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Video plate capture: calibration, edge enhance, auto-detect well borders

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This commit is contained in:
denis defolie
2026-06-03 17:56:23 +02:00
parent 4b42c03756
commit 9bb8fc1bce
58 changed files with 1699 additions and 274 deletions
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etc/1-install-sys.sh
+5 -4
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@@ -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
@@ -24,8 +24,8 @@ sudo apt -y install python3-dev python3-pip python3-venv libpq-dev default-libmy
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/requirements.txt
+2 -1
View File
@@ -11,6 +11,7 @@ twisted[tls,http2]
celery[redis]
python-decouple
PyYaml
requests
reduct-py
python-dateutil
psutil
@@ -20,4 +21,4 @@ mysqlclient
psycopg2
pyserial
scipy
django-stubs[compatible-mypy]
pyrightconfig.json
+16
View File
@@ -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/home/management/commands/export_video.py
+1 -1
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@@ -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
+2 -2
View File
@@ -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
+1 -1
View File
@@ -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/test_L2544.py
+5 -1
View File
@@ -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
+4 -4
View File
@@ -19,7 +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/
@@ -35,10 +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'
@@ -237,7 +237,7 @@ 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
test_tube_scanner/modules/capture_interface.py
+41 -6
View File
@@ -25,7 +25,7 @@ from asgiref.sync import async_to_sync
from django.conf import settings
from modules.planarian_tracker import PlanarianTracker
from modules.planarian_metrics import ExperimentParams
from modules.planarian_metrics import ExperimentParams, EthoVisionMetrics
from modules.tube_aligner import TubeAligner
@@ -81,11 +81,12 @@ 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 = None
self._metrics = None
self._params = None
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
@@ -284,10 +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.
@@ -306,7 +327,11 @@ class VideoCaptureInterface(abc.ABC):
if frame is None:
return jpeg, metrics
try:
# Mode debug
# 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')
@@ -325,6 +350,16 @@ class VideoCaptureInterface(abc.ABC):
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:
test_tube_scanner/modules/circular_crop.py
+1 -1
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@@ -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
+7 -7
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@@ -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
+16 -10
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@@ -15,6 +15,7 @@ import logging
import time
import threading
import math
from typing import Callable, Any
logging.basicConfig(level=logging.INFO)
@@ -47,12 +48,11 @@ 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
# Position courante simulée
self.x, self.y = 0.0, 0.0
self.x: float | None = None
self.y: float | None = None
# État interne de la machine simulée
self._machine_state = 'Idle' # Idle | Run | Alarm
@@ -150,7 +150,7 @@ class GRBLController:
# Homing : retour à l'origine avec délai simulé
self._machine_state = 'Run'
self._state(state='send', msg="SIMULATOR: homing...")
distance = math.hypot(self.x, self.y)
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'
@@ -158,7 +158,9 @@ class GRBLController:
# --- Extraction des coordonnées X, Y et du feed F ---
tokens = cmd_upper.replace(',', ' ').split()
new_x, new_y, feed = self.x, self.y, 1000.0
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'):
@@ -186,8 +188,10 @@ class GRBLController:
# --- Mouvement effectif (G0, G1, G53 G1, etc.) ---
has_move = any(t in tokens for t in ('G0', 'G1', 'G53'))
if has_move and (new_x != self.x or new_y != self.y):
distance = math.hypot(new_x - self.x, new_y - self.y)
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
@@ -208,7 +212,9 @@ class GRBLController:
def get_status(self):
'''Retourne un status GRBL simulé au format <State|MPos:x,y,z>.'''
