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

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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
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test_tube_scanner/planarian/migrations/0001_initial.py
+56
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@@ -0,0 +1,56 @@
# Generated by Django 6.0.5 on 2026-05-31 07:42
import django.db.models.deletion
from django.conf import settings
from django.db import migrations, models
class Migration(migrations.Migration):
initial = True
dependencies = [
migrations.swappable_dependency(settings.AUTH_USER_MODEL),
]
operations = [
migrations.CreateModel(
name='ExperimentConfig',
fields=[
('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('experiment', models.CharField(default='Identifier', max_length=128, null=True, verbose_name='Identifiant expérience')),
('well', models.CharField(choices=[], default='A1', help_text='Nom du puit', max_length=8, null=True, verbose_name='Puit')),
('description', models.TextField(blank=True, default='-', verbose_name='Description')),
('created_at', models.DateTimeField(auto_now_add=True, verbose_name='Créé le')),
('active', models.BooleanField(default=True, verbose_name='Active')),
('px_per_mm', models.FloatField(default=26.25, help_text='Facteur de calibration optique', verbose_name='Pixels par mm')),
('fps', models.FloatField(default=5.0, help_text='Image de capture en img/s', verbose_name='FPS de capture')),
('well_radius_mm', models.FloatField(default=8.0, help_text='En mm', verbose_name='Rayon du puits')),
('thresh_immobile', models.FloatField(default=0.2, verbose_name='Seuil Immobile (mm/s)')),
('thresh_mobile', models.FloatField(default=1.5, verbose_name='Seuil Mobile (mm/s)')),
('tube_axis', models.CharField(choices=[('vertical', 'Vertical'), ('horizontal', 'Horizontal')], default='vertical', max_length=10, verbose_name='Axe du tube')),
('min_area_px', models.IntegerField(default=20, verbose_name='Surface min détection (px²)')),
('max_area_ratio', models.FloatField(default=0.1, help_text='Ratio de la surface du puits, ex: 0.10 pour 10%', verbose_name='Surface max contour (fraction de la frame)')),
('planarian_count', models.IntegerField(default=1, verbose_name='Nombre de planaires')),
('merge_kernel_size', models.PositiveIntegerField(default=15, help_text='taille du kernel elliptique de fusion des fragments (px). Augmenter si fragments résiduels', verbose_name='Taille du kernel')),
('min_contour_dist_px', models.PositiveIntegerField(default=40, help_text='Distance min entre deux contours pour les considérer comme individus distincts. Défaut : 40px. Augmenter si IDs multiples persistent', verbose_name='Distance <contour>')),
('thigmotaxis_wall_dist_mm', models.FloatField(default=1.0, verbose_name='Distance paroi thigmotactisme (mm)')),
('photo_mode', models.CharField(choices=[('none', 'Désactivé'), ('fixed', 'Source fixe'), ('sine', 'Source sinusoïdale'), ('radial', 'Gradient radial')], default='none', max_length=10, verbose_name='Mode phototactisme')),
('photo_strength', models.FloatField(default=0.0, verbose_name='Intensité phototactisme')),
('photo_x', models.FloatField(default=0.5, verbose_name='Source lumière X (0-1)')),
('photo_y', models.FloatField(default=0.5, verbose_name='Source lumière Y (0-1)')),
('chemo_strength', models.FloatField(default=0.0, verbose_name='Intensité chimiotactisme')),
('chemo_x', models.FloatField(default=0.5, verbose_name='Nourriture X (0-1)')),
('chemo_y', models.FloatField(default=0.5, verbose_name='Nourriture Y (0-1)')),
('chemo_radius_mm', models.FloatField(default=2.0, verbose_name='Rayon nourriture (mm)')),
('avoid_radius_mm', models.FloatField(default=3.0, verbose_name='Rayon évitement (mm)')),
('aggreg_radius_mm', models.FloatField(default=6.0, verbose_name='Rayon agrégation (mm)')),
('author', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Auteur')),
],
options={
'verbose_name': "Configuration d'une expérience",
