endoreg-db 0.8.4.2__py3-none-any.whl → 0.8.4.3__py3-none-any.whl

endoreg_db/utils/setup_config.py

@@ -0,0 +1,177 @@
+"""
+Configuration loader for EndoReg DB setup.
+Handles loading and parsing of setup configuration from YAML files.
+"""
+
+import glob
+import logging
+import os
+from pathlib import Path
+from typing import Any, Dict, List, Optional
+
+import yaml
+
+logger = logging.getLogger(__name__)
+
+
+class SetupConfig:
+    """
+    Handles loading and accessing setup configuration from YAML files.
+    Provides methods to get model names, search patterns, and fallback configurations.
+    """
+
+    def __init__(self, config_file: Optional[Path] = None):
+        """
+        Initialize the setup configuration.
+
+        Args:
+            config_file: Path to the setup configuration YAML file.
+                        If None, uses default location.
+        """
+        if config_file is None:
+            # Default to setup_config.yaml in data directory
+            config_file = Path(__file__).parent.parent / "data" / "setup_config.yaml"
+
+        self.config_file = config_file
+        self._config = self._load_config()
+
+    def _load_config(self) -> Dict[str, Any]:
+        """Load configuration from YAML file."""
+        try:
+            if self.config_file.exists():
+                with open(self.config_file, "r") as f:
+                    config = yaml.safe_load(f)
+                    logger.info(f"Loaded setup configuration from {self.config_file}")
+                    return config or {}
+            else:
+                logger.warning(f"Setup config file not found: {self.config_file}")
+                return self._get_default_config()
+        except Exception as e:
+            logger.error(f"Error loading setup config: {e}")
+            return self._get_default_config()
+
+    def _get_default_config(self) -> Dict[str, Any]:
+        """Return default configuration if file is not available."""
+        return {
+            "default_models": {
+                "primary_classification_model": "image_multilabel_classification_colonoscopy_default",
+                "primary_labelset": "multilabel_classification_colonoscopy_default",
+            },
+            "huggingface_fallback": {
+                "enabled": True,
+                "repo_id": "wg-lux/colo_segmentation_RegNetX800MF_base",
+                "filename": "colo_segmentation_RegNetX800MF_base.ckpt",
+                "labelset_name": "multilabel_classification_colonoscopy_default",
+            },
+            "weights_search_patterns": [
+                "colo_segmentation_RegNetX800MF_*.ckpt",
+                "image_multilabel_classification_colonoscopy_default_*.ckpt",
+                "*_colonoscopy_*.ckpt",
+            ],
+            "weights_search_dirs": ["tests/assets", "assets", "data/storage/model_weights", "${STORAGE_DIR}/model_weights"],
+            "auto_generation_defaults": {
+                "activation": "sigmoid",
+                "mean": "0.485,0.456,0.406",
+                "std": "0.229,0.224,0.225",
+                "size_x": 224,
+                "size_y": 224,
+                "axes": "CHW",
+                "batchsize": 32,
+                "num_workers": 4,
+            },
+        }
+
+    def get_primary_model_name(self) -> str:
+        """Get the primary classification model name."""
+        return self._config.get("default_models", {}).get("primary_classification_model", "image_multilabel_classification_colonoscopy_default")
+
+    def get_primary_labelset_name(self) -> str:
+        """Get the primary labelset name."""
+        return self._config.get("default_models", {}).get("primary_labelset", "multilabel_classification_colonoscopy_default")
+
+    def get_huggingface_config(self) -> Dict[str, Any]:
+        """Get HuggingFace fallback configuration."""
+        return self._config.get("huggingface_fallback", {})
+
+    def get_weights_search_patterns(self) -> List[str]:
+        """Get weight file search patterns."""
+        return self._config.get("weights_search_patterns", ["colo_segmentation_RegNetX800MF_*.ckpt", "*_colonoscopy_*.ckpt"])
+
+    def get_weights_search_dirs(self) -> List[Path]:
+        """
+        Get weight file search directories with environment variable substitution.
