denis/PlanarianScanner
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Video plate capture: calibration, edge enhance, auto-detect well borders

Browse Source
This commit is contained in:
denis defolie
2026-06-03 17:56:23 +02:00
parent 4b42c03756
commit 9bb8fc1bce
58 changed files with 1699 additions and 274 deletions
Download Patch File Download Diff File Expand all files Collapse all files
test_tube_scanner/scanner/multiwell.py
+75 -41
View File
@@ -14,7 +14,7 @@ import time
from threading import Thread, Event
#from django.utils.translation import gettext_lazy as _
from django.utils import timezone
from django.utils.html import mark_safe
from django.utils.safestring import mark_safe
from django.conf import settings
from planarian.models import ExperimentConfig
from . import models
@@ -115,42 +115,56 @@ class MultiWellManager:
self._duration = duration or self.process.conf.calibration_default_duration
self.px_per_mm = 50.0
def init_manager_values(self):
wells = models.WellPosition.objects.filter(multiwell_id=self.multiwell.pk).order_by('order').all() # type: ignore[union-attr]
self.well_iterator = WellIterator(wells)
self.position = self.multiwell.position
self._xbase = self.multiwell.xbase
self._ybase = self.multiwell.ybase
self._dx = self.multiwell.dx
self._dy = self.multiwell.dy
def set_multiwell(self, position=None):
if position is None:
self.multiwell = models.MultiWell.objects.filter(default=True).first()
else:
self.multiwell = models.MultiWell.by_position(position)
wells = models.WellPosition.objects.filter(multiwell_id=self.multiwell.id).order_by('order').all()
self.well_iterator = WellIterator(wells)
self.position = self.multiwell.position
self._xbase = self.multiwell.xbase
self._ybase = self.multiwell.ybase
self._dx = self.multiwell.dx
self._dy = self.multiwell.dy
self.init_manager_values()
return self.multiwell.config()
def set_first_multiwell_from_session(self, sid):
experiments = models.SessionExperiment.experiment_by_session(sid)
if experiments:
self.multiwell = experiments[0].multiwell
self.init_manager_values()
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:
for wl in self.well_iterator:
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))
#def _grid_scanning_capture(self, uuid, duration):
def set_circular_crop(self, crop_radius):
crop = self.process.set_crop_radius(crop_radius)
self.process.cam.set_circular_crop(crop)
def update_crop_radius(self, value):
self.multiwell.crop_radius = value
self.multiwell.save()
def _grid_scanning_capture(self, experiment, well_position, simulate=False):
uuid = None
try:
well = well_position.well
multiwell = experiment.multiwell
# En mode video le crop_radius est piloté par _capture_video_simulation
if self.process.conf.capture_type != 'video':
self.set_circular_crop(multiwell.crop_radius)
## create uuid for this capture
uuid = f'{self.process.data.session}-{multiwell.position}-{well.name}'
@@ -198,8 +212,17 @@ class MultiWellManager:
vf = settings.MEDIA_ROOT / 'simulation' / f'{name}.mp4'
if vf.exists():
self.process.cam._video_file = str(vf)
self.process.cam._error_occured = True
logger.info(f"Simulating capture with file {vf}")
self.process.cam._error_occured = True
logger.info(f"Simulating capture with file {vf}")
def _capture_video_simulation(self, well_position):
"""Met à jour VideoPlateCapture : crop_radius depuis MultiWell.crop_radius."""
cam = self.process.cam
r = well_position.multiwell.crop_radius
if hasattr(cam, 'set_crop_radius_px'):
cam.set_crop_radius_px(r)
self.set_circular_crop(r)
logger.info(f"video_simulation: {well_position.well.name} crop_r={r}px")
def _is_well_valid(self, welposition, experiment):
@@ -222,10 +245,12 @@ class MultiWellManager:
if not self._is_well_valid(wl, experiment):
continue
self.cnc_controller.move_to(wl.x, wl.y, feed=wl.multiwell.feed)
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)
self._capture_file_simulation(wl.well.name)
elif self.process.conf.capture_type == 'video':
self._capture_video_simulation(wl)
self._grid_scanning_capture(experiment, wl, simulate=simulate)
msg =f"Scan terminé — retour à l'origine (X={xnext:.1f} Y={ynext:.1f})"
logger.info(msg)
@@ -237,7 +262,7 @@ class MultiWellManager:
self.process._send(state='error', msg=msg)
return False
finally:
self.cnc_controller.move_to(xnext, ynext, feed=multiwell.feed*2)
self.cnc_controller.move_to(xnext, ynext, feed=self.feed*2)
def _start_scanning(self, session, experiments, simulate=False):
@@ -315,38 +340,46 @@ class MultiWellManager:
wl = self.well_iterator.previous()
if self.process.conf.capture_type == 'file':
self._capture_file_simulation(wl.well.name)
elif self.process.conf.capture_type == 'video':
self._capture_video_simulation(wl)
self.cnc_controller.move_to(wl.x, wl.y, feed=wl.multiwell.feed)
return {"state": "previous", "msg": f">>> {wl.well.name}: ({wl.x}, {wl.y})"}
return {"state": "previous", "msg": f">>> {wl.well.name}: ({wl.x}, {wl.y})"}
def next_well(self):
wl = self.well_iterator.next()
if self.process.conf.capture_type == 'file':
self._capture_file_simulation(wl.well.name)
elif self.process.conf.capture_type == 'video':
self._capture_video_simulation(wl)
self.cnc_controller.move_to(wl.x, wl.y, feed=wl.multiwell.feed)
return {"state": "next", "msg": f">>> {wl.well.name}: ({wl.x}, {wl.y})"}
return {"state": "next", "msg": f">>> {wl.well.name}: ({wl.x}, {wl.y})"}
def goto_well(self, numwell):
wl = self.well_iterator.seek(numwell)
if self.process.conf.capture_type == 'file':
self._capture_file_simulation(wl.well.name)
self._capture_file_simulation(wl.well.name)
elif self.process.conf.capture_type == 'video':
self._capture_video_simulation(wl)
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})"}
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._capture_file_simulation(wl.well.name)
elif self.process.conf.capture_type == 'video':
self._capture_video_simulation(wl)
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._capture_file_simulation('zero')
elif self.process.conf.capture_type == 'video':
# Plein cadre : désactiver le masque circulaire pour ne pas rogner la vue d'ensemble
self.process.cam.set_circular_crop(None)
self.cnc_controller.move_to(0, 0, feed=self.feed*2)
def set_well_position(self):
@@ -364,18 +397,19 @@ class MultiWellManager:
self.stop_playing.clear()
cam = self.process.cam
cam._aligner.set_tube_diameter(self.multiwell.diameter)
duration = self.duration if not auto else settings.CALIBRATION_AUTO_DURATION
duration = self.duration if not auto else settings.CALIBRATION_AUTO_DURATION
start_test = time.monotonic()
try:
start_test = time.monotonic()
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._capture_file_simulation(wl.well.name)
elif self.process.conf.capture_type == 'video':
self._capture_video_simulation(wl)
self.process._send(current=wl.order)
start = time.monotonic()
@@ -497,7 +531,7 @@ class MultiWellManager:
if wl:
return wl.order
return None
def set_position(self):
x, y = self.cnc_controller.get_mpos()
self.cnc_controller.wait_for(2.0)