endoreg-db 0.8.4.4__py3-none-any.whl → 0.8.8.0__py3-none-any.whl

endoreg_db/data/_examples/requirement_operator/model_operators.yaml

@@ -0,0 +1,96 @@
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "models_match_all"
+    name_de: "Modelle existieren"
+    name_en: "Models exist"
+    description: "Make sure that all the provided Foreign Key models exist."
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "models_match_any"
+    name_de: "Mindestens ein Modell existiert"
+    name_en: "At least one model exists"
+    description: "Make sure that at least one of the provided Foreign Key models exist."
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "models_match_none"
+    name_de: "Kein Modell existiert"
+    name_en: "No model exists"
+    description: "Make sure that none of the provided Foreign Key models exist."
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "models_match_n"
+    name_de: " Exakt n Modelle existieren"
+    name_en: "Exactly n models exist"
+    description: "Make sure that exactly n of the provided Foreign Key models exist. The number n is defined using the numeric_value_min field."
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "models_match_n_or_more"
+    name_de: "Mindestens n Modelle existieren"
+    name_en: "At least n models exist"
+    description: "Make sure that at least n of the provided Foreign Key models exist. The number n is defined using the numeric_value_min field."
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "models_match_n_or_less"
+    name_de: "Höchstens n Modelle existieren"
+    name_en: "At most n models exist"
+    description: "Make sure that at most n of the provided Foreign Key models exist. The number n is defined using the numeric_value_min field."
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "models_match_count_in_range"
+    name_de: "Anzahl der Modelle liegt im angegebenen Bereich"
+    name_en: "Number of models is in the given range"
+    description: "Make sure that the number of provided Foreign Key models is in the given range. The range is defined using numeric_value_min and numeric_value_max."
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "models_match_any_in_timeframe"
+    name_de: "Mindestens ein Modell existiert im angegebenen Zeitraum"
+    name_en: "At least one model exists in the given timeframe"
+    description: "Make sure that at least one of the provided Foreign Key models exist and its associated date falls within the specified timeframe. Timeframe is defined by numeric_value_min, numeric_value_max, and unit on the Requirement."
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "models_match_all_in_timeframe"
+    name_de: "Modelle existieren im angegebenen Zeitraum"
+    name_en: "Models exist in the given timeframe"
+    description: "Make sure that all the provided Foreign Key models have a date within the given timeframe. The timeframe is defined using numeric_value_min and numeric_value_max and setting the unit to a fitting one (e.g. week)."
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "models_match_none_in_timeframe"
+    name_de: "Kein Modell existiert im angegebenen Zeitraum"
+    name_en: "No model exists in the given timeframe"
+    description: "Make sure that none of the provided Foreign Key models have a date within the given timeframe. The timeframe is defined using numeric_value_min and numeric_value_max and setting the unit to a fitting one (e.g. week)."
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "models_match_n_in_timeframe"
+    name_de: "Exakt n Modelle existieren im angegebenen Zeitraum"
+    name_en: "Exactly n models exist in the given timeframe"
+    description: "Make sure that exactly n of the provided Foreign Key models have a date within the given timeframe. The timeframe is defined using numeric_value_min and numeric_value_max and setting the unit to a fitting one (e.g. week). The number n is defined using the numeric_value_min field."
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "models_match_n_or_more_in_timeframe"
+    name_de: "Mindestens n Modelle existieren im angegebenen Zeitraum"
+    name_en: "At least n models exist in the given timeframe"
+    description: "Make sure that at least n of the provided Foreign Key models have a date within the given timeframe. The timeframe is defined using numeric_value_min and numeric_value_max and setting the unit to a fitting one (e.g. week). The number n is defined using the numeric_value_min field."
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "models_match_n_or_less_in_timeframe"
+    name_de: "Höchstens n Modelle existieren im angegebenen Zeitraum"
+    name_en: "At most n models exist in the given timeframe"
+    description: "Make sure that at most n of the provided Foreign Key models have a date within the given timeframe. The timeframe is defined using numeric_value_min and numeric_value_max and setting the unit to a fitting one (e.g. week). The number n is defined using the numeric_value_min field."
+
+- model: endoreg_db.requirement_operator
+  fields:
+    name: "patient_medication_schedule_matches_template"
+    description: "Checks if any PatientMedication in the input PatientMedicationSchedule matches the profile (medication, dose, unit, intake times) of any MedicationSchedule template linked to the requirement."
+    evaluation_function_name: "_evaluate_patient_medication_schedule_matches_template"

