endoreg-db 0.8.1__tar.gz → 0.8.2__tar.gz

{endoreg_db-0.8.1 → endoreg_db-0.8.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: endoreg-db
-Version: 0.8.1
+Version: 0.8.2
 Summary: EndoReg Db Django App
 Project-URL: Homepage, https://info.coloreg.de
 Project-URL: Repository, https://github.com/wg-lux/endoreg-db
@@ -33,7 +33,7 @@ Requires-Dist: gunicorn>=23.0.0
 Requires-Dist: icecream>=2.1.4
 Requires-Dist: librosa==0.11.0
 Requires-Dist: llvmlite>=0.44.0
-Requires-Dist: lx-anonymizer[llm,ocr]>=0.8.1
+Requires-Dist: lx-anonymizer[llm,ocr]>=0.8.2
 Requires-Dist: moviepy==2.2.1
 Requires-Dist: mypy>=1.16.0
 Requires-Dist: numpy>=2.2.3

{endoreg_db-0.8.1 → endoreg_db-0.8.2}/devenv.nix

@@ -18,7 +18,7 @@ let
   confDir = "./conf"; # Define confDir here
 
   # Pin to specific Python 3.12 version to match pyproject.toml
-  python = pkgs.python312;
+  python = pkgs.python3.withPackages(ps: with ps; [tkinter]); #known devenv issue with python3Packages since python3Full was deprecated
   uvPackage = pkgs.uv;
   
   buildInputs = with pkgs; [
@@ -37,6 +37,7 @@ let
   runtimePackages = with pkgs; [
     stdenv.cc.cc
     ffmpeg-headless.bin
+    python312Packages.tkinter
     tesseract
     uvPackage
     libglvnd # Add libglvnd for libGL.so.1
@@ -86,6 +87,7 @@ in
   };
 
   scripts = {
+
     export-nix-vars.exec = ''
       cat > .devenv-vars.json << EOF
       {
@@ -179,9 +181,7 @@ in
       echo "Warning: uv virtual environment activation script not found. Run 'devenv task run env:clean' and re-enter shell."
     fi
 
-    # . .devenv/state/venv/bin/activate
-    # runtests-dataloader
-    # hello
+    env-setup
   '';
 
   enterTest = ''

endoreg_db-0.8.2/endoreg_db/helpers/download_segmentation_model.py

@@ -0,0 +1,31 @@
+import huggingface_hub
+from typing import Optional
+
+def download_segmentation_model(
+    repo_id: str = "wg-lux/colo_segmentation_RegNetX800MF_base",
+    filename: str = "model.safetensors",
+    cache_dir: Optional[str] = None
+) -> str:
+    """
+    Downloads a segmentation model from Hugging Face and caches it locally.
+
+    Args:
+        repo_id (str): The Hugging Face repository ID (default: wg-lux model).
+        filename (str): The specific file to download from the repo (default: model.safetensors).
+        cache_dir (str): The directory to cache the downloaded model. If None, uses HF default cache.
+
+    Returns:
+        str: The local path to the downloaded model.
+        
+    Example:
+        >>> model_path = download_segmentation_model()
+        >>> # Downloads from wg-lux/colo_segmentation_RegNetX800MF_base
+    """
+    local_path = huggingface_hub.hf_hub_download(
+        repo_id=repo_id,
+        filename=filename,
+        cache_dir=cache_dir,
+        force_download=False,
+        resume_download=True,
+    )
+    return local_path

{endoreg_db-0.8.1 → endoreg_db-0.8.2}/endoreg_db/models/media/video/pipe_1.py

@@ -1,6 +1,7 @@
 import logging
 from typing import TYPE_CHECKING, Optional, Dict, List, Tuple
 from django.db import transaction
+from endoreg_db.helpers.download_segmentation_model import download_segmentation_model
 
 # Added imports
 
@@ -50,6 +51,8 @@ def _pipe_1(
             if not state.frames_extracted:
                 logger.error("Pipe 1 failed: Frame extraction did not complete successfully.")
                 return False
+            
+            
 
             # 3. Perform Initial Prediction
             logger.info(f"Pipe 1: Performing prediction with model '{model_name}'...")
@@ -61,7 +64,16 @@ def _pipe_1(
                     model_meta = ai_model_obj.get_latest_version()
             except AiModel.DoesNotExist:
                 logger.error(f"Pipe 1 failed: Model '{model_name}' not found.")
-                return False
+                try:
+                    model_name = download_segmentation_model()
+                    ai_model_obj = AiModel.objects.get(name=model_name)
+                    if model_meta_version is not None:
+                        model_meta = ai_model_obj.metadata_versions.get(version=model_meta_version)
+                    else:
+                        model_meta = ai_model_obj.get_latest_version()
+                except AiModel.DoesNotExist:
+                    logger.error(f"Pipe 1 failed: Model '{model_name}' not found.")
+                    return False
             except ModelMeta.DoesNotExist:
                 logger.error(
                     f"Pipe 1 failed: ModelMeta version {model_meta_version} for model '{model_name}' not found."

{endoreg_db-0.8.1 → endoreg_db-0.8.2}/endoreg_db/serializers/anonymization.py

@@ -28,6 +28,9 @@ class SensitiveMetaValidateSerializer(serializers.Serializer):
     patient_gender = serializers.CharField(required=False, allow_blank=True)
     center_name = serializers.CharField(required=False, allow_blank=True)
     is_verified = serializers.BooleanField(required=False, default=True)
+    file_type = serializers.ChoiceField(
+        choices=['video', 'pdf'], required=False
+    )  # Optional: "video" oder "pdf"
 
     def validate_patient_dob(self, value):
         """

{endoreg_db-0.8.1 → endoreg_db-0.8.2}/endoreg_db/services/pdf_import.py

@@ -637,36 +637,6 @@ class PdfImportService:
 
         except Exception as e:
             logger.warning("Could not set anonymized file reference: %s", e)
-    
-    '''def _apply_anonymized_pdf(self):
-        """Apply anonymized PDF results."""
-        if not self.current_pdf:
-            logger.warning("Cannot apply anonymized PDF - no PDF instance available")
-            return
-            
-        anonymized_pdf_path = self.processing_context.get('anonymized_pdf_path')
-        
-        if not anonymized_pdf_path:
-            return
-            
-        anonymized_path = Path(anonymized_pdf_path)
-        if anonymized_path.exists():
-            logger.info(f"Anonymized PDF created by ReportReader at: {anonymized_path}")
-            try:
-                from django.core.files.base import File
-                with open(anonymized_path, 'rb') as f:
-                    django_file = File(f)
-                    self.current_pdf.anonymized_file.save(
-                        anonymized_path.name,
-                        django_file,
-                        save=False
-                    )
-            except Exception as e:
-                logger.warning(f"Could not set anonymized file reference: {e}")
-        else:
-            logger.warning(f"Anonymized PDF path returned but file does not exist: {anonymized_path}")'''
-
-
 
 
     def _finalize_processing(self):