endoreg-db 0.4.5__py3-none-any.whl → 0.8.6.3__py3-none-any.whl

{endoreg_db-0.4.5.dist-info → endoreg_db-0.8.6.3.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.9.0
+Generator: hatchling 1.27.0
 Root-Is-Purelib: true
 Tag: py3-none-any

endoreg_db/data/active_model/data.yaml

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

endoreg_db/data/agl_service/data.yaml

@@ -1,19 +0,0 @@
-- model: endoreg_db.agl_service
-  fields:
-    name: "agl-home-django"
-    description: "AGL Home Django service"
-    devices: [
-      "agl-server-04",
-    ]
-    port: 9100
-    url: "https://home.endo-reg.net/"
-
-- model: endoreg_db.agl_service
-  fields:
-    name: "endoreg-client-manager"
-    description: "AGL Home Django service"
-    devices: [
-      "agl-gpu-client-dev",
-    ]
-    port: 9000
-    url: "https://home.endo-reg.net/"

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

@@ -1,18 +0,0 @@
-- 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/management/commands/_load_model_template.py

@@ -1,41 +0,0 @@
-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_all.py

@@ -1,18 +0,0 @@
-from django.core.management.base import BaseCommand
-from django.apps import apps
-from django.db import transaction
-
-class Command(BaseCommand):
-    help = 'Deletes all objects from all models in the "endoreg_db" app.'
-
-    def handle(self, *args, **options):
-        app_models = apps.get_models()
-        app_models = [model for model in app_models if "endoreg_db" in model._meta.app_label]  # Filter models by the "endoreg_db" app
-        for model in app_models:
-            with transaction.atomic():  # Use a separate transaction for each model
-                try:
-                    model.objects.all().delete()
-                    self.stdout.write(self.style.SUCCESS(f'Successfully deleted all objects in {model._meta.db_table}'))
-                except Exception as e:
-                    # This catches exceptions and continues with the next model
-                    self.stdout.write(self.style.ERROR(f'Error deleting objects in {model._meta.db_table}: {e}'))

endoreg_db/management/commands/delete_legacy_images.py

@@ -1,19 +0,0 @@
-# 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

@@ -1,17 +0,0 @@
-# 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

@@ -1,18 +0,0 @@
-# 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

@@ -1,32 +0,0 @@
-# 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'))

endoreg_db/management/commands/fix_auth_permission.py

@@ -1,20 +0,0 @@
-from django.core.management.base import BaseCommand
-from django.contrib.auth.models import Permission
-from django.contrib.contenttypes.models import ContentType
-from django.apps import apps
-
-class Command(BaseCommand):
-    help = 'Sets up default permissions for each model in the app.'
-
-    def handle(self, *args, **options):
-        for model in apps.get_models():
-            content_type = ContentType.objects.get_for_model(model)
-            permissions = ['view', 'add', 'change', 'delete']
-            for perm in permissions:
-                codename = f'{perm}_{model._meta.model_name}'
-                name = f'Can {perm} {model._meta.verbose_name}'
-                Permission.objects.get_or_create(
-                    codename=codename,
-                    defaults={'name': name, 'content_type': content_type},
-                )
-            self.stdout.write(self.style.SUCCESS(f'Set up permissions for {model._meta.verbose_name}'))

