453 lines
22 KiB
Python
453 lines
22 KiB
Python
# Django models for test tube scanner application
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# Created on 10/04/2024
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# denis@linuxtarn.org
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from django.utils.translation import gettext_lazy as _
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import uuid
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import json
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from django_celery_beat.models import PeriodicTask, ClockedSchedule
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from django.dispatch import receiver
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from django.db.models.signals import post_save, post_delete
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from django.utils import timezone
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from django.db import models
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from django.contrib.auth.models import User
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MULTIWELL_POSITION = [
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('HG', _("HG-Haut gauche")),
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('HD', _("HD-Haut droit")),
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('BG', _("BG-Bas gauche")),
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('BD', _("BD-Bas droit")),
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('BM', _("BM-Bas milieu")),
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('HM', _("HM-Haut milieu")),
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]
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FOURCC_FORMAT = [
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('mp4v', _("MP4")),
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('XVID', _("XVID")),
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]
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VIDEO_TYPE = [
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('mp4', _("MP4")),
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('avi', _("AVI")),
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]
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CAPTURE_TYPE = [
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('rpi', _("Arducam")),
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('webcam', _("Webcam")),
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('file', _("Fichier vidéo (mp4, avi)")),
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]
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TUBE_AXIS_TYPE = [
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('vertical', _("Vertical")),
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('horizontal', _("Horizontal")),
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]
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class Configuration(models.Model):
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name = models.CharField(_("Nom de la Configuration"), help_text=_("Nom de la configuration"), max_length=100, null=True, blank=False, default=_("Configuration par défaut"))
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author = models.ForeignKey(User, on_delete=models.CASCADE, verbose_name="Auteur", null=True, blank=True)
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# Dashboard configuration
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sidebar_width = models.CharField(_("Barre latérale"), help_text=_("Largeur barre latérale (css)"), max_length=32, null=True, blank=False, default="350px")
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default_grid_columns = models.PositiveSmallIntegerField(_("Colonnes de la grille par défaut"), help_text=_("Nombre de colonnes de la grille par défaut"), blank=False, default=3)
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# opencv
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opencv_fourcc_format = models.CharField(_("Fourcc"), help_text=_('Opencv fourcc format'), max_length=8, choices=FOURCC_FORMAT, null=True, blank=False, default='mp4v')
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opencv_video_type = models.CharField(_("Video type"), help_text=_('Opencv video type'), max_length=8, choices=VIDEO_TYPE, null=True, blank=False, default='mp4')
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# Grbl configuration
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grbl_xmax = models.FloatField(_("Grbl Xmax"), help_text=_("CNC Grbl Xmax en mm"), blank=False, default=350.0)
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grbl_ymax = models.FloatField(_("Grbl Ymax"), help_text=_("CNC Grbl Ymax en mm"), blank=False, default=250.0)
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# camera configuration
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capture_type = models.CharField(_("Capture"), help_text=_("Type de capture"), default='rpi', max_length=8, choices=CAPTURE_TYPE, null=True, blank=False)
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webcam_device_index = models.PositiveSmallIntegerField(_("Index de la webcam"), help_text=_("Index de la webcam (0, 1, ...) si présente"), default=2)
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image_quality = models.PositiveSmallIntegerField(_("Qualité JPEG"), help_text=_("Qualité JPEG (1-100) pour les images exportées"), default=90)
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video_jpeg_quality = models.PositiveSmallIntegerField(_("Qualité JPEG pour les vidéos"), help_text=_("Qualité JPEG (1-100) pour les images extraites des vidéos"), default=90)
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video_frame_rate = models.FloatField(_("Fréquence vidéos (fps)"), help_text=_("Fréquence d'extraction des images des vidéos (images par seconde)"), default=5.0)
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video_width_capture = models.PositiveSmallIntegerField(_("Largeur de capture vidéo"), help_text=_("Largeur de capture vidéo en pixels"), default=1280)
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video_height_capture = models.PositiveSmallIntegerField(_("Hauteur de capture vidéo"), help_text=_("Hauteur de capture vidéo en pixels"), default=720)
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# Calibration
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scan_simulation = models.BooleanField(_("Simuler balayage"), help_text=_("Autorise la simulation du balayage"), default=False)
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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)
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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')
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calibration_default_feed = models.PositiveIntegerField(_("Vitesse de calibration"), help_text=_("Vitesse de déplacement pour la calibration en mm/mn"), default=1000)
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calibration_default_step = models.FloatField(_("Pas de calibration"), help_text=_("Pas de déplacement pour la calibration en mm"), default=1.0)
