tracking

test_tube_scanner/.env.example

@@ -19,6 +19,7 @@ APP_DATAS=test_tube_scanner
 EXPORTS_LOCAL_PATH=/home/rpi4/exports
 EXPORT_REMOTE_PATH=/mnt/exports
 REDUCTSTORE_PATH=/home/rpi4/medias
+CSV_EXPORT_DIR=/home/rpi4/exports/csv
 
 ####
 # django email

test_tube_scanner/home/settings.py

@@ -393,6 +393,8 @@ EXPORT_REMOTE_PATH = config("EXPORT_REMOTE_PATH")
 EXPORT_DESTINATIONS = ["local", "remote"]
 #EXPORT_DESTINATIONS = ["remote"] # only remote
 
+CSV_EXPORT_DIR = config("CSV_EXPORT_DIR")   # ou None pour mémoire uniquement
+
 ## tracker default parameters
 #
 TRACKER_TUBE_AXIS = "vertical"

test_tube_scanner/modules/planarian_metrics.py

@@ -34,7 +34,7 @@ Métriques résumé (summary) :
 Created on 25 avr. 2026
 @author: denis
 """
-import asyncio
+#import asyncio
 import csv
 import io
 import json
@@ -42,8 +42,8 @@ import logging
 import math
 import os
 import time
+from datetime import datetime, timezone
 
-from datetime import datetime
 from typing import Optional
 
 logger = logging.getLogger(__name__)
@@ -667,14 +667,14 @@ class ReductStoreClient:
         self.bucket_name  = bucket
         self.quota_type = quota_type
         self.quota_size = quota_size
-        self._client      = None
+        self.entry_name   = "metrics"
-        self._bucket = asyncio.run(self.create_bucket())
+        self._client = None
+        self._bucket = None
         
 
-    async def create_bucket(self):
+    async def _create_bucket(self):
         from reduct import Client, BucketSettings
         self._client = Client(self.url, api_token=self.token)
-        
         settings = BucketSettings(
             quota_type=self.quota_type,
             quota_size=self.quota_size,
@@ -682,43 +682,45 @@ class ReductStoreClient:
         )
         return await self._client.create_bucket(self.bucket_name, settings, exist_ok=True)
 
-    '''
+
     async def connect(self):
         """Initialise la connexion et crée le bucket si nécessaire."""
-        from reduct import Client, BucketSettings, QuotaType
+        self._bucket = await self._create_bucket()
-        self._client = Client(self.url, api_token=self.token)
-        self._bucket = await self._client.create_bucket(
-            self.bucket_name,
-            BucketSettings(quota_type=QuotaType.NONE),
-            exist_ok=True,
-        )
         logger.info(f"ReductStore connecté : {self.url} / {self.bucket_name}")
         
-    '''    
-
     async def store_metric(
         self,
         record:      dict,
         experiment:  str,
         well:        str,
-        entry_name:  str = "metrics",
         planarian:   int = 0,
-        record_type: str = "metrics",
+        record_type: str = "frame",
+        uuid:        str = "",
         ts_us:       Optional[int] = None,
     ):
-        """Stocke un enregistrement dans ReductStore."""
+        """
+        Stocke un enregistrement dans ReductStore.
+
+        Le timestamp est rendu unique par planaire en ajoutant l'index
+        du planaire comme offset sub-microseconde — évite le 409 Conflict
+        quand plusieurs planaires du même puits écrivent dans la même frame.
+        """
         if self._bucket is None:
             await self.connect()
-        ts_us = ts_us or int(time.time() * 1_000_000)
+        # ts_us de base + offset planaire (0, 1, 2…) pour unicité garantie
+        base_ts = ts_us or int(time.time() * 1_000_000)
+        unique_ts = base_ts + planarian
+        
         await self._bucket.write(
-            entry_name   = entry_name,
+            entry_name   = "metrics",
             data         = json.dumps(record).encode("utf-8"),
-            timestamp    = ts_us,
+            timestamp    = unique_ts,
             labels       = {
                 "experiment":  experiment,
                 "well":        well,
                 "planarian":   str(planarian),
                 "record_type": record_type,
+                "uuid": uuid,
             },
             content_type = "application/json",
         )
@@ -733,7 +735,7 @@ class ReductStoreClient:
         experiment:  str,
         well:        str,
         planarian:   int = 0,
-        record_type: str = "frame",
+        record_type: str = "metrics",
         start:       Optional[datetime] = None,
         stop:        Optional[datetime] = None,
     ) -> list:
@@ -756,45 +758,121 @@ class ReductStoreClient:
                 logger.warning(f"Entrée illisible ignorée : {e}")
         return records
 