endoreg_db/management/commands/import_legacy_images.py

@@ -1,94 +0,0 @@
-# command expects a directory as an argument
-# directory should contain a img_dicts.jsonl file, a settings.json and an "images" directory
-# images should be in jpeg format
-# reads the img_dicts.jsonl file and creates a new database entry for each image
-# img_dicts contains a line for each image in the following format:
-# {"id": 30604292, "path": "images/30604292.jpg", "labels": ["appendix", "polyp"]}
-
-# import_settings.json example:
-# {
-#     "annotator": "legacy",
-#     "labelset_name": "multilabel_classification",
-#     "labelset_version": 0
-# }
-
-import os
-import json
-from tqdm import tqdm
-from django.core.management.base import BaseCommand
-from endoreg_db.models import LegacyImage, LabelSet, Label, ImageClassificationAnnotation
-from django.core.files import File
-from uuid import uuid4
-
-class Command(BaseCommand):
-    """
-    Imports images from a directory into the database
-
-    Usage:
-        python manage.py import_legacy_images <directory>
-    """
-    help = 'Imports images from a directory into the database'
-
-    def add_arguments(self, parser):
-        parser.add_argument('directory', type=str)
-
-    def handle(self, *args, **options):
-        directory = options['directory']
-        if not os.path.isdir(directory):
-            raise Exception(f"Directory {directory} does not exist")
-
-        # read settings.json
-        with open(os.path.join(directory, 'import_settings.json'), 'r') as f:
-            settings = json.load(f)
-
-        # read img_dicts.jsonl
-        with open(os.path.join(directory, 'img_dicts.jsonl'), 'r') as f:
-            img_dicts = [json.loads(line) for line in f.readlines()]
-
-        # get labelset
-        labelset_name = settings['labelset_name']
-        labelset_version = settings['labelset_version']
-        try:
-            labelset = LabelSet.objects.get(name=labelset_name, version=labelset_version)
-        except LabelSet.DoesNotExist:
-            raise Exception(f"No labelset found with the name {labelset_name} and version {labelset_version}")
-
-
-        # get labels in dict to lookup by name
-        labels = {label.name: label for label in labelset.labels.all()}
-
-        # create images and image_classification_annotations
-        for img_dict in tqdm(img_dicts):
-
-            # Open the image file
-            with open(os.path.join(directory, img_dict['path']), 'rb') as f:
-                # Create the Django File object
-                django_file = File(f)
-                
-                # Extract only the filename
-                filename = os.path.basename(img_dict['path'])
-                img_suffix = os.path.splitext(filename)[1]
-                # assign uuid as new filename
-                filename = str(uuid4()) + img_suffix
-                
-
-                # Create a new LegacyImage instance and save the image
-                image = LegacyImage(image=filename, suffix=img_suffix)
-                image.image.save(filename, django_file, save=True)
-
-                image_annotations = []
-                for label_name, label in labels.items():
-                    if label_name in img_dict['labels']:
-                        value = True
-                    else:
-                        value = False
-
-                    image_annotations.append(ImageClassificationAnnotation(
-                        legacy_image=image,
-                        label=label,
-                        value=value,
-                        annotator=settings['annotator']
-                    ))
-
-                ImageClassificationAnnotation.objects.bulk_create(image_annotations)
-

endoreg_db/management/commands/import_legacy_videos.py

@@ -1,76 +0,0 @@
-from endoreg_db.utils.hashs import get_video_hash
-import subprocess
-from django.core.files import File
-from django.core.management.base import BaseCommand
-from endoreg_db.models.data_file.video import LegacyVideo
-import os
-from tqdm import tqdm
-# import cv2
-
-def convert_mkv_to_mp4(source_path, target_path):
-    """
-    Convert a .mkv file to a .mp4 file using FFmpeg.
-    
-    Parameters:
-        mov_file_path (str): The file path of the input .MOV file.
-        mp4_file_path (str): The file path where the output .mp4 file should be saved.
-        
-    Returns:
-        None
-    """
-    cmd = ["ffmpeg", "-y", "-i", source_path, "-vcodec", "h264", "-acodec", "aac", target_path]
-    subprocess.run(cmd)
-
-
-class Command(BaseCommand):
-    """
-    Imports videos from a directory into the database
-
-    Usage:
-        python manage.py import_legacy_videos <directory>
-    """
-    help = 'Imports videos from a directory into the database'
-
-    def add_arguments(self, parser):
-        parser.add_argument('directory', type=str)
-
-    def handle(self, *args, **options):
-        directory = options['directory']
-        if not os.path.isdir(directory):
-            raise Exception(f"Directory {directory} does not exist")
-
-        # iterate over all subdirectories and gather all .mkv files
-        mkv_files = []
-        for root, dirs, files in os.walk(directory):
-            for file in files:
-                if file.endswith(".mkv"):
-                    mkv_files.append(os.path.join(root, file))
-
-        # create videos
-        for mkv_file in tqdm(mkv_files):
-            # get the name of the video
-            video_name = os.path.basename(mkv_file).replace(".mkv", "")
-
-            # convert the .mkv file to a .mp4 file
-            mp4_file = os.path.join(directory, video_name + ".mp4")
-            if not os.path.isfile(mp4_file):
-                convert_mkv_to_mp4(mkv_file, mp4_file)
-
-            # create the video object
-            video_hash = get_video_hash(mp4_file)
-
-            # check if the video already exists
-            if LegacyVideo.objects.filter(video_hash=video_hash).exists():
-                print(f"Video with hash {video_hash} already exists. Skipping...")
-                continue
-
-            video = LegacyVideo.objects.create(video_hash=video_hash, suffix = "mp4")
-
-            # open the .mp4 file
-            with open(mp4_file, 'rb') as f:
-                # create the Django File object
-                django_file = File(f)
-                # save the file to the video
-                video.file.save(video_name + ".mp4", django_file)
-            raise Exception("Stop here: NEED TO FIX OPENCV DEPENDENCY")
-            video.initialize_video_specs(cv2.VideoCapture(video.file.path))

