endoreg-db 0.8.8.0__py3-none-any.whl → 0.8.8.9__py3-none-any.whl

endoreg_db/data/__init__.py

@@ -13,7 +13,7 @@ ENDOSCOPE_TYPE_DATA_DIR = DATA_DIR / "endoscope_type"
 ENDOSCOPE_DATA_DIR = DATA_DIR / "endoscope"
 ACTIVE_MODEL_DATA_DIR = DATA_DIR / "active_model"
 PROFESSION_DATA_DIR = DATA_DIR / "profession"
-PDF_TYPE_DATA_DIR = DATA_DIR / "pdf_type"
+REPORT_TYPE_DATA_DIR = DATA_DIR / "pdf_type"
 REPORT_READER_FLAG_DATA_DIR = DATA_DIR / "report_reader_flag"
 EVENT_DATA_DIR = DATA_DIR / "event"
 GENDER_DATA_DIR = DATA_DIR / "gender"
@@ -27,17 +27,29 @@ CONTRAINDICATION_DATA_DIR = DATA_DIR / "contraindication"
 
 # Examination
 EXAMINATION_INDICATION_DATA_DIR = DATA_DIR / "examination_indication"
-EXAMINATION_INDICATION_CLASSIFICATION_DATA_DIR = DATA_DIR / "examination_indication_classification"
-EXAMINATION_INDICATION_CLASSIFICATION_CHOICE_DATA_DIR = DATA_DIR / "examination_indication_classification_choice"
+EXAMINATION_INDICATION_CLASSIFICATION_DATA_DIR = (
+    DATA_DIR / "examination_indication_classification"
+)
+EXAMINATION_INDICATION_CLASSIFICATION_CHOICE_DATA_DIR = (
+    DATA_DIR / "examination_indication_classification_choice"
+)
 
 # Finding
 FINDING_TYPE_DATA_DIR = DATA_DIR / "finding_type"
 FINDING_DATA_DIR = DATA_DIR / "finding"
 FINDING_LOCATION_CLASSIFICATION_DATA_DIR = DATA_DIR / "finding_location_classification"
-FINDING_LOCATION_CLASSIFICATION_CHOICE_DATA_DIR = DATA_DIR / "finding_location_classification_choice"
-FINDING_MORPHOLOGY_CLASSIFICATION_DATA_DIR = DATA_DIR / "finding_morphology_classification"
-FINDING_MORPHOLOGY_CLASSIFICATION_CHOICE_DATA_DIR = DATA_DIR / "finding_morphology_classification_choice"
-FINDING_MORPGOLOGY_CLASSIFICATION_TYPE_DATA_DIR = DATA_DIR / "finding_morphology_classification_type"
+FINDING_LOCATION_CLASSIFICATION_CHOICE_DATA_DIR = (
+    DATA_DIR / "finding_location_classification_choice"
+)
+FINDING_MORPHOLOGY_CLASSIFICATION_DATA_DIR = (
+    DATA_DIR / "finding_morphology_classification"
+)
+FINDING_MORPHOLOGY_CLASSIFICATION_CHOICE_DATA_DIR = (
+    DATA_DIR / "finding_morphology_classification_choice"
+)
+FINDING_MORPGOLOGY_CLASSIFICATION_TYPE_DATA_DIR = (
+    DATA_DIR / "finding_morphology_classification_type"
+)
 FINDING_INTERVETION_DATA_DIR = DATA_DIR / "finding_intervention"
 FINIDNG_INTERVENTION_TYPE_DATA_DIR = DATA_DIR / "finding_intervention_type"
 