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calibration_default_duration = models.FloatField(_("Duruée calibration"), help_text=_("Durée de pose entre chaque puits en s"), default=3.0)
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# tracking
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tracking = models.BooleanField(_("Suivi"), help_text=_("Suivi et analyse des planaires"), default=False)
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tube_axis = models.CharField(_("Axe du puit"), help_text=_("Axe du tube"), default='vertical', max_length=16, choices=TUBE_AXIS_TYPE, null=True, blank=False)
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min_area_px = models.PositiveIntegerField(_("Surface minimale"), help_text=_("surface minimale d'un contour pour être considéré valide (px²)"), default=20)
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max_area_ratio = models.FloatField(_("surface maximale "), help_text=_("surface maximale d'un contour en fraction de la frame (défaut 10%)"), default=0.10)
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max_planarians = models.PositiveIntegerField(_("Max planaire"), help_text=_("nombre maximum de planaires à suivre simultanément (1-10)"), default=1)
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merge_kernel_size = models.PositiveIntegerField(_("Taille du kernel"), help_text=_("taille du kernel elliptique de fusion des fragments (px). Augmenter si fragments résiduels"), default=15)
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min_contour_dist_px = models.PositiveIntegerField(_("Distance <contour>"), help_text=_("Distance min entre deux contours pour les considérer comme individus distincts. Défaut : 40px. Augmenter si IDs multiples persistent"), default=40)
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#
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active = models.BooleanField(_("Actif"), default=False)
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@classmethod
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def active_config(cls):
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return Configuration.objects.filter(active=True).first()
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class Meta:
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ordering = ['id', ]
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verbose_name = _("Configuration")
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verbose_name_plural = verbose_name
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def __str__(self):
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return f'{self.name}'
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class Well(models.Model):
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author = models.ForeignKey(User, on_delete=models.CASCADE, verbose_name="Auteur", null=True, blank=True)
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name = models.CharField(_("Nom"), help_text=_("Nom du puit: Ai..Di"), unique=True, max_length=4, null=True, blank=True)
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class Meta:
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ordering = ['name', ]
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verbose_name = _("Puit")
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verbose_name_plural = _("Puits")
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def __str__(self):
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return f'{self.name}'
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class MultiWell(models.Model):
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# Identification
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label = models.CharField(_("Label"), help_text=_("Label du multi-puit"), max_length=100, null=True, blank=True)
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author = models.ForeignKey(User, on_delete=models.CASCADE, verbose_name="Auteur", null=True, blank=True)
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position = models.CharField(_("Position"), help_text=_('Position du multi-puits sur la table'), unique=True, max_length=8, choices=MULTIWELL_POSITION, null=True, blank=False)
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default = models.BooleanField(_("Par défaut"), help_text=_('Multi-puit par défaut'), default=False)
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# Configuration
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cols = models.PositiveSmallIntegerField(_("Colonnes"), help_text=_('Nombre de colonnes'), blank=False, default=6)
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rows = models.PositiveSmallIntegerField(_("Lignes"), help_text=_('Nombre de lignes'), blank=False, default=4)
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diameter = models.FloatField(_("Diamètre"), help_text=_('Diamètre des tubes en mm'), blank=False, default=16.0)
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row_def = models.CharField(_("Définition"), help_text=_('Définition des lignes'), max_length=16, null=True, blank=False, default="A,B,C,D")
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row_order = models.CharField(_("Ordre ligne"), help_text=_('Ordre ligne de puit. Lecture en serpentin dans le sens des +- X'), max_length=16, null=True, blank=False, default="D,C,B,A")
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# Balayage
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order = models.PositiveSmallIntegerField(_("Ordre"), help_text=_('Ordre de lecture du multi-puit'), blank=False, default=0)
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duration = models.PositiveIntegerField(_("Durée"), help_text=_('Durée du film en secondes por la calibration'), blank=False, default=10)
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xbase = models.FloatField(_("Origine X"), help_text=_('Base origine X en mm'), blank=False, default=50.0)
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ybase = models.FloatField(_("Origine Y"), help_text=_('Base origine Y en mm'), blank=False, default=50.0)
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dx = models.FloatField(_("Pas X"), help_text=_('Pas ou interval sur X en mm'), blank=False, default=19.5)
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dy = models.FloatField(_("Pas Y"), help_text=_('Pas ou interval sur Y en mm'), blank=False, default=19.5)
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feed = models.PositiveIntegerField(_("Vitesse"), help_text=_('Vitesse déplacement en mm/mn '), blank=False, default=1000)
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well_position = models.BooleanField(_("Positions"), help_text=_('Positions des puits générées ?. Non => efface WellPosition et recalcule les positions'), default=False)
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active = models.BooleanField(_("Active"), default=True)
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def config(self):