endoreg_db/data/_examples/requirement_set/01_endoscopy_generic.yaml

@@ -0,0 +1,48 @@
+- models: endoreg_db.requirement_set
+  fields:
+    name: "patient_gender_generic"
+    name_de: "Patientengeschlecht (männlich/weiblich)"
+    name_en: "Patient gender generic" 
+    description: "Patient gender (generic)"
+    requirement_set_type: "any"
+    requirements:
+      - patient_gender_is_male
+      - patient_gender_is_female
+
+- models: endoreg_db.requirement_set
+  fields:
+    name: "basic_lab_values_normal"
+    name_de: "Basis-Labortests (Unauffällig)"
+    name_en: "Basic Lab Tests (Normal)"
+    description: "Basic lab tests (normal)"
+    requirement_set_type: "all"
+    requirements:
+      - "lab_value_hb_normal"
+      - "lab_value_leukocytes_normal"
+      - "lab_value_platelets_normal"
+      - "lab_value_creatinine_normal"
+      - "lab_value_inr_normal"
+
+- models: endoreg_db.requirement_set
+  fields:
+    name: "patient_age_generic"
+    name_de: "Patientenalter (18-100 Jahre)"
+    name_en: "Patient Age (18-100 years)"
+    description: "Patient age between 18 and 100 years"
+    requirement_set_type: "all"
+    requirements:
+      - "patient_age_gte_18"
+      - "patient_age_lte_100"
+
+# - models: endoreg_db.requirement_set
+- models: endoreg_db.requirement_set
+  fields:
+    name: "generic_patient"
+    requirement_set_type: "all"
+    description: "Generic patient requirement set"
+    name_de: "Generische Patientenanforderung"
+    name_en: "Generic Patient Requirement"
+    links_to_sets:
+      - "patient_age_generic"
+      - "patient_gender_generic"
+      - "basic_lab_values_normal"

endoreg_db/data/_examples/requirement_set/colonoscopy_austria_screening.yaml

@@ -0,0 +1,57 @@
+
+
+- models: endoreg_db.requirement_set
+  fields:
+    name: "colonoscopy_austria_screening_finding_polyp_required_classifications"
+    name_de: "Vorsorge Koloskopie Österreich: Polyp"
+    requirement_set_type: "all"
+    links_to_sets: []
+    requirements:
+      - "colon_austria_screening_polyp_size"
+      - "colonoscopy_austria_screening_polyp_location"
+      - "colonoscopy_austria_screening_polyp_histology"
+
+- models: endoreg_db.requirement_set
+  fields:
+    name: "colonoscopy_austria_screening_examination_complete"
+    requirement_set_type: "any"
+    requirements:
+      - "colonoscopy_austria_screening_examination_cecum_visualized"
+      - "colonoscopy_austria_screening_examination_reason_incomplete"
+
+- models: endoreg_db.requirement_set
+  fields:
+    name: "colonoscopy_austria_screening_examination_required_findings"
+    links_to_sets:
+      - "colonoscopy_austria_screening_examination_complete"
+    requirement_set_type: "all"
+    requirements:
+      - "colonoscopy_austria_screening_bowel_prep"
+      - "colonoscopy_austria_screening_sedation"
+
+- models: endoreg_db.requirement_set
+  fields:
+    name: "colonoscopy_austria_screening_required_patient_information"
+    name_de: "Vorsorge Koloskopie Österreich: Patienteninformation"
+    requirement_set_type: "all"
+    links_to_sets:
+      - "patient_gender_generic"
+      - "patient_age_generic"
+
+- models: endoreg_db.requirement_set
+  fields:
+    name: "colonoscopy_austria_screening_qa"
+    name_de: "Vorsorge Koloskopie Österreich QA"
+    name_en: "Colonoscopy Austria Screening QA"
+    description: "Colonoscopy Austria Screening QA"
+    requirement_set_type: "all"
+    links_to_sets:
+      - "colonoscopy_austria_screening_finding_polyp_required_classifications"
+      - "colonoscopy_austria_screening_required_patient_information"
+      - "colonoscopy_austria_screening_examination_required_findings"
+    tags:
+      - "report_mask_requirement_set"
+      - "colonoscopy_austria_screening"
+    reqset_exam_links:
+      - "colonoscopy_austria_req_sets"
+      - "colonoscopy_req_sets"

endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml

@@ -5,6 +5,7 @@
     version: "1"
     model: "image_multilabel_classification_colonoscopy_default"
     labelset: "multilabel_classification_colonoscopy_default"
+    labelset_version: 1
     activation: "sigmoid"
     mean: "0.485,0.456,0.406" # ImageNet defaults
     std: "0.229,0.224,0.225" # ImageNet defaults
@@ -20,8 +21,8 @@
   setup_config:
     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.ckpt"
-      - "image_multilabel_classification_colonoscopy_default_v1_*.ckpt"
+      - "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.ckpt"
+      filename: "colo_segmentation_RegNetX800MF_base.safetensors"

endoreg_db/data/event_classification/data.yaml

@@ -0,0 +1,4 @@
+- model: endoreg_db.event_classification
+  fields:
+    name: "stroke_origin_classification"
+    event: "stroke"

endoreg_db/data/event_classification_choice/data.yaml

@@ -0,0 +1,9 @@
+- model: endoreg_db.event_classification
+  fields:
+    name: "stroke_origin_ischemic"
+    event_classification: "stroke_origin_classification"
+
+- model: endoreg_db.event_classification
+  fields:
+    name: "stroke_origin_hemorrhagic"
+    event_classification: "stroke_origin_classification"

endoreg_db/data/finding_classification/colonoscopy_bowel_preparation.yaml

@@ -1,95 +1,68 @@
 - model: endoreg_db.finding_classification
   fields:
     name: "bowel_prep_boston"
-    classification_types: [
-      "bowel_prep"
-    ]
+    classification_types: ["bowel_prep"]
     name_de: "Boston Bowel Preparation Scale"
     name_en: "Boston Bowel Preparation Scale"
-    examinations: [
-      "colonoscopy"
-    ]
-    findings: [
-      "bowel_preparation_lc",
-      "bowel_preparation_tc",
-      "bowel_preparation_rc",
-
-    ] 
-    choices: [
-      "bowel_prep_boston_0",
-      "bowel_prep_boston_1",
-      "bowel_prep_boston_2",
-      "bowel_prep_boston_3"
-    ]
+    examinations: ["colonoscopy"]
+    findings:
+      ["bowel_preparation_lc", "bowel_preparation_tc", "bowel_preparation_rc"]
+    choices:
+      [
+        "bowel_prep_boston_0",
+        "bowel_prep_boston_1",
+        "bowel_prep_boston_2",
+        "bowel_prep_boston_3",
+      ]
 
 - model: endoreg_db.finding_classification
   fields:
     name: "bowel_prep_boston_simplified"
-    classification_types: [
-      "bowel_prep"
-    ]
+    classification_types: ["bowel_prep"]
     name_de: "Boston Bowel Preparation Scale"
     name_en: "Boston Bowel Preparation Scale"
-    examinations: [
-      "colonoscopy"
-    ]
-    findings: [
-      "bowel_preparation_simplified"
-    ] 
-    choices: [
-      "bowel_prep_boston_0",
-      "bowel_prep_boston_1",
-      "bowel_prep_boston_2",
-      "bowel_prep_boston_3"
-    ]
-
+    examinations: ["colonoscopy"]
+    findings: ["bowel_preparation_simplified"]
+    choices:
+      [
+        "bowel_prep_boston_0",
+        "bowel_prep_boston_1",
+        "bowel_prep_boston_2",
+        "bowel_prep_boston_3",
+      ]
 