@@ -69,7 +81,9 @@ MEDICATION_INDICATION_TYPE_DATA_DIR = DATA_DIR / "medication_indication_type"
 DISTRIBUTION_BASE_DIR = DATA_DIR / "distribution"
 DISTRIBUTION_SINGLE_CATEGORICAL_DATA_DIR = DISTRIBUTION_BASE_DIR / "single_categorical"
 DISTRIBUTION_NUMERIC_DATA_DIR = DISTRIBUTION_BASE_DIR / "numeric"
-DISTRIBUTION_MULTIPLE_CATEGORICAL_DATA_DIR = DISTRIBUTION_BASE_DIR / "multiple_categorical"
+DISTRIBUTION_MULTIPLE_CATEGORICAL_DATA_DIR = (
+    DISTRIBUTION_BASE_DIR / "multiple_categorical"
+)
 DISTRIBUTION_DATE_DATA_DIR = DISTRIBUTION_BASE_DIR / "date"
 
 # NETWORK

endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml

@@ -22,7 +22,6 @@
     is_primary_model: true # Mark this as the primary model for setup
     weight_filenames: # Specific weight file patterns for this model
       - "colo_segmentation_RegNetX800MF_6.safetensors"
-      - "image_multilabel_classification_colonoscopy_default_v1_*.safetensors"
     huggingface_fallback: # HF configuration for this model
       repo_id: "wg-lux/colo_segmentation_RegNetX800MF_base"
       filename: "colo_segmentation_RegNetX800MF_base.safetensors"

endoreg_db/data/examination/examinations/data.yaml

@@ -4,6 +4,45 @@
     name_de: "Koloskopie"
     name_en: "Colonoscopy"
     examination_types: ["endoscopy"]
+    indications:
+      - colonoscopy_generic
+      - colonoscopy_screening
+      - colonoscopy_lesion_removal_small
+      - colonoscopy_lesion_removal_large
+      - colonoscopy_lesion_removal_emr
+      - colonoscopy_diagnostic_acute_symptomatic
+    findings:
+      # baseline
+      - examination_setting
+      - bowel_preparation_lc
+      - bowel_preparation_tc
+      - bowel_preparation_rc
+      - bowel_preparation_simplified
+      - colonoscopy_deepest_viewed_location
+      # observations
+      - complication_generic
+      - colon_polyp
+      - colon_post_intervention_wound
+      - colon_tumor_mass
+      - colon_inflammation
+      - colon_erosion
+      - colon_ulcer
+      - colon_scar
+      - anal_fissure
+      - anal_hemorrhoids
+      # hidden
+      - rectum_anus
+      - rectum
+      - sigmoid_colon
+      - descending_colon
+      - left_flexure
+      - transverse_colon
+      - right_flexure
+      - ascending_colon
+      - cecum
+      - appendiceal_orifice
+      - ileocecal_valve
+      - terminal_ileum
 
 - model: endoreg_db.Examination
   fields:
@@ -11,6 +50,43 @@
     name_de: "Gastroskopie"
     name_en: "Gastroscopy"
     examination_types: ["endoscopy"]
+    indications:
+      - gastroscopy_generic
+      # - gastroscopy_diagnostic_acute_symptomatic
+      # - gastroscopy_surveillance_barretts_esophagus
+      # - gastroscopy_surveillance_gastric_atrophy
+      - gastroscopy_lesion_removal_small
+      - gastroscopy_lesion_removal_large
+      # - gastroscopy_lesion_removal_emr
+    findings:
+      # baseline
+      - sedation_endoscopy
+      - gastroscopy_esophagus_mucosa
+      - gastroscopy_gastroesophageal_junction
+      - gastroscopy_fundus_mucosa
+      - gastroscopy_corpus_mucosa
+      - gastroscopy_antrum_mucosa
+      - gastroscopy_pylorus
+      - gastroscopy_angulus_flexure_mucosa
+      - gastroscopy_duodenum_bulbus_mucosa
+      - gastroscopy_duodenum_mucosa
+      # observations
+      - gastroscopy_polyp
+      - gastroscopy_ulcer
+      - gastroscopy_erythema
+      - gastroscopy_subepithelial_tumor
+      - gastroscopy_stenosis
+      - gastroscopy_varices_esophageal
+      - gastroscopy_varices_gastric
+      - gastroscopy_varices_duodenal
+      - gastroscopy_scar
+      - gastroscopy_bleeding
+      - gastroscopy_stenosis
+      - gastroscopy_ectopic_gastric_mucosa
+      - gastroscopy_diverticulum_esophagus
+      - gastroscopy_diverticulum_duodenum
+      - gastroscopy_ectopic_pancreatic_tissue
+      - gastroscopy_obstruction_generic
 
