model multi -well-96

README/CONTEXT

.gitignore

@@ -0,0 +1,41 @@
+# ── Secrets & credentials ──────────────────────────────────────────────────
+test_tube_scanner/.env
+*.pem
+*.key
+*.crt
+*.p12
+*.pfx
+credentials*.json
+secrets*.json
+.secrets
+
+# ── Données capturées / exports / backups ──────────────────────────────────
+datas/
+
+# ── Python / venv ──────────────────────────────────────────────────────────
+.venv/
+__pycache__/
+*.py[cod]
+*.pyo
+
+# ── Django runtime ─────────────────────────────────────────────────────────
+*.sqlite3
+*.db
+test_tube_scanner/staticfiles/
+test_tube_scanner/media/
+test_tube_scanner/logs/
+*.log
+
+# ── Celery ─────────────────────────────────────────────────────────────────
+celerybeat-schedule
+celerybeat.pid
+*.pid
+
+# ── Éditeurs & OS ──────────────────────────────────────────────────────────
+.idea/
+.vscode/
+*.swp
+*.swo
+*~
+.DS_Store
+Thumbs.db

CONTEXT.md

@@ -0,0 +1,257 @@
+# PlanarianScanner — Contexte technique
+
+Système d'imagerie automatisé pour le suivi comportemental de planaires (*Platyhelminthes*).
+Développé par dd@linuxtarn.org pour le **Laboratoire de Biologie, Université Champollion, Albi**.
+
+---
+
+## Matériel cible
+
+| Composant | Détail |
+|---|---|
+| Carte | Raspberry Pi 4 |
+| Caméra | ArduCam haute définition (Picamera2) |
+| Motorisation | Bras CNC L2544 piloté en GRBL via port série |
+| Grille | 4 plaques multi-puits de 6×4 = 96 puits (Ø 16 mm) |
+| Réseau | LAN — export Samba (CIFS) / rsync SSH |
+
+---
+
+## Stack technique
+
+| Couche | Technologie |
+|---|---|
+| Backend | Django 5.1 + Django Channels (WebSocket) |
+| Serveur ASGI | Daphne |
+| Broker/cache | Redis |
+| Tâches async | Celery + django-celery-beat (one-shot via ClockedSchedule) |
+| Vision | OpenCV (headless) + Picamera2 |
+| Stockage frames | ReductStore (base time série haute performance) |
+| BDD | MariaDB (prod) — sqlite3 (dev) |
+| Export distant | Samba client (CIFS) / rsync |
+| Plateforme | Raspberry Pi 4, Debian 64-bit Trixie |
+| Python | 3.13 — venv dans `.venv/` |
+
+---
+
+## Structure du dépôt
+
+```
+PlanarianScanner/
+├── etc/                        # Scripts d'installation et configs système
+│   ├── 1-install-sys.sh        # Dépendances système
+│   ├── 2-cargo-reductstore-install.sh  # Build ReductStore (~15 min sur RPi4)
+│   ├── 3-install-samba-client.sh
+│   ├── 4-install_mariadb.sh
+│   ├── 5-install_adminer.sh
+│   ├── 6-install_django_app.sh # Init Django (migrations, fixtures, collectstatic)
+│   ├── db/                     # Fixtures JSON initiales (configuration, multiwell, well)
+│   ├── requirements.txt
+│   ├── scanner_service.conf    # Supervisor : Django + Celery workers
+│   ├── reductstore_service.conf
+│   └── nginx_service.conf
+├── datas/                      # Données hors Django (gitignored)
+│   ├── medias/                 # Images et vidéos capturées
+│   ├── exports/csv/            # Exports CSV EthoVision
+│   ├── remote/exports/         # Dossier cible des transferts distants
+│   └── backup/mariadb/         # Sauvegardes MariaDB
+├── assets/                     # Logo, screenshots
+├── test_tube_scanner/          # Racine du projet Django
+│   ├── home/                   # Package projet (settings, urls, wsgi, asgi, celery)
+│   ├── scanner/                # App scanner (CNC, multi-puits, sessions, exports)
+│   ├── planarian/              # App suivi planaires (métriques, export CSV)
+│   ├── modules/                # Modules partagés (capture, GRBL, tracker, metrics…)
+│   ├── manage.py
+│   ├── run-server.sh
+│   ├── run-workers.sh
+│   ├── planarian_sim.py        # Simulateur standalone (CLI)
+│   └── .env / .env.example
+└── browser.py                  # Ouverture navigateur local (utilitaire)
+```
+
+---
+
+## Applications Django
+
+### `scanner` — Pilotage CNC et acquisition
+
+Modèles principaux :
+
+| Modèle | Rôle |
+|---|---|
+| `Configuration` | Config globale active (caméra, GRBL, tracking, calibration) |
+| `MultiWell` | Plaque multi-puits (position HG/HD/BG/BD, grille 6×4, pas XY, crop_radius) |
+| `Well` | Puit individuel (nom Ai..Di) |
+| `WellPosition` | Position XY mm d'un puit dans un MultiWell + px_per_mm (calibration optique caméra) |
+| `VideoPlate` | Vidéo plaque entière associée à un MultiWell — champs : `px_per_mm` (échelle vidéo ~15 px/mm), `x_origin_mm` / `y_origin_mm` (origine CNC stable, indépendante de la calibration) |
+| `Experiment` | Session de capture sur un MultiWell (durée, début/fin) |
+| `Session` | Groupe d'expériences avec planification (ClockedSchedule one-shot) |
+| `SessionExperiment` | Liaison Session ↔ Experiment |
+| `ExperimentWell` | Liaison Experiment ↔ Well (puits actifs) |
+
+Signaux Django :
+- `post_save(MultiWell)` → génère automatiquement les `WellPosition` en serpentin
+- `post_save(Session)` → crée les `PeriodicTask` Celery Beat (export + scanning)
+- `post_delete(Session)` → supprime les `PeriodicTask` associées
+
+Tâches Celery (`scanner/tasks.py`, `scanner/export_tasks.py`) :
+- `run_scanning(session_id)` — parcours serpentin des puits (GRBL + capture)
+- `run_session_exports(session_id)` — génération ZIP JPEG + MP4 + transfert distant
+
+### `planarian` — Suivi multi-individus et métriques
+
+Modèle `ExperimentConfig` : paramètres de tracking par puit (px_per_mm, fps, seuils).
+
+---
+
+## Modules partagés (`modules/`)
+
+| Module | Rôle |
+|---|---|
+| `grbl.py` | Pilotage CNC via port série (G-code, homing, déplacement XY) |
+| `grbl_simulator.py` | Simulateur GRBL pour dev sans matériel |
+| `capture_interface.py` | Interface abstraite de capture — crop circulaire, edge enhance, debug overlay, tracking |
+| `picamera2_capture.py` | Capture ArduCam via Picamera2 |
+| `webcam_capture.py` | Capture webcam via OpenCV |
+| `videofile_capture.py` | Lecture fichier vidéo (test/sim) |
+| `videoplate_capture.py` | Capture par crop dynamique dans une vidéo plaque entière — position GRBL → région extraite, hot swap vidéo, plein cadre à l'origine |
+| `planarian_tracker.py` | Tracking multi-individus : MOG2 + algorithme hongrois (`scipy`) |
+| `planarian_metrics.py` | Métriques par frame et summary (mobilité, thigmo, photo, chemo, social) |
+| `tube_aligner.py` | Détection HoughCircles + CLAHE, calibration optique, plage rayon configurable (`set_radius_range`) |
+| `circular_crop.py` | Découpe circulaire des images de puit |
+| `reductstore.py` | Interface ReductStore (stockage/lecture frames time série) |
+| `system_stats.py` | Stats système (CPU, RAM, disque — affichage dashboard) |
+
+---
+
+## Métriques de tracking
+
+**Par frame** : velocity, distance, moving, mobility_state, dist_to_wall_mm, near_wall,
+dist_to_light_mm, heading_to_light_deg, fleeing_light, dist_to_food_mm, heading_to_food_deg,
+approaching_food, in_food_zone, nearest_neighbour_mm, in_avoid_zone, in_aggreg_zone,
+chem_repulsion_level.
+
+**Summary** : totaux et pourcentages EthoVision-compatibles pour mobilité, thigmotactisme,
+phototactisme, chimiotactisme, interactions sociales.
+
+Export CSV compatible **EthoVision XT**.
+
+---
+
+## Configuration runtime
+
+Fichier `.env` (python-decouple) dans `test_tube_scanner/` :
+
+```
+SECRET_KEY, DEBUG, DOMAIN_SERVER, ALLOWED_HOSTS, CSRF_TRUSTED_ORIGINS
+APP_DATAS          # chemin relatif vers datas/ (ex: ../datas)
+DJANGO_APP         # nom de l'app (home)
+REDIS_URL          # ex: redis://localhost:6379/0
+REDUCTSTORE_URL    # ex: http://localhost:8383
+DB_*               # MariaDB credentials
+```
+
+---
+
+## Démarrage des services
+
+Tous gérés par **Supervisor** :
+
+```bash
+# Interface web Supervisor
+http://root:toor@<ip>:9001
+
+# CLI
+sudo supervisorctl start|stop|restart reductstore
+sudo supervisorctl start|stop|restart test_tube:*
+```
+
+En dev :
+```bash
+cd test_tube_scanner
+./manage.py runserver 0.0.0.0:8000
+# Workers Celery séparés :
+./run-workers.sh
+```
+
+Accès réseau : ajouter `<ip-rpi4> scanner.local` dans `/etc/hosts` des clients.
+
+---
+
+## Simulateur standalone
+
+`test_tube_scanner/planarian_sim.py` — simulation CLI d'une arène circulaire (Ø 16 mm, 500×500 px),
+export CSV EthoVision par planaire.
+
+```bash
+python3 planarian_sim.py --count 5 --thigmotaxis 0.4
+python3 planarian_sim.py --count 5 --photo-mode fixed --photo-x 0.2 --photo-y 0.2 --photo-strength 0.6
+```
+
+`test_tube_scanner/make_videos.sh` — génération de 24 vidéos de simulation (une par puit).
+
+---
+
+## Mode capture vidéo plaque (`capture_type == 'video'`)
+
+Alternative à la caméra ArduCam : une **vidéo de la plaque entière** enregistrée une fois,
+rejouée en boucle pendant les scans. Adapté aux labos sans Raspberry Pi ou pour tests hors matériel.
+
+### Flux
+```
+VideoPlateCapture.capture_frame()
+  → lit la frame courante de la vidéo
+  → extrait un carré 2r×2r centré sur (GRBL_x, GRBL_y) converti en pixels
+  → si GRBL à (0,0) : retourne la frame entière (vue plaque)
+  → sinon          : retourne le crop du puit courant
+→ process_frame()
+  → edge_enhance (optionnel, CLAHE + Canny overlay vert)
+  → TubeAligner.detect_tube() (optionnel, debug HoughCircles)
+  → crop circulaire (optionnel)
+```
+
+### Calibration vidéo
+- `VideoPlate.px_per_mm` : échelle de la vidéo (~15 px/mm) — **différent** de `WellPosition.px_per_mm` (~50 px/mm, optique caméra)
+- `VideoPlate.x_origin_mm` / `y_origin_mm` : position CNC correspondant au pixel (0,0) de la vidéo — **stable**, jamais modifiée par la calibration des puits
+- `MultiWell.crop_radius` : rayon du crop en pixels — contrôle la taille de la vue par puit
+
+### Contrôles calibration UI (boutons)
+| Bouton | Action |
+|---|---|
+| Debug | Active `TubeAligner.debug` — détection HoughCircles en continu |
+| Overlay | Affiche/masque les annotations de détection sans couper la détection |
+| Contours | Active edge enhance (CLAHE + Canny overlay vert) sur la frame propre |
+| Recadrer | Active le crop circulaire + navigue vers la position Base (mode vidéo) |
+
+### `TubeAligner.set_radius_range(min_ratio, max_ratio)`
+Ajuste la plage de recherche HoughCircles en fraction de `min(w,h)` :
+- Mode caméra : `0.26–0.37` (tube occupe ~30% du champ)
+- Mode vidéo  : `0.38–0.47` (puit remplit le crop, ratio ~0.43–0.50)
+
+---
+
+## Déploiement réseau isolé (labo sans internet)
+
+```
+GitHub ←→ Portable (internet) ←→ Routeur OpenWrt ←→ Machine labo (SSH)
+```
+
+Mise à jour sans internet :
+```bash
+# Sur la machine labo (une fois)
+git config receive.denyCurrentBranch updateInstead
+
+# Sur le portable — ajouter le labo comme remote
+git remote add labo ssh://user@<ip-labo>/chemin/PlanarianScanner
+
+# Workflow répétable
+git pull origin video-plate-calibration   # portable ← GitHub
+git push labo video-plate-calibration     # labo ← portable
+```
+
+---
+
+## Licence
+
+GPL-3.0
+

README.md

@@ -48,9 +48,18 @@ d'analyse distantes.
 ---
 ## Fonctionnalités
 
+### Application 1: Scanner de tube à essais
+
 - Pilotage du bras CNC en GRBL — déplacement automatique puits par puits
 - Calibration des multi-puits avec synchro base de données
-- Acquisition image haute définition via ArduCam (OpenCV + Picamera2)
+- Trois modes de capture :
+  - **ArduCam** (Picamera2) — caméra haute définition montée sur le bras
+  - **Webcam** — via OpenCV (développement / test)
+  - **Vidéo plaque** (`VideoPlateCapture`) — crop dynamique dans une vidéo plaque entière rejouée en boucle ; adapté aux scans sans caméra embarquée
+- Calibration assistée :
+  - Détection automatique du centre du puit (Hough + CLAHE, plage rayon adaptable selon le mode)
+  - Overlay Canny vert pour visualiser les bords en conditions d'éclairage difficile
+  - Contrôles temps réel : Debug, Overlay annotations, Contours, Recadrage
 - Stockage des frames en base time série ReductStore
 - Sessions de scan paramétrables (grille complète ou sélection de puits)
 - Export asynchrone (Celery) :
@@ -62,12 +71,43 @@ d'analyse distantes.
 - Interface administration Django (sqlite3 ou mariadb ou postgresql)
 - Suivi de progression des tâches longues par polling
 
-Supporte plusieurs planaires avec paramètres configurables via django ou csv.
-
-Export CSV par planaire compatible EthoVision XT.
+### Application 2: Détection de planaires et suivi multi-individus dans un tube.
 
 
-### Seuils EthoVision par défaut (configurables via django ou csv)
+[🎬 Vidéo Simulation planaires](https://youtu.be/pkzClmBp_KM)
+
+
+- Supporte plusieurs planaires avec paramètres configurables via django ou csv.
+
+    - Stratégie :
+    
+        - Soustraction de fond MOG2 (léger sur Raspberry Pi 4)
+        - Détection de tous les contours valides (surface >= min_area_px)
+        - Association frame-à-frame par distance euclidienne minimale
+          via algorithme hongrois (scipy.optimize.linear_sum_assignment)
+        - Un état inter-frame indépendant par individu (PlanarianState)
+        - Retourne une liste de résultats, un par individu suivi
+
+- Export CSV par planaire compatible EthoVision XT.
+- Métriques par frame :
+
+    - Mobilité    : velocity, distance, moving, mobility_state
+    - Thigmo      : dist_to_wall_mm, near_wall
+    - Photo       : dist_to_light_mm, heading_to_light_deg, fleeing_light
+    - Chemo       : dist_to_food_mm, heading_to_food_deg, approaching_food, in_food_zone
+    - Social      : nearest_neighbour_mm, in_avoid_zone, in_aggreg_zone, chem_repulsion_level
+
+- Métriques résumé (summary) :
+
+    - Mobilité    : movedCenter_pointTotal_mm, velocity_mean_mm_s, durations par état
+    - Thigmo      : thigmotaxis_pct_time_near_wall
+    - Photo       : photo_pct_time_fleeing, photo_mean_dist_mm, photo_latency_s
+    - Chemo       : chemo_pct_time_approaching, chemo_pct_time_in_zone,
+                  chemo_latency_s, chemo_mean_dist_mm
+    - Social      : social_pct_time_avoiding, social_pct_time_aggregating,
+                  social_mean_nn_mm, social_contact_events
+
+- Seuils EthoVision par défaut (configurables via django ou csv)
 
     - **Immobile** : déplacement < 0.2 mm/s
     - **Mobile** : 0.2 à 1.5 mm/s
@@ -83,23 +123,43 @@ Export CSV par planaire compatible EthoVision XT.
     | MobileFrequency / Duration | mobility_state | mobility_mobile_frequency/duration_s |
     | Highly mobileFrequency / Duration | mobility_state | mobility_highly_mobile_frequency/duration_s |
 
-### Métriques calculées
-
-- Distance totale parcourue (mm) → movedCenter-pointTotalmm
-- Vitesse instantanée (mm/s) → VelocityCenter-pointMeanmm/s
-- Durée cumulée en mouvement (s) → MovementMoving
-- Durée cumulée à l'arrêt (s) → MovementNot Moving
-- Fréquence et durée par état de mobilité → Mobility state (EthoVision)
-- Distance à la paroi (mm) → thigmotactisme
-
-### Comportements
+- Comportements
     
     - **Thigmotactisme** : attraction vers la paroi (--thigmotaxis)
     - **Phototactisme** : fuite de la lumière (--photo-mode, --photo-strength)
     - **Chimiotactisme** : attraction vers une source de nourriture (--chemo-strength)
     - **Inter-individus** : évitement de contact, agrégation, répulsion chimique
 
+### Application 4: Simulation de planaires
 
+- planarian_sim.py 
+
+    Espace circulaire de 16mm de diamètre, 500x500px
+    Supporte plusieurs planaires avec paramètres configurables via arguments CLI.
+    Export CSV par planaire compatible EthoVision XT.
+
+        Comportements simulés :
+            - Thigmotactisme  : attraction vers la paroi (--thigmotaxis)
+            - Phototactisme   : fuite de la lumière (--photo-mode, --photo-strength)
+            - Chimiotactisme  : attraction vers une source de nourriture (--chemo-strength)
+            - Inter-individus : évitement de contact, agrégation, répulsion chimique
+    
+        Usage:
+            python3 planarian_sim.py [options]
+        
+        Exemples:
+            python3 planarian_sim.py --count 5 --thigmotaxis 0.4
+            python3 planaire_sim.py --count 5 --photo-mode fixed --photo-x 0.2 --photo-y 0.2 --photo-strength 0.6
+            python3 planarian_sim.py --count 5 --chemo-x 0.7 --chemo-y 0.5 --chemo-strength 0.5
+            python3 planarian_sim.py --count 5 --avoid-strength 0.6 --aggreg-strength 0.2
+        
+- make_videos.sh 
+    
+    - Générateur de vidéos paramétrables
+    
+        Usage:
+             - ./make_video.sh  (génère le fichier par défaut)
+             - ./make_video.sh  all (génère 24 vidéos pour 24 tubes à essais)             
 ---
 
 ## Architecture
@@ -185,13 +245,6 @@ ou
 sudo supervisorctl start|stop|restart reductstore
 sudo supervisorctl start|stop|restart test_tube:*
 
-Ajouter scanner.local au fichier hosts des clients web:
-ip.du.rasp.berry scanner.local
-
-- linux  : /etc/hosts
-- windows: C:\Windows\System32\drivers\etc\hosts
-- mac    : /private/etc/hosts"
-
 ```
 
 ## Organisation du dépôt
@@ -199,8 +252,6 @@ ip.du.rasp.berry scanner.local
 ```bash
 PlanarianScanner/
 ├── assets
-│   ├── calibration-auto.jpg
-│   ├── calibration-auto.mp4
 │   ├── calibration-auto.png
 │   └── logo.png
 ├── browser.py
@@ -222,7 +273,6 @@ PlanarianScanner/
 │   ├── scanner_service.conf
 │   └── supervisor-inet_http.conf
 ├── LICENSE
-├── logo.png
 ├── README.md
 └── test_tube_scanner
     ├── home
@@ -312,14 +362,30 @@ PlanarianScanner/
 
 ---
 
-## Procédure de calibration en 4 étapes
-1. Activer "Debug détection" → voir le cercle et les zones sur le stream
+## Procédure de calibration
 
-Calibration auto
+### Mode caméra (ArduCam / Webcam)
+1. **Debug** → active la détection HoughCircles en continu (cercle + zones affiché)
+2. **Overlay** → affiche/masque les annotations sans couper la détection
+3. **Recadrer** → isole le puit et navigue vers la position Base
+4. **Calibrage auto** → centrage automatique puit par puit avec sauvegarde
 
-![Aperçu de la vidéo](assets/calibration-auto.png) Calibration auto
+### Mode vidéo plaque
 
-![Vidéo Calibration auto 🎬](https://www.linuxtarn.org/media/original_videos/calibration-auto.mp4) Vidéo Calibration auto
+> **Note** : ce mode permet de piloter le scanner sans caméra embarquée sur le bras CNC.
+> Une vidéo de la plaque entière est enregistrée une seule fois puis rejouée en boucle ;
+> chaque déplacement GRBL extrait dynamiquement la zone du puit courant dans cette vidéo.
+> Idéal pour les tests sans matériel ou les laboratoires ne disposant pas de caméra ArduCam.
+
+1. Créer un enregistrement `VideoPlate` dans l'admin (upload vidéo, `px_per_mm`, `x_origin_mm`, `y_origin_mm`)
+2. **Contours** → overlay Canny vert pour repérer les bords des puits selon l'éclairage
+3. **Debug** → détection Hough adaptée (plage rayon élargie pour puit plein cadre)
+4. **Recadrer** → active le crop + déplace vers la Base
+5. Naviguer puit par puit, sauvegarder les positions
+
+![Aperçu calibration auto](assets/calibration-auto.png)
+
+[🎬 Vidéo Calibration auto](https://youtu.be/6RueJ3onUoY)
 
 
 

README_EN.md

@@ -0,0 +1,382 @@
+# ![Planarians](assets/logo.png) PlanarianScanner
+
+> Automated imaging system for behavioral tracking of planarians
+
+> (C) dd@linuxtarn.org for the Biology Laboratory, Champollion University, Albi
+
+---
+
+## Overview
+
+**PlanarianScanner** is a web application developed for monitoring the activity
+and movements of **planarians** (*Platyhelminthes*) in laboratory research.
+
+The system controls a motorized multi-well scanner composed of a CNC arm (GRBL)
+and a high-definition ArduCam camera mounted on a Raspberry Pi 4. It enables
+automated image acquisition on a **6×4 wells × 4 plates** grid,
+high-performance storage of captures, and export to remote analysis machines.
+
+---
+
+## Hardware
+
+| Component | Details |
+|---|---|
+| Board | Raspberry Pi 4 |
+| Camera | High-definition ArduCam |
+| Motion system | CNC arm (L2544) controlled by GRBL |
+| Well grid | 6×4 × 4 multi-well plates |
+| Network | Local LAN — Samba/rsync export |
+
+---
+
+## Technical Stack
+
+| Layer | Technology |
+|---|---|
+| Backend | Django + Django Channels |
+| Real-time | Redis (broker + channel layer) |
+| Acquisition | OpenCV + Picamera2 |
+| Storage | ReductStore (high-performance time series) |
+| Asynchronous tasks | Celery + django-celery-beat |
+| Export | Samba (CIFS), rsync/SSH |
+| Platform | Raspberry Pi 4 — Debian Linux |
+
+---
+
+## Features
+
+### Application 1: Test Tube Scanner
+
+- CNC arm control through GRBL — automatic well-by-well movement
+- Multi-well calibration with database synchronization
+- Three capture modes:
+  - **ArduCam** (Picamera2) — high-definition camera mounted on the arm
+  - **Webcam** — via OpenCV (development / testing)
+  - **Plate video** (`VideoPlateCapture`) — dynamic crop from a full-plate video replayed in loop; suitable for scans without an embedded camera
+- Assisted calibration:
+  - Automatic well-center detection (Hough + CLAHE, adjustable radius range per mode)
+  - Green Canny overlay to visualize well borders under difficult lighting
+  - Real-time controls: Debug, Annotation Overlay, Edge Enhance, Crop
+- Frame storage in ReductStore time-series database
+- Configurable scan sessions (full grid or selected wells)
+- Asynchronous export (Celery):
+  - ZIP archive of JPEG images per session
+  - MP4 video generated from captured frames
+- Automatic transfer of exports to remote machines (Linux / Windows)
+- Nightly export scheduling via django-celery-beat
+- Real-time web interface (Django Channels / WebSocket)
+- Django administration interface (sqlite3 or mariadb or postgresql)
+- Long-task progress tracking through polling
+
+### Application 2: Planarian Detection and Multi-Individual Tracking in a Tube
+
+[🎬 Planarian Simulation Video](https://youtu.be/pkzClmBp_KM)
+
+- Supports multiple planarians with configurable parameters via Django or CSV.
+
+    - Strategy:
+    
+        - MOG2 background subtraction (lightweight on Raspberry Pi 4)
+        - Detection of all valid contours (surface >= min_area_px)
+        - Frame-to-frame association using minimum Euclidean distance
+          via the Hungarian algorithm (scipy.optimize.linear_sum_assignment)
+        - Independent inter-frame state per individual (PlanarianState)
+        - Returns a list of results, one for each tracked individual
+
+- Per-planarian CSV export compatible with EthoVision XT.
+- Metrics per frame:
+
+    - Mobility   : velocity, distance, moving, mobility_state
+    - Thigmo     : dist_to_wall_mm, near_wall
+    - Photo      : dist_to_light_mm, heading_to_light_deg, fleeing_light
+    - Chemo      : dist_to_food_mm, heading_to_food_deg, approaching_food, in_food_zone
+    - Social     : nearest_neighbour_mm, in_avoid_zone, in_aggreg_zone, chem_repulsion_level
+
+- Summary metrics:
+
+    - Mobility   : movedCenter_pointTotal_mm, velocity_mean_mm_s, state durations
+    - Thigmo     : thigmotaxis_pct_time_near_wall
+    - Photo      : photo_pct_time_fleeing, photo_mean_dist_mm, photo_latency_s
+    - Chemo      : chemo_pct_time_approaching, chemo_pct_time_in_zone,
+                  chemo_latency_s, chemo_mean_dist_mm
+    - Social     : social_pct_time_avoiding, social_pct_time_aggregating,
+                  social_mean_nn_mm, social_contact_events
+
+- Default EthoVision thresholds (configurable via Django or CSV)
+
+    - **Immobile** : movement < 0.2 mm/s
+    - **Mobile** : 0.2 to 1.5 mm/s
+    - **Highly mobile** : > 1.5 mm/s
+
+    | EthoVision | CSV frames | CSV summary |
+    |---|---|---|
+    | movedCenter-pointTotalmm | total_distance_mm | movedCenter_pointTotal_mm |
+    | VelocityCenter-pointMeanmm/s | velocity_mm_s | velocity_mean_mm_s |
+    | MovementMoving | moving, duration_moving_s | movement_moving_duration_s |
+    | MovementNot Moving | duration_stopped_s | movement_not_moving_duration_s |
+    | ImmobileFrequency / Duration | mobility_state | mobility_immobile_frequency/duration_s |
+    | MobileFrequency / Duration | mobility_state | mobility_mobile_frequency/duration_s |
+    | Highly mobileFrequency / Duration | mobility_state | mobility_highly_mobile_frequency/duration_s |
+
+- Behaviors
+    
+    - **Thigmotaxis** : wall attraction (--thigmotaxis)
+    - **Phototaxis** : fleeing from light (--photo-mode, --photo-strength)
+    - **Chemotaxis** : attraction toward a food source (--chemo-strength)
+    - **Inter-individuals** : contact avoidance, aggregation, chemical repulsion
+
+### Application 4: Planarian Simulation
+
+- planarian_sim.py 
+
+    Circular space of 16 mm diameter, 500x500 px
+    Supports multiple planarians with configurable parameters via CLI arguments.
+    Per-planarian CSV export compatible with EthoVision XT.
+
+        Simulated behaviors:
+            - Thigmotaxis      : wall attraction (--thigmotaxis)
+            - Phototaxis       : fleeing from light (--photo-mode, --photo-strength)
+            - Chemotaxis       : attraction toward a food source (--chemo-strength)
+            - Inter-individual : contact avoidance, aggregation, chemical repulsion
+    
+        Usage:
+            python3 planarian_sim.py [options]
+        
+        Examples:
+            python3 planarian_sim.py --count 5 --thigmotaxis 0.4
+            python3 planarian_sim.py --count 5 --photo-mode fixed --photo-x 0.2 --photo-y 0.2 --photo-strength 0.6
+            python3 planarian_sim.py --count 5 --chemo-x 0.7 --chemo-y 0.5 --chemo-strength 0.5
+            python3 planarian_sim.py --count 5 --avoid-strength 0.6 --aggreg-strength 0.2
+        
+- make_videos.sh 
+    
+    - Configurable video generator
+    
+        Usage:
+             - ./make_video.sh  (generates the default file)
+             - ./make_video.sh all (generates 24 videos for 24 test tubes)
+
+---
+
+## Architecture
+
+```text
+Raspberry Pi 4
+├── Django (web interface + API)
+│   ├── Django Channels  ←→  Redis  (real-time WebSocket)
+│   └── Celery workers
+│       ├── scanning(session_id)       — well traversal
+│       ├── export_images_zip()        — JPEG ZIP generation
+│       ├── export_video_mp4()         — MP4 generation (OpenCV)
+│       └── transfer → /mnt/exports    — Samba share
+│
+├── ArduCam  ←  Picamera2 / OpenCV    — HD capture
+├── CNC GRBL ←  Serial                — XY movement
+└── ReductStore                        — frame time-series storage
+
+Installation
+
+Full documentation coming soon.
+
+Using piImager, install Raspberry Pi OS 64-bit Trixie on the Raspberry Pi 4.<br>
+Customize your Raspberry Pi with at least SSH enabled (SSH key or password).<br>
+Later, for convenience, you may install a VNC server.
+
+ssh rpi4@ip.of.raspi
+
+git clone https://github.com/your-repo/planarianscanner.git
+git@github.com:deunix-educ/PlanarianScanner.git
+
+# modify environment variables if needed
+cp .env.example .env
+# Edit .env : SECRET_KEY, REDIS_URL, REDUCTSTORE_URL, ... 
+
+cd PlanarianScanner/etc
+chmod +x *.sh
+
+# install system libraries
+./1-install-sys.sh
+
+# compile reductstore (~15 min on Raspberry Pi 4)
+./2-cargo-reductstore-install.sh
+
+# install samba client
+./3-install-samba-client.sh
+
+# install mariadb
+./4-install_mariadb.sh
+
+# install adminer
+./5-install_adminer.sh
+
+# Configure Django applications
+./6-install_django_app.sh
+
+# test
+sudo supervisorctl stop test_tube:*
+./manage.py runserver 0.0.0.0:8000
+
+# local test
+# http://127.0.0.1:8000
+
+# remote test
+# http://ip.of.raspi:8000
+
+# end of test
+sudo supervisorctl restart test_tube:*
+
+Starting services:
+
+All services are accessible through supervisor
+http://root:toor@ip-of-raspi:9001
+or 
+sudo supervisorctl start|stop|restart reductstore
+sudo supervisorctl start|stop|restart test_tube:*
+
+Repository Organization
+PlanarianScanner/
+├── assets
+│   ├── calibration-auto.png
+│   └── logo.png
+├── browser.py
+├── etc
+│   ├── 1-install-sys.sh
+│   ├── 2-cargo-reductstore-install.sh
+│   ├── 3-install-samba-client.sh
+│   ├── 4-install_mariadb.sh
+│   ├── 5-install_adminer.sh
+│   ├── 6-install_django_app.sh
+│   ├── db
+│   │   ├── configuration.json
+│   │   ├── multiwell.json
+│   │   └── well.json
+│   ├── install-linux-samba-server.sh
+│   ├── nginx_service.conf
+│   ├── reductstore_service.conf
+│   ├── requirements.txt
+│   ├── scanner_service.conf
+│   └── supervisor-inet_http.conf
+├── LICENSE
+├── README.md
+└── test_tube_scanner
+    ├── home
+    │   ├── apps.py
+    │   ├── asgi.py
+    │   ├── celerymodule.py
+    │   ├── context_processors.py
+    │   ├── __init__.py
+    │   ├── locale
+    │   ├── management
+    │   ├── middleware.py
+    │   ├── __pycache__
+    │   ├── settings.py
+    │   ├── static
+    │   ├── templates
+    │   ├── templatetags
+    │   ├── urls.py
+    │   ├── views.py
+    │   └── wsgi.py
+    ├── logs
+    │   ├── celery.log
+    │   └── test_tube.log
+    ├── manage.py
+    ├── media
+    │   ├── images
+    │   └── simulation
+    ├── modules
+    │   ├── capture_interface.py
+    │   ├── circular_crop.py
+    │   ├── grbl.py
+    │   ├── __init__.py
+    │   ├── picamera2_capture_basic.py
+    │   ├── picamera2_capture.py
+    │   ├── planarian_metrics.py
+    │   ├── planarian_tracker.py
+    │   ├── __pycache__
+    │   ├── reductstore.py
+    │   ├── system_stats.py
+    │   ├── tube_aligner.py
+    │   ├── utils.py
+    │   ├── videofile_capture.py
+    │   └── webcam_capture.py
+    ├── planarian
+    │   ├── admin.py
+    │   ├── apps.py
+    │   ├── forms.py
+    │   ├── __init__.py
+    │   ├── migrations
+    │   ├── models.py
+    │   ├── __pycache__
+    │   ├── templates
+    │   ├── tests.py
+    │   ├── urls.py
+    │   └── views.py
+    ├── run-workers.sh
+    ├── scanner
+    │   ├── admin.py
+    │   ├── apps.py
+    │   ├── constants.py
+    │   ├── consumers.py
+    │   ├── export_tasks.py
+    │   ├── __init__.py
+    │   ├── migrations
+    │   ├── models.py
+    │   ├── multiwell.py
+    │   ├── process.py
+    │   ├── __pycache__
+    │   ├── routing.py
+    │   ├── static
+    │   ├── tasks.py
+    │   ├── templates
+    │   ├── templatetags
+    │   ├── tests.py
+    │   ├── urls.py
+    │   └── views.py
+    ├── staticfiles
+    │   ├── admin
+    │   ├── css
+    │   ├── img
+    │   ├── js
+    │   ├── scanner
+    │   └── webfonts
+    └── templates
+        └── admin
+## Calibration Procedure
+
+### Camera mode (ArduCam / Webcam)
+1. **Debug** → enables continuous HoughCircles detection (circle + zones displayed)
+2. **Overlay** → shows/hides annotations without stopping detection
+3. **Crop** → isolates the well and navigates to the Base position
+4. **Auto calibration** → automatic well-by-well centering with position save
+
+### Plate video mode
+
+> **Note**: this mode lets you drive the scanner without a camera mounted on the CNC arm.
+> A single recording of the full plate is made once and replayed in a loop; each GRBL move
+> dynamically crops the current well's region from that video. Ideal for hardware-free
+> testing or labs without an ArduCam.
+
+1. Create a `VideoPlate` record in admin (upload video, set `px_per_mm`, `x_origin_mm`, `y_origin_mm`)
+2. **Edge Enhance** → green Canny overlay to locate well borders under variable lighting
+3. **Debug** → Hough detection with wider radius range (well fills the crop)
+4. **Crop** → activates circular crop + moves to Base position
+5. Navigate well by well and save positions
+
+![Auto calibration preview](assets/calibration-auto.png)
+
+[🎬 Auto Calibration Video](https://youtu.be/6RueJ3onUoY)
+
+## Status
+
+![status](https://img.shields.io/badge/statut-en%20développement-orange)
+![platform](https://img.shields.io/badge/plateforme-Raspberry%20Pi%204-red)
+![python](https://img.shields.io/badge/python-3.11%2B-blue)
+![django](https://img.shields.io/badge/django-4.2%2B-green)
+![license](https://img.shields.io/badge/licence-GPL3-lightgrey)
+
+---
+
+## License
+
+GPL-3.0 — Open-source project, developed for sharing and scientific reproducibility.

etc/1-install-sys.sh

@@ -1,4 +1,4 @@
-!/bin/bash
+#!/bin/bash
 
 echo "==== System installation for rpi"
 echo
@@ -7,8 +7,8 @@ sudo apt upgrade
 
 ETC="$(pwd)"
 
-mkdir -p $HOME/exports
-mkdir -p$HOME/medias
+mkdir -p "$HOME"/exports
+mkdir -p "$HOME"/medias
 mkdir -p /mnt/exports
 
 cp ../test_tube_scanner/.env.example ../test_tube_scanner/.env
@@ -17,15 +17,15 @@ echo
 
 # system
 echo "==== system essential"
-sudo apt -y install build-essential openssl git pkg-config redis supervisor sqlitebrowser samba-client cifs-utils gettext
+sudo apt -y install build-essential openssl git pkg-config redis supervisor sqlitebrowser samba-client cifs-utils gettext avahi-daemon
 
 echo "==== python3 install"
 sudo apt -y install python3-dev python3-pip python3-venv libpq-dev default-libmysqlclient-dev libmariadb-dev python3-picamera2
 
 echo "==== supervisor http access login:pass => root:toor"
 sudo cp supervisor-inet_http.conf /etc/supervisor/conf.d/
-sudo ln -s $ETC/scanner_service.conf /etc/supervisor/conf.d/
-sudo ln -s $ETC/reductstore_service.conf /etc/supervisor/conf.d/
+sudo ln -s "$ETC"/scanner_service.conf /etc/supervisor/conf.d/
+sudo ln -s "$ETC"/reductstore_service.conf /etc/supervisor/conf.d/
 
 echo "==== restart supervisor "
 sudo systemctl restart supervisor
@@ -33,6 +33,7 @@ sudo systemctl restart supervisor
 echo "==== python env with system site packages for picamera2"
 rm -rf ../.venv
 python -m venv --system-site-packages ../.venv
+# shellcheck disable=SC1091
 source ../.venv/bin/activate
 
 echo "==== pip requirements"

etc/2-cargo-reductstore-install.sh

@@ -1,4 +1,4 @@
-!/bin/bash
+#!/bin/bash
 echo "--- install reductstore"
 echo "    machine raspberry pi4"
 echo "    Compilation finished `release` profile [optimized] target(s) in 16m 31s"
@@ -11,4 +11,4 @@ cargo --version
 rustc --version
 cargo install reductstore
 
-mkdir -p $HOME/medias
+mkdir -p $HOME/reduct-media

etc/3-install-samba-client.sh

@@ -50,6 +50,8 @@ sudo bash -c "echo '//$samba_server/$public_share /mnt/samba/public cifs guest,u
 echo "Montage des partages Samba..."
 sudo mount -a
 
+sudo mkdir -p /mnt/samba/public/images /mnt/samba/public/videos
+
 # Vérification du montage
 echo "Vérification des partages montés :"
 df -h | grep samba

etc/4-install_mariadb.sh

@@ -3,8 +3,7 @@
 # Script d'installation et de configuration de MariaDB
 # Utilisation : source mariadb_config.sh && ./install_mariadb.sh
 
-ENV_FILE="../test_tube_scanner/.env"
-source $ENV_FILE
+source ../test_tube_scanner/.env
 
 # Vérifie que le fichier de configuration est sourcé
 if [ -z "$DATABASE_ROOT_PASSWORD" ] || [ -z "$DATABASE_NAME" ] || [ -z "$DATABASE_USER" ] || [ -z "$DATABASE_PASSWORD" ]; then

etc/reductstore_service.conf

@@ -1,8 +1,8 @@
 [program:reductstore]
 process_name=%(program_name)s
 priority=10
-environment=RS_DATA_PATH="/home/rpi4/medias"
-directory=/home/rpi4/medias
+environment=RS_DATA_PATH="/home/rpi4/reduct-media"
+directory=/home/rpi4/reduct-media
 command=/home/rpi4/.cargo/bin/reductstore
 user=rpi4
 group=rpi4

etc/requirements.txt

@@ -11,6 +11,7 @@ twisted[tls,http2]
 celery[redis]
 python-decouple
 PyYaml
+requests
 reduct-py
 python-dateutil
 psutil
@@ -19,4 +20,5 @@ opencv-python-headless
 mysqlclient
 psycopg2
 pyserial
-
+scipy
+django-stubs[compatible-mypy] 

etc/scanner_service.conf

@@ -4,12 +4,14 @@ programs=webUI,planification,services
 [program:webUI]
 process_name=%(program_name)s
 priority=500
+
 directory=/home/rpi4/PlanarianScanner/test_tube_scanner
-command=
-    /home/rpi4/PlanarianScanner/.venv/bin/daphne
-    -b 0.0.0.0
-    -p 8000
-    home.asgi:application
+command=/home/rpi4/PlanarianScanner/test_tube_scanner/run-server.sh
+#    /home/rpi4/PlanarianScanner/.venv/bin/daphne
+#    -b 0.0.0.0
+#    -p 8000
+#    home.asgi:application
+
 user=rpi4
 group=rpi4
 stopasgroup=true

pyrightconfig.json

@@ -0,0 +1,16 @@
+{
+  "venvPath": ".",
+  "venv": ".venv",
+  "pythonVersion": "3.13",
+  "extraPaths": ["test_tube_scanner"],
+  "typeCheckingMode": "basic",
+  "reportMissingImports": false,
+  "reportMissingModuleSource": false,
+  "reportOptionalMemberAccess": false,
+  "reportOptionalSubscript": false,
+  "reportOptionalIterable": false,
+  "reportPossiblyUnboundVariable": "warning",
+  "reportCallIssue": false,
+  "reportArgumentType": false,
+  "reportAttributeAccessIssue": false
+}

test_tube_scanner/.env.example

@@ -2,6 +2,7 @@
 # django app
 DEBUG=True
 IS_LOGGING=True
+GRBL_SIMULATION = False
 
 # app
 DJANGO_APP=Test Tube Scanner
@@ -19,6 +20,8 @@ APP_DATAS=test_tube_scanner
 EXPORTS_LOCAL_PATH=/home/rpi4/exports
 EXPORT_REMOTE_PATH=/mnt/exports
 REDUCTSTORE_PATH=/home/rpi4/medias
+CSV_EXPORT_DIR=/home/rpi4/exports/csv
+BACKUP_DIR=/home/rpi4/backup/mariadb
 
 ####
 # django email
@@ -39,12 +42,14 @@ SECRET_KEY="django-insecure-0)4_w=pjv1ex7=s=c=ii3g@fx_=8fb=hxk€3bpk1)uj(0ph0t)
 USER=rpi4
 GROUP=rpi4
 
+
 DOMAIN_SERVER=scanner.local
-ALLOWED_HOSTS=127.0.0.1,localhost
-CSRF_TRUSTED_ORIGINS=http://127.0.0.1:8000,http://localhost:8000
+ALLOWED_HOSTS=127.0.0.1,localhost,scanner.local,192.168.250.230,192.168.1.200
+CSRF_TRUSTED_ORIGINS=http://127.0.0.1:8000,http://localhost:8000,http://scanner.local,http://192.168.1.200:8000,http://192.168.250.230:8000
 
 ####
 # server app
+LOCAL_IP_SERVER=192.168.1.200
 SERVER_HOST_IP=0.0.0.0
 SERVER_HOST_PORT=8000
 

test_tube_scanner/backup/services.py

@@ -0,0 +1,61 @@
+'''
+Created on 18 mai 2026
+
+@author: denis
+'''
+from pathlib import Path
+from datetime import datetime
+import subprocess
+import gzip
+import shutil
+
+from django.conf import settings
+
+BACKUP_DIR = Path(settings.BACKUP_DIR)
+
+
+def mariadb_backup():
+    BACKUP_DIR.mkdir(parents=True, exist_ok=True)
+
+    db = settings.DATABASES["default"]
+
+    db_name = db["NAME"]
+    db_user = db["USER"]
+    db_password = db["PASSWORD"]
+    db_host = db.get("HOST", "localhost")
+    db_port = str(db.get("PORT", 3306))
+
+    timestamp = datetime.now().strftime("%Y%m%d_%H%M%S")
+
+    sql_file = BACKUP_DIR / f"{db_name}_{timestamp}.sql"
+    gz_file = BACKUP_DIR / f"{db_name}_{timestamp}.sql.gz"
+
+    cmd = [
+        "mariadb-dump",
+        "--single-transaction",
+        "--quick",
+        "--routines",
+        "--triggers",
+        "-h", db_host,
+        "-P", db_port,
+        "-u", db_user,
+        f"-p{db_password}",
+        db_name,
+    ]
+
+    with open(sql_file, "wb") as f:
+        result = subprocess.run(
+            cmd,
+            stdout=f,
+            stderr=subprocess.PIPE,
+            check=True,
+        )
+
+    with open(sql_file, "rb") as f_in:
+        with gzip.open(gz_file, "wb") as f_out:
+            shutil.copyfileobj(f_in, f_out)
+
+    sql_file.unlink()
+
+    return str(gz_file)
+

test_tube_scanner/backup/tasks.py

@@ -0,0 +1,12 @@
+'''
+Created on 18 mai 2026
+
+@author: denis
+'''
+from celery import shared_task
+from .services import mariadb_backup
+
+@shared_task
+def backup_mariadb_task():
+    path = mariadb_backup()
+    return {"status": "ok", "backup": path, }

test_tube_scanner/home/celerymodule.py

@@ -8,3 +8,6 @@ os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'home.settings')
 appc = Celery('home')
 appc.config_from_object('django.conf:settings', namespace='CELERY')
 appc.autodiscover_tasks()
+
+worker_prefetch_multiplier = 1
+task_acks_late = True

test_tube_scanner/home/management/commands/export_video.py

@@ -31,7 +31,7 @@ class Command(BaseCommand):
             
             )
             print()          
-            print(f"Export video: {job.id}")
+            print(f"Export video: {job.id}")  # type: ignore[union-attr]
         except Exception as e:
             print("Export video uuid error", e)
 

test_tube_scanner/home/management/commands/init_data.py

@@ -13,7 +13,7 @@ def create_user():
         if User.objects.count() == 0:
             for email, username, password, is_superuser in settings.ADMINS:
                 if is_superuser:
-                    User.objects.create_superuser(
+                    User.objects.create_superuser(  # type: ignore[attr-defined]
                         email=email,
                         username=username,
                         password=password,
@@ -21,7 +21,7 @@ def create_user():
                         is_superuser=is_superuser,
                     )
                 else:
-                    User.objects.create_user(
+                    User.objects.create_user(  # type: ignore[attr-defined]
                         email=email,
                         username=username,
                         password=password,

test_tube_scanner/home/management/commands/secret_key.py

@@ -2,7 +2,7 @@
 # encoding: utf-8
 from uuid import uuid4
 from django.core.management import BaseCommand
-from django.core.management.utils import get_random_string;
+from django.utils.crypto import get_random_string
 
 class Command(BaseCommand):
     def add_arguments(self, parser):

test_tube_scanner/home/management/commands/start_workers.py

@@ -7,7 +7,6 @@ from django.core.management.base import BaseCommand
 from scanner import tasks as scanner_tasks
 
 
-
 class Command(BaseCommand):
     help = "Démarre les tâches Celery."
 
@@ -18,9 +17,9 @@ class Command(BaseCommand):
     def handle(self, *args, **options):  # @UnusedVariable
         #task = options['task']
         try:
-
             scanner_tasks.scanner_start.delay()   # @UndefinedVariable
             scanner_tasks.replay_start.delay()     # @UndefinedVariable
+       
         except Exception as e:
             print(e)
 

test_tube_scanner/home/management/commands/test_L2544.py

@@ -4,7 +4,11 @@ Created on 19 janv. 2026
 @author: denis
 '''
 from django.core.management.base import BaseCommand
-from modules.grbl import GRBLController, wait_for
+from modules.grbl import GRBLController
+import threading
+
+def wait_for(delay: float = 1.0) -> None:
+    threading.Event().wait(delay)
 import time
 
 

test_tube_scanner/home/settings.py

@@ -19,9 +19,7 @@ BASE_DIR = Path(__file__).resolve().parent.parent
 print("Django BASE_DIR:", BASE_DIR)
 
 PACKAGE_DIR = BASE_DIR.parent
-APP_DATAS = PACKAGE_DIR / config('APP_DATAS')
-
-
+APP_DATAS = PACKAGE_DIR / str(config('APP_DATAS'))
 
 # Quick-start development settings - unsuitable for production
 # See https://docs.djangoproject.com/en/5.0/howto/deployment/checklist/
@@ -37,10 +35,10 @@ SECRET_KEY = config("SECRET_KEY")
 DEBUG = config('DEBUG', cast=bool)
 
 DOMAIN_SERVER = config("DOMAIN_SERVER")
-ALLOWED_HOSTS = config('ALLOWED_HOSTS', cast=Csv())
+ALLOWED_HOSTS: list = list(config('ALLOWED_HOSTS', cast=Csv()))
 ALLOWED_HOSTS += [DOMAIN_SERVER, '*']
 
-CSRF_TRUSTED_ORIGINS = config('CSRF_TRUSTED_ORIGINS', cast=Csv())
+CSRF_TRUSTED_ORIGINS: list = list(config('CSRF_TRUSTED_ORIGINS', cast=Csv()))
 CSRF_TRUSTED_ORIGINS += [f'http://{DOMAIN_SERVER}', f'https://{DOMAIN_SERVER}']
 
 SECURE_CROSS_ORIGIN_OPENER_POLICY = 'same-origin'
@@ -61,6 +59,7 @@ INSTALLED_APPS = [
     'django_celery_results',
     'celery',
     'home',
+    'backup',
     'scanner',
     'planarian',
 
@@ -216,12 +215,11 @@ LOCALE_PATHS = (
 
 STATIC_URL = '/static/'
 STATIC_ROOT = APP_DATAS / 'staticfiles'
-print("Django application STATIC_ROOT:", STATIC_ROOT)
 
 
 MEDIA_URL = '/media/'
 MEDIA_ROOT = APP_DATAS / 'media'
-print("Django application MEDIA_ROOT:", MEDIA_ROOT)
+print("Django application MEDIA_ROOT:", MEDIA_ROOT, "\nDjango application STATIC_ROOT:", STATIC_ROOT)
 
 
 """
@@ -239,8 +237,9 @@ DEFAULT_AUTO_FIELD = 'django.db.models.BigAutoField'
 ## LOGGING
 # CRITICAL=50, ERROR=40, WARN=30, INFO=20, DEBUG=10 and NOTSET=0
 
-LOGGING_FILE = config('LOGGING_FILE')
+LOGGING_FILE: str = str(config('LOGGING_FILE'))
 IS_LOGGING = config('IS_LOGGING', cast=bool)
+IS_LOGGING = False
 
 LOGGING = None if not IS_LOGGING else {
     'version': 1,
@@ -347,6 +346,7 @@ DJANGO_CELERY_BEAT_TZ_AWARE = False
 CELERY_ENABLE_UTC = True
 CELERY_TASK_TRACK_STARTED = True
 CELERY_TASK_TIME_LIMIT = 30 * 60
+CELERY_TASK_SOFT_TIME_LIMIT = 20 * 60
 CELERY_BEAT_SCHEDULER = 'django_celery_beat.schedulers:DatabaseScheduler'
 CELERY_ACCEPT_CONTENT = ['application/json']
 CELERY_RESULT_SERIALIZER = 'json'
@@ -356,6 +356,15 @@ CELERY_RESULT_EXTENDED = True
 CELERY_RESULT_BACKEND = 'django-db'
 DJANGO_CELERY_RESULTS_TASK_ID_MAX_LENGTH=191
 
+from celery.schedules import crontab
+
+CELERY_BEAT_SCHEDULE = {
+    "mariadb-backup-every-night": {
+        "task": "backup.tasks.backup_mariadb_task",
+        "schedule": crontab(hour=2, minute=0),
+    },
+}
+
 ## reductstore
 #
 REDUCTSTORE_TOKEN = config('REDUCTSTORE_TOKEN')
@@ -364,6 +373,8 @@ REDUCTSTORE_PORT = config('REDUCTSTORE_PORT', cast=int)
 REDUCTSTORE_URL = f'http://{REDUCTSTORE_HOST}:{REDUCTSTORE_PORT}'
 REDUCTSTORE_PATH = config("REDUCTSTORE_PATH")
 
+BACKUP_DIR = config('BACKUP_DIR')
+
 ## servers app
 #
 USER = config('USER')
@@ -371,6 +382,8 @@ GROUP = config('GROUP')
 SERVER_HOST_PORT = config('SERVER_HOST_PORT', cast=int)
 SERVER_HOST_IP = config('SERVER_HOST_IP')
 
+LOCAL_IP_SERVER = config('LOCAL_IP_SERVER')
+
 # ws
 SCANNER_WEBSOCKET_ROUTE = 'ws/scanner'
 REPLAY_WEBSOCKET_ROUTE = 'ws/replay'
@@ -385,20 +398,28 @@ DATETIME_FORMAT = '%d-%m-%Y-%m %H:%M:%S'
 #===========================
 # default configuration
 #
-#===========================
 # rpicam 4056x3040 2028x1080 2028x1520
+#===========================
+
+GRBL_SIMULATION = config('GRBL_SIMULATION', cast=bool)
 
 EXPORTS_LOCAL_PATH = config("EXPORTS_LOCAL_PATH")
 EXPORT_REMOTE_PATH = config("EXPORT_REMOTE_PATH")
+
 EXPORT_DESTINATIONS = ["local", "remote"]
+#EXPORT_DESTINATIONS = ["remote"] # only remote
 
-TEST_VIDEOFILE = False
+CSV_EXPORT_DIR = config("CSV_EXPORT_DIR")   # ou None pour mémoire uniquement
 
-TRACKING = True
+## tracker default parameters
+#
 TRACKER_TUBE_AXIS = "vertical"
-TRACKER_MIN_AREA = 200
+TRACKER_MIN_AREA = 20               # surface min planaire px x px
+TRACKER_MAX_AREA_RATIO = 0.1        # 5% de la frame = surface max acceptable
+TRACKER_MAX_PLANARIANS = 4         
+TRACKER_MERGE_KERNEL_SIZE = 15      # augmenter si fragments résiduels
+TRACKER_MIN_CONTOUR_DIST_PX = 40    # augmenter si IDs multiples persistent
 