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return dict(
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position=self.position,
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cols=self.cols,
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rows=self.rows,
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row_def=self.row_def,
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row_order=self.row_order,
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dx=self.dx,
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dy=self.dy,
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duration=self.duration,
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feed=self.feed,
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xbase=self.xbase,
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ybase=self.ybase,
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)
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return {}
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@classmethod
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def config_by_position(cls, position):
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qs = MultiWell.objects.filter(position__exact=position).values()
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if qs:
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return dict(qs[0])
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return {}
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@classmethod
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def by_position(cls, position):
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return MultiWell.objects.filter(position__exact=position).first()
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@classmethod
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def all(cls):
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return MultiWell.objects.filter(active=True).all()
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class Meta:
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ordering = ['order', ]
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verbose_name = _("Multi-puits")
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verbose_name_plural = _("Multi-puits")
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def __str__(self):
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return f'{self.position}: {self.label}'
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class WellPosition(models.Model):
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author = models.ForeignKey(User, on_delete=models.CASCADE, verbose_name="Auteur", null=True, blank=True)
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well = models.ForeignKey(Well, verbose_name=_("Puit"), on_delete=models.SET_NULL, null=True, blank=True)
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multiwell = models.ForeignKey(MultiWell, verbose_name=_("Multi-puits"), on_delete=models.SET_NULL, null=True, blank=True)
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order = models.PositiveSmallIntegerField(_("Ordre"), help_text=_('Ordre de lecture du puit'), blank=False, default=0)
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x = models.FloatField(_("X"), help_text=_('Axe X en mm'), blank=False, default=10.0)
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y = models.FloatField(_("Y"), help_text=_('Axe Y en mm'), blank=False, default=10.0)
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px_per_mm = models.FloatField( default=50.0, verbose_name=_("Pixels par mm"), help_text=_("Facteur de calibration optique"))
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@classmethod
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def active_well(cls, multiwell, well):
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return WellPosition.objects.filter(multiwell_id=multiwell.id, well_id=well.id).first()
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@classmethod
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def well_by_multiwell(cls, multiwell):
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return WellPosition.objects.filter(multiwell_id=multiwell.id).all()
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class Meta:
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ordering = ['order']
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unique_together = ["multiwell", "well"]
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verbose_name = _("Position du puit")
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verbose_name_plural = _("Position des puits")
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def __str__(self):
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return f'{self.multiwell.position}: {self.well.name}'
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@receiver(post_save, sender=MultiWell)
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def create_well_position(sender, instance, created, **kwargs):
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if created:
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pass
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if not instance.well_position:
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row_order = instance.row_order.split(',')
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n = 0
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for row in range(instance.rows):
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if row % 2 == 0:
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cols = range(instance.cols)
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else:
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cols = range(instance.cols - 1, -1, -1)
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for col in cols:
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x = instance.xbase + col * instance.dx
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y = instance.ybase + row * instance.dy
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try:
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name = f'{row_order[row]}{col+1}'
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well = Well.objects.get(name__exact=name)
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WellPosition.objects.update_or_create(
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multiwell=instance,
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well=well,
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author=instance.author,
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defaults={'order': n, 'x': round(x, 4), 'y': round(y, 4)}
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)
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n += 1
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except:
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pass
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instance.well_position=True
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instance.save()
