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

endoreg_db/models/center/center.py

@@ -1,25 +0,0 @@
-from django.db import models
-
-class CenterManager(models.Manager):
-    def get_by_natural_key(self, name):
-        return self.get(name=name)
-
-class Center(models.Model):
-    objects = CenterManager()
-
-    # import_id = models.IntegerField(primary_key=True)
-    name = models.CharField(max_length=255)
-    name_de = models.CharField(max_length=255, blank=True, null=True)
-    name_en = models.CharField(max_length=255, blank=True, null=True)
-
-    first_names = models.ManyToManyField(
-        'FirstName',
-        related_name='centers',
-    )
-    last_names = models.ManyToManyField('LastName', related_name='centers')
-
-    def natural_key(self):
-        return (self.name,)
-    
-    def __str__(self):
-        return self.name

endoreg_db/models/center/center_product.py

@@ -1,34 +0,0 @@
-from itertools import product
-from django.db import models
-
-class CenterProduct(models.Model):
-    product = models.ForeignKey("Product", on_delete=models.CASCADE)
-    date_used = models.DateField()
-    center = models.ForeignKey("Center", on_delete=models.CASCADE)
-
-
-    def get_product_group(self):
-        product = self.product
-        product_group = product.product_group
-
-        return product_group
-    
-    def get_reference_product(self):
-        product_group = self.get_product_group()
-        reference_product = product_group.reference_product
-
-        return reference_product
-    
-    def get_product_weight(self):
-        product = self.product
-        weight, unit = product.get_product_weight()
-
-        return weight, unit
-    
-    def get_package_weight(self):
-        product = self.product
-        weight, unit = product.get_package_weight()
-
-        return weight, unit
-    
-    

endoreg_db/models/center/center_resource.py

@@ -1,19 +0,0 @@
-from os import name
-from django.db import models
-
-class CenterResource(models.Model):
-    name = models.CharField(max_length=255, null=True)
-    center = models.ForeignKey("Center", on_delete=models.CASCADE)
-    name_de = models.CharField(max_length=255, null=True)
-    name_en = models.CharField(max_length=255, null=True)
-    quantity = models.FloatField()
-    resource = models.ForeignKey("Resource", on_delete=models.CASCADE)
-    transport_emission_factor = models.ForeignKey("EmissionFactor", on_delete=models.SET_NULL, null=True,
-                                                  related_name="center_resource_transport_emission_factor")
-    use_emission_factor = models.ForeignKey("EmissionFactor", on_delete=models.SET_NULL, null=True,
-                                            related_name="center_resource_use_emission_factor")
-    year = models.IntegerField()
-    unit = models.ForeignKey("Unit", on_delete=models.SET_NULL, null=True)
-    
-    def __str__(self):
-        return self.center.name + " - " + self.resource.name + " (" + str(self.year) + ")"

endoreg_db/models/center/center_waste.py

@@ -1,11 +0,0 @@
-from django.db import models
-    
-class CenterWaste(models.Model):
-    center = models.ForeignKey("Center", on_delete=models.CASCADE)
-    year = models.IntegerField()
-    waste = models.ForeignKey("Waste", on_delete=models.CASCADE)
-    quantity = models.FloatField()
-    unit = models.ForeignKey("Unit", on_delete=models.SET_NULL, null=True)
-    emission_factor = models.ForeignKey("EmissionFactor", on_delete=models.SET_NULL, null=True)
-
-    

endoreg_db/models/data_file/__init__.py

@@ -1,6 +0,0 @@
-from .frame import Frame, LegacyFrame
-from .report_file import ReportFile
-from .video import Video, LegacyVideo, VideoImportMeta
-from .video_segment import LegacyLabelVideoSegment, LabelVideoSegment
-from .metadata import *
-from .import_classes import *

endoreg_db/models/data_file/base_classes/__init__.py

@@ -1,2 +0,0 @@
-from .abstract_frame import AbstractFrame
-from .abstract_video import AbstractVideo