endoreg_db/management/commands/load_active_model_data.py

@@ -1,45 +0,0 @@
-from django.conf import settings
-import os
-from django.core.management.base import BaseCommand
-from ...models import ActiveModel
-from ...utils import load_model_data_from_yaml
-from ...data import ACTIVE_MODEL_DATA_DIR
-
-SOURCE_DIR = ACTIVE_MODEL_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
-
-MODEL_0 = ActiveModel
-
-IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
-    MODEL_0.__name__,
-]
-
-IMPORT_METADATA = {
-    MODEL_0.__name__: {
-        "dir": SOURCE_DIR, # e.g. "interventions"
-        "model": MODEL_0, # 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_from_yaml(
-                self,
-                model_name,
-                _metadata,
-                verbose
-            )

endoreg_db/management/commands/load_endoscopy_processor_data.py

@@ -1,45 +0,0 @@
-from django.conf import settings
-import os
-from django.core.management.base import BaseCommand
-from ...models import EndoscopyProcessor
-from ...utils import load_model_data_from_yaml
-from ...data import ENDOSCOPY_PROCESSOR_DATA_DIR
-
-SOURCE_DIR = ENDOSCOPY_PROCESSOR_DATA_DIR # e.g. settings.DATA_DIR_INTERVENTION
-
-MODEL_0 = EndoscopyProcessor
-
-IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
-    MODEL_0.__name__,
-]
-
-IMPORT_METADATA = {
-    MODEL_0.__name__: {
-        "dir": SOURCE_DIR, # e.g. "interventions"
-        "model": MODEL_0, # 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_from_yaml(
-                self,
-                model_name,
-                _metadata,
-                verbose
-            )