 CALIBRATION_AUTO_DURATION = 45.0
 CALIBRATION_AUTO_TIMEOUT = 2.5
 
-

test_tube_scanner/home/static/css/doc_calibration.css

@@ -0,0 +1,98 @@
+/* ============================================================
+   doc_calibration.css
+   Styles spécifiques à la page de calibration du scanner.
+   Dépend de doc_database.css (variables, composants de base).
+   ============================================================ */
+
+/* ─── Badge teal ─── */
+.badge-teal {
+    background: rgba(45,212,191,.12);
+    color: var(--accent-teal);
+    border: 1px solid rgba(45,212,191,.3);
+}
+
+/* ─── Badge blue ─── */
+.badge-blue {
+    background: rgba(88,166,255,.12);
+    color: var(--accent-blue);
+    border: 1px solid rgba(88,166,255,.3);
+}
+
+/* ─── Tag teal ─── */
+.tag-teal {
+    background: rgba(45,212,191,.12);
+    color: var(--accent-teal);
+    border: 1px solid rgba(45,212,191,.2);
+}
+
+/* ─── Schéma des 3 zones de l'écran ─── */
+.screen-layout {
+    display: grid;
+    grid-template-columns: 1fr 2fr 1fr;
+    gap: 8px;
+    margin-bottom: 24px;
+    border: 1px solid var(--border);
+    border-radius: var(--radius);
+    overflow: hidden;
+    background: var(--bg-card);
+}
+
+.screen-zone {
+    display: flex;
+    flex-direction: column;
+    align-items: center;
+    justify-content: center;
+    gap: 8px;
+    padding: 20px 10px;
+    font-size: 12px;
+    font-weight: 600;
+    color: var(--text-secondary);
+    text-align: center;
+    border-right: 1px solid var(--border);
+    transition: background .15s;
+}
+.screen-zone:last-child { border-right: none; }
+.screen-zone i { font-size: 20px; }
+
+.zone-left   { color: var(--accent-indigo); }
+.zone-left   i { color: var(--accent-indigo); }
+.zone-center {
+    background: rgba(45,212,191,.04);
+    color: var(--accent-teal);
+}
+.zone-center i { font-size: 26px; color: var(--accent-teal); }
+.zone-right  { color: var(--accent-orange); }
+.zone-right  i { color: var(--accent-orange); }
+
+/* ─── Barre visuelle des seuils de centrage ─── */
+.center-bar {
+    display: flex;
+    margin-top: 12px;
+    border-radius: var(--radius-sm);
+    overflow: hidden;
+    height: 28px;
+    font-size: 11px;
+    font-weight: 700;
+}
+.cb-seg {
+    flex: 1;
+    display: flex;
+    align-items: center;
+    justify-content: center;
+}
+.cb-red    { background: rgba(248,81,73,.18);  color: var(--accent-red);    border: 1px solid rgba(248,81,73,.3);  }
+.cb-yellow { background: rgba(227,179,65,.18); color: var(--accent-yellow); border: 1px solid rgba(227,179,65,.3); }
+.cb-green  { background: rgba(63,185,80,.18);  color: var(--accent-green);  border: 1px solid rgba(63,185,80,.3);  }
+
+/* ─── Responsive ─── */
+@media (max-width: 768px) {
+    .screen-layout {
+        grid-template-columns: 1fr;
+    }
+    .screen-zone {
+        border-right: none;
+        border-bottom: 1px solid var(--border);
+        padding: 14px;
+    }
+    .screen-zone:last-child { border-bottom: none; }
+}

test_tube_scanner/home/static/css/doc_database.css

@@ -0,0 +1,521 @@
+/* ============================================================
+   doc_database.css
+   Feuille de style de la documentation base de données
+   Dépendances : w3.css, all.css (Font Awesome)
+   Fond sombre, style industriel/technique
+   ============================================================ */
+
+/* ─── Variables globales ─── */
+:root {
+    --bg-base:          #0d1117;
+    --bg-surface:       #161b22;
+    --bg-card:          #1c2128;
+    --bg-card-hover:    #21262d;
+    --border:           #30363d;
+    --border-strong:    #484f58;
+
+    --text-primary:     #e6edf3;
+    --text-secondary:   #8b949e;
+    --text-muted:       #6e7681;
+    --text-code:        #79c0ff;
+
+    --accent-blue:      #58a6ff;
+    --accent-cyan:      #39d353;
+    --accent-green:     #3fb950;
+    --accent-teal:      #2dd4bf;
+    --accent-orange:    #f0883e;
+    --accent-yellow:    #e3b341;
+    --accent-red:       #f85149;
+    --accent-purple:    #bc8cff;
+    --accent-indigo:    #818cf8;
+
+    --nav-width:        240px;
+    --header-h:         90px;
+    --radius:           8px;
+    --radius-sm:        4px;
+    --shadow:           0 4px 16px rgba(0,0,0,.4);
+    --font-mono:        'JetBrains Mono', 'Fira Code', 'Consolas', monospace;
+    --font-body:        'Segoe UI', system-ui, sans-serif;
+}
+
+/* ─── Reset minimal ─── */
+*, *::before, *::after { box-sizing: border-box; }
+
+a { color: var(--accent-blue); text-decoration: none; }
+/*a:hover { text-decoration: underline; }*/
+
+ul { padding: 0; margin: 0; list-style: none; }
+
+/* ─── Mise en page principale ─── */
+.doc-wrapper {
+    display: grid;
+    grid-template-columns: var(--nav-width) 1fr;
+    grid-template-rows: auto 1fr;
+    grid-template-areas:
+        "header  header"
+        "sidenav content";
+    min-height: 100vh;
+    background: var(--bg-base);
+    color: var(--text-primary);
+    font-family: var(--font-body);
+    font-size: 14px;
+    line-height: 1.6;
+}
+
+/* ─── En-tête ─── */
+.doc-header {
+    grid-area: header;
+    background: linear-gradient(135deg, #1a2236 0%, #0d1117 60%, #1a1a2e 100%);
+    border-bottom: 1px solid var(--border-strong);
+    padding: 20px 28px;
+}
+.doc-header-inner {
+    display: flex;
+    align-items: center;
+    gap: 18px;
+    max-width: 1200px;
+}
+.doc-header-icon {
+    width: 52px; height: 52px;
+    background: linear-gradient(135deg, var(--accent-blue), var(--accent-indigo));
+    border-radius: var(--radius);
+    display: flex; align-items: center; justify-content: center;
+    font-size: 22px;
+    color: #fff;
+    flex-shrink: 0;
+    box-shadow: 0 4px 12px rgba(88,166,255,.3);
+}
+.doc-title {
+    margin: 0;
+    font-size: 22px;
+    font-weight: 700;
+    color: var(--text-primary);
+}
+.doc-subtitle {
+    margin: 2px 0 0;
+    font-size: 13px;
+    color: var(--text-secondary);
+}
+
+/* ─── Navigation latérale ─── */
+.doc-sidenav {
+    grid-area: sidenav;
+    background: var(--bg-surface);
+    border-right: 1px solid var(--border);
+    padding: 20px 0;
+    position: sticky;
+    top: 0;
+    height: 100vh;
+    overflow-y: auto;
+}
+.nav-section-label {
+    font-size: 11px;
+    font-weight: 700;
+    text-transform: uppercase;
+    letter-spacing: .08em;
+    color: var(--text-muted);
+    padding: 0 16px 8px;
+    margin: 0;
+}
+.nav-link {
+    display: flex;
+    align-items: center;
+    gap: 8px;
+    padding: 7px 16px;
+    color: var(--text-secondary);
+    font-size: 13px;
+    transition: all .15s;
+    border-left: 2px solid transparent;
+}
+.nav-link:hover {
+    color: var(--text-primary);
+    background: var(--bg-card);
+    text-decoration: none;
+}
+.nav-link.active {
+    color: var(--accent-blue);
+    border-left-color: var(--accent-blue);
+    background: rgba(88,166,255,.08);
+}
+.nav-link.nav-sub {
+    padding-left: 28px;
+    font-size: 12.5px;
+}
+.nav-link.nav-sub-2 {
+    padding-left: 42px;
+    font-size: 12px;
+}
+
+/* ─── Contenu principal ─── */
+.doc-content {
+    grid-area: content;
+    padding: 28px 32px;
+    max-width: 1100px;
+}
+
+/* ─── Sections ─── */
+.doc-section {
+    margin-bottom: 48px;
+}
+.subsection {
+    margin-top: 32px;
+    padding-top: 24px;
+    border-top: 1px solid var(--border);
+}
+.sub-subsection {
+    margin-top: 24px;
+}
+
+.section-header {
+    margin-bottom: 20px;
+}
+.section-header h2 {
+    margin: 6px 0 6px;
+    font-size: 20px;
+    font-weight: 700;
+    color: var(--text-primary);
+    display: flex;
+    align-items: center;
+    gap: 10px;
+}
+.section-desc {
+    margin: 0;
+    color: var(--text-secondary);
+    font-size: 13px;
+}
+
+.subsection-title {
+    font-size: 16px;
+    font-weight: 600;
+    margin: 0 0 14px;
+    color: var(--text-primary);
+    display: flex;
+    align-items: center;
+    gap: 8px;
+}
+.table-title {
+    font-size: 14px;
+    font-weight: 600;
+    margin: 0 0 12px;
+    color: var(--text-primary);
+    display: flex;
+    align-items: center;
+    gap: 8px;
+    flex-wrap: wrap;
+}
+.table-desc {
+    color: var(--text-secondary);
+    font-weight: 400;
+    font-size: 12.5px;
+}
+
+/* ─── Badges de section ─── */
+.section-badge {
+    display: inline-block;
+    font-size: 10px;
+    font-weight: 700;
+    text-transform: uppercase;
+    letter-spacing: .06em;
+    padding: 2px 8px;
+    border-radius: 20px;
+    margin-bottom: 6px;
+}
+.badge-time    { background: rgba(57,211,83,.12);  color: var(--accent-green);  border: 1px solid rgba(57,211,83,.3); }
+.badge-orange  { background: rgba(240,136,62,.12); color: var(--accent-orange); border: 1px solid rgba(240,136,62,.3);}
+
+/* ─── Ligne de cartes ─── */
+.info-row {
+    display: flex;
+    gap: 14px;
+    flex-wrap: wrap;
+    margin-bottom: 14px;
+}
+
+/* ─── Cartes d'information ─── */
+.info-card {
+    background: var(--bg-card);
+    border: 1px solid var(--border);
+    border-radius: var(--radius);
+    padding: 16px;
+    display: flex;
+    gap: 14px;
+    flex: 1;
+    min-width: 220px;
+    transition: background .15s, box-shadow .15s;
+    border-left-width: 3px;
+}
+.info-card:hover {
+    background: var(--bg-card-hover);
+    box-shadow: var(--shadow);
+}
+.info-card.full-width { flex: 1 1 100%; }
+
+.card-icon {
+    width: 36px; height: 36px;
+    border-radius: var(--radius-sm);
+    display: flex; align-items: center; justify-content: center;
+    font-size: 16px;
+    flex-shrink: 0;
+    opacity: .85;
+}
+.card-body { flex: 1; min-width: 0; }
+.card-body h4 {
+    margin: 0 0 6px;
+    font-size: 13.5px;
+    font-weight: 600;
+    color: var(--text-primary);
+    display: flex;
+    align-items: center;
+    gap: 8px;
+    flex-wrap: wrap;
+}
+.card-body p {
+    margin: 0 0 8px;
+    color: var(--text-secondary);
+    font-size: 13px;
+}
+
+/* Accents colorés des cartes */
+.card-accent-blue   { border-left-color: var(--accent-blue);   }
+.card-accent-blue   .card-icon { background: rgba(88,166,255,.12); color: var(--accent-blue); }
+.card-accent-cyan   { border-left-color: var(--accent-cyan);   }
+.card-accent-cyan   .card-icon { background: rgba(57,211,83,.12);  color: var(--accent-cyan); }
+.card-accent-green  { border-left-color: var(--accent-green);  }
+.card-accent-green  .card-icon { background: rgba(63,185,80,.12);  color: var(--accent-green); }
+.card-accent-teal   { border-left-color: var(--accent-teal);   }
+.card-accent-teal   .card-icon { background: rgba(45,212,191,.12); color: var(--accent-teal); }
+.card-accent-orange { border-left-color: var(--accent-orange); }
+.card-accent-orange .card-icon { background: rgba(240,136,62,.12); color: var(--accent-orange); }
+.card-accent-yellow { border-left-color: var(--accent-yellow); }
+.card-accent-yellow .card-icon { background: rgba(227,179,65,.12); color: var(--accent-yellow); }
+.card-accent-red    { border-left-color: var(--accent-red);    }
+.card-accent-red    .card-icon { background: rgba(248,81,73,.12);  color: var(--accent-red); }
+.card-accent-purple { border-left-color: var(--accent-purple); }
+.card-accent-purple .card-icon { background: rgba(188,140,255,.12);color: var(--accent-purple); }
+.card-accent-indigo { border-left-color: var(--accent-indigo); }
+.card-accent-indigo .card-icon { background: rgba(129,140,248,.12);color: var(--accent-indigo); }
+
+/* ─── Lien d'accès ─── */
+.access-link {
+    font-family: var(--font-mono);
+    font-size: 12.5px;
+    color: var(--accent-blue);
+    word-break: break-all;
+}
+.access-link .fa-external-link-alt { font-size: 10px; margin-left: 4px; }
+
+/* ─── Listes documentaires ─── */
+.doc-list {
+    display: flex;
+    flex-direction: column;
+    gap: 6px;
+    margin: 0;
+    padding: 0;
+}
+.doc-list li {
+    display: flex;
+    align-items: flex-start;
+    gap: 8px;
+    color: var(--text-secondary);
+    font-size: 13px;
+    padding: 4px 0;
+    border-bottom: 1px solid rgba(48,54,61,.5);
+}
+.doc-list li:last-child { border-bottom: none; }
+.doc-list li i {
+    width: 16px;
+    text-align: center;
+    margin-top: 2px;
+    flex-shrink: 0;
+}
+
+/* ─── Tags ─── */
+.tag-list {
+    display: flex;
+    flex-wrap: wrap;
+    gap: 6px;
+    margin-top: 8px;
+}
+.tag-list.inline {
+    display: inline-flex;
+    margin-top: 0;
+    margin-left: 4px;
+}
+.tag {
+    font-size: 11px;
+    padding: 2px 8px;
+    border-radius: 20px;
+    font-weight: 600;
+}
+.tag-blue   { background: rgba(88,166,255,.12);  color: var(--accent-blue);   border: 1px solid rgba(88,166,255,.2); }
+.tag-green  { background: rgba(63,185,80,.12);   color: var(--accent-green);  border: 1px solid rgba(63,185,80,.2); }
+.tag-orange { background: rgba(240,136,62,.12);  color: var(--accent-orange); border: 1px solid rgba(240,136,62,.2);}
+.tag-gray   { background: rgba(110,118,129,.12); color: var(--text-secondary);border: 1px solid rgba(110,118,129,.2);}
+
+/* ─── Grille de puits ─── */
+.well-grid {
+    display: flex;
+    flex-wrap: wrap;
+    gap: 6px;
+    margin-top: 10px;
+}
+
+/* Grille serpentin : 6 colonnes fixes, 4 lignes (D/C/B/A) */
+.well-grid--serpentine {
+    display: grid;
+    grid-template-columns: repeat(6, 1fr);
+    gap: 5px;
+    margin-top: 12px;
+}
+
+.well-chip {
+    font-family: var(--font-mono);
+    font-size: 12px;
+    font-weight: 700;
+    padding: 5px 4px;
+    border-radius: var(--radius-sm);
+    text-align: center;
+    letter-spacing: .03em;
+    /* couleur par défaut (teal) */
+    background: rgba(45,212,191,.1);
+    border: 1px solid rgba(45,212,191,.25);
+    color: var(--accent-teal);
+}
+
+/* Couleurs distinctes par ligne */
+.wc-d {
+    background: rgba(248,81,73,.10);
+    border-color: rgba(248,81,73,.25);
+    color: var(--accent-red);
+}
+.wc-c {
+    background: rgba(240,136,62,.10);
+    border-color: rgba(240,136,62,.25);
+    color: var(--accent-orange);
+}
+.wc-b {
+    background: rgba(88,166,255,.10);
+    border-color: rgba(88,166,255,.25);
+    color: var(--accent-blue);
+}
+.wc-a {
+    background: rgba(63,185,80,.10);
+    border-color: rgba(63,185,80,.25);
+    color: var(--accent-green);
+}
+
+/* ─── Grille de position multi-puits ─── */
+.position-grid {
+    display: grid;
+    grid-template-columns: 1fr 1fr;
+    gap: 8px;
+    margin: 10px 0;
+}
+.pos-cell {
+    background: rgba(129,140,248,.08);
+    border: 1px solid rgba(129,140,248,.2);
+    border-radius: var(--radius-sm);
+    padding: 8px 10px;
+    text-align: center;
+    font-weight: 700;
+    font-size: 13px;
+    color: var(--accent-indigo);
+    transition: background .15s;
+}
+.pos-cell.active:hover {
+    background: rgba(129,140,248,.18);
+}
+.pos-cell small {
+    display: block;
+    font-weight: 400;
+    font-size: 11px;
+    color: var(--text-secondary);
+}
+
+/* ─── Badges inline ─── */
+.badge-auto {
+    font-size: 10px;
+    background: rgba(63,185,80,.12);
+    color: var(--accent-green);
+    border: 1px solid rgba(63,185,80,.25);
+    padding: 1px 6px;
+    border-radius: 20px;
+    margin-left: 4px;
+    font-weight: 600;
+}
+.badge-important {
+    font-size: 10px;
+    background: rgba(248,81,73,.15);
+    color: var(--accent-red);
+    border: 1px solid rgba(248,81,73,.3);
+    padding: 1px 6px;
+    border-radius: 20px;
+    margin-left: 4px;
+    font-weight: 700;
+}
+
+/* ─── Boîte d'alerte ─── */
+.alert-box {
+    margin-top: 10px;
+    background: rgba(248,81,73,.08);
+    border: 1px solid rgba(248,81,73,.25);
+    border-radius: var(--radius-sm);
+    padding: 8px 12px;
+    color: var(--accent-red);
+    font-size: 12.5px;
+    font-weight: 600;
+    display: flex;
+    align-items: center;
+    gap: 8px;
+}
+
+/* ─── Description de tâche ─── */
+.task-desc {
+    margin: 3px 0 0;
+    color: var(--text-muted);
+    font-size: 12px;
+}
+
+/* ─── Aide contextuelle ─── */
+.hint {
+    margin: 8px 0 0;
+    color: var(--text-muted);
+    font-size: 12px;
+}
+
+/* ─── Code inline ─── */
+code {
+    font-family: var(--font-mono);
+    font-size: 12.5px;
+    color: var(--text-code);
+    background: rgba(88,166,255,.07);
+    padding: 1px 5px;
+    border-radius: 3px;
+    border: 1px solid rgba(88,166,255,.12);
+}
+
+/* ─── Couleurs utilitaires ─── */
+.text-gold  { color: #d4a017; }
+.text-blue  { color: var(--accent-blue); }
+.text-gray  { color: var(--text-muted); }
+.text-green { color: var(--accent-green); }
+.text-cyan  { color: var(--accent-cyan); }
+
+/* ─── Scrollbar personnalisée ─── */
+::-webkit-scrollbar { width: 6px; }
+::-webkit-scrollbar-track { background: var(--bg-base); }
+::-webkit-scrollbar-thumb { background: var(--border-strong); border-radius: 3px; }
+::-webkit-scrollbar-thumb:hover { background: var(--text-muted); }
+
+/* ─── Responsive ─── */
+@media (max-width: 768px) {
+    .doc-wrapper {
+        grid-template-columns: 1fr;
+        grid-template-areas:
+            "header"
+            "content";
+    }
+    .doc-sidenav { display: none; }
+    .doc-content { padding: 16px; }
+    .info-card { min-width: 100%; }
+}

test_tube_scanner/home/static/css/doc_experiments.css

@@ -0,0 +1,126 @@
+/* ============================================================
+   doc_experiments.css
+   Styles spécifiques à la page "Démarrer des expériences".
+   Dépend de doc_database.css + doc_calibration.css.
+   ============================================================ */
+
+/* ─── Badges supplémentaires ─── */
+.badge-green {
+    background: rgba(63,185,80,.12);
+    color: var(--accent-green);
+    border: 1px solid rgba(63,185,80,.3);
+}
+.badge-purple {
+    background: rgba(188,140,255,.12);
+    color: var(--accent-purple);
+    border: 1px solid rgba(188,140,255,.3);
+}
+.badge-orange {
+    background: rgba(240,136,62,.12);
+    color: var(--accent-orange);
+    border: 1px solid rgba(240,136,62,.3);
+}
+
+/* ─── Tags supplémentaires ─── */
+.tag-purple {
+    background: rgba(188,140,255,.12);
+    color: var(--accent-purple);
+    border: 1px solid rgba(188,140,255,.2);
+}
+.tag-yellow {
+    background: rgba(227,179,65,.12);
+    color: var(--accent-yellow);
+    border: 1px solid rgba(227,179,65,.2);
+}
+
+/* ─── Étapes numérotées ─── */
+ol.doc-steps {
+    list-style: none;
+    padding: 0;
+    margin: 8px 0 0;
+    counter-reset: step-counter;
+    display: flex;
+    flex-direction: column;
+    gap: 8px;
+}
+ol.doc-steps li {
+    display: flex;
+    align-items: flex-start;
+    gap: 10px;
+    color: var(--text-secondary);
+    font-size: 13px;
+    counter-increment: step-counter;
+    padding: 6px 8px;
+    background: rgba(255,255,255,.02);
+    border-radius: var(--radius-sm);
+    border: 1px solid var(--border);
+    transition: background .12s;
+}
+ol.doc-steps li:hover {
+    background: rgba(255,255,255,.05);
+}
+ol.doc-steps li::before {
+    content: counter(step-counter);
+    min-width: 20px;
+    height: 20px;
+    border-radius: 50%;
+    background: rgba(88,166,255,.15);
+    color: var(--accent-blue);
+    font-size: 11px;
+    font-weight: 700;
+    display: flex;
+    align-items: center;
+    justify-content: center;
+    flex-shrink: 0;
+    margin-top: 1px;
+}
+ol.doc-steps li i {
+    width: 16px;
+    text-align: center;
+    margin-top: 2px;
+    flex-shrink: 0;
+}
+
+/* ─── Alert info (bleu, non critique) ─── */
+.alert-box.alert-info {
+    background: rgba(88,166,255,.08);
+    border-color: rgba(88,166,255,.25);
+    color: var(--accent-blue);
+}
+
+/* ─── Titre de groupe de métriques ─── */
+.metrics-group-title {
+    font-size: 13px;
+    font-weight: 600;
+    color: var(--text-secondary);
+    margin: 16px 0 10px;
+    display: flex;
+    align-items: center;
+    gap: 8px;
+    text-transform: uppercase;
+    letter-spacing: .05em;
+}
+.metrics-group-title i {
+    color: var(--text-muted);
+}
+
+/* ─── Cartes métriques : padding réduit ─── */
+.metrics-card {
+    min-width: 180px;
+}
+.metrics-card .card-body h4 {
+    font-size: 13px;
+    margin-bottom: 8px;
+}
+
+/* ─── Tags métriques : inline compact ─── */
+.metric-tags {
+    display: flex;
+    flex-wrap: wrap;
+    gap: 5px;
+    margin-top: 4px;
+}
+.metric-tags .tag {
+    font-family: var(--font-mono);
+    font-size: 11px;
+}

test_tube_scanner/home/static/css/doc_media.css

@@ -0,0 +1,114 @@
+/* ============================================================
+   doc_media.css
+   Styles spécifiques à la page "Gestionnaire de médias".
+   Dépend de doc_database.css + doc_calibration.css
+                              + doc_experiments.css
+                              + doc_scanning.css
+                              + doc_results.css.
+   ============================================================ */
+
+/* ─── Badge purple ─── */
+.badge-purple {
+    background: rgba(188,140,255,.12);
+    color: var(--accent-purple);
+    border: 1px solid rgba(188,140,255,.3);
+}
+
+/* ─── Prévisualisation grille ─── */
+.grid-preview {
+    display: flex;
+    align-items: center;
+    gap: 10px;
+    margin-top: 14px;
+    flex-wrap: wrap;
+}
+
+.gp-col {
+    width: 28px; height: 28px;
+    border-radius: 50%;
+    background: rgba(188,140,255,.12);
+    border: 1px solid rgba(188,140,255,.25);
+    color: var(--accent-purple);
+    display: flex; align-items: center; justify-content: center;
+    font-size: 13px;
+    cursor: default;
+}
+
+/* Chaque démo de grille */
+.gp-demo {
+    display: grid;
+    gap: 3px;
+    flex: 1;
+    min-width: 60px;
+    max-width: 120px;
+}
+.gp-demo span {
+    height: 22px;
+    border-radius: 3px;
+    background: rgba(188,140,255,.15);
+    border: 1px solid rgba(188,140,255,.2);
+}
+.gp-2 { grid-template-columns: repeat(2, 1fr); }
+.gp-3 { grid-template-columns: repeat(3, 1fr); }
+.gp-4 { grid-template-columns: repeat(4, 1fr); }
+
+/* ─── Contrôles lecteur vidéo ─── */
+.player-controls {
+    display: flex;
+    gap: 8px;
+    margin-top: 10px;
+    flex-wrap: wrap;
+}
+
+.player-btn {
+    display: flex;
+    flex-direction: column;
+    align-items: center;
+    gap: 4px;
+    padding: 10px 16px;
+    border-radius: var(--radius-sm);
+    font-size: 11px;
+    font-weight: 600;
+    flex: 1;
+    min-width: 60px;
+    border: 1px solid var(--border);
+    transition: background .15s;
+}
+.player-btn i { font-size: 16px; }
+.player-btn span { color: var(--text-secondary); }
+
+.btn-play {
+    background: rgba(63,185,80,.08);
+    border-color: rgba(63,185,80,.25);
+    color: var(--accent-green);
+}
+.btn-play:hover  { background: rgba(63,185,80,.16); }
+
+.btn-pause {
+    background: rgba(227,179,65,.08);
+    border-color: rgba(227,179,65,.25);
+    color: var(--accent-yellow);
+}
+.btn-pause:hover { background: rgba(227,179,65,.16); }
+
+.btn-stop {
+    background: rgba(248,81,73,.08);
+    border-color: rgba(248,81,73,.25);
+    color: var(--accent-red);
+}
+.btn-stop:hover  { background: rgba(248,81,73,.16); }
+
+/* ─── Badge export différé ─── */
+.deferred-badge {
+    display: inline-flex;
+    align-items: center;
+    gap: 6px;
+    margin-top: 10px;
+    padding: 5px 12px;
+    border-radius: 20px;
+    font-size: 12px;
+    font-weight: 600;
+    background: rgba(45,212,191,.08);
+    border: 1px solid rgba(45,212,191,.25);
+    color: var(--accent-teal);
+}

test_tube_scanner/home/static/css/doc_results.css

@@ -0,0 +1,32 @@
+/* ============================================================
+   doc_results.css
+   Styles spécifiques à la page "Exploiter les résultats".
+   Dépend de doc_database.css + doc_calibration.css
+                              + doc_experiments.css
+                              + doc_scanning.css.
+   ============================================================ */
+
+/* ─── Bloc chemin serveur ─── */
+.path-block {
+    display: flex;
+    align-items: center;
+    gap: 12px;
+    margin-top: 10px;
+    padding: 10px 14px;
+    background: rgba(45,212,191,.06);
+    border: 1px solid rgba(45,212,191,.2);
+    border-radius: var(--radius-sm);
+    color: var(--accent-teal);
+}
+.path-block i {
+    font-size: 16px;
+    flex-shrink: 0;
+}
+.path-block code {
+    color: var(--accent-teal);
+    background: transparent;
+    border: none;
+    font-size: 13px;
+    letter-spacing: .03em;
+    word-break: break-all;
+}

test_tube_scanner/home/static/css/doc_scanning.css

@@ -0,0 +1,54 @@
+/* ============================================================
+   doc_scanning.css
+   Styles spécifiques à la page "Balayage des puits".
+   Dépend de doc_database.css + doc_calibration.css
+                              + doc_experiments.css.
+   ============================================================ */
+
+/* ─── Badge indigo ─── */
+.badge-indigo {
+    background: rgba(129,140,248,.12);
+    color: var(--accent-indigo);
+    border: 1px solid rgba(129,140,248,.3);
+}
+
+/* ─── Badge red ─── */
+.badge-red {
+    background: rgba(248,81,73,.12);
+    color: var(--accent-red);
+    border: 1px solid rgba(248,81,73,.3);
+}
+
+/* ─── Badge superadmin ─── */
+.badge-superadmin {
+    font-size: 10px;
+    background: rgba(188,140,255,.15);
+    color: var(--accent-purple);
+    border: 1px solid rgba(188,140,255,.3);
+    padding: 1px 8px;
+    border-radius: 20px;
+    margin-left: 6px;
+    font-weight: 700;
+    font-family: var(--font-mono);
+}
+
+/* ─── Exemple UUID ─── */
+.uuid-example {
+    display: flex;
+    align-items: center;
+    gap: 10px;
+    margin-top: 10px;
+    padding: 8px 12px;
+    background: rgba(227,179,65,.06);
+    border: 1px dashed rgba(227,179,65,.25);
+    border-radius: var(--radius-sm);
+    color: var(--accent-yellow);
+    font-size: 12.5px;
+}
+.uuid-example code {
+    color: var(--accent-yellow);
+    background: transparent;
+    border: none;
+    font-size: 12.5px;
+    letter-spacing: .04em;
+}

test_tube_scanner/home/static/js/w3-custom.js

@@ -1,6 +1,6 @@
 /*
 ** custom.js
-** GNU GENERAL PUBLIC LICENSE: (c) DD miraceti.net return document.querySelectorAll(id);
+** GNU GENERAL PUBLIC LICENSE: (c) DD miraceti.net 
 */
 let s   = function(sel) 			{ return document.querySelector(sel);  };
 let ss  = function(sel)             { return document.querySelectorAll(sel);  };
@@ -40,3 +40,13 @@ function timestampToLocalISOString(timestamp) {
     return toLocalISOString(date);
 }
 
+function getCookie(name) {
+    const match = document.cookie.match('(?:^|; )' + name + '=([^;]*)');
+    return match ? decodeURIComponent(match[1]) : null;
+}
+
+function csrfFetch(url, options = {}) {
+    options.headers = { ...(options.headers || {}), 'X-CSRFToken': getCookie('csrftoken') };
+    return fetch(url, options);
+}
+

test_tube_scanner/home/templates/docs/doc_calibration.html

@@ -0,0 +1,473 @@
+{% extends 'scanner/base.html' %}
+{% load i18n %}
+{% block columns %}{% endblock %}
+
+{% block styles %}
+    {{ block.super }}
+    <link rel="stylesheet" href="/static/css/doc_database.css">
+    <link rel="stylesheet" href="/static/css/doc_calibration.css">   
+{% endblock %}
+
+{% block content %}
+<div class="doc-wrapper">
+
+    <!-- ─── En-tête ─── -->
+    <header class="doc-header">
+        <div class="doc-header-inner">
+            <div class="doc-header-icon" style="background: linear-gradient(135deg, var(--accent-teal), var(--accent-blue));">
+                <i class="fas fa-crosshairs"></i>
+            </div>
+            <div>
+                <h1 class="doc-title">{% trans "Calibration du scanner" %}</h1>
+                <p class="doc-subtitle">{% trans "Procédure, organisation de l'écran et commandes disponibles" %}</p>
+            </div>
+        </div>
+    </header>
+
+    <!-- ─── Navigation latérale ─── -->
+    <nav class="doc-sidenav" id="sidenav">
+        <p class="nav-section-label">{% trans "Navigation" %}</p>
+        <a href="#section-intro"     class="nav-link active"><i class="fas fa-info-circle"></i>   {% trans "Présentation" %}</a>
+        <a href="#section-screen"    class="nav-link">       <i class="fas fa-desktop"></i>        {% trans "Organisation écran" %}</a>
+        <a href="#section-left"      class="nav-link nav-sub"><i class="fas fa-arrows-alt"></i>   {% trans "Panneau gauche" %}</a>
+        <a href="#section-center"    class="nav-link nav-sub"><i class="fas fa-video"></i>         {% trans "Centre — vidéo live" %}</a>
+        <a href="#section-right"     class="nav-link nav-sub"><i class="fas fa-sliders-h"></i>    {% trans "Panneau droit" %}</a>
+        <a href="#section-centering" class="nav-link nav-sub-2"><i class="fas fa-dot-circle"></i> {% trans "Centrage" %}</a>
+        <a href="#section-base"      class="nav-link nav-sub-2"><i class="fas fa-map-pin"></i>    {% trans "Définir la base" %}</a>
+    </nav>
+
+    <!-- ─── Contenu principal ─── -->
+    <main class="doc-content">
+
+        <!-- ============================================================ -->
+        <!-- SECTION 1 : Présentation                                      -->
+        <!-- ============================================================ -->
+        <section class="doc-section" id="section-intro">
+            <div class="section-header">
+                <span class="section-badge badge-teal">{% trans "Prérequis" %}</span>
+                <h2><i class="fas fa-crosshairs"></i> {% trans "Calibration" %}</h2>
+                <p class="section-desc">
+                    {% trans "La calibration est indispensable au fonctionnement du scanner." %}<br>
+                    <i class="fas fa-exclamation-triangle w3-text-red"></i> {% trans "Affichage des logs en bas de page" %}
+                </p>
+            </div>
+            <div class="info-row">
+                <!-- Pourquoi calibrer -->
+                <div class="info-card card-accent-teal">
+                    <div class="card-icon"><i class="fas fa-bullseye"></i></div>
+                    <div class="card-body">
+                        <h4>{% trans "Objectifs" %}</h4>
+                        <ul class="doc-list">
+                            <li>
+                                <i class="fas fa-camera text-blue"></i>
+                                {% trans "Pointer l'axe de la caméra dans l'axe du tube." %}
+                            </li>
+                            <li>
+                                <i class="fas fa-crop-alt text-cyan"></i>
+                                {% trans "Recadrer l'image pour porter l'origine du suivi des planaires au centre du tube." %}
+                            </li>
+                        </ul>
+                    </div>
+                </div>
+
+                <!-- Avantage recadrage -->
+                <div class="info-card card-accent-green">
+                    <div class="card-icon"><i class="fas fa-compress-arrows-alt"></i></div>
+                    <div class="card-body">
+                        <h4>{% trans "Avantage du recadrage" %}</h4>
+                        <ul class="doc-list">
+                            <li>
+                                <i class="fas fa-hdd text-green"></i>
+                                {% trans "Réduit la taille des images stockées." %}
+                            </li>
+                        </ul>
+                    </div>
+                </div>
+            </div>
+
+            <!-- IMPORTANT : base de départ -->
+            <div class="info-row">
+                <div class="info-card card-accent-red full-width">
+                    <div class="card-icon"><i class="fas fa-exclamation-triangle"></i></div>
+                    <div class="card-body">
+                        <h4>{% trans "IMPORTANT — Avant toute manipulation" %} <span class="badge-important">{% trans "IMPORTANT" %}</span></h4>
+                        <p>{% trans "Pour tout multi-puits, trouver la base de départ avant de commencer." %}</p>
+                    </div>
+                </div>
+            </div>
+        </section>
+
+        <!-- ============================================================ -->
+        <!-- SECTION 2 : Organisation de l'écran                          -->
+        <!-- ============================================================ -->
+        <section class="doc-section" id="section-screen">
+            <div class="section-header">
+                <span class="section-badge badge-blue">{% trans "Interface" %}</span>
+                <h2><i class="fas fa-desktop"></i> {% trans "Organisation de l'écran" %}</h2>
+                <p class="section-desc">{% trans "L'écran de calibration est divisé en trois zones fonctionnelles." %}</p>
+            </div>
+
+            <!-- Schéma des 3 zones -->
+            <div class="screen-layout">
+                <div class="screen-zone zone-left">
+                    <i class="fas fa-arrows-alt"></i>
+                    <span>{% trans "Déplacements" %}</span>
+                </div>
+                <div class="screen-zone zone-center">
+                    <i class="fas fa-video"></i>
+                    <span>{% trans "Vidéo live" %}</span>
+                </div>
+                <div class="screen-zone zone-right">
+                    <i class="fas fa-sliders-h"></i>
+                    <span>{% trans "Commandes" %}</span>
+                </div>
+            </div>
+
+            <!-- ─── Panneau GAUCHE ─── -->
+            <div class="subsection" id="section-left">
+                <h3 class="subsection-title">
+                    <i class="fas fa-arrow-left"></i> {% trans "Panneau gauche — Déplacements caméra" %}
+                </h3>
+
+                <div class="info-row">
+                    <!-- Sélection & vitesse -->
+                    <div class="info-card card-accent-indigo">
+                        <div class="card-icon"><i class="fas fa-exchange-alt"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Sélection & vitesse" %}</h4>
+                            <ul class="doc-list">
+                                <li><i class="fas fa-th"></i> {% trans "Changer de multi-puits" %}</li>
+                                <li><i class="fas fa-tachometer-alt"></i> {% trans "Modifier la vitesse (mm/mn)" %}</li>
+                                <li><i class="fas fa-ruler-horizontal"></i> {% trans "Modifier le pas de déplacement (mm)" %}</li>
+                            </ul>
+                        </div>
+                    </div>
+
+                    <!-- Manœuvre manuelle -->
+                    <div class="info-card card-accent-blue">
+                        <div class="card-icon"><i class="fas fa-gamepad"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Manœuvre manuelle" %}</h4>
+                            <ul class="doc-list">
+                                <li>
+                                    <i class="fas fa-arrows-alt"></i>
+                                    {% trans "Déplacement" %}
+                                    <div class="tag-list inline">
+                                        <span class="tag tag-blue">±X</span>
+                                        <span class="tag tag-blue">±Y</span>
+                                    </div>
+                                </li>
+                                <li><i class="fas fa-save"></i> {% trans "Sauver la position courante" %}</li>
+                            </ul>
+                        </div>
+                    </div>
+
+                    <!-- Déplacement puit à puit -->
+                    <div class="info-card card-accent-cyan">
+                        <div class="card-icon"><i class="fas fa-step-forward"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Navigation puit à puit" %}</h4>
+                            <ul class="doc-list">
+                                <li><i class="fas fa-arrow-right text-cyan"></i> {% trans "Boutons de déplacement puit à puit" %}</li>
+                                <li><i class="fas fa-compress-arrows-alt text-cyan"></i> {% trans "Bouton centrage manuel" %}</li>
+                                <li><i class="fas fa-magic text-cyan"></i> {% trans "Bouton calibrage automatique" %}</li>
+                            </ul>
+                        </div>
+                    </div>
+                </div>
+
+                <!-- Sous-section : Définir la base -->
+                <div class="sub-subsection" id="section-base">
+                    <h4 class="table-title">
+                        <i class="fas fa-map-pin"></i>
+                        {% trans "Définir la base" %}
+                        <span class="badge-important">{% trans "IMPORTANT" %}</span>
+                    </h4>
+
+                    <div class="info-row">
+                        <!-- Création en BDD -->
+                        <div class="info-card card-accent-orange">
+                            <div class="card-icon"><i class="fas fa-database"></i></div>
+                            <div class="card-body">
+                                <h4>{% trans "À la création du multi-puits en base" %}</h4>
+                                <ul class="doc-list">
+                                    <li>
+                                        <i class="fas fa-map-marker-alt text-orange"></i>
+                                        {% trans "Fixe la base par défaut en" %} <code>(50, 50)</code>
+                                    </li>
+                                    <li>
+                                        <i class="fas fa-calculator text-orange"></i>
+                                        {% trans "Calcule et enregistre toutes les positions des puits dans" %}
+                                        <code>scanner.wellposition</code>
+                                        <p class="task-desc">
+                                            <i class="fas fa-bolt text-green"></i>
+                                            {% trans "Permet de gagner du temps au centrage manuel ou automatique." %}
+                                        </p>
+                                    </li>
+                                </ul>
+                            </div>
+                        </div>
+
+                        <!-- Donnée positions générées -->
+                        <div class="info-card card-accent-yellow">
+                            <div class="card-icon"><i class="fas fa-sync-alt"></i></div>
+                            <div class="card-body">
+                                <h4>
+                                    {% trans "Positions générées" %} — <code>scanner.multiwell</code>
+                                    <span class="badge-important">{% trans "ATTENTION" %}</span>
+                                </h4>
+                                <ul class="doc-list">
+                                    <li>
+                                        <i class="fas fa-check-circle text-green"></i>
+                                        {% trans "À la création : donnée fixée à" %} <strong>{% trans "Oui" %}</strong>
+                                    </li>
+                                    <li>
+                                        <i class="fas fa-times-circle text-red"></i>
+                                        {% trans "Non → efface" %} <code>WellPosition</code>
+                                        {% trans "et recalcule toutes les positions" %}
+                                    </li>
+                                </ul>
+                            </div>
+                        </div>
+                    </div>
+
+                    <!-- Bouton Définir la base -->
+                    <div class="info-row">
+                        <div class="info-card card-accent-blue full-width">
+                            <div class="card-icon"><i class="fas fa-flag-checkered"></i></div>
+                            <div class="card-body">
+                                <h4>{% trans "Bouton « Définir la base »" %}</h4>
+                                <ul class="doc-list">
+                                    <li>
+                                        <i class="fas fa-map-marker text-blue"></i>
+                                        {% trans "Fixe la base aux coordonnées" %} <code>(X, Y)</code> {% trans "courantes" %}
+                                    </li>
+                                    <li>
+                                        <i class="fas fa-redo text-blue"></i>
+                                        {% trans "Recalcule toutes les positions des puits dans" %} <code>scanner.wellposition</code>
+                                    </li>
+                                </ul>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+
+                <!-- Sous-section : Centrage -->
+                <div class="sub-subsection" id="section-centering">
+                    <h4 class="table-title">
+                        <i class="fas fa-dot-circle"></i>
+                        {% trans "Centrage manuel / automatique" %}
+                        <span class="badge-important">{% trans "ATTENTION" %}</span>
+                    </h4>
+
+                    <div class="info-row">
+                        <!-- Conditions -->
+                        <div class="info-card card-accent-purple">
+                            <div class="card-icon"><i class="fas fa-lightbulb"></i></div>
+                            <div class="card-body">
+                                <h4>{% trans "Conditions requises" %}</h4>
+                                <ul class="doc-list">
+                                    <li>
+                                        <i class="fas fa-sun text-yellow"></i>
+                                        {% trans "Éclairage important des puits — éviter les ombres." %}
+                                    </li>
+                                    <li>
+                                        <i class="fas fa-toggle-on text-blue"></i>
+                                        {% trans "Actif uniquement si Debug" %} <strong>{% trans "ET" %}</strong> {% trans "Recadrage activés (commandes à droite)." %}
+                                    </li>
+                                </ul>
+                            </div>
+                        </div>
+
+                        <!-- Indicateurs visuels -->
+                        <div class="info-card card-accent-indigo">
+                            <div class="card-icon"><i class="fas fa-circle-notch"></i></div>
+                            <div class="card-body">
+                                <h4>{% trans "Indicateurs visuels de centrage" %}</h4>
+                                <ul class="doc-list">
+                                    <li>
+                                        <i class="fas fa-circle" style="color:#f85149;"></i>
+                                        <strong class="text-red">{% trans "Cercle rouge" %}</strong>
+                                        — {% trans "déplacement centre" %} <code>&lt; 20 px</code>
+                                    </li>
+                                    <li>
+                                        <i class="fas fa-circle" style="color:#e3b341;"></i>
+                                        <strong style="color:var(--accent-yellow);">{% trans "Cercle jaune" %}</strong>
+                                        — {% trans "au plus près" %} <code>&lt; 5 px</code>
+                                    </li>
+                                    <li>
+                                        <i class="fas fa-circle" style="color:#3fb950;"></i>
+                                        <strong class="text-green">{% trans "Cercle vert" %}</strong>
+                                        — {% trans "centré" %}
+                                    </li>
+                                </ul>
+                                <!-- Barre visuelle des seuils -->
+                                <div class="center-bar">
+                                    <div class="cb-seg cb-red">
+                                        <span>&lt; 20 px</span>
+                                    </div>
+                                    <div class="cb-seg cb-yellow">
+                                        <span>&lt; 5 px</span>
+                                    </div>
+                                    <div class="cb-seg cb-green">
+                                        <span>{% trans "OK" %}</span>
+                                    </div>
+                                </div>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+            </div>
+
+            <!-- ─── CENTRE ─── -->
+            <div class="subsection" id="section-center">
+                <h3 class="subsection-title">
+                    <i class="fas fa-video"></i> {% trans "Centre — Vidéo live" %}
+                </h3>
+                <div class="info-row">
+                    <div class="info-card card-accent-teal full-width">
+                        <div class="card-icon"><i class="fas fa-film"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Flux vidéo en temps réel" %}</h4>
+                            <p>{% trans "Affiche le flux caméra en direct, avec ou sans recadrage selon l'état de la commande." %}</p>
+                            <div class="tag-list">
+                                <span class="tag tag-teal">{% trans "Recadrage actif" %}</span>
+                                <span class="tag tag-gray">{% trans "Image pleine" %}</span>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+            </div>
+
+            <!-- ─── PANNEAU DROIT ─── -->
+            <div class="subsection" id="section-right">
+                <h3 class="subsection-title">
+                    <i class="fas fa-arrow-right"></i> {% trans "Panneau droit — Commandes" %}
+                </h3>
+
+                <div class="info-row">
+                    <!-- Navigation rapide -->
+                    <div class="info-card card-accent-blue">
+                        <div class="card-icon"><i class="fas fa-location-arrow"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Navigation rapide" %}</h4>
+                            <ul class="doc-list">
+                                <li><i class="fas fa-home text-blue"></i> {% trans "Déplacer à l'origine (0, 0)" %}</li>
+                                <li><i class="fas fa-map-pin text-blue"></i> {% trans "Aller à la base du multi-puits" %}</li>
+                            </ul>
+                        </div>
+                    </div>
+
+                    <!-- Bascules -->
+                    <div class="info-card card-accent-indigo">
+                        <div class="card-icon"><i class="fas fa-toggle-on"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Bascules" %}</h4>
+                            <ul class="doc-list">
+                                <li>
+                                    <i class="fas fa-bug text-purple"></i>
+                                    {% trans "Debug" %}
+                                    <div class="tag-list inline">
+                                        <span class="tag tag-green">{% trans "Oui" %}</span>
+                                        <span class="tag tag-gray">{% trans "Non" %}</span>
+                                    </div>
+                                </li>
+                                <li>
+                                    <i class="fas fa-ruler-combined text-purple"></i>
+                                    {% trans "Tracer axes" %}
+                                    <div class="tag-list inline">
+                                        <span class="tag tag-green">{% trans "Oui" %}</span>
+                                        <span class="tag tag-gray">{% trans "Non" %}</span>
+                                    </div>
+                                </li>
+                                <li>
+                                    <i class="fas fa-crop-alt text-purple"></i>
+                                    {% trans "Recadrage" %}
+                                    <div class="tag-list inline">
+                                        <span class="tag tag-green">{% trans "Oui" %}</span>
+                                        <span class="tag tag-gray">{% trans "Non" %}</span>
+                                    </div>
+                                </li>
+                            </ul>
+                        </div>
+                    </div>
+                </div>
+
+                <div class="info-row">
+                    <!-- Rayon de recadrage -->
+                    <div class="info-card card-accent-cyan">
+                        <div class="card-icon"><i class="fas fa-circle-notch"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Rayon de recadrage" %}</h4>
+                            <p>{% trans "Ajuster le recadrage en pixels." %}</p>
+                        </div>
+                    </div>
+
+                    <!-- Durée test -->
+                    <div class="info-card card-accent-orange">
+                        <div class="card-icon"><i class="fas fa-stopwatch"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Durée entre puits" %}</h4>
+                            <p>{% trans "Durée de pause entre chaque puit lors du test du circuit." %}</p>
+                        </div>
+                    </div>
+
+                    <!-- Tester le circuit -->
+                    <div class="info-card card-accent-green">
+                        <div class="card-icon"><i class="fas fa-route"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Tester le circuit" %}</h4>
+                            <p>{% trans "Vérifier les déplacements en parcourant automatiquement tous les puits." %}</p>
+                        </div>
+                    </div>
+                </div>
+
+                <!-- ARRÊT -->
+                <div class="info-row">
+                    <div class="info-card card-accent-red full-width">
+                        <div class="card-icon"><i class="fas fa-hand-paper"></i></div>
+                        <div class="card-body">
+                            <h4>
+                                {% trans "ARRÊT" %}
+                                <span class="badge-important">{% trans "URGENCE" %}</span>
+                            </h4>
+                            <div class="alert-box">
+                                <i class="fas fa-stop-circle"></i>
+                                {% trans "Stoppe immédiatement tout mouvement du scanner." %}
+                            </div>
+                        </div>
+                    </div>
+                </div>
+
+            </div><!-- end section-right -->
+        </section><!-- end section-screen -->
+
+    </main>
+</div>
+{% endblock %}
+
+{% block js_footer %}
+    {{ block.super }}
+	<script>
+	/* Mise en évidence du lien actif dans la navigation latérale */
+	(function () {
+	    const links    = document.querySelectorAll('.nav-link');
+	    const sections = document.querySelectorAll('[id^="section-"]');
+	
+	    const observer = new IntersectionObserver(
+	        (entries) => {
+	            entries.forEach(entry => {
+	                if (entry.isIntersecting) {
+	                    links.forEach(l => l.classList.remove('active'));
+	                    const target = document.querySelector(`.nav-link[href="#${entry.target.id}"]`);
+	                    if (target) target.classList.add('active');
+	                }
+	            });
+	        },
+	        { rootMargin: '-10% 0px -80% 0px' }
+	    );
+	
+	    sections.forEach(s => observer.observe(s));
+	})();
+	</script> 
+{% endblock %}

test_tube_scanner/home/templates/docs/doc_database.html

@@ -0,0 +1,510 @@
+{% extends 'scanner/base.html' %}
+{% load i18n %}
+
+{% block columns %}{% endblock %}
+
+{% block styles %}
+    {{ block.super }}
+    <link href="/static/css/doc_database.css" rel="stylesheet">
+{% endblock %}
+
+{% block content %}
+<div class="doc-wrapper">
+
+    <!-- En-tête de la documentation -->
+    <header class="doc-header">
+        <div class="doc-header-inner">
+            <div class="doc-header-icon">
+                <i class="fas fa-database"></i>
+            </div>
+            <div>
+                <h1 class="doc-title">{% trans "Architecture des bases de données" %}</h1>
+                <p class="doc-subtitle">{% trans "Planarian Scanner — Infrastructure de stockage et modèles de données" %}</p>
+            </div>
+        </div>
+    </header>
+
+    <!-- Navigation latérale -->
+    <nav class="doc-sidenav" id="sidenav">
+        <p class="nav-section-label">{% trans "Navigation" %}</p>
+        <a href="#section-reductstore" class="nav-link active">
+            <i class="fas fa-wave-square"></i> ReductStore
+        </a>
+        <a href="#section-mariadb" class="nav-link">
+            <i class="fas fa-server"></i> MariaDB
+        </a>
+        <a href="#section-auth" class="nav-link nav-sub">
+            <i class="fas fa-shield-alt"></i> {% trans "Authentification" %}
+        </a>
+        <a href="#section-planarian" class="nav-link nav-sub">
+            <i class="fas fa-microscope"></i> Planarian
+        </a>
+        <a href="#section-scanner" class="nav-link nav-sub">
+            <i class="fas fa-camera"></i> Scanner
+        </a>
+        <a href="#section-config" class="nav-link nav-sub-2">
+            <i class="fas fa-sliders-h"></i> {% trans "Configuration" %}
+        </a>
+        <a href="#section-wells" class="nav-link nav-sub-2">
+            <i class="fas fa-circle"></i> {% trans "Puits" %}
+        </a>
+        <a href="#section-multiwell" class="nav-link nav-sub-2">
+            <i class="fas fa-th"></i> {% trans "Multi-puits" %}
+        </a>
+        <a href="#section-wellpos" class="nav-link nav-sub-2">
+            <i class="fas fa-map-marker-alt"></i> {% trans "Positions" %}
+        </a>
+        <a href="#section-experiments" class="nav-link nav-sub-2">
+            <i class="fas fa-flask"></i> {% trans "Expériences" %}
+        </a>
+        <a href="#section-sessions" class="nav-link nav-sub-2">
+            <i class="fas fa-play-circle"></i> {% trans "Sessions" %}
+        </a>
+        <a href="#section-celery" class="nav-link nav-sub-2">
+            <i class="fas fa-tasks"></i> Celery Beat
+        </a>
+    </nav>
+
+    <!-- Contenu principal -->
+    <main class="doc-content">
+
+        <!-- ============================================================ -->
+        <!-- SECTION 1 : ReductStore                                       -->
+        <!-- ============================================================ -->
+        <section class="doc-section" id="section-reductstore">
+            <div class="section-header">
+                <span class="section-badge badge-time">{% trans "Séries temporelles" %}</span>
+                <h2><i class="fas fa-wave-square"></i> ReductStore</h2>
+                <p class="section-desc">{% trans "Base de données de séries temporelles pour les images et métriques de l'application." %}</p>
+            </div>
+
+            <div class="info-row">
+                <div class="info-card card-accent-blue">
+                    <div class="card-icon"><i class="fas fa-link"></i></div>
+                    <div class="card-body">
+                        <h4>{% trans "Accès" %}</h4>
+                        <a href="http://192.168.1.200:8383/ui/dashboard" target="_blank" class="access-link">
+                            192.168.1.200:8383/ui/dashboard <i class="fas fa-external-link-alt"></i>
+                        </a>
+                    </div>
+                </div>
+            </div>
+
+            <h3 class="subsection-title"><i class="fas fa-bucket"></i> {% trans "Buckets" %}</h3>
+            <div class="info-row">
+                <div class="info-card card-accent-cyan">
+                    <div class="card-icon"><i class="fas fa-images"></i></div>
+                    <div class="card-body">
+                        <h4><code>camera</code></h4>
+                        <p>{% trans "Stockage des images capturées par la caméra." %}</p>
+                        <div class="tag-list">
+                            <span class="tag tag-blue">JPEG</span>
+                            <span class="tag tag-gray">{% trans "Séries temporelles" %}</span>
+                        </div>
+                    </div>
+                </div>
+                <div class="info-card card-accent-cyan">
+                    <div class="card-icon"><i class="fas fa-chart-line"></i></div>
+                    <div class="card-body">
+                        <h4><code>planarian_metrics</code></h4>
+                        <p>{% trans "Métriques de suivi des planaires." %}</p>
+                        <div class="tag-list">
+                            <span class="tag tag-green">JSON</span>
+                            <span class="tag tag-gray">{% trans "Séries temporelles" %}</span>
+                        </div>
+                    </div>
+                </div>
+            </div>
+        </section>
+
+        <!-- ============================================================ -->
+        <!-- SECTION 2 : MariaDB                                           -->
+        <!-- ============================================================ -->
+        <section class="doc-section" id="section-mariadb">
+            <div class="section-header">
+                <span class="section-badge badge-orange">{% trans "Base relationnelle" %}</span>
+                <h2><i class="fas fa-server"></i> MariaDB</h2>
+                <p class="section-desc">{% trans "Base de données relationnelle principale de l'application Django." %}</p>
+            </div>
+
+            <div class="info-row">
+                <div class="info-card card-accent-orange">
+                    <div class="card-icon"><i class="fas fa-database"></i></div>
+                    <div class="card-body">
+                        <h4>Adminer</h4>
+                        <a href="http://192.168.1.200/adminer/" target="_blank" class="access-link">
+                            192.168.1.200/adminer/ <i class="fas fa-external-link-alt"></i>
+                        </a>
+                    </div>
+                </div>
+                <div class="info-card card-accent-orange">
+                    <div class="card-icon"><i class="fas fa-user-shield"></i></div>
+                    <div class="card-body">
+                        <h4>{% trans "Administration Django" %}</h4>
+                        <a href="http://192.168.1.200/admin" target="_blank" class="access-link">
+                            192.168.1.200/admin <i class="fas fa-external-link-alt"></i>
+                        </a>
+                    </div>
+                </div>
+            </div>
+
+            <!-- -------------------------------------------------------- -->
+            <!-- Authentification                                          -->
+            <!-- -------------------------------------------------------- -->
+            <div class="subsection" id="section-auth">
+                <h3 class="subsection-title"><i class="fas fa-shield-alt"></i> {% trans "Authentification & Autorisation" %}</h3>
+
+                <div class="info-row">
+                    <div class="info-card card-accent-purple">
+                        <div class="card-icon"><i class="fas fa-users-cog"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Groupes" %}</h4>
+                            <ul class="doc-list">
+                                <li><i class="fas fa-crown text-gold"></i> Admin</li>
+                                <li><i class="fas fa-user-tie text-blue"></i> Staff</li>
+                                <li><i class="fas fa-user text-gray"></i> {% trans "Staff limité" %}</li>
+                            </ul>
+                        </div>
+                    </div>
+                    <div class="info-card card-accent-purple">
+                        <div class="card-icon"><i class="fas fa-user-circle"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Utilisateurs" %}</h4>
+                            <ul class="doc-list">
+                                <li><i class="fas fa-star text-gold"></i> superadmin</li>
+                            </ul>
+                        </div>
+                    </div>
+                </div>
+            </div>
+
+            <!-- -------------------------------------------------------- -->
+            <!-- Planarian                                                 -->
+            <!-- -------------------------------------------------------- -->
+            <div class="subsection" id="section-planarian">
+                <h3 class="subsection-title"><i class="fas fa-microscope"></i> {% trans "Application Planarian" %}</h3>
+                <div class="info-row">
+                    <div class="info-card card-accent-green full-width">
+                        <div class="card-icon"><i class="fas fa-vials"></i></div>
+                        <div class="card-body">
+                            <h4><code>planarian_experimentconfig</code></h4>
+                            <p>{% trans "Configurations des expériences de suivi des planaires." %}</p>
+                        </div>
+                    </div>
+                </div>
+            </div>
+
+            <!-- -------------------------------------------------------- -->
+            <!-- Scanner                                                   -->
+            <!-- -------------------------------------------------------- -->
+            <div class="subsection" id="section-scanner">
+                <h3 class="subsection-title"><i class="fas fa-camera"></i> {% trans "Application Scanner" %}</h3>
+
+                <!-- Configuration -->
+                <div class="sub-subsection" id="section-config">
+                    <h4 class="table-title">
+                        <i class="fas fa-sliders-h"></i>
+                        <code>scanner_configuration</code>
+                        <span class="table-desc">{% trans "Constantes et valeurs par défaut" %}</span>
+                    </h4>
+                    <div class="info-row">
+                        <div class="info-card card-accent-blue">
+                            <div class="card-icon"><i class="fas fa-camera-retro"></i></div>
+                            <div class="card-body">
+                                <h4>{% trans "Caméra" %}</h4>
+                                <ul class="doc-list">
+                                    <li>
+                                        <i class="fas fa-plug"></i>
+                                        {% trans "Capture" %} :
+                                        <div class="tag-list inline">
+                                            <span class="tag tag-blue">Arducam</span>
+                                            <span class="tag tag-gray">Webcam</span>
+                                            <span class="tag tag-gray">{% trans "Fichier vidéo" %}</span>
+                                        </div>
+                                    </li>
+                                    <li><i class="fas fa-film"></i> {% trans "Fréquence vidéos (fps)" %}</li>
+                                    <li><i class="fas fa-arrows-alt-h"></i> {% trans "Largeur de capture vidéo" %}</li>
+                                    <li><i class="fas fa-arrows-alt-v"></i> {% trans "Hauteur de capture vidéo" %}</li>
+                                </ul>
+                            </div>
+                        </div>
+                        <div class="info-card card-accent-blue">
+                            <div class="card-icon"><i class="fas fa-crosshairs"></i></div>
+                            <div class="card-body">
+                                <h4>{% trans "Suivi / Tracking" %}</h4>
+                                <ul class="doc-list">
+                                    <li><i class="fas fa-cog"></i> {% trans "Valeurs par défaut du tracking" %}</li>
+                                </ul>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+
+                <!-- Puits -->
+                <div class="sub-subsection" id="section-wells">
+                    <h4 class="table-title">
+                        <i class="fas fa-circle"></i>
+                        <code>scanner_well</code>
+                        <span class="table-desc">{% trans "Noms des puits" %}</span>
+                    </h4>
+                    <div class="info-row">
+                        <div class="info-card card-accent-teal full-width">
+                            <div class="card-icon"><i class="fas fa-th-large"></i></div>
+                            <div class="card-body">
+                                <p>{% trans "Contient uniquement les noms des puits disponibles." %}</p>
+                                <p class="hint"><i class="fas fa-exchange-alt"></i> {% trans "Lecture en serpentin dans le sens des ±X" %}</p>
+                                <!-- Grille serpentin : D1→D6 / C6←C1 / B1→B6 / A6←A1 -->
+                                <div class="well-grid well-grid--serpentine">
+                                    {# Ligne D : gauche → droite (D1..D6) #}
+                                    <span class="well-chip wc-d">D1</span><span class="well-chip wc-d">D2</span>
+                                    <span class="well-chip wc-d">D3</span><span class="well-chip wc-d">D4</span>
+                                    <span class="well-chip wc-d">D5</span><span class="well-chip wc-d">D6</span>
+                                    {# Ligne C : droite → gauche (C6..C1) #}
+                                    <span class="well-chip wc-c">C6</span><span class="well-chip wc-c">C5</span>
+                                    <span class="well-chip wc-c">C4</span><span class="well-chip wc-c">C3</span>
+                                    <span class="well-chip wc-c">C2</span><span class="well-chip wc-c">C1</span>
+                                    {# Ligne B : gauche → droite (B1..B6) #}
+                                    <span class="well-chip wc-b">B1</span><span class="well-chip wc-b">B2</span>
+                                    <span class="well-chip wc-b">B3</span><span class="well-chip wc-b">B4</span>
+                                    <span class="well-chip wc-b">B5</span><span class="well-chip wc-b">B6</span>
+                                    {# Ligne A : droite → gauche (A6..A1) #}
+                                    <span class="well-chip wc-a">A6</span><span class="well-chip wc-a">A5</span>
+                                    <span class="well-chip wc-a">A4</span><span class="well-chip wc-a">A3</span>
+                                    <span class="well-chip wc-a">A2</span><span class="well-chip wc-a">A1</span>
+                                </div>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+
+                <!-- Multi-puits -->
+                <div class="sub-subsection" id="section-multiwell">
+                    <h4 class="table-title">
+                        <i class="fas fa-th"></i>
+                        <code>scanner_multiwell</code>
+                        <span class="table-desc">{% trans "Géométrie et déplacements" %}</span>
+                    </h4>
+                    <div class="info-row">
+                        <div class="info-card card-accent-indigo">
+                            <div class="card-icon"><i class="fas fa-map"></i></div>
+                            <div class="card-body">
+                                <h4>{% trans "Position sur la table" %}</h4>
+                                <div class="position-grid">
+                                    <div class="pos-cell active">HG<br><small>{% trans "Haut gauche" %}</small></div>
+                                    <div class="pos-cell active">HD<br><small>{% trans "Haut droit" %}</small></div>
+                                    <div class="pos-cell active">BG<br><small>{% trans "Bas gauche" %}</small></div>
+                                    <div class="pos-cell active">BD<br><small>{% trans "Bas droit" %}</small></div>
+                                </div>
+                                <p class="hint"><i class="fas fa-info-circle"></i> {% trans "4 positions disponibles sur la table" %}</p>
+                                <p class="hint"><i class="fas fa-info-circle"></i> {% trans "(0, 0) de le CNC est en HD" %}</p>
+                                <p class="hint"><i class="fas fa-info-circle"></i> {% trans "HD --> HG +X" %}</p>
+                                <p class="hint"><i class="fas fa-info-circle"></i> {% trans "HD --> BD +Y" %}</p>
+                            </div>
+                        </div>
+                        <div class="info-card card-accent-indigo">
+                            <div class="card-icon"><i class="fas fa-ruler-combined"></i></div>
+                            <div class="card-body">
+                                <h4>{% trans "Géométrie" %}</h4>
+                                <ul class="doc-list">
+                                    <li><i class="fas fa-grip-lines"></i> {% trans "Nombre de lignes" %}</li>
+                                    <li><i class="fas fa-grip-lines-vertical"></i> {% trans "Nombre de colonnes" %}</li>
+                                    <li><i class="fas fa-circle"></i> {% trans "Diamètre des puits" %}</li>
+                                    <li><i class="fas fa-font"></i> {% trans "Définition des lignes (A, B, C, D)" %}</li>
+                                    <li><i class="fas fa-exchange-alt"></i> {% trans "Lecture en serpentin ±X (D→C→B→A)" %}</li>
+                                </ul>
+                            </div>
+                        </div>
+                        <div class="info-card card-accent-indigo">
+                            <div class="card-icon"><i class="fas fa-route"></i></div>
+                            <div class="card-body">
+                                <h4>{% trans "Déplacements" %}</h4>
+                                <ul class="doc-list">
+                                    <li><i class="fas fa-sort-numeric-down"></i> {% trans "Ordre de lecture" %}</li>
+                                    <li><i class="fas fa-stopwatch"></i> {% trans "Durée de capture (calibration)" %}</li>
+                                    <li>
+                                        <i class="fas fa-location-arrow"></i>
+                                        {% trans "Origine X" %}
+                                        <span class="badge-auto">{% trans "Calibration" %}</span>
+                                    </li>
+                                    <li>
+                                        <i class="fas fa-location-arrow fa-rotate-90"></i>
+                                        {% trans "Origine Y" %}
+                                        <span class="badge-auto">{% trans "Calibration" %}</span>
+                                    </li>
+                                    <li><i class="fas fa-arrows-alt-h"></i> {% trans "Pas X mesuré" %}</li>
+                                    <li><i class="fas fa-arrows-alt-v"></i> {% trans "Pas Y mesuré" %}</li>
+                                    <li><i class="fas fa-tachometer-alt"></i> {% trans "Vitesse (mm/mn)" %}</li>
+                                </ul>
+                            </div>
+                        </div>
+                    </div>
+                    <div class="info-row">
+                        <div class="info-card card-accent-yellow full-width">
+                            <div class="card-icon"><i class="fas fa-exclamation-triangle"></i></div>
+                            <div class="card-body">
+                                <h4>{% trans "Positions générées" %}</h4>
+                                <p>{% trans "Si les positions ne sont pas encore générées, le système efface" %} <code>WellPosition</code> {% trans "et recalcule toutes les positions des puits." %}</p>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+
+                <!-- Position des puits -->
+                <div class="sub-subsection" id="section-wellpos">
+                    <h4 class="table-title">
+                        <i class="fas fa-map-marker-alt"></i>
+                        <code>scanner_wellposition</code>
+                        <span class="table-desc">{% trans "Positions calibrées des puits" %}</span>
+                    </h4>
+                    <div class="info-row">
+                        <div class="info-card card-accent-cyan">
+                            <div class="card-icon"><i class="fas fa-drafting-compass"></i></div>
+                            <div class="card-body">
+                                <h4>{% trans "Calibration" %}</h4>
+                                <p>{% trans "Manuelle ou automatique." %}</p>
+                                <ul class="doc-list">
+                                    <li><i class="fas fa-arrows-alt-h"></i> {% trans "Axe X (mm)" %} <span class="badge-auto">{% trans "Calibration" %}</span></li>
+                                    <li><i class="fas fa-arrows-alt-v"></i> {% trans "Axe Y (mm)" %} <span class="badge-auto">{% trans "Calibration" %}</span></li>
+                                </ul>
+                            </div>
+                        </div>
+                        <div class="info-card card-accent-red">
+                            <div class="card-icon"><i class="fas fa-exclamation-circle"></i></div>
+                            <div class="card-body">
+                                <h4>{% trans "Pixels par mm" %} <span class="badge-important">{% trans "IMPORTANT" %}</span></h4>
+                                <p>{% trans "Facteur de calibration optique calculé en fonction de la taille de l'image." %}</p>
+                                <div class="alert-box">
+                                    <i class="fas fa-redo"></i>
+                                    {% trans "Recalibrer si la taille de l'image est modifiée !" %}
+                                </div>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+
+                <!-- Expériences -->
+                <div class="sub-subsection" id="section-experiments">
+                    <h4 class="table-title">
+                        <i class="fas fa-flask"></i>
+                        <code>scanner_experiment</code> &amp; <code>scanner_experimentwell</code>
+                        <span class="table-desc">{% trans "Expériences et puits associés" %}</span>
+                    </h4>
+                    <div class="info-row">
+                        <div class="info-card card-accent-green">
+                            <div class="card-icon"><i class="fas fa-vial"></i></div>
+                            <div class="card-body">
+                                <h4>{% trans "Valeurs importantes" %}</h4>
+                                <ul class="doc-list">
+                                    <li><i class="fas fa-link"></i> {% trans "Multi-puits lié" %}</li>
+                                    <li><i class="fas fa-clock"></i> {% trans "Durée de capture (secondes)" %}</li>
+                                    <li><i class="fas fa-fingerprint"></i> {% trans "Identifiant d'expérience" %}</li>
+                                </ul>
+                            </div>
+                        </div>
+                        <div class="info-card card-accent-green">
+                            <div class="card-icon"><i class="fas fa-magic"></i></div>
+                            <div class="card-body">
+                                <h4>{% trans "Création automatique" %}</h4>
+                                <p>{% trans "À la création d'une expérience, les puits liés sont automatiquement créés dans" %} <code>scanner_experimentwell</code>.</p>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+
+                <!-- Sessions -->
+                <div class="sub-subsection" id="section-sessions">
+                    <h4 class="table-title">
+                        <i class="fas fa-play-circle"></i>
+                        <code>scanner_session</code> &amp; <code>scanner_sessionexperiment</code>
+                        <span class="table-desc">{% trans "Sessions d'expériences" %}</span>
+                    </h4>
+                    <div class="info-row">
+                        <div class="info-card card-accent-blue">
+                            <div class="card-icon"><i class="fas fa-layer-group"></i></div>
+                            <div class="card-body">
+                                <h4>{% trans "Regroupement" %}</h4>
+                                <p>{% trans "Regroupe les expériences lors d'un balayage dans" %} <code>scanner_sessionexperiment</code>.</p>
+                                <div class="tag-list">
+                                    <span class="tag tag-blue">{% trans "4 multi-puits maximum" %}</span>
+                                </div>
+                            </div>
+                        </div>
+                        <div class="info-card card-accent-blue">
+                            <div class="card-icon"><i class="fas fa-tasks"></i></div>
+                            <div class="card-body">
+                                <h4>{% trans "2 tâches Celery créées" %}</h4>
+                                <ul class="doc-list">
+                                    <li>
+                                        <i class="fas fa-play text-green"></i>
+                                        <code>scanning_session</code>
+                                        <p class="task-desc">{% trans "Lancement différé d'un balayage de session." %}</p>
+                                    </li>
+                                    <li>
+                                        <i class="fas fa-file-export text-cyan"></i>
+                                        <code>export_session</code>
+                                        <p class="task-desc">
+                                            {% trans "Export images et vidéos :" %}
+                                            <span class="tag tag-gray">{% trans "Local" %}</span>
+                                            <span class="tag tag-gray">{% trans "Support distant" %}</span>
+                                        </p>
+                                    </li>
+                                </ul>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+
+                <!-- Celery Beat -->
+                <div class="sub-subsection" id="section-celery">
+                    <h4 class="table-title">
+                        <i class="fas fa-tasks"></i>
+                        <code>django_celery_beat_periodictask</code>
+                        <span class="table-desc">{% trans "Gestion des tâches différées" %}</span>
+                    </h4>
+                    <div class="info-row">
+                        <div class="info-card card-accent-orange full-width">
+                            <div class="card-icon"><i class="fas fa-clock"></i></div>
+                            <div class="card-body">
+                                <p>{% trans "Gère le déclenchement et la planification des tâches Celery différées." %}</p>
+                                <div class="tag-list">
+                                    <span class="tag tag-orange">Celery Beat</span>
+                                    <span class="tag tag-gray">{% trans "Tâches périodiques" %}</span>
+                                </div>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+
+            </div><!-- end section-scanner -->
+        </section><!-- end section-mariadb -->
+
+    </main><!-- end doc-content -->
+</div><!-- end doc-wrapper -->
+{% endblock %}
+
+{% block js_footer %}
+    {{ block.super }}
+	<script>
+	/* Mise en évidence du lien actif dans la navigation latérale */
+	(function () {
+	    const links = document.querySelectorAll('.nav-link');
+	    const sections = document.querySelectorAll('.doc-section, .subsection, .sub-subsection');
+	
+	    /* Observer d'intersection pour la navigation active */
+	    const observer = new IntersectionObserver(
+	        (entries) => {
+	            entries.forEach(entry => {
+	                if (entry.isIntersecting) {
+	                    links.forEach(l => l.classList.remove('active'));
+	                    const target = document.querySelector(`.nav-link[href="#${entry.target.id}"]`);
+	                    if (target) target.classList.add('active');
+	                }
+	            });
+	        },
+	        { rootMargin: '-10% 0px -80% 0px' }
+	    );
+	
+	    sections.forEach(s => { if (s.id) observer.observe(s); });
+	})();
+	</script>
+{% endblock %}