+        """
+        dirs = self._config.get("weights_search_dirs", [])
+        resolved_dirs = []
+
+        for dir_str in dirs:
+            # Handle environment variable substitution
+            if "${" in dir_str:
+                dir_str = os.path.expandvars(dir_str)
+
+            resolved_dirs.append(Path(dir_str))
+
+        return resolved_dirs
+
+    def get_auto_generation_defaults(self) -> Dict[str, Any]:
+        """Get default values for auto-generated metadata."""
+        return self._config.get("auto_generation_defaults", {})
+
+    def find_model_weights_files(self) -> List[Path]:
+        """
+        Find model weight files using configured search patterns and directories.
+
+        Returns:
+            List of paths to found weight files
+        """
+        found_files = []
+        search_dirs = self.get_weights_search_dirs()
+        search_patterns = self.get_weights_search_patterns()
+
+        for search_dir in search_dirs:
+            if not search_dir.exists():
+                continue
+
+            for pattern in search_patterns:
+                # Use glob to find files matching pattern
+                pattern_path = search_dir / pattern
+                matches = glob.glob(str(pattern_path))
+                for match in matches:
+                    path = Path(match)
+                    if path.exists() and path not in found_files:
+                        found_files.append(path)
+                        logger.info(f"Found weight file: {path}")
+
+        return found_files
+
+    def get_model_specific_config(self, model_name: str) -> Optional[Dict[str, Any]]:
+        """
+        Get model-specific configuration from YAML metadata files.
+
+        Args:
+            model_name: Name of the model to get config for
+
+        Returns:
+            Model-specific setup configuration if found
+        """
+        # This would need to parse the ai_model_meta YAML files
+        # and extract setup_config sections for the specified model
+        try:
+            from endoreg_db.data import AI_MODEL_META_DATA_DIR
+
+            for yaml_file in AI_MODEL_META_DATA_DIR.glob("*.yaml"):
+                with open(yaml_file, "r") as f:
+                    data = yaml.safe_load(f)
+
+                if isinstance(data, list):
+                    for item in data:
+                        if item.get("fields", {}).get("name") == model_name or item.get("fields", {}).get("model") == model_name:
+                            return item.get("setup_config", {})
+        except Exception as e:
+            logger.warning(f"Error loading model-specific config for {model_name}: {e}")
+
+        return None
+
+
+# Global instance for easy access
+setup_config = SetupConfig()

{endoreg_db-0.8.4.2.dist-info → endoreg_db-0.8.4.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: endoreg-db
-Version: 0.8.4.2
+Version: 0.8.4.3
