scanning

test_tube_scanner/scanner/admin.py

@@ -26,10 +26,10 @@ class ConfigurationAdmin(admin.ModelAdmin):
             "classes": ("collapse",),
         }),
         (_("Camera"), {
-            "fields": ("capture_type", "webcam_device_index", "image_quality", "video_jpeg_quality", "video_frame_rate", "video_width_capture", "video_height_capture"),
+            "fields": ("scan_simulation", "capture_type", "webcam_device_index", "image_quality", "video_jpeg_quality", "video_frame_rate", "video_width_capture", "video_height_capture"),
             "classes": ("collapse",),
         }),
-        (_("Calibration"), {
+        (_("Calibration / Balayage"), {
             "fields": ("calibration_crop_radius", "calibration_default_multiwell", "calibration_default_feed", "calibration_default_step", "calibration_default_duration"),
             "classes": ("collapse",),
         }),
@@ -64,13 +64,14 @@ class MultiWellAdmin(admin.ModelAdmin):
 class WellPositionAdmin(admin.ModelAdmin):
     list_filter = ('author', 'multiwell')
     list_display = ('multiwell__position', 'well__name', 'order', 'x', 'y', 'px_per_mm', 'author',)
-    
+  
-
+  
 class ExperimentWellInline(admin.TabularInline):
     model = models.ExperimentWell
     extra = 0
-
+    #ordering = ('experiment__multiwell__wellposition__order',)
-
+    
+    
 class ExperimentAdmin(admin.ModelAdmin):
     inlines = (ExperimentWellInline, )
     list_filter = ('session_experiments__session', 'author', )

test_tube_scanner/scanner/constants.py

@@ -22,6 +22,7 @@ class DefaultConfig:
     video_frame_rate: int = 5.0
     video_width_capture: int = 2028
     video_height_capture: int = 1520
+    scan_simulation: bool = False
     calibration_crop_radius: int = 500
     calibration_default_multiwell: str = 'HD'
     calibration_default_feed: int = 1000

test_tube_scanner/scanner/models.py

@@ -64,6 +64,7 @@ class Configuration(models.Model):
     video_width_capture = models.PositiveSmallIntegerField(_("Largeur de capture vidéo"), help_text=_("Largeur de capture vidéo en pixels"), default=1280)
     video_height_capture = models.PositiveSmallIntegerField(_("Hauteur de capture vidéo"), help_text=_("Hauteur de capture vidéo en pixels"), default=720)
     # Calibration
+    scan_simulation = models.BooleanField(_("Simuler balayage"), help_text=_("Autorise la simulation du balayage"), default=False)
     calibration_crop_radius = models.PositiveSmallIntegerField(_("Rayon de découpe pour la calibration"), help_text=_("Rayon en pixels pour découper les images de calibration en px"), default=150)
     calibration_default_multiwell = models.CharField(_("Multi-puits de calibration par défaut"), help_text=_("Position du multi-puits de calibration par défaut"), max_length=8, choices=MULTIWELL_POSITION, default='HG')
     calibration_default_feed = models.PositiveIntegerField(_("Vitesse de calibration"), help_text=_("Vitesse de déplacement pour la calibration en mm/mn"), default=1000)
@@ -308,7 +309,7 @@ class Session(models.Model):
 
     def __str__(self):
         state = _("Terminée") if not self.active else _("Active")
-        return f'{self.name}: {state}'
+        return f'{self.id}: {self.name} {state}'
     
 
 @receiver(post_save, sender=Session)
@@ -409,10 +410,10 @@ class ExperimentWell(models.Model):
  
     @classmethod
     def wellname_by_experiment(cls, experiment_id):
-        return [ ew.well.name for ew in ExperimentWell.objects.filter(experiment__id=experiment_id, active=True).order_by('well__order') ]
+        return [ ew.well.name for ew in ExperimentWell.objects.filter(experiment__id=experiment_id, active=True).order_by('well__name') ]
 
     class Meta:
-        ordering = ['experiment',]
+        ordering = ['experiment', 'well']
         unique_together = ["experiment", "well", ]
         verbose_name = _("Expérience puit")
         verbose_name_plural = _("Expériences puitd")

test_tube_scanner/scanner/multiwell.py

@@ -78,8 +78,7 @@ class MultiWellManager:
     def __init__(self, process):
         
         self.process = process
-        self.cnc_controller = process.grbl
+        self.cnc_controller = process.grbl     
-        
         logger.info(f"MultiWellManager initialized with CNC controller: {self.cnc_controller}")
         
         self.stop_playing = Event()
@@ -99,8 +98,6 @@ class MultiWellManager:
             min_contour_dist_px = self.process.conf.min_contour_dist_px,
         )
         
