endoreg-db 0.1.0__py3-none-any.whl → 0.2.1__py3-none-any.whl

endoreg_db/data/__init__.py

@@ -0,0 +1,14 @@
+from pathlib import Path
+
+DATA_DIR = Path(__file__).parent
+
+INFORMATION_DATA_DIR = DATA_DIR / "information_source"
+UNIT_DATA_DIR = DATA_DIR / "unit"
+CENTER_DATA_DIR = DATA_DIR / "center"
+EXAMINATION_DATA_DIR = DATA_DIR / "examination"
+LABEL_DATA_DIR = DATA_DIR / "label"
+MODEL_TYPE_DATA_DIR = DATA_DIR / "model_type"
+ENDOSCOPY_PROCESSOR_DATA_DIR = DATA_DIR / "endoscopy_processor"
+ENDOSCOPE_TYPE_DATA_DIR = DATA_DIR / "endoscope_type"
+ACTIVE_MODEL_DATA_DIR = DATA_DIR / "active_model"
+PROFESSION_DATA_DIR = DATA_DIR / "profession"

endoreg_db/data/active_model/data.yaml

@@ -0,0 +1,3 @@
+- model: endoreg_db.active_model
+  data:
+    - name: "multilabel_image_classification"

endoreg_db/data/center/data.yaml

@@ -0,0 +1,7 @@
+# center/data.yaml
+
+- model: endoreg_db.center
+  fields:
+    name: "university_hospital_wuerzburg"
+    name_de: "Universitätsklinikum Würzburg"
+    name_en: "University Hospital Würzburg"

endoreg_db/data/endoscope_type/data.yaml

@@ -0,0 +1,11 @@
+- model: endoreg_db.endoscope_type
+  fields:
+    name: "gastroscope"
+    name_de: "Gastroskop"
+    name_en: "Gastroscope"
+
+- model: endoreg_db.endoscope_type
+  fields:
+    name: "colonoscope"
+    name_de: "Koloskop"
+    name_en: "Colonoscope"

endoreg_db/data/endoscopy_processor/data.yaml

@@ -0,0 +1,45 @@
+- model: endoreg_db.endoscopy_processor
+  fields:
+    name: "olympus_cv_1500"
+    image_width: 1920
+    image_height: 1080
+
+    endoscope_image_x: 550
+    endoscope_image_y: 0
+    endoscope_image_width: 1350
+    endoscope_image_height: 1080
+
+    examination_date_x: 0
+    examination_date_y: 0
+    examination_date_width: 390
+    examination_date_height: 40
+
+    examination_time_x: 240
+    examination_time_y: 7
+    examination_time_width: 115
+    examination_time_height: 35
+
+    patient_first_name_x: 80
+    patient_first_name_y: 110
+    patient_first_name_width: 440
+    patient_first_name_height: 33
+
+    patient_last_name_x: 70
+    patient_last_name_y: 83
+    patient_last_name_width: 450
+    patient_last_name_height: 27
+
+    patient_dob_x: 70
+    patient_dob_y: 180
+    patient_dob_width: 160
+    patient_dob_height: 50
+
+    endoscope_type_x: 70
+    endoscope_type_y: 630
+    endoscope_type_width: 280
+    endoscope_type_height: 35
+
+    endoscope_sn_x: 70
+    endoscope_sn_y: 670
+    endoscope_sn_width: 280
+    endoscope_sn_height: 35

endoreg_db/data/examination/examinations/data.yaml

@@ -0,0 +1,17 @@
+- model: report.Examination
+  fields:
+    name: "colonoscopy"
+    name_de: "Koloskopie"
+    name_en: "Colonoscopy"
+    examination_types: [
+      "endoscopy"
+    ]
+
+- model: report.Examination
+  fields:
+    name: "gastroscopy"
+    name_de: "Gastroskopie"
+    name_en: "Gastroscopy"
+    examination_types: [
+      "endoscopy"
+    ]