 Summary: EndoReg Db Django App
 Project-URL: Homepage, https://info.coloreg.de
 Project-URL: Repository, https://github.com/wg-lux/endoreg-db

{endoreg_db-0.8.4.2.dist-info → endoreg_db-0.8.4.3.dist-info}/RECORD

@@ -18,13 +18,14 @@ endoreg_db/config/env.py,sha256=S244AQRkDP0PpP0MPaShgqeBJgI1BQknfER1_vUFMD4,2673
 endoreg_db/data/__init__.py,sha256=Wqu24f5-FVKE5pis0wGDYsMHOTkieN40b10S5zU5240,5932
 endoreg_db/data/db_summary.csv,sha256=K4PcufVHQ64H1i2MbCShMxReEa96I8cL6IfwCVpqF2M,1225
 endoreg_db/data/db_summary.xlsx,sha256=pwsc_IcxNETNrYjDXjpSW83b8f-WsSunRDiJLZXENZ0,5829
+endoreg_db/data/setup_config.yaml,sha256=ZlL_DwHNqdulPzfZzNDlsMEHC9hSrZZ3Ri9OUDJKXn8,1301
 endoreg_db/data/ai_model/data.yaml,sha256=9XIRMS_meioGu-vYY6zUvz4RUXhRLdalaHhCTdaq4nA,306
 endoreg_db/data/ai_model_label/label/data.yaml,sha256=qkt0FfrLvPrcW_N0GUzu3q9TpiXrvZU047xAIOk_33A,1737
 endoreg_db/data/ai_model_label/label/polyp_classification.yaml,sha256=lHx2VwwVgKzOM_3PcuHuSIStgvMK6rHVi3WP67Qjv70,936
 endoreg_db/data/ai_model_label/label-set/data.yaml,sha256=ocaxnkqiZgwi4sY561TbP_DEQWkPG1hBZ3olwPOqiXQ,789
 endoreg_db/data/ai_model_label/label-set/polyp_classifications.yaml,sha256=GVmctJCgnr2lPUMttgPThNXoLcUl4XpliiuSjvE6h_Q,443
 endoreg_db/data/ai_model_label/label-type/data.yaml,sha256=vffKYpTae_gu63_wza6LONs5ys4pna1EbrUUO6CafQs,136
-endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml,sha256=JhrFP6WXSFRa4kKujKAtgNVmnFYMiz8-J_oN-JQsSi0,182
+endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml,sha256=VelCJXavWT4HYbPko1S8O1gv7wBZBsvz6r5FvjXTm2o,1196
 endoreg_db/data/ai_model_type/data.yaml,sha256=vCMMo8wiI5uL2zrQROmgsHq1GrC8IdagGIgNdQunUeQ,149
 endoreg_db/data/ai_model_video_segmentation_label/base_segmentation.yaml,sha256=EZ83vq02Cf2KfflWQ4HEe1NHmuzSCsmKtWW5Bv8jet0,4060
 endoreg_db/data/ai_model_video_segmentation_labelset/data.yaml,sha256=07uB1ousJVNpp8B9enJ_YIdZf3y4sBPlME4bZwDv6ho,404
@@ -257,7 +258,7 @@ endoreg_db/management/commands/import_report.py,sha256=vFst-NeQdL-w62yoH4kDamq-2
 endoreg_db/management/commands/import_video.py,sha256=AMvgi1eN0F_hjhgnNNYIFkJtHfjalBfh2lfDxw6VTzE,17980
 endoreg_db/management/commands/import_video_with_classification.py,sha256=ulZH5jvAWu_pJ1kI9B3hbIO1-p_BReY0zbIQDS_d9OI,14726
 endoreg_db/management/commands/init_default_ai_model.py,sha256=98yBigGZ5gkA-b1LPcvzS5x2jAms3pX58fU-TEAcjKw,4669
-endoreg_db/management/commands/load_ai_model_data.py,sha256=QDyWPjIC1ga13Ou67_mnE8HUGTAK0uF2LLQ12sE-95E,2747
+endoreg_db/management/commands/load_ai_model_data.py,sha256=O_mzGGcpnVacC4EZmEGbTp4EADNXJRsvaZoNFgh2wFU,2867
 endoreg_db/management/commands/load_ai_model_label_data.py,sha256=jnm2720TsnRTBKF6guwnjLo7sropW_YoRjgyjo1TUr8,2143
 endoreg_db/management/commands/load_base_db_data.py,sha256=0Go2cYbqfx6MBSeQaHPAq22yeJxOyX25xpmcBcE9Auw,9374
 endoreg_db/management/commands/load_center_data.py,sha256=GQpbe7dxgbTgd66oBqrBXax-os3ibnPmCeSEFDVauPU,2570