test_tube_scanner/home/templates/docs/doc_experiment.html

@@ -0,0 +1,541 @@
+{% extends 'scanner/base.html' %}
+{% load i18n %}
+{% block columns %}{% endblock %}
+
+{% block styles %}
+    {{ block.super }}
+	<link rel="stylesheet" href="/static/css/doc_database.css">
+	<link rel="stylesheet" href="/static/css/doc_calibration.css>
+	<link rel="stylesheet" href="/static/css/doc_experiments.css">
+{% endblock %}
+
+{% block content %}
+<div class="doc-wrapper">
+
+    <!-- ─── En-tête ─── -->
+    <header class="doc-header">
+        <div class="doc-header-inner">
+            <div class="doc-header-icon" style="background: linear-gradient(135deg, var(--accent-green), var(--accent-teal));">
+                <i class="fas fa-flask"></i>
+            </div>
+            <div>
+                <h1 class="doc-title">{% trans "Démarrer des expériences" %}</h1>
+                <p class="doc-subtitle">{% trans "Sessions, expériences, configurations et import CSV — interface Administration Django" %}</p>
+            </div>
+        </div>
+    </header>
+
+    <!-- ─── Navigation latérale ─── -->
+    <nav class="doc-sidenav" id="sidenav">
+        <p class="nav-section-label">{% trans "Navigation" %}</p>
+        <a href="#section-intro"       class="nav-link active"><i class="fas fa-info-circle"></i>   {% trans "Présentation" %}</a>
+        <a href="#section-workflow"    class="nav-link">       <i class="fas fa-random"></i>         {% trans "Ordre de création" %}</a>
+        <a href="#section-session"     class="nav-link">       <i class="fas fa-play-circle"></i>    {% trans "Session" %}</a>
+        <a href="#section-session-data"  class="nav-link nav-sub"><i class="fas fa-table"></i>      {% trans "Données" %}</a>
+        <a href="#section-session-tasks" class="nav-link nav-sub"><i class="fas fa-clock"></i>      {% trans "Tâches périodiques" %}</a>
+        <a href="#section-experiment"  class="nav-link">       <i class="fas fa-vial"></i>           {% trans "Expérience" %}</a>
+        <a href="#section-exp-data"    class="nav-link nav-sub"><i class="fas fa-table"></i>        {% trans "Données" %}</a>
+        <a href="#section-exp-create"  class="nav-link nav-sub"><i class="fas fa-magic"></i>        {% trans "Création automatique" %}</a>
+        <a href="#section-metrics"     class="nav-link nav-sub"><i class="fas fa-chart-line"></i>   {% trans "Métriques" %}</a>
+        <a href="#section-config"      class="nav-link">       <i class="fas fa-cog"></i>            {% trans "Configuration puits" %}</a>
+        <a href="#section-csv"         class="nav-link">       <i class="fas fa-file-csv"></i>       {% trans "Import CSV" %}</a>
+    </nav>
+
+    <!-- ─── Contenu principal ─── -->
+    <main class="doc-content">
+
+        <!-- ============================================================ -->
+        <!-- SECTION 1 : Présentation                                      -->
+        <!-- ============================================================ -->
+        <section class="doc-section" id="section-intro">
+            <div class="section-header">
+                <span class="section-badge badge-green">{% trans "Administration Django" %}</span>
+                <h2><i class="fas fa-flask"></i> {% trans "Démarrer des expériences" %}</h2>
+                <p class="section-desc">
+                    {% trans "C'est l'interface Administration Django qui est chargée de créer les données." %}
+                </p>
+            </div>
+
+            <div class="info-row">
+                <div class="info-card card-accent-green full-width">
+                    <div class="card-icon"><i class="fas fa-th-large"></i></div>
+                    <div class="card-body">
+                        <h4>{% trans "Principe général" %}</h4>
+                        <ul class="doc-list">
+                            <li>
+                                <i class="fas fa-link text-green"></i>
+                                {% trans "Une expérience est toujours affectée à un multi-puits." %}
+                            </li>
+                            <li>
+                                <i class="fas fa-th text-green"></i>
+                                {% trans "Il y a 4 emplacements multi-puits, donc" %}
+                                <strong>{% trans "4 expériences maximum par session." %}</strong>
+                            </li>
+                        </ul>
+                    </div>
+                </div>
+            </div>
+        </section>
+
+        <!-- ============================================================ -->
+        <!-- SECTION 2 : Ordre de création                                 -->
+        <!-- ============================================================ -->
+        <section class="doc-section" id="section-workflow">
+            <div class="section-header">
+                <span class="section-badge badge-blue">{% trans "Workflow" %}</span>
+                <h2><i class="fas fa-random"></i> {% trans "Ordre de création" %}</h2>
+                <p class="section-desc">{% trans "Les deux approches sont équivalentes — au choix." %}</p>
+            </div>
+
+            <div class="info-row">
+                <!-- Option A -->
+                <div class="info-card card-accent-indigo">
+                    <div class="card-icon"><i class="fas fa-list-ol"></i></div>
+                    <div class="card-body">
+                        <h4><i class="fas fa-play-circle text-indigo"></i> {% trans "Option A — Session en premier" %}</h4>
+                        <ol class="doc-steps">
+                            <li><i class="fas fa-plus-circle"></i> {% trans "Créer la session" %}</li>
+                            <li><i class="fas fa-vial"></i> {% trans "Créer les expériences (4 maxi)" %}</li>
+                            <li><i class="fas fa-link"></i> {% trans "Revenir sur la session et ajouter les expériences" %}</li>
+                        </ol>
+                    </div>
+                </div>
+
+                <!-- Option B -->
+                <div class="info-card card-accent-blue">
+                    <div class="card-icon"><i class="fas fa-list-ol"></i></div>
+                    <div class="card-body">
+                        <h4><i class="fas fa-vial text-blue"></i> {% trans "Option B — Expériences en premier" %}</h4>
+                        <ol class="doc-steps">
+                            <li><i class="fas fa-vial"></i> {% trans "Créer les expériences" %}</li>
+                            <li><i class="fas fa-plus-circle"></i> {% trans "Créer la session" %}</li>
+                            <li><i class="fas fa-link"></i> {% trans "Ajouter les expériences à la session" %}</li>
+                        </ol>
+                    </div>
+                </div>
+            </div>
+        </section>
+
+        <!-- ============================================================ -->
+        <!-- SECTION 3 : Session                                           -->
+        <!-- ============================================================ -->
+        <section class="doc-section" id="section-session">
+            <div class="section-header">
+                <span class="section-badge badge-purple">scanner_session</span>
+                <h2><i class="fas fa-play-circle"></i> {% trans "Session" %}</h2>
+            </div>
+
+            <!-- Données importantes -->
+            <div class="sub-subsection" id="section-session-data">
+                <h4 class="table-title">
+                    <i class="fas fa-table"></i> {% trans "Données importantes" %}
+                </h4>
+                <div class="info-row">
+                    <div class="info-card card-accent-purple">
+                        <div class="card-icon"><i class="fas fa-id-card"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Identification" %}</h4>
+                            <ul class="doc-list">
+                                <li><i class="fas fa-heading text-purple"></i> {% trans "Titre" %}</li>
+                                <li><i class="fas fa-user text-purple"></i> {% trans "Auteur" %}</li>
+                            </ul>
+                        </div>
+                    </div>
+
+                    <!-- Expériences de la session -->
+                    <div class="info-card card-accent-indigo">
+                        <div class="card-icon"><i class="fas fa-layer-group"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Expériences d'une session" %}</h4>
+                            <p>{% trans "Ajouter les expériences à la suite dans l'inline" %} <code>scanner_sessionexperiment</code>.</p>
+                            <div class="tag-list">
+                                <span class="tag tag-blue">{% trans "4 maximum" %}</span>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Tâches périodiques -->
+            <div class="sub-subsection" id="section-session-tasks">
+                <h4 class="table-title">
+                    <i class="fas fa-clock"></i> {% trans "Options tâches périodiques" %}
+                </h4>
+                <div class="info-row">
+                    <div class="info-card card-accent-orange">
+                        <div class="card-icon"><i class="fas fa-file-export"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Date d'exportation" %}</h4>
+                            <p>{% trans "Crée une tâche différée pour exporter automatiquement les images et vidéos à la date choisie." %}</p>
+                            <div class="tag-list">
+                                <span class="tag tag-orange">export_session</span>
+                            </div>
+                        </div>
+                    </div>
+                    <div class="info-card card-accent-teal">
+                        <div class="card-icon"><i class="fas fa-calendar-alt"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Date du balayage" %}</h4>
+                            <p>{% trans "Planifie le déclenchement du balayage de la session à une date ultérieure." %}</p>
+                            <div class="tag-list">
+                                <span class="tag tag-teal">scanning_session</span>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+            </div>
+        </section>
+
+        <!-- ============================================================ -->
+        <!-- SECTION 4 : Expérience                                        -->
+        <!-- ============================================================ -->
+        <section class="doc-section" id="section-experiment">
+            <div class="section-header">
+                <span class="section-badge badge-green">scanner_experiment</span>
+                <h2><i class="fas fa-vial"></i> {% trans "Expérience" %}</h2>
+            </div>
+
+            <!-- Données -->
+            <div class="sub-subsection" id="section-exp-data">
+                <h4 class="table-title"><i class="fas fa-table"></i> {% trans "Données" %}</h4>
+                <div class="info-row">
+                    <div class="info-card card-accent-green">
+                        <div class="card-icon"><i class="fas fa-id-card"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Identification" %}</h4>
+                            <ul class="doc-list">
+                                <li><i class="fas fa-heading text-green"></i> {% trans "Titre" %}</li>
+                                <li><i class="fas fa-user text-green"></i> {% trans "Auteur" %}</li>
+                                <li><i class="fas fa-comment-alt text-green"></i> {% trans "Commentaires" %}</li>
+                            </ul>
+                        </div>
+                    </div>
+                    <div class="info-card card-accent-red">
+                        <div class="card-icon"><i class="fas fa-exclamation-circle"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Paramètres critiques" %} <span class="badge-important">{% trans "IMPORTANT" %}</span></h4>
+                            <ul class="doc-list">
+                                <li>
+                                    <i class="fas fa-th text-red"></i>
+                                    {% trans "Choix du multi-puits" %}
+                                </li>
+                                <li>
+                                    <i class="fas fa-stopwatch text-red"></i>
+                                    {% trans "Durée de la prise de vue (secondes)" %}
+                                </li>
+                            </ul>
+                        </div>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Création automatique -->
+            <div class="sub-subsection" id="section-exp-create">
+                <h4 class="table-title">
+                    <i class="fas fa-magic"></i> {% trans "Fonctionnement à la création" %}
+                </h4>
+                <div class="info-row">
+                    <!-- experimentwell -->
+                    <div class="info-card card-accent-blue">
+                        <div class="card-icon"><i class="fas fa-circle-notch"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Création/MAJ" %} <code>scanner.experimentwell</code></h4>
+                            <ul class="doc-list">
+                                <li>
+                                    <i class="fas fa-plus text-blue"></i>
+                                    {% trans "Création de chaque puit individuel." %}
+                                </li>
+                                <li>
+                                    <i class="fas fa-check-circle text-green"></i>
+                                    {% trans "Par défaut, tous les puits sont actifs." %}
+                                </li>
+                            </ul>
+                            <div class="alert-box alert-info">
+                                <i class="fas fa-info-circle"></i>
+                                {% trans "Il est possible d'ignorer le balayage d'un ou plusieurs puits au choix." %}
+                            </div>
+                        </div>
+                    </div>
+
+                    <!-- experimentconfig -->
+                    <div class="info-card card-accent-cyan">
+                        <div class="card-icon"><i class="fas fa-sliders-h"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Création/MAJ" %} <code>planarian.experimentconfig</code></h4>
+                            <p>{% trans "Paramètres d'une expérience PlanarianScanner." %}</p>
+                            <ul class="doc-list">
+                                <li>
+                                    <i class="fas fa-user-cog text-cyan"></i>
+                                    {% trans "Créé depuis Django admin" %}
+                                </li>
+                                <li>
+                                    <i class="fas fa-file-csv text-cyan"></i>
+                                    {% trans "Ou import CSV depuis l'admin" %}
+                                </li>
+                                <li>
+                                    <i class="fas fa-pencil-alt text-muted"></i>
+                                    <em>{% trans "Données descriptives supplémentaires (à définir)" %}</em>
+                                </li>
+                            </ul>
+                        </div>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Métriques -->
+            <div class="sub-subsection" id="section-metrics">
+                <h4 class="table-title">
+                    <i class="fas fa-chart-line"></i>
+                    {% trans "Intégration métriques EthoVision XT + comportementales" %}
+                </h4>
+
+                <!-- Métriques par frame -->
+                <h5 class="metrics-group-title">
+                    <i class="fas fa-film"></i> {% trans "Métriques par frame" %}
+                </h5>
+                <div class="info-row">
+                    <div class="info-card card-accent-blue metrics-card">
+                        <div class="card-icon"><i class="fas fa-running"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Mobilité" %}</h4>
+                            <div class="metric-tags">
+                                <span class="tag tag-blue">velocity</span>
+                                <span class="tag tag-blue">distance</span>
+                                <span class="tag tag-blue">moving</span>
+                                <span class="tag tag-blue">mobility_state</span>
+                            </div>
+                        </div>
+                    </div>
+                    <div class="info-card card-accent-orange metrics-card">
+                        <div class="card-icon"><i class="fas fa-border-style"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Thigmotaxie" %}</h4>
+                            <div class="metric-tags">
+                                <span class="tag tag-orange">dist_to_wall_mm</span>
+                                <span class="tag tag-orange">near_wall</span>
+                            </div>
+                        </div>
+                    </div>
+                    <div class="info-card card-accent-yellow metrics-card">
+                        <div class="card-icon"><i class="fas fa-sun"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Phototaxie" %}</h4>
+                            <div class="metric-tags">
+                                <span class="tag tag-yellow">dist_to_light_mm</span>
+                                <span class="tag tag-yellow">heading_to_light_deg</span>
+                                <span class="tag tag-yellow">fleeing_light</span>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+                <div class="info-row">
+                    <div class="info-card card-accent-green metrics-card">
+                        <div class="card-icon"><i class="fas fa-utensils"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Chimiotaxie" %}</h4>
+                            <div class="metric-tags">
+                                <span class="tag tag-green">dist_to_food_mm</span>
+                                <span class="tag tag-green">heading_to_food_deg</span>
+                                <span class="tag tag-green">approaching_food</span>
+                                <span class="tag tag-green">in_food_zone</span>
+                            </div>
+                        </div>
+                    </div>
+                    <div class="info-card card-accent-purple metrics-card">
+                        <div class="card-icon"><i class="fas fa-users"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Social" %}</h4>
+                            <div class="metric-tags">
+                                <span class="tag tag-purple">nearest_neighbour_mm</span>
+                                <span class="tag tag-purple">in_avoid_zone</span>
+                                <span class="tag tag-purple">in_aggreg_zone</span>
+                                <span class="tag tag-purple">chem_repulsion_level</span>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+
+                <!-- Métriques résumé -->
+                <h5 class="metrics-group-title" style="margin-top:20px;">
+                    <i class="fas fa-clipboard-list"></i> {% trans "Métriques résumé (summary)" %}
+                </h5>
+                <div class="info-row">
+                    <div class="info-card card-accent-blue metrics-card">
+                        <div class="card-icon"><i class="fas fa-running"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Mobilité" %}</h4>
+                            <div class="metric-tags">
+                                <span class="tag tag-blue">movedCenter_pointTotal_mm</span>
+                                <span class="tag tag-blue">velocity_mean_mm_s</span>
+                                <span class="tag tag-blue">{% trans "durations par état" %}</span>
+                            </div>
+                        </div>
+                    </div>
+                    <div class="info-card card-accent-orange metrics-card">
+                        <div class="card-icon"><i class="fas fa-border-style"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Thigmotaxie" %}</h4>
+                            <div class="metric-tags">
+                                <span class="tag tag-orange">thigmotaxis_pct_time_near_wall</span>
+                            </div>
+                        </div>
+                    </div>
+                    <div class="info-card card-accent-yellow metrics-card">
+                        <div class="card-icon"><i class="fas fa-sun"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Phototaxie" %}</h4>
+                            <div class="metric-tags">
+                                <span class="tag tag-yellow">photo_pct_time_fleeing</span>
+                                <span class="tag tag-yellow">photo_mean_dist_mm</span>
+                                <span class="tag tag-yellow">photo_latency_s</span>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+                <div class="info-row">
+                    <div class="info-card card-accent-green metrics-card">
+                        <div class="card-icon"><i class="fas fa-utensils"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Chimiotaxie" %}</h4>
+                            <div class="metric-tags">
+                                <span class="tag tag-green">chemo_pct_time_approaching</span>
+                                <span class="tag tag-green">chemo_pct_time_in_zone</span>
+                                <span class="tag tag-green">chemo_latency_s</span>
+                                <span class="tag tag-green">chemo_mean_dist_mm</span>
+                            </div>
+                        </div>
+                    </div>
+                    <div class="info-card card-accent-purple metrics-card">
+                        <div class="card-icon"><i class="fas fa-users"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Social" %}</h4>
+                            <div class="metric-tags">
+                                <span class="tag tag-purple">social_pct_time_avoiding</span>
+                                <span class="tag tag-purple">social_pct_time_aggregating</span>
+                                <span class="tag tag-purple">social_mean_nn_mm</span>
+                                <span class="tag tag-purple">social_contact_events</span>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+            </div>
+        </section>
+
+        <!-- ============================================================ -->
+        <!-- SECTION 5 : Configuration des puits                           -->
+        <!-- ============================================================ -->
+        <section class="doc-section" id="section-config">
+            <div class="section-header">
+                <span class="section-badge badge-teal">{% trans "Interface Scanner" %}</span>
+                <h2><i class="fas fa-cog"></i> {% trans "Configuration des expériences" %}</h2>
+                <p class="section-desc">{% trans "Sélectionner l'expérience et le puit à modifier pour compléter la fiche." %}</p>
+            </div>
+            <div class="info-row">
+                <div class="info-card card-accent-teal full-width">
+                    <div class="card-icon"><i class="fas fa-edit"></i></div>
+                    <div class="card-body">
+                        <h4>{% trans "Procédure" %}</h4>
+                        <ol class="doc-steps">
+                            <li><i class="fas fa-mouse-pointer"></i> {% trans "Sélectionner l'expérience dans la liste" %}</li>
+                            <li><i class="fas fa-circle"></i> {% trans "Sélectionner le puit à modifier" %}</li>
+                            <li><i class="fas fa-pen"></i> {% trans "Compléter la fiche de configuration" %}</li>
+                        </ol>
+                    </div>
+                </div>
+            </div>
+        </section>
+
+        <!-- ============================================================ -->
+        <!-- SECTION 6 : Import CSV                                        -->
+        <!-- ============================================================ -->
+        <section class="doc-section" id="section-csv">
+            <div class="section-header">
+                <span class="section-badge badge-orange">{% trans "Import" %}</span>
+                <h2><i class="fas fa-file-csv"></i> {% trans "Importer des configurations depuis CSV" %}</h2>
+            </div>
+
+            <div class="info-row">
+                <!-- Menu gauche -->
+                <div class="info-card card-accent-indigo">
+                    <div class="card-icon"><i class="fas fa-bars"></i></div>
+                    <div class="card-body">
+                        <h4>{% trans "Menu gauche" %}</h4>
+                        <ol class="doc-steps">
+                            <li><i class="fas fa-play-circle"></i> {% trans "Sélectionner la session" %}</li>
+                            <li><i class="fas fa-check-square"></i> {% trans "Cocher l'expérience souhaitée" %}</li>
+                        </ol>
+                    </div>
+                </div>
+
+                <!-- Zone de dépôt -->
+                <div class="info-card card-accent-blue">
+                    <div class="card-icon"><i class="fas fa-cloud-upload-alt"></i></div>
+                    <div class="card-body">
+                        <h4>{% trans "Zone d'import" %}</h4>
+                        <ol class="doc-steps">
+                            <li><i class="fas fa-file-csv"></i> {% trans "Glisser-déposer le fichier CSV" %}</li>
+                            <li><i class="fas fa-upload"></i> {% trans "Cliquer sur Importer" %}</li>
+                        </ol>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Astuce CSV -->
+            <div class="info-row">
+                <div class="info-card card-accent-yellow full-width">
+                    <div class="card-icon"><i class="fas fa-lightbulb"></i></div>
+                    <div class="card-body">
+                        <h4>{% trans "Astuce — Générer le template CSV depuis Django admin" %}</h4>
+                        <ol class="doc-steps">
+                            <li>
+                                <i class="fas fa-th-list"></i>
+                                {% trans "Aller dans" %}
+                                <strong>{% trans "Planarian › Configurations des expériences" %}</strong>
+                            </li>
+                            <li>
+                                <i class="fas fa-check-square"></i>
+                                {% trans "Cocher le puit de l'expérience ou un groupe d'expériences" %}
+                            </li>
+                            <li>
+                                <i class="fas fa-bolt"></i>
+                                {% trans "Action :" %} <strong>{% trans "Exporter un template CSV…" %}</strong>
+                            </li>
+                            <li>
+                                <i class="fas fa-download"></i>
+                                {% trans "Vérifier l'emplacement du fichier téléchargé (dossier Download)." %}
+                            </li>
+                        </ol>
+                    </div>
+                </div>
+            </div>
+        </section>
+
+    </main>
+</div>
+{% endblock %}
+
+{% block js_footer %}
+    {{ block.super }}
+    <script>
+	/* Mise en évidence du lien actif dans la navigation latérale */
+	(function () {
+	    const links    = document.querySelectorAll('.nav-link');
+	    const sections = document.querySelectorAll('[id^="section-"]');
+	
+	    const observer = new IntersectionObserver(
+	        (entries) => {
+	            entries.forEach(entry => {
+	                if (entry.isIntersecting) {
+	                    links.forEach(l => l.classList.remove('active'));
+	                    const target = document.querySelector(`.nav-link[href="#${entry.target.id}"]`);
+	                    if (target) target.classList.add('active');
+	                }
+	            });
+	        },
+	        { rootMargin: '-10% 0px -80% 0px' }
+	    );
+	
+	    sections.forEach(s => observer.observe(s));
+	})();
+	</script>
+{% endblock %}

test_tube_scanner/home/templates/docs/doc_medias.html

@@ -0,0 +1,287 @@
+{% extends 'scanner/base.html' %}
+{% load i18n %}
+{% block columns %}{% endblock %}
+
+{% block styles %}
+    {{ block.super }}
+    <link rel="stylesheet" href="/static/css/doc_database.css">
+    <link rel="stylesheet" href="/static/css/doc_calibration.css>
+    <link rel="stylesheet" href="/static/css/doc_experiments.css">
+    <link rel="stylesheet" href="/static/css/doc_scanning.css"> 
+    <link rel="stylesheet" href="/static/css/doc_results.css">     
+    <link rel="stylesheet" href="/static/css/doc_media.css">
+{% endblock %}
+
+{% block content %}
+<div class="doc-wrapper">
+
+    <!-- ─── En-tête ─── -->
+    <header class="doc-header">
+        <div class="doc-header-inner">
+            <div class="doc-header-icon" style="background: linear-gradient(135deg, var(--accent-purple), var(--accent-blue));">
+                <i class="fas fa-photo-video"></i>
+            </div>
+            <div>
+                <h1 class="doc-title">{% trans "Gestionnaire de médias" %}</h1>
+                <p class="doc-subtitle">{% trans "Consultation, rediffusion et export des images et vidéos" %}</p>
+            </div>
+        </div>
+    </header>
+
+    <!-- ─── Navigation latérale ─── -->
+    <nav class="doc-sidenav" id="sidenav">
+        <p class="nav-section-label">{% trans "Navigation" %}</p>
+        <a href="#section-grid"    class="nav-link active"><i class="fas fa-th"></i>            {% trans "Grille d'affichage" %}</a>
+        <a href="#section-images"  class="nav-link">       <i class="fas fa-images"></i>        {% trans "Gestionnaire d'images" %}</a>
+        <a href="#section-img-nav" class="nav-link nav-sub"><i class="fas fa-bars"></i>        {% trans "Menu gauche" %}</a>
+        <a href="#section-img-view"class="nav-link nav-sub"><i class="fas fa-eye"></i>         {% trans "Affichage & export" %}</a>
+        <a href="#section-videos"  class="nav-link">       <i class="fas fa-film"></i>          {% trans "Rediffusion vidéos" %}</a>
+        <a href="#section-vid-nav" class="nav-link nav-sub"><i class="fas fa-bars"></i>        {% trans "Menu gauche" %}</a>
+        <a href="#section-vid-view"class="nav-link nav-sub"><i class="fas fa-play-circle"></i> {% trans "Lecteur & export" %}</a>
+    </nav>
+
+    <!-- ─── Contenu principal ─── -->
+    <main class="doc-content">
+
+        <!-- ============================================================ -->
+        <!-- SECTION 1 : Grille d'affichage                                -->
+        <!-- ============================================================ -->
+        <section class="doc-section" id="section-grid">
+            <div class="section-header">
+                <span class="section-badge badge-purple">{% trans "Affichage" %}</span>
+                <h2><i class="fas fa-th"></i> {% trans "Grille d'affichage" %}</h2>
+                <p class="section-desc">{% trans "Contrôle situé en haut à gauche de l'interface." %}</p>
+            </div>
+            <div class="info-row">
+                <div class="info-card card-accent-purple full-width">
+                    <div class="card-icon"><i class="fas fa-columns"></i></div>
+                    <div class="card-body">
+                        <h4>{% trans "Nombre de colonnes" %}</h4>
+                        <p>{% trans "Réduire ou augmenter dynamiquement le nombre de colonnes d'affichage des médias." %}</p>
+                        <!-- Visualisation colonnes -->
+                        <div class="grid-preview">
+                            <div class="gp-col"><i class="fas fa-minus"></i></div>
+                            <div class="gp-demo gp-2">
+                                <span></span><span></span>
+                            </div>
+                            <div class="gp-demo gp-3">
+                                <span></span><span></span><span></span>
+                            </div>
+                            <div class="gp-demo gp-4">
+                                <span></span><span></span><span></span><span></span>
+                            </div>
+                            <div class="gp-col"><i class="fas fa-plus"></i></div>
+                        </div>
+                    </div>
+                </div>
+            </div>
+        </section>
+
+        <!-- ============================================================ -->
+        <!-- SECTION 2 : Gestionnaire d'images                             -->
+        <!-- ============================================================ -->
+        <section class="doc-section" id="section-images">
+            <div class="section-header">
+                <span class="section-badge badge-blue">{% trans "Images" %}</span>
+                <h2><i class="fas fa-images"></i> {% trans "Gestionnaire d'images" %}</h2>
+            </div>
+
+            <!-- Menu gauche -->
+            <div class="sub-subsection" id="section-img-nav">
+                <h4 class="table-title"><i class="fas fa-bars"></i> {% trans "Menu gauche — Sélection" %}</h4>
+                <div class="info-row">
+                    <div class="info-card card-accent-indigo full-width">
+                        <div class="card-icon"><i class="fas fa-mouse-pointer"></i></div>
+                        <div class="card-body">
+                            <ol class="doc-steps">
+                                <li><i class="fas fa-play-circle"></i> {% trans "Sélectionner la session" %}</li>
+                                <li><i class="fas fa-check-square"></i> {% trans "Cocher l'expérience" %}</li>
+                                <li><i class="fas fa-circle"></i> {% trans "Choisir le puit" %}</li>
+                            </ol>
+                        </div>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Affichage & export -->
+            <div class="sub-subsection" id="section-img-view">
+                <h4 class="table-title"><i class="fas fa-eye"></i> {% trans "Affichage des images & export" %}</h4>
+                <div class="info-row">
+                    <!-- Téléchargement unitaire -->
+                    <div class="info-card card-accent-blue">
+                        <div class="card-icon"><i class="fas fa-download"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Téléchargement unitaire" %}</h4>
+                            <p>{% trans "Chaque image affichée dispose d'un bouton de téléchargement individuel." %}</p>
+                        </div>
+                    </div>
+
+                    <!-- Export global images -->
+                    <div class="info-card card-accent-orange">
+                        <div class="card-icon"><i class="fas fa-file-archive"></i></div>
+                        <div class="card-body">
+                            <h4>
+                                {% trans "Exporter l'ensemble des images" %}
+                                <span class="badge-important">{% trans "ATTENTION" %}</span>
+                            </h4>
+                            <ul class="doc-list">
+                                <li>
+                                    <i class="fas fa-hourglass-half text-orange"></i>
+                                    {% trans "La procédure peut être longue." %}
+                                </li>
+                                <li>
+                                    <i class="fas fa-clock text-orange"></i>
+                                    {% trans "Préférer l'export différé." %}
+                                </li>
+                            </ul>
+                            <div class="deferred-badge">
+                                <i class="fas fa-calendar-alt"></i>
+                                {% trans "Export différé recommandé" %}
+                            </div>
+                        </div>
+                    </div>
+                </div>
+            </div>
+        </section>
+
+        <!-- ============================================================ -->
+        <!-- SECTION 3 : Rediffusion de vidéos                            -->
+        <!-- ============================================================ -->
+        <section class="doc-section" id="section-videos">
+            <div class="section-header">
+                <span class="section-badge badge-teal">{% trans "Vidéos" %}</span>
+                <h2><i class="fas fa-film"></i> {% trans "Rediffusion de vidéos" %}</h2>
+            </div>
+
+            <!-- Menu gauche -->
+            <div class="sub-subsection" id="section-vid-nav">
+                <h4 class="table-title"><i class="fas fa-bars"></i> {% trans "Menu gauche — Sélection" %}</h4>
+                <div class="info-row">
+                    <div class="info-card card-accent-indigo full-width">
+                        <div class="card-icon"><i class="fas fa-mouse-pointer"></i></div>
+                        <div class="card-body">
+                            <ol class="doc-steps">
+                                <li><i class="fas fa-play-circle"></i> {% trans "Sélectionner la session" %}</li>
+                                <li><i class="fas fa-check-square"></i> {% trans "Cocher l'expérience" %}</li>
+                                <li><i class="fas fa-circle"></i> {% trans "Choisir le puit" %}</li>
+                            </ol>
+                        </div>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Lecteur & export -->
+            <div class="sub-subsection" id="section-vid-view">
+                <h4 class="table-title"><i class="fas fa-play-circle"></i> {% trans "Lecteur vidéo & export" %}</h4>
+                <div class="info-row">
+                    <!-- Contrôles lecture -->
+                    <div class="info-card card-accent-teal">
+                        <div class="card-icon"><i class="fas fa-gamepad"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Contrôles de lecture" %}</h4>
+                            <!-- Boutons transport -->
+                            <div class="player-controls">
+                                <div class="player-btn btn-play">
+                                    <i class="fas fa-play"></i>
+                                    <span>{% trans "Marche" %}</span>
+                                </div>
+                                <div class="player-btn btn-pause">
+                                    <i class="fas fa-pause"></i>
+                                    <span>{% trans "Pause" %}</span>
+                                </div>
+                                <div class="player-btn btn-stop">
+                                    <i class="fas fa-stop"></i>
+                                    <span>{% trans "Arrêt" %}</span>
+                                </div>
+                            </div>
+                            <!-- Sliders -->
+                            <ul class="doc-list" style="margin-top:12px;">
+                                <li>
+                                    <i class="fas fa-tachometer-alt text-teal"></i>
+                                    {% trans "Slider vitesse de lecture" %}
+                                </li>
+                                <li>
+                                    <i class="fas fa-stream text-teal"></i>
+                                    {% trans "Slider timeline (position dans la vidéo)" %}
+                                </li>
+                            </ul>
+                        </div>
+                    </div>
+
+                    <!-- Téléchargements -->
+                    <div class="info-card card-accent-blue">
+                        <div class="card-icon"><i class="fas fa-download"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Téléchargements" %}</h4>
+                            <ul class="doc-list">
+                                <li>
+                                    <i class="fas fa-image text-blue"></i>
+                                    {% trans "Télécharger l'image courante" %}
+                                </li>
+                                <li>
+                                    <i class="fas fa-film text-blue"></i>
+                                    {% trans "Télécharger la vidéo complète" %}
+                                </li>
+                            </ul>
+                        </div>
+                    </div>
+                </div>
+
+                <!-- Export global vidéos -->
+                <div class="info-row">
+                    <div class="info-card card-accent-orange full-width">
+                        <div class="card-icon"><i class="fas fa-file-video"></i></div>
+                        <div class="card-body">
+                            <h4>
+                                {% trans "Exporter l'ensemble des vidéos" %}
+                                <span class="badge-important">{% trans "ATTENTION" %}</span>
+                            </h4>
+                            <ul class="doc-list">
+                                <li>
+                                    <i class="fas fa-hourglass-half text-orange"></i>
+                                    {% trans "La procédure peut être longue." %}
+                                </li>
+                                <li>
+                                    <i class="fas fa-clock text-orange"></i>
+                                    {% trans "Préférer l'export différé." %}
+                                </li>
+                            </ul>
+                            <div class="deferred-badge">
+                                <i class="fas fa-calendar-alt"></i>
+                                {% trans "Export différé recommandé" %}
+                            </div>
+                        </div>
+                    </div>
+                </div>
+            </div>
+        </section>
+
+    </main>
+</div>
+{% endblock %}
+
+{% block js_footer %}
+    {{ block.super }}
+	<script>
+	/* Mise en évidence du lien actif dans la navigation latérale */
+	(function () {
+	    const links    = document.querySelectorAll('.nav-link');
+	    const sections = document.querySelectorAll('[id^="section-"]');
+	
+	    const observer = new IntersectionObserver(
+	        (entries) => {
+	            entries.forEach(entry => {
+	                if (entry.isIntersecting) {
+	                    links.forEach(l => l.classList.remove('active'));
+	                    const target = document.querySelector(`.nav-link[href="#${entry.target.id}"]`);
+	                    if (target) target.classList.add('active');
+	                }
+	            });
+	        },
+	        { rootMargin: '-10% 0px -80% 0px' }
+	    );
+	
+	    sections.forEach(s => observer.observe(s));
+	})();
+	</script> 
+{% endblock %}

test_tube_scanner/home/templates/docs/doc_results.html

@@ -0,0 +1,204 @@
+{% extends 'scanner/base.html' %}
+{% load i18n %}
+{% block columns %}{% endblock %}
+
+{% block styles %}
+    {{ block.super }}
+    <link rel="stylesheet" href="/static/css/doc_database.css">
+    <link rel="stylesheet" href="/static/css/doc_calibration.css>
+    <link rel="stylesheet" href="/static/css/doc_experiments.css">
+    <link rel="stylesheet" href="/static/css/doc_scanning.css"> 
+    <link rel="stylesheet" href="/static/css/doc_results.css">       
+{% endblock %}
+
+{% block content %}
+<div class="doc-wrapper">
+
+    <!-- ─── En-tête ─── -->
+    <header class="doc-header">
+        <div class="doc-header-inner">
+            <div class="doc-header-icon" style="background: linear-gradient(135deg, var(--accent-green), var(--accent-blue));">
+                <i class="fas fa-chart-bar"></i>
+            </div>
+            <div>
+                <h1 class="doc-title">{% trans "Exploiter les résultats" %}</h1>
+                <p class="doc-subtitle">{% trans "Export CSV des métriques par session, expérience et planaire" %}</p>
+            </div>
+        </div>
+    </header>
+
+    <!-- ─── Navigation latérale ─── -->
+    <nav class="doc-sidenav" id="sidenav">
+        <p class="nav-section-label">{% trans "Navigation" %}</p>
+        <a href="#section-intro"    class="nav-link active"><i class="fas fa-info-circle"></i>  {% trans "Présentation" %}</a>
+        <a href="#section-left"     class="nav-link">       <i class="fas fa-bars"></i>          {% trans "Menu gauche" %}</a>
+        <a href="#section-export"   class="nav-link nav-sub"><i class="fas fa-server"></i>      {% trans "Export serveur" %}</a>
+        <a href="#section-right"    class="nav-link">       <i class="fas fa-download"></i>      {% trans "Partie droite" %}</a>
+        <a href="#section-generate" class="nav-link nav-sub"><i class="fas fa-file-csv"></i>    {% trans "Générer le CSV" %}</a>
+    </nav>
+
+    <!-- ─── Contenu principal ─── -->
+    <main class="doc-content">
+
+        <!-- ============================================================ -->
+        <!-- SECTION 1 : Présentation                                      -->
+        <!-- ============================================================ -->
+        <section class="doc-section" id="section-intro">
+            <div class="section-header">
+                <span class="section-badge badge-green">{% trans "Export CSV" %}</span>
+                <h2><i class="fas fa-chart-bar"></i> {% trans "Exploiter les résultats des expériences" %}</h2>
+                <p class="section-desc">{% trans "Les métriques de suivi des planaires sont exportables au format CSV depuis l'interface Scanner." %}</p>
+            </div>
+        </section>
+
+        <!-- ============================================================ -->
+        <!-- SECTION 2 : Menu gauche                                       -->
+        <!-- ============================================================ -->
+        <section class="doc-section" id="section-left">
+            <div class="section-header">
+                <span class="section-badge badge-blue">{% trans "Sélection" %}</span>
+                <h2><i class="fas fa-bars"></i> {% trans "Menu gauche" %}</h2>
+            </div>
+
+            <div class="info-row">
+                <div class="info-card card-accent-indigo">
+                    <div class="card-icon"><i class="fas fa-mouse-pointer"></i></div>
+                    <div class="card-body">
+                        <h4>{% trans "Sélection" %}</h4>
+                        <ol class="doc-steps">
+                            <li><i class="fas fa-play-circle"></i> {% trans "Sélectionner la session" %}</li>
+                            <li><i class="fas fa-check-square"></i> {% trans "Cocher l'expérience souhaitée" %}</li>
+                            <li><i class="fas fa-file-export"></i> {% trans "Cliquer sur Exporter les métriques de l'expérience" %}</li>
+                        </ol>
+                    </div>
+                </div>
+            </div>
+
+            <!-- Export serveur -->
+            <div class="sub-subsection" id="section-export">
+                <h4 class="table-title">
+                    <i class="fas fa-server"></i> {% trans "Export côté serveur" %}
+                    <span class="badge-important">{% trans "ATTENTION" %}</span>
+                </h4>
+
+                <div class="info-row">
+                    <!-- Durée -->
+                    <div class="info-card card-accent-orange">
+                        <div class="card-icon"><i class="fas fa-hourglass-half"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Durée variable" %}</h4>
+                            <div class="alert-box" style="margin-bottom:0;">
+                                <i class="fas fa-exclamation-triangle"></i>
+                                {% trans "La procédure peut être longue selon le nombre de planaires à suivre." %}
+                            </div>
+                        </div>
+                    </div>
+
+                    <!-- Tâche de fond -->
+                    <div class="info-card card-accent-blue">
+                        <div class="card-icon"><i class="fas fa-cogs"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Tâche de fond" %}</h4>
+                            <p>{% trans "Le service est exécuté en arrière-plan (Celery)." %}</p>
+                            <div class="tag-list">
+                                <span class="tag tag-blue">export_session</span>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+
+                <!-- Emplacement fichiers -->
+                <div class="info-row">
+                    <div class="info-card card-accent-teal full-width">
+                        <div class="card-icon"><i class="fas fa-folder-open"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Emplacement des fichiers sur le serveur" %}</h4>
+                            <div class="path-block">
+                                <i class="fas fa-hdd"></i>
+                                <code>/home/rpi4/export/csv/*.csv</code>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+            </div>
+        </section>
+
+        <!-- ============================================================ -->
+        <!-- SECTION 3 : Partie droite — téléchargement client            -->
+        <!-- ============================================================ -->
+        <section class="doc-section" id="section-right">
+            <div class="section-header">
+                <span class="section-badge badge-green">{% trans "Téléchargement" %}</span>
+                <h2><i class="fas fa-download"></i> {% trans "Partie droite — Téléchargement client" %}</h2>
+            </div>
+
+            <div class="sub-subsection" id="section-generate">
+                <div class="info-row">
+                    <!-- Sélections -->
+                    <div class="info-card card-accent-indigo">
+                        <div class="card-icon"><i class="fas fa-sliders-h"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Paramètres" %}</h4>
+                            <ul class="doc-list">
+                                <li>
+                                    <i class="fas fa-circle text-teal"></i>
+                                    {% trans "Choisir le puit" %}
+                                </li>
+                                <li>
+                                    <i class="fas fa-hashtag text-indigo"></i>
+                                    {% trans "Choisir l'index du planaire" %}
+                                    <p class="task-desc">
+                                        <i class="fas fa-info-circle"></i>
+                                        {% trans "Le nombre de planaires est défini dans" %}
+                                        <em>{% trans "Paramètres d'une expérience" %}</em>.
+                                    </p>
+                                </li>
+                            </ul>
+                        </div>
+                    </div>
+
+                    <!-- Bouton Générer -->
+                    <div class="info-card card-accent-green">
+                        <div class="card-icon"><i class="fas fa-file-download"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Bouton Générer" %}</h4>
+                            <p>{% trans "Télécharge le fichier CSV directement sur le poste client." %}</p>
+                            <div class="alert-box alert-info">
+                                <i class="fas fa-hourglass-half"></i>
+                                {% trans "La procédure peut être longue." %}
+                            </div>
+                        </div>
+                    </div>
+                </div>
+            </div>
+        </section>
+
+    </main>
+</div>
+{% endblock %}
+
+{% block js_footer %}
+    {{ block.super }}
+	<script>
+	/* Mise en évidence du lien actif dans la navigation latérale */
+	(function () {
+	    const links    = document.querySelectorAll('.nav-link');
+	    const sections = document.querySelectorAll('[id^="section-"]');
+	
+	    const observer = new IntersectionObserver(
+	        (entries) => {
+	            entries.forEach(entry => {
+	                if (entry.isIntersecting) {
+	                    links.forEach(l => l.classList.remove('active'));
+	                    const target = document.querySelector(`.nav-link[href="#${entry.target.id}"]`);
+	                    if (target) target.classList.add('active');
+	                }
+	            });
+	        },
+	        { rootMargin: '-10% 0px -80% 0px' }
+	    );
+	
+	    sections.forEach(s => observer.observe(s));
+	})();
+	</script>    
+{% endblock %}

test_tube_scanner/home/templates/docs/doc_scanning.html

@@ -0,0 +1,266 @@
+{% extends 'scanner/base.html' %}
+{% load i18n %}
+{% block columns %}{% endblock %}
+
+{% block styles %}
+    {{ block.super }}
+    <link rel="stylesheet" href="/static/css/doc_database.css">
+    <link rel="stylesheet" href="/static/css/doc_calibration.css>
+    <link rel="stylesheet" href="/static/css/doc_experiments.css">
+    <link rel="stylesheet" href="/static/css/doc_scanning.css">
+{% endblock %}
+
+{% block content %}
+<div class="doc-wrapper">
+
+    <!-- ─── En-tête ─── -->
+    <header class="doc-header">
+        <div class="doc-header-inner">
+            <div class="doc-header-icon" style="background: linear-gradient(135deg, var(--accent-indigo), var(--accent-purple));">
+                <i class="fas fa-route"></i>
+            </div>
+            <div>
+                <h1 class="doc-title">{% trans "Balayage des puits" %}</h1>
+                <p class="doc-subtitle">{% trans "Lancement, suivi et procédure en cas d'arrêt" %}</p>
+            </div>
+        </div>
+    </header>
+
+    <!-- ─── Navigation latérale ─── -->
+    <nav class="doc-sidenav" id="sidenav">
+        <p class="nav-section-label">{% trans "Navigation" %}</p>
+        <a href="#section-intro"   class="nav-link active"><i class="fas fa-info-circle"></i>  {% trans "Présentation" %}</a>
+        <a href="#section-cmd"     class="nav-link">       <i class="fas fa-gamepad"></i>       {% trans "Commandes" %}</a>
+        <a href="#section-start"   class="nav-link nav-sub"><i class="fas fa-play"></i>        {% trans "Lancer le balayage" %}</a>
+        <a href="#section-stop"    class="nav-link nav-sub"><i class="fas fa-stop"></i>        {% trans "Arrêt" %}</a>
+        <a href="#section-recover" class="nav-link">       <i class="fas fa-undo-alt"></i>      {% trans "Procédure après arrêt" %}</a>
+        <a href="#section-reduct"  class="nav-link nav-sub"><i class="fas fa-database"></i>   ReductStore</a>
+    </nav>
+
+    <!-- ─── Contenu principal ─── -->
+    <main class="doc-content">
+
+        <!-- ============================================================ -->
+        <!-- SECTION 1 : Présentation                                      -->
+        <!-- ============================================================ -->
+        <section class="doc-section" id="section-intro">
+            <div class="section-header">
+                <span class="section-badge badge-indigo">{% trans "Balayage" %}</span>
+                <h2><i class="fas fa-route"></i> {% trans "Balayage des puits" %}</h2>
+            </div>
+
+            <div class="info-row">
+                <div class="info-card card-accent-indigo">
+                    <div class="card-icon"><i class="fas fa-crop-alt"></i></div>
+                    <div class="card-body">
+                        <h4>{% trans "Recadrage forcé" %}</h4>
+                        <p>{% trans "Le balayage force toujours le recadrage de l'image." %}</p>
+                        <p>{% trans "Le balayage est disponible quand la session est marquée ACTIVE" %}</p>
+                        <div class="alert-box alert-info">
+                            <i class="fas fa-info-circle"></i>
+                            {% trans "Les boutons Axes et Recadrer sont affichés à titre indicatif uniquement." %}
+                        </div>
+                    </div>
+                </div>
+            </div>
+        </section>
+
+        <!-- ============================================================ -->
+        <!-- SECTION 2 : Commandes                                         -->
+        <!-- ============================================================ -->
+        <section class="doc-section" id="section-cmd">
+            <div class="section-header">
+                <span class="section-badge badge-blue">{% trans "Interface" %}</span>
+                <h2><i class="fas fa-gamepad"></i> {% trans "Commandes importantes" %}</h2>
+            </div>
+
+            <!-- Lancer le balayage -->
+            <div class="sub-subsection" id="section-start">
+                <h4 class="table-title">
+                    <i class="fas fa-play"></i> {% trans "Lancer le balayage" %}
+                </h4>
+                <div class="info-row">
+                    <div class="info-card card-accent-green full-width">
+                        <div class="card-icon"><i class="fas fa-play-circle"></i></div>
+                        <div class="card-body">
+                            <ul class="doc-list">
+                                <li>
+                                    <i class="fas fa-shoe-prints text-green"></i>
+                                    {% trans "Suivi pas à pas de tous les puits de la session." %}
+                                </li>
+                                <li>
+                                    <i class="fas fa-terminal text-green"></i>
+                                    {% trans "Les logs s'affichent en bas de l'écran en temps réel." %}
+                                </li>
+                            </ul>
+                        </div>
+                    </div>
+                </div>
+            </div>
+
+            <!-- ARRÊT -->
+            <div class="sub-subsection" id="section-stop">
+                <h4 class="table-title">
+                    <i class="fas fa-stop"></i> {% trans "ARRÊT" %}
+                    <span class="badge-important">{% trans "ATTENTION" %}</span>
+                </h4>
+                <div class="info-row">
+                    <div class="info-card card-accent-green">
+                        <div class="card-icon"><i class="fas fa-images"></i></div>
+                        <div class="card-body">
+                            <h4><i class="fas fa-check-circle text-green"></i> {% trans "Images" %}</h4>
+                            <p>{% trans "Les images capturées jusqu'à l'arrêt seront enregistrées." %}</p>
+                        </div>
+                    </div>
+                    <div class="info-card card-accent-red">
+                        <div class="card-icon"><i class="fas fa-chart-line"></i></div>
+                        <div class="card-body">
+                            <h4><i class="fas fa-times-circle text-red"></i> {% trans "Données" %}</h4>
+                            <p>{% trans "Les données de suivi ne seront pas enregistrées." %}</p>
+                        </div>
+                    </div>
+                </div>
+            </div>
+        </section>
+
+        <!-- ============================================================ -->
+        <!-- SECTION 3 : Procédure après arrêt                            -->
+        <!-- ============================================================ -->
+        <section class="doc-section" id="section-recover">
+            <div class="section-header">
+                <span class="section-badge badge-red">{% trans "Récupération" %}</span>
+                <h2><i class="fas fa-undo-alt"></i> {% trans "Procédure en cas d'arrêt" %}</h2>
+            </div>
+
+            <!-- Étapes Django -->
+            <div class="info-row">
+                <div class="info-card card-accent-orange full-width">
+                    <div class="card-icon"><i class="fas fa-redo-alt"></i></div>
+                    <div class="card-body">
+                        <h4>{% trans "Réinitialiser la session" %}</h4>
+                        <ol class="doc-steps">
+                            <li>
+                                <i class="fas fa-trash-alt text-red"></i>
+                                {% trans "Supprimer la session en cours depuis l'administration Django." %}
+                            </li>
+                            <li>
+                                <i class="fas fa-plus-circle text-green"></i>
+                                {% trans "Créer une nouvelle session." %}
+                            </li>
+                        </ol>
+                    </div>
+                </div>
+            </div>
+
+            <!-- ReductStore — superadmin -->
+            <div class="sub-subsection" id="section-reduct">
+                <h4 class="table-title">
+                    <i class="fas fa-database"></i>
+                    {% trans "Nettoyage ReductStore" %}
+                    <span class="badge-superadmin">superadmin</span>
+                </h4>
+
+                <div class="info-row">
+                    <div class="info-card card-accent-red full-width">
+                        <div class="card-icon"><i class="fas fa-exclamation-triangle"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Accès ReductStore" %}</h4>
+                            <a href="http://192.168.1.200:8383/ui/dashboard" target="_blank" class="access-link">
+                                192.168.1.200:8383/ui/dashboard <i class="fas fa-external-link-alt"></i>
+                            </a>
+                        </div>
+                    </div>
+                </div>
+
+                <div class="info-row">
+                    <!-- Bucket camera -->
+                    <div class="info-card card-accent-cyan">
+                        <div class="card-icon"><i class="fas fa-images"></i></div>
+                        <div class="card-body">
+                            <h4>
+                                {% trans "Bucket" %} <code>camera</code>
+                            </h4>
+                            <ol class="doc-steps">
+                                <li>
+                                    <i class="fas fa-search"></i>
+                                    {% trans "Localiser les entrées correspondant aux UUIDs des expériences." %}
+                                </li>
+                                <li>
+                                    <i class="fas fa-trash-alt text-red"></i>
+                                    {% trans "Supprimer les UUIDs des expériences concernées." %}
+                                </li>
+                            </ol>
+                        </div>
+                    </div>
+
+                    <!-- Bucket planarian_metrics -->
+                    <div class="info-card card-accent-green">
+                        <div class="card-icon"><i class="fas fa-chart-line"></i></div>
+                        <div class="card-body">
+                            <h4>
+                                {% trans "Bucket" %} <code>planarian_metrics</code>
+                            </h4>
+                            <ol class="doc-steps">
+                                <li>
+                                    <i class="fas fa-tag"></i>
+                                    {% trans "Repérer les enregistrements dont le label correspond aux UUIDs." %}
+                                </li>
+                                <li>
+                                    <i class="fas fa-trash-alt text-red"></i>
+                                    {% trans "Supprimer ces enregistrements." %}
+                                </li>
+                            </ol>
+                            <div class="tag-list" style="margin-top:10px;">
+                                <span class="tag tag-gray">label: uuid</span>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+
+                <!-- Résumé visuel uuid -->
+                <div class="info-row">
+                    <div class="info-card card-accent-yellow full-width">
+                        <div class="card-icon"><i class="fas fa-key"></i></div>
+                        <div class="card-body">
+                            <h4>{% trans "Identifier les UUIDs à supprimer" %}</h4>
+                            <p>{% trans "Les UUIDs des expériences sont visibles dans l'administration Django, dans la session supprimée ou dans les logs affichés pendant le balayage." %}</p>
+                            <div class="uuid-example">
+                                <i class="fas fa-fingerprint"></i>
+                                <code>3-HD-A4</code>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+
+            </div>
+        </section>
+
+    </main>
+</div>
+{% endblock %}
+
+{% block js_footer %}
+    {{ block.super }}
+	<script>
+	/* Mise en évidence du lien actif dans la navigation latérale */
+	(function () {
+	    const links    = document.querySelectorAll('.nav-link');
+	    const sections = document.querySelectorAll('[id^="section-"]');
+	
+	    const observer = new IntersectionObserver(
+	        (entries) => {
+	            entries.forEach(entry => {
+	                if (entry.isIntersecting) {
+	                    links.forEach(l => l.classList.remove('active'));
+	                    const target = document.querySelector(`.nav-link[href="#${entry.target.id}"]`);
+	                    if (target) target.classList.add('active');
+	                }
+	            });
+	        },
+	        { rootMargin: '-10% 0px -80% 0px' }
+	    );
+	
+	    sections.forEach(s => observer.observe(s));
+	})();
+	</script>
+{% endblock %}