 #Aronchick
 - model: endoreg_db.finding_classification
   fields:
     name: "bowel_prep_aronchick"
-    classification_types: [
-      "bowel_prep"
-    ]
+    classification_types: ["bowel_prep"]
     name_de: "Aronchick Bowel Preparation Scale"
     name_en: "Aronchick Bowel Preparation Scale"
-    examinations: [
-      "colonoscopy"
-    ]
-    findings: [
-      "bowel_preparation_lc",
-      "bowel_preparation_tc",
-      "bowel_preparation_rc",
-    ]
-    choices: [
-      "bowel_prep_aronchick_0",
-      "bowel_prep_aronchick_1",
-      "bowel_prep_aronchick_2",
-      "bowel_prep_aronchick_3"
-    ]
+    examinations: ["colonoscopy"]
+    findings:
+      ["bowel_preparation_lc", "bowel_preparation_tc", "bowel_preparation_rc"]
+    choices:
+      [
+        "bowel_prep_aronchick_0",
+        "bowel_prep_aronchick_1",
+        "bowel_prep_aronchick_2",
+        "bowel_prep_aronchick_3",
+      ]
 
 # Screening Austria
-# Choices are "bowel_prep_perfect", "bowel_prep_good", 
-# "bowel_prep_fair", "bowel_prep_poor", "bowel_prep_poor_in_rc_only"
-
 - model: endoreg_db.finding_classification
   fields:
     name: "bowel_prep_screening_austria"
-    classification_types: [
-      "bowel_prep"
-    ]
+    classification_types: ["bowel_prep"]
     name_de: "Darmvorbereitung Screening Österreich"
     name_en: "Bowel Preparation Screening Austria"
-    examinations: [
-      "colonoscopy_austria_screening"
-    ]
-    findings: [
-      "bowel_prep_screening_austria"
-    ]
-    choices: [
-      "bowel_prep_perfect",
-      "bowel_prep_good",
-      "bowel_prep_fair",
-      "bowel_prep_poor",
-      "bowel_prep_poor_in_rc_only"
-    ]
+    examinations: ["colonoscopy_austria_screening"]
+    findings: ["bowel_prep_screening_austria"]
+    choices:
+      [
+        "bowel_prep_perfect",
+        "bowel_prep_good",
+        "bowel_prep_fair",
+        "bowel_prep_poor",
+        "bowel_prep_poor_in_rc_only",
+      ]

endoreg_db/data/finding_classification/colonoscopy_lesion_size.yaml

@@ -1,68 +1,38 @@
 - model: endoreg_db.finding_classification
   fields:
     name: "colon_lesion_size_categorical"
-    classification_types: [
-      "colon_lesion_size",
-      "morphology"
-    ]
+    classification_types: ["colon_lesion_size", "morphology"]
     name_de: "Größenklassifikation Kolonläsion (kategorisch)"
     name_en: "Colon Lesion Size Classification (categorical)"
-    examinations: [
-      "colonoscopy"
-    ]
-    findings: [
-      "colon_polyp",
-      "tumor",
-      "erosion",
-      "ulcer",
-      "scar"
-    ]
+    examinations: ["colonoscopy"]
+    findings: ["colon_polyp", "tumor", "erosion", "ulcer", "scar"]
     choices: [
-      "colon_lesion_size_categorical_diminutive",
-      "colon_lesion_size_categorical_small",
-      "colon_lesion_size_categorical_medium",
-      "colon_lesion_size_categorical_large"
-    ]
+        "colon_lesion_size_categorical_diminutive", # 0 - 5 mm
+        "colon_lesion_size_categorical_small", # 6 - 9 mm
+        "colon_lesion_size_categorical_medium", # 10 - 20 mm
+        "colon_lesion_size_categorical_large", # 21+ mm
+      ]
 