@@ -290,10 +291,11 @@ endoreg_db/management/commands/load_unit_data.py,sha256=tcux-iL-ByT2ApgmHEkLllZS
 endoreg_db/management/commands/load_user_groups.py,sha256=D7SK2FvZEHoE4TIXNGCjDw5_12MH9bpGZvoS7eEv0Os,1031
 endoreg_db/management/commands/register_ai_model.py,sha256=KixTfuQR6TUfRmzB5GOos16BFOz7NL4TzLzBkgtPPgE,2510
 endoreg_db/management/commands/reset_celery_schedule.py,sha256=U-m_FNRTw6LAwJoT9RUE4qrhmQXm7AyFToPcHYyJpIE,386
-endoreg_db/management/commands/setup_endoreg_db.py,sha256=efOXE6IQs4ey84tIncf6zXI2VVVRd7CYXbeuACFgkgI,9095
+endoreg_db/management/commands/setup_endoreg_db.py,sha256=C0ooVVmrzX-_ksoma3s3rZtJUcUsxvO4ddm1VhlYiiU,17640
 endoreg_db/management/commands/start_filewatcher.py,sha256=3jESBqRiYPa9f35--zd70qQaYnyT0tzRO_b_HJuyteQ,4093
 endoreg_db/management/commands/storage_management.py,sha256=NpToX59ndwTFNmnSoeppmiPdMvpjSHH7mAdIe4SvUoI,22396
 endoreg_db/management/commands/summarize_db_content.py,sha256=pOIz3qbY4Ktmh0zV_DKFx971VD0pPx027gCD7a47EL0,10766
+endoreg_db/management/commands/validate_ai_models.py,sha256=Z7Ga-PndTFVG8GnkYbS58h8ofiyhnxZDcyP5Qqpl1c8,4684
 endoreg_db/management/commands/validate_video.py,sha256=cns_kNgztyp6XTeXuDeLEet8vAATkpxZwJuSWuQ5Olk,11302
 endoreg_db/management/commands/validate_video_files.py,sha256=0lvA0Z8BKiibjyqc4ueI646IIc5bKI3sIOxiiF5_bTk,6509
 endoreg_db/management/commands/video_validation.py,sha256=xnAoCPB44dmnRbn6FqUjqRXQ-ZhDPNX1T5kCpAU8sgc,771
@@ -435,7 +437,7 @@ endoreg_db/models/medical/finding/finding_intervention.py,sha256=FBwjI15yitMpTXk
 endoreg_db/models/medical/finding/finding_type.py,sha256=ohDEmLcgEpYjG5q0uhCaq2xQS8jH_rj4qyKQ2DUumqQ,1117
 endoreg_db/models/medical/hardware/__init__.py,sha256=uX2-UpBzX2chpZEeCyqbv2BSrv3OZNG9PrB8sHEWpHQ,178
 endoreg_db/models/medical/hardware/endoscope.py,sha256=8T8R2Bo2T29psQ3C_HTrhBogN8hiysuZkJOxUefqGoI,1657
-endoreg_db/models/medical/hardware/endoscopy_processor.py,sha256=DLKMXPWValfJCf4rZ1u6PdpeBa2ST0WTjkcuruFlzG0,6201
+endoreg_db/models/medical/hardware/endoscopy_processor.py,sha256=9HMTgODfJo36gDg4N3QtcH3_NOriOanwYMtIPTlULVk,6626
 endoreg_db/models/medical/laboratory/__init__.py,sha256=595XF1ikkwzQWbUsyasU23v1kDRugrgTp3eUfrMd0UQ,62
 endoreg_db/models/medical/laboratory/lab_value.py,sha256=uw4mjguVrqvsxQ-NzGO0DoNlSCaydI8KaJgUhuM16wo,20258
 endoreg_db/models/medical/medication/__init__.py,sha256=BHh6ARvm2uVNswN12EQAEMFPnoGBiVwl7RCjKrW6C2I,761
@@ -464,7 +466,7 @@ endoreg_db/models/medical/risk/risk_type.py,sha256=kEugcaWSTEWH_Vxq4dcF80Iv1L4_K
 endoreg_db/models/metadata/__init__.py,sha256=8I6oLj3YTmeaPGJpL0AWG5gLwp38QzrEggxSkTisv7c,474
 endoreg_db/models/metadata/frame_ocr_result.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 endoreg_db/models/metadata/model_meta.py,sha256=F_r-PTLeNi4J-4EaGCQkGIguhdl7Bwba7_i56ZAjc-4,7589
-endoreg_db/models/metadata/model_meta_logic.py,sha256=pcpKf9J5DUiEG-D-VhOPcnFjBznkx5jK7EGv0zDMQm8,12440
+endoreg_db/models/metadata/model_meta_logic.py,sha256=wESdSRvnA0SthaZD2W29nbMGrichRCwaKQGnE5uCAao,16046