test_tube_scanner/home/templates/inc/alert.html

@@ -2,12 +2,14 @@
 {% if messages %}
 <div class="alert">
 	{% for message in messages %}
-		<div class="w3-bar {% if message.tags %}{{ message.tags }}{% endif %}" style="width: 100%" >
+	<div class="w3-panel w3-round 
+        {% if message.tags == 'success' %}w3-green
+        {% elif message.tags == 'error'   %}w3-red
+        {% elif message.tags == 'warning' %}w3-orange
+        {% else %}w3-blue{% endif %}" style="width: 100%" >
 		<div class="w3-bar-item">{{ message }}</div>
 		<div class="w3-bar-item w3-button w3-right" onclick="this.parentElement.style.display='none'">&times;</div>
 	</div>
 	{% endfor %}
 </div>
 {% endif %}
-
-

test_tube_scanner/home/urls.py

@@ -38,6 +38,7 @@ urlpatterns += i18n_patterns(
 
     path('', RedirectView.as_view(url='/scanner/calibration/', permanent=True), name='redirect_to_mainboard'),
     path('scanner/', include('scanner.urls', namespace='scanner')),
+    path('planarian/', include('planarian.urls', namespace='planarian')),
 )
 
 if settings.DEBUG:

test_tube_scanner/make_videos.sh

@@ -0,0 +1,102 @@
+#!/bin/bash
+
+# Génère 24 vidéos pour simuler le balayage d'un multi-puit de 6x24 
+#   A1..A6, B1..B6, C1..C6, D1..D6
+#  
+MODE="$1"
+PATH="./media/simulation"
+default_width=1000      # px
+default_height=1000     # px
+default_diameter=16.0   # mm
+
+     #fps duration bg-color arena-color arena-border shadow-color body-color body-dark body-light head-color thresh-immobile thresh-mobile
+BASE="15  60       #EBEBEB  #FAFAFA     #8C8C8C      #C8C8C8      #A5A5A5    #373737   #D2D2D2    #828282    0.2             1.5"
+
+        #photo-mode photo-strength photo-x photo-y photo-sine-freq photo-radius
+PHOTO_0="none       0.50           0.50    0.50    0.10            0.30"
+PHOTO_1="fixed      0.50           0.50    0.50    0.10            0.40"
+PHOTO_2="sine       0.50           0.50    0.50    0.10            0.50"
+PHOTO_3="radial     0.50           0.50    0.50    0.10            0.60"
+
+        #chemo-strength chemo-x chemo-y chemo-radius
+CHEMO_0="0.0            0.70    0.70    2.0"
+CHEMO_1="0.5            0.70    0.70    2.0"
+CHEMO_2="1.0            0.70    0.70    2.0"
+
+        #avoid-strength avoid-radius aggreg-strength aggreg-radius chem-repulsion chem-decay
+AVOID_0="0.0            3.0          0.0             6.0           0.0            0.95"
+AVOID_1="0.5            3.0          0.0             6.0           0.5            0.75"
+AVOID_2="1.0            3.0          0.0             6.0           1.0            0.65"
+
+       #length width
+SIZE_0="0.40   0.30"
+SIZE_1="0.45   0.35"
+SIZE_2="0.50   0.40"
+SIZE_3="0.55   0.45"
+SIZE_4="0.65   0.45"
+SIZE_5="0.7    0.25"
+
+declare -A DEFAULT
+declare -A ALL
+
+#=========================== count size    seed  base  thigmotaxis photo    chemo    avoid
+DEFAULT[default_simulation]="4     $SIZE_0  32   $BASE 0.45        $PHOTO_0 $CHEMO_0 $AVOID_1"
+
+    
+#======= count size    seed  base  thigmotaxis photo    chemo    avoid
+ALL[A1]="4     $SIZE_0  32   $BASE 0.45        $PHOTO_0 $CHEMO_0 $AVOID_0"
+ALL[A2]="4     $SIZE_1  64   $BASE 0.50        $PHOTO_1 $CHEMO_1 $AVOID_1"
+ALL[A3]="4     $SIZE_2  96   $BASE 0.55        $PHOTO_1 $CHEMO_2 $AVOID_2"
+ALL[A4]="4     $SIZE_3  128  $BASE 0.60        $PHOTO_2 $CHEMO_0 $AVOID_1"   
+ALL[A5]="4     $SIZE_4  192  $BASE 0.65        $PHOTO_2 $CHEMO_1 $AVOID_0"
+ALL[A6]="4     $SIZE_5  240  $BASE 0.75        $PHOTO_3 $CHEMO_2 $AVOID_2"
+ALL[B1]="4     $SIZE_0  32   $BASE 0.45        $PHOTO_3 $CHEMO_0 $AVOID_0"
+ALL[B2]="4     $SIZE_1  64   $BASE 0.50        $PHOTO_0 $CHEMO_1 $AVOID_1"    
+ALL[B3]="4     $SIZE_2  96   $BASE 0.55        $PHOTO_0 $CHEMO_2 $AVOID_0"
+ALL[B4]="4     $SIZE_3  128  $BASE 0.65        $PHOTO_0 $CHEMO_1 $AVOID_2" 
+ALL[B5]="4     $SIZE_4  192  $BASE 0.85        $PHOTO_0 $CHEMO_2 $AVOID_0"
+ALL[B6]="4     $SIZE_5  240  $BASE 0.95        $PHOTO_0 $CHEMO_0 $AVOID_0" 
+ALL[C1]="4     $SIZE_0  32   $BASE 0.40        $PHOTO_0 $CHEMO_0 $AVOID_1"    
+ALL[C2]="4     $SIZE_1  64   $BASE 0.30        $PHOTO_0 $CHEMO_0 $AVOID_0"      
+ALL[C3]="4     $SIZE_2  96   $BASE 0.55        $PHOTO_0 $CHEMO_1 $AVOID_0"    
+ALL[C4]="4     $SIZE_3  128  $BASE 0.45        $PHOTO_0 $CHEMO_2 $AVOID_2"    
+ALL[C5]="4     $SIZE_4  192  $BASE 0.50        $PHOTO_0 $CHEMO_0 $AVOID_0"    
+ALL[C6]="4     $SIZE_5  240  $BASE 0.65        $PHOTO_0 $CHEMO_1 $AVOID_0"    
+ALL[D1]="4     $SIZE_0  32   $BASE 0.70        $PHOTO_0 $CHEMO_2 $AVOID_1"    
+ALL[D2]="4     $SIZE_1  64   $BASE 0.65        $PHOTO_0 $CHEMO_0 $AVOID_0"
+ALL[D3]="4     $SIZE_2  96   $BASE 0.75        $PHOTO_0 $CHEMO_1 $AVOID_2"    
+ALL[D4]="4     $SIZE_3  128  $BASE 0.85        $PHOTO_0 $CHEMO_0 $AVOID_0"
+ALL[D5]="4     $SIZE_4  192  $BASE 0.65        $PHOTO_0 $CHEMO_2 $AVOID_0"    
+ALL[D6]="4     $SIZE_5  240  $BASE 0.45        $PHOTO_0 $CHEMO_0 $AVOID_0"        
+
+
+export_video() {
+    local -n arguments=$1
+    
+    for key in "${!arguments[@]}"; do
+        args="${arguments[$key]}"
+        read -r count length width seed fps duration bg_color arena_color arena_border shadow_color \
+                body_color body_dark body_light head_color thresh_immobile thresh_mobile thigmotaxis \
+                photo_mode photo_strength photo_x photo_y photo_sine_freq photo_radius chemo_strength chemo_x chemo_y chemo_radius \
+                avoid_strength avoid_radius aggreg_strength aggreg_radius chem_repulsion chem_decay <<< "$args"
+                
+        echo "==== Exécution de $PATH/$key.mp4"
+        
+        ./planarian_sim.py --output "$PATH/$key.mp4" --default_width "$default_width" --default_height "$default_height" --default_diameter "$default_diameter"  --no-csv \
+            --count "$count" --length "$length" --width "$width" --duration "$duration" --fps "$fps" --seed "$seed" \
+            --bg-color "$bg_color" --arena-color "$arena_color" --arena-border "$arena_border" --shadow-color "$shadow_color" \
+            --body-color "$body_color" --body-dark  "$body_dark" --body-light "$body_light" --head-color "$head_color" \
+            --thresh-immobile "$thresh_immobile" --thresh-mobile "$thresh_mobile" --thigmotaxis "$thigmotaxis"  \
+            --photo-mode "$photo_mode" --photo-strength "$photo_strength" --photo-x "$photo_x" --photo-y "$photo_y" --photo-sine-freq "$photo_sine_freq" --photo-radius "$photo_radius"  \
+            --chemo-strength "$chemo_strength" --chemo-x "$chemo_x" --chemo-y "$chemo_y" --chemo-radius "$chemo_radius"  \
+            --avoid-strength "$avoid_strength" --avoid-radius "$avoid_radius" --aggreg-strength "$aggreg_strength" --aggreg-radius "$aggreg_radius" \
+            --chem-repulsion "$chem_repulsion" --chem-decay "$chem_decay"
+    done
+}
+
+if [ "$MODE" = "all" ]; then
+    export_video ALL
+else
+    export_video DEFAULT
+fi
+

test_tube_scanner/modules/capture_interface.py

@@ -21,11 +21,14 @@ import logging
 from datetime import datetime, timezone
 from pathlib import Path
 from typing import Optional, Callable, TYPE_CHECKING
+from asgiref.sync import async_to_sync
 
 from django.conf import settings
 from modules.planarian_tracker import PlanarianTracker
+from modules.planarian_metrics import ExperimentParams, EthoVisionMetrics
 from modules.tube_aligner import TubeAligner
 
+
 if TYPE_CHECKING:
     from .circular_crop import CircularCrop     # Evite l'import circulaire au runtime
 
@@ -49,16 +52,27 @@ class VideoCaptureInterface(abc.ABC):
     # Cadence par défaut en images par seconde
     DEFAULT_FPS: float = 5.0
 
-    def __init__(self, fps: float = DEFAULT_FPS, use_tracking: bool = False, display=None, parent=None):
+    DEFAULT_TRACKER_CONFIG = dict(
+        tube_axis = settings.TRACKER_TUBE_AXIS,
+        min_area_px = settings.TRACKER_MIN_AREA,
+        max_area_ratio = settings.TRACKER_MAX_AREA_RATIO,
+        max_planarians = settings.TRACKER_MAX_PLANARIANS,
+        merge_kernel_size = settings.TRACKER_MERGE_KERNEL_SIZE,
+        min_contour_dist_px = settings.TRACKER_MIN_CONTOUR_DIST_PX,       
+    )
+    
+
+    def __init__(self, fps: float = DEFAULT_FPS, use_tracking: bool = False, display=None, parent=None, jpeg_quality=85):
         """
         Initialise l'interface de capture.
 
         :param fps: Cadence cible en images par seconde
         """
         self._fps: float = fps
-        self.use_tracking = use_tracking
         self.display = display
         self.parent = parent
+        self.use_tracking = use_tracking
+        self.jpeg_quality = jpeg_quality
         self._interval: float = 1.0 / fps       # Intervalle en secondes entre chaque capture
         self._running: bool = False              # Indique si la capture est en cours
         self._thread: Optional[threading.Thread] = None
@@ -67,12 +81,17 @@ class VideoCaptureInterface(abc.ABC):
         self._circular_crop: Optional["CircularCrop"] = None  # Recadrage circulaire optionnel
         self._active_median = False
         self._active_crop = False
+        self._active_edge_enhance = False
         self._error_occured = False
         
-        self._tracker = PlanarianTracker(
-            tube_axis = settings.TRACKER_TUBE_AXIS,
-            min_area_px = settings.TRACKER_MIN_AREA,
-        )
+        self._tracker: PlanarianTracker | None = None
+        self._metrics: list[EthoVisionMetrics] | None = None
+        self._params: ExperimentParams | None = None
+        self._clientDB = self.parent.metricDB
+
+        # Tracker générique, pour simulation
+        self.on_test_well_change(**self.DEFAULT_TRACKER_CONFIG)
+
         self._aligner = TubeAligner(
             grbl_threshold_px = 20,      # au-delà → correction GRBL
             dead_zone_px      = 5,       # en-dessous → rien à faire
@@ -80,13 +99,66 @@ class VideoCaptureInterface(abc.ABC):
         )
         self.align_detection  = None     # résultat du test
 
-    def on_well_change(self):
-        """
-        Appelé par le CNC lors du changement de puits.
-        Réinitialise le fond appris et l'état inter-frame du tracker.
-        """
-        self._tracker.reset()  
 
+    def on_test_well_change(self, **cfg):
+        try:
+            if self.use_tracking and cfg:
+                self._tracker = PlanarianTracker(**cfg)
+                logger.info(f"Create test with conf: {cfg}")
+        except Exception as e:
+            logger.error(f"Error creating tracker with conf {cfg}: {e}")
+            self._tracker = None
+    
+    def _flush_current_well(self, uuid=""):
+        """Stocke les résumés du puits courant — appelé avant tout changement."""
+        if not self._metrics or not self._params:
+            return
+        for pid, m in enumerate(self._metrics):
+            async_to_sync(self._clientDB.store_summary)(
+                summary    = m.summary(),
+                experiment = self._params.experiment,
+                well       = self._params.well,
+                planarian  = pid,
+                uuid       = uuid,
+            )
+            logger.warning(f'_flush_current_well: {self._params.well} planaire: {pid}')
+        self._metrics.clear()    
+
+
+    def on_well_change(self, cfg, uuid="", draw_contours=False):
+        """
+        Appelé par la CNC lors du changement de puits.
+        Réinitialise le fond appris et l'état inter-frame du tracker.
+        Construit les métriques aussi
+        """
+        if not self.use_tracking or not cfg:
+            return
+        
+        # 1. Sauvegarder les résumés du puits qu'on quitte
+        self._flush_current_well(uuid)          # ← ferme le puits courant
+        
+        # 2. Reconstruire pour le nouveau puit _metrics_list
+        params = cfg.to_params_dict()
+        self._params = ExperimentParams(params)        
+        self._metrics = [self._params.build_metrics() for _ in range(self._params.planarian_count)]
+        
+        self._tracker = PlanarianTracker(
+            tube_axis      = self._params.tube_axis,
+            min_area_px    = self._params.min_area_px,
+            max_area_ratio = self._params.max_area_ratio,
+            max_planarians = self._params.planarian_count,
+            merge_kernel_size = self._params.merge_kernel_size,
+            min_contour_dist_px = self._params.min_contour_dist_px,
+            draw_contours = draw_contours,
+        )
+
+    def on_scan_complete(self):
+        if self.use_tracking:
+            self._flush_current_well()          # ← ferme le dernier puits
+
+    def set_draw_contours(self, draw: bool = True):
+        if self._tracker:
+            self._tracker.draw_contours = draw
             
     # ------------------------------------------------------------------
     # Méthodes abstraites — obligatoires dans les sous-classes
@@ -213,10 +285,30 @@ class VideoCaptureInterface(abc.ABC):
             msg= f"{self.__class__.__name__}: recadrage circulaire désactivé"
         
         logger.info(msg)
+        if self.display is not None:
             self.display(state='circular_crop', msg=msg)
             
 
-    def process_frame(self, jpeg_bytes: bytes) -> bytes:
+    def set_edge_enhance(self, enabled: bool) -> None:
+        """Active ou désactive le filtre de mise en évidence des contours (calibration)."""
+        self._active_edge_enhance = enabled
+        logger.info(f"{self.__class__.__name__}: edge_enhance={enabled}")
+        if self.display is not None:
+            self.display(state='edge_enhance', value=enabled, msg=f"Edge enhance: {enabled}")
+
+    def _apply_edge_enhance(self, frame: np.ndarray) -> np.ndarray:
+        """Overlay Canny vert additif sur l'image originale.
+        Flou fort avant détection pour ne garder que les bords dominants (rebord du puit).
+        """
+        gray = cv2.cvtColor(frame, cv2.COLOR_BGR2GRAY)
+        blurred = cv2.GaussianBlur(gray, (9, 9), 2)
+        edges = cv2.Canny(blurred, 80, 200)
+        edges = cv2.dilate(edges, np.ones((3, 3), np.uint8), iterations=1)
+        overlay = np.zeros_like(frame)
+        overlay[edges > 0] = [0, 255, 0]  # vert sur fond noir
+        return cv2.addWeighted(frame, 1.0, overlay, 1.0, 0)  # additif : image inchangée hors bords
+
+    def process_frame(self, jpeg_bytes: bytes) -> tuple[bytes, dict]:
         """
         Applique le post-traitement configuré sur une image brute.
 
@@ -227,30 +319,47 @@ class VideoCaptureInterface(abc.ABC):
         :return:           Image traitée (JPEG ou PNG selon la stratégie)
         """
         metrics = {"detected": False}
+        
         if self._circular_crop is not None:
             jpeg  = self._circular_crop.process(jpeg_bytes)
             nparr = np.frombuffer(jpeg, np.uint8)
             frame = cv2.imdecode(nparr, cv2.IMREAD_COLOR)
             if frame is None:
                 return jpeg, metrics        
-            
-            # Mode debug
+            try:
+                # Edge enhance sur la frame propre, avant les annotations
+                if self._active_edge_enhance:
+                    frame = self._apply_edge_enhance(frame)
+                ##
+                # Mode debug (annotations par-dessus)
                 if self._aligner.debug:
                     self.align_detection = self._aligner.detect_tube(frame)
                     annotated = self.align_detection.get('frame_annotated')
                     frame = annotated if annotated is not None else frame
-            
-            # mode racking
+                ##
+                # mode tracking
                 if self.use_tracking:
                     ts = datetime.now(timezone.utc).timestamp()
                     frame, metrics = self._tracker.process(frame, ts)
-                
-            ok, buf = cv2.imencode(".jpg", frame, [cv2.IMWRITE_JPEG_QUALITY, 85])
+                ##
+                ok, buf = cv2.imencode(".jpg", frame, [cv2.IMWRITE_JPEG_QUALITY, self.jpeg_quality])
                 if ok:
                     jpeg = buf.tobytes()
-                    
                 return jpeg, metrics
             
+            except Exception as e:
+                logger.error(e)
+
+        # Pas de circular crop — appliquer edge enhance si actif
+        if self._active_edge_enhance:
+            nparr = np.frombuffer(jpeg_bytes, np.uint8)
+            frame = cv2.imdecode(nparr, cv2.IMREAD_COLOR)
+            if frame is not None:
+                frame = self._apply_edge_enhance(frame)
+                ok, buf = cv2.imencode(".jpg", frame, [cv2.IMWRITE_JPEG_QUALITY, self.jpeg_quality])
+                if ok:
+                    return buf.tobytes(), metrics
+
         return jpeg_bytes, metrics
 
     def save_frame(self, jpeg_bytes: bytes, directory: str = ".", prefix: str = "frame") -> Path:
@@ -325,16 +434,12 @@ class VideoCaptureInterface(abc.ABC):
                 ## 
                 jpeg, metrics = self.process_frame(jpeg)  # Recadrage circulaire si configuré
 
-                metrics.update({
-                    "count": self._frame_count,
-                }) 
-
                 self._frame_count += 1
                 ts = datetime.now(timezone.utc)
 
                 if self._on_frame:
                     try:
-                        self._on_frame(jpeg, ts, metrics)
+                        self._on_frame(jpeg, ts, metrics, self._frame_count)
                     except Exception as cb_err:  # noqa: BLE001
                         logger.error("Erreur dans le callback image : %s", cb_err)
 

test_tube_scanner/modules/circular_crop.py

@@ -66,7 +66,7 @@ class CircularCrop:
 
         # Cache du masque pour éviter de le recalculer à chaque frame
         self._mask_cache: Optional[np.ndarray] = None
-        self._mask_shape: Optional[tuple[int, int, int]] = None  # (H, W, strategy)
+        self._mask_shape: Optional[tuple[int, ...]] = None  # (H, W, cx, cy, radius)
 
     # ------------------------------------------------------------------
     # API publique

test_tube_scanner/modules/grbl.py

@@ -12,6 +12,7 @@ import logging
 import serial
 import time
 import threading
+from typing import Callable, Any
 
 
 logging.basicConfig(level=logging.INFO)
@@ -41,11 +42,10 @@ class GRBLController:
         if y_max is not None:
             self.Y_MAX = y_max
 
-        self._state = send_callback
-        if self._state is None:
-            self._state = self._send_msg
+        self._state: Callable[..., Any] = send_callback if send_callback is not None else self._send_msg
 
-        self.x, self.y = 0, 0
+        self.x: float | None = None
+        self.y: float | None = None
         
         #self.start_connection()
 
@@ -67,8 +67,8 @@ class GRBLController:
             try:
                 self.ser = serial.Serial(self.port, self.baudrate, timeout=self.timeout, exclusive=True)
                 # CRITIQUE :
-                self.ser.setDTR(False)
-                self.ser.setRTS(False)
+                self.ser.setDTR(False)  # type: ignore[attr-defined]
+                self.ser.setRTS(False)  # type: ignore[attr-defined]
                 self.clear_buffer()
                 
                 self._wake_up()
@@ -192,7 +192,7 @@ class GRBLController:
         
     def move_relative(self, dx=0, dy=0, feed=1000):
         x, y = self.get_mpos()  # Position actuelle
-        self.move_to(x + dx, y + dy, feed=feed)
+        self.move_to((x or 0) + dx, (y or 0) + dy, feed=feed)
         
     def move_relative__(self, dx=0, dy=0, feed=1000):
         self.send("G91")  # Mode relatif

test_tube_scanner/modules/grbl_simulator.py

@@ -0,0 +1,300 @@
+'''
+Simulateur GCode pour tester sans CNC physique.
+
+    GRBLController (simulé):
+        Reproduit fidèlement l'API de grbl.py
+        Simule les mouvements (X, Y) avec délai proportionnel au feed rate
+        Le mode absolu est retenu
+        Aucune dépendance à pyserial
+
+Created on 07 mai 2026
+
+@author: denis@miraceti.net
+'''
+import logging
+import time
+import threading
+import math
+from typing import Callable, Any
+
+
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+
+class GRBLController:
+    '''
+    Simulateur du contrôleur GRBL 1.1f (L2544 Laser Engraving Machine).
+    API 100% identique à grbl.py — interchangeable sans modifier le code appelant.
+    Les délais de déplacement sont calculés à partir du feed rate et de la distance.
+    '''
+    X_MAX = 350
+    Y_MAX = 250
+    X_MIN = 0
+    Y_MIN = 0
+
+    # Facteur de compression du temps simulé (1.0 = temps réel, 0.1 = 10x plus rapide)
+    TIME_SCALE = 0.1
+
+    def __init__(self, port='/dev/ttyUSB0', baudrate=115200, timeout=1, send_callback=None, x_max=None, y_max=None):
+        logger.info(f"GRBLController SIMULATOR::init begin {port} device port")
+
+        self.port = port
+        self.baudrate = baudrate
+        self.timeout = timeout
+
+        if x_max is not None:
+            self.X_MAX = x_max
+        if y_max is not None:
+            self.Y_MAX = y_max
+
+        self._state: Callable[..., Any] = send_callback if send_callback is not None else self._send_msg
+
+        # Position courante simulée
+        self.x: float | None = None
+        self.y: float | None = None
+
+        # État interne de la machine simulée
+        self._machine_state = 'Idle'   # Idle | Run | Alarm
+        self._connected = False
+
+    # -------------------------------------------------------------------------
+    # Méthodes utilitaires
+    # -------------------------------------------------------------------------
+
+    def wait_for(self, delay=1.0):
+        # Applique le facteur de compression temporelle
+        threading.Event().wait(delay * self.TIME_SCALE)
+
+    def _send_msg(self, **msg):
+        # Callback par défaut : simple affichage console
+        print(msg)
+
+    # -------------------------------------------------------------------------
+    # Simulation de la couche série (pas de port réel)
+    # -------------------------------------------------------------------------
+
+    def clear_buffer(self):
+        # Rien à vider : pas de port série physique
+        logger.debug("SIMULATOR::clear_buffer (no-op)")
+
+    def start_connection(self):
+        '''Simule l'ouverture de la connexion série et l'initialisation GRBL.'''
+        logger.info(f"SIMULATOR::start_connection on {self.port} @ {self.baudrate} baud")
+        self._state(state='serial', msg="Grbl 1.1f ['$' for help]")
+        self._connected = True
+        self._wake_up()
+        self._init_machine()
+        logger.info("SIMULATOR::start_connection started")
+
+    def _init_machine(self):
+        # Envoie les commandes d'initialisation (simulées)
+        self.send("G21")   # Unités en mm
+        self.send("G90")   # Mode absolu
+
+    def _clamp(self, x, y):
+        self.clear_buffer()
+        x = max(self.X_MIN, min(self.X_MAX, x))
+        y = max(self.Y_MIN, min(self.Y_MAX, y))
+        return x, y
+
+    def _wake_up(self):
+        # Simule l'envoi des octets de réveil et la réponse GRBL
+        logger.debug("SIMULATOR::_wake_up")
+        self.wait_for(1)
+        self._state(state='serial', msg="")   # ligne vide typique de GRBL au démarrage
+        self.clear_buffer()
+
+    # -------------------------------------------------------------------------
+    # Envoi de commandes
+    # -------------------------------------------------------------------------
+
+    def send(self, cmd, wait_ok=True, timeout=5):
+        try:
+            return self._send(cmd, wait_ok, timeout)
+        except Exception as e:
+            self._state(state='error', msg=f"Error send {cmd} command: {e}")
+            self.close()
+            self.start_connection()
+
+    def recover(self):
+        self._state(state='recover', msg="Erreur, récupération de GRBL...")
+        self.wait_for(1)
+        self._wake_up()
+
+    def _send(self, cmd, wait_ok=True, timeout=5):
+        '''Simule l'envoi d'une commande GCode et retourne "ok".'''
+        self._state(state='send', msg=f">>> {cmd}")
+        logger.debug(f"SIMULATOR::_send {cmd}")
+
+        # Interprète les commandes de mouvement pour mettre à jour la position interne
+        self._interpret_gcode(cmd)
+
+        if not wait_ok:
+            return None
+
+        # Simule une réponse "ok" immédiate
+        return "ok"
+
+    def _interpret_gcode(self, cmd):
+        '''
+        Analyse le GCode pour mettre à jour x, y et simuler le délai de déplacement.
+        Gère : G0, G1, G53 G1, G92, G21, G90, G91, $X, $H.
+        '''
+        cmd_upper = cmd.strip().upper()
+
+        # --- Commandes sans mouvement ---
+        if cmd_upper in ("G21", "G90", "G91", "$X"):
+            return
+        if cmd_upper == "$H":
+            # Homing : retour à l'origine avec délai simulé
+            self._machine_state = 'Run'
+            self._state(state='send', msg="SIMULATOR: homing...")
+            distance = math.hypot(self.x or 0.0, self.y or 0.0)
+            self._simulate_move_delay(distance, feed=3000)
+            self.x, self.y = 0.0, 0.0
+            self._machine_state = 'Idle'
+            return
+
+        # --- Extraction des coordonnées X, Y et du feed F ---
+        tokens = cmd_upper.replace(',', ' ').split()
+        new_x: float = self.x or 0.0
+        new_y: float = self.y or 0.0
+        feed: float = 1000.0
+
+        for token in tokens:
+            if token.startswith('X'):
+                try:
+                    new_x = float(token[1:])
+                except ValueError:
+                    pass
+            elif token.startswith('Y'):
+                try:
+                    new_y = float(token[1:])
+                except ValueError:
+                    pass
+            elif token.startswith('F'):
+                try:
+                    feed = float(token[1:])
+                except ValueError:
+                    pass
+
+        # --- G92 : redéfinit la position courante sans déplacement ---
+        if 'G92' in tokens:
+            self.x = new_x
+            self.y = new_y
+            logger.debug(f"SIMULATOR: G92 position set to ({self.x:.2f}, {self.y:.2f})")
+            return
+
+        # --- Mouvement effectif (G0, G1, G53 G1, etc.) ---
+        has_move = any(t in tokens for t in ('G0', 'G1', 'G53'))
+        cur_x = self.x or 0.0
+        cur_y = self.y or 0.0
+        if has_move and (new_x != cur_x or new_y != cur_y):
+            distance = math.hypot(new_x - cur_x, new_y - cur_y)
+            self._machine_state = 'Run'
+            self._simulate_move_delay(distance, feed)
+            self.x = new_x
+            self.y = new_y
+            self._machine_state = 'Idle'
+            logger.debug(f"SIMULATOR: moved to ({self.x:.2f}, {self.y:.2f})")
+
+    def _simulate_move_delay(self, distance_mm, feed):
+        '''Simule le temps de déplacement : distance / feed (mm/min) → secondes.'''
+        if feed <= 0:
+            return
+        duration = (distance_mm / feed) * 60.0   # feed est en mm/min
+        self.wait_for(duration)
+
+    # -------------------------------------------------------------------------
+    # Status machine
+    # -------------------------------------------------------------------------
+
+    def get_status(self):
+        '''Retourne un status GRBL simulé au format <State|MPos:x,y,z>.'''
+        x = self.x or 0.0
+        y = self.y or 0.0
+        status = f"<{self._machine_state}|MPos:{x:.3f},{y:.3f},0.000|FS:0,0>"
+        logger.debug(f"SIMULATOR::get_status → {status}")
+        return status
+
+    def reset_grbl(self):
+        self.send("$X")   # Réinitialise les alarmes
+        self.wait_idle()
+        self.send("$H")   # Homing
+        self.wait_idle()
+
+    def _mpos(self, status):
+        if "MPos" in status:
+            mpos = status.split("MPos:")[1].split("|")[0]
+            x, y, *_ = mpos.split(",")
+            self._state(state='Mpos', msg=f"pos >>> ({x}, {y})")
+            return float(x), float(y)
+        return None, None
+
+    def get_mpos(self):
+        return self._mpos(self.get_status())
+
+    def wait_idle(self, timeout=20):
+        '''Attend que la machine soit à l'état Idle (immédiat en simulation).'''
+        start = time.time()
+        while True:
+            if time.time() - start > timeout:
+                raise TimeoutError("Délai d'attente pour Idle dépassé")
+            status = self.get_status()
+            self.x, self.y = self._mpos(status)
+            self._state(xy=True, x=self.x, y=self.y)
+            if status and "Idle" in status:
+                break
+            self.wait_for(0.1)
+
+    # -------------------------------------------------------------------------
+    # Commandes de haut niveau (identiques à grbl.py)
+    # -------------------------------------------------------------------------
+
+    def send_command(self, cmd):
+        self.send(cmd)
+        self.wait_idle()
+
+    def move_to(self, x, y, feed=1000):
+        x, y = self._clamp(x, y)
+        cmd = f"G53 G1 X{x:.2f} Y{y:.2f} F{feed}"
+        self.send_command(cmd)
+
+    def move_relative(self, dx=0, dy=0, feed=1000):
+        x, y = self.get_mpos()   # Position actuelle
+        self.move_to((x or 0.0) + dx, (y or 0.0) + dy, feed=feed)
+
+    def move_relative__(self, dx=0, dy=0, feed=1000):
+        self.send("G91")   # Mode relatif
+        cmd = f"G0 X{dx} Y{dy} F{feed}"
+        self.send(cmd)
+        self.send("G90")   # Retour en mode absolu
+        self.wait_idle()
+
+    def go_origin(self, feed=1000):
+        self.move_to(0, 0, feed=feed)
+        self.wait_for(2.0)
+
+    def set_position(self, x, y):
+        x, y = self._clamp(x, y)
+        cmd = f"G92 X{x:.2f} Y{y:.2f}"
+        self.send(cmd)
+        self.wait_for(2.0)
+
+    def move_up(self, step=10, feed=1000):
+        self.move_relative(dy=step, feed=feed)
+
+    def move_down(self, step=10, feed=1000):
+        self.move_relative(dy=-step, feed=feed)
+
+    def move_left(self, step=10, feed=1000):
+        self.move_relative(dx=-step, feed=feed)
+
+    def move_right(self, step=10, feed=1000):
+        self.move_relative(dx=step, feed=feed)
+
+    def close(self):
+        # Simule la fermeture du port série
+        self._connected = False
+        logger.info("SIMULATOR::close — connexion simulée fermée")

test_tube_scanner/modules/picamera2_capture.py

@@ -59,7 +59,7 @@ class PiCamera2Capture(VideoCaptureInterface):
         :param use_video_config: True = VideoConfiguration (flux continu, basse latence)
                                  False = StillConfiguration (haute résolution, plus lent)
         """
-        super().__init__(fps=fps, use_tracking=use_tracking, display=display, parent=parent)
+        super().__init__(fps=fps, use_tracking=use_tracking, display=display, parent=parent, jpeg_quality=jpeg_quality)
         self._width: int = width
         self._height: int = height
         self._jpeg_quality: int = jpeg_quality

test_tube_scanner/modules/planarian_tracker.py

@@ -1,36 +1,221 @@
-# modules/planarian_tracker.py
-'''
-Created on 16 avr. 2026
+"""
+modules/planarian_tracker.py
 
+Détection et suivi multi-individus de planaires dans un tube.
+Supporte de 1 à MAX_PLANARIANS planaires par tube.
+
+Stratégie :
+    - Soustraction de fond MOG2 (léger sur Raspberry Pi 4)
+    - Détection de tous les contours valides (surface >= min_area_px)
+    - Association frame-à-frame par distance euclidienne minimale
+      via algorithme hongrois (scipy.optimize.linear_sum_assignment)
+    - Un état inter-frame indépendant par individu (PlanarianState)
+    - Retourne une liste de résultats, un par individu suivi
+
+Created on 25 avr. 2026
 @author: denis
-'''
+"""
 
 import cv2
-import logging
 import numpy as np
 
+from scipy.optimize import linear_sum_assignment
+import logging
+
+
 logger = logging.getLogger(__name__)
 
+# Nombre maximum de planaires suivis simultanément par tube
+MAX_PLANARIANS = 10
+
+# Distance maximale en pixels entre deux positions consécutives
+# pour qu'une association soit acceptée (évite les sauts aberrants)
+MAX_ASSOC_DIST_PX = 80
+
+# Couleurs d'annotation par individu (BGR)
+# Cycle automatique si plus de planaires que de couleurs
+INDIVIDUAL_COLORS = [
+    (255, 255,   0),  # cyan
+    (  0, 165, 255),  # orange
+    (255,   0, 255),  # magenta
+    (  0, 255, 255),  # jaune
+    (128,   0, 255),  # violet
+    (  0, 255, 128),  # vert clair
+    (255, 128,   0),  # bleu clair
+    (  0, 128, 255),  # orange foncé
+    (128, 255,   0),  # vert-jaune
+    (255,   0, 128),  # rose
+]
+
+# Couleur du contour principal (individu le plus grand)
+COLOR_LARGEST  = (255, 255,   0)   # cyan
+COLOR_OTHER    = (  0, 255,   0)   # vert
+COLOR_CENTER   = (  0,   0, 255)   # rouge
+
+
+# ---------------------------------------------------------------------------
+# État inter-frame d'un individu
+# ---------------------------------------------------------------------------
+
+class PlanarianState:
+    """
+    Mémorise la position et le timestamp de la dernière détection
+    pour un planaire individuel.
+
+    Un PlanarianState par slot (index 0 à max_planarians-1).
+    Quand un slot n'est pas associé à un contour sur plusieurs frames
+    consécutives, il est marqué comme perdu (lost).
+    """
+
+    # Nombre de frames sans détection avant de considérer l'individu perdu
+    MAX_LOST_FRAMES = 5
+
+    def __init__(self, idx: int):
+        """
+        Args:
+            idx : index de l'individu (0-based)
+        """
+        self.idx:    int          = idx
+        self.cx:     int | None  = None
+        self.cy:     int | None  = None
+        self.ts:     float | None = None
+        self.lost:   int         = 0     # compteur de frames sans détection
+        self.active: bool        = False # vrai si l'individu a été détecté au moins une fois
+
+    def update(self, cx: int, cy: int, ts: float):
+        """
+        Met à jour la position suite à une association réussie.
+
+        Args:
+            cx, cy : position du centre de masse en pixels
+            ts     : timestamp de la frame
+        """
+        self.cx     = cx
+        self.cy     = cy
+        self.ts     = ts
+        self.lost   = 0
+        self.active = True
+
+    def mark_lost(self):
+        """Incrémente le compteur de perte — appelé quand aucun contour n'est associé."""
+        self.lost += 1
+
+    @property
+    def is_lost(self) -> bool:
+        """Retourne True si l'individu est considéré perdu (trop de frames sans détection)."""
+        return self.lost >= self.MAX_LOST_FRAMES
+
+    def compute_speed(self, cx: int, cy: int, ts: float, tube_axis: str) -> tuple:
+        """
+        Calcule la vitesse instantanée depuis la position précédente.
+
+        Args:
+            cx, cy    : position courante en pixels
+            ts        : timestamp courant
+            tube_axis : "vertical" ou "horizontal"
+
+        Returns:
+            tuple (speed_px_s, axial_speed) ou (0.0, 0.0) si état vide
+        """
+        if self.cx is None or self.cy is None or self.ts is None:
+            return 0.0, 0.0
+
+        dt = ts - self.ts
+        if dt <= 0:
+            return 0.0, 0.0
+
+        dx          = cx - self.cx
+        dy          = cy - self.cy
+        speed_px_s  = float(np.sqrt(dx**2 + dy**2) / dt)
+        axial_speed = float((dy / dt) if tube_axis == "vertical" else (dx / dt))
+
+        return speed_px_s, axial_speed
+
+    def reset(self):
+        """Réinitialise l'état de cet individu."""
+        self.cx     = None
+        self.cy     = None
+        self.ts     = None
+        self.lost   = 0
+        self.active = False
+
+
+# ---------------------------------------------------------------------------
+# Tracker multi-individus
+# ---------------------------------------------------------------------------
 
 class PlanarianTracker:
     """
-    Détection et suivi d'une planaire dans un tube.
+    Détection et suivi multi-individus de planaires dans un tube.
+
     Instancié une fois par caméra active, réutilisé frame à frame.
     Utilise la soustraction de fond MOG2 — léger sur Raspberry Pi 4.
+    Association frame-à-frame par algorithme hongrois (distance euclidienne).
+
+    Usage :
+        tracker = PlanarianTracker(tube_axis="vertical", max_planarians=3)
+        while capturing:
+            frame_out, results = tracker.process(frame, ts)
+            # results : liste de dicts, un par individu détecté
+            for r in results:
+                metrics.update(r, planarian_id=r["planarian_id"])
     """
 
-    def __init__(self, tube_axis: str = "vertical", min_area_px: int = 20):
-        # Axe du tube : "vertical" (cy) ou "horizontal" (cx)
+    # Nombre de frames d'initialisation MOG2 ignorées (fond non appris)
+    WARMUP_FRAMES = 10
+
+    def __init__(
+        self,
+        tube_axis:          str   = "vertical",
+        min_area_px:        int   = 20,
+        max_area_ratio:     float = 0.10,
+        max_planarians:     int   = 1,
+        merge_kernel_size:  int   = 15,
+        min_contour_dist_px:int   = 40,
+        draw_contours:       bool = True,
+    ):
+        """
+        Args:
+            tube_axis      : axe principal du tube — "vertical" (cy) ou "horizontal" (cx)
+            min_area_px    : surface minimale d'un contour pour être considéré valide (px²)
+            max_area_ratio : surface maximale d'un contour en fraction de la frame (défaut 10%)
+                             filtre les faux positifs du fond non encore appris par MOG2
+            max_planarians      : nombre maximum de planaires à suivre simultanément (1-10)
+            merge_kernel_size   : taille du kernel elliptique de fusion des fragments (px).
+                                  Régler ≈ largeur du planaire en pixels. Défaut : 15.
+            min_contour_dist_px : distance min entre deux contours pour les considérer
+                                  comme individus distincts. Défaut : 40px.
+        """
         self.tube_axis      = tube_axis
         self.min_area_px    = min_area_px
+        self.max_area_ratio = max_area_ratio
+        self.max_planarians = max(1, min(max_planarians, MAX_PLANARIANS))
+        self.draw_contours  = draw_contours
 
-        # Etat inter-frame
-        self._prev_cx  = None
-        self._prev_cy  = None
-        self._prev_ts  = None
+        # Un état inter-frame par slot individu
+        self._states = [PlanarianState(i) for i in range(self.max_planarians)]
+
+        # Taille du kernel de fusion morphologique (pixels) —
+        # doit être proche de la largeur du planaire en pixels.
+        # Trop petit : fragments non fusionnés → IDs multiples.
+        # Trop grand : deux planaires proches fusionnés en un seul.
+        self.merge_kernel_size    = merge_kernel_size
+
+        # Distance minimale en pixels entre deux contours distincts.
+        # En-dessous : le plus petit est considéré comme fragment du plus grand.
+        self.min_contour_dist_px  = min_contour_dist_px
 
         # Soustracteur de fond adaptatif MOG2
-        self._bg_sub = cv2.createBackgroundSubtractorMOG2(
+        self._bg_sub = self._make_bg_sub()
+
+        # Compteur de frames d'initialisation — MOG2 retourne du bruit
+        # pendant les premières WARMUP_FRAMES frames
+        self._warmup_count = 0
+
+    @staticmethod
+    def _make_bg_sub():
+        """Crée et retourne un soustracteur de fond MOG2."""
+        return cv2.createBackgroundSubtractorMOG2(
             history      = 50,
             varThreshold = 25,
             detectShadows= False,
@@ -38,205 +223,321 @@ class PlanarianTracker:
 
     def reset(self):
         """
-        Réinitialise l'état inter-frame — appeler lors du changement de puits.
+        Réinitialise l'état inter-frame complet.
+        À appeler lors du changement de puits.
         """
-        self._prev_cx = None
-        self._prev_cy = None
-        self._prev_ts = None
-        # Réinitialise le fond appris
-        self._bg_sub  = cv2.createBackgroundSubtractorMOG2(
-            history      = 50,
-            varThreshold = 25,
-            detectShadows= False,
-        )
-
-    '''
-    def process(self, frame: np.ndarray, ts: float) -> dict:
-        """
-        Analyse une frame décodée numpy.
-        Retourne un dict de métriques attachable aux labels ReductStore.
-
-        :param frame: Frame BGR décodée (numpy array)
-        :param ts:    Timestamp epoch secondes (float)
-        :return:      dict métriques
-        """
-        result = self._empty_result(ts)
-
-        gray    = cv2.cvtColor(frame, cv2.COLOR_BGR2GRAY)
-        fg_mask = self._bg_sub.apply(gray)
-
-        # Nettoyage morphologique du masque
-        kernel  = np.ones((3, 3), np.uint8)
-        fg_mask = cv2.morphologyEx(fg_mask, cv2.MORPH_OPEN,  kernel)
-        fg_mask = cv2.morphologyEx(fg_mask, cv2.MORPH_CLOSE, kernel)
-
-        contours, _ = cv2.findContours(
-            fg_mask, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE
-        )
-
-        if not contours:
-            self._update_prev(None, None, ts)
-            return result
-
-        # Plus grand contour = planaire
-        largest = max(contours, key=cv2.contourArea)
-        area    = cv2.contourArea(largest)
-
-        if area < self.min_area_px:
-            self._update_prev(None, None, ts)
-            return result
-
-        # Centre de masse
-        M = cv2.moments(largest)
-        if M["m00"] == 0:
-            return result
-
-        cx = int(M["m10"] / M["m00"])
-        cy = int(M["m01"] / M["m00"])
-        h, w = frame.shape[:2]
-
-        # Position normalisée sur l'axe du tube (0.0 → 1.0)
-        axial_pos = (cy / h) if self.tube_axis == "vertical" else (cx / w)
-
-        # Vitesse calculée entre frames
-        speed_px_s  = None
-        axial_speed = None
-
-        if self._prev_cx is not None and self._prev_ts is not None:
-            dt = ts - self._prev_ts
-            if dt > 0:
-                dx          = cx - self._prev_cx
-                dy          = cy - self._prev_cy
-                speed_px_s  = float(np.sqrt(dx**2 + dy**2) / dt)
-                # Vitesse signée sur l'axe du tube
-                # + = vers bas/droite, - = vers haut/gauche
-                axial_speed = float((dy / dt) if self.tube_axis == "vertical" else (dx / dt))
-
-        result.update({
-            "detected"    : True,
-            "cx"          : cx,
-            "cy"          : cy,
-            "area_px"     : int(area),
-            "speed_px_s"  : round(speed_px_s,  3) if speed_px_s  is not None else 0.0,
-            "axial_speed" : round(axial_speed,  3) if axial_speed is not None else 0.0,
-            "axial_pos"   : round(axial_pos,    4),
-        })
-
-        self._update_prev(cx, cy, ts)
-        return result
-    '''
-        
-    def process(self, frame: np.ndarray, ts: float) -> tuple[np.ndarray, dict]:
-        """
-        Analyse une frame et dessine les contours détectés directement sur l'image.
-        Retourne (frame_annotée, métriques).
-        
-            Contours fins    Vert (0,255,0)    Tous les contours valides détectés
-            Contour épais    Cyan (255,255,0)    Planaire principale (plus grand contour)
-            Croix + cercle    Rouge (0,0,255)    Centre de masse exact
-            Texte    Blanc    Vitesse px/s + position axiale normalisée
-        """
-        result       = self._empty_result(ts)
-        frame_out    = frame.copy()    # copie pour ne pas modifier l'original
-    
-        gray    = cv2.cvtColor(frame, cv2.COLOR_BGR2GRAY)
-        fg_mask = self._bg_sub.apply(gray)
-    
-        kernel  = np.ones((3, 3), np.uint8)
-        fg_mask = cv2.morphologyEx(fg_mask, cv2.MORPH_OPEN,  kernel)
-        fg_mask = cv2.morphologyEx(fg_mask, cv2.MORPH_CLOSE, kernel)
-    
-        contours, _ = cv2.findContours(
-            fg_mask, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE
-        )
-    
-        if not contours:
-            self._update_prev(None, None, ts)
-            return frame_out, result
-    
-        # Filtre les contours significatifs
-        valid_contours = [c for c in contours if cv2.contourArea(c) >= self.min_area_px]
-    
-        if not valid_contours:
-            self._update_prev(None, None, ts)
-            return frame_out, result
-    
-        # Dessine tous les contours valides en vert fin
-        cv2.drawContours(frame_out, valid_contours, -1, (0, 255, 0), 1)
-    
-        # Plus grand contour = planaire principale
-        largest = max(valid_contours, key=cv2.contourArea)
-        area    = cv2.contourArea(largest)
-    
-        # Contour principal en cyan plus épais
-        cv2.drawContours(frame_out, [largest], -1, (255, 255, 0), 2)
-    
-        M = cv2.moments(largest)
-        if M["m00"] == 0:
-            return frame_out, result
-    
-        cx = int(M["m10"] / M["m00"])
-        cy = int(M["m01"] / M["m00"])
-        h, w = frame.shape[:2]
-    
-        axial_pos   = (cy / h) if self.tube_axis == "vertical" else (cx / w)
-        speed_px_s  = None
-        axial_speed = None
-    
-        if self._prev_cx is not None and self._prev_ts is not None:
-            dt = ts - self._prev_ts
-            if dt > 0:
-                dx          = cx - self._prev_cx
-                dy          = cy - self._prev_cy
-                speed_px_s  = float(np.sqrt(dx**2 + dy**2) / dt)
-                axial_speed = float((dy / dt) if self.tube_axis == "vertical" else (dx / dt))
-    
-        # Croix sur le centre de masse
-        cross_size = 8
-        cv2.line(frame_out, (cx - cross_size, cy), (cx + cross_size, cy), (0, 0, 255), 1)
-        cv2.line(frame_out, (cx, cy - cross_size), (cx, cy + cross_size), (0, 0, 255), 1)
-    
-        # Cercle centré sur la planaire
-        cv2.circle(frame_out, (cx, cy), 12, (0, 0, 255), 1)
-    
-        # Texte vitesse + position axiale
-        label = f"v={speed_px_s:.1f}px/s  ax={axial_pos:.2f}" if speed_px_s is not None else f"ax={axial_pos:.2f}"
-        cv2.putText(
-            frame_out, label,
-            (max(cx - 60, 0), max(cy - 18, 12)),
-            cv2.FONT_HERSHEY_SIMPLEX, 0.4, (255, 255, 255), 1, cv2.LINE_AA,
-        )
-    
-        result.update({
-            "detected"    : True,
-            "cx"          : cx,
-            "cy"          : cy,
-            "area_px"     : int(area),
-            "speed_px_s"  : round(speed_px_s,  3) if speed_px_s  is not None else 0.0,
-            "axial_speed" : round(axial_speed,  3) if axial_speed is not None else 0.0,
-            "axial_pos"   : round(axial_pos,    4),
-        })
-    
-        self._update_prev(cx, cy, ts)
-        return frame_out, result              
-        
+        for s in self._states:
+            s.reset()
+        self._bg_sub       = self._make_bg_sub()
+        self._warmup_count = 0
+        # Les paramètres morphologiques (merge_kernel_size, min_contour_dist_px)
+        # sont conservés — ils ne dépendent pas du puits
 
     # ------------------------------------------------------------------ #
-    def _empty_result(self, ts: float) -> dict:
-        return {
+    # Interface principale
+    # ------------------------------------------------------------------ #
+
+    def process(self, frame: np.ndarray, ts: float) -> tuple:
+        """
+        Analyse une frame, associe les contours aux individus connus,
+        dessine les annotations et retourne les métriques.
+
+        Args:
+            frame : image BGR (numpy array)
+            ts    : timestamp de la frame (float, secondes epoch)
+
+        Returns:
+            tuple (frame_annotée, results)
+
+            frame_annotée : copie BGR avec contours, croix et textes
+            results       : liste de dicts — un dict par planaire actif détecté.
+                            Chaque dict contient :
+                                planarian_id  int     index de l'individu (0-based)
+                                detected      bool    True si détecté cette frame
+                                cx, cy        int     centre de masse en pixels
+                                area_px       int     surface du contour (px²)
+                                speed_px_s    float   vitesse totale (px/s)
+                                axial_speed   float   vitesse axiale (px/s)
+                                axial_pos     float   position axiale normalisée (0-1)
+                                timestamp     float   ts de la frame
+        """
+        frame_out = frame.copy()
+        h, w      = frame.shape[:2]
+
+        # --- Extraction du premier plan ---
+        gray    = cv2.cvtColor(frame, cv2.COLOR_BGR2GRAY)
+        fg_mask = self._bg_sub.apply(gray)
+
+        # --- Morphologie : fusion des fragments du corps ---
+        # Un planaire ondulant est souvent segmenté en plusieurs contours
+        # (tête, milieu, queue). La dilatation fusionne les fragments proches
+        # avant la détection des contours.
+        # Kernel 3×3 : supprime le bruit fin (OPEN)
+        # Kernel merge_kernel : fusionne les fragments du corps (CLOSE + DILATE)
+        noise_kernel = np.ones((3, 3), np.uint8)
+        merge_kernel  = cv2.getStructuringElement(
+            cv2.MORPH_ELLIPSE, (self.merge_kernel_size, self.merge_kernel_size)
+        )
+        fg_mask = cv2.morphologyEx(fg_mask, cv2.MORPH_OPEN,   noise_kernel)
+        fg_mask = cv2.morphologyEx(fg_mask, cv2.MORPH_CLOSE,  merge_kernel)
+        fg_mask = cv2.dilate(fg_mask, merge_kernel, iterations=1)
+
+        # Warmup MOG2 : les premières WARMUP_FRAMES frames retournent du bruit
+        # (fond non encore appris) — on les alimente mais on ne détecte rien
+        self._warmup_count += 1
+        if self._warmup_count <= self.WARMUP_FRAMES:
+            return frame_out, []
+
+        contours, _ = cv2.findContours(
+            fg_mask, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE
+        )
+
+        # Surface maximale admissible : fraction de la frame
+        # Filtre les faux positifs du fond (contours couvrant toute l'image)
+        max_area_px = h * w * self.max_area_ratio
+
+        # Filtrage : surface min ET surface max, triés par surface décroissante
+        valid = sorted(
+            [c for c in contours
+             if self.min_area_px <= cv2.contourArea(c) <= max_area_px],
+            key=cv2.contourArea,
+            reverse=True,
+        )
+
+        # --- Suppression des fragments résiduels trop proches ---
+        # Si plusieurs contours valides ont leur centre à moins de
+        # min_contour_dist_px les uns des autres, seul le plus grand est conservé.
+        # Évite les cas où la fusion morphologique est incomplète.
+        filtered = []
+        for c in valid:
+            M = cv2.moments(c)
+            if M["m00"] == 0:
+                continue
+            cx_c = int(M["m10"] / M["m00"])
+            cy_c = int(M["m01"] / M["m00"])
+            too_close = False
+            for kept in filtered:
+                Mk = cv2.moments(kept)
+                if Mk["m00"] == 0:
+                    continue
+                cx_k = int(Mk["m10"] / Mk["m00"])
+                cy_k = int(Mk["m01"] / Mk["m00"])
+                dist = np.sqrt((cx_c - cx_k)**2 + (cy_c - cy_k)**2)
+                if dist < self.min_contour_dist_px:
+                    too_close = True
+                    break
+            if not too_close:
+                filtered.append(c)
+
+        # Limiter au nombre maximum de planaires attendus
+        valid = filtered[:self.max_planarians]
+
+        # --- Calcul des centres de masse des contours détectés ---
+        detections = []   # liste de (cx, cy, area, contour)
+        for c in valid:
+            M = cv2.moments(c)
+            if M["m00"] == 0:
+                continue
+            cx   = int(M["m10"] / M["m00"])
+            cy   = int(M["m01"] / M["m00"])
+            area = cv2.contourArea(c)
+            detections.append((cx, cy, int(area), c))
+
+        # --- Association hongroise détections → slots individus ---
+        assignments = self._hungarian_assign(detections)
+
+        # --- Mise à jour des états et construction des résultats ---
+        results = []
+
+        for slot_idx, det_idx in assignments.items():
+            state = self._states[slot_idx]
+
+            if det_idx is None:
+                # Aucune détection associée à ce slot
+                state.mark_lost()
+                if state.active and not state.is_lost:
+                    # L'individu était suivi : on retourne un résultat "perdu"
+                    results.append(self._lost_result(slot_idx, ts))
+                continue
+
+            cx, cy, area, contour = detections[det_idx]
+
+            # Calcul de la vitesse depuis la position précédente
+            speed_px_s, axial_speed = state.compute_speed(cx, cy, ts, self.tube_axis)
+
+            axial_pos = (cy / h) if self.tube_axis == "vertical" else (cx / w)
+
+            # Mise à jour de l'état
+            state.update(cx, cy, ts)
+
+            
+            if self.draw_contours:
+                
+                # Annotation visuelle
+                color = INDIVIDUAL_COLORS[slot_idx % len(INDIVIDUAL_COLORS)]
+                cv2.drawContours(frame_out, [contour], -1, color, 2)        
+                self._draw_center(frame_out, cx, cy, slot_idx, speed_px_s, axial_pos, color)
+
+            results.append({
+                "planarian_id": slot_idx,
+                "detected":     True,
+                "cx":           cx,
+                "cy":           cy,
+                "area_px":      area,
+                "speed_px_s":   round(speed_px_s,  3),
+                "axial_speed":  round(axial_speed,  3),
+                "axial_pos":    round(axial_pos,    4),
                 "timestamp":    ts,
+            })
+
+        # Marquer les slots non présents dans les assignments comme perdus
+        assigned_slots = set(assignments.keys())
+        for state in self._states:
+            if state.idx not in assigned_slots:
+                state.mark_lost()
+        return frame_out, results
+
+    # ------------------------------------------------------------------ #
+    # Association hongroise
+    # ------------------------------------------------------------------ #
+
+    def _hungarian_assign(self, detections: list) -> dict:
+        """
+        Associe les détections courantes aux slots individus connus
+        via l'algorithme hongrois (coût = distance euclidienne).
+
+        Contrainte : une association n'est acceptée que si la distance
+        est inférieure à MAX_ASSOC_DIST_PX (évite les sauts aberrants).
+
+        Args:
+            detections : liste de (cx, cy, area, contour)
+
+        Returns:
+            dict {slot_idx: det_idx | None}
+            det_idx = None si aucune détection assignée à ce slot
+        """
+        n_slots = self.max_planarians
+        n_dets  = len(detections)
+
+        if n_dets == 0:
+            # Aucune détection : tous les slots sont "perdus"
+            return {i: None for i in range(n_slots)}
+
+        # Slots actifs (déjà vus au moins une fois et non perdus)
+        active_slots = [s for s in self._states if s.active and not s.is_lost]
+
+        if not active_slots:
+            # Première frame ou tous perdus : attribution séquentielle simple
+            assignment = {}
+            for i in range(n_slots):
+                assignment[i] = i if i < n_dets else None
+            return assignment
+
+        # --- Construction de la matrice de coût (distance euclidienne) ---
+        cost = np.full((len(active_slots), n_dets), fill_value=1e6)
+
+        for si, state in enumerate(active_slots):
+            for di, (cx, cy, _, _) in enumerate(detections):
+                dist = np.sqrt((cx - state.cx)**2 + (cy - state.cy)**2)
+                cost[si, di] = dist
+
+        # --- Algorithme hongrois ---
+        row_ind, col_ind = linear_sum_assignment(cost)
+
+        # Construire le dict d'association
+        assignment: dict[int, int | None] = {i: None for i in range(n_slots)}
+
+        assigned_dets = set()
+        for ri, ci in zip(row_ind, col_ind):
+            if cost[ri, ci] <= MAX_ASSOC_DIST_PX:
+                slot_idx = active_slots[ri].idx
+                assignment[slot_idx] = ci
+                assigned_dets.add(ci)
+
+        # --- Nouvelles détections non assignées → slots inactifs libres ---
+        free_slots = [s for s in self._states if not s.active or s.is_lost]
+        new_dets   = [di for di in range(n_dets) if di not in assigned_dets]
+
+        for state, det_idx in zip(free_slots, new_dets):
+            assignment[state.idx] = det_idx
+
+        return assignment
+
+    # ------------------------------------------------------------------ #
+    # Dessin des annotations
+    # ------------------------------------------------------------------ #
+
+    def _draw_center(
+        self,
+        frame:      np.ndarray,
+        cx:         int,
+        cy:         int,
+        idx:        int,
+        speed_px_s: float,
+        axial_pos:  float,
+        color:      tuple,
+    ):
+        """
+        Dessine la croix, le cercle et le label de vitesse/position
+        pour un individu.
+
+        Args:
+            frame      : image à annoter (en place)
+            cx, cy     : centre de masse en pixels
+            idx        : index de l'individu
+            speed_px_s : vitesse en px/s
+            axial_pos  : position axiale normalisée
+            color      : couleur BGR de l'individu
+        """
+        cross = 8
+        cv2.line(frame, (cx - cross, cy), (cx + cross, cy), COLOR_CENTER, 1)
+        cv2.line(frame, (cx, cy - cross), (cx, cy + cross), COLOR_CENTER, 1)
+        cv2.circle(frame, (cx, cy), 12, color, 1)
+
+        # Badge numéro individu
+        cv2.circle(frame, (cx + 14, cy - 14), 8, color, -1)
+        cv2.putText(
+            frame, str(idx),
+            (cx + 10, cy - 10),
+            cv2.FONT_HERSHEY_SIMPLEX, 0.35, (0, 0, 0), 1, cv2.LINE_AA,
+        )
+
+        # Texte vitesse + position axiale
+        label = (
+            f"#{idx} v={speed_px_s:.1f}px/s ax={axial_pos:.2f}"
+            if speed_px_s > 0
+            else f"#{idx} ax={axial_pos:.2f}"
+        )
+        cv2.putText(
+            frame, label,
+            (max(cx - 60, 0), max(cy - 22, 12)),
+            cv2.FONT_HERSHEY_SIMPLEX, 0.35, (255, 255, 255), 1, cv2.LINE_AA,
+        )
+
+    # ------------------------------------------------------------------ #
+    # Résultats vides / perdus
+    # ------------------------------------------------------------------ #
+
+    def _lost_result(self, planarian_id: int, ts: float) -> dict:
+        """
+        Retourne un résultat pour un individu temporairement non détecté.
+
+        Args:
+            planarian_id : index de l'individu
+            ts           : timestamp de la frame courante
+
+        Returns:
+            dict avec detected=False et les dernières coordonnées connues
+        """
+        state = self._states[planarian_id]
+        return {
+            "planarian_id": planarian_id,
             "detected":     False,
-            "cx"         : 0,
-            "cy"         : 0,
+            "cx":           state.cx or 0,
+            "cy":           state.cy or 0,
             "area_px":      0,
             "speed_px_s":   0.0,
             "axial_speed":  0.0,
             "axial_pos":    0.0,
+            "timestamp":    ts,
         }
-
-    def _update_prev(self, cx, cy, ts):
-        self._prev_cx = cx
-        self._prev_cy = cy
-        self._prev_ts = ts
-  
-        

test_tube_scanner/modules/reductstore.py

@@ -27,12 +27,11 @@ class ReductStoreBase(ABC):
         self.bucket: Bucket = asyncio.run(self.create_bucket())
         logger.info(f"====  {url} token:{api_token}")
 