status = f"<{self._machine_state}|MPos:{self.x:.3f},{self.y:.3f},0.000|FS:0,0>"
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
@@ -257,7 +263,7 @@ 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 0.0) + dx, (y or 0.0) + dy, feed=feed)
def move_relative__(self, dx=0, dy=0, feed=1000):
self.send("G91") # Mode relatif
test_tube_scanner/modules/planarian_metrics.py
+31 -1
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@@ -282,7 +282,7 @@ class EthoVisionMetrics:
self.total_distance_mm += dist_mm
# Vecteur de déplacement (pour calculs d'angle)
if self._prev_cx_mm is not None:
if self._prev_cx_mm is not None and self._prev_cy_mm is not None:
move_dx = cx_mm - self._prev_cx_mm
move_dy = cy_mm - self._prev_cy_mm
else:
@@ -570,6 +570,36 @@ class ExperimentParams:
**BEHAVIOUR_DEFAULTS,
}
# Attributs issus de REQUIRED
experiment: str
well: str
px_per_mm: float
fps: float
# Attributs issus de DEFAULTS
well_radius_mm: float
thresh_immobile: float
thresh_mobile: float
planarian_count: int
tube_axis: str
min_area_px: int
max_area_ratio: float
merge_kernel_size: int
min_contour_dist_px: int
# Attributs issus de BEHAVIOUR_DEFAULTS
thigmotaxis_wall_dist_mm: float
photo_mode: str
photo_strength: float
photo_x: float
photo_y: float
photo_flee_angle_deg: float
chemo_strength: float
chemo_x: float
chemo_y: float
chemo_radius_mm: float
chemo_approach_angle_deg: float
avoid_radius_mm: float
aggreg_radius_mm: float
def __init__(self, data: dict):
missing = self.REQUIRED - set(data.keys())
if missing:
test_tube_scanner/modules/planarian_tracker.py
+8 -8
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@@ -75,12 +75,12 @@ class PlanarianState:
Args:
idx : index de l'individu (0-based)
"""
self.idx = idx
self.cx = None
self.cy = None
self.ts = None
self.lost = 0 # compteur de frames sans détection
self.active = False # vrai si l'individu a été détecté au moins une fois
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):
"""
@@ -117,7 +117,7 @@ class PlanarianState:
Returns:
tuple (speed_px_s, axial_speed) ou (0.0, 0.0) si état vide
"""
if self.cx is None or self.ts is None:
if self.cx is None or self.cy is None or self.ts is None:
return 0.0, 0.0
dt = ts - self.ts
@@ -445,7 +445,7 @@ class PlanarianTracker:
row_ind, col_ind = linear_sum_assignment(cost)
# Construire le dict d'association
assignment = {i: None for i in range(n_slots)}
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):
test_tube_scanner/modules/reductstore.py
-1
View File
@@ -32,7 +32,6 @@ class ReductStoreBase(ABC):
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
+1 -1
View File
@@ -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
+21 -6
View File
@@ -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
+3
View File
@@ -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
+4 -4
View File
@@ -33,7 +33,7 @@ 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,
@@ -50,7 +50,7 @@ class VideoFileCapture(VideoCaptureInterface):
:param height: Hauteur souhaitée (None = valeur par défaut du pilote)
"""
super().__init__(fps=fps, use_tracking=use_tracking, display=display, parent=parent, jpeg_quality=jpeg_quality)
self._video_file: str = video_file
self._video_file: str | None = video_file
self._jpeg_quality: int = jpeg_quality
self._width: Optional[int] = width
self._height: Optional[int] = height
@@ -134,8 +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
+226
View File
@@ -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/planarian/migrations/0001_initial.py
+56
View File
@@ -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
+26
View File
@@ -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/migrations/__init__.py
View File
test_tube_scanner/planarian/tasks.py
+1 -1
View File
@@ -33,7 +33,7 @@ def export_experiment_metrics_task(experiment_id):
return
jobs = []
configs = (ExperimentConfig.objects.filter(experiment_key_id=experiment.id).order_by("well"))
configs = (ExperimentConfig.objects.filter(experiment_key_id=experiment.pk).order_by("well"))
for conf in configs:
well = conf.well
count = conf.planarian_count
test_tube_scanner/planarian/templates/planarian/base.html
+1 -1
View File
@@ -1,5 +1,5 @@
{% extends "scanner/base.html" %}
{% load i18n home_tags scanner_tags %}
{% load i18n home_tags %}
{% block styles %}
{{ block.super }}
<link href="/static/planarian/css/planarian.css" rel="stylesheet">
test_tube_scanner/planarian/views.py
+7 -7
View File
@@ -93,7 +93,7 @@ def export_metrics(request):
if action=='experiment_csv':
experiment = models.Experiment.objects.filter(pk=pid).first()
if experiment:
export_experiment_metrics_task.delay(experiment.id) # @UndefinedVariable
