calibration

test_tube_scanner/home/static/js/w3-custom.js

@@ -1,6 +1,6 @@
 /*
 ** custom.js
-** GNU GENERAL PUBLIC LICENSE: (c) DD miraceti.net return document.querySelectorAll(id);
+** GNU GENERAL PUBLIC LICENSE: (c) DD miraceti.net 
 */
 let s   = function(sel) 			{ return document.querySelector(sel);  };
 let ss  = function(sel)             { return document.querySelectorAll(sel);  };

test_tube_scanner/scanner/admin.py

@@ -66,14 +66,15 @@ class WellPositionAdmin(admin.ModelAdmin):
     list_display = ('multiwell__position', 'well__name', 'order', 'x', 'y', 'px_per_mm', 'author',)
     
 
-#class ExperimentConfigInline(admin.TabularInline):
+class ExperimentWellInline(admin.TabularInline):
-#    model = models.ExperimentConfig
+    model = models.ExperimentWell
-#    extra = 0
+    extra = 0
+
 
 class ExperimentAdmin(admin.ModelAdmin):
-    #inlines = (ExperimenConfigInline,)
+    inlines = (ExperimentWellInline, )
     list_filter = ('session_experiments__session', 'author', )
-    list_display = ('title', 'author', 'identifier',  'multiwell', 'created', 'started', 'finished')
+    list_display = ('title', 'author', 'identifier', 'duration',  'multiwell', 'created', 'started', 'finished')
     readonly_fields = ('created', 'identifier',  'started',  'finished', )
     
 

test_tube_scanner/scanner/models.py

@@ -238,6 +238,7 @@ class Experiment(models.Model):
     author = models.ForeignKey(User, on_delete=models.CASCADE, verbose_name="Auteur", null=True, blank=True)
     multiwell = models.ForeignKey(MultiWell, verbose_name=_("Multi-puits"), on_delete=models.SET_NULL, null=True, blank=True)
     duration = models.PositiveIntegerField(_("Durée"), help_text=_('Durée de la prise de vue en secondes'), blank=False, default=120)
+    
     created = models.DateTimeField(_("Date de création"), default=timezone.now)
     started = models.DateTimeField (_("Date de début"), null=True, blank=True)
     finished = models.DateTimeField (_("Date de fin"), null=True, blank=True)
@@ -400,3 +401,29 @@ class SessionExperiment(models.Model):
         return f'{self.session.name}'
 
 
+class ExperimentWell(models.Model):
+    author = models.ForeignKey(User, on_delete=models.CASCADE, verbose_name="Auteur", null=True, blank=True)
+    experiment = models.ForeignKey(Experiment, verbose_name=_("Expérience"), on_delete=models.SET_NULL, null=True, blank=True, related_name="experimentwell")
+    well = models.ForeignKey(Well, verbose_name=_("Puit"), on_delete=models.SET_NULL, null=True, blank=True, related_name="wellexperiment")
+    active = models.BooleanField(_("Active"), default=True)
+ 
+    @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') ]
+
+    class Meta:
+        ordering = ['experiment',]
+        unique_together = ["experiment", "well", ]
+        verbose_name = _("Expérience puit")
+        verbose_name_plural = _("Expériences puitd")
+
+    def __str__(self):
+        return f'{self.experiment.title}'
+    
+
+@receiver(post_save, sender=Experiment)
+def create_experiment_well(sender, instance, created, **kwargs):
+    wells = Well.objects.all()
+    for well in wells:
+        ExperimentWell.objects.get_or_create(experiment=instance, well=well, author=instance.author, defaults={'active':True})
+     

test_tube_scanner/scanner/multiwell.py

@@ -137,11 +137,11 @@ class MultiWellManager:
         return self.multiwell.config()
     
     
-    def multiwell_buttons(self):
+    def multiwell_buttons(self, btn_class="w3-button", onclick=''' onclick="goto_well(this)"'''):
         multiwells = []
         multiwells.append('''<div class="w3-border well-btn">''')
         for wl in self.well_iterator:
-            multiwells.append(f"""<button class="w3-button well" value="{wl.order}" onclick="goto_well(this)">{wl.well.name}</button>""")
+            multiwells.append(f"""<button class="{btn_class} well" value="{wl.order}"{onclick}>{wl.well.name}</button>""")
         multiwells.append('''</div>''')
         self.well_iterator.reset()
         return mark_safe("\n".join(multiwells))         
@@ -152,6 +152,7 @@ class MultiWellManager:
         try:
             well = well_position.well
             multiwell = experiment.multiwell
+            
             if self.process.use_tracking:               
                 cfg = ExperimentConfig.objects.filter(experiment_id=experiment.id, well_id=well.id).first()
                 if not cfg:
@@ -159,15 +160,19 @@ class MultiWellManager:
                 # reset PlanarianTracker => on_well_change
                 self.process.cam.on_well_change(cfg, draw_contours=False)
 