 - model: endoreg_db.finding_classification
   fields:
     name: "colon_lesion_size_mm"
-    classification_types: [
-      "colon_lesion_size",
-      "morphology"
-    ]
+    classification_types: ["colon_lesion_size", "morphology"]
     name_de: "Größenklassifikation Kolonläsion (numerisch)"
     name_en: "Colon Lesion Size Classification (numerical)"
-    examinations: [
-      "colonoscopy"
-    ]
-    findings: [
-      "colon_polyp",
-      "tumor",
-      "erosion",
-      "ulcer",
-      "scar"
-    ]
-    choices: [
-      "colon_lesion_size_oval_mm"
-    ]
+    examinations: ["colonoscopy"]
+    findings: ["colon_polyp", "tumor", "erosion", "ulcer", "scar"]
+    choices: ["colon_lesion_size_oval_mm"]
 
 - model: endoreg_db.finding_classification
   fields:
     name: "colon_lesion_size_austria_categorical"
-    classification_types: [
-      "colon_lesion_size",
-      "morphology"
-    ]
-    examinations: [
-      "colonoscopy_austria_screening"
-    ]
-    findings: [
-      "colon_polyp",
-    ]
-    choices: [
-      "colon_lesion_size_austria_categorical_0_5",
-      "colon_lesion_size_austria_categorical_6_9",
-      "colon_lesion_size_austria_categorical_10_20",
-      "colon_lesion_size_austria_categorical_21_x"
-    ]
+    classification_types: ["colon_lesion_size", "morphology"]
+    examinations: ["colonoscopy_austria_screening"]
+    findings: ["colon_polyp"]
+    choices:
+      [
+        "colon_lesion_size_austria_categorical_0_5",
+        "colon_lesion_size_austria_categorical_6_9",
+        "colon_lesion_size_austria_categorical_10_20",
+        "colon_lesion_size_austria_categorical_21_x",
+      ]

endoreg_db/data/finding_classification/colonoscopy_location.yaml

@@ -3,78 +3,47 @@
     name: "colonoscopy_location_default"
     name_de: "Koloskopie Standard"
     name_en: "Colonoscopy Default"
-    classification_types: [
-      "location",
-    ]
-    examinations: [
-      "colonoscopy"
-    ]
-    finding_types: [
-      "macroscopic"
-    ]
-    findings: [
-      "colon_polyp",
-      "tumor",
-      "erosion",
-      "ulcer",
-      "scar"
-    ]
-    choices: [
-      "terminal_ileum",
-      "cecum",
-      "ascending_colon",
-      "right_flexure",
-      "transverse_colon",
-      "descending_colon",
-      "sigmoid_colon",
-      "rectum",
-      "anal_canal"
-    ]
+    classification_types: ["location"]
+    examinations: ["colonoscopy"]
+    finding_types: ["macroscopic"]
+    findings: ["colon_polyp", "tumor", "erosion", "ulcer", "scar"]
+    choices:
+      [
+        "terminal_ileum",
+        "cecum",
+        "ascending_colon",
+        "right_flexure",
+        "transverse_colon",
+        "left_flexure",
+        "descending_colon",
+        "sigmoid_colon",
+        "rectum",
+        "anal_canal",
+      ]
 