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:
@@ -118,7 +118,7 @@ def export_csv_view(request):
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.id, experiment.multiwell.position, well_name)
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:
@@ -126,7 +126,7 @@ def export_csv_view(request):
response["Content-Disposition"] = f'attachment; filename="{filename}"'
return response'''
csv_content, n = export_csv_sync(
experiment=experiment.identifier,
experiment=experiment.identifier, # type: ignore[union-attr]
well=well_name,
uuid=uuid,
planarian=request.POST.get("planarian"),
@@ -136,7 +136,7 @@ def export_csv_view(request):
)
if csv_content:
filename = (
f"{experiment.identifier}_{well_name}-{request.POST.get('planarian')}_"
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)}")
@@ -223,8 +223,8 @@ def import_csv_view(request):
return import_csv(request, current_experiment, rows, overwrite)
except Exception as e:
messages.error(request, msg)
logger.error(msg)
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))
@@ -266,6 +266,6 @@ class TrackingDataView(View):
return JsonResponse({"count": len(records), "records": records})
def get_context_data(self, **kwargs):
context = super().get_context_data(**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/planarian_sim.py
+10 -5
View File
@@ -29,6 +29,7 @@ try:
from planarian_metrics import EthoVisionMetrics
HAS_METRICS = True
except ImportError:
EthoVisionMetrics = None # type: ignore[assignment]
HAS_METRICS = False
import numpy as np
import math
@@ -1007,8 +1008,8 @@ def draw_arena(frame, cfg, width, height, arena_center, arena_radius_px, mm_to_p
cv2.circle(overlay, arena_center, arena_radius_px + r_off, (245, 243, 238), 3)
cv2.addWeighted(overlay, alpha / 255.0, frame, 1 - alpha / 255.0, 0, frame)
cv2.circle(frame, arena_center, arena_radius_px, arena_border, 2)
cv2.circle(frame, arena_center, arena_radius_px + 4, (200, 198, 192), 1)
cv2.circle(frame, arena_center, arena_radius_px, arena_border, 4)
cv2.circle(frame, arena_center, arena_radius_px + 8, (200, 198, 192), 1)
bar_len = int(mm_to_px)
bx, by = width - 40, height - 25
@@ -1191,14 +1192,18 @@ def main():
}
metrics_list = []
if HAS_METRICS:
assert EthoVisionMetrics is not None
for _ in planaires:
metrics_list.append(EthoVisionMetrics(
metric = EthoVisionMetrics(
px_per_mm = MM_TO_PX,
fps = args.fps,
thresh_immobile = args.thresh_immobile,
thresh_mobile = args.thresh_mobile,
behaviour = behaviour,
))
)
if metric:
metrics_list.append(metric)
# --- Arène de base ---
arena_base = np.zeros((HEIGHT, WIDTH, 3), dtype=np.uint8)
@@ -1208,7 +1213,7 @@ def main():
output_path = args.output
if not output_path.endswith(".mp4"):
output_path += ".mp4"
fourcc = cv2.VideoWriter_fourcc(*'mp4v')
fourcc = cv2.VideoWriter_fourcc(*'mp4v') # type: ignore[attr-defined]
out = cv2.VideoWriter(output_path, fourcc, args.fps, (WIDTH, HEIGHT))
print(f"Simulation : {args.count} planaire(s), {TOTAL_FRAMES} frames ({args.duration}s à {args.fps} fps)")
test_tube_scanner/scanner/admin.py
+107 -4
View File
@@ -1,4 +1,6 @@
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
@@ -43,14 +45,14 @@ class ConfigurationAdmin(admin.ModelAdmin):
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", "active"),
"fields": ("label", "author", "position", "default", "capture_video", "active"),
}),
(_("Géométrie"), {
"fields": ("cols", "rows", "diameter", "row_def", "row_order"),"classes": ("collapse",),
"fields": ("cols", "rows", "diameter", "crop_radius", "row_def", "row_order"),"classes": ("collapse",),
}),
(_("Déplacement"), {
"fields": ("order", "duration", "xbase", "ybase", "dx", "dy", "feed"),"classes": ("collapse",),
@@ -113,6 +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
+9 -1
View File
@@ -19,7 +19,7 @@ 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
@@ -52,4 +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/export_tasks.py
+10 -7
View File
@@ -34,19 +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):
await remove_video_by_uuid(uuid, start_ts, end_ts, when=when)
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)
@@ -77,12 +78,13 @@ async def shm_download_video(uuid, start_ts, end_ts, frame_rate=5, opencv_fourcc
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)
@@ -95,6 +97,7 @@ async def shm_download_video(uuid, start_ts, end_ts, frame_rate=5, opencv_fourcc
progress_bar(i + 1, total, prefix=f'Progress {uuid}:', suffix='Ended', length=30)
i+=1
if video:
video.release()
# Nettoie la mémoire partagée
@@ -183,7 +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(
@@ -340,7 +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(
@@ -390,7 +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
