endoreg-db 0.4.0__tar.gz → 0.4.2__tar.gz

{endoreg_db-0.4.0 → endoreg_db-0.4.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: endoreg-db
-Version: 0.4.0
+Version: 0.4.2
 Summary: EndoReg Db Django App
 License: GNU3
 Author: Thomas J. Lux
@@ -9,15 +9,13 @@ Classifier: License :: Other/Proprietary License
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Requires-Dist: agl-report-reader (>=0.3.0,<0.4.0)
-Requires-Dist: django (>=4.2,<4.3)
+Requires-Dist: django (>=5.1,<6.0)
 Requires-Dist: django-bootstrap5 (>=23.4,<24.0)
 Requires-Dist: djangorestframework (>=3.14.0,<4.0.0)
 Requires-Dist: ffmpeg-python (>=0.2.0,<0.3.0)
-Requires-Dist: icecream (>=2.1.3,<3.0.0)
 Requires-Dist: opencv-python (>=4.9.0.80,<5.0.0.0)
 Requires-Dist: pandas (>=2.2.2,<3.0.0)
-Requires-Dist: pillow (>=10.2.0,<11.0.0)
+Requires-Dist: pillow (>=10,<11)
 Requires-Dist: pytesseract (>=0.3.10,<0.4.0)
 Requires-Dist: pyyaml (>=6.0.1,<7.0.0)
 Requires-Dist: scipy (>=1.14.0,<2.0.0)

{endoreg_db-0.4.0 → endoreg_db-0.4.2}/endoreg_db/data/endoscopy_processor/data.yaml

@@ -43,3 +43,5 @@
     endoscope_sn_y: 670
     endoscope_sn_width: 280
     endoscope_sn_height: 35
+
+    

endoreg_db-0.4.2/endoreg_db/migrations/0002_anonymizedimagelabel_anonymousimageannotation_and_more.py

@@ -0,0 +1,55 @@
+# Generated by Django 4.2.15 on 2024-08-28 11:05
+
+import django.core.files.storage
+import django.core.validators
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('endoreg_db', '0001_initial'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='AnonymizedImageLabel',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(max_length=255, unique=True)),
+                ('description', models.TextField(blank=True, null=True)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='AnonymousImageAnnotation',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('image_name', models.CharField(max_length=255)),
+                ('slug', models.SlugField(blank=True, null=True, unique=True)),
+                ('polyp_count', models.IntegerField()),
+                ('comments', models.CharField(max_length=255)),
+                ('gender', models.CharField(max_length=255)),
+                ('name_image_url', models.CharField(max_length=255)),
+                ('date_created', models.DateTimeField(auto_now_add=True)),
+                ('label', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.label')),
+            ],
+        ),
+        migrations.AlterField(
+            model_name='rawpdffile',
+            name='file',
+            field=models.FileField(storage=django.core.files.storage.FileSystemStorage(location='/home/agl-admin/agl-validator-backend/agl_validator_backend/erc_data/raw_pdf'), upload_to='raw_pdf/', validators=[django.core.validators.FileExtensionValidator(allowed_extensions=['pdf'])]),
+        ),
+        migrations.CreateModel(
+            name='DroppedName',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(max_length=255)),
+                ('gender', models.CharField(max_length=255)),
+                ('x', models.FloatField()),
+                ('y', models.FloatField()),
+                ('name_image_url', models.CharField(max_length=255)),
+                ('annotation', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='dropped_names', to='endoreg_db.anonymousimageannotation')),
+            ],
+        ),
+    ]

endoreg_db-0.4.2/endoreg_db/migrations/0003_anonymousimageannotation_original_image_url_and_more.py

@@ -0,0 +1,39 @@
+# Generated by Django 4.2.15 on 2024-08-29 07:15
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('endoreg_db', '0002_anonymizedimagelabel_anonymousimageannotation_and_more'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='anonymousimageannotation',
+            name='original_image_url',
+            field=models.CharField(default='https://example.com/placeholder.jpg', max_length=255),
+        ),
+        migrations.AddField(
+            model_name='anonymousimageannotation',
+            name='processed',
+            field=models.BooleanField(default=False),
+        ),
+        migrations.AddField(
+            model_name='droppedname',
+            name='box_coordinates',
+            field=models.CharField(blank=True, max_length=255, null=True),
+        ),
+        migrations.AlterField(
+            model_name='anonymousimageannotation',
+            name='comments',
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AlterField(
+            model_name='anonymousimageannotation',
+            name='label',
+            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='endoreg_db.anonymizedimagelabel'),
+        ),
+    ]