endoreg_db/data/examination/time/data.yaml

@@ -0,0 +1,48 @@
+- model: report.ExaminationTime
+  fields:
+    name: "colonoscopy-total-time"
+    name_de: "Koloskopie Zeiten"
+    name_en: "Colonoscopy Times"
+    time_types: [
+      "colonoscopy-time"
+    ]
+  
+# withdrawal-time
+- model: report.ExaminationTime
+  fields:
+    name: "withdrawal-time"
+    name_de: "Withdrawal Time"
+    name_en: "Withdrawal Time"
+    time_types: [
+      "colonoscopy-time"
+    ]
+
+# cecum-time
+- model: report.ExaminationTime
+  fields:
+    name: "cecum-time"
+    name_de: "Zökum Zeit"
+    name_en: "Cecum Time"
+    time_types: [
+      "colonoscopy-time"
+    ]
+
+# intubation-time
+- model: report.ExaminationTime
+  fields:
+    name: "intubation-time"
+    name_de: "Intubationszeit"
+    name_en: "Intubation Time"
+    time_types: [
+      "colonoscopy-time"
+    ]
+
+# colonoscopy-intervention-time
+- model: report.ExaminationTimeType
+  fields:
+    name: "colonoscopy-intervention-time"
+    name_de: "Interventionszeit"
+    name_en: "Intervention Time"
+    time_types: [
+      "colonoscopy-time"
+    ]

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

@@ -0,0 +1,8 @@
+- model:
+  fields:
+    name: "colonoscopy-time"
+    name_de: "Koloskopie-Zeit"
+    name_en: "Colonoscopy Time"
+    examinations: [
+      "colonoscopy"
+    ]

endoreg_db/data/examination/type/data.yaml

@@ -0,0 +1,5 @@
+- model: report.ExaminationType
+  fields:
+    name: "endoscopy"
+    name_de: "Endoskopie"
+    name_en: "Endoscopy"

endoreg_db/data/information_source/data.yaml

@@ -0,0 +1,30 @@
+- model: endoreg_db.InformationSource
+  fields:
+    name: treating_physician
+- model: endoreg_db.InformationSource
+  fields:
+    name: treating_physician_anamnestic
+- model: endoreg_db.InformationSource
+  fields:
+    name: physicians_note_anamnestic
+- model: endoreg_db.InformationSource
+  fields:
+    name: patient_anamnestic
+- model: endoreg_db.InformationSource
+  fields:
+    name: physical_measurement
+- model: endoreg_db.InformationSource
+  fields:
+    name: family_anamnestic
+- model: endoreg_db.InformationSource
+  fields:
+    name: physical_examination
+- model: endoreg_db.InformationSource
+  fields:
+    name: unknown
+- model: endoreg_db.InformationSource
+  fields:
+    name: prediction
+- model: endoreg_db.InformationSource
+  fields:
+    name: annotation

endoreg_db/data/label/label/data.yaml

@@ -0,0 +1,62 @@
+# labels are: "appendix", "ileocecal_valve", "polyp", "water_jet", "digital_chromo_endoscopy", "instrument", "wound", "blood", "ileum", "low_quality", "clip", "outside"
+
+- model: endoreg_db.Label
+  fields:
+    name: "appendix"
+    label_type: "classification"
+
+- model: endoreg_db.Label
+  fields:
+    name: "ileocecal_valve"
+    label_type: "classification"
+
+- model: endoreg_db.Label
+  fields:
+    name: "polyp"
+    label_type: "classification"
+
+- model: endoreg_db.Label
+  fields:
+    name: "water_jet"
+    label_type: "classification"
+
+- model: endoreg_db.Label
+  fields:
+    name: "digital_chromo_endoscopy"
+    label_type: "classification"
+
+- model: endoreg_db.Label
+  fields:
+    name: "instrument"
+    label_type: "classification"
+
+- model: endoreg_db.Label
+  fields:
+    name: "wound"
+    label_type: "classification"
+
+- model: endoreg_db.Label
+  fields:
+    name: "blood"
+    label_type: "classification"
+
+- model: endoreg_db.Label
+  fields:
+    name: "ileum"
+    label_type: "classification"
+
+- model: endoreg_db.Label
+  fields:
+    name: "low_quality"
+    label_type: "classification"
+
+- model: endoreg_db.Label
+  fields:
+    name: "clip"
+    label_type: "classification"
+
+- model: endoreg_db.Label
+  fields:
+    name: "outside"
+    label_type: "classification"
+