test_tube_scanner/scanner/migrations/0001_initial.py
+197
View File
@@ -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
+17
View File
@@ -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
+18
View File
@@ -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
+44
View File
@@ -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
+22
View File
@@ -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
+23
View File
@@ -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
+18
View File
@@ -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
+29
View File
@@ -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
+23
View File
@@ -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/migrations/__init__.py
View File
test_tube_scanner/scanner/models.py
+128 -14
View File
@@ -4,6 +4,7 @@
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
@@ -13,10 +14,22 @@ 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")),
('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")),
]
FOURCC_FORMAT = [
@@ -32,7 +45,8 @@ VIDEO_TYPE = [
CAPTURE_TYPE = [
('rpi', _("Arducam")),
('webcam', _("Webcam")),
('file', _("Fichier vidéo (mp4, avi)")),
('file', _("Simulation Fichier vidéo (mp4, avi)")),
('video', _("Fichier vidéo (mp4, avi)")),
]
TUBE_AXIS_TYPE = [
@@ -81,7 +95,6 @@ class Configuration(models.Model):
#
active = models.BooleanField(_("Actif"), default=False)
@classmethod
def active_config(cls):
return Configuration.objects.filter(active=True).first()
@@ -103,7 +116,6 @@ class Well(models.Model):
verbose_name = _("Puit")
verbose_name_plural = _("Puits")
def __str__(self):
return f'{self.name}'
@@ -113,13 +125,15 @@ class MultiWell(models.Model):
label = models.CharField(_("Label"), help_text=_("Label du multi-puit"), max_length=100, 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 de capture en secondes pour la calibration'), blank=False, default=10)
@@ -131,9 +145,9 @@ 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,
@@ -166,7 +180,7 @@ 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")
@@ -206,8 +220,8 @@ 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
@@ -302,7 +316,7 @@ class Session(models.Model):
@classmethod
def get_session(self, sid):
def get_session(cls, sid):
return Session.objects.filter(pk=sid).first()
@@ -313,7 +327,7 @@ class Session(models.Model):
def __str__(self):
state = _("Terminée") if not self.active else _("Active")
return f'[ {self.id} ] {self.name} ({state})'
return f'[ {self.pk} ] {self.name} ({state})'
@receiver(post_save, sender=Session)
@@ -444,6 +458,106 @@ class ExperimentWell(models.Model):
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
test_tube_scanner/scanner/multiwell.py
+51 -17
View File
@@ -14,7 +14,7 @@ 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
@@ -115,24 +115,28 @@ class MultiWellManager:
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, btn_class="w3-button", onclick=''' onclick="goto_well(this)"'''):
multiwells = []
@@ -143,14 +147,24 @@ class MultiWellManager:
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 update_crop_radius(self, value):
self.multiwell.crop_radius = value
self.multiwell.save()
#def _grid_scanning_capture(self, uuid, duration):
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}'
@@ -201,6 +215,15 @@ class MultiWellManager:
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)
@@ -225,6 +248,8 @@ class MultiWellManager:
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._grid_scanning_capture(experiment, wl, simulate=simulate)
msg =f"Scan terminé — retour à l'origine (X={xnext:.1f} Y={ynext:.1f})"
@@ -237,7 +262,7 @@ class MultiWellManager:
self.process._send(state='error', msg=msg)
return False
finally:
self.cnc_controller.move_to(xnext, ynext, feed=multiwell.feed*2)
self.cnc_controller.move_to(xnext, ynext, feed=self.feed*2)
def _start_scanning(self, session, experiments, simulate=False):
@@ -315,6 +340,8 @@ class MultiWellManager:
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.well.name}: ({wl.x}, {wl.y})"}
@@ -323,7 +350,8 @@ class MultiWellManager:
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.well.name}: ({wl.x}, {wl.y})"}
@@ -332,21 +360,26 @@ class MultiWellManager:
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.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):
@@ -365,17 +398,18 @@ class MultiWellManager:
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)
## change file
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()
test_tube_scanner/scanner/process.py
+96 -14
View File
@@ -27,6 +27,7 @@ from modules import reductstore, utils, planarian_metrics
from modules.circular_crop import CircularCrop, CropStrategy