endoreg_db/management/commands/load_g_play_data.py

@@ -1,113 +0,0 @@
-from django.core.management.base import BaseCommand
-from endoreg_db.models import (
-    CaseTemplateRuleType,
-    CaseTemplateRuleValueType,
-    CaseTemplateRuleValue,
-    CaseTemplateRule,
-    CaseTemplateType,
-    CaseTemplate,
-    SingleCategoricalValueDistribution,
-    NumericValueDistribution,
-    MultipleCategoricalValueDistribution,
-    DateValueDistribution,
-
-    QuizQuestionType,
-    QuizAnswerType,
-    QuizQuestion,
-    QuizAnswer,
-
-    # Other models for ForeignKeys
-    Unit, Center
-)
-from collections import OrderedDict
-
-from ...utils import load_model_data_from_yaml
-from ...data import (
-    CASE_TEMPLATE_RULE_TYPE_DATA_DIR,
-    CASE_TEMPLATE_RULE_DATA_DIR,
-    CASE_TEMPLATE_RULE_VALUE_TYPE_DATA_DIR,
-    CASE_TEMPLATE_RULE_VALUE_DATA_DIR,
-    CASE_TEMPLATE_TYPE_DATA_DIR,
-    CASE_TEMPLATE_DATA_DIR,
-)
-
-IMPORT_METADATA = OrderedDict({
-    CaseTemplateRuleType.__name__: {
-        "dir": CASE_TEMPLATE_RULE_TYPE_DATA_DIR,
-        "model": CaseTemplateRuleType, 
-        "foreign_keys": [], 
-        "foreign_key_models": [] 
-    },
-    CaseTemplateRuleValueType.__name__: {
-        "dir": CASE_TEMPLATE_RULE_VALUE_TYPE_DATA_DIR,
-        "model": CaseTemplateRuleValueType, 
-        "foreign_keys": [], 
-        "foreign_key_models": [] 
-    },
-    CaseTemplateRuleValue.__name__: {
-        "dir": CASE_TEMPLATE_RULE_VALUE_DATA_DIR,
-        "model": CaseTemplateRuleValue, 
-        "foreign_keys": ["value_type"], 
-        "foreign_key_models": [CaseTemplateRuleValueType] 
-    },
-    CaseTemplateRule.__name__: {
-        "dir": CASE_TEMPLATE_RULE_DATA_DIR,
-        "model": CaseTemplateRule, 
-        "foreign_keys": [
-            "rule_type", 
-            # "rule_values",
-            "chained_rules", 
-            "value_type",
-            "single_categorical_value_distribution",
-            "numerical_value_distribution",
-            "multiple_categorical_value_distribution",
-            "date_value_distribution"
-        ], 
-        "foreign_key_models": [
-            CaseTemplateRuleType,
-            # CaseTemplateRuleValue,
-            CaseTemplateRule,
-            CaseTemplateRuleValueType,
-            SingleCategoricalValueDistribution,
-            NumericValueDistribution,
-            MultipleCategoricalValueDistribution,
-            DateValueDistribution
-
-        ] 
-    },
-    CaseTemplateType.__name__: {
-        "dir": CASE_TEMPLATE_TYPE_DATA_DIR,
-        "model": CaseTemplateType, 
-        "foreign_keys": [], 
-        "foreign_key_models": [] 
-    },
-    CaseTemplate.__name__: {
-        "dir": CASE_TEMPLATE_DATA_DIR,
-        "model": CaseTemplate, 
-        "foreign_keys": ["template_type", "rules"], 
-        "foreign_key_models": [CaseTemplateType, CaseTemplateRule] 
-    },
-    
-})
-
-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_METADATA.keys():
-            _metadata = IMPORT_METADATA[model_name]
-            load_model_data_from_yaml(
-                self,
-                model_name,
-                _metadata,
-                verbose
-            )

endoreg_db/management/commands/load_label_data.py

@@ -1,67 +0,0 @@
-from django.conf import settings
-from django.core.management.base import BaseCommand
-from ...models import (
-    Label,
-    LabelType,
-    LabelSet
-)
-import os
-from ...utils import load_model_data_from_yaml
-from ...data import LABEL_DATA_DIR
-
-SOURCE_DIR = LABEL_DATA_DIR 
-
-IMPORT_MODELS = [ # string as model key, serves as key in IMPORT_METADATA
-    "LabelType",
-    "Label",
-    "LabelSet",
-]
-
-IMPORT_METADATA = {
-    # "": { # same as model name in "import models", e.g. "Intervention"
-    #     "subdir": 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]
-    # },
-    "LabelType": {
-        "dir": os.path.join(SOURCE_DIR,"label-type"), # e.g. "interventions"
-        "model": LabelType, # e.g. Intervention
-        "foreign_keys": [], # e.g. ["intervention_types"]
-        "foreign_key_models": [] # e.g. [InterventionType]
-    },
-    "Label": {
-        "dir": os.path.join(SOURCE_DIR,"label"), # e.g. "interventions"
-        "model": Label, # e.g. Intervention
-        "foreign_keys": ["label_type"], # e.g. ["intervention_types"]
-        "foreign_key_models": [LabelType] # e.g. [InterventionType]
-    },
-    "LabelSet": {
-        "dir": os.path.join(SOURCE_DIR,"label-set"), # e.g. "interventions"
-        "model": LabelSet, # e.g. Intervention
-        "foreign_keys": ["labels"], # e.g. ["intervention_types"]
-        "foreign_key_models": [Label] # 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_from_yaml(
-                self,
-                model_name,
-                _metadata,
-                verbose
-            )