+            ## create uuid for this capture
             uuid = f'{self.process.data.session}-{multiwell.position}-{well.name}'
+            
             ## start recording   
             self.process.data.uuid = uuid
             if not simulate:
                 self.process.data.record = True
+            self.process._send(current=well_position.order)
             
             start = time.monotonic()
             while not self.stop_playing.is_set():
-                if time.monotonic() - start > multiwell.duration:
+                ## stop after duration in experiemnt now
+                if time.monotonic() - start > experiment.duration:
                     break
                 self.cnc_controller.wait_for(0.1)
                 
@@ -191,19 +196,26 @@ class MultiWellManager:
         logger.info(f"Simulating capture with file {vf}")           
 
 
+    def _is_well_valid(self, welposition):
+        names = models.ExperimentWell.wellname_by_experiment(welposition.experiment.id)       
+        if welposition.well.name not in names:
+            return False
+        return True
+        
     def _grid_scanning(self, experiment, xnext=0, ynext=0, simulate=False):
         try:
             multiwell = experiment.multiwell
-            wells = models.WellPosition.objects.filter(multiwell_id=multiwell.id).order_by('order').all()
+            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 wells:
+            for wl in wellpositions:
                 if self.stop_playing.is_set():
                     break
-                self.cnc_controller.move_to(wl.x, wl.y, feed=wl.multiwell.feed)  
+                if not self._is_well_valid(wl):
+                    continue
                 
-                ## change file 
+                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)   
                 
@@ -308,6 +320,18 @@ class MultiWellManager:
         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) 
+        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')  
+        self.cnc_controller.move_to(0, 0, feed=self.feed*2)
+        
     def set_well_position(self):
         wl = self.well_iterator.get_current()
         if wl:
@@ -329,8 +353,12 @@ class MultiWellManager:
             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)                  
                 self.process._send(current=wl.order)
     
                 start = time.monotonic()
@@ -374,8 +402,8 @@ class MultiWellManager:
         self.process.cam._aligner.debug = False
 
         logger.info(f"Scan terminé — retour à l'origine (X=0, Y=0) en {int(time.monotonic()-start_test)} s")
-        self.cnc_controller.move_to(0, 0, feed=self.multiwell.feed*2)
+        self.goto_0()
-        
+        self.process._send(current=self.get_well_order())
 
     def scan_test(self, auto=False):
         if self.test_thread:
@@ -467,12 +495,12 @@ class MultiWellManager:
         """    Active / désactive le mode debug sur le stream."""
         aligner = self.process.cam._aligner
         aligner.debug = not aligner.debug       
-        return {"state": "debug", "msg": f"Debug: {aligner.debug}"}
+        return {"state": "debug", "value": aligner.debug, "msg": f"Debug: {aligner.debug}"}
     
     def set_calib_debug(self, value=True):
         """    Active / désactive le mode debug sur le stream."""
         aligner = self.process.cam._aligner
         aligner.debug = value      
-        return {"state": "debug", "msg": f"Debug: {aligner.debug}"}    
+        return {"state": "debug", "value": aligner.debug, "msg": f"Debug: {aligner.debug}"}    
     
     

test_tube_scanner/scanner/process.py

@@ -373,6 +373,8 @@ 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="")
+                            self._send(buttons=buttons) 
                             
                         elif topic == 'scan' or topic == 'simulate':                           
                             logger.info(f"==== Scan {cmd}")
@@ -390,9 +392,12 @@ class ScannerProcess(Task):
                                 except Exception as e:
                                     logger.error(f"Scan error: {e}")
                                     self._send(state='error', msg=str(_('Erreur lors du démarrage du balayage...')))  
-                                    
                             continue
                         
+                        self._send(
+                            buttons=buttons,
+                            current=self.manager.get_well_order(),
+                        )                                
                     elif cmd["type"]=="calibrate":
                         topic = cmd.get("topic")
                         value = cmd.get("value")
@@ -424,11 +429,13 @@ class ScannerProcess(Task):
                             
                         elif topic == 'median':
                             self.cam._active_median = not self.cam._active_median
+                            self._send(state="median", value=self.cam._active_median, msg=f"Median: {self.cam._active_median}")
                             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)
+                            self._send(state="crop", value=self.cam._active_crop, msg=f"Crop: {self.cam._active_crop}")
                             continue
                         
                         elif topic == 'crop_radius':
@@ -452,17 +459,10 @@ class ScannerProcess(Task):
                             self.manager.duration = float(value)   
                                  
                         elif topic == 'goto_0':
-                            self.grbl.go_origin(feed=self.manager.feed)
+                            self.manager.goto_0()
-                            self.manager.well_iterator.reset()
-                            self.manager.well_iterator.seek(0)
-                            if self.conf.capture_type == 'file':
-                                self.manager._capture_file_simulation('zero')                            
 