from .multiwell import MultiWellManager
from .constants import ScannerConstants
from .models import MultiWell
# CNC
if not settings.GRBL_SIMULATION:
@@ -38,7 +39,7 @@ else:
class ProcessData:
play: bool = True
record: bool = False
uuid: str = None
uuid: str | None = None
session: int = 0
tube_diameter: float = 16.0
@@ -173,7 +174,8 @@ class ScannerProcess(Task):
Constants:
reset si besoin les constantes vidéo
'''
self.conf = ScannerConstants().get()
self.constants = ScannerConstants()
self.conf = self.constants.get()
self.use_tracking = self.conf.tracking
self.video_quality = self.conf.video_jpeg_quality
@@ -181,19 +183,22 @@ 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
@@ -209,6 +214,29 @@ class ScannerProcess(Task):
display=self._display,
parent=self,
)
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
self.cam = WebcamCapture(
@@ -237,7 +265,12 @@ class ScannerProcess(Task):
self.cam._active_median = False
self.cam.set_circular_crop(None)
self.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
@@ -354,11 +387,10 @@ class ScannerProcess(Task):
def _listen_to_redis(self):
try:
logger.info(f"==== Scanner {self.group}: listen via redisDB")
pubsub = redisDB.pubsub()
pubsub.subscribe(self.group)
try:
for message in pubsub.listen():
try:
#logger.info(f"{message}")
@@ -372,15 +404,29 @@ 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.cam.set_edge_enhance(False)
if self.conf.capture_type == 'video':
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)
buttons = self.manager.multiwell_buttons(btn_class="w3-btn well", onclick="")
self._send(buttons=buttons)
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}")
@@ -391,6 +437,7 @@ class ScannerProcess(Task):
else:
try:
self.cam._active_median = False
self.cam.set_edge_enhance(False)
simulate = (topic=='simulate')
self.manager.scan_process(sid, simulate)
@@ -401,8 +448,10 @@ class ScannerProcess(Task):
continue
self._send(
buttons=buttons,
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")
@@ -418,6 +467,7 @@ 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()
@@ -438,17 +488,31 @@ class ScannerProcess(Task):
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':
@@ -480,6 +544,12 @@ 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
@@ -495,10 +565,21 @@ class ScannerProcess(Task):
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)
@@ -536,6 +617,7 @@ 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:
@@ -697,12 +779,11 @@ 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():
@@ -754,6 +835,7 @@ 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
+1 -1
View File
@@ -5,7 +5,7 @@
.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/scanning.css
+1 -1
View File
@@ -5,7 +5,7 @@
.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/video_upload.css
+72
View File
@@ -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
+21 -10
View File
@@ -33,12 +33,14 @@ 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;
@@ -62,33 +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" }); });
try {
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) {}
} catch(e) {console.log(e);}
}
registerSocket(socket) {
@@ -104,8 +108,12 @@ class ScannerManager {
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';
}
@@ -113,7 +121,10 @@ class ScannerManager {
}
if (payload.ts) { this.ts.textContent = timestampToLocalISOString(payload.ts); }
if (payload.buttons) { this.well_btn.innerHTML = payload.buttons; }
if (payload.buttons) {
this.well_btn.innerHTML = payload.buttons;
document.documentElement.style.setProperty('--well-columns', payload.columns);
}
if (payload.current >= 0) {
document.querySelectorAll('button.w3-button.well').forEach(btn => {
if (btn.value==payload.current) { btn.classList.add('w3-green'); return; }
test_tube_scanner/scanner/static/scanner/js/scanning.js
+2 -1
View File
@@ -62,6 +62,7 @@ class ScannerManager {
if (payload.buttons) {
this.well_btn.innerHTML = payload.buttons;
const span = this.crop.querySelector("span.crop"); span.style.color = '#f0f';
document.documentElement.style.setProperty('--well-columns', payload.columns);
}
if (payload.current >= 0) {
document.querySelectorAll('button.w3-btn.well').forEach(btn => {
@@ -72,7 +73,7 @@ class ScannerManager {
} catch(e) { console.log(e); }
}
init() { this.axes = 0; this.cropping = 1; this._send({ type: 'scanner', topic: "init", }); }
init() { this.axes = 0; this.cropping = 1; this._send({ type: 'scanner', topic: "init", sid: this.session.value }); }
scan() { this._send({ type: 'scanner', topic: "scan", session: this.session.value ? this.session.value: "0" }); }