endoreg_db-0.4.2/endoreg_db/migrations/0004_alter_rawpdffile_file.py

@@ -0,0 +1,20 @@
+# Generated by Django 4.2.14 on 2024-09-04 19:48
+
+import django.core.files.storage
+import django.core.validators
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('endoreg_db', '0003_anonymousimageannotation_original_image_url_and_more'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='rawpdffile',
+            name='file',
+            field=models.FileField(storage=django.core.files.storage.FileSystemStorage(location='/home/agl-admin/agl_anonymizer/agl_anonymizer/erc_data/raw_pdf'), upload_to='raw_pdf/', validators=[django.core.validators.FileExtensionValidator(allowed_extensions=['pdf'])]),
+        ),
+    ]

endoreg_db-0.4.2/endoreg_db/migrations/0005_uploadedfile_alter_rawpdffile_file_anonymizedfile.py

@@ -0,0 +1,40 @@
+# Generated by Django 4.2.15 on 2024-09-17 11:46
+
+import django.core.files.storage
+import django.core.validators
+from django.db import migrations, models
+import django.db.models.deletion
+import django.utils.timezone
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('endoreg_db', '0004_alter_rawpdffile_file'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='UploadedFile',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('original_file', models.FileField(upload_to='uploads/original/')),
+                ('upload_date', models.DateTimeField(default=django.utils.timezone.now)),
+                ('description', models.TextField(blank=True, null=True)),
+            ],
+        ),
+        migrations.AlterField(
+            model_name='rawpdffile',
+            name='file',
+            field=models.FileField(storage=django.core.files.storage.FileSystemStorage(location='/mnt/hdd-sensitive/Pseudo/import/pdf'), upload_to='raw_pdf/', validators=[django.core.validators.FileExtensionValidator(allowed_extensions=['pdf'])]),
+        ),
+        migrations.CreateModel(
+            name='AnonymizedFile',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('anonymized_file', models.FileField(upload_to='uploads/anonymized/')),
+                ('anonymization_date', models.DateTimeField(default=django.utils.timezone.now)),
+                ('original_file', models.OneToOneField(on_delete=django.db.models.deletion.CASCADE, related_name='anonymized_file', to='endoreg_db.uploadedfile')),
+            ],
+        ),
+    ]

{endoreg_db-0.4.0 → endoreg_db-0.4.2}/endoreg_db/models/__init__.py

@@ -39,11 +39,7 @@ from .patient_examination import PatientExamination
 
 from .label import Label, LabelType, LabelSet
 
-from .annotation import (
-    ImageClassificationAnnotation,
-    LegacyBinaryClassificationAnnotationTask,
-    BinaryClassificationAnnotationTask,
-)
+from .annotation import *
 
 from .legacy_data import (
     LegacyImage,
@@ -74,3 +70,4 @@ from .hardware import (
 )
 
 from .questionnaires import TtoQuestionnaire
+from .annotation import AnonymousImageAnnotation, AnonymizedImageLabel, DroppedName

endoreg_db-0.4.2/endoreg_db/models/annotation/__init__.py

@@ -0,0 +1,3 @@
+from .image_classification import ImageClassificationAnnotation
+from .binary_classification_annotation_task import LegacyBinaryClassificationAnnotationTask, BinaryClassificationAnnotationTask
+from .anonymized_image_annotation import AnonymousImageAnnotation, DroppedName, AnonymizedImageLabel, AnonymizedFile, UploadedFile

