simulate

test_tube_scanner/home/settings.py

@@ -396,8 +396,8 @@ EXPORT_DESTINATIONS = ["local", "remote"]
 
 
 TRACKER_TUBE_AXIS = "vertical"
-TRACKER_MIN_AREA = 20           # surface min planaire
-TRACKER_MAX_AREA_RATIO = 0.05   # 5% de la frame = surface max acceptable
+TRACKER_MIN_AREA = 8           # surface min planaire px x px
+TRACKER_MAX_AREA_RATIO = 0.1   # 5% de la frame = surface max acceptable
 TRACKER_MAX_PLANARIANS = 3
 
 

test_tube_scanner/scanner/multiwell.py

@@ -122,7 +122,7 @@ class MultiWellManager:
        
         
     #def _grid_scanning_capture(self, uuid, duration):
-    def _grid_scanning_capture(self, experiment, well_position):
+    def _grid_scanning_capture(self, experiment, well_position, simulate=False):
         well = well_position.well
         multiwell = experiment.multiwell
         
@@ -134,12 +134,15 @@ class MultiWellManager:
         uuid = f'{self.process.data.session}-{multiwell.position}-{well.name}'
         ## start recording   
         self.process.data.uuid = uuid
-        self.process.data.record = True
+        if not simulate:
+            self.process.data.record = True
+        
         start = time.monotonic()
         while not self.stop_playing.is_set():
             if time.monotonic() - start > multiwell.duration:
                 break
             self.cnc_controller.wait_for(1.0)
+            
         self.process.data.record = False
         self.process.data.uuid = None
         
@@ -148,7 +151,7 @@ class MultiWellManager:
         self.process._send(scan_state=msg)      
                
         
-    def _grid_scanning(self, experiment, xnext=0, ynext=0):
+    def _grid_scanning(self, experiment, xnext=0, ynext=0, simulate=False):
         multiwell = experiment.multiwell
         wells = models.WellPosition.objects.filter(multiwell_id=multiwell.id).order_by('order').all()
         cam = self.process.cam
@@ -159,10 +162,7 @@ class MultiWellManager:
             if self.stop_playing.is_set():
                 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)
-            self._grid_scanning_capture(experiment, wl)
+            self._grid_scanning_capture(experiment, wl, simulate=simulate)
             
             ## change file 
             if self.process.conf.capture_type == 'file':
@@ -172,7 +172,7 @@ class MultiWellManager:
         self.cnc_controller.move_to(xnext, ynext, feed=multiwell.feed*2)
              
 
-    def _start_scanning(self, session, experiments):
+    def _start_scanning(self, session, experiments, simulate=False):
         self.process.cam._aligner.debug = False
         xynext = []
         for obs in experiments:
@@ -189,7 +189,7 @@ class MultiWellManager:
             obs.save()
             xnext, ynext = xynext[pos]
             pos +=1
-            self._grid_scanning(obs, xnext=xnext, ynext=ynext)
+            self._grid_scanning(obs, xnext=xnext, ynext=ynext, simulate=simulate)
             obs.finished = timezone.now()
             obs.save()
             
@@ -197,10 +197,12 @@ class MultiWellManager:
         if self.stop_playing.is_set():
             msg = f"Session {session.name} abandonnée à {session.finished} après {session.finished - started} secondes."
         else:
-            session.active = False
-            if session.scanning_task:
-                session.scanning_task.enabled = False
-            session.save()
+            if not simulate:
+                session.active = False
+                if session.scanning_task:
+                    session.scanning_task.enabled = False
+                session.save()
+            
             msg = f"Session {session.name} terminée à {session.finished} après {session.finished - started} secondes."
         logger.info(msg)
         self.process._send(scan_state=msg)
@@ -214,13 +216,13 @@ class MultiWellManager:
         self.process.cam._aligner.debug = False   
 