endoreg_db/data/label/label-set/data.yaml

@@ -0,0 +1,18 @@
+- model: endoreg_db.LabelSet
+  fields:
+    name: "multilabel_classification"
+    version: 0
+    labels: [
+      "appendix",
+      "ileocecal_valve",
+      "polyp",
+      "water_jet",
+      "digital_chromo_endoscopy",
+      "instrument",
+      "wound",
+      "blood",
+      "ileum",
+      "low_quality",
+      "clip",
+      "outside",
+    ]

endoreg_db/data/label/label-type/data.yaml

@@ -0,0 +1,7 @@
+- model: endoreg_db.LabelType
+  fields:
+    name: "classification"
+
+- model: endoreg_db.LabelType
+  fields:
+    name: "object_detection"

endoreg_db/data/model_type/data.yaml

@@ -0,0 +1,7 @@
+- model: endoreg_db.model_type
+  fields:
+    name: "multilabel_classification"
+
+- model: endoreg_db.model_type
+  fields:
+    name: "object_detection"

endoreg_db/data/profession/data.yaml

@@ -0,0 +1,70 @@
+- model: endoreg_db.Profession
+  fields:
+    name: "nurse"
+    name_de: "Pflegekraft"
+    name_en: "Nurse"
+    description: "Not further specified nurse"
+
+# endoscopy nurse
+- model: endoreg_db.Profession
+  fields:
+    name: "endoscopy-nurse"
+    name_de: "Pflegekraft (Endoskopie)"
+    name_en: "Endoscopy nurse"
+    description: "Endoscopy nurse"
+
+- model: endoreg_db.Profession
+  fields:
+    name: "physician"
+    name_de: "Arzt"
+    name_en: "Physician"
+    description: "Not further specified doctor"
+
+# Physician in training (gastroenterology)
+- model: endoreg_db.Profession
+  fields:
+    name: "physician-in-training-gastroenterology"
+    name_de: "Arzt in Weiterbildung Gastroenterologie"
+    name_en: "Physician in training (gastroenterology)"
+    description: "Physician in training (gastroenterology)"
+  
+# Physician in training (internal medicine)
+- model: endoreg_db.Profession
+  fields:
+    name: "physician-in-training-internal-medicine"
+    name_de: "Arzt in Weiterbildung Innere Medizin"
+    name_en: "Physician in training (internal medicine)"
+    description: "Physician in training (internal medicine)"
+
+# Physician in training (general surgery)
+- model: endoreg_db.Profession
+  fields:
+    name: "physician-in-training-general-surgery"
+    name_de: "Arzt in Weiterbildung Allgemeinchirurgie"
+    name_en: "Physician in training (general surgery)"
+    description: "Physician in training (general surgery)"
+
+# Physician (Internal Medicine)
+- model: endoreg_db.Profession
+  fields:
+    name: "physician-internal-medicine"
+    name_de: "Arzt Innere Medizin"
+    name_en: "Physician (Internal Medicine)"
+    description: "Physician (Internal Medicine)"
+
+# Physician (Gastroenterology)
+- model: endoreg_db.Profession
+  fields:
+    name: "physician-gastroenterology"
+    name_de: "Arzt Gastroenterologie"
+    name_en: "Physician (Gastroenterology)"
+    description: "Physician (Gastroenterology)"
+
+# Physician (General Surgery)
+- model: endoreg_db.Profession
+  fields:
+    name: "physician-general-surgery"
+    name_de: "Arzt Allgemeinchirurgie"
+    name_en: "Physician (General Surgery)"
+    description: "Physician (General Surgery)"
+

endoreg_db/data/unit/data.yaml

@@ -0,0 +1,17 @@
+- model: endoreg_db.Unit
+  fields:
+    name: "liters-per-minute"
+    abbreviation: "l/min"
+    name_de: "Liter pro Minute"
+    name_en: "Liters per Minute"
+    description: "liters per minute"
+
+
+# kilowatt-hours
+- model: endoreg_db.Unit
+  fields:
+    name: "kilowatt-hours"
+    abbreviation: "kWh"
+    name_de: "Kilowattstunden"
+    name_en: "Kilowatt-hours"
+    description: "kilowatt-hours"