-
     async def create_bucket(self):
+        
         settings = BucketSettings(
             quota_type=self.quota_type,
             quota_size=self.quota_size,
-            exist_ok=True,
         )
         return await self.client.create_bucket(self.bucket_name, settings, exist_ok=True)
 

test_tube_scanner/modules/system_stats.py

@@ -111,7 +111,7 @@ def _update_cache():
         _timer.start()
 
 
-def start_background_updater(interval_seconds: int = None):
+def start_background_updater(interval_seconds: int = 0):
     global REFRESH_INTERVAL, _timer
     if interval_seconds:
         REFRESH_INTERVAL = interval_seconds

test_tube_scanner/modules/tube_aligner.py

@@ -29,6 +29,17 @@ class TubeAligner:
         self.debug             = debug
         self.display           = display
         self.TUBE_DIAMETER_MM  = 16.0
+        # Plage de recherche du rayon en fraction de min(w,h)
+        # Défaut : tube occupe ~30% du champ (camera).
+        # Mode vidéo : puit remplit le crop → ratio ~0.50 → appeler set_radius_range(0.35, 0.52)
+        self._min_radius_ratio = 0.26
+        self._max_radius_ratio = 0.37
+        self.draw_annotations  = True   # masquer l'overlay sans couper la détection
+
+    def set_radius_range(self, min_ratio: float, max_ratio: float) -> None:
+        """Ajuste la plage de recherche HoughCircles. Appeler avant detect_tube()."""
+        self._min_radius_ratio = min_ratio
+        self._max_radius_ratio = max_ratio
 
 
     def set_tube_diameter(self, tube_diameter: float = 16.0) -> None:
@@ -64,14 +75,18 @@ class TubeAligner:
         frame_out = frame.copy()
         
         gray    = cv2.cvtColor(frame, cv2.COLOR_BGR2GRAY)
+        # CLAHE pour renforcer le contraste local (paroi du puit sur fond gris uniforme)
+        clahe   = cv2.createCLAHE(clipLimit=3.0, tileGridSize=(8, 8))
+        gray    = clahe.apply(gray)
         blurred = cv2.GaussianBlur(gray, (15, 15), 3)
 
+        lo = self._min_radius_ratio
+        hi = self._max_radius_ratio
         # 3 configurations légèrement différentes — vote majoritaire
-        # Fonctionne sur fond sombre ET fond clair
         configs = [
-            dict(param1=50, param2=30, minRadius=int(min(w,h)*0.26), maxRadius=int(min(w,h)*0.36)),
-            dict(param1=60, param2=30, minRadius=int(min(w,h)*0.26), maxRadius=int(min(w,h)*0.37)),
-            dict(param1=50, param2=28, minRadius=int(min(w,h)*0.25), maxRadius=int(min(w,h)*0.365)),
+            dict(param1=50, param2=30, minRadius=int(min(w,h)*lo),        maxRadius=int(min(w,h)*hi)),
+            dict(param1=60, param2=28, minRadius=int(min(w,h)*lo),        maxRadius=int(min(w,h)*(hi+0.01))),
+            dict(param1=50, param2=26, minRadius=int(min(w,h)*(lo-0.01)), maxRadius=int(min(w,h)*(hi+0.005))),
         ]
         
         all_cx, all_cy, all_r = [], [], []
@@ -93,7 +108,7 @@ class TubeAligner:
         if not all_cx:
             msg = f"TubeAligner: aucun cercle détecté ({w}x{h})"
             result["msg"] =msg
-            if self.debug:
+            if self.debug and self.draw_annotations:
                 frame_out = self._draw_debug_no_detection(frame_out, cx_img, cy_img)
             result["frame_annotated"] = frame_out
             return result        
@@ -120,7 +135,7 @@ class TubeAligner:
         else:
             action = "grbl"
     
-        if self.debug:
+        if self.debug and self.draw_annotations:
             frame_out = self._draw_debug(
                 frame_out, cx_img, cy_img,
                 tx, ty, tr,

test_tube_scanner/modules/utils.py

@@ -70,6 +70,7 @@ def get_tmpfs_info(mount_point="/ramdisk"):
         return f"{n:.1f}PB"
 
     usage = None
+    part = None
     for part in psutil.disk_partitions(all=True):
         if part.mountpoint == mount_point and part.fstype.lower() == "tmpfs":
             usage = psutil.disk_usage(part.mountpoint)
@@ -81,6 +82,7 @@ def get_tmpfs_info(mount_point="/ramdisk"):
             print(f"  Free:  {usage.free} bytes ({sizeof(usage.free)})")
             print(f"  Percent used: {usage.percent}%")
             break
+    if usage and part:
         return {
             "percent": usage.percent,
             "mount": part.mountpoint,
@@ -92,6 +94,7 @@ def get_tmpfs_info(mount_point="/ramdisk"):
         }
 
 
+
 def get_cpu_info():
     # cpu percent par coeur et moyennes load
     return {

test_tube_scanner/modules/videofile_capture.py

@@ -33,12 +33,11 @@ class VideoFileCapture(VideoCaptureInterface):
 
     def __init__(
         self,
-        video_file: str = None,
+        video_file: str | None = None,
         fps: float = VideoCaptureInterface.DEFAULT_FPS,
         jpeg_quality: int = 85,
         width: Optional[int] = None,
         height: Optional[int] = None,
-        video_lists = [],
         use_tracking: bool = False,
         display = None,
         parent = None,
@@ -50,33 +49,23 @@ class VideoFileCapture(VideoCaptureInterface):
         :param width:         Largeur souhaitée (None = valeur par défaut du pilote)
         :param height:        Hauteur souhaitée (None = valeur par défaut du pilote)
         """
-        super().__init__(fps=fps, use_tracking=use_tracking, display=display, parent=parent)
-        self._video_file: str = video_file
+        super().__init__(fps=fps, use_tracking=use_tracking, display=display, parent=parent, jpeg_quality=jpeg_quality)
+        self._video_file: str | None = video_file
         self._jpeg_quality: int = jpeg_quality
         self._width: Optional[int] = width
         self._height: Optional[int] = height
-        self._video_lists = video_lists
-        
-        self.ptf = 0
         self._cap = None                          # Instance cv2.VideoCapture
 
-    def get_file(self):
-        if self._video_lists:
-            self._video_file = self._video_lists[self.ptf]
-            self.ptf += 1
-            if self.ptf >= len(self._video_lists):
-                self.ptf = 0
+    def set_video_file(self, vf):
+        self._video_file = vf
         return self._video_file
             
-
     # ------------------------------------------------------------------
     # Implémentation des méthodes abstraites
     # ------------------------------------------------------------------
 
     def open(self) -> None:
         """Ouvre le flux V4L2 via OpenCV et configure la résolution."""
-        self.get_file()
-
         self._cap = cv2.VideoCapture(self._video_file)
 
         if not self._cap.isOpened():
@@ -145,8 +134,8 @@ class VideoFileCapture(VideoCaptureInterface):
     # ------------------------------------------------------------------
 
     @property
-    def video_file(self) -> int:
-        """Index du périphérique V4L2."""
+    def video_file(self) -> str | None:
+        """Fichier vidéo."""
         return self._video_file
 
     @property

test_tube_scanner/modules/videoplate_capture.py

@@ -0,0 +1,226 @@
+"""
+VideoPlateCapture — capture par extraction de région dans une vidéo plaque entière.
+
+La vidéo montre l'ensemble de la plaque multi-puits (vue de dessus).
+La position GRBL (x, y en mm) détermine la région extraite via px_per_mm.
+Le résultat est un carré centré sur le puits courant, compatible avec
+le recadrage circulaire de process_frame() comme pour toute autre capture.
+
+Flux : video frame → crop carré (GRBL pos) → CircularCrop → tracking/display
+
+Hot swap : set_video_file(path) remplace la vidéo sans arrêter la capture.
+Thread-safe via _cap_lock.
+"""
+import os
+os.environ['OPENCV_LOG_LEVEL'] = "0"
+os.environ['OPENCV_FFMPEG_LOGLEVEL'] = "0"
+import cv2
+import numpy as np
+import logging
+import threading
+from pathlib import Path
+
+from modules.capture_interface import VideoCaptureInterface, CaptureError
+
+logger = logging.getLogger(__name__)
+
+
+class VideoPlateCapture(VideoCaptureInterface):
+    """
+    Lecture d'une vidéo de plaque complète avec crop dynamique à la position GRBL.
+
+    La position GRBL (x_mm, y_mm) est convertie en coordonnées pixel via px_per_mm.
+    Un carré de côté 2*crop_radius_px est extrait à cette position, puis
+    process_frame() applique le masque circulaire habituel.
+
+    La vidéo boucle automatiquement. La cadence est adaptée via frame_step
+    pour correspondre au fps cible.
+
+    Calibration : set_px_per_mm() met à jour le facteur de conversion à chaud.
+    Hot swap    : set_video_file(path) change la vidéo sans interruption.
+    """
+
+    def __init__(
+        self,
+        video_dir,
+        fps: float = 5.0,
+        jpeg_quality: int = 90,
+        use_tracking: bool = False,
+        display=None,
+        parent=None,
+        crop_radius_px: int = 150,
+        px_per_mm: float = 15.0,
+        x_offset_mm: float = 0.0,
+        y_offset_mm: float = 0.0,
+        initial_video_path: str | None = None,
+    ):
+        super().__init__(fps, use_tracking, display, parent, jpeg_quality)
+        self._video_dir = Path(video_dir)
+        self._cap: cv2.VideoCapture | None = None
+        self._cap_lock = threading.Lock()
+        self._video_path: Path | None = (
+            Path(initial_video_path) if initial_video_path else None
+        )
+        self._frame_w: int = 0
+        self._frame_h: int = 0
+        self._crop_radius_px: int = crop_radius_px
+        self._px_per_mm: float = px_per_mm
+        self._x_offset_mm: float = x_offset_mm
+        self._y_offset_mm: float = y_offset_mm
+        self._frame_step: int = 1
+
+    # ------------------------------------------------------------------
+    # API publique
+    # ------------------------------------------------------------------
+
+    def set_px_per_mm(self, px_per_mm: float) -> None:
+        """Met à jour le facteur de conversion mm → pixel à chaud (depuis WellPosition)."""
+        self._px_per_mm = px_per_mm
+        logger.info(f"VideoPlateCapture: px_per_mm={px_per_mm:.3f}")
+
+    def set_crop_radius_px(self, r: int) -> None:
+        """Met à jour le rayon de découpe en pixels à chaud (depuis MultiWell.crop_radius)."""
+        self._crop_radius_px = r
+        logger.info(f"VideoPlateCapture: crop_radius_px={r}")
+
+    def set_offset_mm(self, x_offset_mm: float, y_offset_mm: float) -> None:
+        """Met à jour l'offset d'origine (xbase, ybase du MultiWell) à chaud."""
+        self._x_offset_mm = x_offset_mm
+        self._y_offset_mm = y_offset_mm
+
+    def set_video_file(self, path: str) -> None:
+        """
+        Hot swap : remplace la vidéo courante sans arrêter la capture.
+        Thread-safe — peut être appelé depuis n'importe quel thread.
+        """
+        new_cap = cv2.VideoCapture(path)
+        if not new_cap.isOpened():
+            logger.error(f"VideoPlateCapture hot swap: impossible d'ouvrir {path}")
+            return
+
+        new_w    = int(new_cap.get(cv2.CAP_PROP_FRAME_WIDTH))
+        new_h    = int(new_cap.get(cv2.CAP_PROP_FRAME_HEIGHT))
+        nat_fps  = new_cap.get(cv2.CAP_PROP_FPS) or self._fps
+        new_step = max(1, round(nat_fps / self._fps))
+
+        with self._cap_lock:
+            old_cap          = self._cap
+            self._cap        = new_cap
+            self._video_path = Path(path)
+            self._frame_w    = new_w
+            self._frame_h    = new_h
+            self._frame_step = new_step
+
+        if old_cap:
+            old_cap.release()
+
+        logger.info(f"VideoPlateCapture: hot swap → {Path(path).name} {new_w}×{new_h}")
+
+    @property
+    def video_path(self) -> Path | None:
+        return self._video_path
+
+    # ------------------------------------------------------------------
+    # Implémentation VideoCaptureInterface
+    # ------------------------------------------------------------------
+
+    def open(self) -> None:
+        path = self._video_path if (self._video_path and self._video_path.exists()) \
+               else self._find_video()
+        if path is None:
+            raise CaptureError(f"Aucune vidéo trouvée dans {self._video_dir}")
+
+        cap = cv2.VideoCapture(str(path))
+        if not cap.isOpened():
+            raise CaptureError(f"Impossible d'ouvrir {path.name}")
+
+        nat_fps = cap.get(cv2.CAP_PROP_FPS) or self._fps
+
+        with self._cap_lock:
+            self._cap        = cap
+            self._video_path = path
+            self._frame_w    = int(cap.get(cv2.CAP_PROP_FRAME_WIDTH))
+            self._frame_h    = int(cap.get(cv2.CAP_PROP_FRAME_HEIGHT))
+            self._frame_step = max(1, round(nat_fps / self._fps))
+
+        logger.info(
+            f"VideoPlateCapture: {path.name} {self._frame_w}×{self._frame_h} "
+            f"@ {nat_fps:.1f} fps → step={self._frame_step}, "
+            f"px_per_mm={self._px_per_mm:.2f}"
+        )
+
+    def close(self) -> None:
+        with self._cap_lock:
+            cap, self._cap = self._cap, None
+        if cap:
+            cap.release()
+
+    def is_available(self) -> bool:
+        with self._cap_lock:
+            return self._cap is not None and self._cap.isOpened()
+
+    def capture_frame(self) -> bytes:
+        with self._cap_lock:
+            if self._cap is None or not self._cap.isOpened():
+                raise CaptureError("Vidéo non disponible")
+
+            # Avancer dans la vidéo pour correspondre au fps cible
+            for _ in range(self._frame_step - 1):
+                self._cap.grab()
+
+            ret, frame = self._cap.read()
+            if not ret:
+                self._cap.set(cv2.CAP_PROP_POS_FRAMES, 0)
+                ret, frame = self._cap.read()
+                if not ret:
+                    raise CaptureError("Impossible de relire la vidéo")
+
+            frame_w = self._frame_w
+            frame_h = self._frame_h
+
+        # Position GRBL (mm) → coordonnées pixel dans la vidéo plaque
+        grbl  = getattr(self.parent, 'grbl', None) if self.parent else None
+        x_mm  = float(getattr(grbl, 'x', None) or 0.0)
+        y_mm  = float(getattr(grbl, 'y', None) or 0.0)
+
+        # À l'origine CNC (0, 0) : retourner la plaque entière à sa résolution native
+        if x_mm == 0.0 and y_mm == 0.0:
+            ok, buf = cv2.imencode('.jpg', frame, [cv2.IMWRITE_JPEG_QUALITY, self.jpeg_quality])
+            if not ok:
+                raise CaptureError("Encodage JPEG échoué")
+            return buf.tobytes()
+
+        cx = int((x_mm - self._x_offset_mm) * self._px_per_mm)
+        cy = int((y_mm - self._y_offset_mm) * self._px_per_mm)
+        r  = self._crop_radius_px
+
+        # Extraction du carré centré sur le puits courant
+        x1 = max(0, cx - r)
+        y1 = max(0, cy - r)
+        x2 = min(frame_w, cx + r)
+        y2 = min(frame_h, cy + r)
+        crop = frame[y1:y2, x1:x2]
+
+        # Padding noir si le crop déborde du bord de la vidéo
+        if crop.shape[0] != 2 * r or crop.shape[1] != 2 * r:
+            padded = np.zeros((2 * r, 2 * r, 3), dtype=np.uint8)
+            padded[:crop.shape[0], :crop.shape[1]] = crop
+            crop = padded
+
+        ok, buf = cv2.imencode('.jpg', crop, [cv2.IMWRITE_JPEG_QUALITY, self.jpeg_quality])
+        if not ok:
+            raise CaptureError("Encodage JPEG échoué")
+        return buf.tobytes()
+
+    # ------------------------------------------------------------------
+    # Privé
+    # ------------------------------------------------------------------
+
+    def _find_video(self) -> Path | None:
+        """Retourne le premier fichier vidéo trouvé dans video_dir."""
+        self._video_dir.mkdir(parents=True, exist_ok=True)
+        for ext in ('*.mp4', '*.avi', '*.MP4', '*.AVI'):
+            files = sorted(self._video_dir.glob(ext))
+            if files:
+                return files[0]
+        return None

test_tube_scanner/modules/webcam_capture.py

@@ -49,7 +49,7 @@ class WebcamCapture(VideoCaptureInterface):
         :param width:         Largeur souhaitée (None = valeur par défaut du pilote)
         :param height:        Hauteur souhaitée (None = valeur par défaut du pilote)
         """
-        super().__init__(fps=fps, use_tracking=use_tracking, display=display, parent=parent)
+        super().__init__(fps=fps, use_tracking=use_tracking, display=display, parent=parent, jpeg_quality=jpeg_quality)
         self._device_index: int = device_index
         self._jpeg_quality: int = jpeg_quality
         self._width: Optional[int] = width

test_tube_scanner/planarian/admin.py

@@ -8,29 +8,34 @@ from .models import ExperimentConfig
 @admin.register(ExperimentConfig)
 class ExperimentConfigAdmin(admin.ModelAdmin):
     """Admin Django pour les configurations d'expérience."""
-    readonly_fields = ('experiment',  )
-    list_display  = ("experiment", "well", "px_per_mm", "fps",
+    readonly_fields = ('experiment', 'px_per_mm',  'fps', 'well_radius_mm',)
+    list_display  = ("experiment_key", "well", "active", "planarian_count", "px_per_mm", "fps",
                      "thresh_immobile", "thresh_mobile",
-                     "photo_mode", "chemo_strength", "created_at")
-    list_filter   = ("photo_mode", "tube_axis")
-    search_fields = ("experiment", "well", "description")
+                     "photo_mode", "chemo_strength", "created_at", )
+    
+    list_filter   = ("experiment_key__session_experiments__session", "experiment_key", "photo_mode", "thigmotaxis_wall_dist_mm", "planarian_count")
+    search_fields = ("experiment_key", "well_name", "description")
     ordering      = ("-created_at",)
 
     fieldsets = (
         (_("Identification"), {
-            "fields": ("experiment", "well", "description"),
+            "fields": ("experiment_key", "well", "active", "description"),
         }),        
-        (_("Calibration optique"), {
+        (_("Calibration optique:  générée lors de la calibration"), {
             "fields": ("px_per_mm", "fps", "well_radius_mm"),
+            "classes": ("collapse",),
         }),
         (_("Seuils de mobilité EthoVision"), {
             "fields": ("thresh_immobile", "thresh_mobile"), 
+            "classes": ("collapse",),
         }),
         (_("Tracker"), {
-            "fields": ("tube_axis", "min_area_px", "planarian_count"),
+            "fields": ("tube_axis", "min_area_px", "max_area_ratio", "planarian_count", "merge_kernel_size", "min_contour_dist_px"),
+            "classes": ("collapse",),
         }),
         (_("Thigmotactisme"), {
             "fields": ("thigmotaxis_wall_dist_mm",),
+            "classes": ("collapse",),
         }),
         (_("Phototactisme"), {
             "fields": ("photo_mode", "photo_strength", "photo_x", "photo_y"),
@@ -52,19 +57,19 @@ class ExperimentConfigAdmin(admin.ModelAdmin):
     @admin.action(description=_("Exporter un template CSV de ces configurations"))
     def export_csv_template(self, request, queryset):
         import csv
-        from django.http import HttpResponse
+        from django.http import FileResponse
         from io import StringIO
 
         output = StringIO()
         fields = [f.name for f in ExperimentConfig._meta.fields if f.name != "id"]  # @UndefinedVariable
+        
         writer = csv.DictWriter(output, fieldnames=fields)
         writer.writeheader()
         for obj in queryset:
             row = {f: getattr(obj, f) for f in fields}
             writer.writerow(row)
 
-        response = HttpResponse(output.getvalue(), content_type="text/csv")
+        response = FileResponse(output.getvalue(), content_type='text/csv')
         response["Content-Disposition"] = 'attachment; filename="experiment_configs.csv"'       
-        
         return response
 

test_tube_scanner/planarian/export_service.py

@@ -0,0 +1,68 @@
+
+import logging
+import asyncio
+
+from asgiref.sync import async_to_sync
+from django.conf import settings
+from modules.planarian_metrics import ReductStoreClient
+
+logger = logging.getLogger(__name__)
+
+
+def _get_reduct_client() -> ReductStoreClient:
+    """Instancie le client ReductStore depuis les settings Django."""
+    return ReductStoreClient(url=settings.REDUCTSTORE_URL, token=settings.REDUCTSTORE_TOKEN)
+
+
+def export_csv_sync(
+    *,
+    experiment,
+    well,
+    uuid,
+    planarian,
+    record_type,
+    start=None,
+    stop=None,
+):
+    #@async_to_sync
+    async def _run():
+        client = _get_reduct_client()
+
+        await client.connect()
+        return await client.export_csv_response(
+            experiment=experiment,
+            well=well,
+            uuid=uuid,
+            planarian=planarian,
+            record_type=record_type,
+            start=start,
+            stop=stop,
+        )
+    #return _run()
+    return asyncio.run(_run())
+
+def export_csv_file_sync(
+    *,
+    experiment,
+    well,
+    uuid,
+    planarian,
+    record_type,
+):
+    async def _run():
+        client = _get_reduct_client()
+
+        await client.connect()
+        try:
+            return await client.export_csv(
+                experiment=experiment,
+                well=well,
+                uuid=uuid,
+                planarian=planarian,
+                record_type=record_type,
+                output_dir=settings.CSV_EXPORT_DIR,
+            )
+        finally:
+            await client.close()
+    return asyncio.run(_run())
+

test_tube_scanner/planarian/forms.py

@@ -1,91 +0,0 @@
-# planarian/forms.py
-
-import csv
-import io
-
-from django import forms
-from django.utils.translation import gettext_lazy as _
-from .models import ExperimentConfig
-
-
-class ExperimentConfigForm(forms.ModelForm):
-    """Formulaire de saisie/modification d'un ExperimentConfig."""
-
-    class Meta:
-        model  = ExperimentConfig
-        fields = "__all__"
-        widgets = {
-            "description": forms.Textarea(attrs={"rows": 3}),
-        }
-
-    def clean(self):
-        cleaned = super().clean()
-        if cleaned.get("thresh_immobile", 0) >= cleaned.get("thresh_mobile", 1):
-            raise forms.ValidationError(
-                _("Le seuil Immobile doit être inférieur au seuil Mobile.")
-            )
-        if cleaned.get("avoid_radius_mm", 0) >= cleaned.get("aggreg_radius_mm", 1):
-            raise forms.ValidationError(
-                _("Le rayon d'évitement doit être inférieur au rayon d'agrégation.")
-            )
-        return cleaned
-
-
-class CsvImportForm(forms.Form):
-    """Formulaire d'import de paramètres depuis un fichier CSV."""
-
-    csv_file = forms.FileField(
-        label=_("Fichier CSV"),
-        help_text=_(
-            "Colonnes obligatoires : experiment, well, px_per_mm, fps. "
-            "Toutes les autres colonnes sont optionnelles."
-        ),
-    )
-    overwrite = forms.BooleanField(
-        required=False,
-        initial=False,
-        label=_("Écraser les configurations existantes"),
-    )
-
-    def clean_csv_file(self):
-        f = self.cleaned_data["csv_file"]
-        try:
-            content = f.read().decode("utf-8")
-            reader  = csv.DictReader(io.StringIO(content))
-            rows    = list(reader)
-        except Exception as e:
-            raise forms.ValidationError(_("Fichier CSV invalide : %(err)s") % {"err": e})
-
-        required = {"experiment", "well", "px_per_mm", "fps"}
-        if rows:
-            missing = required - set(rows[0].keys())
-            if missing:
-                raise forms.ValidationError(
-                    _("Colonnes manquantes : %(cols)s") % {"cols": ", ".join(missing)}
-                )
-        self.csv_rows = rows
-        return f
-
-
-class ExportCsvForm(forms.Form):
-    """Formulaire de demande d'export CSV depuis ReductStore."""
-
-    experiment  = forms.CharField(label=_("Expérience"), max_length=100)
-    well        = forms.CharField(label=_("Puits"), max_length=20)
-    planarian   = forms.IntegerField(label=_("Index planaire"), initial=0, min_value=0)
-    record_type = forms.ChoiceField(
-        label=_("Type d'enregistrement"),
-        choices=[("frame", _("Frame par frame")), ("summary", _("Résumé"))],
-        initial="frame",
-    )
-    start_dt = forms.DateTimeField(
-        label=_("Début (UTC)"),
-        required=False,
-        widget=forms.DateTimeInput(attrs={"type": "datetime-local"}),
-    )
-    stop_dt = forms.DateTimeField(
-        label=_("Fin (UTC)"),
-        required=False,
-        widget=forms.DateTimeInput(attrs={"type": "datetime-local"}),
-    )
-

test_tube_scanner/planarian/migrations/0001_initial.py

@@ -0,0 +1,56 @@
+# Generated by Django 6.0.5 on 2026-05-31 07:42
+
+import django.db.models.deletion
+from django.conf import settings
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = [
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='ExperimentConfig',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('experiment', models.CharField(default='Identifier', max_length=128, null=True, verbose_name='Identifiant expérience')),
+                ('well', models.CharField(choices=[], default='A1', help_text='Nom du puit', max_length=8, null=True, verbose_name='Puit')),
+                ('description', models.TextField(blank=True, default='-', verbose_name='Description')),
+                ('created_at', models.DateTimeField(auto_now_add=True, verbose_name='Créé le')),
+                ('active', models.BooleanField(default=True, verbose_name='Active')),
+                ('px_per_mm', models.FloatField(default=26.25, help_text='Facteur de calibration optique', verbose_name='Pixels par mm')),
+                ('fps', models.FloatField(default=5.0, help_text='Image de capture en img/s', verbose_name='FPS de capture')),
+                ('well_radius_mm', models.FloatField(default=8.0, help_text='En mm', verbose_name='Rayon du puits')),
+                ('thresh_immobile', models.FloatField(default=0.2, verbose_name='Seuil Immobile (mm/s)')),
+                ('thresh_mobile', models.FloatField(default=1.5, verbose_name='Seuil Mobile (mm/s)')),
+                ('tube_axis', models.CharField(choices=[('vertical', 'Vertical'), ('horizontal', 'Horizontal')], default='vertical', max_length=10, verbose_name='Axe du tube')),
+                ('min_area_px', models.IntegerField(default=20, verbose_name='Surface min détection (px²)')),
+                ('max_area_ratio', models.FloatField(default=0.1, help_text='Ratio de la surface du puits, ex: 0.10 pour 10%', verbose_name='Surface max contour (fraction de la frame)')),
+                ('planarian_count', models.IntegerField(default=1, verbose_name='Nombre de planaires')),
+                ('merge_kernel_size', models.PositiveIntegerField(default=15, help_text='taille du kernel elliptique de fusion des fragments (px). Augmenter si fragments résiduels', verbose_name='Taille du kernel')),
+                ('min_contour_dist_px', models.PositiveIntegerField(default=40, help_text='Distance min entre deux contours pour les considérer comme individus distincts. Défaut : 40px. Augmenter si IDs multiples persistent', verbose_name='Distance <contour>')),
+                ('thigmotaxis_wall_dist_mm', models.FloatField(default=1.0, verbose_name='Distance paroi thigmotactisme (mm)')),
+                ('photo_mode', models.CharField(choices=[('none', 'Désactivé'), ('fixed', 'Source fixe'), ('sine', 'Source sinusoïdale'), ('radial', 'Gradient radial')], default='none', max_length=10, verbose_name='Mode phototactisme')),
+                ('photo_strength', models.FloatField(default=0.0, verbose_name='Intensité phototactisme')),
+                ('photo_x', models.FloatField(default=0.5, verbose_name='Source lumière X (0-1)')),
+                ('photo_y', models.FloatField(default=0.5, verbose_name='Source lumière Y (0-1)')),
+                ('chemo_strength', models.FloatField(default=0.0, verbose_name='Intensité chimiotactisme')),
+                ('chemo_x', models.FloatField(default=0.5, verbose_name='Nourriture X (0-1)')),
+                ('chemo_y', models.FloatField(default=0.5, verbose_name='Nourriture Y (0-1)')),
+                ('chemo_radius_mm', models.FloatField(default=2.0, verbose_name='Rayon nourriture (mm)')),
+                ('avoid_radius_mm', models.FloatField(default=3.0, verbose_name='Rayon évitement (mm)')),
+                ('aggreg_radius_mm', models.FloatField(default=6.0, verbose_name='Rayon agrégation (mm)')),
+                ('author', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Auteur')),
+            ],
+            options={
+                'verbose_name': "Configuration d'une expérience",
+                'verbose_name_plural': 'Configurations des expériences',
+                'ordering': ['-created_at'],
+            },
+        ),
+    ]

test_tube_scanner/planarian/migrations/0002_initial.py

@@ -0,0 +1,26 @@
+# Generated by Django 6.0.5 on 2026-05-31 07:42
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = [
+        ('planarian', '0001_initial'),
+        ('scanner', '0001_initial'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='experimentconfig',
+            name='experiment_key',
+            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='scanner.experiment', verbose_name='Expérience'),
+        ),
+        migrations.AlterUniqueTogether(
+            name='experimentconfig',
+            unique_together={('experiment_key', 'well')},
+        ),
+    ]

test_tube_scanner/planarian/models.py

@@ -1,13 +1,17 @@
 # planarian/models.py
 
 from django.db import models
-from django.dispatch import receiver
-from django.db.models.signals import post_save
-from django.conf import settings
+#from django.conf import settings
 from django.utils.translation import gettext_lazy as _
 from django.contrib.auth.models import User
-from scanner.models import Experiment, Well, WellPosition
-from scanner.constants import ScannerConstants
+from scanner.models import Experiment, Well
+
+WELL_CHOICES = []
+def get_well_choices():
+    wells = Well.objects.order_by('name').all()
+    for well in wells:
+        WELL_CHOICES.append((well.name, well.name))
+
 
 class ExperimentConfig(models.Model):
     """
@@ -15,22 +19,15 @@ class ExperimentConfig(models.Model):
     Peut être créé depuis Django admin, une vue formulaire ou un import CSV.
     """
     author = models.ForeignKey(User, on_delete=models.CASCADE, verbose_name="Auteur", null=True, blank=True)   
+    experiment_key = models.ForeignKey(Experiment, verbose_name="Expérience", on_delete=models.CASCADE, null=True, blank=False)
+    experiment = models.CharField(_("Identifiant expérience"), max_length=128, null=True, blank=False, default='Identifier' )
+    well = models.CharField(_("Puit"), help_text=_("Nom du puit"), max_length=8, choices=WELL_CHOICES, null=True, blank=False, default='A1' )
     
-    # --- Identification ---
-    idendifier = models.CharField(
-        max_length=100,
-        verbose_name=_("Identifiant d'expérience"),
-        help_text=_("Ex : exp_2026_04_25_ctrl"),
-    )
+    description = models.TextField( blank=True, verbose_name=_("Description"), default="-")
     
-    experiment = models.ForeignKey(Experiment, on_delete=models.CASCADE, related_name="experiment_well" , null=True, blank=True)
-    well = models.ForeignKey(Well, verbose_name="Puit", on_delete=models.CASCADE, related_name="well_experiment", null=True, blank=True )
 
-    description = models.TextField(
-        blank=True,
-        verbose_name=_("Description"),
-    )
     created_at = models.DateTimeField(auto_now_add=True, verbose_name=_("Créé le"))
+    active = models.BooleanField(_("Active"), default=True)
 
     # --- Calibration optique ---
     # px_per_mm, fps, well_radius_mm 
@@ -42,10 +39,12 @@ class ExperimentConfig(models.Model):
     fps = models.FloatField(
         default=5.0,
         verbose_name=_("FPS de capture"),
+        help_text=_("Image de capture en img/s"),
     )
     well_radius_mm = models.FloatField(
         default=8.0,
-        verbose_name=_("Rayon du puits (mm)"),
+        verbose_name=_("Rayon du puits"),
+        help_text=_("En mm"),
     )
 
     # --- Seuils de mobilité EthoVision ---
@@ -69,11 +68,30 @@ class ExperimentConfig(models.Model):
         default=20,
         verbose_name=_("Surface min détection (px²)"),
     )
+    
+    max_area_ratio = models.FloatField(
+        default=0.10,
+        verbose_name=_("Surface max contour (fraction de la frame)"),
+        help_text=_("Ratio de la surface du puits, ex: 0.10 pour 10%"),
+    )
+        
     planarian_count = models.IntegerField(
         default=1,
         verbose_name=_("Nombre de planaires"),
     )
 
+    merge_kernel_size = models.PositiveIntegerField(
+        _("Taille du kernel"), 
+        help_text=_("taille du kernel elliptique de fusion des fragments (px). Augmenter si fragments résiduels"), 
+        default=15
+    )
+    
+    min_contour_dist_px = models.PositiveIntegerField(
+        _("Distance <contour>"), 
+        help_text=_("Distance min entre deux contours pour les considérer comme individus distincts. Défaut : 40px. Augmenter si IDs multiples persistent"), 
+        default=40
+    )
+
     # --- Thigmotactisme ---
     thigmotaxis_wall_dist_mm = models.FloatField(
         default=1.0,
@@ -107,23 +125,33 @@ class ExperimentConfig(models.Model):
     avoid_radius_mm  = models.FloatField(default=3.0, verbose_name=_("Rayon évitement (mm)"))
     aggreg_radius_mm = models.FloatField(default=6.0, verbose_name=_("Rayon agrégation (mm)"))
 
+
     class Meta:
-        verbose_name        = _("Configuration expérience")
-        verbose_name_plural = _("Configurations expériences")
-        unique_together     = ("experiment", "well")
+        verbose_name        = _("Configuration d'une expérience")
+        verbose_name_plural = _("Configurations des expériences")
+        unique_together     = ("experiment_key", "well")
         ordering            = ["-created_at"]       
 
     def __str__(self):
-        return f"{self.experiment} / {self.well.name}"
+        return f"{self.experiment_key}:{self.well}"
+    
+    def save(self, *args, **kwargs):
+        if not self.author:
+            self.author = self.experiment_key.author
+        self.experiment = self.experiment_key.identifier   
+        super().save(*args, **kwargs)    
+    
     
     def get_session(self):
-        return self.experiment.session_experiments.first() if self.experiment else None
+        se = self.experiment_key.session_experiments.first() if self.experiment_key else None
+        return se.session
+    
 
     def to_params_dict(self) -> dict:
         """Retourne un dict compatible avec ExperimentParams."""
         return {
-            "experiment":            self.idendifier,
-            "well":                  self.well.name,
+            "experiment":            self.experiment,
+            "well":                  self.well,        
             "px_per_mm":             self.px_per_mm,
             "fps":                   self.fps,
             "well_radius_mm":        self.well_radius_mm,
@@ -131,6 +159,9 @@ class ExperimentConfig(models.Model):
             "thresh_mobile":         self.thresh_mobile,
             "tube_axis":             self.tube_axis,
             "min_area_px":           self.min_area_px,
+            "max_area_ratio":        self.max_area_ratio,
+            "merge_kernel_size":     self.merge_kernel_size,
+            "min_contour_dist_px":   self.min_contour_dist_px,
             "planarian_count":       self.planarian_count,
             "thigmotaxis_wall_dist_mm": self.thigmotaxis_wall_dist_mm,
             "photo_mode":            self.photo_mode,
@@ -143,23 +174,3 @@ class ExperimentConfig(models.Model):
             "aggreg_radius_mm":      self.aggreg_radius_mm,
         }
         
-    def save(self, *args, **kwargs):
-        session = self.get_session()
-        position = self.experiment.multiwell.position
-        dte = self.experiment.multiwell.finished.isoformat()
-        self.idendifier = f'{session}-{position}-{self.well.name}-{dte}'
-        super().save(*args, **kwargs)
-        
-        
-@receiver(post_save, sender=ExperimentConfig)
-def create_well_position(sender, instance, created, **kwargs):
-    active_well = WellPosition.active_well(instance.multiwel, instance.well)
-    instance.px_per_mm = active_well.px_per_mm
-    instance.well_radius_mm = instance.experiment.multiwell.diameter / 2
-    conf = ScannerConstants().get()
-    instance.fps = conf.video_frame_rate
-    instance.save()        
-        
-        
-        
-        

test_tube_scanner/planarian/static/planarian/css/planarian.css

@@ -0,0 +1,12 @@
+
+.multiwell_cards {
+  display: grid;
+  grid-template-columns: repeat(6, 1fr);
+  justify-items: center; 
+  align-items: center; 
+}
+
+button.multiwell {
+    padding: 0.2em ;
+}
+

test_tube_scanner/planarian/tasks.py

@@ -0,0 +1,80 @@
+# tasks.py
+from celery import shared_task, group
+from celery.utils.log import get_task_logger
+
+from scanner.models import SessionExperiment, get_uuid_from_session, Experiment
+from .models import ExperimentConfig
+from .export_service import export_csv_file_sync
+
+logger = get_task_logger(__name__)
+
+
+@shared_task(bind=True, autoretry_for=(Exception,), retry_backoff=True, retry_kwargs={"max_retries": 3},)
+def export_single_metric(self, *, experiment, well, uuid, planarian, record_type,):
+    """
+    Exporte UN fichier CSV.
+    """
+    logger.info( f"Export start {experiment} {well} {planarian} {record_type}")
+    f, n = export_csv_file_sync(
+        experiment=experiment,
+        well=well,
+        uuid=uuid,
+        planarian=planarian,
+        record_type=record_type,
+    )
+    logger.info( f"Export done {f} ({n} rows)" )
+    return {"file": f, "rows": n, }
+
+
+@shared_task
+def export_experiment_metrics_task(experiment_id):
+    experiment = Experiment.objects.filter(pk=experiment_id).first()
+    if not experiment:
+        return
+    
+    jobs = []
+    configs = (ExperimentConfig.objects.filter(experiment_key_id=experiment.pk).order_by("well"))
+    for conf in configs:
+        well = conf.well
+        count = conf.planarian_count
+        session = conf.get_session()
+        uuid = get_uuid_from_session(session.id, conf.experiment_key.multiwell.position, well, )
+
+        for record_type in ["frame", "summary"]:
+            for planarian in range(count):
+                '''
+                jobs.append(
+                    export_single_metric.s(
+                        experiment=experiment.identifier,
+                        well=well,
+                        uuid=uuid,
+                        planarian=planarian,
+                        record_type=record_type,
+                    )
+                )
+                     
+                '''
+                try:
+                    f, n = export_csv_file_sync(
+                        experiment=experiment.identifier,
+                        well=well,
+                        uuid=uuid,
+                        planarian=planarian,
+                        record_type=record_type,
+                    )
+                    logger.info( f"Export done {f} ({n} rows)" )
+                except Exception as e:
+                    logger.exception(e)
+        '''      
+        result = group(jobs).apply_async()
+        logger.info(f"{len(jobs)} exports launched group_id={result.id}")        
+        return {"group_id": result.id,"jobs": len(jobs), }'''
+    
+ 
+@shared_task
+def export_session_metrics_task(session_id):
+    experiments = SessionExperiment.experiment_by_session(session_id, active=False)
+    for experiment in experiments:
+        export_experiment_metrics_task.delay(experiment.id)
+
+    

test_tube_scanner/planarian/templates/planarian/base.html

@@ -0,0 +1,76 @@
+{% extends "scanner/base.html" %}
+{% load i18n home_tags %}
+{% block styles %}
+    {{ block.super }}
+    <link href="/static/planarian/css/planarian.css" rel="stylesheet">
+{% endblock %}
+{% block columns %}{% endblock %}
+
+{% block sidebar_list %}
+    <a href="/"  class="w3-bar-item w3-btn w3-hover-opacity"><i class="fa-solid fa-house w3-text-orange w3-xlarge"></i> {% trans "Retour accueil" %}</a>
+    <form method="post" class="w3-bar-item" action="">
+        {% csrf_token %}
+        <select id="_sid" name="_sid" class="w3-select w3-margin-bottom" onchange="this.form.submit()" title="{% trans "Ensemble d'expériences" %}">
+            <option value="0">---- {% trans "Session" %}</option>
+            {% for s in sessions %}
+            <option value="{{ s.id }}" {% if s.id == current_session.id %}selected{% endif %}>{{ s }}</option>
+            {% endfor %}
+        </select>
+        <div class="w3-margin-left w3-margin-bottom">
+            {% include "scanner/experiment-inc.html" %} 
+        </div>
+    </form>
+    {% block export_csv %}
+	    {% if current_session and current_experiment %}
+	    {% url "planarian:api-export-csv"  as url_export %}
+	    <a href="#" class="w3-bar-item w3-btn w3-hover-opacity" onclick="export_csv('{{ url_export }}', {{ current_experiment.id }}, 'experiment_csv')">
+	        <i class="fa-solid fa-file-export w3-text-red w3-xlarge"></i> {% trans "Exporter les metrics de l'expérience" %}<br>
+	        <span class="w3-margin-left-5">&nbsp;$> {{ export_csv_destination }}
+	    </a>
+	    
+        <a href="#" class="w3-bar-item w3-btn w3-hover-opacity" onclick="export_csv('{{ url_export }}', {{ current_session.id }}, 'session_csv')">
+            <i class="fa-solid fa-file-export w3-text-pink w3-xxlarge"></i> {% trans "Exporter les metrics de la session" %}<br>
+            <span class="w3-margin-left-5">&nbsp;$> {{ export_csv_destination }}
+        </a>	    
+	  
+	    {% endif %}   
+    {% endblock %}
+{% endblock %}
+
+{% block js_footer %}
+    {{ block.super }}
+	<script>
+	    const export_msg = "{% trans "Confirmer l'export des vidéos. ATTENTION le processus peut être long!" %}";
+	    // Auto-dismiss messages after 5 seconds
+	    document.addEventListener('DOMContentLoaded', function() {
+	        const messages = document.querySelectorAll('.alert');
+	        messages.forEach(function(message) {
+	            setTimeout(function() {
+	                // Fade out effect
+	                message.style.transition = 'opacity 0.5s ease-out';
+	                message.style.opacity = '0';
+	                
+	                // Remove from DOM after fade
+	                setTimeout(function() {
+	                    message.remove();
+	                }, 500);
+	            }, 15000); // 15 seconds
+	        });
+	    });
+	    function export_csv(url, pid, mode) {
+	        csrfFetch(url, {
+	            method: 'POST',
+	            headers: { 'Content-Type': 'application/json' },
+	            body: JSON.stringify({
+	                action: mode,
+	                pid: pid,
+	            })
+	        })
+	        .then(response => response.json())
+	        .then(res      => { alert(res.msg);  })
+	        .catch(error   => { console.error('Erreur:', error); });       
+	    }
+   
+	   
+	</script>
+{% endblock %}