+    @staticmethod
+    def _convert_timestamps(records: list) -> list:
+        """
+        Convertit le champ 'timestamp' (epoch float secondes) en ISO 8601 UTC
+        dans chaque enregistrement.
+
+        Args:
+            records : liste de dicts issus de ReductStore
+
+        Returns:
+            nouvelle liste avec timestamp converti (originaux non modifiés)
+        """
+        converted = []
+        for r in records:
+            row = dict(r)
+            ts  = row.get("timestamp")
+            if ts is not None:
+                try:
+                    row["timestamp"] = (
+                        datetime.fromtimestamp(float(ts), tz=timezone.utc)
+                        .strftime("%Y-%m-%dT%H:%M:%S.%f") + "Z"
+                    )
+                except (ValueError, TypeError, OSError):
+                    pass
+            converted.append(row)
+        return converted
+
+    @staticmethod
+    def _build_filepath(output_dir: str, experiment: str,
+                        well: str, planarian: int, record_type: str) -> str:
+        """
+        Construit le chemin du fichier CSV de sortie.
+        Nom : <experiment>_<well>_planaire<NN>_<record_type>.csv
+
+        Args:
+            output_dir  : répertoire de sortie (créé si absent)
+            experiment  : identifiant de l'expérience
+            well        : identifiant du puits
+            planarian   : index du planaire
+            record_type : "frame" ou "summary"
+
+        Returns:
+            chemin absolu du fichier CSV
+        """
+        dirpath  = os.path.abspath(output_dir)
+        os.makedirs(dirpath, exist_ok=True)
+        filename = f"{experiment}_{well}_planaire{planarian:02d}_{record_type}.csv"
+        return os.path.join(dirpath, filename)
+
     async def export_csv(
         self,
-        filepath:    str,
         experiment:  str,
         well:        str,
         planarian:   int = 0,
-        record_type: str = "frame",
+        record_type: str = "metrics",
+        output_dir:  str = ".",
         start:       Optional[datetime] = None,
         stop:        Optional[datetime] = None,
-    ) -> int:
+    ) -> tuple:
-        """Exporte les données vers un fichier CSV."""
+        """
+        Exporte les données depuis ReductStore vers un fichier CSV.
+        Le répertoire de sortie est choisi via output_dir.
+        Le champ timestamp est converti en ISO 8601 UTC.
+
+        Args:
+            experiment  : identifiant de l'expérience
+            well        : identifiant du puits
+            planarian   : index du planaire
+            record_type : "frame" | "summary"
+            output_dir  : répertoire de sortie (défaut : répertoire courant)
+            start, stop : plage temporelle (datetime UTC, optionnel)
+
+        Returns:
+            tuple (filepath, nb_lignes)
+        """
         records = await self.get_tracking_data(
             experiment, well, planarian, record_type, start, stop)
         if not records:
             logger.warning(f"Aucune donnée pour {experiment}/{well}/{planarian}")
-            return 0
+            return "", 0
-        os.makedirs(os.path.dirname(os.path.abspath(filepath)), exist_ok=True)
+
+        records    = self._convert_timestamps(records)
+        filepath   = self._build_filepath(output_dir, experiment, well,
+                                          planarian, record_type)
         fieldnames = list(dict.fromkeys(k for r in records for k in r.keys()))
+
         with open(filepath, "w", newline="", encoding="utf-8") as f:
             writer = csv.DictWriter(f, fieldnames=fieldnames, extrasaction="ignore")
             writer.writeheader()
             writer.writerows(records)
+
         logger.info(f"Export CSV : {len(records)} lignes → {filepath}")
-        return len(records)
+        return filepath, len(records)
 
     async def export_csv_response(
         self,
         experiment:  str,
         well:        str,
         planarian:   int = 0,
-        record_type: str = "frame",
+        record_type: str = "metrics",
         start:       Optional[datetime] = None,
         stop:        Optional[datetime] = None,
     ) -> tuple:
-        """Génère le contenu CSV en mémoire (pour réponse HTTP Django)."""
+        """
+        Génère le contenu CSV en mémoire (pour réponse HTTP Django).
+        Le champ timestamp est converti en ISO 8601 UTC.
+
+        Returns:
+            tuple (contenu_csv_str, nb_lignes)
+        """
         records = await self.get_tracking_data(
             experiment, well, planarian, record_type, start, stop)
         if not records:
             return "", 0
+        records    = self._convert_timestamps(records)
         fieldnames = list(dict.fromkeys(k for r in records for k in r.keys()))
         out = io.StringIO()
         writer = csv.DictWriter(out, fieldnames=fieldnames, extrasaction="ignore")
@@ -803,7 +881,12 @@ class ReductStoreClient:
         return out.getvalue(), len(records)
 
     async def close(self):
-        """Ferme la connexion ReductStore."""
+        """
-        if self._client:
+        Ferme la connexion ReductStore.
-            await self._client.close()
+        Note : reduct-py >= 1.x ne nécessite pas de fermeture explicite —
-            logger.info("ReductStore déconnecté")
+        la méthode est conservée pour compatibilité d'interface.
+        """
+        self._client = None
+        self._bucket = None
+        logger.info("ReductStore déconnecté")        
+        

test_tube_scanner/planarian/views.py

@@ -19,6 +19,7 @@ from modules.planarian_metrics import ExperimentParams, ReductStoreClient
 from modules.system_stats import get_cached_stats, start_background_updater
 from scanner.constants import ScannerConstants
 