 # endosonography_upper_gi
 - model: endoreg_db.Examination
@@ -19,6 +95,27 @@
     name_de: "Endosonographie oberer GI-Trakt"
     name_en: "Endosonography Upper GI Tract"
     examination_types: ["endoscopy"]
+    indications:
+      - gastroscopy_baseline
+      - gastroscopy_diagnostic_acute_symptomatic
+      - gastroscopy_acute_bleeding
+      - gastroscopy_percutane_enterostomy
+      - gastroscopy_varicosis_therapeutic_esophagus
+      - gastroscopy_varicosis_therapeutic_stomach
+      - gastroscopy_therapeutic_varicosis_intestine
+      - gastroscopy_lesion_removal_small
+      - gastroscopy_lesion_removal_large
+      - gastroscopy_obstruction_generic
+
+- model: endoreg_db.Examination
+  fields:
+    name: "endosonography_upper_gi"
+    name_de: "Endosonographie unterer GI-Trakt"
+    name_en: "Endosonography Lower GI Tract"
+    examination_types: ["endoscopy"]
+    indications:
+      - endosonography_upper_gi_non_invasive
+      - endosonography_upper_gi_invasive
 
 - model: endoreg_db.Examination
   fields:
@@ -26,6 +123,9 @@
     name_de: "Endosonographie unterer GI-Trakt"
     name_en: "Endosonography Lower GI Tract"
     examination_types: ["endoscopy"]
+    indications:
+      - endosonography_lower_gi_non_invasive
+      - endosonography_lower_gi_invasive
 
 # ERCP
 - model: endoreg_db.Examination
@@ -34,6 +134,12 @@
     name_de: "ERCP"
     name_en: "ERCP"
     examination_types: ["endoscopy"]
+    indications:
+      - erc
+      - erc_no_est
+      - ercp
+      - ercp_no_est
+      - ercp_therapeutic_stenosis
 
 # small bowel endoscopy
 - model: endoreg_db.Examination
@@ -42,6 +148,8 @@
     name_de: "Dünndarmendoskopie"
     name_en: "Small Bowel Endoscopy"
     examination_types: ["endoscopy"]
+    indications:
+      - small_bowel_endoscopy_generic
 
 # capsule endoscopy
 - model: endoreg_db.Examination
@@ -50,23 +158,15 @@
     name_de: "Kapselendoskopie"
     name_en: "Capsule Endoscopy"
     examination_types: ["endoscopy"]
+    indications:
+      - capsule_endoscopy_generic
 
 - model: endoreg_db.Examination
   fields:
-    name: "percutaneous_transhepatic_biliary_drainage"
+    name: "percutaneous_transhepatic_biliary_intervention"
     name_de: "Perkutane transhepatische Gallengangdrainage"
     name_en: "Percutaneous Transhepatic Biliary Drainage"
     examination_types: ["endoscopy", "sonography", "xray"]
-
-# percutaneous_transhepatic_cholangiography
-- model: endoreg_db.Examination
-  fields:
-    name: "percutaneous_transhepatic_cholangiography"
-    name_de: "Perkutane transhepatische Cholangiographie"
-    name_en: "Percutaneous Transhepatic Cholangiography"
-    examination_types: ["endoscopy", "sonography", "xray"]
-
-- model: endoreg_db.Examination
-  fields:
-    name: "colonoscopy_austria_screening"
-    examination_types: ["endoscopy"]
+    indications:
+      - percutaneous_transhepatic_cholangiography
+      - percutaneous_transhepatic_biliary_drainage

endoreg_db/data/examination/time-type/data.yaml

@@ -3,6 +3,3 @@
     name: "colonoscopy-time"
     name_de: "Koloskopie-Zeit"
     name_en: "Colonoscopy Time"
-    examinations: [
-      "colonoscopy"
-    ]