simulate() { this._send({ type: 'scanner', topic: "simulate", session: this.session.value ? this.session.value: "0" }); }
halt() { this._send({ type: 'calibrate', topic: "halt" }); }
test_tube_scanner/scanner/static/scanner/js/video_upload.js
+141
View File
@@ -0,0 +1,141 @@
(function () {
"use strict";
function initDropZone(input) {
var zone = document.createElement("div");
zone.className = "video-drop-zone";
var hint = document.createElement("span");
hint.className = "video-drop-hint";
hint.textContent = "⬇ Glisser une vidéo ici ou cliquer pour parcourir";
zone.appendChild(hint);
// Progress bar (hidden by default)
var progressWrap = document.createElement("div");
progressWrap.className = "video-progress-wrap";
var progressTrack = document.createElement("div");
progressTrack.className = "video-progress-bar-track";
var progressBar = document.createElement("div");
progressBar.className = "video-progress-bar";
progressTrack.appendChild(progressBar);
progressWrap.appendChild(progressTrack);
var progressLabel = document.createElement("span");
progressLabel.className = "video-progress-label";
progressWrap.appendChild(progressLabel);
zone.appendChild(progressWrap);
input.parentNode.insertBefore(zone, input.nextSibling);
function setFilename(name) {
hint.textContent = "✓ " + name;
zone.classList.add("has-file");
}
function showProgress(pct) {
progressWrap.style.display = "block";
progressBar.style.width = pct + "%";
progressLabel.textContent = Math.round(pct) + " %";
}
function hideProgress() {
progressWrap.style.display = "none";
}
// Drag events
zone.addEventListener("dragenter", function (e) { e.preventDefault(); zone.classList.add("drag-over"); });
zone.addEventListener("dragover", function (e) { e.preventDefault(); zone.classList.add("drag-over"); });
zone.addEventListener("dragleave", function () { zone.classList.remove("drag-over"); });
zone.addEventListener("dragend", function () { zone.classList.remove("drag-over"); });
zone.addEventListener("drop", function (e) {
e.preventDefault();
zone.classList.remove("drag-over");
var files = e.dataTransfer.files;
if (!files.length) return;
var file = files[0];
try {
var dt = new DataTransfer();
dt.items.add(file);
input.files = dt.files;
input.dispatchEvent(new Event("change", { bubbles: true }));
} catch (_) {}
setFilename(file.name);
});
// Click on zone → open file picker
zone.addEventListener("click", function () { input.click(); });
// Sync when user picks via dialog
input.addEventListener("change", function () {
if (input.files && input.files.length > 0) {
setFilename(input.files[0].name);
}
});
// Pre-fill if a file is already set (edit form)
if (input.value) {
var parts = input.value.split(/[\\/]/);
setFilename(parts[parts.length - 1]);
}
return { showProgress: showProgress, hideProgress: hideProgress, input: input };
}
function interceptFormSubmit(form, dropZones) {
form.addEventListener("submit", function (e) {
// Only intercept if at least one file input has a file selected
var hasFile = dropZones.some(function (dz) {
return dz.input.files && dz.input.files.length > 0;
});
if (!hasFile) return; // normal submit, no big file
e.preventDefault();
var data = new FormData(form);
var xhr = new XMLHttpRequest();
// Show progress on the first drop zone that has a file
var active = dropZones.find(function (dz) {
return dz.input.files && dz.input.files.length > 0;
});
if (active) active.showProgress(0);
xhr.upload.addEventListener("progress", function (ev) {
if (ev.lengthComputable && active) {
active.showProgress((ev.loaded / ev.total) * 100);
}
});
xhr.addEventListener("load", function () {
if (active) active.hideProgress();
// Django admin redirects after save — follow the final URL
var finalUrl = xhr.responseURL || form.action;
// The response itself is the resulting admin page; navigate to it
window.location.href = finalUrl;
});
xhr.addEventListener("error", function () {
if (active) {
active.hideProgress();
active.showProgress(0); // reset bar
}
alert("Erreur lors de l'envoi du fichier.");
});
xhr.open(form.method || "POST", form.action || window.location.href, true);
xhr.send(data);
});
}
document.addEventListener("DOMContentLoaded", function () {
var inputs = Array.from(document.querySelectorAll('input[type="file"]'));
var dropZones = inputs.map(initDropZone);
// Hook into the closest form that contains these inputs
var form = inputs.length && inputs[0].closest("form");
if (form && dropZones.length) {
interceptFormSubmit(form, dropZones);
}
});
}());
test_tube_scanner/scanner/tasks.py
+5 -8
View File
@@ -68,15 +68,13 @@ def export_all_images(session_id=None):
conf = ScannerConstants().get()
if session_id is None:
sessions = [s.id for s in models.Session.objects.filter(active=False)]