                         elif topic == 'goto_xy':
-                            self.grbl.move_to(self.manager.xbase, self.manager.ybase, feed=self.manager.feed)
+                            self.manager.goto_xy()  
-                            wl = self.manager.well_iterator.seek(0)
-                            if self.conf.capture_type == 'file':
-                                self.manager._capture_file_simulation(wl.well.name)
 
                         elif topic == 'xy_base':
                             self.manager.set_position()
@@ -488,7 +488,6 @@ class ScannerProcess(Task):
                         elif topic == 'halt':
                             self.manager.halt_scanning()
                             
-                        
                         elif topic == 'calib_debug':
                             msg = self.manager.calib_toggle_debug()
                             self._send(**msg)    

test_tube_scanner/scanner/static/scanner/css/scanning.css

@@ -1 +1,11 @@
 
+.well {
+    padding: 0.2em;
+}
+
+.well-btn {
+  display: grid; 
+  grid-template-columns: repeat(6, 1fr);
+  justify-items: center; 
+  align-items: center; 
+}

test_tube_scanner/scanner/static/scanner/js/calibration.js

@@ -101,7 +101,16 @@ class ScannerManager {
             if (payload.jpeg)   { this.container.src = `data:image/jpeg;base64,${payload.jpeg}`; }
             if (payload.xbase)  { this.xbase.textContent = payload.xbase;  this.ybase.textContent = payload.ybase; }
             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 == 'debug') {
+                    const span = this.calib_debug.querySelector("span.debug"); span.style.color = payload.value ? '#f0f': '#fff';
+                } else 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.buttons) { this.well_btn.innerHTML = payload.buttons; }

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

@@ -24,6 +24,7 @@ class ScannerManager {
         this.frame_count  = options.frame_count; 
         this.scan_state   = options.scan_state;
         this.sim_bt       = options.simulate;
+        this.well_btn     = options.well_btn;  
     }
 
     init_controls() {
@@ -47,14 +48,14 @@ class ScannerManager {
             if (payload.ts)     { this.ts.textContent = timestampToLocalISOString(payload.ts); }
             if (payload.scan_state) { this.scan_state.textContent=payload.scan_state;}
             
-            if (payload.detected && use_tracking) { 
+            if (payload.buttons) { this.well_btn.innerHTML = payload.buttons; }
-                this.cx.textContent = payload.cx; this.cy.textContent = payload.cy;
+            if (payload.current >= 0) {                 
-                this.speed_px_s.textContent = payload.speed_px_s; 
+                document.querySelectorAll('button.w3-button.well').forEach(btn => {
-                this.axial_speed.textContent = payload.axial_speed; 
+                    if (btn.value==payload.current) { btn.classList.add('w3-green'); return; }
-                this.axial_pos.textContent = payload.axial_pos;
+                    btn.classList.remove('w3-green'); 
-                this.area_px.textContent = payload.area_px; 
+                });
-                this.frame_count.textContent = payload.count;           
             }
+                      
         } catch(e) { console.log(e); }
     }
 

test_tube_scanner/scanner/templates/scanner/calibration.html

@@ -86,6 +86,7 @@
         </div>
         <div class="w3-row w3-row-padding">
             <div id="_well_btn" class="w3-col w3-margin-bottom"></div>  
+            
             <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>
@@ -134,17 +135,17 @@
         <div class="w3-row w3-row-padding">
             <div class="w3-half">
 	            <button id="_calib_debug" class="w3-button w3-dark-xlight w3-round-large w3-padding-1 w3-block" title="{% trans 'Ce mode permet les réglages graphiques' %}">
-	                {% trans 'Debug' %}<br><i class="fa-solid fa-triangle-exclamation w3-text-amber w3-xlarge"></i>
+	                <span class="debug">{% trans 'Debug' %}</span><br><i class="fa-solid fa-triangle-exclamation 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-block">
-	                {% trans 'Axes' %}<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-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' %}">
-	                {% trans 'Recadrer' %}<br><i class="fa-solid fa-crop w3-text-amber w3-xlarge"></i>
+	                 <span class="crop">{% trans 'Recadrer pour calibrer / suivre' %}</span><br><i class="fa-solid fa-crop w3-text-amber w3-xlarge"></i>
 	            </button>               
             </div>
         </div>    

test_tube_scanner/scanner/templates/scanner/scanning.html

@@ -48,6 +48,9 @@
 	                {% 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">
+	            <div id="_well_btn" class="w3-margin-top"></div>  	
+	        </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>
@@ -94,7 +97,8 @@
             area_px     : sId("_area_px"),
             frame_count : sId("_count"),
             scan_state  : sId("_scan_state"),
-            simulate    : sId("_simulate")
+            simulate    : sId("_simulate"),
+            well_btn    : sId("_well_btn")
         };                      
     </script>        
     <script src="/static/scanner/js/scanning.js"></script>