test_tube_scanner/planarian/templates/planarian/experiment_form.html

@@ -1,503 +0,0 @@
-{% extends "scanner/base.html" %}
-{% load i18n %}
-
-{% block content %}
-
-<div class="w3-container w3-padding-32" style="max-width:960px; margin:auto;">
-
-    <!-- En-tête de la page -->
-    <div class="w3-panel w3-teal w3-round-large w3-padding-16" style="margin-bottom:2rem;">
-        <div class="w3-row w3-bar-item">
-            <span class="w3-xlarge">
-                <i class="w3-margin-right">🔬</i>
-                {% if object %}
-                    {% trans "Modifier la configuration" %} — {{ object }}
-                {% else %}
-                    {% trans "Nouvelle configuration d'expérience" %}
-                {% endif %}
-            </span>
-        </div>
-    </div>
-
-    <!-- Messages Django -->
-    {% for message in messages %}
-    <div class="w3-panel w3-round
-        {% if message.tags == 'success' %}w3-green
-        {% elif message.tags == 'error'   %}w3-red
-        {% elif message.tags == 'warning' %}w3-orange
-        {% else %}w3-blue{% endif %}">
-        <p>{{ message }}</p>
-    </div>
-    {% endfor %}
-
-    <form method="post" novalidate>
-        {% csrf_token %}
-
-        <!-- Erreurs globales du formulaire -->
-        {% if form.non_field_errors %}
-        <div class="w3-panel w3-red w3-round">
-            {% for error in form.non_field_errors %}
-            <p>⚠ {{ error }}</p>
-            {% endfor %}
-        </div>
-        {% endif %}
-
-        <!-- ============================================================
-             Section 1 : Identification
-        ============================================================ -->
-        <div class="w3-card-4 w3-round-large w3-margin-bottom">
-            <header class="w3-container w3-teal w3-round-top-large">
-                <h3 class="w3-text-white">{% trans "Identification" %}</h3>
-            </header>
-            <div class="w3-container w3-padding-24">
-                <div class="w3-row-padding">
-
-                    <!-- Experiment -->
-                    <div class="w3-col m6 s12 w3-margin-bottom">
-                        <label class="w3-text-teal"><b>{{ form.experiment.label }}</b></label>
-                        {% if form.experiment.help_text %}
-                        <p class="w3-small w3-text-grey" style="margin:0 0 4px;">{{ form.experiment.help_text }}</p>
-                        {% endif %}
-                        {{ form.experiment }}
-                        {% if form.experiment.errors %}
-                        <span class="w3-text-red w3-small">{{ form.experiment.errors|join:", " }}</span>
-                        {% endif %}
-                    </div>
-
-                    <!-- Well -->
-                    <div class="w3-col m6 s12 w3-margin-bottom">
-                        <label class="w3-text-teal"><b>{{ form.well.label }}</b></label>
-                        {% if form.well.help_text %}
-                        <p class="w3-small w3-text-grey" style="margin:0 0 4px;">{{ form.well.help_text }}</p>
-                        {% endif %}
-                        {{ form.well }}
-                        {% if form.well.errors %}
-                        <span class="w3-text-red w3-small">{{ form.well.errors|join:", " }}</span>
-                        {% endif %}
-                    </div>
-
-                </div>
-
-                <!-- Description -->
-                <div class="w3-margin-bottom">
-                    <label class="w3-text-teal"><b>{{ form.description.label }}</b></label>
-                    {{ form.description }}
-                    {% if form.description.errors %}
-                    <span class="w3-text-red w3-small">{{ form.description.errors|join:", " }}</span>
-                    {% endif %}
-                </div>
-
-            </div>
-        </div>
-
-        <!-- ============================================================
-             Section 2 : Calibration optique
-        ============================================================ -->
-        <div class="w3-card-4 w3-round-large w3-margin-bottom">
-            <header class="w3-container w3-blue-grey w3-round-top-large">
-                <h3 class="w3-text-white">{% trans "Calibration optique" %}</h3>
-            </header>
-            <div class="w3-container w3-padding-24">
-                <div class="w3-row-padding">
-
-                    <div class="w3-col m4 s12 w3-margin-bottom">
-                        <label class="w3-text-blue-grey"><b>{{ form.px_per_mm.label }}</b></label>
-                        {% if form.px_per_mm.help_text %}
-                        <p class="w3-small w3-text-grey" style="margin:0 0 4px;">{{ form.px_per_mm.help_text }}</p>
-                        {% endif %}
-                        {{ form.px_per_mm }}
-                        {% if form.px_per_mm.errors %}
-                        <span class="w3-text-red w3-small">{{ form.px_per_mm.errors|join:", " }}</span>
-                        {% endif %}
-                    </div>
-
-                    <div class="w3-col m4 s12 w3-margin-bottom">
-                        <label class="w3-text-blue-grey"><b>{{ form.fps.label }}</b></label>
-                        {{ form.fps }}
-                        {% if form.fps.errors %}
-                        <span class="w3-text-red w3-small">{{ form.fps.errors|join:", " }}</span>
-                        {% endif %}
-                    </div>
-
-                    <div class="w3-col m4 s12 w3-margin-bottom">
-                        <label class="w3-text-blue-grey"><b>{{ form.well_radius_mm.label }}</b></label>
-                        {{ form.well_radius_mm }}
-                        {% if form.well_radius_mm.errors %}
-                        <span class="w3-text-red w3-small">{{ form.well_radius_mm.errors|join:", " }}</span>
-                        {% endif %}
-                    </div>
-
-                </div>
-            </div>
-        </div>
-
-        <!-- ============================================================
-             Section 3 : Seuils de mobilité EthoVision
-        ============================================================ -->
-        <div class="w3-card-4 w3-round-large w3-margin-bottom">
-            <header class="w3-container w3-indigo w3-round-top-large">
-                <h3 class="w3-text-white">{% trans "Seuils de mobilité EthoVision XT" %}</h3>
-            </header>
-            <div class="w3-container w3-padding-24">
-
-                <!-- Visualisation des seuils -->
-                <div class="w3-light-grey w3-round w3-margin-bottom" style="height:32px; position:relative; overflow:hidden;">
-                    <div style="position:absolute; left:0; width:13%; height:100%; background:#c0392b; display:flex; align-items:center; justify-content:center;">
-                        <span class="w3-small w3-text-white"><b>{% trans "Immobile" %}</b></span>
-                    </div>
-                    <div style="position:absolute; left:13%; width:27%; height:100%; background:#e67e22; display:flex; align-items:center; justify-content:center;">
-                        <span class="w3-small w3-text-white"><b>{% trans "Mobile" %}</b></span>
-                    </div>
-                    <div style="position:absolute; left:40%; right:0; height:100%; background:#27ae60; display:flex; align-items:center; justify-content:center;">
-                        <span class="w3-small w3-text-white"><b>{% trans "Très mobile" %}</b></span>
-                    </div>
-                </div>
-                <p class="w3-small w3-text-grey" style="margin-top:-8px; margin-bottom:16px;">
-                    {% trans "Représentation indicative des zones de mobilité (défauts EthoVision : 0.2 / 1.5 mm/s)" %}
-                </p>
-
-                <div class="w3-row-padding">
-                    <div class="w3-col m6 s12 w3-margin-bottom">
-                        <label class="w3-text-indigo"><b>{{ form.thresh_immobile.label }}</b></label>
-                        <p class="w3-small w3-text-grey" style="margin:0 0 4px;">{% trans "En-dessous : Immobile (mm/s)" %}</p>
-                        {{ form.thresh_immobile }}
-                        {% if form.thresh_immobile.errors %}
-                        <span class="w3-text-red w3-small">{{ form.thresh_immobile.errors|join:", " }}</span>
-                        {% endif %}
-                    </div>
-                    <div class="w3-col m6 s12 w3-margin-bottom">
-                        <label class="w3-text-indigo"><b>{{ form.thresh_mobile.label }}</b></label>
-                        <p class="w3-small w3-text-grey" style="margin:0 0 4px;">{% trans "En-dessous : Mobile, au-delà : Très mobile (mm/s)" %}</p>
-                        {{ form.thresh_mobile }}
-                        {% if form.thresh_mobile.errors %}
-                        <span class="w3-text-red w3-small">{{ form.thresh_mobile.errors|join:", " }}</span>
-                        {% endif %}
-                    </div>
-                </div>
-            </div>
-        </div>
-
-        <!-- ============================================================
-             Section 4 : Tracker
-        ============================================================ -->
-        <div class="w3-card-4 w3-round-large w3-margin-bottom">
-            <header class="w3-container w3-dark-grey w3-round-top-large">
-                <h3 class="w3-text-white">{% trans "Tracker" %}</h3>
-            </header>
-            <div class="w3-container w3-padding-24">
-                <div class="w3-row-padding">
-
-                    <div class="w3-col m4 s12 w3-margin-bottom">
-                        <label class="w3-text-dark-grey"><b>{{ form.tube_axis.label }}</b></label>
-                        {{ form.tube_axis }}
-                        {% if form.tube_axis.errors %}
-                        <span class="w3-text-red w3-small">{{ form.tube_axis.errors|join:", " }}</span>
-                        {% endif %}
-                    </div>
-
-                    <div class="w3-col m4 s12 w3-margin-bottom">
-                        <label class="w3-text-dark-grey"><b>{{ form.min_area_px.label }}</b></label>
-                        {{ form.min_area_px }}
-                        {% if form.min_area_px.errors %}
-                        <span class="w3-text-red w3-small">{{ form.min_area_px.errors|join:", " }}</span>
-                        {% endif %}
-                    </div>
-
-                    <div class="w3-col m4 s12 w3-margin-bottom">
-                        <label class="w3-text-dark-grey"><b>{{ form.planarian_count.label }}</b></label>
-                        {{ form.planarian_count }}
-                        {% if form.planarian_count.errors %}
-                        <span class="w3-text-red w3-small">{{ form.planarian_count.errors|join:", " }}</span>
-                        {% endif %}
-                    </div>
-
-                </div>
-            </div>
-        </div>
-
-        <!-- ============================================================
-             Section 5 : Comportements (accordéon W3.CSS)
-        ============================================================ -->
-        <div class="w3-card-4 w3-round-large w3-margin-bottom">
-            <header class="w3-container w3-teal w3-round-top-large">
-                <h3 class="w3-text-white">{% trans "Comportements" %}</h3>
-            </header>
-
-            <!-- --- Thigmotactisme --- -->
-            <div class="w3-container w3-padding-16 w3-border-bottom">
-                <button type="button" class="w3-button w3-block w3-left-align w3-hover-light-grey"
-                        onclick="toggleSection('thigmo')">
-                    <span class="w3-large">🫧</span>
-                    <b class="w3-margin-left">{% trans "Thigmotactisme" %}</b>
-                    <span class="w3-small w3-text-grey w3-margin-left">
-                        {% trans "Attraction vers la paroi du puits" %}
-                    </span>
-                    <span id="thigmo-icon" class="w3-right">▼</span>
-                </button>
-                <div id="thigmo" class="w3-padding-top">
-                    <div class="w3-row-padding">
-                        <div class="w3-col m6 s12">
-                            <label class="w3-text-teal"><b>{{ form.thigmotaxis_wall_dist_mm.label }}</b></label>
-                            <p class="w3-small w3-text-grey" style="margin:0 0 4px;">
-                                {% trans "Distance à la paroi considérée « près du bord » (mm)" %}
-                            </p>
-                            {{ form.thigmotaxis_wall_dist_mm }}
-                            {% if form.thigmotaxis_wall_dist_mm.errors %}
-                            <span class="w3-text-red w3-small">{{ form.thigmotaxis_wall_dist_mm.errors|join:", " }}</span>
-                            {% endif %}
-                        </div>
-                    </div>
-                </div>
-            </div>
-
-            <!-- --- Phototactisme --- -->
-            <div class="w3-container w3-padding-16 w3-border-bottom">
-                <button type="button" class="w3-button w3-block w3-left-align w3-hover-light-grey"
-                        onclick="toggleSection('photo')">
-                    <span class="w3-large">💡</span>
-                    <b class="w3-margin-left">{% trans "Phototactisme" %}</b>
-                    <span class="w3-small w3-text-grey w3-margin-left">
-                        {% trans "Fuite de la lumière" %}
-                    </span>
-                    <span id="photo-icon" class="w3-right">▼</span>
-                </button>
-                <div id="photo" class="w3-hide w3-padding-top">
-                    <div class="w3-row-padding">
-
-                        <div class="w3-col m6 s12 w3-margin-bottom">
-                            <label class="w3-text-teal"><b>{{ form.photo_mode.label }}</b></label>
-                            {{ form.photo_mode }}
-                            {% if form.photo_mode.errors %}
-                            <span class="w3-text-red w3-small">{{ form.photo_mode.errors|join:", " }}</span>
-                            {% endif %}
-                        </div>
-
-                        <div class="w3-col m6 s12 w3-margin-bottom">
-                            <label class="w3-text-teal"><b>{{ form.photo_strength.label }}</b></label>
-                            <p class="w3-small w3-text-grey" style="margin:0 0 4px;">{% trans "0.0 = désactivé  →  1.0 = fort" %}</p>
-                            {{ form.photo_strength }}
-                            {% if form.photo_strength.errors %}
-                            <span class="w3-text-red w3-small">{{ form.photo_strength.errors|join:", " }}</span>
-                            {% endif %}
-                        </div>
-
-                        <div class="w3-col m6 s12 w3-margin-bottom">
-                            <label class="w3-text-teal"><b>{{ form.photo_x.label }}</b></label>
-                            {{ form.photo_x }}
-                            {% if form.photo_x.errors %}
-                            <span class="w3-text-red w3-small">{{ form.photo_x.errors|join:", " }}</span>
-                            {% endif %}
-                        </div>
-
-                        <div class="w3-col m6 s12 w3-margin-bottom">
-                            <label class="w3-text-teal"><b>{{ form.photo_y.label }}</b></label>
-                            {{ form.photo_y }}
-                            {% if form.photo_y.errors %}
-                            <span class="w3-text-red w3-small">{{ form.photo_y.errors|join:", " }}</span>
-                            {% endif %}
-                        </div>
-
-                    </div>
-                </div>
-            </div>
-
-            <!-- --- Chimiotactisme --- -->
-            <div class="w3-container w3-padding-16 w3-border-bottom">
-                <button type="button" class="w3-button w3-block w3-left-align w3-hover-light-grey"
-                        onclick="toggleSection('chemo')">
-                    <span class="w3-large">🍖</span>
-                    <b class="w3-margin-left">{% trans "Chimiotactisme" %}</b>
-                    <span class="w3-small w3-text-grey w3-margin-left">
-                        {% trans "Attraction vers une source de nourriture" %}
-                    </span>
-                    <span id="chemo-icon" class="w3-right">▼</span>
-                </button>
-                <div id="chemo" class="w3-hide w3-padding-top">
-                    <div class="w3-row-padding">
-
-                        <div class="w3-col m4 s12 w3-margin-bottom">
-                            <label class="w3-text-teal"><b>{{ form.chemo_strength.label }}</b></label>
-                            <p class="w3-small w3-text-grey" style="margin:0 0 4px;">{% trans "0.0 = désactivé  →  1.0 = fort" %}</p>
-                            {{ form.chemo_strength }}
-                            {% if form.chemo_strength.errors %}
-                            <span class="w3-text-red w3-small">{{ form.chemo_strength.errors|join:", " }}</span>
-                            {% endif %}
-                        </div>
-
-                        <div class="w3-col m4 s12 w3-margin-bottom">
-                            <label class="w3-text-teal"><b>{{ form.chemo_x.label }}</b></label>
-                            {{ form.chemo_x }}
-                            {% if form.chemo_x.errors %}
-                            <span class="w3-text-red w3-small">{{ form.chemo_x.errors|join:", " }}</span>
-                            {% endif %}
-                        </div>
-
-                        <div class="w3-col m4 s12 w3-margin-bottom">
-                            <label class="w3-text-teal"><b>{{ form.chemo_y.label }}</b></label>
-                            {{ form.chemo_y }}
-                            {% if form.chemo_y.errors %}
-                            <span class="w3-text-red w3-small">{{ form.chemo_y.errors|join:", " }}</span>
-                            {% endif %}
-                        </div>
-
-                        <div class="w3-col m6 s12 w3-margin-bottom">
-                            <label class="w3-text-teal"><b>{{ form.chemo_radius_mm.label }}</b></label>
-                            {{ form.chemo_radius_mm }}
-                            {% if form.chemo_radius_mm.errors %}
-                            <span class="w3-text-red w3-small">{{ form.chemo_radius_mm.errors|join:", " }}</span>
-                            {% endif %}
-                        </div>
-
-                    </div>
-                </div>
-            </div>
-
-            <!-- --- Interactions inter-individus --- -->
-            <div class="w3-container w3-padding-16">
-                <button type="button" class="w3-button w3-block w3-left-align w3-hover-light-grey"
-                        onclick="toggleSection('social')">
-                    <span class="w3-large">🔀</span>
-                    <b class="w3-margin-left">{% trans "Interactions inter-individus" %}</b>
-                    <span class="w3-small w3-text-grey w3-margin-left">
-                        {% trans "Évitement et agrégation" %}
-                    </span>
-                    <span id="social-icon" class="w3-right">▼</span>
-                </button>
-                <div id="social" class="w3-hide w3-padding-top">
-                    <div class="w3-row-padding">
-
-                        <div class="w3-col m6 s12 w3-margin-bottom">
-                            <label class="w3-text-teal"><b>{{ form.avoid_radius_mm.label }}</b></label>
-                            <p class="w3-small w3-text-grey" style="margin:0 0 4px;">{% trans "Rayon de répulsion courte portée (mm)" %}</p>
-                            {{ form.avoid_radius_mm }}
-                            {% if form.avoid_radius_mm.errors %}
-                            <span class="w3-text-red w3-small">{{ form.avoid_radius_mm.errors|join:", " }}</span>
-                            {% endif %}
-                        </div>
-
-                        <div class="w3-col m6 s12 w3-margin-bottom">
-                            <label class="w3-text-teal"><b>{{ form.aggreg_radius_mm.label }}</b></label>
-                            <p class="w3-small w3-text-grey" style="margin:0 0 4px;">{% trans "Rayon d'attraction longue portée — doit être > rayon évitement (mm)" %}</p>
-                            {{ form.aggreg_radius_mm }}
-                            {% if form.aggreg_radius_mm.errors %}
-                            <span class="w3-text-red w3-small">{{ form.aggreg_radius_mm.errors|join:", " }}</span>
-                            {% endif %}
-                        </div>
-
-                    </div>
-                </div>
-            </div>
-
-        </div><!-- fin card comportements -->
-
-        <!-- ============================================================
-             Boutons d'action
-        ============================================================ -->
-        <div class="w3-row-padding w3-margin-top">
-
-            <div class="w3-col m8 s12 w3-margin-bottom">
-                <button type="submit" class="w3-button w3-teal w3-round w3-large w3-padding-large">
-                    {% if object %}
-                        💾 {% trans "Enregistrer les modifications" %}
-                    {% else %}
-                        ➕ {% trans "Créer la configuration" %}
-                    {% endif %}
-                </button>
-                <a href="{% url 'planarian:experiment-list' %}"
-                   class="w3-button w3-light-grey w3-round w3-large w3-padding-large w3-margin-left">
-                    ✖ {% trans "Annuler" %}
-                </a>
-            </div>
-
-            {% if object %}
-            <div class="w3-col m4 s12 w3-right-align w3-margin-bottom">
-                <a href="{% url 'planarian:export-csv' %}?experiment={{ object.experiment }}&well={{ object.well }}"
-                   class="w3-button w3-blue w3-round w3-large w3-padding-large">
-                    📥 {% trans "Exporter CSV" %}
-                </a>
-            </div>
-            {% endif %}
-
-        </div>
-
-    </form><!-- fin form -->
-
-</div><!-- fin container -->
-
-<!-- ============================================================
-     Styles W3.CSS pour les champs de formulaire Django
-     (Django génère des <input> bruts sans classes — on les stylise ici)
-============================================================ -->
-<style>
-    /* Champs texte, number, select */
-    input[type="text"],
-    input[type="number"],
-    input[type="email"],
-    textarea,
-    select {
-        width: 100%;
-        padding: 8px 12px;
-        border: 1px solid #ccc;
-        border-radius: 4px;
-        font-size: 15px;
-        box-sizing: border-box;
-        margin-top: 2px;
-        background-color: #fafafa;
-        transition: border-color 0.2s;
-    }
-    input[type="text"]:focus,
-    input[type="number"]:focus,
-    textarea:focus,
-    select:focus {
-        border-color: #009688;  /* teal W3.CSS */
-        outline: none;
-        background-color: #fff;
-    }
-    /* Champ en erreur */
-    input.errorfield, select.errorfield, textarea.errorfield {
-        border-color: #f44336;
-        background-color: #fff8f8;
-    }
-    /* Label au-dessus du champ */
-    label {
-        display: block;
-        margin-bottom: 2px;
-        font-size: 14px;
-    }
-    /* Sections accordéon */
-    [id$="-icon"] {
-        transition: transform 0.2s;
-    }
-</style>
-
-<script>
-    /**
-     * Bascule la visibilité d'une section accordéon.
-     * @param {string} id - Identifiant de la section (sans le préfixe)
-     */
-    function toggleSection(id) {
-        const section = document.getElementById(id);
-        const icon    = document.getElementById(id + '-icon');
-        if (section.classList.contains('w3-hide')) {
-            section.classList.remove('w3-hide');
-            if (icon) icon.textContent = '▲';
-        } else {
-            section.classList.add('w3-hide');
-            if (icon) icon.textContent = '▼';
-        }
-    }
-
-    /* Ouvrir automatiquement les sections qui contiennent des erreurs */
-    document.addEventListener('DOMContentLoaded', function () {
-        ['thigmo', 'photo', 'chemo', 'social'].forEach(function (id) {
-            const section = document.getElementById(id);
-            if (section && section.querySelector('.w3-text-red')) {
-                section.classList.remove('w3-hide');
-                const icon = document.getElementById(id + '-icon');
-                if (icon) icon.textContent = '▲';
-            }
-        });
-    });
-</script>
-
-{% endblock %}

test_tube_scanner/planarian/templates/planarian/experiment_list.html

@@ -1,334 +0,0 @@
-{% extends "base.html" %}
-{% load i18n %}
-
-{% block content %}
-
-<div class="w3-container w3-padding-32" style="max-width:1200px; margin:auto;">
-
-    <!-- En-tête -->
-    <div class="w3-panel w3-teal w3-round-large w3-padding-16 w3-margin-bottom">
-        <div class="w3-row">
-            <div class="w3-col s12 m8 w3-bar-item">
-                <span class="w3-xlarge">
-                    <i class="w3-margin-right">🔬</i>
-                    {% trans "Configurations d'expériences" %}
-                </span>
-            </div>
-            <div class="w3-col s12 m4 w3-bar-item w3-right-align" style="padding-top:6px;">
-                <a href="{% url 'planarian:experiment-new' %}"
-                   class="w3-button w3-white w3-round w3-text-teal">
-                    ➕ {% trans "Nouvelle configuration" %}
-                </a>
-            </div>
-        </div>
-    </div>
-
-    <!-- Messages Django -->
-    {% for message in messages %}
-    <div class="w3-panel w3-round
-        {% if message.tags == 'success' %}w3-green
-        {% elif message.tags == 'error'   %}w3-red
-        {% elif message.tags == 'warning' %}w3-orange
-        {% else %}w3-blue{% endif %}">
-        <p>{{ message }}</p>
-    </div>
-    {% endfor %}
-
-    <!-- Barre d'outils : recherche + import -->
-    <div class="w3-row-padding w3-margin-bottom">
-
-        <!-- Recherche côté client -->
-        <div class="w3-col m7 s12 w3-margin-bottom">
-            <div class="w3-border w3-round" style="display:flex; align-items:center; background:#fafafa;">
-                <span style="padding:0 10px; font-size:18px; color:#888;">🔍</span>
-                <input type="text" id="search-input"
-                       placeholder="{% trans 'Filtrer par expérience, puits…' %}"
-                       class="w3-input w3-border-0"
-                       style="background:transparent;"
-                       oninput="filterTable(this.value)">
-            </div>
-        </div>
-
-        <!-- Boutons import / export -->
-        <div class="w3-col m5 s12 w3-right-align w3-margin-bottom">
-            <a href="{% url 'planarian:import-params' %}"
-               class="w3-button w3-blue-grey w3-round w3-margin-right">
-                📂 {% trans "Importer CSV" %}
-            </a>
-            <a href="{% url 'planarian:export-csv' %}"
-               class="w3-button w3-blue w3-round">
-                📥 {% trans "Exporter CSV" %}
-            </a>
-        </div>
-
-    </div>
-
-    <!-- ============================================================
-         Tableau des configurations
-    ============================================================ -->
-    {% if configs %}
-
-    <!-- Compteur -->
-    <p class="w3-text-grey w3-small" id="row-count">
-        {{ configs|length }} {% trans "configuration(s)" %}
-    </p>
-
-    <div class="w3-responsive w3-card-4 w3-round-large">
-        <table class="w3-table w3-striped w3-hoverable w3-bordered" id="config-table">
-            <thead>
-                <tr class="w3-teal">
-                    <th onclick="sortTable(0)" class="sortable" title="{% trans 'Trier' %}">
-                        {% trans "Expérience" %} <span class="sort-icon">↕</span>
-                    </th>
-                    <th onclick="sortTable(1)" class="sortable" title="{% trans 'Trier' %}">
-                        {% trans "Puits" %} <span class="sort-icon">↕</span>
-                    </th>
-                    <th onclick="sortTable(2)" class="sortable w3-hide-small" title="{% trans 'Trier' %}">
-                        {% trans "px/mm" %} <span class="sort-icon">↕</span>
-                    </th>
-                    <th class="w3-hide-small">{% trans "FPS" %}</th>
-                    <th class="w3-hide-small">{% trans "Seuils (mm/s)" %}</th>
-                    <th class="w3-hide-small">{% trans "Comportements" %}</th>
-                    <th onclick="sortTable(6)" class="sortable w3-hide-small" title="{% trans 'Trier' %}">
-                        {% trans "Créé le" %} <span class="sort-icon">↕</span>
-                    </th>
-                    <th>{% trans "Actions" %}</th>
-                </tr>
-            </thead>
-            <tbody id="config-tbody">
-                {% for cfg in configs %}
-                <tr class="config-row">
-
-                    <!-- Expérience -->
-                    <td>
-                        <b>{{ cfg.experiment }}</b>
-                        {% if cfg.description %}
-                        <br><span class="w3-small w3-text-grey">{{ cfg.description|truncatechars:40 }}</span>
-                        {% endif %}
-                    </td>
-
-                    <!-- Puits -->
-                    <td>
-                        <span class="w3-tag w3-teal w3-round">{{ cfg.well }}</span>
-                    </td>
-
-                    <!-- px/mm -->
-                    <td class="w3-hide-small">{{ cfg.px_per_mm }}</td>
-
-                    <!-- FPS -->
-                    <td class="w3-hide-small">{{ cfg.fps }}</td>
-
-                    <!-- Seuils de mobilité -->
-                    <td class="w3-hide-small">
-                        <span class="w3-tag w3-red w3-round w3-small"
-                              title="{% trans 'Immobile' %}">
-                            &lt; {{ cfg.thresh_immobile }}
-                        </span>
-                        <span class="w3-tag w3-orange w3-round w3-small"
-                              title="{% trans 'Mobile' %}">
-                            &lt; {{ cfg.thresh_mobile }}
-                        </span>
-                    </td>
-
-                    <!-- Comportements actifs -->
-                    <td class="w3-hide-small">
-                        {% if cfg.thigmotaxis_wall_dist_mm > 0 %}
-                        <span class="w3-tag w3-blue-grey w3-round w3-small w3-margin-right"
-                              title="{% trans 'Thigmotactisme actif' %}">🫧</span>
-                        {% endif %}
-                        {% if cfg.photo_mode != 'none' and cfg.photo_strength > 0 %}
-                        <span class="w3-tag w3-yellow w3-round w3-small w3-margin-right"
-                              title="{% trans 'Phototactisme actif' %} ({{ cfg.photo_mode }})">💡</span>
-                        {% endif %}
-                        {% if cfg.chemo_strength > 0 %}
-                        <span class="w3-tag w3-green w3-round w3-small w3-margin-right"
-                              title="{% trans 'Chimiotactisme actif' %}">🍖</span>
-                        {% endif %}
-                        {% if cfg.avoid_radius_mm > 0 or cfg.aggreg_radius_mm > 0 %}
-                        <span class="w3-tag w3-purple w3-round w3-small"
-                              title="{% trans 'Interactions inter-individus' %}">🔀</span>
-                        {% endif %}
-                    </td>
-
-                    <!-- Date de création -->
-                    <td class="w3-hide-small w3-small w3-text-grey">
-                        {{ cfg.created_at|date:"d/m/Y H:i" }}
-                    </td>
-
-                    <!-- Actions -->
-                    <td style="white-space:nowrap;">
-                        <a href="{% url 'planarian:experiment-edit' cfg.pk %}"
-                           class="w3-button w3-small w3-teal w3-round"
-                           title="{% trans 'Modifier' %}">✏</a>
-                        <a href="{% url 'planarian:export-csv' %}?experiment={{ cfg.experiment }}&well={{ cfg.well }}"
-                           class="w3-button w3-small w3-blue w3-round"
-                           title="{% trans 'Exporter CSV' %}">📥</a>
-                        <button type="button"
-                                class="w3-button w3-small w3-red w3-round"
-                                title="{% trans 'Supprimer' %}"
-                                onclick="confirmDelete('{{ cfg.pk }}', '{{ cfg.experiment }}', '{{ cfg.well }}')">
-                            🗑
-                        </button>
-                    </td>
-
-                </tr>
-                {% endfor %}
-            </tbody>
-        </table>
-    </div><!-- fin responsive -->
-
-    <!-- Message "aucun résultat" (filtrage JS) -->
-    <div id="no-results" class="w3-panel w3-pale-yellow w3-round w3-margin-top" style="display:none;">
-        <p>{% trans "Aucune configuration ne correspond à la recherche." %}</p>
-    </div>
-
-    {% else %}
-    <!-- Liste vide -->
-    <div class="w3-panel w3-pale-blue w3-round-large w3-padding-32" style="text-align:center;">
-        <p style="font-size:3rem; margin:0;">🔬</p>
-        <h3>{% trans "Aucune configuration pour l'instant." %}</h3>
-        <p class="w3-text-grey">
-            {% trans "Créez une première configuration ou importez un fichier CSV." %}
-        </p>
-        <a href="{% url 'planarian:experiment-new' %}"
-           class="w3-button w3-teal w3-round w3-large w3-margin-right">
-            ➕ {% trans "Nouvelle configuration" %}
-        </a>
-        <a href="{% url 'planarian:import-params' %}"
-           class="w3-button w3-blue-grey w3-round w3-large">
-            📂 {% trans "Importer CSV" %}
-        </a>
-    </div>
-    {% endif %}
-
-</div><!-- fin container -->
-
-<!-- ============================================================
-     Modal de confirmation de suppression
-============================================================ -->
-<div id="delete-modal" class="w3-modal">
-    <div class="w3-modal-content w3-round-large w3-card-4" style="max-width:420px; margin:auto; margin-top:10%;">
-        <header class="w3-container w3-red w3-round-top-large">
-            <h3 class="w3-text-white">🗑 {% trans "Confirmer la suppression" %}</h3>
-        </header>
-        <div class="w3-container w3-padding-24">
-            <p id="delete-msg"></p>
-            <form id="delete-form" method="post" action="">
-                {% csrf_token %}
-                <input type="hidden" name="_method" value="delete">
-                <button type="submit" class="w3-button w3-red w3-round w3-margin-right">
-                    🗑 {% trans "Supprimer" %}
-                </button>
-                <button type="button" class="w3-button w3-light-grey w3-round"
-                        onclick="document.getElementById('delete-modal').style.display='none'">
-                    ✖ {% trans "Annuler" %}
-                </button>
-            </form>
-        </div>
-    </div>
-</div>
-
-<!-- ============================================================
-     Styles
-============================================================ -->
-<style>
-    /* En-têtes de colonnes triables */
-    th.sortable {
-        cursor: pointer;
-        user-select: none;
-    }
-    th.sortable:hover {
-        background-color: #00796b;
-    }
-    .sort-icon {
-        font-size: 11px;
-        opacity: 0.7;
-        margin-left: 4px;
-    }
-    th.sort-asc  .sort-icon::after { content: " ▲"; opacity: 1; }
-    th.sort-desc .sort-icon::after { content: " ▼"; opacity: 1; }
-
-    /* Tableau responsive */
-    #config-table td, #config-table th {
-        vertical-align: middle;
-        padding: 10px 12px;
-    }
-</style>
-
-<!-- ============================================================
-     JavaScript : filtrage + tri + modal suppression
-============================================================ -->
-<script>
-    // --- Filtrage dynamique ---
-    function filterTable(query) {
-        const q      = query.toLowerCase().trim();
-        const rows   = document.querySelectorAll('.config-row');
-        const noRes  = document.getElementById('no-results');
-        const count  = document.getElementById('row-count');
-        let visible  = 0;
-
-        rows.forEach(function (row) {
-            const text = row.textContent.toLowerCase();
-            if (!q || text.includes(q)) {
-                row.style.display = '';
-                visible++;
-            } else {
-                row.style.display = 'none';
-            }
-        });
-
-        noRes.style.display = (visible === 0 && q) ? 'block' : 'none';
-        if (count) {
-            count.textContent = visible + ' {% trans "configuration(s)" %}';
-        }
-    }
-
-    // --- Tri de colonnes ---
-    let sortDir = {};
-
-    function sortTable(colIdx) {
-        const tbody = document.getElementById('config-tbody');
-        const rows  = Array.from(tbody.querySelectorAll('.config-row'));
-        const th    = document.querySelectorAll('#config-table thead th')[colIdx];
-
-        // Alterner ascendant / descendant
-        sortDir[colIdx] = sortDir[colIdx] === 'asc' ? 'desc' : 'asc';
-
-        // Réinitialiser les classes de toutes les colonnes
-        document.querySelectorAll('#config-table thead th').forEach(function (h) {
-            h.classList.remove('sort-asc', 'sort-desc');
-        });
-        th.classList.add(sortDir[colIdx] === 'asc' ? 'sort-asc' : 'sort-desc');
-
-        rows.sort(function (a, b) {
-            const cellA = a.querySelectorAll('td')[colIdx]?.textContent.trim() || '';
-            const cellB = b.querySelectorAll('td')[colIdx]?.textContent.trim() || '';
-            // Tri numérique si possible, sinon alphabétique
-            const numA  = parseFloat(cellA);
-            const numB  = parseFloat(cellB);
-            const cmp   = (!isNaN(numA) && !isNaN(numB))
-                ? numA - numB
-                : cellA.localeCompare(cellB, '{{ LANGUAGE_CODE|default:"fr" }}');
-            return sortDir[colIdx] === 'asc' ? cmp : -cmp;
-        });
-
-        rows.forEach(function (row) { tbody.appendChild(row); });
-    }
-
-    // --- Modal de suppression ---
-    function confirmDelete(pk, experiment, well) {
-        document.getElementById('delete-msg').textContent =
-            '{% trans "Supprimer la configuration" %} ' + experiment + ' / ' + well + ' ?';
-        document.getElementById('delete-form').action =
-            '{% url "planarian:experiment-list" %}' + pk + '/delete/';
-        document.getElementById('delete-modal').style.display = 'block';
-    }
-
-    // Fermer le modal en cliquant en dehors
-    window.onclick = function (e) {
-        const modal = document.getElementById('delete-modal');
-        if (e.target === modal) modal.style.display = 'none';
-    };
-</script>
-
-{% endblock %}

test_tube_scanner/planarian/templates/planarian/export_csv.html

@@ -1,38 +1,10 @@
-{% extends "base.html" %}
+{% extends "planarian/base.html" %}
 {% load i18n %}
 
 {% block content %}
-
-<div class="w3-container w3-padding-32" style="max-width:760px; margin:auto;">
-
-    <!-- En-tête -->
-    <div class="w3-panel w3-blue w3-round-large w3-padding-16 w3-margin-bottom">
-        <div class="w3-row">
-            <div class="w3-col s12 m8 w3-bar-item">
-                <span class="w3-xlarge">
-                    📥 {% trans "Exporter les données vers CSV" %}
-                </span>
-            </div>
-            <div class="w3-col s12 m4 w3-bar-item w3-right-align" style="padding-top:6px;">
-                <a href="{% url 'planarian:experiment-list' %}"
-                   class="w3-button w3-white w3-round w3-text-blue">
-                    ← {% trans "Retour à la liste" %}
-                </a>
-            </div>
-        </div>
-    </div>
-
-    <!-- Messages Django -->
-    {% for message in messages %}
-    <div class="w3-panel w3-round
-        {% if message.tags == 'success' %}w3-green
-        {% elif message.tags == 'error'   %}w3-red
-        {% elif message.tags == 'warning' %}w3-orange
-        {% else %}w3-blue{% endif %}">
-        <p>{{ message }}</p>
-    </div>
-    {% endfor %}
-
+<div class="w3-container w3-padding" style="max-width:760px; margin:auto;">
+{% if current_session and current_experiment %}
+    {% include "inc/alert.html" %}
     <!-- Explication -->
     <div class="w3-panel w3-pale-blue w3-round w3-margin-bottom">
         <p>
@@ -43,104 +15,54 @@
             {% trans "Colonnes exportées compatibles EthoVision XT : distance, vitesse, états de mobilité, thigmotactisme." %}
         </p>
     </div>
-
     <!-- Formulaire -->
     <form method="post" novalidate>
         {% csrf_token %}
+        <input type="hidden" id="_sid" name="_sid" value="{{ current_session.id }}">
+        <input type="hidden" id="_expid" name="_expid" value="{{ current_experiment.id }}">
         
-        {% if form.non_field_errors %}
-        <div class="w3-panel w3-red w3-round">
-            {% for error in form.non_field_errors %}
-            <p>⚠ {{ error }}</p>
-            {% endfor %}
-        </div>
-        {% endif %}
         
-        <div class="w3-card-4 w3-round-large">
-            <header class="w3-container w3-blue w3-round-top-large">
+        <div class="w3-card-4 w3-border w3-round w3-round-large">
+            <header class="w3-container w3-blue w3-round w3-round-top-large">
                 <h3 class="w3-text-white">{% trans "Paramètres d'export" %}</h3>
             </header>
             <div class="w3-container w3-padding-24">
-
                 <!-- Ligne 1 : expérience + puits -->
                 <div class="w3-row-padding w3-margin-bottom">
 
                     <div class="w3-col m7 s12 w3-margin-bottom">
-                        <label class="w3-text-blue"><b>{{ form.experiment.label }}</b></label>
-                        {% if form.experiment.help_text %}
-                        <p class="w3-small w3-text-grey" style="margin:0 0 4px;">{{ form.experiment.help_text }}</p>
-                        {% endif %}
-                        <!-- Saisie libre ou sélection depuis les configs existantes -->
-                        <input list="experiment-list" name="experiment" id="id_experiment"
-                               value="{{ form.experiment.value|default:'' }}"
-                               class="w3-input w3-border w3-round"
-                               placeholder="{% trans 'Ex : exp_2026_04_25' %}">
-                        <datalist id="experiment-list">
-                            {% for cfg in experiment_choices %}
-                            <option value="{{ cfg }}">
-                            {% endfor %}
-                        </datalist>
-                        {% if form.experiment.errors %}
-                        <span class="w3-text-red w3-small">{{ form.experiment.errors|join:", " }}</span>
-                        {% endif %}
+                        <label class="w3-text-blue"><b>{% trans "Expérience" %}</b></label>
+                        <input type="text" name="experiment" value="{{ current_experiment.identifier }}" readonly/>
                     </div>
-
                     <div class="w3-col m5 s12 w3-margin-bottom">
-                        <label class="w3-text-blue"><b>{{ form.well.label }}</b></label>
-                        <input list="well-list" name="well" id="id_well"
-                               value="{{ form.well.value|default:'' }}"
-                               class="w3-input w3-border w3-round"
-                               placeholder="{% trans 'Ex : A1' %}">
-                        <datalist id="well-list">
-                            {% for w in well_choices %}
-                            <option value="{{ w }}">
+                        <label class="w3-text-blue"><b>{% trans "Puits" %}</b></label>
+                        <select name="well">
+                            {% for well in well_choices %}
+                            <option value="{{ well.name }}">{{ well.name }}</option>
                             {% endfor %}
-                        </datalist>
-                        {% if form.well.errors %}
-                        <span class="w3-text-red w3-small">{{ form.well.errors|join:", " }}</span>
-                        {% endif %}
+                        </select>
                     </div>
-
                 </div>
-
                 <!-- Ligne 2 : planaire + type d'enregistrement -->
                 <div class="w3-row-padding w3-margin-bottom">
-
                     <div class="w3-col m4 s12 w3-margin-bottom">
-                        <label class="w3-text-blue"><b>{{ form.planarian.label }}</b></label>
-                        <p class="w3-small w3-text-grey" style="margin:0 0 4px;">
+                        <label class="w3-text-blue"><b>{% trans "Index planaire" %}</b></label>        
+                        <p class="w3-small w3-text-light-grey" style="margin:0 0 4px;">
                             {% trans "Index du planaire dans le puits (commence à 0)" %}
                         </p>
-                        {{ form.planarian }}
-                        {% if form.planarian.errors %}
-                        <span class="w3-text-red w3-small">{{ form.planarian.errors|join:", " }}</span>
-                        {% endif %}
+                        <input type="number" name="planarian" step="1"  min="0" max="20" value="{{ planarian }}" />
                     </div>
-
                     <div class="w3-col m8 s12 w3-margin-bottom">
-                        <label class="w3-text-blue"><b>{{ form.record_type.label }}</b></label>
-                        <p class="w3-small w3-text-grey" style="margin:0 0 4px;">
+                        <label class="w3-text-blue"><b>{% trans "Type d'enregistrement" %}</b></label>
+                        <p class="w3-small w3-text-light-grey" style="margin:0 0 4px;">
                             {% trans "Frame par frame : une ligne par image. Résumé : métriques agrégées de la session." %}
                         </p>
-                        <!-- Radio buttons stylisés W3 -->
-                        <div class="w3-row-padding" style="margin-top:6px;">
-                            {% for radio in form.record_type %}
-                            <div class="w3-col m6 s12">
-                                <label class="w3-button w3-block w3-round w3-border
-                                    {% if radio.data.value == form.record_type.value %}w3-blue w3-text-white{% else %}w3-white{% endif %}"
-                                    style="text-align:center; margin-bottom:6px; cursor:pointer;">
-                                    {{ radio.tag }} {{ radio.choice_label }}
-                                </label>
+                        <select name="record_type">
+                            <option value="frame">{% trans "Frame par frame" %}</option>
+                            <option value="summary">{% trans "Résumé" %}</option>
+                        </select>                       
                     </div>
-                            {% endfor %}
                 </div>
-                        {% if form.record_type.errors %}
-                        <span class="w3-text-red w3-small">{{ form.record_type.errors|join:", " }}</span>
-                        {% endif %}
-                    </div>
-
-                </div>
-
                 <!-- Ligne 3 : plage temporelle (optionnel) -->
                 <div class="w3-border-top w3-padding-top w3-margin-top">
                     <p class="w3-text-blue-grey">
@@ -150,36 +72,26 @@
                         </span>
                     </p>
                     <div class="w3-row-padding">
-
                         <div class="w3-col m6 s12 w3-margin-bottom">
-                            <label class="w3-text-blue-grey">{{ form.start_dt.label }}</label>
-                            {{ form.start_dt }}
-                            {% if form.start_dt.errors %}
-                            <span class="w3-text-red w3-small">{{ form.start_dt.errors|join:", " }}</span>
-                            {% endif %}
+                            <label class="w3-text-blue-grey">{% trans "Début (UTC)" %}</label>
+                            <input type="datetime-local" class="datetime" name="start_dt">
                         </div>
-
                         <div class="w3-col m6 s12 w3-margin-bottom">
-                            <label class="w3-text-blue-grey">{{ form.stop_dt.label }}</label>
-                            {{ form.stop_dt }}
-                            {% if form.stop_dt.errors %}
-                            <span class="w3-text-red w3-small">{{ form.stop_dt.errors|join:", " }}</span>
-                            {% endif %}
-                        </div>
-
+                            <label class="w3-text-blue-grey">{% trans "Fin (UTC)" %}</label>
+                            <input type="datetime-local" class="datetime" name="stop_dt">
+                        </div>
                     </div>
                 </div>
-
             </div><!-- fin padding -->
         </div><!-- fin card -->
 
         <!-- Boutons -->
         <div class="w3-row-padding w3-margin-top">
             <div class="w3-col s12">
-                <button type="submit" class="w3-button w3-blue w3-round w3-large w3-padding-large">
+                <button type="submit" name="valid" class="w3-button w3-blue w3-large w3-padding-large" value="ok">
                     📥 {% trans "Générer et télécharger le CSV" %}
                 </button>
-                <a href="{% url 'planarian:experiment-list' %}"
+                <a href="/"
                    class="w3-button w3-light-grey w3-round w3-large w3-padding-large w3-margin-left">
                     ✖ {% trans "Annuler" %}
                 </a>
@@ -187,10 +99,9 @@
         </div>
 
     </form>
-
     <!-- Rappel des colonnes exportées -->
-    <div class="w3-card w3-round-large w3-margin-top">
-        <header class="w3-container w3-blue-grey w3-round-top-large">
+    <div class="w3-card w3-round-large w3-margin-top w3-border w3-round w3-round-large w3-margin-bottom">
+        <header class="w3-container w3-blue-grey w3-round w3-round-top-large">
             <h4 class="w3-text-white" style="margin:8px 0;">
                 {% trans "Colonnes du fichier CSV exporté" %}
             </h4>
@@ -223,9 +134,7 @@
             </div>
         </div>
     </div>
-
 </div><!-- fin container -->
-
 <style>
     input[type="text"],
     input[type="number"],
@@ -245,10 +154,25 @@
         outline: none;
         background-color: #fff;
     }
-    /* Masquer le radio natif, laisser le label stylisé */
-    .w3-button input[type="radio"] {
-        display: none;
-    }
 </style>
-
+{% else %}
+<div class="w3-container w3-padding-64" style="max-width:760px; margin:auto;">
+    <h3 class="w3-panel w3-blue w3-round-xlarge w3-padding-64 w3-center"> {% trans "Choisir une session" %}</h3>
+</div>
+{% endif %}
 {% endblock %}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

test_tube_scanner/planarian/templates/planarian/import_params.html

@@ -1,55 +1,25 @@
-{% extends "base.html" %}
+{% extends "planarian/base.html" %}
 {% load i18n %}
-
+{% block export_csv %}{% endblock %}
 {% block content %}
-
 <div class="w3-container w3-padding-32" style="max-width:760px; margin:auto;">
-
-    <!-- En-tête -->
-    <div class="w3-panel w3-blue-grey w3-round-large w3-padding-16 w3-margin-bottom">
-        <div class="w3-row">
-            <div class="w3-col s12 m8 w3-bar-item">
-                <span class="w3-xlarge">
-                    📂 {% trans "Importer des configurations depuis CSV" %}
-                </span>
-            </div>
-            <div class="w3-col s12 m4 w3-bar-item w3-right-align" style="padding-top:6px;">
-                <a href="{% url 'planarian:experiment-list' %}"
-                   class="w3-button w3-white w3-round w3-text-blue-grey">
-                    ← {% trans "Retour à la liste" %}
-                </a>
-            </div>
-        </div>
-    </div>
-
-    <!-- Messages Django -->
-    {% for message in messages %}
-    <div class="w3-panel w3-round
-        {% if message.tags == 'success' %}w3-green
-        {% elif message.tags == 'error'   %}w3-red
-        {% elif message.tags == 'warning' %}w3-orange
-        {% else %}w3-blue{% endif %}">
-        <p>{{ message }}</p>
-    </div>
-    {% endfor %}
+{% if current_session and current_experiment %}
+    {% include "inc/alert.html" %}
     
     <!-- Formulaire d'import -->
     <form method="post" enctype="multipart/form-data" novalidate id="import-form">
         {% csrf_token %}
+        <input type="hidden" id="_sid" name="_sid" value="{{ current_session.id }}">
+        <input type="hidden" id="_expid" name="_expid" value="{{ current_experiment.id }}">
          
-        {% if form.non_field_errors %}
-        <div class="w3-panel w3-red w3-round">
-            {% for error in form.non_field_errors %}
-            <p>⚠ {{ error }}</p>
-            {% endfor %}
-        </div>
-        {% endif %}
-
-        <div class="w3-card-4 w3-round-large w3-margin-bottom">
-            <header class="w3-container w3-blue-grey w3-round-top-large">
-                <h3 class="w3-text-white">{% trans "Fichier CSV à importer" %}</h3>
+        <div class="w3-card-4 w3-margin-bottom w3-border w3-round w3-round-large">
+            <header class="w3-container w3-blue-grey w3-round  w3-round-top-large">
+                <h3 class="w3-text-white">{% trans "Fichier CSV à importer" %}: <span class="w3-large w3-text-lime">{{ current_experiment }}</span></h3>
             </header>
             <div class="w3-container w3-padding-24">
+                <p class="w3-light-blue w3-padding w3-border w3-round" style="margin:0 0 4px;">
+                    {% trans "Colonnes obligatoires : well, px_per_mm, fps." %}<br>
+                    {% trans "Toutes les autres colonnes sont optionnelles." %}
             
                 <!-- Zone de dépôt de fichier -->
                 <div id="drop-zone"
@@ -68,22 +38,12 @@
                             {% trans "ou cliquez pour sélectionner" %}
                         </span>
                     </p>
-
                     <!-- Input fichier caché -->
                     <input type="file" id="id_csv_file" name="csv_file"
                            accept=".csv,text/csv"
                            style="display:none;"
                            onchange="fileSelected(this)">
                 </div>
-
-                {% if form.csv_file.errors %}
-                <div class="w3-panel w3-red w3-round w3-margin-top">
-                    {% for error in form.csv_file.errors %}
-                    <p>⚠ {{ error }}</p>
-                    {% endfor %}
-                </div>
-                {% endif %}
-
                 <!-- Aperçu du fichier sélectionné -->
                 <div id="file-info" class="w3-panel w3-pale-green w3-round w3-margin-top" style="display:none;">
                     <p id="file-name" class="w3-text-green"><b></b></p>
@@ -93,44 +53,37 @@
                 <!-- Option : écraser -->
                 <div class="w3-margin-top w3-padding-top w3-border-top">
                     <label class="w3-text-blue-grey" style="cursor:pointer; display:flex; align-items:center; gap:10px;">
-                        {{ form.overwrite }}
+                        <input type="checkbox" name="overwriteoverwrite" class="w3-check" value="1" />
                         <span>
-                            <b>{{ form.overwrite.label }}</b><br>
+                            <b>{% trans "Écraser les configurations existantes" %}</b><br>
                             <span class="w3-small w3-text-grey">
                                 {% trans "Si décoché, les configurations déjà existantes (même experiment + well) seront ignorées." %}
                             </span>
                         </span>
                     </label>
-                    {% if form.overwrite.errors %}
-                    <span class="w3-text-red w3-small">{{ form.overwrite.errors|join:", " }}</span>
-                    {% endif %}
-                </div>
-
                 </div>
             </div>
-
+        </div>
         <!-- Boutons -->
         <div class="w3-row-padding w3-margin-bottom">
             <div class="w3-col s12">
-                <button type="submit" id="submit-btn"
+                <button type="submit" id="submit-btn" name="valid" value="ok"
                         class="w3-button w3-blue-grey w3-round w3-large w3-padding-large"
                         disabled>
                     📂 {% trans "Importer" %}
                 </button>
-                <a href="{% url 'planarian:experiment-list' %}"
+                <a href="/"
                    class="w3-button w3-light-grey w3-round w3-large w3-padding-large w3-margin-left">
                     ✖ {% trans "Annuler" %}
                 </a>
             </div>
         </div>
-
     </form>
-
     <!-- ============================================================
          Format attendu du CSV
     ============================================================ -->
-    <div class="w3-card-4 w3-round-large">
-        <header class="w3-container w3-teal w3-round-top-large">
+    <div class="w3-card-4 w3-round-large w3-border w3-round w3-round-large">
+        <header class="w3-container w3-teal w3-round w3-round-top-large">
             <h3 class="w3-text-white">{% trans "Format du fichier CSV" %}</h3>
         </header>
         <div class="w3-container w3-padding-24">
@@ -191,42 +144,30 @@
                     </thead>
                     <tbody>
                         <tr><td><code>well_radius_mm</code></td>    <td>8.0</td>       <td>{% trans "Rayon du puits (mm)" %}</td></tr>
-                        <tr><td><code>thresh_immobile</code></td>   <td>0.2</td>       <td>{% trans "Seuil Immobile EthoVision (mm/s)" %}</td></tr>
+                        <tr class="w3-grey"><td><code>thresh_immobile</code></td>   <td>0.2</td>       <td>{% trans "Seuil Immobile EthoVision (mm/s)" %}</td></tr>
                         <tr><td><code>thresh_mobile</code></td>     <td>1.5</td>       <td>{% trans "Seuil Mobile EthoVision (mm/s)" %}</td></tr>
-                        <tr><td><code>tube_axis</code></td>         <td>vertical</td>  <td>{% trans "Axe du tube : vertical | horizontal" %}</td></tr>
+                        <tr class="w3-grey"><td><code>tube_axis</code></td>         <td>vertical</td>  <td>{% trans "Axe du tube : vertical | horizontal" %}</td></tr>
                         <tr><td><code>min_area_px</code></td>       <td>20</td>        <td>{% trans "Surface min de détection (px²)" %}</td></tr>
-                        <tr><td><code>planarian_count</code></td>   <td>1</td>         <td>{% trans "Nombre de planaires par puits" %}</td></tr>
+                        <tr class="w3-grey"><td><code>planarian_count</code></td>   <td>1</td>         <td>{% trans "Nombre de planaires par puits" %}</td></tr>
                         <tr><td><code>photo_mode</code></td>        <td>none</td>      <td>{% trans "Phototactisme : none | fixed | sine | radial" %}</td></tr>
-                        <tr><td><code>photo_strength</code></td>    <td>0.0</td>       <td>{% trans "Intensité phototactisme (0-1)" %}</td></tr>
+                        <tr class="w3-grey"><td><code>photo_strength</code></td>    <td>0.0</td>       <td>{% trans "Intensité phototactisme (0-1)" %}</td></tr>
                         <tr><td><code>chemo_strength</code></td>    <td>0.0</td>       <td>{% trans "Intensité chimiotactisme (0-1)" %}</td></tr>
-                        <tr><td><code>chemo_radius_mm</code></td>   <td>2.0</td>       <td>{% trans "Rayon zone nourriture (mm)" %}</td></tr>
+                        <tr class="w3-grey"><td><code>chemo_radius_mm</code></td>   <td>2.0</td>       <td>{% trans "Rayon zone nourriture (mm)" %}</td></tr>
                         <tr><td><code>avoid_radius_mm</code></td>   <td>3.0</td>       <td>{% trans "Rayon évitement inter-individus (mm)" %}</td></tr>
-                        <tr><td><code>aggreg_radius_mm</code></td>  <td>6.0</td>       <td>{% trans "Rayon agrégation inter-individus (mm)" %}</td></tr>
+                        <tr class="w3-grey"><td><code>aggreg_radius_mm</code></td>  <td>6.0</td>       <td>{% trans "Rayon agrégation inter-individus (mm)" %}</td></tr>
                     </tbody>
                 </table>
             </div>
 
             <!-- Exemple de fichier -->
             <p><b>{% trans "Exemple minimal" %}</b></p>
-            <div class="w3-code w3-round" style="font-size:12px; overflow-x:auto;">
+            <div class="w3-code w3-round w3-text-grey" style="font-size:12px; overflow-x:auto;">
 experiment,well,px_per_mm,fps,thresh_immobile,thresh_mobile,photo_mode<br>
 exp_ctrl_01,A1,26.25,10,0.2,1.5,none<br>
 exp_ctrl_01,A2,26.25,10,0.2,1.5,none<br>
 exp_light_01,B1,26.25,10,0.2,1.5,fixed<br>
 exp_light_01,B2,26.25,10,0.2,1.5,fixed<br>
             </div>
-
-            <!-- Téléchargement du template -->
-            <div class="w3-margin-top">
-                <a href="{% url 'planarian:experiment-list' %}?export_template=1"
-                   class="w3-button w3-teal w3-round w3-small">
-                    ⬇ {% trans "Télécharger un template CSV vide" %}
-                </a>
-                <span class="w3-small w3-text-grey w3-margin-left">
-                    {% trans "Ou exportez vos configurations existantes depuis l'admin Django." %}
-                </span>
-            </div>
-
         </div>
     </div>
 
@@ -322,5 +263,9 @@ exp_light_01,B2,26.25,10,0.2,1.5,fixed<br>
         return (bytes / 1048576).toFixed(1) + ' MB';
     }
 </script>
-
+{% else %}
+<div class="w3-container w3-padding-64 w3-margin" style="max-width:760px; margin:auto;">
+    <h3 class="w3-panel w3-blue w3-round-xlarge w3-padding-64 w3-center"> {% trans "Choisir une session" %}<br>{% trans "Puis une expérience." %}</h3>
+</div>
+{% endif %}
 {% endblock %}

test_tube_scanner/planarian/urls.py

@@ -6,16 +6,12 @@ from planarian import views
 app_name = "planarian"
 
 urlpatterns = [
-    # Configurations expériences
-    path("experiments/",         views.ExperimentConfigListView.as_view(), name="experiment-list"),
-    path("experiments/new/",     views.ExperimentConfigFormView.as_view(), name="experiment-new"),
-    path("experiments/<int:pk>/",views.ExperimentConfigFormView.as_view(), name="experiment-edit"),
-
     # Import / export   
-    path("import/",              views.ImportParamsView.as_view(),         name="import-params"),
-    path("export/",              views.ExportCsvView.as_view(),            name="export-csv"),
-
+    path("import/csv/",     views.import_csv_view,              name="import-params"),
+    path("export/csv/",     views.export_csv_view,              name="export-csv"),
+    path("api/export/csv/", views.export_metrics,               name="api-export-csv"),
     # API JSON pour le front-end
     path("api/tracking/",   views.TrackingDataView.as_view(),   name="tracking-data-api"),
+    
 ]
 

test_tube_scanner/planarian/views.py

@@ -2,89 +2,154 @@
 
 #import asyncio
 import logging
-
+import csv
+import io
+import json
 from asgiref.sync import async_to_sync
 from django.conf import settings
 from django.contrib import messages
-from django.http import HttpResponse, JsonResponse
-from django.shortcuts import get_object_or_404, redirect    #, render
+from django.http import JsonResponse, FileResponse
+from django.shortcuts import redirect
 from django.utils.translation import gettext_lazy as _
+from django.shortcuts import render #, redirect
+from django.views.decorators.http import require_GET
+from django.contrib.auth.decorators import login_required
 from django.views import View
-from django.views.generic import FormView, ListView
 
-
-from .forms import CsvImportForm, ExperimentConfigForm, ExportCsvForm
-from .models import ExperimentConfig
 from modules.planarian_metrics import ExperimentParams, ReductStoreClient
+from modules.system_stats import get_cached_stats, start_background_updater
+from scanner.constants import ScannerConstants
+
+from .tasks import export_experiment_metrics_task, export_session_metrics_task
+from .export_service import export_csv_sync
+from scanner import models, views as scanner_views
+from .models import ExperimentConfig
 
 
 logger = logging.getLogger(__name__)
+start_background_updater()
+
+
+def is_staff_or_admin(user):
+    return user.is_staff or user.is_superuser   
+
+
+@require_GET
+def stats_view(request):
+    """
+    Retourne tout le cache (shm, cpu_info, memory_info, disk_info, updated_at)
+    """
+    try:
+        data = get_cached_stats()
+        return JsonResponse(data, safe=False)
+    except Exception as e:
+        return JsonResponse({"error": str(e)}, status=500)
 
 
 def _get_reduct_client() -> ReductStoreClient:
     """Instancie le client ReductStore depuis les settings Django."""
-    return ReductStoreClient(
-        url    = getattr(settings, "REDUCTSTORE_URL",    "http://localhost:8383"),
-        token  = getattr(settings, "REDUCTSTORE_TOKEN",  ""),
-        bucket = getattr(settings, "REDUCTSTORE_BUCKET", "planarian_metrics"),
+    return ReductStoreClient(url=settings.REDUCTSTORE_URL, token=settings.REDUCTSTORE_TOKEN)
+
+
+def global_context(request, **ctx):
+    conf = ScannerConstants().get()
+    return dict(
+        app_title=settings.APP_TITLE,
+        app_sub_title=settings.APP_SUB_TITLE,
+        domain_server=settings.DOMAIN_SERVER,
+        local_ip_server=settings.LOCAL_IP_SERVER,
+        host_port=settings.SERVER_HOST_PORT,
+        export_csv_destination=settings.CSV_EXPORT_DIR,
+        conf=conf,
+        **ctx
     )
 
 
-# ---------------------------------------------------------------------------
-# Vue : liste des configurations
-# ---------------------------------------------------------------------------
-
-class ExperimentConfigListView(ListView):
-    """Liste toutes les configurations expériences."""
-
-    model               = ExperimentConfig
-    template_name       = "planarian/experiment_list.html"
-    context_object_name = "configs"
-    ordering            = ["-created_at"]
+def get_active_session(request, session_id=None, experiment_id=None):
+    cursid = session_id or request.POST.get('_sid')
+    expid = experiment_id or request.POST.get('_expid')
 
+    current_session = models.Session.get_session(cursid)
+    experiments, current_experiment = scanner_views.get_not_active_experiments(current_session, expid) 
+    context = dict(
+        current_session = current_session,
+        current_experiment = current_experiment,
+        experiments=experiments or [],
+        sessions=models.Session.objects.filter(active=False).all(),
+        well_choices=models.Well.objects.order_by('name').all(),
+    )
+    return context    
     
 # ---------------------------------------------------------------------------
-# Vue : création / modification d'une configuration
+# Vue :Export CSV depuis ReductStore
 # ---------------------------------------------------------------------------
+@login_required
+def export_metrics(request):
+    data = json.loads(request.body.decode() or "{}")
+    action = data.get("action")
+    pid = data.get("pid")
+    if action=='experiment_csv':    
+        experiment = models.Experiment.objects.filter(pk=pid).first()
+        if experiment:
+            export_experiment_metrics_task.delay(experiment.pk)  # @UndefinedVariable
+            return JsonResponse({"success":  True,  "msg": str(_("Métrics en cours de téléchargement"))})
+    if action=='session_csv':   
+        if pid:
+            export_session_metrics_task(pid)  # @UndefinedVariable
+            return JsonResponse({"success":  True,  "msg": str(_("Métrics en cours de téléchargement"))})
+    return JsonResponse({"success":  False,  "msg": str(_("Erreur: les métrics non pas été téléchargés"))})
 
-class ExperimentConfigFormView(FormView):
-    """Formulaire de saisie des paramètres d'une expérience."""
 
