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planarian

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denis defolie
2026-04-27 23:28:41 +02:00
parent 922d89bf8d
commit cf0230a28b
34 changed files with 2832 additions and 191 deletions
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test_tube_scanner/scanner/models.py
+35 -41
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@@ -12,7 +12,7 @@ from django.utils import timezone
from django.db import models
from django.contrib.auth.models import User
# Multi-well positions on the table for calibration and observation
MULTIWELL_POSITION = [
('HG', _("HG-Haut gauche")),
('HD', _("HD-Haut droit")),
@@ -51,9 +51,7 @@ class Configuration(models.Model):
grbl_xmax = models.FloatField(_("Grbl Xmax"), help_text=_("CNC Grbl Xmax en mm"), blank=False, default=350.0)
grbl_ymax = models.FloatField(_("Grbl Ymax"), help_text=_("CNC Grbl Ymax en mm"), blank=False, default=250.0)
# camera configuration
use_rpicam = models.BooleanField(_("Utiliser rpicam"), help_text=_("Par défaaut. Sinon USB webcam"), default=True)
capture_type = models.CharField(_("Capture"), help_text=_("Type de capture"), default='rpi', max_length=8, choices=CAPTURE_TYPE, null=True, blank=False)
webcam_device_index = models.PositiveSmallIntegerField(_("Index de la webcam"), help_text=_("Index de la webcam (0, 1, ...) si présente"), default=2)
image_quality = models.PositiveSmallIntegerField(_("Qualité JPEG"), help_text=_("Qualité JPEG (1-100) pour les images exportées"), default=90)
video_jpeg_quality = models.PositiveSmallIntegerField(_("Qualité JPEG pour les vidéos"), help_text=_("Qualité JPEG (1-100) pour les images extraites des vidéos"), default=90)
@@ -68,9 +66,13 @@ class Configuration(models.Model):
calibration_default_duration = models.FloatField(_("Duruée calibration"), help_text=_("Durée de pose entre chaque puits en s"), default=3.0)
# tracking
tracking = models.BooleanField(_("Suivi"), help_text=_("Suivi et analyse des planaires"), default=False)
#
active = models.BooleanField(_("Actif"), default=False)
@classmethod
def active_config(cls):
return Configuration.objects.filter(active=True).first()
class Meta:
ordering = ['id', ]
@@ -116,7 +118,7 @@ class MultiWell(models.Model):
dy = models.FloatField(_("Pas Y"), help_text=_('Pas ou interval sur Y en mm'), blank=False, default=19.5)
feed = models.PositiveIntegerField(_("Vitesse"), help_text=_('Vitesse déplacement en mm/mn '), blank=False, default=1000)
well_position = models.BooleanField(_("Positions"), help_text=_('Positions des puits générées ?. Non => efface WellPostion et recalcule les positions'), default=False)
well_position = models.BooleanField(_("Positions"), help_text=_('Positions des puits générées ?. Non => efface WellPosition et recalcule les positions'), default=False)
active = models.BooleanField(_("Active"), default=True)
@@ -161,7 +163,7 @@ class MultiWell(models.Model):
return f'{self.position}: {self.label}'
class WellPostion(models.Model):
class WellPosition(models.Model):
author = models.ForeignKey(User, on_delete=models.CASCADE, verbose_name="Auteur", null=True, blank=True)
well = models.ForeignKey(Well, verbose_name=_("Puit"), on_delete=models.SET_NULL, null=True, blank=True)
multiwell = models.ForeignKey(MultiWell, verbose_name=_("Multi-puits"), on_delete=models.SET_NULL, null=True, blank=True)
@@ -169,8 +171,13 @@ class WellPostion(models.Model):
order = models.PositiveSmallIntegerField(_("Ordre"), help_text=_('Ordre de lecture du puit'), blank=False, default=0)
x = models.FloatField(_("X"), help_text=_('Axe X en mm'), blank=False, default=10.0)
y = models.FloatField(_("Y"), help_text=_('Axe Y en mm'), blank=False, default=10.0)
px_per_mm = models.FloatField( default=50.0, verbose_name=_("Pixels par mm"), help_text=_("Facteur de calibration optique"))
@classmethod
def active_well(cls, multiwel, well):
return WellPosition.objects.filter(multiwel_id=multiwel.id, well_id=well.id).first()
class Meta:
ordering = ['order']
unique_together = ["multiwell", "well"]
@@ -183,6 +190,8 @@ class WellPostion(models.Model):
@receiver(post_save, sender=MultiWell)
def create_well_position(sender, instance, created, **kwargs):
if created:
pass
if not instance.well_position:
row_order = instance.row_order.split(',')
n = 0
@@ -197,7 +206,7 @@ def create_well_position(sender, instance, created, **kwargs):
try:
name = f'{row_order[row]}{col+1}'
well = Well.objects.get(name__exact=name)
WellPostion.objects.update_or_create(
WellPosition.objects.update_or_create(
multiwell=instance,
well=well,
author=instance.author,
@@ -210,9 +219,9 @@ def create_well_position(sender, instance, created, **kwargs):
instance.save()
class Observation(models.Model):
title = models.CharField(_("Titre de l'observation"), max_length=100, null=True, blank=False)
