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calibration

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This commit is contained in:
denis defolie
2026-05-09 09:45:27 +02:00
parent 563069d3c6
commit 5ba8e04ddf
10 changed files with 135 additions and 55 deletions
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test_tube_scanner/scanner/admin.py
+6 -5
View File
@@ -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):
# model = models.ExperimentConfig
# extra = 0
class ExperimentWellInline(admin.TabularInline):
model = models.ExperimentWell
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
+27
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@@ -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
+44 -16
View File
@@ -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))
@@ -152,22 +152,27 @@ 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:
raise Exception(f"Configuration d'expérience introuvable pour {experiment} / {well}")
# 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)
@@ -190,20 +195,27 @@ class MultiWellManager:
self.process.cam._error_occured = True
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)
@@ -305,9 +317,21 @@ class MultiWellManager:
self._capture_file_simulation(wl.well.name)
self.cnc_controller.move_to(wl.x, wl.y, feed=wl.multiwell.feed)
return {"state": "goto", "msg": f">>> {wl.well.name}: ({wl.x}, {wl.y})"}
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()
@@ -374,9 +402,9 @@ 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:
return
@@ -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
+15 -16
View File
@@ -373,7 +373,9 @@ 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}")
sid = cmd.get("session", '0')
@@ -389,10 +391,13 @@ class ScannerProcess(Task):
self._send(state=topic, msg=str(_('Balayage démarré...')))
except Exception as e:
logger.error(f"Scan error: {e}")
self._send(state='error', msg=str(_('Erreur lors du démarrage du balayage...')))
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':
@@ -452,18 +459,11 @@ class ScannerProcess(Task):
self.manager.duration = float(value)
elif topic == 'goto_0':
self.grbl.go_origin(feed=self.manager.feed)
self.manager.well_iterator.reset()
self.manager.well_iterator.seek(0)
if self.conf.capture_type == 'file':
self.manager._capture_file_simulation('zero')
self.manager.goto_0()
elif topic == 'goto_xy':
self.grbl.move_to(self.manager.xbase, self.manager.ybase, feed=self.manager.feed)
wl = self.manager.well_iterator.seek(0)
if self.conf.capture_type == 'file':
self.manager._capture_file_simulation(wl.well.name)
self.manager.goto_xy()
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
+10
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@@ -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
+12 -3
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@@ -101,16 +101,25 @@ 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; }
if (payload.current >= 0) {
document.querySelectorAll('button.w3-button.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/static/scanner/js/scanning.js
+10 -9
View File
@@ -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() {
@@ -46,15 +47,15 @@ class ScannerManager {
if (payload.state) { 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.detected && use_tracking) {
this.cx.textContent = payload.cx; this.cy.textContent = payload.cy;
this.speed_px_s.textContent = payload.speed_px_s;
this.axial_speed.textContent = payload.axial_speed;
this.axial_pos.textContent = payload.axial_pos;
this.area_px.textContent = payload.area_px;
this.frame_count.textContent = payload.count;
}
if (payload.buttons) { this.well_btn.innerHTML = payload.buttons; }
if (payload.current >= 0) {
document.querySelectorAll('button.w3-button.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/calibration.html
+5 -4
View File
@@ -85,7 +85,8 @@
</div>
</div>
<div class="w3-row w3-row-padding">
<div id="_well_btn" class="w3-col w3-margin-bottom"></div>
<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
+5 -1
View File
@@ -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>