'verbose_name_plural': 'Configurations des expériences',
'ordering': ['-created_at'],
},
),
]
test_tube_scanner/planarian/migrations/0002_initial.py
+26
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@@ -0,0 +1,26 @@
# Generated by Django 6.0.5 on 2026-05-31 07:42
import django.db.models.deletion
from django.db import migrations, models
class Migration(migrations.Migration):
initial = True
dependencies = [
('planarian', '0001_initial'),
('scanner', '0001_initial'),
]
operations = [
migrations.AddField(
model_name='experimentconfig',
name='experiment_key',
field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='scanner.experiment', verbose_name='Expérience'),
),
migrations.AlterUniqueTogether(
name='experimentconfig',
unique_together={('experiment_key', 'well')},
),
]
test_tube_scanner/planarian/migrations/__init__.py
View File
test_tube_scanner/planarian/tasks.py
+1 -1
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@@ -33,7 +33,7 @@ def export_experiment_metrics_task(experiment_id):
return
jobs = []
configs = (ExperimentConfig.objects.filter(experiment_key_id=experiment.id).order_by("well"))
configs = (ExperimentConfig.objects.filter(experiment_key_id=experiment.pk).order_by("well"))
for conf in configs:
well = conf.well
count = conf.planarian_count
test_tube_scanner/planarian/templates/planarian/base.html
+1 -1
View File
@@ -1,5 +1,5 @@
{% extends "scanner/base.html" %}
{% load i18n home_tags scanner_tags %}
{% load i18n home_tags %}
{% block styles %}
{{ block.super }}
<link href="/static/planarian/css/planarian.css" rel="stylesheet">
test_tube_scanner/planarian/views.py
+7 -7
View File
@@ -93,7 +93,7 @@ def export_metrics(request):
if action=='experiment_csv':
experiment = models.Experiment.objects.filter(pk=pid).first()
if experiment:
export_experiment_metrics_task.delay(experiment.id) # @UndefinedVariable
export_experiment_metrics_task.delay(experiment.pk) # @UndefinedVariable
return JsonResponse({"success": True, "msg": str(_("Métrics en cours de téléchargement"))})
if action=='session_csv':
if pid:
@@ -118,7 +118,7 @@ def export_csv_view(request):
experiment = session_context['current_experiment']
if valid == 'ok' and session and experiment:
well_name = request.POST.get('well')
uuid = models.get_uuid_from_session(session.id, experiment.multiwell.position, well_name)
uuid = models.get_uuid_from_session(session.pk, experiment.multiwell.position, well_name) # type: ignore[union-attr]
'''
csv_content, filename = export_csv(request, uuid)
if csv_content:
@@ -126,7 +126,7 @@ def export_csv_view(request):
response["Content-Disposition"] = f'attachment; filename="{filename}"'
return response'''
csv_content, n = export_csv_sync(
experiment=experiment.identifier,
experiment=experiment.identifier, # type: ignore[union-attr]
well=well_name,
uuid=uuid,
planarian=request.POST.get("planarian"),
@@ -136,7 +136,7 @@ def export_csv_view(request):
)
if csv_content:
filename = (
f"{experiment.identifier}_{well_name}-{request.POST.get('planarian')}_"
f"{experiment.identifier}_{well_name}-{request.POST.get('planarian')}_" # type: ignore[union-attr]
f"{request.POST.get('record_type')}.csv"
)
logger.info(f"Export CSV: {n} lignes, content size={len(csv_content)}")
@@ -223,8 +223,8 @@ def import_csv_view(request):
return import_csv(request, current_experiment, rows, overwrite)
except Exception as e:
messages.error(request, msg)
logger.error(msg)
messages.error(request, e)
logger.error(e)
ctx = { 'choice_title': _("Importer des configurations depuis un fichier CSV"), **session_context }
return render(request, "planarian/import_params.html", context=global_context(request, **ctx))
@@ -266,6 +266,6 @@ class TrackingDataView(View):
return JsonResponse({"count": len(records), "records": records})
def get_context_data(self, **kwargs):
context = super().get_context_data(**kwargs)
context = super().get_context_data(**kwargs) # type: ignore[attr-defined]
return global_context(self.request, choice_title=str(_("Métriques de tracking d'un planaire")), **context)