+
 logger = logging.getLogger(__name__)
 
 start_background_updater()
@@ -49,11 +50,7 @@ def global_context(request, **ctx):
 
 def _get_reduct_client() -> ReductStoreClient:
     """Instancie le client ReductStore depuis les settings Django."""
-    return ReductStoreClient(
+    return ReductStoreClient(url=settings.REDUCTSTORE_URL, token=settings.REDUCTSTORE_TOKEN)
-        url    = getattr(settings, "REDUCTSTORE_URL",    "http://localhost:8383"),
-        token  = getattr(settings, "REDUCTSTORE_TOKEN",  ""),
-        bucket = getattr(settings, "REDUCTSTORE_BUCKET", "planarian_metrics"),
-    )
 
 
 # ---------------------------------------------------------------------------
@@ -212,12 +209,17 @@ class ExportCsvView(FormView):
                     start       = d.get("start_dt"),
                     stop        = d.get("stop_dt"),
                 )          
-            finally:
+                print(f"Export CSV: export_csv_response done, {n} lignes, content size={len(csv_content)}, {csv_content}")
-                await client.close()
+            except Exception as e:
+                logger.error(f"Erreur export CSV: {e}")
+                messages.error(self.request, _("Erreur lors de l'export CSV: %(error)s") % {"error": str(e)})
+                return None, 0
+            
             return csv_content, n
 
         csv_content, n = _do_export()
 
+        print(f"Export CSV: {n} lignes, content size={len(csv_content)}")
         if not csv_content:
             messages.warning(self.request, _("Aucune donnée trouvée."))
             return self.form_invalid(form)
@@ -268,8 +270,8 @@ class TrackingDataView(View):
                     planarian   = planarian,
                     record_type = record_type,
                 )
-            finally:
+            except Exception as e:
-                await client.close()
+                logger.error(f"Erreur fetching tracking data: {e}")
 
         records = _fetch()
         return JsonResponse({"count": len(records), "records": records})

test_tube_scanner/scanner/process.py

@@ -43,6 +43,7 @@ logger = get_task_logger(__name__)
 redisDB = Redis(host=settings.REDIS_HOST, port=settings.REDIS_PORT, db=0, decode_responses=True)
 cameraDB = reductstore.ReductStore(name='camera')
 planarianDB = planarian_metrics.ReductStoreClient(url=settings.REDUCTSTORE_URL, token=settings.REDUCTSTORE_TOKEN)
+async_to_sync(planarianDB.connect)()
 
 
 class CameraRecordManager():
@@ -281,9 +282,10 @@ class ScannerProcess(Task):
                 record,
                 self.cam._params.experiment,
                 self.cam._params.well,
-                entry_name=uuid,
+                uuid=uuid,
                 planarian=pid,
                 record_type='metrics',
+                ts_us=ts,
             )
                   
     def _store_frame(self, uuid, frame, ts, frame_count):
@@ -311,7 +313,7 @@ class ScannerProcess(Task):
             try:
                 (uuid, ts, frame, metrics, frame_count) = self.record_queue.get()
                 if self.cam.use_tracking:
-                    self._store_metric(uuid, metrics, ts)
+                    self._store_metric(uuid, metrics, ts.timestamp())
                                               
                 self._store_frame(uuid, frame, ts, frame_count)
                 

test_tube_scanner/scanner/templates/scanner/scanning.html

@@ -58,8 +58,8 @@
            <div class="w3-margin-top w3-padding w3-small">
                <span id="_ts"></span>
            </div>
-            <div class="w3-margin-top w3-padding w3-small">
+            <div class="w3-margin-top w3-small">
-               <span id="_scan_state" class="w3-text-amber w3-border"></span>
+               <span id="_scan_state" class="w3-text-amber w3-padding"></span>
            </div>    
         </div>                      
     </div>

test_tube_scanner/scanner/urls.py

@@ -19,6 +19,5 @@ urlpatterns = [
     path('replay/', views.replay_view, name='replay'),
     path('api/stats/', views.stats_view, name='api_stats'),
     path('api/video/', views.download_api, name='download_api'),
-    path('api/restart/', views.restart_all, name='restart_all'),
     path('api/export/', views.export_api, name='export_api'),
 ]

test_tube_scanner/scanner/views.py

@@ -156,18 +156,6 @@ def images_view(request):
     return render(request, "scanner/images.html", context=global_context(request, **ctx))
 
 
-## replay
-@require_GET
-@csrf_exempt
-def restart_all(request):
-    #http://scanner.local:9001/index.html?processname=test_tube%3Aservices&action=restart
-    #http://scanner.local:9001/index.html?processname=test_tube%3AwebUI&action=start
-    #http://scanner.local:9001/index.html?action=restartall
-    #supervisor_restart_service('index.html?action=restartall')
-    supervisor_restart_service('index.html?processname=test_tube%3Aservices&action=restart')
-    return JsonResponse({"state":  True})
-
-
 @require_POST
 @csrf_exempt
 def download_api(request):