comment = models.TextField(_("Commentaires"), help_text=_("Descriptions de l'observations"), null=True, blank=True)
class Experiment(models.Model):
title = models.CharField(_("Titre de l'expérience"), max_length=100, null=True, blank=False)
comment = models.TextField(_("Commentaires"), help_text=_("Descriptions de l'expérience"), null=True, blank=True)
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)
created = models.DateTimeField(_("Date de création"), default=timezone.now)
@@ -221,28 +230,12 @@ class Observation(models.Model):
class Meta:
ordering = ['-created', ]
verbose_name = _("Observation")
verbose_name_plural = _("Observations")
verbose_name = _("Expérience")
verbose_name_plural = _("Expériences")
def __str__(self):
return f'{self.title}: {self.created} {self.multiwell.order}'
class ObservationMultiWellDetail(models.Model):
author = models.ForeignKey(User, on_delete=models.CASCADE, verbose_name="Auteur", null=True, blank=True)
observation = models.ForeignKey(Observation, on_delete=models.CASCADE, related_name="multiwell_details" , null=True, blank=True)
well = models.ForeignKey(Well, verbose_name="Puit", on_delete=models.CASCADE, related_name="observation_details", null=True, blank=True )
detail = models.CharField("Détail", max_length=255)
comment = models.TextField("Commentaire", blank=True)
class Meta:
ordering = ['observation', 'well__name']
unique_together = ["observation", "well"]
verbose_name = _("Observation multi-puits détail")
verbose_name_plural = _("Observations multi-puits détails")
def __str__(self):
return f"{self.observation.title} - {self.well} - {self.detail}"
class Session(models.Model):
@@ -252,7 +245,7 @@ class Session(models.Model):
DONE = "done", _("Terminé")
ERROR = "error", _("Erreur")
name = models.CharField(_("Nom de la session"), help_text=_("Session d'observations. 4 Multi-puits maximum"), max_length=100, null=True, blank=False)
name = models.CharField(_("Nom de la session"), help_text=_("Session d'expérience. 4 Multi-puits maximum"), max_length=100, null=True, blank=False)
author = models.ForeignKey(User, on_delete=models.CASCADE, verbose_name="Auteur", null=True, blank=True)
active = models.BooleanField(_("Active"), default=True)
expected_export = models.DateTimeField(_("Date d'exportation"), help_text=_("Date d'exportation prévue"), null=True, blank=True)
@@ -280,8 +273,8 @@ class Session(models.Model):
class Meta:
ordering = ['-created', ]
verbose_name = _("Session d'observation")
verbose_name_plural = _("Sessions d'observation")
verbose_name = _("Session d'expérience")
verbose_name_plural = _("Sessions d'expériences")
def __str__(self):
state = _("Terminée") if not self.active else _("Active")
@@ -346,20 +339,21 @@ def delete_periodic_task(sender, instance, **kwargs):
if instance.scanning_task:
instance.scanning_task.delete()
class SessionObservation(models.Model):
class SessionExperiment(models.Model):
author = models.ForeignKey(User, on_delete=models.CASCADE, verbose_name="Auteur", null=True, blank=True)
session = models.ForeignKey(Session, verbose_name=_("Session"), on_delete=models.SET_NULL, null=True, blank=True)
observation = models.ForeignKey(Observation, verbose_name=_("Observation"), on_delete=models.SET_NULL, null=True, blank=True)
experiment = models.ForeignKey(Experiment, verbose_name=_("Expérience"), on_delete=models.SET_NULL, null=True, blank=True, related_name="session_experiments")
@classmethod
def observation_by_session(cls, session_id, active=True):
return [ ss.observation for ss in SessionObservation.objects.filter(session__id=session_id, session__active=active).order_by('observation__multiwell__order') ]
def experiment_by_session(cls, session_id, active=True):
return [ ss.experiment for ss in SessionExperiment.objects.filter(session__id=session_id, session__active=active).order_by('experiment__multiwell__order') ]
@classmethod
def uuid_from_session(cls, sid):
observations = [ss.observation for ss in SessionObservation.objects.filter(session__id=sid, session__active=False)]
experiments = [ss.experiment for ss in SessionExperiment.objects.filter(session__id=sid, session__active=False)]
uuid_list = []
for obs in observations:
for obs in experiments:
row_def = obs.multiwell.row_def.split(',')
for row in range(obs.multiwell.rows):
for col in range(obs.multiwell.cols):
@@ -369,9 +363,9 @@ class SessionObservation(models.Model):
class Meta:
ordering = ['session',]
unique_together = ["session", "observation"]
verbose_name = _("Session observations")
verbose_name_plural = _("Sessions observations")
unique_together = ["session", "experiment"]
verbose_name = _("Session expérience")
verbose_name_plural = _("Sessions expériences")
def __str__(self):
return f'{self.session.name}'