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class Experiment(models.Model):
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title = models.CharField(_("Titre de l'expérience"), max_length=100, null=True, blank=False)
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comment = models.TextField(_("Commentaires"), help_text=_("Descriptions de l'expérience"), null=True, blank=True)
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identifier = models.CharField(_("Identifiant d'expérience"), unique=True, max_length=100, null=True, blank=False )
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author = models.ForeignKey(User, on_delete=models.CASCADE, verbose_name="Auteur", null=True, blank=True)
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multiwell = models.ForeignKey(MultiWell, verbose_name=_("Multi-puits"), on_delete=models.SET_NULL, null=True, blank=True)
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duration = models.PositiveIntegerField(_("Durée"), help_text=_('Durée de la prise de vue en secondes'), blank=False, default=120)
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created = models.DateTimeField(_("Date de création"), default=timezone.now)
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started = models.DateTimeField (_("Date de début"), null=True, blank=True)
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finished = models.DateTimeField (_("Date de fin"), null=True, blank=True)
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def save(self, *args, **kwargs):
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self.identifier = f'{self.id}-{self.multiwell.position}_{self.created.isoformat()[:19]}'
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super().save(*args, **kwargs)
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@classmethod
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def by_identifier(cls, identifier):
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return Experiment.objects.filter(identifier__exact=identifier).first()
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class Meta:
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ordering = ['-created', ]
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verbose_name = _("Expérience")
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verbose_name_plural = _("Expériences")
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def __str__(self):
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return f'{self.identifier}'
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class Session(models.Model):
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class Status(models.TextChoices):
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PENDING = "pending", _("En attente")
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RUNNING = "running", _("En cours")
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DONE = "done", _("Terminé")
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ERROR = "error", _("Erreur")
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name = models.CharField(_("Nom de la session"), help_text=_("Session d'expérience. 4 Multi-puits maximum"), max_length=100, null=True, blank=False)
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author = models.ForeignKey(User, on_delete=models.CASCADE, verbose_name="Auteur", null=True, blank=True)
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active = models.BooleanField(_("Active"), default=True)
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expected_export = models.DateTimeField(_("Date d'exportation"), help_text=_("Date d'exportation prévue"), null=True, blank=True)
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expected_scanning = models.DateTimeField(_("Date du balayage"), help_text=_("Date du balayage prévue"), null=True, blank=True)
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created = models.DateTimeField(_("Date de création"), default=timezone.now)
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finished = models.DateTimeField (_("Date de fin"), null=True, blank=True)
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export_status = models.CharField(_("Status exportation"), max_length=16, choices=Status.choices, default=Status.PENDING)
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export_task = models.OneToOneField(
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"django_celery_beat.PeriodicTask",
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verbose_name=_("Export médias"),
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help_text=_("Programmation de l'exportation des vidéos et images"),
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null=True, blank=True, on_delete=models.SET_NULL, related_name="export_session")
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export_exported_at = models.DateTimeField(_("Exportation terminée à"), null=True, blank=True)
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scanning_status = models.CharField(_("Status scanning"), max_length=16, choices=Status.choices, default=Status.PENDING)
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scanning_task = models.OneToOneField(
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"django_celery_beat.PeriodicTask",
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verbose_name=_("Lancer le balayage"),
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help_text=_("Programmation du lancement du balayage"),
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null=True, blank=True, on_delete=models.SET_NULL, related_name="scanning_session")
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scanning_finished_at = models.DateTimeField(_("Balayage terminé à"), null=True, blank=True)
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@classmethod
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def get_session(self, sid):
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return Session.objects.filter(pk=sid).first()
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class Meta:
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ordering = ['-created', ]
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verbose_name = _("Session")
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verbose_name_plural = _("Sessions")
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def __str__(self):
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state = _("Terminée") if not self.active else _("Active")
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return f'{self.id}: {self.name} {state}'
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@receiver(post_save, sender=Session)
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def create_periodic_task(sender, instance, created, **kwargs):
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"""
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Crée automatiquement une PeriodicTask à la création d'une session.
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La tâche est one-shot : elle se désactive après exécution (one_off=True).