-    template_name = "planarian/experiment_form.html"
-    form_class    = ExperimentConfigForm
+@login_required
+def export_csv_view(request):   
+    session_context = get_active_session(request)
+    ctx = {
+        'choice_title': _("Export vers un fichier CSV depuis ReductStore"), 
+        'well': 'A1',
+        'planarian': "0",
+        'record_type': 'frame',        
+        **session_context
+    }    
+    if request.method == 'POST':
+        valid = request.POST.get('valid')       
+        session = session_context['current_session']
+        experiment = session_context['current_experiment']         
+        if valid == 'ok' and session and experiment:
+            well_name = request.POST.get('well')
+            uuid = models.get_uuid_from_session(session.pk, experiment.multiwell.position, well_name)  # type: ignore[union-attr]
+            '''
+            csv_content, filename = export_csv(request, uuid)
+            if csv_content:
+                response = FileResponse(csv_content, content_type="text/csv; charset=utf-8")
+                response["Content-Disposition"] = f'attachment; filename="{filename}"'
+                return response'''
+            csv_content, n = export_csv_sync(
+                experiment=experiment.identifier,  # type: ignore[union-attr]
+                well=well_name,
+                uuid=uuid,
+                planarian=request.POST.get("planarian"),
+                record_type=request.POST.get("record_type"),
+                start=request.POST.get("start_dt"),
+                stop=request.POST.get("stop_dt"),
+            )
+            if csv_content:
+                filename = (
+                    f"{experiment.identifier}_{well_name}-{request.POST.get('planarian')}_"  # type: ignore[union-attr]
+                    f"{request.POST.get('record_type')}.csv"
+                )
+                logger.info(f"Export CSV: {n} lignes, content size={len(csv_content)}")
+                response = FileResponse(csv_content, content_type="text/csv; charset=utf-8")
+                response["Content-Disposition"] = (f'attachment; filename="{filename}"')
+                return response
 
-    def get_form(self, form_class=None):
-        pk = self.kwargs.get("pk")
-        if pk:
-            instance = get_object_or_404(ExperimentConfig, pk=pk)
-            return ExperimentConfigForm(self.request.POST or None, instance=instance)
-        return ExperimentConfigForm(self.request.POST or None)
-
-    def form_valid(self, form):
-        form.save()
-        messages.success(self.request, _("Configuration sauvegardée."))
-        return redirect("planarian:experiment-list")
+            messages.warning(request, _("Aucune donnée trouvée."))
+    return render(request, "planarian/export_csv.html", context=global_context(request, **ctx))
 
 
 # ---------------------------------------------------------------------------
 # Vue : import CSV de paramètres
 # ---------------------------------------------------------------------------
-
-class ImportParamsView(FormView):
-    """
-    Import de configurations d'expérience depuis un fichier CSV.
-    Une ligne CSV = un puits = un ExperimentConfig.
-
-    Colonnes CSV obligatoires : experiment, well, px_per_mm, fps
-    Toutes les autres colonnes correspondent aux champs du modèle.
-    """
-
-    template_name = "planarian/import_params.html"
-    form_class    = CsvImportForm
-
-    def form_valid(self, form):
-        rows      = form.csv_rows
-        overwrite = form.cleaned_data["overwrite"]
+def import_csv(request, current_experiment, rows, overwrite):
     created   = 0
     updated   = 0
     errors    = 0
@@ -95,13 +160,13 @@ class ImportParamsView(FormView):
             d      = params.to_dict()
           
             obj, is_new = ExperimentConfig.objects.get_or_create(
-                    experiment = d["experiment"],
-                    well       = d["well"],
+                experiment = current_experiment.identifier,
+                well       = d.get("well"),
             )
 
             if is_new or overwrite:
                 for k, v in d.items():
-                        if k not in ("experiment", "well") and hasattr(obj, k):
+                    if k not in ["well", "experiment", "author", "experiment_key", "active"] and hasattr(obj, k):
                         setattr(obj, k, v)              
                 obj.save()
                 if is_new:
@@ -112,68 +177,58 @@ class ImportParamsView(FormView):
         except Exception as e:
             logger.warning(f"Ligne ignorée ({row}): {e}")
             errors += 1
-
     messages.success(
-            self.request,
+        request,
         _("Import terminé : %(c)d créés, %(u)d mis à jour, %(e)d erreurs.")
         % {"c": created, "u": updated, "e": errors},
     )
-        return redirect("planarian:experiment-list")
+
+    return redirect("redirect_to_mainboard")
     
     
-# ---------------------------------------------------------------------------
-# Vue : export CSV depuis ReductStore
-# ---------------------------------------------------------------------------
-
-class ExportCsvView(FormView):
+@login_required
+def import_csv_view(request):  
     """
-    Export des données de tracking depuis ReductStore vers un fichier CSV.
-    Retourne le fichier en téléchargement HTTP.
+    Import de configurations d'expérience depuis un fichier CSV.
+    Une ligne CSV = un puits = un ExperimentConfig.
+
+    Colonnes CSV obligatoires: well, px_per_mm, fps
+    Toutes les autres colonnes correspondent aux champs du modèle.
     """
+    session_context = get_active_session(request)
+    if request.method == 'POST':
+        valid = request.POST.get('valid')
+        current_experiment = session_context.get('current_experiment')
         
-    template_name = "planarian/export_csv.html"
-    form_class    = ExportCsvForm
-
-    def form_valid(self, form):
-        d = form.cleaned_data
-
-        @async_to_sync
-        async def _do_export():
-            client = _get_reduct_client()
-            await client.connect()
+        if valid == 'ok' and current_experiment:
             try:
-                csv_content, n = await client.export_csv_response(
-                    experiment  = d["experiment"],
-                    well        = d["well"],
-                    planarian   = d["planarian"],
-                    record_type = d["record_type"],
-                    start       = d.get("start_dt"),
-                    stop        = d.get("stop_dt"),
-                )
-            finally:
-                await client.close()
-            return csv_content, n
+                f = request.FILES.get('csv_file')
+                overwrite = request.POST.get("overwrite")
+                try:
+                    content = f.read().decode("utf-8-sig")
+                    reader  = csv.DictReader(io.StringIO(content))
+                    rows    = list(reader)
+                except Exception as e:
+                    msg = f'Fichier CSV invalide : {e}'
+                    raise Exception(msg)
 
-        csv_content, n = _do_export()
-
-        if not csv_content:
-            messages.warning(self.request, _("Aucune donnée trouvée."))
-            return self.form_invalid(form)
-
-        filename = (
-            f"{d['experiment']}_{d['well']}_planaire{d['planarian']}"
-            f"_{d['record_type']}.csv"
-        )
-        response = HttpResponse(csv_content, content_type="text/csv; charset=utf-8")
-        response["Content-Disposition"] = f'attachment; filename="{filename}"'       
-        messages.success(self.request, _("%(n)d lignes exportées.") % {"n": n})
-        return response
+                required = {"well", "px_per_mm", "fps"}
+                if rows:
+                    missing = required - set(rows[0].keys())
+                    if missing:
+                        msg = _("Colonnes manquantes : %(cols)s") % {"cols": ", ".join(missing)}
+                        raise Exception(msg)
             
+                    return import_csv(request, current_experiment, rows, overwrite)
+            except Exception as e:
+                messages.error(request, e)
+                logger.error(e) 
+    ctx = { 'choice_title': _("Importer des configurations depuis un fichier CSV"), **session_context }
+    return render(request, "planarian/import_params.html", context=global_context(request, **ctx))    
 
 # ---------------------------------------------------------------------------
 # Vue API JSON : données de tracking (pour polling front-end)
 # ---------------------------------------------------------------------------
-
 class TrackingDataView(View):
     """
     API JSON retournant les métriques de tracking d'un planaire.
@@ -202,9 +257,13 @@ class TrackingDataView(View):
                     planarian   = planarian,
                     record_type = record_type,
                 )
-            finally:
-                await client.close()
+            except Exception as e:
+                logger.error(f"Erreur fetching tracking data: {e}")
 
         records = _fetch()
         return JsonResponse({"count": len(records), "records": records})
     
+    def get_context_data(self, **kwargs):
+        context = super().get_context_data(**kwargs)  # type: ignore[attr-defined]
+        return global_context(self.request, choice_title=str(_("Métriques de tracking d'un planaire")), **context)
+    

test_tube_scanner/run-server.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+echo "==== Starting server development in debug mode port 8000 ..."
+echo "===="
+../.venv/bin/python manage.py runserver 0.0.0.0:8000

test_tube_scanner/scanner/admin.py

@@ -1,8 +1,10 @@
+from pathlib import Path
+from django.utils.translation import gettext_lazy as _
+from django.utils.html import format_html
 from django.contrib import admin
 from django.db.models import Q
 from . import models
 
-
 class WellAdmin(admin.ModelAdmin):
     model = models.Well
     list_display = ('name', 'author',)
@@ -10,24 +12,74 @@ class WellAdmin(admin.ModelAdmin):
 class ConfigurationAdmin(admin.ModelAdmin):
     list_display = ('name', 'author', 'capture_type', 'video_width_capture', 'video_height_capture', 'video_frame_rate', 'active',)
     
+    
+    fieldsets = (
+        (_("Identification"), {
+            "fields": ("name", "author", "active"),
+        }),
+        (_("Dashboard"), {
+            "fields": ("sidebar_width", "default_grid_columns",),"classes": ("collapse",),
+        }),
+        (_("opencv"), {
+            "fields": ("opencv_fourcc_format", "opencv_video_type"),"classes": ("collapse",),
+        }),
+        (_("Grbl"), {
+            "fields": ("grbl_xmax", "grbl_ymax"),            
+            "classes": ("collapse",),
+        }),
+        (_("Camera"), {
+            "fields": ("scan_simulation", "capture_type", "webcam_device_index", "image_quality", "video_jpeg_quality", "video_frame_rate", "video_width_capture", "video_height_capture"),
+            "classes": ("collapse",),
+        }),
+        (_("Calibration / Balayage"), {
+            "fields": ("tube_axis", "calibration_crop_radius", "calibration_default_multiwell", "calibration_default_feed", "calibration_default_step", "calibration_default_duration"),
+            "classes": ("collapse",),
+        }),
+        (_("Tracking: valeurs par défaut"), {
+            "fields": ("tracking", "tracking_setting", "min_area_px", "max_area_ratio", "max_planarians", "merge_kernel_size", "min_contour_dist_px"),
+            "classes": ("collapse",),
+        }),
+
+    
+    )
+
 class MultiWellAdmin(admin.ModelAdmin):
     list_filter = ('author', )
-    list_display = ('label', 'position', 'author', 'order', 'xbase', 'ybase', 'duration', 'feed', 'default', 'well_position', 'active',)
+    list_display = ('label', 'position', 'author', 'order', 'xbase', 'ybase', 'duration', 'feed', 'default', 'well_position', 'capture_video', 'active',)
+    ordering = ('label', 'order')
+    fieldsets = (
+        (_("Identification"), {
+            "fields": ("label", "author", "position", "default", "capture_video", "active"),
+        }),
+        (_("Géométrie"), {
+            "fields": ("cols", "rows", "diameter", "crop_radius", "row_def", "row_order"),"classes": ("collapse",),
+        }),
+        (_("Déplacement"), {
+            "fields": ("order", "duration", "xbase", "ybase", "dx", "dy", "feed"),"classes": ("collapse",),
+        }),
+        (_("Positions générées"), {
+            "fields": ("well_position",),
+        }),
+
+    )
 
 class WellPositionAdmin(admin.ModelAdmin):
     list_filter = ('author', 'multiwell')
     list_display = ('multiwell__position', 'well__name', 'order', 'x', 'y', 'px_per_mm', 'author',)
   
   
-#class ExperimentConfigInline(admin.TabularInline):
-#    model = models.ExperimentConfig
-#    extra = 0
+class ExperimentWellInline(admin.TabularInline):
+    model = models.ExperimentWell
+    extra = 0
+    #ordering = ('experiment__multiwell__wellposition__order',)
+    
     
 class ExperimentAdmin(admin.ModelAdmin):
-    #inlines = (ExperimenConfigInline,)
+    inlines = (ExperimentWellInline, )
     list_filter = ('session_experiments__session', 'author', )
-    list_display = ('title', 'author',  'multiwell', 'created', 'started', 'finished')
-    readonly_fields = ('created',  'started',  'finished', )
+    list_display = ('title', 'author', 'identifier', 'duration',  'multiwell', 'created', 'started', 'finished')
+    readonly_fields = ('created', 'identifier',  'started',  'finished', )
+    
 
 class SessionExperimentInlineAdmin(admin.TabularInline):
     model = models.SessionExperiment
@@ -51,7 +103,7 @@ class SessionExperimentInlineAdmin(admin.TabularInline):
 class SessionAdmin(admin.ModelAdmin):
     list_filter = ('author',)
     inlines = (SessionExperimentInlineAdmin, )
-    list_display = ('name', 'author', 'created', 'finished', 'active', 'expected_export', 'expected_scanning', )
+    list_display = ('name', 'id', 'author', 'created', 'finished', 'active', 'expected_export', 'expected_scanning', )
     readonly_fields = (
         'created', 
         'finished',
@@ -63,6 +115,107 @@ class SessionAdmin(admin.ModelAdmin):
         'scanning_finished_at'
     )
 
+@admin.register(models.VideoPlate)
+class VideoPlateAdmin(admin.ModelAdmin):
+
+    list_display  = ['multiwell', 'label', 'video_filename', 'active',
+                     'fps_display', 'duration_display', 'resolution_display', 'uploaded_at']
+    list_filter   = ['multiwell', 'active']
+    list_editable = ['active']
+    readonly_fields = [
+        'native_fps', 'duration_s', 'frame_w', 'frame_h',
+        'uploaded_at', 'resolution_display', 'video_preview',
+    ]
+    fields = [
+        'multiwell', 'label', 'video_file', 'active', 'px_per_mm',
+        'x_origin_mm', 'y_origin_mm',
+        'video_preview',
+        'native_fps', 'duration_s', 'frame_w', 'frame_h', 'uploaded_at',
+    ]
+
+    class Media:
+        css = {'all': ('scanner/css/video_upload.css',)}
+        js  = ('scanner/js/video_upload.js',)
+
+    # ------------------------------------------------------------------
+    # Colonnes liste
+    # ------------------------------------------------------------------
+
+    @admin.display(description=_("Fichier"), ordering='video_file')
+    def video_filename(self, obj):
+        return obj.video_filename
+
+    @admin.display(description=_("FPS"))
+    def fps_display(self, obj):
+        return f"{obj.native_fps:.2f}" if obj.native_fps else "—"
+
+    @admin.display(description=_("Durée"))
+    def duration_display(self, obj):
+        if not obj.duration_s:
+            return "—"
+        m, s = divmod(int(obj.duration_s), 60)
+        return f"{m}:{s:02d}"
+
+    @admin.display(description=_("Résolution"))
+    def resolution_display(self, obj):
+        return obj.resolution
+
+    # ------------------------------------------------------------------
+    # Aperçu vidéo (readonly field)
+    # ------------------------------------------------------------------
+
+    @admin.display(description=_("Aperçu"))
+    def video_preview(self, obj):
+        if not obj.video_file:
+            return "—"
+        return format_html(
+            '<video src="{}" controls style="max-width:480px;max-height:320px;'
+            'border-radius:4px;"></video>',
+            obj.video_file.url,
+        )
+
+    # ------------------------------------------------------------------
+    # Sauvegarde : extraction des métadonnées
+    # ------------------------------------------------------------------
+
+    def save_model(self, request, obj, form, change):
+        super().save_model(request, obj, form, change)
+        if obj.video_file:
+            self._extract_metadata(obj)
+
+    def _extract_metadata(self, obj):
+        try:
+            import cv2
+            cap = cv2.VideoCapture(obj.video_file.path)
+            if cap.isOpened():
+                fps = cap.get(cv2.CAP_PROP_FPS)
+                fc  = cap.get(cv2.CAP_PROP_FRAME_COUNT)
+                models.VideoPlate.objects.filter(pk=obj.pk).update(
+                    native_fps = fps,
+                    duration_s = (fc / fps) if fps else None,
+                    frame_w    = int(cap.get(cv2.CAP_PROP_FRAME_WIDTH)),
+                    frame_h    = int(cap.get(cv2.CAP_PROP_FRAME_HEIGHT)),
+                )
+                cap.release()
+        except Exception:
+            pass
+
+    # ------------------------------------------------------------------
+    # Suppression : efface aussi le fichier physique
+    # ------------------------------------------------------------------
+
+    def delete_model(self, request, obj):
+        if obj.video_file:
+            Path(obj.video_file.path).unlink(missing_ok=True)
+        super().delete_model(request, obj)
+
+    def delete_queryset(self, request, queryset):
+        for obj in queryset:
+            if obj.video_file:
+                Path(obj.video_file.path).unlink(missing_ok=True)
+        super().delete_queryset(request, queryset)
+
+
 admin.site.register(models.Configuration, ConfigurationAdmin)
 admin.site.register(models.Well, WellAdmin)
 admin.site.register(models.MultiWell, MultiWellAdmin)

test_tube_scanner/scanner/constants.py

@@ -19,15 +19,23 @@ class DefaultConfig:
     webcam_device_index: int = 2
     image_quality: int = 90
     video_jpeg_quality: int = 90
-    video_frame_rate: int = 5.0
+    video_frame_rate: float = 5.0
     video_width_capture: int = 2028
     video_height_capture: int = 1520
+    scan_simulation: bool = False
     calibration_crop_radius: int = 500
     calibration_default_multiwell: str = 'HD'
     calibration_default_feed: int = 1000
     calibration_default_step: float = 1.0
     calibration_default_duration: float = 3.0
     tracking: bool = False 
+    tracking_setting: bool = False 
+    tube_axis: str = 'vertical'
+    min_area_px: int = 20
+    max_area_ratio: float = 0.10
+    max_planarians: int = 1
+    merge_kernel_size: int = 15
+    min_contour_dist_px: int = 40
    
     
 class ScannerConstants:
@@ -44,4 +52,12 @@ class ScannerConstants:
     def get(self):
         return self.conf
     
+    @classmethod
+    def get_config(cls):
+        return Configuration.objects.filter(active=True).first()
+    
+    def save_config(self):
+        d = asdict(self.conf)
+        Configuration.objects.filter(active=True).update(**d)
+    
     

test_tube_scanner/scanner/consumers.py

@@ -33,9 +33,6 @@ class ScannerConsumer(AsyncWebsocketConsumer):
         if msg_type in ["scanner", "calibrate"]:
             redisDB.publish(self.this_group, json.dumps(data))
 
-    async def replay_message(self, event):
-        await self.send(text_data=json.dumps(event["text"]))
-
 
 class ReplayConsumer(AsyncWebsocketConsumer):
 

test_tube_scanner/scanner/export_tasks.py

@@ -7,7 +7,7 @@ import posix_ipc
 import mmap
 import cv2
 import numpy as np
-from django.http import JsonResponse, HttpResponse
+#from django.http import JsonResponse, HttpResponse
 from django.conf import settings
 from reduct.time import unix_timestamp_to_iso
 
@@ -34,24 +34,20 @@ def delete_file_later(path):
 
 async def remove_video_by_uuid(uuid, start_ts=None, end_ts=None, when=None):
     record_manager = CameraRecordManager(cameraDB)
-    await record_manager.remove(uuid, start_ts, end_ts)
+    await record_manager.remove_uuid(uuid, start_ts, end_ts)
 
 
 async def remove_video(uuid, start_ts, end_ts, when=None):
-    try:
     await remove_video_by_uuid(uuid, start_ts, end_ts, when=when)
-        return JsonResponse({'state': 'ok'}, status=200)
-    except Exception as e:
-        return JsonResponse({'error': str(e)}, status=500)
-
 
 async def shm_download_video(uuid, start_ts, end_ts, frame_rate=5, opencv_fourcc_format='mp4v', opencv_video_type='mp4'):
+    video_path = os.path.join(settings.MEDIA_ROOT, f"output.{opencv_video_type}")
     try:        
         record_manager = CameraRecordManager(cameraDB)
         total_size = await record_manager.size(uuid, start_ts, end_ts)
 
         # segment de mémoire partagée pour stocker les frames
-        shm_size = int(total_size * 1.5)
+        shm_size = int((total_size or 0) * 1.5)
         shm_name = f"/video_frames_{uuid}"
         try:
             shm = posix_ipc.SharedMemory(shm_name, posix_ipc.O_CREAT | posix_ipc.O_EXCL, size=shm_size)
@@ -79,14 +75,16 @@ async def shm_download_video(uuid, start_ts, end_ts, frame_rate=5, opencv_fourcc
             total += 1
 
         if not frame_sizes:
-            return JsonResponse({'error': 'Aucune frame trouvée'}, status=404)
+            raise Exception("No frame found!")
+            #return JsonResponse({'error': 'Aucune frame trouvée'}, status=404)
 
-        video_path = os.path.join(settings.MEDIA_ROOT, f"output.{opencv_video_type}")
-        fourcc = cv2.VideoWriter_fourcc(* opencv_fourcc_format)
+        #video_path = os.path.join(settings.MEDIA_ROOT, f"output.{opencv_video_type}")
+        fourcc = cv2.VideoWriter_fourcc(*opencv_fourcc_format)  # type: ignore[attr-defined]
 
         # Lit les frames depuis la mémoire partagée
         current_offset = 0
         i = 0
+        video = None
         for size in frame_sizes:
             frame_bytes = mm[current_offset:current_offset + size]
             nparr = np.frombuffer(frame_bytes, np.uint8)
@@ -97,36 +95,17 @@ async def shm_download_video(uuid, start_ts, end_ts, frame_rate=5, opencv_fourcc
             video.write(frame)
             current_offset += size
             
-            progress_bar(i + 1, total, prefix=f'Progression {uuid}:', suffix='Terminé', length=30)
+            progress_bar(i + 1, total, prefix=f'Progress {uuid}:', suffix='Ended', length=30)
             i+=1
-            
+        if video:                        
             video.release()
 
         # Nettoie la mémoire partagée
         shm.unlink()
             
-        # Vérifier que le fichier existe
-        if not os.path.exists(video_path):
-            logger.error(f"Fichier non créé: {video_path}")
-            return JsonResponse({'error': 'Erreur création vidéo'}, status=500)
-
-        # Lit le fichier vidéo généré
-        with open(video_path, 'rb') as f:
-            video_bytes = f.read()
-
-        # Retourne la vidéo en réponse
-        response = HttpResponse(video_bytes, content_type='video/mp4')
-        response['Content-Disposition'] = f'attachment; filename="{video_path}"'
-        response['Content-Length'] = os.path.getsize(video_path)
-
-
-        # Supprime le fichier temporaire
-        os.remove(video_path)
-        return response
-
+        return { "status": 404, "success": True, "video_path": video_path}        
     except Exception as e:
-        logger.error(f"shm_download_video: {e}")
-        return JsonResponse({'error': str(e)}, status=500)
+        return {"status": 500, "success": False, "video_path": video_path, "error": str(e)}
 
 # ─────────────────────────────────────────────
 ##
@@ -145,6 +124,10 @@ def _copy_to_destinations(source_path: str, filename: str) -> dict:
     """
     results = {"local": None, "remote": None}
     
+    filename = filename.replace(':', '_')
+    
+    logger.info("%s %s", source_path, filename)
+
     for dest in settings.EXPORT_DESTINATIONS:
 
         if dest == "local":
@@ -152,9 +135,9 @@ def _copy_to_destinations(source_path: str, filename: str) -> dict:
             results["local"] = source_path
 
         elif dest == "remote":            
-            remote_path = os.path.join(settings.EXPORT_REMOTE_DIR, filename)
+            remote_path = os.path.join(settings.EXPORT_REMOTE_PATH, filename)
             try:
-                if not remote_mount_available(settings.EXPORT_REMOTE_DIR):
+                if not remote_mount_available(settings.EXPORT_REMOTE_PATH):
                     logger.warning("Partage Samba non disponible, copie ignorée")
                     results["remote_error"] = "Montage indisponible"
                     continue                
@@ -203,7 +186,7 @@ async def export_images_zip(
         # --- Chargement des frames en mémoire partagée ---
         record_manager = CameraRecordManager(cameraDB)
         total_size = await record_manager.size(uuid, start_ts, end_ts)
-        shm_size = int(total_size * 1.5)
+        shm_size = int((total_size or 0) * 1.5)
 
         try:
             shm = posix_ipc.SharedMemory(
@@ -243,11 +226,12 @@ async def export_images_zip(
             total += 1
 
         if not frame_sizes:
-            return {"status": "error", "message": "Aucune frame trouvée"}
+            return {"status": "error", "message": "No frame found!..."}
 
         # --- Génération du ZIP ---
         max_zip_bytes = max_zip_size_mb * 1024 * 1024 if max_zip_size_mb > 0 else 0
         ts_s = unix_timestamp_to_iso(start_ts)
+        
         zip_filename = f"{uuid}_{ts_s}.zip"
         zip_path = os.path.join(settings.EXPORTS_LOCAL_PATH, 'images', zip_filename)
         os.makedirs(os.path.dirname(zip_path), exist_ok=True)
@@ -292,19 +276,21 @@ async def export_images_zip(
                     zf.writestr(f"{uuid}_{ts_iso}.jpg", buf.tobytes())
                     written += 1
                     
-                progress_bar(i + 1, total, prefix=f'Progression {uuid}:', suffix='Terminé', length=30)
+                progress_bar(i + 1, total, prefix=f'Progress {uuid}:', suffix='Ended', length=30)
                 i+=1                   
                 current_offset += size
         
         ## Copie vers les destinations (local + Samba)    
-        #destinations = _copy_to_destinations(zip_path, zip_filename)   
+        filename = os.path.join('images', zip_filename)
+        
+        destinations = _copy_to_destinations(zip_path, filename)   
         return {
             "status": "success",
             "zip_path": zip_path,
             "frames_written": written,
             "frames_skipped": skipped,
             "jpeg_quality": jpeg_quality,
-            #"destinations": destinations,
+            "destinations": destinations,
         }
 
     except Exception as exc:
@@ -357,7 +343,7 @@ async def export_video_mp4(
         # --- Chargement des frames en mémoire partagée ---
         record_manager = CameraRecordManager(cameraDB)
         total_size = await record_manager.size(uuid, start_ts, end_ts)
-        shm_size = int(total_size * 1.5)
+        shm_size = int((total_size or 0) * 1.5)
 
         try:
             shm = posix_ipc.SharedMemory(
@@ -395,7 +381,7 @@ async def export_video_mp4(
             total +=1
 
         if not frame_sizes:
-            return {"status": "error", "message": "Aucune frame trouvée"}
+            return {"status": "error", "message": "No frame found!..."}
 
 
         # --- Génération du MP4 ---
@@ -407,7 +393,7 @@ async def export_video_mp4(
         )
         os.makedirs(os.path.dirname(video_path), exist_ok=True)
 
-        fourcc = cv2.VideoWriter_fourcc(*opencv_fourcc_format)
+        fourcc = cv2.VideoWriter_fourcc(*opencv_fourcc_format)  # type: ignore[attr-defined]
         skipped = 0
         written = 0
         current_offset = 0
@@ -451,18 +437,20 @@ async def export_video_mp4(
             written += 1
             current_offset += size
 
-            progress_bar(i + 1, total, prefix=f'Progression {uuid}:', suffix='Terminé', length=30)
+            progress_bar(i + 1, total, prefix=f'Progress {uuid}:', suffix='Ended', length=30)
             i+=1
 
         if video:
             video.release()
 
         if not os.path.exists(video_path):
-            return {"status": "error", "message": f"Fichier {opencv_video_type} non créé"}
+            return {"status": "error", "message": f"File {opencv_video_type} not created!..."}
         
         ## Copie vers les destinations (local + Samba)
-        #filename = os.path.basename(video_path)
-        #destinations = _copy_to_destinations(video_path, filename)
+        filename = os.path.basename(video_path)
+        filename = os.path.join('videos', filename)
+        
+        destinations = _copy_to_destinations(video_path, filename)
         return {
             "status": "success",
             "video_path": video_path,
@@ -470,7 +458,7 @@ async def export_video_mp4(
             "frames_skipped": skipped,
             "frame_rate": frame_rate,
             "file_size_mb": round(os.path.getsize(video_path) / 1024 / 1024, 2),
-            #"destinations": destinations,
+            "destinations": destinations,
         }
 
     except Exception as exc:

test_tube_scanner/scanner/migrations/0001_initial.py

@@ -0,0 +1,197 @@
+# Generated by Django 6.0.5 on 2026-05-31 07:42
+
+import django.db.models.deletion
+import django.utils.timezone
+from django.conf import settings
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = [
+        ('django_celery_beat', '0019_alter_periodictasks_options'),
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='Configuration',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(default='Configuration par défaut', help_text='Nom de la configuration', max_length=100, null=True, verbose_name='Nom de la Configuration')),
+                ('sidebar_width', models.CharField(default='350px', help_text='Largeur barre latérale (css)', max_length=32, null=True, verbose_name='Barre latérale')),
+                ('default_grid_columns', models.PositiveSmallIntegerField(default=3, help_text='Nombre de colonnes de la grille par défaut', verbose_name='Colonnes de la grille par défaut')),
+                ('opencv_fourcc_format', models.CharField(choices=[('mp4v', 'MP4'), ('XVID', 'XVID')], default='mp4v', help_text='Opencv fourcc format', max_length=8, null=True, verbose_name='Fourcc')),
+                ('opencv_video_type', models.CharField(choices=[('mp4', 'MP4'), ('avi', 'AVI')], default='mp4', help_text='Opencv video type', max_length=8, null=True, verbose_name='Video type')),
+                ('grbl_xmax', models.FloatField(default=350.0, help_text='CNC Grbl Xmax en mm', verbose_name='Grbl Xmax')),
+                ('grbl_ymax', models.FloatField(default=250.0, help_text='CNC Grbl Ymax en mm', verbose_name='Grbl Ymax')),
+                ('capture_type', models.CharField(choices=[('rpi', 'Arducam'), ('webcam', 'Webcam'), ('file', 'Simulation Fichier vidéo (mp4, avi)'), ('video', 'Fichier vidéo (mp4, avi)')], default='rpi', help_text='Type de capture. Nécessite un redémarrage en cas de modification à chaud!', max_length=8, null=True, verbose_name='Capture')),
+                ('webcam_device_index', models.PositiveSmallIntegerField(default=2, help_text='Index de la webcam (0, 1, ...) si présente', verbose_name='Index de la webcam')),
+                ('image_quality', models.PositiveSmallIntegerField(default=90, help_text='Qualité JPEG (1-100) pour les images exportées', verbose_name='Qualité JPEG')),
+                ('video_jpeg_quality', models.PositiveSmallIntegerField(default=90, help_text='Qualité JPEG (1-100) pour les images extraites des vidéos', verbose_name='Qualité JPEG pour les vidéos')),
+                ('video_frame_rate', models.FloatField(default=5.0, help_text="Fréquence d'extraction des images des vidéos (images par seconde)", verbose_name='Fréquence vidéos (fps)')),
+                ('video_width_capture', models.PositiveSmallIntegerField(default=1280, help_text='Largeur de capture vidéo en pixels', verbose_name='Largeur de capture vidéo')),
+                ('video_height_capture', models.PositiveSmallIntegerField(default=720, help_text='Hauteur de capture vidéo en pixels', verbose_name='Hauteur de capture vidéo')),
+                ('scan_simulation', models.BooleanField(default=False, help_text='Autorise la simulation du balayage', verbose_name='Simuler balayage')),
+                ('calibration_crop_radius', models.PositiveSmallIntegerField(default=150, help_text='Rayon en pixels pour découper les images de calibration en px', verbose_name='Rayon de découpe pour la calibration')),
+                ('calibration_default_multiwell', models.CharField(choices=[('HG', 'HG-Haut gauche'), ('HD', 'HD-Haut droit'), ('BG', 'BG-Bas gauche'), ('BD', 'BD-Bas droit')], default='HG', help_text='Position du multi-puits de calibration par défaut', max_length=8, verbose_name='Multi-puits de calibration par défaut')),
+                ('calibration_default_feed', models.PositiveIntegerField(default=1000, help_text='Vitesse de déplacement pour la calibration en mm/mn', verbose_name='Vitesse de calibration')),
+                ('calibration_default_step', models.FloatField(default=1.0, help_text='Pas de déplacement pour la calibration en mm', verbose_name='Pas de calibration')),
+                ('calibration_default_duration', models.FloatField(default=3.0, help_text='Durée de pose entre chaque puits en s', verbose_name='Duruée calibration')),
+                ('tracking', models.BooleanField(default=False, help_text='Suivi et analyse des planaires', verbose_name='Suivi')),
+                ('tracking_setting', models.BooleanField(default=False, help_text='Autorise le réglage des valeurs par défaut dans la calibration', verbose_name='Réglage dans calibration')),
+                ('tube_axis', models.CharField(choices=[('vertical', 'Vertical'), ('horizontal', 'Horizontal')], default='vertical', help_text='Axe du tube', max_length=16, null=True, verbose_name='Axe du puit')),
+                ('min_area_px', models.PositiveIntegerField(default=20, help_text="surface minimale d'un contour pour être considéré valide (px²)", verbose_name='Surface minimale')),
+                ('max_area_ratio', models.FloatField(default=0.1, help_text="surface maximale d'un contour en fraction de la frame (défaut 10%)", verbose_name='surface maximale ')),
+                ('max_planarians', models.PositiveIntegerField(default=1, help_text='nombre maximum de planaires à suivre simultanément (1-10)', verbose_name='Max planaire')),
+                ('merge_kernel_size', models.PositiveIntegerField(default=15, help_text='taille du kernel elliptique de fusion des fragments (px). Augmenter si fragments résiduels', verbose_name='Taille du kernel')),
+                ('min_contour_dist_px', models.PositiveIntegerField(default=40, help_text='Distance min entre deux contours pour les considérer comme individus distincts. Défaut : 40px. Augmenter si IDs multiples persistent', verbose_name='Distance <contour>')),
+                ('active', models.BooleanField(default=False, verbose_name='Actif')),
+                ('author', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to=settings.AUTH_USER_MODEL, verbose_name='Auteur')),
+            ],
+            options={
+                'verbose_name': 'Configuration',
+                'verbose_name_plural': 'Configuration',
+                'ordering': ['id'],
+            },
+        ),
+        migrations.CreateModel(
+            name='MultiWell',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('label', models.CharField(blank=True, help_text='Label du multi-puit', max_length=100, null=True, verbose_name='Label')),
+                ('position', models.CharField(choices=[('HG', 'HG-Haut gauche'), ('HD', 'HD-Haut droit'), ('BG', 'BG-Bas gauche'), ('BD', 'BD-Bas droit')], help_text='Position du multi-puits sur la table', max_length=8, null=True, unique=True, verbose_name='Position')),
+                ('default', models.BooleanField(default=False, help_text='Multi-puit par défaut', verbose_name='Par défaut')),
+                ('cols', models.PositiveSmallIntegerField(default=6, help_text='Nombre de colonnes', verbose_name='Colonnes')),
+                ('rows', models.PositiveSmallIntegerField(default=4, help_text='Nombre de lignes', verbose_name='Lignes')),
+                ('diameter', models.FloatField(default=16.0, help_text='Diamètre des tubes en mm', verbose_name='Diamètre')),
+                ('row_def', models.CharField(default='A,B,C,D', help_text='Définition des lignes', max_length=16, null=True, verbose_name='Définition')),
+                ('row_order', models.CharField(default='D,C,B,A', help_text='Ordre ligne de puit. Lecture en serpentin dans le sens des +- X', max_length=16, null=True, verbose_name='Ordre ligne')),
+                ('crop_radius', models.PositiveSmallIntegerField(default=500, help_text='Rayon en pixels pour recadrer les images en px', verbose_name='Rayon de découpe recadrage')),
+                ('order', models.PositiveSmallIntegerField(default=0, help_text='Ordre de lecture du multi-puit', verbose_name='Ordre')),
+                ('duration', models.PositiveIntegerField(default=10, help_text='Durée de capture en secondes pour la calibration', verbose_name='Durée')),
+                ('xbase', models.FloatField(default=50.0, help_text='Base origine X en mm', verbose_name='Origine X')),
+                ('ybase', models.FloatField(default=50.0, help_text='Base origine Y en mm', verbose_name='Origine Y')),
+                ('dx', models.FloatField(default=19.5, help_text='Pas ou interval sur X en mm', verbose_name='Pas X')),
+                ('dy', models.FloatField(default=19.5, help_text='Pas ou interval sur Y en mm', verbose_name='Pas Y')),
+                ('feed', models.PositiveIntegerField(default=1000, help_text='Vitesse déplacement en mm/mn ', verbose_name='Vitesse')),
+                ('well_position', models.BooleanField(default=False, help_text='Positions des puits générées ?. Non => efface WellPosition et recalcule les positions', verbose_name='Positions')),
+                ('active', models.BooleanField(default=True, verbose_name='Active')),
+                ('author', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to=settings.AUTH_USER_MODEL, verbose_name='Auteur')),
+            ],
+            options={
+                'verbose_name': 'Multi-puits',
+                'verbose_name_plural': 'Multi-puits',
+                'ordering': ['order'],
+            },
+        ),
+        migrations.CreateModel(
+            name='Experiment',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('title', models.CharField(max_length=100, null=True, verbose_name="Titre de l'expérience")),
+                ('comment', models.TextField(blank=True, help_text="Descriptions de l'expérience", null=True, verbose_name='Commentaires')),
+                ('identifier', models.CharField(max_length=100, null=True, unique=True, verbose_name="Identifiant d'expérience")),
+                ('duration', models.PositiveIntegerField(default=120, help_text='Durée de la prise de vue en secondes', verbose_name='Durée')),
+                ('created', models.DateTimeField(default=django.utils.timezone.now, verbose_name='Date de création')),
+                ('started', models.DateTimeField(blank=True, null=True, verbose_name='Date de début')),
+                ('finished', models.DateTimeField(blank=True, null=True, verbose_name='Date de fin')),
+                ('author', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to=settings.AUTH_USER_MODEL, verbose_name='Auteur')),
+                ('multiwell', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='scanner.multiwell', verbose_name='Multi-puits')),
+            ],
+            options={
+                'verbose_name': 'Expérience',
+                'verbose_name_plural': 'Expériences',
+                'ordering': ['-created'],
+            },
+        ),
+        migrations.CreateModel(
+            name='Session',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(help_text="Session d'expérience. 4 Multi-puits maximum", max_length=100, null=True, verbose_name='Nom de la session')),
+                ('active', models.BooleanField(default=True, verbose_name='Active')),
+                ('expected_export', models.DateTimeField(blank=True, help_text="Date d'exportation prévue", null=True, verbose_name='Exportation auto')),
+                ('expected_scanning', models.DateTimeField(blank=True, help_text='Date du balayage prévue', null=True, verbose_name='Bbalayage auto')),
+                ('created', models.DateTimeField(default=django.utils.timezone.now, verbose_name='Date de création')),
+                ('finished', models.DateTimeField(blank=True, null=True, verbose_name='Date de fin')),
+                ('export_status', models.CharField(choices=[('pending', 'En attente'), ('running', 'En cours'), ('done', 'Terminé'), ('error', 'Erreur')], default='pending', max_length=16, verbose_name='Status exportation')),
+                ('export_exported_at', models.DateTimeField(blank=True, null=True, verbose_name='Exportation terminée à')),
+                ('scanning_status', models.CharField(choices=[('pending', 'En attente'), ('running', 'En cours'), ('done', 'Terminé'), ('error', 'Erreur')], default='pending', max_length=16, verbose_name='Status scanning')),
+                ('scanning_finished_at', models.DateTimeField(blank=True, null=True, verbose_name='Balayage terminé à')),
+                ('author', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to=settings.AUTH_USER_MODEL, verbose_name='Auteur')),
+                ('export_task', models.OneToOneField(blank=True, help_text="Programmation de l'exportation des vidéos et images", null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='export_session', to='django_celery_beat.periodictask', verbose_name='Export médias')),
+                ('scanning_task', models.OneToOneField(blank=True, help_text='Programmation du lancement du balayage', null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='scanning_session', to='django_celery_beat.periodictask', verbose_name='Lancer le balayage')),
+            ],
+            options={
+                'verbose_name': 'Session',
+                'verbose_name_plural': 'Sessions',
+                'ordering': ['-created'],
+            },
+        ),
+        migrations.CreateModel(
+            name='Well',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(blank=True, help_text='Nom du puit: Ai..Di', max_length=4, null=True, unique=True, verbose_name='Nom')),
+                ('author', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to=settings.AUTH_USER_MODEL, verbose_name='Auteur')),
+            ],
+            options={
+                'verbose_name': 'Puit',
+                'verbose_name_plural': 'Puits',
+                'ordering': ['name'],
+            },
+        ),
+        migrations.CreateModel(
+            name='SessionExperiment',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('author', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to=settings.AUTH_USER_MODEL, verbose_name='Auteur')),
+                ('experiment', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='session_experiments', to='scanner.experiment', verbose_name='Expérience')),
+                ('session', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='scanner.session', verbose_name='Session')),
+            ],
+            options={
+                'verbose_name': "Expérience d'une session",
+                'verbose_name_plural': "Expériences d'une session",
+                'ordering': ['session'],
+                'unique_together': {('session', 'experiment')},
+            },
+        ),
+        migrations.CreateModel(
+            name='ExperimentWell',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('active', models.BooleanField(default=True, verbose_name='Active')),
+                ('author', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to=settings.AUTH_USER_MODEL, verbose_name='Auteur')),
+                ('experiment', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='experimentwell', to='scanner.experiment', verbose_name='Expérience')),
+                ('well', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='wellexperiment', to='scanner.well', verbose_name='Puit')),
+            ],
+            options={
+                'verbose_name': 'Expérience puit',
+                'verbose_name_plural': 'Expériences puits',
+                'ordering': ['experiment', 'well'],
+                'unique_together': {('experiment', 'well')},
+            },
+        ),
+        migrations.CreateModel(
+            name='WellPosition',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('order', models.PositiveSmallIntegerField(default=0, help_text='Ordre de lecture du puit', verbose_name='Ordre')),
+                ('x', models.FloatField(default=10.0, help_text='Axe X en mm', verbose_name='X')),
+                ('y', models.FloatField(default=10.0, help_text='Axe Y en mm', verbose_name='Y')),
+                ('px_per_mm', models.FloatField(default=50.0, help_text='Facteur de calibration optique', verbose_name='Pixels par mm')),
+                ('author', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to=settings.AUTH_USER_MODEL, verbose_name='Auteur')),
+                ('multiwell', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='scanner.multiwell', verbose_name='Multi-puits')),
+                ('well', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='scanner.well', verbose_name='Puit')),
+            ],
+            options={
+                'verbose_name': 'Position du puit',
+                'verbose_name_plural': 'Position des puits',
+                'ordering': ['order'],
+                'unique_together': {('multiwell', 'well')},
+            },
+        ),
+    ]

test_tube_scanner/scanner/migrations/0002_remove_multiwell_crop_radius.py

@@ -0,0 +1,17 @@
+# Generated by Django 6.0.5 on 2026-05-31 07:43
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('scanner', '0001_initial'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='multiwell',
+            name='crop_radius',
+        ),
+    ]

test_tube_scanner/scanner/migrations/0003_multiwell_crop_radius.py

@@ -0,0 +1,18 @@
+# Generated by Django 6.0.5 on 2026-05-31 07:43
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('scanner', '0002_remove_multiwell_crop_radius'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='multiwell',
+            name='crop_radius',
+            field=models.PositiveSmallIntegerField(default=500, help_text='Rayon en pixels pour recadrer les images en px', verbose_name='Rayon de découpe recadrage'),
+        ),
+    ]

test_tube_scanner/scanner/migrations/0004_add_videoplate.py

@@ -0,0 +1,44 @@
+# Generated by Django 6.0.5 on 2026-05-31 11:01
+
+import django.db.models.deletion
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('scanner', '0003_multiwell_crop_radius'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='configuration',
+            name='calibration_default_multiwell',
+            field=models.CharField(choices=[('HG', 'MP 6x24: HG-Haut gauche'), ('HD', 'MP 6x24: HD-Haut droit'), ('BG', 'MP 6x24: BG-Bas gauche'), ('BD', 'MP 6x24: BD-Bas droit'), ('HG_6', 'MP 2x3: HG-Haut gauche'), ('HD_6', 'MP 2x3: HD-Haut droit'), ('BG_6', 'MP 2x3: BG-Bas gauche'), ('BD_6', 'MP 2x3: BD-Bas droit'), ('HG_12', 'MP 3x4: HG-Haut gauche'), ('HD_12', 'MP 3x4: HD-Haut droit'), ('BG_12', 'MP 3x4: BG-Bas gauche'), ('BD_12', 'MP 3x4: BD-Bas droit'), ('HG_48', 'MP 6x8: HG-Haut gauche'), ('HD_48', 'MP 6x8: HD-Haut droit'), ('BG_48', 'MP 6x8: BG-Bas gauche'), ('BD_48', 'MP 6x8: BD-Bas droit')], default='HG', help_text='Position du multi-puits de calibration par défaut', max_length=8, verbose_name='Multi-puits de calibration par défaut'),
+        ),
+        migrations.AlterField(
+            model_name='multiwell',
+            name='position',
+            field=models.CharField(choices=[('HG', 'MP 6x24: HG-Haut gauche'), ('HD', 'MP 6x24: HD-Haut droit'), ('BG', 'MP 6x24: BG-Bas gauche'), ('BD', 'MP 6x24: BD-Bas droit'), ('HG_6', 'MP 2x3: HG-Haut gauche'), ('HD_6', 'MP 2x3: HD-Haut droit'), ('BG_6', 'MP 2x3: BG-Bas gauche'), ('BD_6', 'MP 2x3: BD-Bas droit'), ('HG_12', 'MP 3x4: HG-Haut gauche'), ('HD_12', 'MP 3x4: HD-Haut droit'), ('BG_12', 'MP 3x4: BG-Bas gauche'), ('BD_12', 'MP 3x4: BD-Bas droit'), ('HG_48', 'MP 6x8: HG-Haut gauche'), ('HD_48', 'MP 6x8: HD-Haut droit'), ('BG_48', 'MP 6x8: BG-Bas gauche'), ('BD_48', 'MP 6x8: BD-Bas droit')], help_text='Position du multi-puits sur la table', max_length=8, null=True, unique=True, verbose_name='Position'),
+        ),
+        migrations.CreateModel(
+            name='VideoPlate',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('label', models.CharField(blank=True, max_length=200, verbose_name='Label')),
+                ('video_file', models.FileField(blank=True, null=True, upload_to='videos/', verbose_name='Fichier vidéo')),
+                ('active', models.BooleanField(default=True, verbose_name='Active')),
+                ('uploaded_at', models.DateTimeField(auto_now_add=True, verbose_name='Déposé le')),
+                ('native_fps', models.FloatField(blank=True, null=True, verbose_name='FPS natif')),
+                ('duration_s', models.FloatField(blank=True, null=True, verbose_name='Durée (s)')),
+                ('frame_w', models.PositiveIntegerField(blank=True, null=True, verbose_name='Largeur (px)')),
+                ('frame_h', models.PositiveIntegerField(blank=True, null=True, verbose_name='Hauteur (px)')),
+                ('multiwell', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='video_plates', to='scanner.multiwell', verbose_name='Multi-puits')),
+            ],
+            options={
+                'verbose_name': 'Vidéo plaque',
+                'verbose_name_plural': 'Vidéos plaque',
+                'ordering': ['multiwell__order', '-uploaded_at'],
+            },
+        ),
+    ]

test_tube_scanner/scanner/migrations/0005_alter_multiwell_options_multiwell_capture_video.py

@@ -0,0 +1,22 @@
+# Generated by Django 6.0.5 on 2026-06-02 08:25
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('scanner', '0004_add_videoplate'),
+    ]
+
+    operations = [
+        migrations.AlterModelOptions(
+            name='multiwell',
+            options={'ordering': ['label', 'order'], 'verbose_name': 'Multi-puits', 'verbose_name_plural': 'Multi-puits'},
+        ),
+        migrations.AddField(
+            model_name='multiwell',
+            name='capture_video',
+            field=models.BooleanField(default=False, help_text='Ce multi-puit servira pour la capture vidéo', verbose_name='Capture vidéo'),
+        ),
+    ]

test_tube_scanner/scanner/migrations/0006_alter_multiwell_capture_video_and_more.py

@@ -0,0 +1,23 @@
+# Generated by Django 6.0.5 on 2026-06-02 08:28
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('scanner', '0005_alter_multiwell_options_multiwell_capture_video'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='multiwell',
+            name='capture_video',
+            field=models.BooleanField(default=False, help_text='Ce multi-puit servira pour la capture vidéo', verbose_name='Vidéo'),
+        ),
+        migrations.AlterField(
+            model_name='multiwell',
+            name='default',
+            field=models.BooleanField(default=False, help_text='Multi-puit par défaut', verbose_name='Défaut'),
+        ),
+    ]

test_tube_scanner/scanner/migrations/0007_add_videoplate_px_per_mm.py

@@ -0,0 +1,18 @@
+# Generated by Django 6.0.5 on 2026-06-02 09:51
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('scanner', '0006_alter_multiwell_capture_video_and_more'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='videoplate',
+            name='px_per_mm',
+            field=models.FloatField(default=15.0, help_text='Facteur pixels/mm dans la vidéo plaque. À calibrer selon la résolution de la caméra plaque.', verbose_name='Pixels par mm (vidéo plaque)'),
+        ),
+    ]

test_tube_scanner/scanner/migrations/0008_add_videoplate_origin.py

@@ -0,0 +1,29 @@
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('scanner', '0007_add_videoplate_px_per_mm'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='videoplate',
+            name='x_origin_mm',
+            field=models.FloatField(
+                default=0.0,
+                verbose_name='Origine X (mm)',
+                help_text='Position CNC X correspondant au pixel 0 de la vidéo plaque (mm). Défaut 0.',
+            ),
+        ),
+        migrations.AddField(
+            model_name='videoplate',
+            name='y_origin_mm',
+            field=models.FloatField(
+                default=0.0,
+                verbose_name='Origine Y (mm)',
+                help_text='Position CNC Y correspondant au pixel 0 de la vidéo plaque (mm). Défaut 0.',
+            ),
+        ),
+    ]

test_tube_scanner/scanner/migrations/0009_alter_videoplate_x_origin_mm_and_more.py

@@ -0,0 +1,23 @@
+# Generated by Django 6.0.5 on 2026-06-03 09:13
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('scanner', '0008_add_videoplate_origin'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='videoplate',
+            name='x_origin_mm',
+            field=models.FloatField(default=0.0, help_text='Position CNC X correspondant au bord gauche de la vidéo plaque (mm). Défaut 0.', verbose_name='Origine X (mm)'),
+        ),
+        migrations.AlterField(
+            model_name='videoplate',
+            name='y_origin_mm',
+            field=models.FloatField(default=0.0, help_text='Position CNC Y correspondant au bord haut de la vidéo plaque (mm). Défaut 0.', verbose_name='Origine Y (mm)'),
+        ),
+    ]

test_tube_scanner/scanner/models.py

@@ -4,22 +4,36 @@
 from django.utils.translation import gettext_lazy as _
 import uuid
 import json
+from pathlib import Path
 from django_celery_beat.models import PeriodicTask, ClockedSchedule
 from django.dispatch import receiver
 from django.db.models.signals import post_save, post_delete
-
 from django.utils import timezone
 from django.db import models
 from django.contrib.auth.models import User
 
 
 MULTIWELL_POSITION = [
-    ('HG', _("HG-Haut gauche")),
-    ('HD', _("HD-Haut droit")),
-    ('BG', _("BG-Bas gauche")),
-    ('BD', _("BD-Bas droit")),
-    ('BM', _("BM-Bas milieu")),
-    ('HM', _("HM-Haut milieu")),
+    ('HG',    _("MP 4x6: HG-Haut gauche")),
+    ('HD',    _("MP 4x6: HD-Haut droit")),
+    ('BG',    _("MP 4x6: BG-Bas gauche")),
+    ('BD',    _("MP 4x6: BD-Bas droit")),
+    ('HG_6',  _("MP 2x3: HG-Haut gauche")),
+    ('HD_6',  _("MP 2x3: HD-Haut droit")),
+    ('BG_6',  _("MP 2x3: BG-Bas gauche")),
+    ('BD_6',  _("MP 2x3: BD-Bas droit")),
+    ('HG_12', _("MP 3x4: HG-Haut gauche")),
+    ('HD_12', _("MP 3x4: HD-Haut droit")),
+    ('BG_12', _("MP 3x4: BG-Bas gauche")),
+    ('BD_12', _("MP 3x4: BD-Bas droit")),
+    ('HG_48', _("MP 6x8: HG-Haut gauche")),
+    ('HD_48', _("MP 6x8: HD-Haut droit")),
+    ('BG_48', _("MP 6x8: BG-Bas gauche")),
+    ('BD_48', _("MP 6x8: BD-Bas droit")),    
+    ('HG_96', _("MP 8x12: HG-Haut gauche")),
+    ('HD_96', _("MP 8x12: HD-Haut droit")),
+    ('BG_96', _("MP 8x12: BG-Bas gauche")),
+    ('BD_96', _("MP 8x12: BD-Bas droit")),      
 ]
 
 FOURCC_FORMAT = [
@@ -35,12 +49,18 @@ VIDEO_TYPE = [
 CAPTURE_TYPE = [
     ('rpi', _("Arducam")),
     ('webcam', _("Webcam")),
-    ('file', _("mp4")),
+    ('file', _("Simulation Fichier vidéo (mp4, avi)")),
+    ('video', _("Fichier vidéo (mp4, avi)")),
+]
+
+TUBE_AXIS_TYPE = [
+    ('vertical', _("Vertical")),
+    ('horizontal', _("Horizontal")),
 ]
     
 class Configuration(models.Model):
     name = models.CharField(_("Nom de la Configuration"), help_text=_("Nom de la configuration"), max_length=100, null=True, blank=False, default=_("Configuration par défaut"))
-    author = models.ForeignKey(User, on_delete=models.CASCADE, verbose_name="Auteur", null=True, blank=True)
+    author = models.ForeignKey(User, on_delete=models.SET_NULL, verbose_name="Auteur", null=True, blank=True)
     # Dashboard configuration
     sidebar_width = models.CharField(_("Barre latérale"), help_text=_("Largeur barre latérale (css)"), max_length=32, null=True, blank=False, default="350px")
     default_grid_columns = models.PositiveSmallIntegerField(_("Colonnes de la grille par défaut"), help_text=_("Nombre de colonnes de la grille par défaut"), blank=False, default=3)
@@ -51,7 +71,8 @@ class Configuration(models.Model):
     grbl_xmax = models.FloatField(_("Grbl Xmax"), help_text=_("CNC Grbl Xmax en mm"), blank=False, default=350.0)
     grbl_ymax = models.FloatField(_("Grbl Ymax"), help_text=_("CNC Grbl Ymax en mm"), blank=False, default=250.0)
     # camera configuration
-    capture_type = models.CharField(_("Capture"), help_text=_("Type de capture"), default='rpi', max_length=8, choices=CAPTURE_TYPE, null=True, blank=False)
+    capture_type = models.CharField(_("Capture"), help_text=_("Type de capture. Nécessite un redémarrage en cas de modification à chaud!"), default='rpi', max_length=8, choices=CAPTURE_TYPE, null=True, blank=False)
+    
     webcam_device_index = models.PositiveSmallIntegerField(_("Index de la webcam"), help_text=_("Index de la webcam (0, 1, ...) si présente"), default=2)
     image_quality = models.PositiveSmallIntegerField(_("Qualité JPEG"), help_text=_("Qualité JPEG (1-100) pour les images exportées"), default=90)
     video_jpeg_quality = models.PositiveSmallIntegerField(_("Qualité JPEG pour les vidéos"), help_text=_("Qualité JPEG (1-100) pour les images extraites des vidéos"), default=90)
@@ -59,6 +80,7 @@ class Configuration(models.Model):
     video_width_capture = models.PositiveSmallIntegerField(_("Largeur de capture vidéo"), help_text=_("Largeur de capture vidéo en pixels"), default=1280)
     video_height_capture = models.PositiveSmallIntegerField(_("Hauteur de capture vidéo"), help_text=_("Hauteur de capture vidéo en pixels"), default=720)
     # Calibration
+    scan_simulation = models.BooleanField(_("Simuler balayage"), help_text=_("Autorise la simulation du balayage"), default=False)
     calibration_crop_radius = models.PositiveSmallIntegerField(_("Rayon de découpe pour la calibration"), help_text=_("Rayon en pixels pour découper les images de calibration en px"), default=150)
     calibration_default_multiwell = models.CharField(_("Multi-puits de calibration par défaut"), help_text=_("Position du multi-puits de calibration par défaut"), max_length=8, choices=MULTIWELL_POSITION, default='HG')
     calibration_default_feed = models.PositiveIntegerField(_("Vitesse de calibration"), help_text=_("Vitesse de déplacement pour la calibration en mm/mn"), default=1000)
@@ -66,10 +88,17 @@ class Configuration(models.Model):
     calibration_default_duration = models.FloatField(_("Duruée calibration"), help_text=_("Durée de pose entre chaque puits en s"), default=3.0)
     # tracking
     tracking = models.BooleanField(_("Suivi"), help_text=_("Suivi et analyse des planaires"), default=False)
+    tracking_setting = models.BooleanField(_("Réglage dans calibration"), help_text=_("Autorise le réglage des valeurs par défaut dans la calibration"), default=False)
+    
+    tube_axis = models.CharField(_("Axe du puit"), help_text=_("Axe du tube"), default='vertical', max_length=16, choices=TUBE_AXIS_TYPE, null=True, blank=False)
+    min_area_px = models.PositiveIntegerField(_("Surface minimale"), help_text=_("surface minimale d'un contour pour être considéré valide (px²)"), default=20)
+    max_area_ratio = models.FloatField(_("surface maximale "), help_text=_("surface maximale d'un contour en fraction de la frame (défaut 10%)"), default=0.10)
+    max_planarians = models.PositiveIntegerField(_("Max planaire"), help_text=_("nombre maximum de planaires à suivre simultanément (1-10)"), default=1)
+    merge_kernel_size = models.PositiveIntegerField(_("Taille du kernel"), help_text=_("taille du kernel elliptique de fusion des fragments (px). Augmenter si fragments résiduels"), default=15)
+    min_contour_dist_px = models.PositiveIntegerField(_("Distance <contour>"), help_text=_("Distance min entre deux contours pour les considérer comme individus distincts. Défaut : 40px. Augmenter si IDs multiples persistent"), default=40)
     #
     active = models.BooleanField(_("Actif"), default=False)
 
-    
     @classmethod
     def active_config(cls):
         return Configuration.objects.filter(active=True).first()
@@ -83,7 +112,7 @@ class Configuration(models.Model):
         return f'{self.name}'
 
 class Well(models.Model):
-    author = models.ForeignKey(User, on_delete=models.CASCADE, verbose_name="Auteur", null=True, blank=True)
+    author = models.ForeignKey(User, on_delete=models.SET_NULL, verbose_name="Auteur", null=True, blank=True)
     name =  models.CharField(_("Nom"), help_text=_("Nom du puit: Ai..Di"), unique=True, max_length=4, null=True, blank=True)
 
     class Meta:
@@ -91,26 +120,27 @@ class Well(models.Model):
         verbose_name = _("Puit")
         verbose_name_plural = _("Puits")
 
-
     def __str__(self):
         return f'{self.name}'
 
 
 class MultiWell(models.Model):
+    # Identification
     label =  models.CharField(_("Label"), help_text=_("Label du multi-puit"), max_length=100, null=True, blank=True)
-    author = models.ForeignKey(User, on_delete=models.CASCADE, verbose_name="Auteur", null=True, blank=True)
+    author = models.ForeignKey(User, on_delete=models.SET_NULL, verbose_name="Auteur", null=True, blank=True)
     position = models.CharField(_("Position"), help_text=_('Position du multi-puits sur la table'), unique=True, max_length=8, choices=MULTIWELL_POSITION, null=True, blank=False)
-    default = models.BooleanField(_("Par défaut"), help_text=_('Multi-puit par défaut'), default=False)
-    
+    default = models.BooleanField(_("Défaut"), help_text=_('Multi-puit par défaut'), default=False)
+    # Configuration   
     cols = models.PositiveSmallIntegerField(_("Colonnes"), help_text=_('Nombre de colonnes'), blank=False, default=6)
     rows = models.PositiveSmallIntegerField(_("Lignes"), help_text=_('Nombre de lignes'), blank=False, default=4)  
     diameter = models.FloatField(_("Diamètre"), help_text=_('Diamètre des tubes en mm'), blank=False, default=16.0)
-      
     row_def = models.CharField(_("Définition"), help_text=_('Définition des lignes'), max_length=16, null=True, blank=False, default="A,B,C,D")
     row_order = models.CharField(_("Ordre ligne"), help_text=_('Ordre ligne de puit. Lecture en serpentin dans le sens des +- X'), max_length=16, null=True, blank=False, default="D,C,B,A")
+    crop_radius = models.PositiveSmallIntegerField(_("Rayon de découpe recadrage"), help_text=_("Rayon en pixels pour recadrer les images en px"), blank=False, default=500)
     
+    # Balayage
     order = models.PositiveSmallIntegerField(_("Ordre"), help_text=_('Ordre de lecture du multi-puit'), blank=False, default=0)
-    duration = models.PositiveIntegerField(_("Durée"), help_text=_('Durée du film en secondes'), blank=False, default=120)
+    duration = models.PositiveIntegerField(_("Durée"), help_text=_('Durée de capture en secondes pour la calibration'), blank=False, default=10)
     xbase = models.FloatField(_("Origine X"), help_text=_('Base origine X en mm'), blank=False, default=50.0)
     ybase = models.FloatField(_("Origine Y"), help_text=_('Base origine Y en mm'), blank=False, default=50.0)
 
@@ -119,9 +149,9 @@ class MultiWell(models.Model):
     feed = models.PositiveIntegerField(_("Vitesse"), help_text=_('Vitesse déplacement en mm/mn '), blank=False, default=1000)
 
     well_position = models.BooleanField(_("Positions"), help_text=_('Positions des puits générées ?. Non => efface WellPosition et recalcule les positions'), default=False)
+    capture_video = models.BooleanField(_("Vidéo"), help_text=_('Ce multi-puit servira pour la capture vidéo'), default=False)
     active = models.BooleanField(_("Active"), default=True)
     
-
     def config(self):
         return dict(
             position=self.position,
@@ -154,7 +184,7 @@ class MultiWell(models.Model):
         return MultiWell.objects.filter(active=True).all()
 
     class Meta:
-        ordering = ['order', ]
+        ordering = ['label', 'order', ]
         verbose_name = _("Multi-puits")
         verbose_name_plural = _("Multi-puits")
 
@@ -164,7 +194,7 @@ class MultiWell(models.Model):
 
 
 class WellPosition(models.Model):
-    author = models.ForeignKey(User, on_delete=models.CASCADE, verbose_name="Auteur", null=True, blank=True)
+    author = models.ForeignKey(User, on_delete=models.SET_NULL, verbose_name="Auteur", null=True, blank=True)
     well = models.ForeignKey(Well, verbose_name=_("Puit"), on_delete=models.SET_NULL, null=True, blank=True)
     multiwell = models.ForeignKey(MultiWell, verbose_name=_("Multi-puits"), on_delete=models.SET_NULL, null=True, blank=True)
     
@@ -175,13 +205,17 @@ class WellPosition(models.Model):
 
 
     @classmethod
-    def active_well(cls, multiwel, well):
-        return WellPosition.objects.filter(multiwel_id=multiwel.id, well_id=well.id).first()    
+    def active_well(cls, multiwell, well):
+        return WellPosition.objects.filter(multiwell_id=multiwell.id, well_id=well.id).first()
+    
+    @classmethod
+    def well_by_multiwell(cls, multiwell):
+        return WellPosition.objects.filter(multiwell_id=multiwell.id).all()   
 
     class Meta:
         ordering = ['order']
         unique_together = ["multiwell", "well"]
-        verbose_name = _("Position d'un puit")
+        verbose_name = _("Position du puit")
         verbose_name_plural = _("Position des puits")
 
     def __str__(self):
@@ -190,8 +224,8 @@ class WellPosition(models.Model):
 
 @receiver(post_save, sender=MultiWell)
 def create_well_position(sender, instance, created, **kwargs):
-    if created:
-        pass
+    #if created:
+    #    pass
     if not instance.well_position:
         row_order = instance.row_order.split(',')
         n = 0
@@ -222,19 +256,33 @@ def create_well_position(sender, instance, created, **kwargs):
 class Experiment(models.Model):
     title = models.CharField(_("Titre de l'expérience"), max_length=100, null=True, blank=False)
     comment =  models.TextField(_("Commentaires"), help_text=_("Descriptions de l'expérience"), null=True, blank=True)
-    author = models.ForeignKey(User, on_delete=models.CASCADE, verbose_name="Auteur", null=True, blank=True)
+    identifier = models.CharField(_("Identifiant d'expérience"), unique=True, max_length=100, null=True, blank=False )
+
+    author = models.ForeignKey(User, on_delete=models.SET_NULL, verbose_name="Auteur", null=True, blank=True)
     multiwell = models.ForeignKey(MultiWell, verbose_name=_("Multi-puits"), on_delete=models.SET_NULL, null=True, blank=True)   
+    duration = models.PositiveIntegerField(_("Durée"), help_text=_('Durée de la prise de vue en secondes'), blank=False, default=120)
+    
     created = models.DateTimeField(_("Date de création"), default=timezone.now)
     started = models.DateTimeField (_("Date de début"), null=True, blank=True)
     finished = models.DateTimeField (_("Date de fin"), null=True, blank=True)
     