endoreg_db/data/unit/length.yaml

@@ -0,0 +1,31 @@
+- model: endoreg_db.Unit
+  fields:
+    name: "millimeter"
+    abbreviation: "mm"
+    name_de: "Millimeter"
+    name_en: "Millimeter"
+    description: "millimeters"
+
+- model: endoreg_db.Unit
+  fields:
+    name: "centimeter"
+    abbreviation: "cm"
+    name_de: "Zentimeter"
+    name_en: "Centimeter"
+    description: "centimeters"
+
+- model: endoreg_db.Unit
+  fields:
+    name: "meter"
+    abbreviation: "m"
+    name_de: "Meter"
+    name_en: "Meter"
+    description: "meters"
+
+- model: endoreg_db.Unit
+  fields:
+    name: "kilometer"
+    abbreviation: "km"
+    name_de: "Kilometer"
+    name_en: "Kilometer"
+    description: "kilometers"

endoreg_db/data/unit/volume.yaml

@@ -0,0 +1,26 @@
+# Units/data.yaml
+
+- model: endoreg_db.Unit
+  fields:
+    name: "milliliter"
+    abbreviation: "ml"
+    name_de: "Milliliter"
+    name_en: "Milliliter"
+    description: "milliliters"
+
+- model: endoreg_db.Unit
+  fields:
+    name: "liter"
+    abbreviation: "l"
+    name_de: "Liter"
+    name_en: "Liter"
+    description: "liters"
+
+# cubic_meter
+- model: endoreg_db.Unit
+  fields:
+    name: "cubic_meter"
+    abbreviation: "m³"
+    name_de: "Kubikmeter"
+    name_en: "Cubic Meter"
+    description: "cubic meters"

endoreg_db/data/unit/weight.yaml

@@ -0,0 +1,31 @@
+- model: endoreg_db.Unit
+  fields:
+    name: "microgram"
+    abbreviation: "µg"
+    name_de: "Mikrogramm"
+    name_en: "Microgram"
+    description: "micrograms"
+
+- model: endoreg_db.Unit
+  fields:
+    name: "milligram"
+    abbreviation: "mg"
+    name_de: "Milligramm"
+    name_en: "Milligram"
+    description: "milligrams"
+
+- model: endoreg_db.Unit
+  fields:
+    name: "gram"
+    abbreviation: "g"
+    name_de: "Gramm"
+    name_en: "Gram"
+    description: "grams"
+
+- model: endoreg_db.Unit
+  fields:
+    name: "kilogram"
+    abbreviation: "kg"
+    name_de: "Kilogramm"
+    name_en: "Kilogram"
+    description: "kilograms"

endoreg_db/forms/__init__.py

@@ -0,0 +1,2 @@
+from .unit import Unit
+from .settings import ActiveModelForm

endoreg_db/forms/settings/__init__.py

@@ -0,0 +1,8 @@
+# forms.py
+from django import forms
+from endoreg_db.models import ActiveModel
+
+class ActiveModelForm(forms.ModelForm):
+    class Meta:
+        model = ActiveModel
+        fields = ["model_meta"]  # Or list the specific fields you want to include in the form.

endoreg_db/forms/unit.py

@@ -0,0 +1,6 @@
+from django import forms
+from ..models import Unit
+
+class UnitForm(forms.Form):
+    class Meta:
+        model = Unit