 endoreg_db/models/metadata/pdf_meta.py,sha256=BTmpSgqxmPKi0apcNjyrZAS4AFKCPXVdBd6VBeyyv6E,3174
 endoreg_db/models/metadata/sensitive_meta.py,sha256=ekLHrW-b5uYcjfkRd0EW5ncx5ef8Bu-K6msDkpWCAbk,13034
 endoreg_db/models/metadata/sensitive_meta_logic.py,sha256=by3eCW8CgglK1SHiDOepHhTOGaugswxJhkH0BZp7-gs,33909
@@ -602,7 +604,7 @@ endoreg_db/services/pseudonym_service.py,sha256=CJhbtRa6K6SPbphgCZgEMi8AFQtB18CU
 endoreg_db/services/requirements_object.py,sha256=290zf8AEbVtCoHhW4Jr7_ud-RvrqYmb1Nz9UBHtTnc0,6164
 endoreg_db/services/segment_sync.py,sha256=YgHvIHkbW4mqCu0ACf3zjRSZnNfxWwt4gh5syUVXuE0,6400
 endoreg_db/services/storage_aware_video_processor.py,sha256=kKFK64vXLeBSVkp1YJonU3gFDTeXZ8C4qb9QZZB99SE,13420
-endoreg_db/services/video_import.py,sha256=0eeY5etJ4rg6uxC-uUis_yoa6cvGgwY2VaiD3mVFosg,46369
+endoreg_db/services/video_import.py,sha256=FTFXb4A7cGp6uphDds5hyjdOcXnWAV-3LbjSIfaswvg,46241
 endoreg_db/tasks/upload_tasks.py,sha256=OJq7DhNwcbWdXzHY8jz5c51BCVkPN5gSWOz-6Fx6W5M,7799
 endoreg_db/tasks/video_ingest.py,sha256=kxFuYkHijINV0VabQKCFVpJRv6eCAw07tviONurDgg8,5265
 endoreg_db/tasks/video_processing_tasks.py,sha256=rZ7Kr49bAR4Q-vALO2SURebrhcJ5hSFGwjF4aULrOao,14089
@@ -644,6 +646,7 @@ endoreg_db/utils/parse_and_generate_yaml.py,sha256=k7y0fl9Jbb_LNryeJYd6tebklRlu1
 endoreg_db/utils/paths.py,sha256=ncXtB_l6FBVXXdk59U7v4FhSvLO7Yb0DQ-GQMcOqiTw,3398
 endoreg_db/utils/permissions.py,sha256=IqxG9IqJBSZuxvT1ItVgGS8fMzkA2OLdDV6y8mKHSuo,5096
 endoreg_db/utils/requirement_helpers.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+endoreg_db/utils/setup_config.py,sha256=yeDPStTEJm8Xy6ah5AJTpXMoPUyouxuPIsRUpqdiXf4,6775
 endoreg_db/utils/translation.py,sha256=77Xel12pAGo0rQ0NxB7nfejvMb0GBjEmhC3I7mcU91I,1256
 endoreg_db/utils/uuid.py,sha256=T4HXqYtKwXFqE5kPyvlgWHyllBBF6LL6N48nl9TpwBk,53
 endoreg_db/utils/validate_endo_roi.py,sha256=Ct2H0JJW9gxYZc7099NYee4kxdKL90a3LGYahqibwms,925
@@ -786,7 +789,7 @@ endoreg_db/views/video/video_meta.py,sha256=C1wBMTtQb_yzEUrhFGAy2UHEWMk_CbU75WXX
 endoreg_db/views/video/video_processing_history.py,sha256=mhFuS8RG5GV8E-lTtuD0qrq-bIpnUFp8vy9aERfC-J8,770
 endoreg_db/views/video/video_remove_frames.py,sha256=2FmvNrSPM0fUXiBxINN6vBUUDCqDlBkNcGR3WsLDgKo,1696
 endoreg_db/views/video/video_stream.py,sha256=kLyuf0ORTmsLeYUQkTQ6iRYqlIQozWhMMR3Lhfe_trk,12148
-endoreg_db-0.8.4.2.dist-info/METADATA,sha256=xSaPMvzzc7HovOmkl2Gn0lYVoRNTPk4yqIBFcz0kc70,14758
-endoreg_db-0.8.4.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-endoreg_db-0.8.4.2.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-endoreg_db-0.8.4.2.dist-info/RECORD,,
+endoreg_db-0.8.4.3.dist-info/METADATA,sha256=KnYipnhERrjdiE4CzHQjRa9sPk9NYl62tJ3UY3cIgZk,14758
+endoreg_db-0.8.4.3.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+endoreg_db-0.8.4.3.dist-info/licenses/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+endoreg_db-0.8.4.3.dist-info/RECORD,,