-
-        
     def set_tracker_config(self):
         self.tracker_config = dict(
             tube_axis = settings.TRACKER_TUBE_AXIS,
@@ -169,6 +166,8 @@ class MultiWellManager:
                 self.process.data.record = True
             self.process._send(current=well_position.order)
             
+            logger.info(f"Starting capture for {uuid} ordre: {well_position.order}")
+            
             start = time.monotonic()
             while not self.stop_playing.is_set():
                 ## stop after duration in experiemnt now
@@ -196,8 +195,8 @@ class MultiWellManager:
         logger.info(f"Simulating capture with file {vf}")           
 
 
-    def _is_well_valid(self, welposition):
+    def _is_well_valid(self, welposition, experiment):
-        names = models.ExperimentWell.wellname_by_experiment(welposition.experiment.id)       
+        names = models.ExperimentWell.wellname_by_experiment(experiment.id)       
         if welposition.well.name not in names:
             return False
         return True
@@ -206,13 +205,14 @@ class MultiWellManager:
         try:
             multiwell = experiment.multiwell
             wellpositions = models.WellPosition.objects.filter(multiwell_id=multiwell.id).order_by('order').all()
+            
             cam = self.process.cam
             cam._aligner.set_tube_diameter(multiwell.diameter)    
     
             for wl in wellpositions:
                 if self.stop_playing.is_set():
                     break
-                if not self._is_well_valid(wl):
+                if not self._is_well_valid(wl, experiment):
                     continue
                 
                 self.cnc_controller.move_to(wl.x, wl.y, feed=wl.multiwell.feed)  
@@ -223,17 +223,18 @@ class MultiWellManager:
             msg =f"Scan terminé — retour à l'origine (X={xnext:.1f}  Y={ynext:.1f})"
             logger.info(msg)
             self.process._send(state='scan_finished', msg=msg)
-                  
+            return True
         except Exception as e: 
             msg = f"Error during grid scanning - {e}"
             logger.error(msg)
             self.process._send(state='error', msg=msg)
-            
+            return False
         finally: 
             self.cnc_controller.move_to(xnext, ynext, feed=multiwell.feed*2)
              
 
     def _start_scanning(self, session, experiments, simulate=False):
+        result = False
         try:
             self.process.cam._aligner.debug = False
             self.stop_playing.clear()
@@ -247,18 +248,21 @@ class MultiWellManager:
             self.process.data.session = session.id
             started = timezone.now()
             for obs in experiments:
+                
+                logger.warning(f"Starting scan for {obs} (well {pos}/{len(experiments)})")
+                
                 if self.stop_playing.is_set():
                     break
                 obs.started = timezone.now()
                 obs.save()
                 xnext, ynext = xynext[pos]
                 pos +=1
-                self._grid_scanning(obs, xnext=xnext, ynext=ynext, simulate=simulate)
+                result = self._grid_scanning(obs, xnext=xnext, ynext=ynext, simulate=simulate)
                 obs.finished = timezone.now()
                 obs.save()
                 
             session.finished = timezone.now()
-            if self.stop_playing.is_set():
+            if self.stop_playing.is_set() or not result:
                 msg = f"Session {session.name} abandonnée à {session.finished} après {session.finished - started} secondes."
             else:
                 if not simulate:
@@ -273,6 +277,8 @@ class MultiWellManager:
             logger.error("Error during scanning process", e)
         finally:
             self.scan_thread = None
+            self.goto_0()
+            self.process._send(current=self.get_well_order())
 
 
     def halt_scanning(self):

test_tube_scanner/scanner/process.py

@@ -373,7 +373,7 @@ class ScannerProcess(Task):
                             self.cam._active_median = False
                             self.grbl.go_origin(feed=self.manager.feed)
                             self.cam.set_draw_contours(False)
-                            buttons = self.manager.multiwell_buttons(btn_class="w3-btn", onclick="")
+                            buttons = self.manager.multiwell_buttons(btn_class="w3-btn well", onclick="")
                             self._send(buttons=buttons) 
                             
                         elif topic == 'scan' or topic == 'simulate':                           

test_tube_scanner/scanner/static/scanner/js/scanning.js

@@ -23,7 +23,7 @@ class ScannerManager {
         this.area_px      = options.area_px; 
         this.frame_count  = options.frame_count; 
         this.scan_state   = options.scan_state;
-        this.sim_bt       = options.simulate;
+        this.sim_bt       = options.simulate || null;
         this.well_btn     = options.well_btn;  
     }
 