sessions = [s.pk for s in models.Session.objects.filter(active=False)]
else:
sessions = [session_id]
job_zip = []
for session_id in sessions:
uuid_list = models.SessionExperiment.uuid_from_session(session_id)
job_zip = []
for uuid in uuid_list:
job = export_images.delay( # @UndefinedVariable
uuid,
start_ts=None,
@@ -109,13 +107,12 @@ def export_all_videos(session_id=None):
try:
conf = ScannerConstants().get()
if session_id is None:
sessions = [s.id for s in models.Session.objects.filter(active=False)]
sessions = [s.pk for s in models.Session.objects.filter(active=False)]
else:
sessions = [session_id]
job_mp4 = []
for session_id in sessions:
uuid_list = models.SessionExperiment.uuid_from_session(session_id)
job_mp4 = []
for uuid in uuid_list:
job = export_videos.delay( # @UndefinedVariable
@@ -146,7 +143,7 @@ def run_session_exports(self, session_id: str):
logger.error("run_session_exports: session %s introuvable", session_id)
return {"status": "error", "message": "Session introuvable"}
session.status = models.Session.Status.RUNNING
session.export_status = models.Session.Status.RUNNING
session.save(update_fields=["export_status"])
logger.info(f"run_session_exports [{session_id}]: export démarré")
chord(
test_tube_scanner/scanner/templates/scanner/base.html
+2 -2
View File
@@ -133,10 +133,10 @@
</a>
<hr class="w3-bar-item divider w3-grey w3-margin-bottom">
{% endif %}
<a href="{% url 'scanner:scanning' %}" class="w3-bar-item w3-btn w3-hover-opacity">
<a href="{% url 'scanner:scanning' %}" class="w3-bar-item w3-btn w3-hover-opacity w3-margin-bottom">
<i class="fa-solid fa-film w3-text-green w3-xlarge""></i> {% trans "Balayage multi-puits" %}
</a>
<div class="w3-bar-item w3-blue-grey"><i class="fa-solid fa-square-poll-vertical w3-text-amber"></i> {% trans "Résultats " %}</div>
<div class="w3-bar-item w3-border-top w3-center"><i class="fa-solid fa-square-poll-vertical w3-text-amber"></i> {% trans "Résultats " %}</div>
{% if conf.tracking %}
<a href="{% url 'planarian:export-csv' %}" class="w3-bar-item w3-btn w3-hover-opacity">
<i class="fa-solid fa-file-export w3-text-lime w3-xlarge"></i> {% trans "Export CSV des expériences" %}
test_tube_scanner/scanner/templates/scanner/calibration.html
+25 -5
View File
@@ -1,8 +1,14 @@
{% extends 'scanner/base.html' %}
{% load i18n home_tags scanner_tags %}
{% load i18n home_tags %}
{% block styles %}
{{ block.super }}
<style>
:root {
--well-columns: 3;
}
</style>
<link href="/static/scanner/css/calibration.css" rel="stylesheet">
{% endblock %}
{% block columns %}{% endblock %}
@@ -84,9 +90,10 @@
</button>
</div>
</div>
<div class="w3-row w3-row-padding">
<div id="_well_btn" class="w3-col w3-margin-bottom"></div>
<div {% if capture_type == "file" %}class="w3-hide"{% endif %}>
<div class="w3-third">
<button id="_previous" class="w3-button w3-dark-xlight w3-round-large w3-padding-small">
<span class="w3-small">{% trans 'Précéd.' %}</span><br><i class="fa-solid fa-circle-left w3-xlarge"></i>
@@ -110,8 +117,9 @@
</div>
</div>
</div>
<div class="w3-col" style="width: 50%">
{% include 'scanner/scan-image.html' %}
</div>
<div class="w3-col" style="width: 50%; display: flex; align-items: center; justify-content: center;">
<img id="scan-img" class="w3-image">
</div>
<div class="w3-col w3-center" style="width: 25%">
<div class="w3-row w3-row-padding">
@@ -139,10 +147,20 @@
</button>
</div>
<div class="w3-half">
<button id="_median" class="w3-button w3-dark-xlight w3-round-large w3-padding-1 w3-block">
<button id="_draw_debug" class="w3-button w3-dark-xlight w3-round-large w3-padding-1 w3-block" title="{% trans 'Afficher / masquer les annotations de détection' %}">
<span class="draw_debug" style="color:#0ff">{% trans 'Overlay' %}</span><br><i class="fa-solid fa-chart-simple w3-text-amber w3-xlarge"></i>
</button>
</div>
<div class="w3-half">
<button id="_median" class="w3-button w3-dark-xlight w3-round-large w3-padding-1 w3-margin-top-1 w3-block">
<span class="median">{% trans 'Axes' %}</span><br><i class="fa-solid fa-crosshairs w3-text-amber w3-xlarge"></i>
</button>
</div>
<div class="w3-half">
<button id="_edge_enhance" class="w3-button w3-dark-xlight w3-round-large w3-padding-1 w3-margin-top-1 w3-block" title="{% trans 'Mettre en évidence les bords du puit' %}">
<span class="edge_enhance">{% trans 'Contours' %}</span><br><i class="fa-solid fa-circle-dot w3-text-amber w3-xlarge"></i>
</button>
</div>
<div class="w3-col">
<button id="_crop" class="w3-button w3-dark-xlight w3-round-large w3-padding-small w3-margin-top w3-block" title="{% trans 'Ce mode actionne le pointage graphique' %}">