 - model: endoreg_db.finding_classification
   fields:
     name: "colonoscopy_location_coarse"
     name_de: "Koloskopie Grob"
     name_en: "Colonoscopy Coarse"
-    classification_types: [
-      "location",
-    ]
-    examinations: [
-      "colonoscopy"
-    ]
-    finding_types: [
-      "macroscopic"
-    ]
+    classification_types: ["location"]
+    examinations: ["colonoscopy"]
+    finding_types: ["macroscopic"]
     findings: [
-      "colon_polyp",
-      # "tumor",
-      # "erosion",
-      # "ulcer",
-      # "scar"
-    ]
-    choices: [
-      "left_colon",
-      "right_colon",
-      "rectum"
-    ]
+        "colon_polyp",
+        # "tumor",
+        # "erosion",
+        # "ulcer",
+        # "scar"
+      ]
+    choices: ["left_colon", "right_colon", "rectum"]
 
 - model: endoreg_db.finding_classification
   fields:
     name: "colonoscopy_austria_screening_location"
     name_de: "Koloskopie Österreich Screening Lokalisation"
     name_en: "Colonoscopy Austria Screening Location"
-    classification_types: [
-      "location",
-    ]
-    examinations: [
-      "colonoscopy_austria_screening"
-    ]
-    findings: [
-      "colon_polyp",
-    ]
-    choices: [
-      "left_colon",
-      "right_colon",
-      "sigmoid_colon",
-      "rectum",
-    ]
+    classification_types: ["location"]
+    examinations: ["colonoscopy_austria_screening"]
+    findings: ["colon_polyp"]
+    choices: ["left_colon", "right_colon", "sigmoid_colon", "rectum"]

endoreg_db/data/finding_classification/histology_colo.yaml

@@ -2,50 +2,42 @@
   fields:
     name: "colonoscopy_polyp_histology"
     classification_types: []
-    examinations: [
-      "colonoscopy",
-      "colonoscopy_austria_screening",
-    ]
-    findings: [
-      "colon_polyp",
-    ]
+    examinations: ["colonoscopy", "colonoscopy_austria_screening"]
+    findings: ["colon_polyp"]
     choices: [
-      "histology_polyp_hyperplastic",
-      "histology_polyp_adenoma_tubular",
-      "histology_polyp_adenoma_tubulovillous",
-      "histology_polyp_adenoma_villous",
-      "histology_polyp_sessile_serrated_lesion"
-    ]
+        "histology_polyp_hyperplastic",
+        "histology_polyp_adenoma_tubular",
+        "histology_polyp_adenoma_tubulovillous",
+        "histology_polyp_adenoma_villous",
+        "histology_polyp_sessile_serrated_lesion",
+        # unknown?
+      ]
 
 - model: endoreg_db.finding_classification_choice
   fields:
     name: "colonoscopy_polyp_histology_dysplasia"
     classification_types: []
-    examinations: [
-      "colonoscopy",
-      "colonoscopy_austria_screening",
-    ]
-    findings: [
-      "colon_polyp",
-    ]
-    choices: [
-      "histology_dysplasia_none",
-      "histology_dysplasia_low_grade",
-      "histology_dysplasia_high_grade",
-    ]
+    examinations: ["colonoscopy", "colonoscopy_austria_screening"]
+    findings: ["colon_polyp"]
+    choices:
+      [
+        "histology_dysplasia_none",
+        "histology_dysplasia_low_grade",
+        "histology_dysplasia_high_grade",
+      ]
 
 - model: endoreg_db.finding_classification
   fields:
     name: "colonoscopy_histology_dignity"
     classification_types: []
-    examinations: [
-      "colonoscopy",
-      "colonoscopy_austria_screening",
-    ]
-    findings: [
-      "colon_polyp",
-    ]
-    choices: [
-      "histology_dignity_benign",
-      "histology_dignity_malign",
-    ]
+    examinations: ["colonoscopy", "colonoscopy_austria_screening"]
+    findings: ["colon_polyp"]
+    choices: ["histology_dignity_benign", "histology_dignity_malign"]
+
+- model: endoreg_db.finding_classification_choice
+  fields:
+    name: "colonoscopy_default_histology_in_sano"
+    classification_types: []
+    examinations: ["colonoscopy"]
+    findings: ["colon_polyp"]
+    choices: ["yes", "no", "na"]