endoreg_db-0.4.2/endoreg_db/models/annotation/anonymized_image_annotation.py

@@ -0,0 +1,60 @@
+from django.db import models
+from django.utils.text import slugify
+
+class AnonymizedImageLabel(models.Model):
+    name = models.CharField(max_length=255, unique=True)  # Ensuring label names are unique
+    description = models.TextField(blank=True, null=True)  # Optional description field
+
+    def __str__(self):
+        return self.name
+
+class AnonymousImageAnnotation(models.Model):
+    label = models.ForeignKey(AnonymizedImageLabel, on_delete=models.CASCADE)
+    image_name = models.CharField(max_length=255)
+    original_image_url = models.CharField(max_length=255, default='https://example.com/placeholder.jpg') # Field for the original image
+    slug = models.SlugField(unique=True, blank=True, null=True)
+    polyp_count = models.IntegerField()
+    comments = models.TextField(blank=True, null=True)  # Comments can be longer
+    gender = models.CharField(max_length=255)  # Overall gender (if applicable)
+    name_image_url = models.CharField(max_length=255)
+    date_created = models.DateTimeField(auto_now_add=True)
+    processed = models.BooleanField(default=False)  # Track if this annotation has been processed
+
+    def save(self, *args, **kwargs):
+        if not self.slug:
+            self.slug = slugify(f"{self.label}-{self.image_name}")
+        super().save(*args, **kwargs)
+
+    def __str__(self):
+        return f"{self.image_name} - {self.label}"
+
+class DroppedName(models.Model):
+    annotation = models.ForeignKey(AnonymousImageAnnotation, related_name='dropped_names', on_delete=models.CASCADE)
+    name = models.CharField(max_length=255)
+    gender = models.CharField(max_length=255)  # Gender of the individual name
+    x = models.FloatField()
+    y = models.FloatField()
+    name_image_url = models.CharField(max_length=255)
+    box_coordinates = models.CharField(max_length=255, blank=True, null=True)  # Store box coordinates if needed
+
+    def __str__(self):
+        return f"{self.name} ({self.gender}) at ({self.x}, {self.y})"
+
+from django.db import models
+from django.utils import timezone
+
+class UploadedFile(models.Model):
+    original_file = models.FileField(upload_to='uploads/original/')
+    upload_date = models.DateTimeField(default=timezone.now)
+    description = models.TextField(blank=True, null=True)
+    
+    def __str__(self):
+        return self.original_file.name
+    
+class AnonymizedFile(models.Model):
+    original_file = models.OneToOneField(UploadedFile, on_delete=models.CASCADE, related_name='anonymized_file')
+    anonymized_file = models.FileField(upload_to='uploads/anonymized/')
+    anonymization_date = models.DateTimeField(default=timezone.now)
+    
+    def __str__(self):
+        return f"Anonymized version of {self.original_file.original_file.name}"

{endoreg_db-0.4.0 → endoreg_db-0.4.2}/endoreg_db/models/data_file/import_classes/raw_pdf.py

@@ -67,7 +67,7 @@ class RawPdfFile(models.Model):
         cls,
         file_path,
         center_name,
-        pdf_type_name,
+        pdf_type_name, # to be depreceated / changed since we now import all pdfs from same directory
         destination_dir,
         save=True,
     ):

{endoreg_db-0.4.0 → endoreg_db-0.4.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "endoreg-db"
-version = "0.4.0"
+version = "0.4.2"
 description = "EndoReg Db Django App"
 authors = ["Thomas J. Lux"]
 license = "GNU3"
@@ -8,22 +8,24 @@ readme = "README.md"
 
 [tool.poetry.dependencies]
 python = "^3.11"
-django = "~4.2"
+django = "^5.1"
 djangorestframework = "^3.14.0"
 django-bootstrap5 = "^23.4"
 tqdm = "^4.66.2"
 pyyaml = "^6.0.1"
-icecream = "^2.1.3"
-pillow = "^10.2.0"
-# opencv-python
 opencv-python = "^4.9.0.80"
 ffmpeg-python = "^0.2.0"
 pytesseract = "^0.3.10"
-agl-report-reader = "^0.3.0"
 scipy = "^1.14.0"
 pandas = "^2.2.2"
+pillow = "~10"
 
+[tool.poetry.group.nixProvided.dependencies]
+icecream = "^2.1.3"
+# agl-report-reader = "^0.3"
 
+[tool.poetry.group.dev.dependencies]
+pytest = "^8.3.3"
 
 [build-system]
 requires = ["poetry-core"]

endoreg_db-0.4.0/endoreg_db/models/annotation/__init__.py

@@ -1,2 +0,0 @@
-from .image_classification import ImageClassificationAnnotation
-from .binary_classification_annotation_task import LegacyBinaryClassificationAnnotationTask, BinaryClassificationAnnotationTask