<span class="crop">{% trans 'Recadrer pour calibrer / suivre' %}</span><br><i class="fa-solid fa-crop w3-text-amber w3-xlarge"></i>
@@ -248,6 +266,7 @@
well : sId("_well"),
debug : sId("_debug"),
calib_debug : sId("_calib_debug"),
draw_debug : sId("_draw_debug"),
calib_auto : sId("_calib_auto"),
calib_center: sId("_calib_center"),
previous : sId("_previous"),
@@ -255,6 +274,7 @@
set_well : sId("_set_well"),
well_btn : sId("_well_btn"),
median : sId("_median"),
edge_enhance : sId("_edge_enhance"),
crop : sId("_crop"),
crop_radius : sId("_crop_radius"),
min_area_px : sId("_min_area_px"),
test_tube_scanner/scanner/templates/scanner/images.html
+1 -1
View File
@@ -1,5 +1,5 @@
{% extends 'scanner/base.html' %}
{% load i18n home_tags scanner_tags %}
{% load i18n home_tags %}
{% block styles %}
{{ block.super }}
test_tube_scanner/scanner/templates/scanner/replay.html
+1 -1
View File
@@ -1,5 +1,5 @@
{% extends 'scanner/base.html' %}
{% load i18n home_tags scanner_tags %}
{% load i18n home_tags %}
{% block styles %}
{{ block.super }}
test_tube_scanner/scanner/templates/scanner/scan-image.html
+2 -2
View File
@@ -12,7 +12,7 @@
<div>Ax pos: <span id="_axial_pos"></span></div>
</div-->
{#% endif %#}
<div class="w3-rest">
<img id="scan-img" class="w3-image">
<div class="w3-col">
<img id="scan-img" class="w3-image w3-margin-auto">
</div>
</div>
test_tube_scanner/scanner/templates/scanner/scanning.html
+11 -2
View File
@@ -3,6 +3,11 @@
{% block styles %}
{{ block.super }}
<style>
:root {
--well-columns: 6;
}
</style>
<link href="/static/scanner/css/scanning.css" rel="stylesheet">
{% endblock %}
{% block columns %}{% endblock %}
@@ -12,11 +17,15 @@
<div class="w3-col w3-center" style="width: 30%">
<div class="w3-col">
<div>{% trans "Choix de la session" %}</div>
<select id="_session" class="w3-select">
<form method="post" class="w3-bar-item" action="">
{% csrf_token %}
<select id="_session" name="_session" class="w3-select" onchange="this.form.submit()">
{% for s in sessions %}
<option value="{{ s.id }}">{{ s }}</option>
<option value="{{ s.id }}" {% if s.id == cursid %}selected{% endif %}>{{ s }}</option>
{% endfor %}
</select>
</form>
</div>
<div class="w3-col">
<div class="w3-row w3-bold">
test_tube_scanner/scanner/templatetags/scanner_tags.py
+1 -1
View File
@@ -1,6 +1,6 @@
# encoding: utf-8
from django import template
from django.utils.html import mark_safe
from django.utils.safestring import mark_safe
register = template.Library()
test_tube_scanner/scanner/views.py
+27 -11
View File
@@ -55,7 +55,6 @@ def global_context(request, **ctx):
**ctx
)
@login_required
@user_passes_test(is_staff_or_admin)
def admin_view(request):
@@ -126,9 +125,16 @@ def documentation(request, template=None):
## Mainboard
@login_required
def scanning_view(request):
cursid = 0
if request.method == 'POST':
cursid = request.POST.get('_session', 0)
if not cursid:
current_session = models.Session.objects.filter(active=True).first()
cursid = current_session.pk
ctx = dict(
ws_route=settings.SCANNER_WEBSOCKET_ROUTE,
columns=1,
cursid=int(cursid),
sessions=models.Session.objects.filter(active=True).all(),
choice_title=_("Balayage multi-puits")
)
@@ -137,26 +143,36 @@ def scanning_view(request):
## Calibration
@login_required
def calibration_view(request):
context = global_context(request)
wells = models.MultiWell.objects.filter(capture_video=False).all()
capture_type = context['conf'].capture_type
config = ScannerConstants.get_config()
if capture_type == 'video':
mw = models.MultiWell.objects.filter(default=True, capture_video=True).first()
if mw:
context['conf'].default_position = mw.position
wells = models.MultiWell.objects.filter(capture_video=True).all()
ctx = dict(
ws_route=settings.SCANNER_WEBSOCKET_ROUTE,
columns=1,
choice_title=_("Calibration"),
wells = models.MultiWell.objects.all(),
choice_title=f'{str(_("Calibration"))} {config.get_capture_type_display()}',
wells = wells,
capture_type=capture_type,
)
return render(request, "scanner/calibration.html", context=global_context(request, **ctx))
context.update(ctx)
return render(request, "scanner/calibration.html", context=context)
def get_not_active_experiments(session, expid=None):
def get_not_active_experiments(session, expid=None) -> tuple[list, "models.Experiment | None"]:
if session:
experiments = models.SessionExperiment.experiment_by_session(session.id, active=False) or []
experiments = models.SessionExperiment.experiment_by_session(session.pk, active=False) or []
if experiments and not expid:
return experiments, experiments[0]
for e in experiments:
if expid == str(e.id):
if expid == str(e.pk):
return experiments, e
return [], None
## images
def get_images(uuid):
oldest, latest, n, images = 0, 0, 0, []