@@ -32,7 +32,9 @@ class ScannerManager {
         this.crop.addEventListener('click',  (e) => { this._send({ type: 'calibrate', topic: "crop" }); });
         this.scan_bt.addEventListener('click',  (e) => { this.scan(); });
         this.halt_bt.addEventListener('click',  (e) => { this.halt(); });
-        this.sim_bt.addEventListener('click',  (e) => { this.simulate(); });
+        
+        if (this.sim_bt)  
+            this.sim_bt.addEventListener('click',  (e) => { this.simulate(); });
     }
 
     registerSocket(socket)  {
@@ -44,18 +46,29 @@ class ScannerManager {
         try {
             if (payload.jpeg)   { this.container.src = `data:image/jpeg;base64,${payload.jpeg}`; }
             if (payload.xy)     { this.x.textContent=payload.x.toFixed(2); this.y.textContent=payload.y.toFixed(2); }
-            if (payload.state)  { this.debug.insertAdjacentHTML('afterbegin', `<li>[ ${++this.debug_count} - ${payload.state} ]: ${payload.msg}</li>`); }
+            if (payload.state)  { 
+                if (payload.state == 'median') {
+                    const span = this.median.querySelector("span.median"); span.style.color = payload.value ? '#f0f' : '#fff';
+                } else if (payload.state == 'crop') {
+                    const span = this.crop.querySelector("span.crop"); span.style.color = payload.value ? '#f0f' : '#fff';
+                }
+                this.debug.insertAdjacentHTML('afterbegin', `<li>[ ${++this.debug_count} - ${payload.state} ]: ${payload.msg}</li>`); 
+            }
             if (payload.ts)     { this.ts.textContent = timestampToLocalISOString(payload.ts); }
             if (payload.scan_state) { this.scan_state.textContent=payload.scan_state;}
             
-            if (payload.buttons) { this.well_btn.innerHTML = payload.buttons; }
+            if (payload.buttons) { 
+                this.well_btn.innerHTML = payload.buttons; 
+                const span = this.crop.querySelector("span.crop"); span.style.color = '#f0f';
+            }
             if (payload.current >= 0) {                 
-                document.querySelectorAll('button.w3-button.well').forEach(btn => {
+                document.querySelectorAll('button.w3-btn.well').forEach(btn => {
                     if (btn.value==payload.current) { btn.classList.add('w3-green'); return; }
                     btn.classList.remove('w3-green'); 
                 });
             }
-                      
+           
+                                
         } catch(e) { console.log(e); }
     }
 

test_tube_scanner/scanner/templates/scanner/images.html

@@ -12,7 +12,7 @@
 	    <select id="_sid" name="_sid" class="w3-select w3-margin-bottom" onchange="this.form.submit()" title="{% trans "Ensemble d'expériences" %}">
 	        <option value="0">---- {% trans "Session" %}</option>
 	        {% for s in sessions %}
-	        <option value="{{ s.id }}" {% if s.id == current_session.id %}selected{% endif %}>{{ s.name }}</option>
+	        <option value="{{ s.id }}" {% if s.id == current_session.id %}selected{% endif %}>{{ s }}</option>
 	        {% endfor %}
 	    </select>
 	    <div class="w3-margin-left w3-margin-bottom">

test_tube_scanner/scanner/templates/scanner/replay.html

@@ -13,7 +13,7 @@
         <select id="_sid" name="_sid" class="w3-select w3-margin-bottom" onchange="this.form.submit()">
             <option value="0">---- {% trans "Session" %}</option>
             {% for s in sessions %}
-            <option value="{{ s.id }}" {% if s.id == current_session.id %}selected{% endif %}>{{ s.name }}</option>
+            <option value="{{ s.id }}" {% if s.id == current_session.id %}selected{% endif %}>{{ s }}</option>
             {% endfor %}
         </select>
         <div class="w3-margin-left w3-margin-bottom">