+    
+    def save(self, *args, **kwargs):
+        self.identifier = f'{self.multiwell.position}_{self.created.isoformat()[:19]}'
+        super().save(*args, **kwargs)
+
+
+    @classmethod
+    def by_identifier(cls, identifier):
+        return Experiment.objects.filter(identifier__exact=identifier).first()
+
     class Meta:
         ordering = ['-created', ]
         verbose_name = _("Expérience")
         verbose_name_plural = _("Expériences")
 
     def __str__(self):
-        return f'{self.title}: {self.created} {self.multiwell.order}'
+        return f'{self.identifier} [ {self.title} ]'
 
 
 class Session(models.Model):
@@ -246,10 +294,10 @@ class Session(models.Model):
         ERROR     = "error",     _("Erreur")    
     
     name = models.CharField(_("Nom de la session"), help_text=_("Session d'expérience. 4 Multi-puits maximum"), max_length=100, null=True, blank=False)
-    author = models.ForeignKey(User, on_delete=models.CASCADE, verbose_name="Auteur", null=True, blank=True)
+    author = models.ForeignKey(User, on_delete=models.SET_NULL, verbose_name="Auteur", null=True, blank=True)
     active = models.BooleanField(_("Active"), default=True)
-    expected_export  = models.DateTimeField(_("Date d'exportation"), help_text=_("Date d'exportation prévue"), null=True, blank=True)
-    expected_scanning  = models.DateTimeField(_("Date du balayage"), help_text=_("Date du balayage prévue"), null=True, blank=True)    
+    expected_export = models.DateTimeField(_("Exportation auto"), help_text=_("Date d'exportation prévue"), null=True, blank=True)
+    expected_scanning = models.DateTimeField(_("Bbalayage auto"), help_text=_("Date du balayage prévue"), null=True, blank=True)    
     
     created = models.DateTimeField(_("Date de création"), default=timezone.now)
     finished = models.DateTimeField (_("Date de fin"), null=True, blank=True)
@@ -271,14 +319,19 @@ class Session(models.Model):
     scanning_finished_at = models.DateTimeField(_("Balayage terminé à"), null=True, blank=True)    
     
     
+    @classmethod
+    def get_session(cls, sid):
+        return Session.objects.filter(pk=sid).first()   
+    
+    
     class Meta:
         ordering = ['-created', ]
-        verbose_name = _("Session d'expérience")
-        verbose_name_plural = _("Sessions d'expériences")
+        verbose_name = _("Session")
+        verbose_name_plural = _("Sessions")
 
     def __str__(self):
         state = _("Terminée") if not self.active else _("Active")
-        return f'{self.name}: {state}'
+        return f'[ {self.pk} ] {self.name} ({state})'
     
 
 @receiver(post_save, sender=Session)
@@ -305,8 +358,8 @@ def create_periodic_task(sender, instance, created, **kwargs):
             )
             # Sauvegarde sans re-déclencher le signal
             Session.objects.filter(pk=instance.pk).update(export_task=export_task)
-        except:
-            pass
+        except Exception as e:
+            print("create_periodic_task error", e)
         
     if instance.expected_scanning:
         try:
@@ -340,15 +393,21 @@ def delete_periodic_task(sender, instance, **kwargs):
         instance.scanning_task.delete()       
     
     
+def get_uuid_from_session(session_id, multiwel_position, well_name):
+    return f'{session_id}-{multiwel_position}-{well_name}'
+
+
 class SessionExperiment(models.Model):
-    author = models.ForeignKey(User, on_delete=models.CASCADE, verbose_name="Auteur", null=True, blank=True)
-    session = models.ForeignKey(Session, verbose_name=_("Session"), on_delete=models.SET_NULL, null=True, blank=True)
-    experiment = models.ForeignKey(Experiment, verbose_name=_("Expérience"), on_delete=models.SET_NULL, null=True, blank=True, related_name="session_experiments")
+    author = models.ForeignKey(User, on_delete=models.SET_NULL, verbose_name="Auteur", null=True, blank=True)
+    session = models.ForeignKey(Session, verbose_name=_("Session"), on_delete=models.CASCADE, null=True, blank=True)
+    experiment = models.ForeignKey(Experiment, verbose_name=_("Expérience"), on_delete=models.CASCADE, null=True, blank=True, related_name="session_experiments")
+
 
     @classmethod
     def experiment_by_session(cls, session_id, active=True):
         return [ ss.experiment for ss in SessionExperiment.objects.filter(session__id=session_id, session__active=active).order_by('experiment__multiwell__order') ]
     
+    
     @classmethod
     def uuid_from_session(cls, sid):
         experiments = [ss.experiment for ss in SessionExperiment.objects.filter(session__id=sid, session__active=False)]
@@ -361,13 +420,166 @@ class SessionExperiment(models.Model):
                     uuid_list.append(uuid)
         return uuid_list
 
+
+    @classmethod
+    def get_uuid(cls, session_id, experiment_id, well_name):
+        ss = SessionExperiment.objects.filter(session__id=session_id, experiment_id=experiment_id).first()
+        if ss:
+            return get_uuid_from_session(session_id, ss.experiment.multiwel.position, well_name)
+        return None
+
+
     class Meta:
         ordering = ['session',]
         unique_together = ["session", "experiment"]
-        verbose_name = _("Session expérience")
-        verbose_name_plural = _("Sessions expériences")
+        verbose_name = _("Expérience d'une session")
+        verbose_name_plural = _("Expériences d'une session")
 
     def __str__(self):
-        return f'{self.session.name}'
+        return f'{self.session.id}: {self.experiment.title}'
 
 
+class ExperimentWell(models.Model):
+    author = models.ForeignKey(User, on_delete=models.SET_NULL, verbose_name="Auteur", null=True, blank=True)
+    experiment = models.ForeignKey(Experiment, verbose_name=_("Expérience"), on_delete=models.CASCADE, null=True, blank=True, related_name="experimentwell")
+    well = models.ForeignKey(Well, verbose_name=_("Puit"), on_delete=models.SET_NULL, null=True, blank=True, related_name="wellexperiment")
+    active = models.BooleanField(_("Active"), default=True)
+ 
+    @classmethod
+    def well_by_experiment(cls, experiment_id):
+        return ExperimentWell.objects.filter(experiment__id=experiment_id, active=True).order_by('well__name')
+    
+    @classmethod
+    def wellname_by_experiment(cls, experiment_id):
+        return [ ew.well.name for ew in ExperimentWell.objects.filter(experiment__id=experiment_id, active=True).order_by('well__name') ]    
+
+    class Meta:
+        ordering = ['experiment', 'well']
+        unique_together = ["experiment", "well", ]
+        verbose_name = _("Expérience puit")
+        verbose_name_plural = _("Expériences puits")
+
+    def __str__(self):
+        return f'{self.experiment.title}'
+    
+class VideoPlate(models.Model):
+    """Vidéo d'une plaque multi-puits entière, utilisée en mode capture_type='video'."""
+    multiwell = models.ForeignKey(
+        MultiWell,
+        on_delete=models.CASCADE,
+        verbose_name=_("Multi-puits"),
+        related_name='video_plates',
+    )
+    label = models.CharField(_("Label"), max_length=200, blank=True)
+    video_file = models.FileField(
+        _("Fichier vidéo"),
+        upload_to='videos/',
+        null=True,
+        blank=True,
+    )
+    active = models.BooleanField(_("Active"), default=True)
+    uploaded_at = models.DateTimeField(_("Déposé le"), auto_now_add=True)
+    # Calibration vidéo plaque : pixels par mm dans la vidéo (≠ calibration caméra individuelle)
+    px_per_mm = models.FloatField(
+        _("Pixels par mm (vidéo plaque)"),
+        default=15.0,
+        help_text=_("Facteur pixels/mm dans la vidéo plaque. À calibrer selon la résolution de la caméra plaque."),
+    )
+    # Origine : position CNC (mm) correspondant au pixel (0, 0) de la vidéo.
+    # Indépendant de MultiWell.xbase — ne change pas à la recalibration des puits.
+    x_origin_mm = models.FloatField(
+        _("Origine X (mm)"),
+        default=0.0,
+        help_text=_("Position CNC X correspondant au bord gauche de la vidéo plaque (mm). Défaut 0."),
+    )
+    y_origin_mm = models.FloatField(
+        _("Origine Y (mm)"),
+        default=0.0,
+        help_text=_("Position CNC Y correspondant au bord haut de la vidéo plaque (mm). Défaut 0."),
+    )
+    # Métadonnées extraites automatiquement à l'upload
+    native_fps = models.FloatField(_("FPS natif"), null=True, blank=True)
+    duration_s = models.FloatField(_("Durée (s)"), null=True, blank=True)
+    frame_w = models.PositiveIntegerField(_("Largeur (px)"), null=True, blank=True)
+    frame_h = models.PositiveIntegerField(_("Hauteur (px)"), null=True, blank=True)
+
+    @classmethod
+    def active_for(cls, multiwell_position: str) -> "VideoPlate | None":
+        return cls.objects.filter(multiwell__position=multiwell_position, active=True).first()
+    
+    @classmethod
+    def active_video(cls) -> "VideoPlate | None":
+        return cls.objects.filter(active=True).first()
+    
+    @property
+    def video_filename(self) -> str:
+        return Path(self.video_file.name).name if self.video_file else "—"
+
+    @property
+    def resolution(self) -> str:
+        if self.frame_w and self.frame_h:
+            return f"{self.frame_w}×{self.frame_h}"
+        return "—"
+
+    class Meta:
+        ordering = ['multiwell__order', '-uploaded_at']
+        verbose_name = _("Vidéo plaque")
+        verbose_name_plural = _("Vidéos plaque")
+
+    def __str__(self) -> str:
+        return f"{self.multiwell.position} — {self.label or self.video_filename}"
+
+
+@receiver(post_save, sender=VideoPlate)
+def notify_video_plate_change(sender, instance, **kwargs):
+    """Hot swap : publie sur Redis quand une vidéo active est enregistrée."""
+    if not instance.active or not instance.video_file:
+        return
+    try:
+        from redis import Redis
+        from django.conf import settings as django_settings
+        r = Redis(
+            host=django_settings.REDIS_HOST,
+            port=django_settings.REDIS_PORT,
+            db=0,
+            decode_responses=True,
+        )
+        r.publish('scanner_proc', json.dumps({
+            'type': 'scanner',
+            'topic': 'video_plate',
+            'multiwell': instance.multiwell.position,
+            'path': instance.video_file.path,
+        }))
+    except Exception:
+        pass
+
+
+@receiver(post_delete, sender=VideoPlate)
+def delete_video_file(sender, instance, **kwargs):
+    """Supprime le fichier physique quand l'enregistrement est effacé."""
+    if instance.video_file:
+        path = Path(instance.video_file.path)
+        path.unlink(missing_ok=True)
+
+
+@receiver(post_save, sender=Experiment)
+def create_experiment_well(sender, instance, created, **kwargs):
+    from planarian.models import ExperimentConfig
+    from .constants import ScannerConstants
+    
+    wellposition = WellPosition.well_by_multiwell(instance.multiwell)
+    for wp in wellposition:
+        ExperimentWell.objects.get_or_create(experiment=instance, well=wp.well, author=instance.author, defaults={'active':True})
+        
+        ExperimentConfig.objects.get_or_create(
+            experiment_key=instance, 
+            well=wp.well.name, 
+            author=instance.author, 
+            experiment=instance.identifier,
+            defaults={
+                'px_per_mm': wp.px_per_mm,
+                'fps': ScannerConstants().get().video_frame_rate,
+                'well_radius_mm': instance.multiwell.diameter / 2, 
+            }
+        )       
+        

test_tube_scanner/scanner/multiwell.py

@@ -7,20 +7,21 @@ Created on 20 avr. 2026
 
 @author: denis
 '''
+
+
 import logging
 import time
 from threading import Thread, Event
 #from django.utils.translation import gettext_lazy as _
 from django.utils import timezone
-from django.utils.html import mark_safe
+from django.utils.safestring import mark_safe
 from django.conf import settings
+from planarian.models import ExperimentConfig
 from . import models
 
 
-logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
-
 class WellIterator:
     """Itérateur personnalisé pour naviguer dans les Wells"""
     
@@ -75,8 +76,11 @@ class WellIterator:
 class MultiWellManager:
 
     def __init__(self, process):
+        
         self.process = process
         self.cnc_controller = process.grbl     
+        logger.info(f"MultiWellManager initialized with CNC controller: {self.cnc_controller}")
+        
         self.stop_playing = Event()
         self.well_iterator = None       
         self.multiwel = None
@@ -85,83 +89,190 @@ class MultiWellManager:
         self.scan_thread = None
         self.test_thread = None
         
+        self.tracker_config =  dict(
+            tube_axis = settings.TRACKER_TUBE_AXIS,
+            min_area_px = self.process.conf.min_area_px,
+            max_area_ratio = self.process.conf.max_area_ratio,
+            max_planarians = self.process.conf.max_planarians,
+            merge_kernel_size = self.process.conf.merge_kernel_size,
+            min_contour_dist_px = self.process.conf.min_contour_dist_px,
+        )
+        
+    def set_tracker_config(self):
+        self.tracker_config = dict(
+            tube_axis = settings.TRACKER_TUBE_AXIS,
+            min_area_px = self.process.conf.min_area_px,
+            max_area_ratio = self.process.conf.max_area_ratio,
+            max_planarians = self.process.conf.max_planarians,
+            merge_kernel_size = self.process.conf.merge_kernel_size,
+            min_contour_dist_px = self.process.conf.min_contour_dist_px,
+        )
+        logger.info(f"Tracker config: {self.tracker_config}")
+
     def set_default_values(self, feed=None, step=None, duration=None):
         self._feed = feed or self.process.conf.calibration_default_feed
         self._step = step or self.process.conf.calibration_default_step
         self._duration = duration or self.process.conf.calibration_default_duration
         self.px_per_mm = 50.0
 
-
-    def set_multiwell(self, position=None):
-        if position is None:
-            self.multiwell = models.MultiWell.objects.filter(default=True).first()
-        else:
-            self.multiwell = models.MultiWell.by_position(position)
-            
-        wells = models.WellPosition.objects.filter(multiwell_id=self.multiwell.id).order_by('order').all()
+    def init_manager_values(self):
+        wells = models.WellPosition.objects.filter(multiwell_id=self.multiwell.pk).order_by('order').all()  # type: ignore[union-attr]
         self.well_iterator = WellIterator(wells)        
-        
         self.position = self.multiwell.position
         self._xbase = self.multiwell.xbase
         self._ybase = self.multiwell.ybase       
         self._dx = self.multiwell.dx
         self._dy = self.multiwell.dy
 
+    def set_multiwell(self, position=None):
+        if position is None:
+            self.multiwell = models.MultiWell.objects.filter(default=True).first()
+        else:
+            self.multiwell = models.MultiWell.by_position(position)
+        self.init_manager_values()
         return self.multiwell.config()
     
+    def set_first_multiwell_from_session(self, sid):
+        experiments = models.SessionExperiment.experiment_by_session(sid)
+        if experiments:
+            self.multiwell = experiments[0].multiwell
+            self.init_manager_values()
 
-    def multiwell_buttons(self):
+    def multiwell_buttons(self, btn_class="w3-button", onclick=''' onclick="goto_well(this)"'''):
         multiwells = []
         multiwells.append('''<div class="w3-border well-btn">''')
         for wl in self.well_iterator: 
-            multiwells.append(f"""<button class="w3-button well" value="{wl.order}" onclick="goto_well(this)">{wl.well.name}</button>""")
+            multiwells.append(f"""<button class="{btn_class} well" value="{wl.order}"{onclick}>{wl.well.name}</button>""")
         multiwells.append('''</div>''')
         self.well_iterator.reset()
         return mark_safe("\n".join(multiwells))         
     
+    def set_circular_crop(self, crop_radius):
+        crop = self.process.set_crop_radius(crop_radius)
+        self.process.cam.set_circular_crop(crop)
 
-    def _grid_scanning_capture(self, uuid, duration):
+    def update_crop_radius(self, value):
+        self.multiwell.crop_radius = value
+        self.multiwell.save()
+
+    def _grid_scanning_capture(self, experiment, well_position, simulate=False):
+        uuid = None
+        try:
+            well = well_position.well
+            multiwell = experiment.multiwell
+            
+            # En mode video le crop_radius est piloté par _capture_video_simulation
+            if self.process.conf.capture_type != 'video':
+                self.set_circular_crop(multiwell.crop_radius)
+
+            ## create uuid for this capture
+            uuid = f'{self.process.data.session}-{multiwell.position}-{well.name}'
+            
+            if self.process.use_tracking:               
+                cfg = ExperimentConfig.objects.filter(experiment_key_id=experiment.id, well=well.name).first()
+                if not cfg:
+                    raise Exception(f"Configuration d'expérience introuvable pour {experiment} / {well}")
+                # reset PlanarianTracker => on_well_change
+                self.process.cam.on_well_change(cfg, uuid=uuid, draw_contours=False)
+              
+            ## start recording   
             self.process.data.uuid = uuid
+            if not simulate:
                 self.process.data.record = True
+            self.process._send(current=well_position.order)
+            
+            msg = f"Starting capture for {uuid} ordre: {well_position.order}"
+            logger.info(msg)
+            self.process._send(well_state=msg)
             
             start = time.monotonic()
             while not self.stop_playing.is_set():
-            if time.monotonic() - start > duration:
+                ## stop after duration in experiemnt now
+                if time.monotonic() - start > experiment.duration:
                     break
-            self.cnc_controller.wait_for(1.0)
+                self.cnc_controller.wait_for(0.1)
+            
+            self.process.cam._flush_current_well(uuid)
             
-        logger.info(f"Arrêter l'enregistrement {uuid}")
             self.process.data.record = False
             self.process.data.uuid = None
 
+            msg = f"{uuid}: capture done..."
+        except Exception as e:
+            msg = f"error during capture - {e}"
+            logger.error(msg)
+        finally:
+            self.process.cam._flush_current_well(uuid)
 
-    def _grid_scanning(self, experiment, xnext=0, ynext=0):
+        logger.info(msg)
+        self.process._send(scan_state=msg)               
+    
+    
+    def _capture_file_simulation(self, name):
+        vf = settings.MEDIA_ROOT / 'simulation' / f'{name}.mp4'
+        if vf.exists():
+            self.process.cam._video_file = str(vf)
+        self.process.cam._error_occured = True
+        logger.info(f"Simulating capture with file {vf}")
+
+    def _capture_video_simulation(self, well_position):
+        """Met à jour VideoPlateCapture : crop_radius depuis MultiWell.crop_radius."""
+        cam = self.process.cam
+        r = well_position.multiwell.crop_radius
+        if hasattr(cam, 'set_crop_radius_px'):
+            cam.set_crop_radius_px(r)
+        self.set_circular_crop(r)
+        logger.info(f"video_simulation: {well_position.well.name} crop_r={r}px")
+
+
+    def _is_well_valid(self, welposition, experiment):
+        names = models.ExperimentWell.wellname_by_experiment(experiment.id)       
+        if welposition.well.name not in names:
+            return False
+        return True
+        
+    def _grid_scanning(self, experiment, xnext=0, ynext=0, simulate=False):
+        try:
             multiwell = experiment.multiwell
-        wells = models.WellPosition.objects.filter(multiwell_id=multiwell.id).order_by('order').all()
+            wellpositions = models.WellPosition.objects.filter(multiwell_id=multiwell.id).order_by('order').all()
+            
             cam = self.process.cam
             cam._aligner.set_tube_diameter(multiwell.diameter)    
     
-        self.stop_playing = Event()
-        for wl in wells:
+            for wl in wellpositions:
                 if self.stop_playing.is_set():
                     break
+                if not self._is_well_valid(wl, experiment):
+                    continue
+                
                 self.cnc_controller.move_to(wl.x, wl.y, feed=wl.multiwell.feed)
-            
-            uuid = f'{self.process.data.session}-{multiwell.position}-{wl.well.name}'
-            self._grid_scanning_capture(uuid, multiwell.duration)
-            
-            ## change file 
                 if self.process.conf.capture_type == 'file':
-                self.process.cam._error_occured = True            
+                    self._capture_file_simulation(wl.well.name)
+                elif self.process.conf.capture_type == 'video':
+                    self._capture_video_simulation(wl)
 
-            self.process._send(scan_state=f"{uuid}: capture")
-            
-        logger.info(f"Scan terminé — retour à l'origine (X={xnext:.1f}  Y={ynext:.1f})")
-        self.cnc_controller.move_to(xnext, ynext, feed=multiwell.feed*2)
+                self._grid_scanning_capture(experiment, wl, simulate=simulate)
+            msg =f"Scan terminé — retour à l'origine (X={xnext:.1f}  Y={ynext:.1f})"
+            logger.info(msg)
+            self.process._send(state='scan_finished', msg=msg)
+            return True
+        except Exception as e: 
+            msg = f"Error during grid scanning - {e}"
+            logger.error(msg)
+            self.process._send(state='error', msg=msg)
+            return False
+        finally: 
+            self.cnc_controller.move_to(xnext, ynext, feed=self.feed*2)
              
 
-    def _start_scanning(self, session, experiments):
+    def _start_scanning(self, session, experiments, simulate=False):
+        result = False
+        try:
+            self.process.get_config()   # get video configuration if updated
+            
             self.process.cam._aligner.debug = False
+            self.stop_playing.clear()
+            
             xynext = []
             for obs in experiments:
                 xynext.append((obs.multiwell.xbase, obs.multiwell.ybase))
@@ -171,20 +282,26 @@ class MultiWellManager:
             self.process.data.session = session.id
             started = timezone.now()
             for obs in experiments:
+                
+                msg = f"Starting scan for {obs} (well {pos}/{len(experiments)})"
+                logger.warning(msg)
+                self.process._send(well_state=msg)
+                
                 if self.stop_playing.is_set():
                     break
                 obs.started = timezone.now()
                 obs.save()
                 xnext, ynext = xynext[pos]
                 pos +=1
-            self._grid_scanning(obs, xnext=xnext, ynext=ynext)
+                result = self._grid_scanning(obs, xnext=xnext, ynext=ynext, simulate=simulate)
                 obs.finished = timezone.now()
                 obs.save()
                 
             session.finished = timezone.now()
-        if self.stop_playing.is_set():
+            if self.stop_playing.is_set() or not result:
                 msg = f"Session {session.name} abandonnée à {session.finished} après {session.finished - started} secondes."
             else:
+                if not simulate:
                     session.active = False
                     if session.scanning_task:
                         session.scanning_task.enabled = False
@@ -192,7 +309,12 @@ class MultiWellManager:
                 msg = f"Session {session.name} terminée à {session.finished} après {session.finished - started} secondes."
             logger.info(msg)
             self.process._send(scan_state=msg)
+        except Exception as e:
+            logger.error("Error during scanning process", e)
+        finally:
             self.scan_thread = None
+            self.goto_0()
+            self.process._send(current=self.get_well_order())
 
 
     def halt_scanning(self):
@@ -200,36 +322,65 @@ class MultiWellManager:
         self.stop_playing.set()
         self.well_iterator.reset()
         self.process.cam._aligner.debug = False
+        self.scan_thread = None
+        self.test_thread = None
 
          
-    def scanning(self, sid):
-        try:
+    def scan_process(self, sid, simulate=False):
         if self.scan_thread:
             return
         session = models.Session.objects.get(pk=sid)
         experiments = models.SessionExperiment.experiment_by_session(sid)      
-            self.scan_thread = Thread(target=self._start_scanning, args=(session, experiments, ), daemon=True).start()
-        except Exception as e:
-            print("MultiWellManager::scan error", e)       
+
+        self.scan_thread = Thread(target=self._start_scanning, args=(session, experiments, simulate, ), daemon=True)
+        self.scan_thread.start()
 
 
     def previous_well(self):
         wl = self.well_iterator.previous()
+        if self.process.conf.capture_type == 'file':
+            self._capture_file_simulation(wl.well.name)
+        elif self.process.conf.capture_type == 'video':
+            self._capture_video_simulation(wl)
         self.cnc_controller.move_to(wl.x, wl.y, feed=wl.multiwell.feed)
-        return {"state": "previous", "msg": f">>> ({wl.x}, {wl.y})"} 
+        return {"state": "previous", "msg": f">>> {wl.well.name}: ({wl.x}, {wl.y})"}
 
 
     def next_well(self):
         wl = self.well_iterator.next()
+        if self.process.conf.capture_type == 'file':
+            self._capture_file_simulation(wl.well.name)
+        elif self.process.conf.capture_type == 'video':
+            self._capture_video_simulation(wl)
         self.cnc_controller.move_to(wl.x, wl.y, feed=wl.multiwell.feed)
-        return {"state": "next", "msg": f">>> ({wl.x}, {wl.y})"} 
+        return {"state": "next", "msg": f">>> {wl.well.name}: ({wl.x}, {wl.y})"}
 
 
     def goto_well(self, numwell):
         wl = self.well_iterator.seek(numwell)
+        if self.process.conf.capture_type == 'file':
+            self._capture_file_simulation(wl.well.name)
+        elif self.process.conf.capture_type == 'video':
+            self._capture_video_simulation(wl)
         self.cnc_controller.move_to(wl.x, wl.y, feed=wl.multiwell.feed)
-        return {"state": "goto", "msg": f">>> ({wl.x}, {wl.y})"}    
+        return {"state": "goto", "msg": f">>> {wl.well.name}: ({wl.x}, {wl.y})"}
 
+    def goto_xy(self):
+        wl = self.well_iterator.seek(0)
+        if self.process.conf.capture_type == 'file':
+            self._capture_file_simulation(wl.well.name)
+        elif self.process.conf.capture_type == 'video':
+            self._capture_video_simulation(wl)
+        self.cnc_controller.move_to(self.xbase, self.ybase, feed=self.feed)
+
+    def goto_0(self):
+        self.well_iterator.reset()
+        if self.process.conf.capture_type == 'file':
+            self._capture_file_simulation('zero')
+        elif self.process.conf.capture_type == 'video':
+            # Plein cadre : désactiver le masque circulaire pour ne pas rogner la vue d'ensemble
+            self.process.cam.set_circular_crop(None)
+        self.cnc_controller.move_to(0, 0, feed=self.feed*2)
         
     def set_well_position(self):
         wl = self.well_iterator.get_current()
@@ -243,17 +394,22 @@ class MultiWellManager:
                                    
 
     def _scanning_test(self, auto=False):       
-        self.stop_playing = Event()
+        self.stop_playing.clear()
         cam = self.process.cam
         cam._aligner.set_tube_diameter(self.multiwell.diameter)
         duration = self.duration if not auto else settings.CALIBRATION_AUTO_DURATION      
-        try:
         start_test = time.monotonic()    
+        try:
             for wl in self.well_iterator:
                 if self.stop_playing.is_set():
                     break
+                
                 self.cnc_controller.wait_for(2.0)
                 self.cnc_controller.move_to(wl.x, wl.y, feed=wl.multiwell.feed)
+                if self.process.conf.capture_type == 'file':
+                    self._capture_file_simulation(wl.well.name)
+                elif self.process.conf.capture_type == 'video':
+                    self._capture_video_simulation(wl)
                 self.process._send(current=wl.order)
     
                 start = time.monotonic()
@@ -287,23 +443,24 @@ class MultiWellManager:
                             self.process._send(state='center', msg=msg)
 
                     self.cnc_controller.wait_for(0.1)
-            logger.info("Fin du centrage")        
+            logger.info("Fin du test")        
         except Exception as e:
-            print(e)
+            logger.error("Error during scanning test", e)
+        finally:
+            self.test_thread = None
             
         self.well_iterator.reset()
         self.process.cam._aligner.debug = False
 
         logger.info(f"Scan terminé — retour à l'origine (X=0, Y=0) en {int(time.monotonic()-start_test)} s")
-        self.cnc_controller.move_to(0, 0, feed=self.multiwell.feed*2)
-        self.test_thread = None
-        
+        self.goto_0()
+        self.process._send(current=self.get_well_order())
 
     def scan_test(self, auto=False):
         if self.test_thread:
             return
-        self.test_thread = Thread(target=self._scanning_test, args=(auto, ), daemon=True).start()
-
+        self.test_thread = Thread(target=self._scanning_test, args=(auto, ), daemon=True)
+        self.test_thread.start()
 
     @property
     def position(self):
@@ -369,14 +526,12 @@ class MultiWellManager:
     def dy(self, value):
         self._dy = value
 
-
     def get_well_order(self):
         wl = self.well_iterator.get_current() 
         if wl:
             return wl.order
         return None
     
-
     def set_position(self):
         x, y = self.cnc_controller.get_mpos()
         self.cnc_controller.wait_for(2.0)
@@ -387,17 +542,16 @@ class MultiWellManager:
         wl.px_per_mm = self.px_per_mm
         wl.save()
         
-        
     def calib_toggle_debug(self):
         """    Active / désactive le mode debug sur le stream."""
         aligner = self.process.cam._aligner
         aligner.debug = not aligner.debug       
-        return {"state": "debug", "msg": f"Debug: {aligner.debug}"}
+        return {"state": "debug", "value": aligner.debug, "msg": f"Debug: {aligner.debug}"}
     
     def set_calib_debug(self, value=True):
         """    Active / désactive le mode debug sur le stream."""
         aligner = self.process.cam._aligner
         aligner.debug = value      
-        return {"state": "debug", "msg": f"Debug: {aligner.debug}"}    
+        return {"state": "debug", "value": aligner.debug, "msg": f"Debug: {aligner.debug}"}    
     
     

test_tube_scanner/scanner/process.py

@@ -21,20 +21,25 @@ from celery.exceptions import Ignore
 from celery.utils.log import get_task_logger
 from redis import Redis
 from dataclasses import dataclass
-from modules import reductstore, grbl, utils
+from modules import reductstore, utils, planarian_metrics
 
 ## camera devices
 from modules.circular_crop import CircularCrop, CropStrategy
 from .multiwell import MultiWellManager
 from .constants import ScannerConstants
-from . import models
+from .models import MultiWell
 
+# CNC
+if not settings.GRBL_SIMULATION:
+    from modules.grbl import GRBLController  # @UnusedImport
+else:
+    from modules.grbl_simulator import GRBLController  # @Reimport
 
 @dataclass
 class ProcessData:
     play: bool = True
     record: bool = False
-    uuid: str = None
+    uuid: str | None = None
     session: int = 0
     tube_diameter: float = 16.0 
 
@@ -42,6 +47,8 @@ class ProcessData:
 logger = get_task_logger(__name__)
 redisDB = Redis(host=settings.REDIS_HOST, port=settings.REDIS_PORT, db=0, decode_responses=True)
 cameraDB = reductstore.ReductStore(name='camera')
+planarianDB = planarian_metrics.ReductStoreClient(url=settings.REDUCTSTORE_URL, token=settings.REDUCTSTORE_TOKEN)
+async_to_sync(planarianDB.connect)()
 
 
 class CameraRecordManager():
@@ -139,11 +146,12 @@ class CameraRecordManager():
 
 
 class ScannerProcess(Task):
-
+    name='scanner.scanner_process'
     def __init__(self):
         super().__init__()
+        
         self.channel_layer = get_channel_layer()
-        self.group = f'scanner_proc'
+        self.group = 'scanner_proc'
         self.stop_event = Event()
         self.cam = None
         self.grbl = None
@@ -153,6 +161,7 @@ class ScannerProcess(Task):
         self.data = ProcessData()
         self.manager = None
         self.recordDB = CameraRecordManager(cameraDB)
+        self.metricDB = planarianDB
 
     def __call__(self, *args, **kwargs):
         return self.start(*args, **kwargs)
@@ -160,9 +169,13 @@ class ScannerProcess(Task):
     def set_crop_radius(self, radius):
         return CircularCrop(radius=radius, strategy=CropStrategy.CROP_JPEG, jpeg_quality=self.image_quality)
     
-    def start(self, *args, **kwargs):
-        try:
-            self.conf = ScannerConstants().get()
+    def get_config(self):
+        '''
+        Constants:
+            reset si besoin les constantes vidéo
+        '''
+        self.constants = ScannerConstants()
+        self.conf = self.constants.get()
         self.use_tracking = self.conf.tracking
         
         self.video_quality = self.conf.video_jpeg_quality
@@ -170,25 +183,29 @@ class ScannerProcess(Task):
         self.video_fps = self.conf.video_frame_rate
         self.video_width = self.conf.video_width_capture
         self.video_height = self.conf.video_height_capture 
+        
         self.crop_radius = self.conf.calibration_crop_radius
 
         self.video_jpg_quality = [int(cv2.IMWRITE_JPEG_QUALITY), self.video_quality]
         self.image_jpg_quality = [int(cv2.IMWRITE_JPEG_QUALITY), self.image_quality]
+        return self.conf
+    
+    def save_config(self):
+        pass
+    
+
+    def start(self, *args, **kwargs):
+        try:            
+            self.get_config()
             self.grbl_xmax = self.conf.grbl_xmax
             self.grbl_ymax = self.conf.grbl_ymax   
-                    
             self.crop = self.set_crop_radius(self.crop_radius)
             
             capture_type = self.conf.capture_type
             if capture_type == 'file':
-                video_lists = []
-                wells = models.Well.objects.all()
-                for wl in wells:
-                    video_lists.append(str( settings.MEDIA_ROOT / 'simulation' / f'{wl.name}.mp4') )
-                
                 from modules.videofile_capture import VideoFileCapture
                 self.cam = VideoFileCapture(
-                    video_file=settings.MEDIA_ROOT / 'simulation' / 'A1.mp4',
+                    video_file=settings.MEDIA_ROOT / 'simulation' / 'default_simulation.mp4',
                     fps=self.video_fps,
                     width=self.video_width,
                     height=self.video_height,
@@ -196,7 +213,29 @@ class ScannerProcess(Task):
                     use_tracking=self.use_tracking,
                     display=self._display,
                     parent=self,
-                    video_lists=video_lists,
+                )
+            elif capture_type == 'video':
+                from modules.videoplate_capture import VideoPlateCapture
+                from .models import VideoPlate
+
+                vp = VideoPlate.active_video()
+                if not vp:
+                    raise Exception("Aucun VideoPlate actif trouvé — créer un enregistrement dans l'admin.")
+                initial_path = vp.video_file.path if vp.video_file else None
+                mw = vp.multiwell
+
+                self.cam = VideoPlateCapture(
+                    video_dir=settings.MEDIA_ROOT / 'videos',
+                    fps=self.video_fps,
+                    jpeg_quality=self.video_quality,
+                    use_tracking=self.use_tracking,
+                    display=self._display,
+                    parent=self,
+                    crop_radius_px=mw.crop_radius,
+                    px_per_mm=vp.px_per_mm,
+                    x_offset_mm=vp.x_origin_mm,
+                    y_offset_mm=vp.y_origin_mm,
+                    initial_video_path=initial_path,
                 )
             elif capture_type == 'webcam':
                 from modules.webcam_capture import WebcamCapture
@@ -226,7 +265,12 @@ class ScannerProcess(Task):
             self.cam._active_median = False
             self.cam.set_circular_crop(None)
             
-            self.grbl = grbl.GRBLController(
+            # Mode vidéo : toujours simuler le GRBL (pas de CNC physique)
+            if capture_type == 'video':
+                from modules.grbl_simulator import GRBLController as _GRBLCtrl
+            else:
+                _GRBLCtrl = GRBLController
+            self.grbl = _GRBLCtrl(
                 send_callback=self._display,
                 x_max=self.conf.grbl_xmax,
                 y_max=self.conf.grbl_ymax
@@ -234,6 +278,8 @@ class ScannerProcess(Task):
 
             self.stop_event.clear()
             self.start_services()
+            
+            return self.name
         except Exception as e:
             logger.error(f"Scanner started error: {e}")
             raise Ignore()
@@ -250,11 +296,14 @@ class ScannerProcess(Task):
             self.stop_event.set()
 
     def start_services(self):
-        Thread(target=self._listen_to_redis, daemon=True).start()
+        Thread(target=self._init_manager, daemon=True).start()
         Thread(target=self._recording, daemon=True).start()
         Thread(target=self._init_grbl, daemon=True).start()
+        Thread(target=self._listen_to_redis, daemon=True).start()
         self.cam.start()
 
+        logger.warning(f"Scanner services started ...")
+
     def _send(self, **payload):
         async_to_sync(self.channel_layer.group_send)(
             self.group, {
@@ -267,30 +316,53 @@ class ScannerProcess(Task):
         if self.grbl:
             self._send(**msg)
     
-    def _on_frame(self, jpeg_bytes: bytes, ts: datetime, metrics: dict) -> None:
+    
+    def _store_metric(self, uuid, metrics, ts):
+        
+        if not isinstance(metrics, list):
+            return
+        for r in metrics:
+            pid = r["planarian_id"]            
+            record = self.cam._metrics[pid].update(r, well_radius_mm=self.cam._params.well_radius_mm)
+
+            async_to_sync(planarianDB.store_metric)(
+                record,
+                self.cam._params.experiment,
+                self.cam._params.well,
+                uuid=uuid,
+                planarian=pid,
+                ts_us=ts,
+            )
+                  
+    def _store_frame(self, uuid, frame, ts, frame_count):
+        labels = {
+            "fps":  self.video_fps,
+            "record_type": 'frame',
+            "frame_count": frame_count,
+        }
+        self.recordDB.write(uuid, frame, ts=ts, labels=labels)
+                 
+    def _on_frame(self, jpeg_bytes: bytes, ts: datetime, metrics: dict, frame_count: int = 0) -> None:
+        try:
             if self.data.record:
-            self.record_queue.put((self.data.uuid, ts, jpeg_bytes, metrics))
+                self.record_queue.put((self.data.uuid, ts, jpeg_bytes, metrics, frame_count))
             if self.data.play:
-            self._send(ts=ts.timestamp(), jpeg=base64.b64encode(jpeg_bytes).decode(), **metrics)
+                    jpeg=base64.b64encode(jpeg_bytes).decode()
+                    self._send(ts=ts.timestamp(), jpeg=jpeg, frame_count=frame_count)
+        except Exception as e:
+            logger.error(e)
+
                 
     def _recording(self):
         logger.info(f"Scanner {self.group}: start recorder")
         while not self.stop_event.is_set():
             try:
-                (uuid, ts, frame, metrics) = self.record_queue.get()
-                labels = dict(fps=self.video_fps, session=self.data.session, detected="1" if metrics.get("detected") else "0")
+                (uuid, ts, frame, metrics, frame_count) = self.record_queue.get()
+                if self.cam.use_tracking:
+                    self._store_metric(uuid, metrics, ts.timestamp())
                                               
-                if metrics.get("detected"):
-                    labels.update({
-                        "cx"          : str(metrics["cx"]),
-                        "cy"          : str(metrics["cy"]),
-                        "area_px"     : str(metrics["area_px"]),
-                        "speed_px_s"  : str(metrics["speed_px_s"]),
-                        "axial_pos"   : str(metrics["axial_pos"]),
-                        "axial_speed" : str(metrics["axial_speed"]),
-                    })    
+                self._store_frame(uuid, frame, ts, frame_count)
                 
-                self.recordDB.write(uuid, frame, labels, ts=ts)
                 self.record_queue.task_done()
             except Exception as e:
                 logger.error(f'recorder: {e}')
@@ -302,18 +374,23 @@ class ScannerProcess(Task):
         self._send(state='serial', msg=f"Connected {self.grbl.port}")        
         
         self.grbl.go_origin(feed=feed)
+        if self.conf.capture_type == 'file':
+            self.manager._capture_file_simulation('zero')  
         self.grbl.wait_for(2.0)
 
 
+    def _init_manager(self):
+        logger.info(f"==== Start MultiWellManager!")
+        self.manager = MultiWellManager(process=self)
+        self.manager.set_calib_debug(False)
+        Event().wait(2.0)
+
+
     def _listen_to_redis(self):
-        try:
         logger.info(f"==== Scanner {self.group}: listen via redisDB")
         pubsub = redisDB.pubsub()
         pubsub.subscribe(self.group)        
-            #self._init_grbl()
-            self.manager = MultiWellManager(process=self)
-            self.manager.set_calib_debug(False)
-            
+        try:
             for message in pubsub.listen():
                 try:
                     #logger.info(f"{message}")
@@ -327,21 +404,58 @@ class ScannerProcess(Task):
                         continue
 
                     self._send(state=cmd["type"], msg=f"Cmd: {cmd.get('topic')} {cmd.get('value', '')}")      
+                    ctx = {}             
                     if cmd["type"]=="scanner":
                         topic = cmd.get("topic")
                         if topic == 'init':
-                            self.cam.set_circular_crop(self.crop)
+                            sid = cmd.get("sid")
+                            self.manager.set_first_multiwell_from_session(sid)     
                             self.cam._active_median = False
-                            self.grbl.go_origin(feed=self.manager.feed)
+                            self.cam.set_edge_enhance(False)
+                            if self.conf.capture_type == 'video':
                                 
-                        elif topic == 'scan':
+                                self.cam._active_crop = False
+                                
+                                
+                                self.cam.set_circular_crop(None)
+                                ctx = dict(state="crop", value=self.cam._active_crop)
+                            else:
+                                self.cam.set_circular_crop(self.crop)
+                            self.grbl.go_origin(feed=self.manager.feed)
+                            self.cam.set_draw_contours(False)
+    
+                        elif topic == 'video_plate':
+                            new_path = cmd.get('path')
+                            if new_path and hasattr(self.cam, 'set_video_file'):
+                                self.cam.set_video_file(new_path)
+                                self._send(state='video_plate', msg=f"Vidéo: {new_path}")
+                            continue
+
+                        elif topic == 'scan' or topic == 'simulate':
+                            logger.info(f"==== Scan {cmd}")
                             sid = cmd.get("session", '0')
+                            
                             if sid == "0":
                                 self._send(state='error', msg=str(_('La session est nulle!...')))
                             else:
+                                try:
                                     self.cam._active_median = False
-                                self.manager.scanning(sid)
+                                    self.cam.set_edge_enhance(False)
+                                    simulate = (topic=='simulate')   
+                                    self.manager.scan_process(sid, simulate)
 
+                                    self._send(state=topic, msg=str(_('Balayage démarré...')))
+                                except Exception as e:
+                                    logger.error(f"Scan error: {e}")
+                                    self._send(state='error', msg=str(_('Erreur lors du démarrage du balayage...')))  
+                            continue
+                        
+                        self._send(
+                            buttons=self.manager.multiwell_buttons(btn_class="w3-btn well", onclick=""),
+                            columns=self.manager.multiwell.cols,
+                            current=self.manager.get_well_order(),
+                            **ctx
+                        )                                
                     elif cmd["type"]=="calibrate":
                         topic = cmd.get("topic")
                         value = cmd.get("value")
@@ -356,6 +470,8 @@ class ScannerProcess(Task):
                             self.manager.set_multiwell(position)
                             self.cam.set_circular_crop(None)
                             self.cam._active_median = False
+                            self.cam.set_edge_enhance(False)
+                            self.cam.set_draw_contours(False)
                             buttons = self.manager.multiwell_buttons()
 
                         elif topic == 'up':
@@ -372,18 +488,34 @@ class ScannerProcess(Task):
                             
                         elif topic == 'median':
                             self.cam._active_median = not self.cam._active_median
+                            self._send(state="median", value=self.cam._active_median, msg=f"Median: {self.cam._active_median}")
+                            continue
+
+                        elif topic == 'edge_enhance':
+                            self.cam.set_edge_enhance(not self.cam._active_edge_enhance)
                             continue
                         
                         elif topic == 'crop':
                             self.cam._active_crop = not self.cam._active_crop
-                            self.cam.set_circular_crop(self.crop) if self.cam._active_crop else self.cam.set_circular_crop(None)
+                            if self.cam._active_crop:
+                                self.cam.set_circular_crop(self.crop)
+                                # En mode vidéo, naviguer vers le premier puit (Base)
+                                # pour que le crop circulaire soit aligné sur un puit réel
+                                if self.conf.capture_type == 'video':
+                                    self.manager.goto_xy()
+                            else:
+                                self.cam.set_circular_crop(None)
+                            self._send(state="crop", value=self.cam._active_crop, msg=f"Crop: {self.cam._active_crop}")
                             continue
                         
                         elif topic == 'crop_radius':
                             self.conf.calibration_crop_radius=int(value)
                             self.crop = self.set_crop_radius(self.conf.calibration_crop_radius)
-                            self.conf.save()
+                            self.constants.save_config()  # type: ignore[attr-defined]
+                            
                             self.cam.set_circular_crop(self.crop)
+                            
+                            self.manager.update_crop_radius(int(value))
                             continue   
                                              
                         elif topic == 'position':
@@ -400,12 +532,10 @@ class ScannerProcess(Task):
                             self.manager.duration = float(value)   
                                  
                         elif topic == 'goto_0':
-                            self.grbl.go_origin(feed=self.manager.feed)
-                            self.manager.well_iterator.reset()
+                            self.manager.goto_0()
 
                         elif topic == 'goto_xy':
-                            self.grbl.move_to(self.manager.xbase, self.manager.ybase, feed=self.manager.feed)
-                            self.manager.well_iterator.seek(0)
+                            self.manager.goto_xy()  
 
                         elif topic == 'xy_base':
                             self.manager.set_position()
@@ -417,6 +547,12 @@ class ScannerProcess(Task):
                         elif topic == 'auto':
                             self.manager.set_calib_debug(True)
                             self.cam.set_circular_crop(self.crop)
+                            # En mode vidéo le puit remplit le crop (ratio ~0.50) ;
+                            # en mode caméra le tube occupe ~30% du champ.
+                            if self.conf.capture_type == 'video':
+                                self.cam._aligner.set_radius_range(0.38, 0.47)
+                            else:
+                                self.cam._aligner.set_radius_range(0.26, 0.37)
                             self.manager.scan_test(auto=True)
                             continue
                            
@@ -431,12 +567,22 @@ class ScannerProcess(Task):
                         elif topic == 'halt':
                             self.manager.halt_scanning()
                             
-                        
                         elif topic == 'calib_debug':
+                            if self.conf.capture_type == 'video':
+                                self.cam._aligner.set_radius_range(0.38, 0.47)
+                            else:
+                                self.cam._aligner.set_radius_range(0.26, 0.37)
                             msg = self.manager.calib_toggle_debug()
                             self._send(**msg)
                             continue
 
+                        elif topic == 'draw_debug':
+                            a = self.cam._aligner
+                            a.draw_annotations = not a.draw_annotations
+                            self._send(state='draw_debug', value=a.draw_annotations,
+                                       msg=f"Draw debug: {a.draw_annotations}")
+                            continue
+                        
                         elif topic == 'previous':
                             msg = self.manager.previous_well()
                             self._send(**msg)  
@@ -453,6 +599,17 @@ class ScannerProcess(Task):
                             msg = self.manager.set_well_position()
                             self._send(**msg)
                             
+                        elif topic == 'draw':
+                            draw = (value=="1")
+                            self.cam.set_draw_contours(draw)
+                            self._send(state=topic, msg=f"Tracking contour: {draw}")                                
+                                                    
+                        elif topic in ['min_area_px', 'max_area_ratio', 'max_planarians', 'merge_kernel_size', 'min_contour_dist_px']:
+                            value = int(value) if topic in ['min_area_px', 'max_planarians', 'merge_kernel_size', 'min_contour_dist_px'] else float(value)
+                            self.manager.tracker_config[topic] = value
+                            self.cam.on_test_well_change(**self.manager.tracker_config)
+                            self._send(state=topic, msg=f"Value changed {value}")                            
+                            
                         self._send(
                             xbase=self.manager.xbase, 
                             ybase=self.manager.ybase, 
@@ -463,6 +620,7 @@ class ScannerProcess(Task):
                             dx=self.manager.dx, 
                             dy=self.manager.dy,
                             buttons=buttons,
+                            columns=self.manager.multiwell.cols,
                             current=self.manager.get_well_order(),
                         )
                 except Exception as e:
@@ -624,12 +782,11 @@ class ReplayProcess(Task):
         logger.info(f"==== ReplayProcess stopped.")
 
     def _listen_to_redis(self):
-        try:
         loop = None
         logger.info(f"==== ReplayProcess {self.group}: listen via redisDB")
         pubsub = redisDB.pubsub()
         pubsub.subscribe(self.group)
-
+        try:
             for message in pubsub.listen():
                 try:
                     if self.stop_event.is_set():
@@ -681,6 +838,7 @@ class ReplayProcess(Task):
                     logger.error(f'ReplayProcess::listen_to_redis: {e}')
         finally:
             self.running.set()
+            if loop:
                 utils.stop_async(loop)
             pubsub.unsubscribe()
             pubsub.close()

test_tube_scanner/scanner/static/scanner/css/calibration.css

@@ -5,10 +5,8 @@
 
 .well-btn {
   display: grid; 
-  grid-template-columns: repeat(6, 1fr);
+  grid-template-columns: repeat(var(--well-columns, 6), 1fr);
   justify-items: center; 
   align-items: center; 
 }
 
-
-

test_tube_scanner/scanner/static/scanner/css/main.css

@@ -1 +0,0 @@
-

test_tube_scanner/scanner/static/scanner/css/scanning.css

@@ -0,0 +1,11 @@
+
+.well {
+    padding: 0.2em;
+}
+
+.well-btn {
+  display: grid; 
+  grid-template-columns: repeat(var(--well-columns, 6), 1fr);
+  justify-items: center; 
+  align-items: center; 
+}

test_tube_scanner/scanner/static/scanner/css/video_upload.css

@@ -0,0 +1,72 @@
+.video-drop-zone {
+    display: flex;
+    flex-direction: column;
+    align-items: center;
+    justify-content: center;
+    min-height: 80px;
+    margin-top: 8px;
+    padding: 12px 20px;
+    border: 2px dashed #aaa;
+    border-radius: 6px;
+    background: #f9f9f9;
+    cursor: pointer;
+    transition: border-color 0.2s, background 0.2s;
+    gap: 8px;
+}
+
+.video-drop-zone:hover,
+.video-drop-zone.drag-over {
+    border-color: #417690;
+    background: #e8f3fb;
+}
+
+.video-drop-zone.has-file {
+    border-style: solid;
+    border-color: #28a745;
+    background: #f0fff4;
+}
+
+.video-drop-hint {
+    font-size: 0.9em;
+    color: #555;
+    pointer-events: none;
+    text-align: center;
+}
+
+.video-drop-zone.has-file .video-drop-hint {
+    color: #28a745;
+    font-weight: 600;
+}
+
+/* ---- Progress bar ---- */
+
+.video-progress-wrap {
+    display: none;
+    width: 100%;
+    max-width: 360px;
+}
+
+.video-progress-bar-track {
+    width: 100%;
+    height: 10px;
+    background: #ddd;
+    border-radius: 5px;
+    overflow: hidden;
+    margin-bottom: 2px;
+}
+
+.video-progress-bar {
+    height: 10px;
+    width: 0%;
+    background: #417690;
+    border-radius: 5px;
+    transition: width 0.3s ease;
+}
+
+.video-progress-label {
+    display: block;
+    text-align: right;
+    font-size: 0.8em;
+    color: #417690;
+    font-weight: 600;
+}

test_tube_scanner/scanner/static/scanner/js/calibration.js

@@ -33,15 +33,26 @@ class ScannerManager {
         this.well    = options.well; 
         this.debug   = options.debug; 
         this.calib_debug = options.calib_debug;
+        this.draw_debug  = options.draw_debug;
         this.calib_center= options.calib_center;
         this.previous    = options.previous;   
         this.next        = options.next;     
         this.set_well    = options.set_well; 
         this.well_btn    = options.well_btn;  
         this.median       = options.median;
+        this.edge_enhance = options.edge_enhance;
         this.crop         = options.crop;
         this.crop_radius = options.crop_radius;
         this.calib_auto  = options.calib_auto;
+        
+        try {
+            this.min_area_px = options.min_area_px;
+            this.max_area_ratio = options.max_area_ratio;
+            this.max_planarians = options.max_planarians;
+            this.merge_kernel_size = options.merge_kernel_size;
+            this.min_contour_dist_px = options.min_contour_dist_px;
+            this.draw = options.draw;
+        } catch(e) {}    
     }
     
     init_controls() {
@@ -53,24 +64,35 @@ class ScannerManager {
         this.goto_0.addEventListener('click',      (e) => { this.clear_buttons(); this._send({ type: 'calibrate', topic: "goto_0" }); });
         this.goto_xy.addEventListener('click',     (e) => { this.clear_buttons(); this._send({ type: 'calibrate', topic: "goto_xy" }); });
         this.xy_base.addEventListener('click',     (e) => { this._send({ type: 'calibrate', topic: "xy_base" }); });
-        
-        this.calib_debug.addEventListener('click', (e) => { this._send({ type: 'calibrate', topic: "calib_debug" }); });       
-        this.previous.addEventListener('click',    (e) => { this._send({ type: 'calibrate', topic: "previous" }); });
-        this.next.addEventListener('click',        (e) => { this._send({ type: 'calibrate', topic: "next" }); });       
         this.set_well.addEventListener('click',    (e) => { this._send({ type: 'calibrate', topic: "set_well" }); });       
-        
         this.median.addEventListener('click',       (e) => { this._send({ type: 'calibrate', topic: "median" }); });
+        this.edge_enhance.addEventListener('click', (e) => { this._send({ type: 'calibrate', topic: "edge_enhance" }); });
         this.crop.addEventListener('click',         (e) => { this._send({ type: 'calibrate', topic: "crop" }); });
         this.crop_radius.addEventListener('change',(e) => { this._send({ type: 'calibrate', topic: "crop_radius", value: this.crop_radius.value }); });
+
         this.well.addEventListener("change",       (e) => { this._send({ type: 'calibrate', topic: "position", value: e.target.value }); });
         this.step.addEventListener("change",       (e) => { this._send({ type: 'calibrate', topic: "step", value: e.target.value }); });
         this.feed.addEventListener("change",       (e) => { this._send({ type: 'calibrate', topic: "feed", value: e.target.value }); });
         this.duration.addEventListener("change",   (e) => { this._send({ type: 'calibrate', topic: "duration", value: e.target.value }); });
 
         this.test.addEventListener('click',         (e) => { this._send({ type: 'calibrate', topic: "test" }); });
+
+        this.halt.addEventListener('click',         (e) => { this._send({ type: 'calibrate', topic: "halt" }); });
+        this.calib_debug.addEventListener('click', (e) => { this._send({ type: 'calibrate', topic: "calib_debug" }); });
+        this.draw_debug.addEventListener('click',  (e) => { this._send({ type: 'calibrate', topic: "draw_debug" }); });
+        try { 
+   
+            this.previous.addEventListener('click',    (e) => { this._send({ type: 'calibrate', topic: "previous" }); });
+            this.next.addEventListener('click',        (e) => { this._send({ type: 'calibrate', topic: "next" }); }); 
             this.calib_center.addEventListener('click', (e) => { this._send({ type: 'calibrate', topic: "center" }); });
             this.calib_auto.addEventListener('click',   (e) => { this._send({ type: 'calibrate', topic: "auto" }); });            
-        this.halt.addEventListener('click',         (e) => { this._send({ type: 'calibrate', topic: "halt" }); });
+            this.min_area_px.addEventListener('change',         (e) => { this._send({ type: 'calibrate', topic: "min_area_px", value: e.target.value }); });
+            this.max_area_ratio.addEventListener('change',      (e) => { this._send({ type: 'calibrate', topic: "max_area_ratio", value: e.target.value }); });
+            this.max_planarians.addEventListener('change',      (e) => { this._send({ type: 'calibrate', topic: "max_planarians",  value: e.target.value}); });
+            this.merge_kernel_size.addEventListener('change',   (e) => { this._send({ type: 'calibrate', topic: "merge_kernel_size",  value: e.target.value}); });
+            this.min_contour_dist_px.addEventListener('change', (e) => { this._send({ type: 'calibrate', topic: "min_contour_dist_px", value: e.target.value }); });
+            this.draw.addEventListener('click',                (e) => { this._send({ type: 'calibrate', topic: "draw", value: e.target.value }); });
+        } catch(e) {console.log(e);}    
     }
 
     registerSocket(socket)  {
@@ -83,25 +105,32 @@ class ScannerManager {
             if (payload.jpeg)   { this.container.src = `data:image/jpeg;base64,${payload.jpeg}`; }
             if (payload.xbase)  { this.xbase.textContent = payload.xbase;  this.ybase.textContent = payload.ybase; }
             if (payload.xy)     { this.x.textContent=payload.x.toFixed(2); this.y.textContent=payload.y.toFixed(2); }
-            if (payload.state)  { this.debug.insertAdjacentHTML('afterbegin', `<li>[ ${++this.debug_count} - ${payload.state} ]: ${payload.msg}</li>`); }
+            if (payload.state)  { 
+                if (payload.state == 'debug') {
+                    const span = this.calib_debug.querySelector("span.debug"); span.style.color = payload.value ? '#f0f': '#fff';
+                } else if (payload.state == 'draw_debug') {
+                    const span = this.draw_debug.querySelector("span.draw_debug"); span.style.color = payload.value ? '#0ff' : '#888';
+                } else if (payload.state == 'median') {
+                    const span = this.median.querySelector("span.median"); span.style.color = payload.value ? '#f0f' : '#fff';
+                } else if (payload.state == 'edge_enhance') {
+                    const span = this.edge_enhance.querySelector("span.edge_enhance"); span.style.color = payload.value ? '#0ff' : '#fff';
+                } else if (payload.state == 'crop') {
+                    const span = this.crop.querySelector("span.crop"); span.style.color = payload.value ? '#f0f' : '#fff';
+                }
+                this.debug.insertAdjacentHTML('afterbegin', `<li>[ ${++this.debug_count} - ${payload.state} ]: ${payload.msg}</li>`); 
+            }
             if (payload.ts)     { this.ts.textContent = timestampToLocalISOString(payload.ts); }
                         
-            if (payload.detected && use_tracking) { 
-                this.cx.textContent = payload.cx; this.cy.textContent = payload.cy;
-                this.speed_px_s.textContent = payload.speed_px_s; 
-                this.axial_speed.textContent = payload.axial_speed; 
-                this.axial_pos.textContent = payload.axial_pos;
-                this.area_px.textContent = payload.area_px; 
-                this.frame_count.textContent = payload.count;           
+            if (payload.buttons) { 
+                this.well_btn.innerHTML = payload.buttons; 
+                document.documentElement.style.setProperty('--well-columns', payload.columns);
             }
-            if (payload.buttons) { this.well_btn.innerHTML = payload.buttons; }
             if (payload.current >= 0) {                 
                 document.querySelectorAll('button.w3-button.well').forEach(btn => {
                     if (btn.value==payload.current) { btn.classList.add('w3-green'); return; }
                     btn.classList.remove('w3-green'); 
                 });
             }
-
         } catch(e) { console.log(e); }
     }
     

test_tube_scanner/scanner/static/scanner/js/replay.js

@@ -171,7 +171,7 @@ class ReplayManager {
         const ok = confirm(`Télécharger le fichier ?\n\n${filename}`);
         if (!ok) return false;
 
-        fetch(this.video_endpoint, {
+        csrfFetch(this.video_endpoint, {
             method: 'POST',
             headers: { 'Content-Type': 'application/json' },
             body: JSON.stringify({