          
-    def scanning(self, sid):
+    def scanning(self, sid, simulate=False):
         try:
             if self.scan_thread:
                 return
             session = models.Session.objects.get(pk=sid)
             experiments = models.SessionExperiment.experiment_by_session(sid)
-            self.scan_thread = Thread(target=self._start_scanning, args=(session, experiments, ), daemon=True).start()
+            self.scan_thread = Thread(target=self._start_scanning, args=(session, experiments, simulate, ), daemon=True).start()
         except Exception as e:
             print("MultiWellManager::scan error", e)       
 

test_tube_scanner/scanner/process.py

@@ -278,7 +278,7 @@ class ScannerProcess(Task):
         if self.data.play:
             try:
                 jpeg=base64.b64encode(jpeg_bytes).decode()
-                logger.warning(f"{jpeg[:100]}")
+                #logger.warning(f"{jpeg[:100]}")
                 self._send(ts=ts.timestamp(), jpeg=jpeg, frame_count=frame_count)
             except Exception as e:
                 logger.error(f"----_on_frame: {e}")
@@ -289,6 +289,8 @@ class ScannerProcess(Task):
         while not self.stop_event.is_set():
             try:
                 (uuid, ts, frame, metrics, frame_count) = self.record_queue.get()
+                
+                
                 labels = dict(fps=self.video_fps, session=self.data.session, detected="1" if metrics.get("detected") else "0")
                 
                 if metrics.get("detected"):
@@ -345,15 +347,15 @@ class ScannerProcess(Task):
                             self.cam._active_median = False
                             self.grbl.go_origin(feed=self.manager.feed)
 
-                        elif topic == 'scan':
-                            
+                        elif topic == 'scan' or topic == 'simulate':                           
                             logger.info(f"==== Scan {cmd}")
                             sid = cmd.get("session", '0')
                             if sid == "0":
                                 self._send(state='error', msg=str(_('La session est nulle!...')))
                             else:
                                 self.cam._active_median = False
-                                self.manager.scanning(sid)
+                                self.manager.scanning(sid, simulate=(topic=='simulate'))
+                                self._send(state=topic, msg=str(_('Balayage démarré...')))
                                 
                     elif cmd["type"]=="calibrate":
                         topic = cmd.get("topic")

test_tube_scanner/scanner/templates/scanner/base.html

@@ -104,22 +104,24 @@
                 </a>         
             {% endif %}
             
-            <a href="{% url 'scanner:main' %}"  class="w3-bar-item w3-btn w3-hover-opacity">
+            <a href="{% url 'scanner:scanning' %}"  class="w3-bar-item w3-btn w3-hover-opacity">
                 <i class="fa-solid fa-film w3-text-green w3-xlarge""></i> {% trans "Balayage multi-puits" %}
             </a>
-             <a href="{% url 'planarian:experiment-list' %}"  class="w3-bar-item w3-btn w3-hover-opacity">
+            {% if conf.tracking %}
+            <a href="{% url 'planarian:experiment-list' %}"  class="w3-bar-item w3-btn w3-hover-opacity">
                 <i class="fa-solid fa-vials w3-text-lime w3-xlarge"></i> {% trans "Préparation des expériences" %}
             </a>    
+            {% endif %}       
             <a href="{% url 'scanner:images' %}"  class="w3-bar-item w3-btn w3-hover-opacity">
                  <i class="fa-regular fa-images w3-text-cyan w3-xlarge" w3-xlarge""></i> {% trans "Gestionnaire d'images" %}
             </a>
              <a href="{% url 'scanner:replay' %}"  class="w3-bar-item w3-btn w3-hover-opacity">
                 <i class="fa-solid fa-podcast w3-text-ambe w3-xlarge"r"></i>  {% trans "Redifusion vidéos" %}
             </a>
-        {% endblock  %}
+        {% endblock %}
 
 	</div>
-	{% endblock  %}
+	{% endblock %}
 {% endblock  %}
 {% block content %}{% endblock %}
 

test_tube_scanner/scanner/templates/scanner/scanning.html

@@ -3,7 +3,7 @@
 
 {% block styles %}
     {{ block.super }}
-    <link href="/static/scanner/css/main.css" rel="stylesheet">
+    <link href="/static/scanner/css/scanning.css" rel="stylesheet">
 {% endblock %}
 {% block columns %}{% endblock %}
 