test_tube_scanner/scanner/templates/scanner/scanning.html

@@ -14,7 +14,7 @@
             <div>{% trans "Choix de la session" %}</div>
             <select id="_session" class="w3-select">
                 {% for s in sessions %}
-                <option value="{{ s.id }}">{{ s.name }}</option>
+                <option value="{{ s.id }}">{{ s }}</option>
                 {% endfor %}
             </select>
         </div>
@@ -28,26 +28,28 @@
         <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>
+		             <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="_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>
+		            <span class="crop" style="color: red">{% trans 'Recadrer' %}</span><br><i class="fa-solid fa-crop w3-text-amber w3-xlarge"></i>
 		        </button>
 	        </div>
         </div>
         <div class="w3-row w3-row-padding">
-	        <div class="w3-twothird w3-center">             
+	        <div class="{% if conf.scan_simulation %}w3-twothird{% else %}w3-col{% endif %} w3-center">             
 		        <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>
+		            <span class="w3-bold">{% trans 'Lancer' %}<br>{% trans 'le balayage' %}</span><br><i class="fa-solid fa-circle-check w3-text-blue w3-xlarge"></i>
 		        </button>
 	        </div>  
+	        {% if conf.scan_simulation %}
 	        <div class="w3-third w3-center">             
 	            <button id="_simulate" 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>
+	                <span class="w3-bold">{% trans 'Simuler' %}<br>{% trans 'le balayage' %}</span><br><i class="fa-solid fa-triangle-exclamation w3-text-orange w3-xlarge"></i>
 	            </button>
 	        </div>
+	        {% endif %}
 	        <div class="w3-col">
 	            <div id="_well_btn" class="w3-margin-top"></div>  	
 	        </div>         
@@ -58,10 +60,10 @@
 	        </div>        
         </div>
         <div class="w3-col">
-           <div class="w3-margin-top w3-padding w3-small">
+           <div class="w3-margin-top w3-padding-small w3-small">
                <span id="_ts"></span>
            </div>
-            <div class="w3-margin-top w3-small">
+           <div class="w3-margin-top w3-small w3-center w3-justify">
                <span id="_scan_state" class="w3-text-amber w3-padding"></span>
            </div>    
         </div>                      

test_tube_scanner/scanner/views.py

@@ -6,7 +6,7 @@ from django.http import JsonResponse
 from django.utils.translation import gettext_lazy as _
 from django.views.decorators.http import require_GET, require_POST
 from django.views.decorators.csrf import csrf_exempt
-from django.contrib.auth.decorators import login_required
+from django.contrib.auth.decorators import login_required, user_passes_test
 from django.conf import settings
 from reduct.time import unix_timestamp_to_iso
 from modules.system_stats import get_cached_stats, start_background_updater
@@ -20,6 +20,10 @@ from .constants import ScannerConstants
 record_manager = CameraRecordManager(cameraDB)
 start_background_updater()
 
+
+def is_staff_or_admin(user):
+    return user.is_staff or user.is_superuser
+
     
 @require_GET
 def stats_view(request):
@@ -48,10 +52,12 @@ def global_context(request, **ctx):
     )
 
 @login_required
+@user_passes_test(is_staff_or_admin)
 def admin_view(request):
     return render(request, "scanner/iframe.html", context=global_context(request, link='/admin/'))
 
 @login_required
+
 def admin_session_view(request):
     return render(request, "scanner/iframe.html", context=global_context(request, link='/admin/scanner/session/'))
 
@@ -68,26 +74,33 @@ def admin_periodictask_view(request):
     return render(request, "scanner/iframe.html", context=global_context(request, link='/admin/django_celery_beat/periodictask/'))
 
 @login_required
+@user_passes_test(is_staff_or_admin)
 def reductstore_view(request):
+    
     return render(request, "scanner/redirection.html", context=global_context(request, link=f'http://{settings.LOCAL_IP_SERVER}:8383/'))
 
 @login_required
+@user_passes_test(is_staff_or_admin)
 def adminer_view(request):
     return render(request, "scanner/redirection.html", context=global_context(request, link=f'http://{settings.LOCAL_IP_SERVER}/adminer/'))
 
 @login_required
+@user_passes_test(is_staff_or_admin)
 def portainer_view(request):
     return render(request, "scanner/redirection.html", context=global_context(request, link=f'http://{settings.LOCAL_IP_SERVER}:9000/'))
 
 @login_required
+@user_passes_test(is_staff_or_admin)
 def supervisor_view(request):
     return render(request, "scanner/redirection.html", context=global_context(request, link=f'http://{settings.LOCAL_IP_SERVER}:9001/'))
 
 @login_required
+@user_passes_test(is_staff_or_admin)
 def supervisor_worker(request):
     return render(request, "scanner/redirection.html", context=global_context(request, link=f'http://{settings.LOCAL_IP_SERVER}:9001/logtail/test_tube:services'))
 
 @login_required
+@user_passes_test(is_staff_or_admin)
 def supervisor_scheduler(request):
     return render(request, "scanner/redirection.html", context=global_context(request, link=f'http://{settings.LOCAL_IP_SERVER}:9001/logtail/test_tube:planification'))