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"""
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if instance.expected_export:
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try:
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clocked, _ = ClockedSchedule.objects.get_or_create(clocked_time=instance.expected_export)
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export_task = PeriodicTask.objects.create(
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name = f"export_session_{instance.id}",
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task = "scanner.tasks.run_session_exports",
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clocked = clocked,
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one_off = True, # se désactive après la première exécution
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enabled = True,
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last_run_at = None, # force Celery Beat à ne pas la considérer déjà exécutée
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start_time = None, # pas de contrainte de démarrage
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kwargs = json.dumps({ # paramètres passés à la tâche
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"session_id": str(instance.id),
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}),
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description = f"Export expected at {instance.expected_export} — {instance.name}",
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)
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# Sauvegarde sans re-déclencher le signal
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Session.objects.filter(pk=instance.pk).update(export_task=export_task)
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except:
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pass
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if instance.expected_scanning:
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try:
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clocked, _ = ClockedSchedule.objects.get_or_create(clocked_time=instance.expected_scanning)
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scanning_task = PeriodicTask.objects.create(
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name = f"scanning_session_{instance.id}",
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task = "scanner.tasks.run_scanning",
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clocked = clocked,
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one_off = True, # se désactive après la première exécution
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enabled = True,
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last_run_at = None, # force Celery Beat à ne pas la considérer déjà exécutée
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start_time = None, # pas de contrainte de démarrage
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kwargs = json.dumps({ # paramètres passés à la tâche
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"session_id": str(instance.id),
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}),
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description = f"Scanning expected at {instance.expected_scanning} — {instance.name}",
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)
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# Sauvegarde sans re-déclencher le signal
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Session.objects.filter(pk=instance.pk).update(scanning_task=scanning_task)
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except:
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pass
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@receiver(post_delete, sender=Session)
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def delete_periodic_task(sender, instance, **kwargs):
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"""
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Supprime la PeriodicTask associée quand la session est supprimée.
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"""
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if instance.export_task:
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instance.export_task.delete()
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if instance.scanning_task:
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instance.scanning_task.delete()
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class SessionExperiment(models.Model):
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author = models.ForeignKey(User, on_delete=models.CASCADE, verbose_name="Auteur", null=True, blank=True)
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session = models.ForeignKey(Session, verbose_name=_("Session"), on_delete=models.SET_NULL, null=True, blank=True)
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experiment = models.ForeignKey(Experiment, verbose_name=_("Expérience"), on_delete=models.SET_NULL, null=True, blank=True, related_name="session_experiments")
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|
|
|
@classmethod
|
|
def experiment_by_session(cls, session_id, active=True):
|
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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):
|
|
experiments = [ss.experiment for ss in SessionExperiment.objects.filter(session__id=sid, session__active=False)]
|
|
uuid_list = []
|
|
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):
|
|
uuid = f'{sid}-{obs.multiwell.position}-{row_def[row]}{col+1}'
|
|
uuid_list.append(uuid)
|
|
return uuid_list
|
|
|
|
class Meta:
|
|
ordering = ['session',]
|
|
unique_together = ["session", "experiment"]
|
|
verbose_name = _("Session expérience")
|
|
verbose_name_plural = _("Sessions expériences")
|
|
|
|
def __str__(self):
|
|
return f'{self.session.id}: {self.experiment.title}'
|
|
|
|
|
|
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 well_by_experiment(cls, experiment_id):
|
|
return ExperimentWell.objects.filter(experiment__id=experiment_id, active=True).order_by('well__name')
|
|
|
|
@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__name') ]
|
|
|
|
class Meta:
|
|
ordering = ['experiment', 'well']
|
|
unique_together = ["experiment", "well", ]
|
|
verbose_name = _("Expérience puit")
|
|
verbose_name_plural = _("Expériences puits")
|
|
|
|
def __str__(self):
|
|
return f'{self.experiment.title}'
|
|
|
|
@receiver(post_save, sender=Experiment)
|
|
def create_experiment_well(sender, instance, created, **kwargs):
|
|
from planarian.models import ExperimentConfig
|
|
from .constants import ScannerConstants
|
|
|
|
wellposition = WellPosition.well_by_multiwell(instance.multiwell)
|
|
for wp in wellposition:
|
|
ExperimentWell.objects.get_or_create(experiment=instance, well=wp.well, author=instance.author, defaults={'active':True})
|
|
|
|
ExperimentConfig.objects.get_or_create(
|
|
experiment_key=instance,
|
|
well=wp.well.name,
|
|
author=instance.author,
|
|
experiment=instance.identifier,
|
|
defaults={
|
|
'px_per_mm': wp.px_per_mm,
|
|
'fps': ScannerConstants().get().video_frame_rate,
|
|
'well_radius_mm': instance.multiwell.diameter / 2,
|
|
}
|
|
)
|
|
|