planarian

test_tube_scanner/modules/capture_interface.py

@@ -24,8 +24,10 @@ from typing import Optional, Callable, TYPE_CHECKING
 
 from django.conf import settings
 from modules.planarian_tracker import PlanarianTracker
+from modules.planarian_metrics import ExperimentParams
 from modules.tube_aligner import TubeAligner
 
+
 if TYPE_CHECKING:
     from .circular_crop import CircularCrop     # Evite l'import circulaire au runtime
 
@@ -58,6 +60,7 @@ class VideoCaptureInterface(abc.ABC):
         self._fps: float = fps
         self.display = display
         self.parent = parent
+        self.use_tracking = use_tracking
         self.jpeg_quality = jpeg_quality
         self._interval: float = 1.0 / fps       # Intervalle en secondes entre chaque capture
         self._running: bool = False              # Indique si la capture est en cours
@@ -70,6 +73,8 @@ class VideoCaptureInterface(abc.ABC):
         self._error_occured = False
         
         self._tracker = None
+        self._metrics = None
+        self._paramss = None
         if use_tracking:
             self._tracker = PlanarianTracker(
                 tube_axis = settings.TRACKER_TUBE_AXIS,
@@ -77,8 +82,7 @@ class VideoCaptureInterface(abc.ABC):
                 max_area_ratio = settings.TRACKER_MAX_AREA_RATIO,
                 max_planarians = settings.TRACKER_MAX_PLANARIANS,
             )
-        
-        
+
         self._aligner = TubeAligner(
             grbl_threshold_px = 20,      # au-delà → correction GRBL
             dead_zone_px      = 5,       # en-dessous → rien à faire
@@ -87,13 +91,22 @@ class VideoCaptureInterface(abc.ABC):
         self.align_detection   = None     # résultat du test
 
 
-    def on_well_change(self):
+    def on_well_change(self, cfg):
         """
         Appelé par le CNC lors du changement de puits.
         Réinitialise le fond appris et l'état inter-frame du tracker.
+        Construit les métriques aussi
         """
-        if self._tracker:
-            self._tracker.reset()  
+        if  self.use_tracking and self._tracker:
+            self._tracker.reset()
+            self._params = ExperimentParams(cfg.to_params_dict())
+            self._metrics = self._params.build_metrics()
+            self._tracker = PlanarianTracker(
+                tube_axis      = self._params.tube_axis,
+                min_area_px    = self._params.min_area_px,
+                max_area_ratio = self._params.max_area_ratio,
+                max_planarians = self._params.planarian_count,
+            )
 
 
     # ------------------------------------------------------------------

test_tube_scanner/planarian/admin.py

@@ -30,7 +30,7 @@ class ExperimentConfigAdmin(admin.ModelAdmin):
             "classes": ("collapse",),
         }),
         (_("Tracker"), {
-            "fields": ("tube_axis", "min_area_px", "planarian_count"),
+            "fields": ("tube_axis", "min_area_px", "max_area_ratio", "planarian_count"),
             "classes": ("collapse",),
         }),
         (_("Thigmotactisme"), {

test_tube_scanner/planarian/models.py

@@ -63,6 +63,12 @@ class ExperimentConfig(models.Model):
         default=20,
         verbose_name=_("Surface min détection (px²)"),
     )
+    
+    max_area_ratio = models.FloatField(
+        default=0.05,
+        verbose_name=_("Filtre surface max acceptable"),
+    )
+        
     planarian_count = models.IntegerField(
         default=1,
         verbose_name=_("Nombre de planaires"),

test_tube_scanner/planarian/templates/planarian/experiment_form.html

@@ -172,6 +172,14 @@
                         <span class="w3-text-red w3-small">{{ form.min_area_px.errors|join:", " }}</span>
                         {% endif %}
                     </div>
+                    
+                    <div class="w3-col m4 s12 w3-margin-bottom">
+                        <label class="w3-text-grey"><b>{{ form.max_area_ratio.label }}</b></label>
+                        {{ form.max_area_ratio }}
+                        {% if form.max_area_ratio.errors %}
+                        <span class="w3-text-red w3-small">{{ form.max_area_ratio.errors|join:", " }}</span>
+                        {% endif %}
+                    </div>
 
                     <div class="w3-col m4 s12 w3-margin-bottom">
                         <label class="w3-text-grey"><b>{{ form.planarian_count.label }}</b></label>

test_tube_scanner/scanner/multiwell.py

@@ -14,6 +14,7 @@ from threading import Thread, Event
 from django.utils import timezone
 from django.utils.html import mark_safe
 from django.conf import settings
+from planarian.models import ExperimentConfig
 from . import models
 
 
@@ -120,22 +121,31 @@ class MultiWellManager:
         return mark_safe("\n".join(multiwells))         
        
         
-    def _grid_scanning_capture(self, uuid, duration):
+    #def _grid_scanning_capture(self, uuid, duration):
+    def _grid_scanning_capture(self, experiment, well_position):
+        well = well_position.well
+        multiwell = experiment.multiwell
+        
+        # Paramètres d'une expérience PlanarianScanner
+        cfg = ExperimentConfig.objects.get(experiment_id=experiment.id, well_id=well.id)
+        # reset PlanarianTracker => on_well_change
+        self.process.cam.on_well_change(cfg)
+        
+        uuid = f'{self.process.data.session}-{multiwell.position}-{well.name}'
+        ## start recording   
         self.process.data.uuid = uuid
         self.process.data.record = True
-        
-        # reset PlanarianTracker => on_well_change
-        self.process.cam.on_well_change()
-
         start = time.monotonic()
         while not self.stop_playing.is_set():
-            if time.monotonic() - start > duration:
+            if time.monotonic() - start > multiwell.duration:
                 break
             self.cnc_controller.wait_for(1.0)
-
-        logger.info(f"Arrêter l'enregistrement {uuid}")
         self.process.data.record = False
         self.process.data.uuid = None
+        
+        msg = f"{uuid}: capture done"
+        logger.info(msg)
+        self.process._send(scan_state=msg)      
                
         
     def _grid_scanning(self, experiment, xnext=0, ynext=0):
@@ -150,15 +160,14 @@ class MultiWellManager:
                 break
             self.cnc_controller.move_to(wl.x, wl.y, feed=wl.multiwell.feed)  
             
-            uuid = f'{self.process.data.session}-{multiwell.position}-{wl.well.name}'
-            self._grid_scanning_capture(uuid, multiwell.duration)
+            #uuid = f'{self.process.data.session}-{multiwell.position}-{wl.well.name}'
+            #self._grid_scanning_capture(uuid, multiwell.duration)
+            self._grid_scanning_capture(experiment, wl)
             
             ## change file 
             if self.process.conf.capture_type == 'file':
                 self.process.cam._error_occured = True            
             
-            self.process._send(scan_state=f"{uuid}: capture")
-            
         logger.info(f"Scan terminé — retour à l'origine (X={xnext:.1f}  Y={ynext:.1f})")
         self.cnc_controller.move_to(xnext, ynext, feed=multiwell.feed*2)
              

test_tube_scanner/scanner/process.py

@@ -162,9 +162,7 @@ class ScannerProcess(Task):
         return CircularCrop(radius=radius, strategy=CropStrategy.CROP_JPEG, jpeg_quality=self.image_quality)
 
     def start(self, *args, **kwargs):
-        try:
-            logger.warning("ScannerProcess==================", self.name)
-            
+        try:            
             self.conf = ScannerConstants().get()
             self.use_tracking = self.conf.tracking