endoreg_db/management/commands/_load_model_template.py

@@ -0,0 +1,41 @@
+from django.conf import settings
+from django.core.management.base import BaseCommand
+from reports.models import Intervention, InterventionType  # Replace 'your_app_name' with the actual app name
+import os
+from reports.dataloader_utils import load_model_data
+
+SOURCE_DIR = None # e.g. settings.DATA_DIR_INTERVENTION
+
+IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
+]
+
+IMPORT_METADATA = {
+    # "": { # same as model name in "import models", e.g. "Intervention"
+    #     "dir": os.path.join(SOURCE_DIR,""), # e.g. "interventions"
+    #     "model": None, # e.g. Intervention
+    #     "foreign_keys": [], # e.g. ["intervention_types"]
+    #     "foreign_key_models": [] # e.g. [InterventionType]
+    # },
+}
+
+class Command(BaseCommand):
+    help = """Load all .yaml files in the data/intervention directory
+    into the Intervention and InterventionType model"""
+
+    def add_arguments(self, parser):
+        parser.add_argument(
+            '--verbose',
+            action='store_true',
+            help='Display verbose output',
+        )
+
+    def handle(self, *args, **options):
+        verbose = options['verbose']
+        for model_name in IMPORT_MODELS:
+            _metadata = IMPORT_METADATA[model_name]
+            load_model_data(
+                self,
+                model_name,
+                _metadata,
+                verbose
+            )

endoreg_db/management/commands/delete_legacy_images.py

@@ -0,0 +1,19 @@
+# django command to delete all LegacyImage objects
+
+from django.core.management.base import BaseCommand, CommandError
+from endoreg_db.models import LegacyImage
+from tqdm import tqdm
+
+class Command(BaseCommand):
+    help = 'Deletes all LegacyImage objects including the linked files (legacy_image.image)'
+
+    def handle(self, *args, **options):
+        legacy_images = LegacyImage.objects.all()
+
+        for legacy_image in tqdm(legacy_images):
+            legacy_image.image.delete()
+            legacy_image.delete()
+
+        self.stdout.write(self.style.SUCCESS('Successfully deleted all LegacyImage objects and linked image files'))
+
+

endoreg_db/management/commands/delete_legacy_videos.py

@@ -0,0 +1,17 @@
+# Django command to fetch all LegacyVideo objects, delete the associated file and delete the object from the database
+
+from endoreg_db.models.data_file.video import LegacyVideo
+from tqdm import tqdm
+from django.core.management.base import BaseCommand
+
+class Command(BaseCommand):
+    """
+    Deletes all LegacyVideos in the database.
+    """
+    help = 'Deletes all LegacyVideos in the database.'
+
+    def handle(self, *args, **options):
+        videos = LegacyVideo.objects.all()
+        for video in tqdm(videos):
+            video.file.delete()
+            video.delete()

endoreg_db/management/commands/extract_legacy_video_frames.py

@@ -0,0 +1,18 @@
+# Django Command to:
+# fetch all LegacyVideos and extract frames from them 
+# track progress for all videos and for each video with tqdm
+
+from endoreg_db.models.data_file.video import LegacyVideo
+from tqdm import tqdm
+from django.core.management.base import BaseCommand
+
+class Command(BaseCommand):
+    """
+    Extracts frames from all LegacyVideos in the database.
+    """
+    help = 'Extracts frames from all LegacyVideos in the database.'
+
+    def handle(self, *args, **options):
+        videos = LegacyVideo.objects.all()
+        for video in tqdm(videos):
+            video.extract_all_frames()

endoreg_db/management/commands/fetch_legacy_image_dataset.py

@@ -0,0 +1,32 @@
+# command to fetch the legacy dataset and save it to a json file.
+from django.core.management.base import BaseCommand, CommandError
+from endoreg_db.queries import generate_legacy_dataset_output 
+import json
+
+LABELSET_NAME = "multilabel_classification"
+LABELSET_VERSION = 0
+
+class Command(BaseCommand):
+    help = 'Fetches the legacy dataset and saves it to a jsonl file'
+
+    def handle(self, *args, **options):
+        output, labelset = generate_legacy_dataset_output(LABELSET_NAME, LABELSET_VERSION)
+        # output is a list of dicts, each dict is an image
+        labels_in_order = labelset.get_labels_in_order()
+
+        # write to file
+        with open('legacy_dataset.jsonl', 'w') as f:
+            for img_dict in output:
+                f.write(json.dumps(img_dict) + '\n')
+
+
+        _dict = {
+            "labels": [label.name for label in labels_in_order],
+            "name": LABELSET_NAME,
+            "version": LABELSET_VERSION
+        }
+
+        with open('legacy_dataset_info.json', 'w') as f:
+            f.write(json.dumps(_dict))
+
+        self.stdout.write(self.style.SUCCESS('Successfully fetched and saved the legacy dataset'))