@@ -25,26 +25,34 @@
 	            <div class="w3-col w3-padding"><span id="_uuid"></span></div>
 	        </div>     
 	    </div>
-
-	    <div class="w3-col"> 
-	        <button id="_median" class="w3-button w3-dark-xlight w3-round-large w3-padding-small w3-block">
-	             {% trans 'Axes' %}&nbsp;<br><i class="fa-solid fa-crosshairs w3-text-amber w3-xlarge"></i>
-	        </button>  
+        <div class="w3-row w3-row-padding">
+		    <div class="w3-half"> 
+		        <button id="_median" class="w3-button w3-dark-xlight w3-round-large w3-block">
+		             {% trans 'Axes' %}&nbsp;<br><i class="fa-solid fa-crosshairs w3-text-amber w3-xlarge"></i>
+		        </button>  
+	        </div>
+	        <div class="w3-half">     
+		        <button id="_crop" class="w3-button w3-dark-xlight w3-round-large w3-block">
+		            {% trans 'Recadrer' %}<br><i class="fa-solid fa-crop w3-text-amber w3-xlarge"></i>
+		        </button>
+	        </div>
         </div>
-        <div class="w3-col">     
-	        <button id="_crop" class="w3-button w3-dark-xlight w3-round-large w3-padding-top w3-margin-top w3-block">
-	            {% trans 'Recadrer' %}<br><i class="fa-solid fa-crop w3-text-amber w3-xlarge"></i>
-	        </button>
-        </div>
-        <div class="w3-col">             
-	        <button id="_scan" class="w3-button w3-dark-xlight w3-round-large w3-margin-top w3-block">
-	            {% trans 'Lancer le balayage' %}<br><i class="fa-solid fa-circle-check w3-text-orange w3-xlarge"></i>
-	        </button>
-        </div>  
-        <div class="w3-col">
-            <button id="_halt" class="w3-button w3-red w3-round-large w3-margin-top w3-block">
-                {% trans 'ARRET' %}<br><i class="fa-solid fa-hand w3-xlarge"></i>
-            </button>
+        <div class="w3-row w3-row-padding">
+	        <div class="w3-twothird">             
+		        <button id="_scan" class="w3-button w3-light-blue w3-round-large w3-margin-top w3-block">
+		            {% trans 'Lancer' %}<br>{% trans 'le balayage' %}<br><i class="fa-solid fa-circle-check w3-text-blue w3-xlarge"></i>
+		        </button>
+	        </div>  
+	        <div class="w3-third">             
+	            <button id="_scan" class="w3-button w3-dark-xlight w3-round-large w3-margin-top w3-block">
+	                {% trans 'Simuler' %}<br>{% trans 'le balayage' %}<br><i class="fa-solid fa-triangle-exclamation w3-text-orange w3-xlarge"></i>
+	            </button>
+	        </div>
+            <div class="w3-col">  
+	            <button id="_halt" class="w3-button w3-red w3-round-large w3-margin-top w3-block">
+	                {% trans 'ARRET' %}<br><i class="fa-solid fa-hand w3-xlarge"></i>
+	            </button>
+	        </div>        
         </div>
         <div class="w3-col">
            <div class="w3-margin-top w3-padding w3-small">
@@ -85,10 +93,11 @@
             axial_pos   : sId("_axial_pos"),
             area_px     : sId("_area_px"),
             frame_count : sId("_count"),
-            scan_state: sId("_scan_state")
+            scan_state  : sId("_scan_state"),
+            simulate    : sId("_simulate")
         };                      
     </script>        
-    <script src="/static/scanner/js/main.js"></script>
+    <script src="/static/scanner/js/scanning.js"></script>
     <script>
         const manager  = new ScannerManager(container, options);
         const protocol = location.protocol === "https:" ? "wss" : "ws";

test_tube_scanner/scanner/urls.py

@@ -14,7 +14,7 @@ urlpatterns = [
     path('logs/worker', views.supervisor_worker, name='logs_worker'),
     path('logs/scheduler', views.supervisor_scheduler, name='logs_scheduler'),
     
-    path('main/', views.main_view, name='main'),
+    path('scanning/', views.scanning_view, name='scanning'),
     path('images/', views.images_view, name='images'),
     path('replay/', views.replay_view, name='replay'),
     path('api/stats/', views.stats_view, name='api_stats'),

test_tube_scanner/scanner/views.py

@@ -75,14 +75,14 @@ def supervisor_scheduler(request):
 
 ## Mainboard
 @login_required
-def main_view(request):
+def scanning_view(request):
     ctx = dict(
         ws_route=settings.SCANNER_WEBSOCKET_ROUTE,
         columns=1,
         sessions=models.Session.objects.filter(active=True).all(),
         choice_title=_("Balayage multi-puits")
     )
-    return render(request, "scanner/main.html", context=global_context(request, **ctx))
+    return render(request, "scanner/scanning.html", context=global_context(request, **ctx))
 
 ## Calibration
 @login_required