endoreg_db/models/data_file/base_classes/abstract_frame.py

@@ -1,51 +0,0 @@
-from endoreg_db.models.annotation.image_classification import ImageClassificationAnnotation
-from endoreg_db.models.label.label import Label
-
-from django.db import models
-
-
-class AbstractFrame(models.Model):
-    video = None # Placeholder for the video field, to be defined in derived classes
-    frame_number = models.IntegerField()
-    # Add any other fields you need to store frame-related information
-    image = models.ImageField(upload_to="frames")  # Or some other field type, depending on how you're storing the frame
-    suffix = models.CharField(max_length=255)
-    # ImageClassificationAnnotation has a foreign key to this model (related name: image_classification_annotations)
-
-    class Meta:
-        # Ensure that for each video, the frame_number is unique
-        abstract = True
-        unique_together = ('video', 'frame_number')
-        # Optimize for retrieval in frame_number order
-        indexes = [models.Index(fields=['video', 'frame_number'])]
-
-
-    def __str__(self):
-        return self.video.file.path + " - " + str(self.frame_number)
-
-    def get_frame_model(self):
-        assert 1 == 2, "This method should be overridden in derived classes"
-
-    def get_classification_annotations(self):
-        """
-        Get all image classification annotations for this frame.
-        """
-        return ImageClassificationAnnotation.objects.filter(frame=self)
-
-    def get_classification_annotations_by_label(self, label:Label):
-        """
-        Get all image classification annotations for this frame with the given label.
-        """
-        return ImageClassificationAnnotation.objects.filter(frame=self, label=label)
-
-    def get_classification_annotations_by_value(self, value:bool):
-        """
-        Get all image classification annotations for this frame with the given value.
-        """
-        return ImageClassificationAnnotation.objects.filter(frame=self, value=value)
-
-    def get_classification_annotations_by_label_and_value(self, label:Label, value:bool):
-        """
-        Get all image classification annotations for this frame with the given label and value.
-        """
-        return ImageClassificationAnnotation.objects.filter(frame=self, label=label, value=value)

endoreg_db/models/data_file/base_classes/abstract_video.py

@@ -1,201 +0,0 @@
-# import cv2
-from PIL import Image
-from django.core.files.base import ContentFile
-from django.db import models, transaction
-from tqdm import tqdm
-# import cv2
-import io
-from datetime import date
-
-BATCH_SIZE = 1000
-
-class AbstractVideo(models.Model):
-    file = models.FileField(upload_to="raw_videos", blank=True, null=True)
-    video_hash = models.CharField(max_length=255, unique=True)
-    patient = models.ForeignKey("Patient", on_delete=models.CASCADE, blank=True, null=True)
-    date = models.DateField(blank=True, null=True)
-    suffix = models.CharField(max_length=255)
-    fps = models.FloatField()
-    duration = models.FloatField()
-    width = models.IntegerField()
-    height = models.IntegerField()
-    endoscope_image_x = models.IntegerField(blank=True, null=True)
-    endoscope_image_y = models.IntegerField(blank=True, null=True)
-    endoscope_image_width = models.IntegerField(blank=True, null=True)
-    endoscope_image_height = models.IntegerField(blank=True, null=True)
-    center = models.ForeignKey("Center", on_delete=models.CASCADE, blank=True, null=True)
-    endoscopy_processor = models.ForeignKey("EndoscopyProcessor", on_delete=models.CASCADE, blank=True, null=True)
-    frames_extracted = models.BooleanField(default=False)
-
-    meta = models.JSONField(blank=True, null=True)
-
-    class Meta:
-        abstract = True
-
-    def get_roi_endoscope_image(self):
-        return {
-            'x': self.endoscope_image_content_x,
-            'y': self.endoscope_image_content_y,
-            'width': self.endoscope_image_content_width,
-            'height': self.endoscope_image_content_height,
-        }
-
-    def initialize_metadata_in_db(self, video_meta=None):
-        if not video_meta:
-            video_meta = self.meta
-        self.set_examination_date_from_video_meta(video_meta)
-        self.patient, created = self.get_or_create_patient(video_meta)
-        self.save()
-
-    def get_or_create_patient(self, video_meta=None):
-        from ...persons import Patient
-        if not video_meta:
-            video_meta = self.meta
-
-        patient_first_name = video_meta['patient_first_name']
-        patient_last_name = video_meta['patient_last_name']
-        patient_dob = video_meta['patient_dob']
-
-        # assert that we got all the necessary information
-        assert patient_first_name and patient_last_name and patient_dob, "Missing patient information"
-
-        patient, created = Patient.objects.get_or_create(
-            first_name=patient_first_name,
-            last_name=patient_last_name,
-            dob=patient_dob
-        )
-
-        return patient, created
-
-    def get_frame_model(self):
-        assert 1 == 2, "This method should be overridden in derived classes"
-
-    def get_video_model(self):
-        assert 1 == 2, "This method should be overridden in derived classes"
-
-    def get_frame_number(self):
-        """
-        Get the number of frames in the video.
-        """
-        frame_model = self.get_frame_model()
-        framecount = frame_model.objects.filter(video=self).count()
-        return framecount
-    
-    def set_frames_extracted(self, value:bool=True):
-        self.frames_extracted = value
-        self.save()
-        
-    def get_frames(self):
-        """
-        Retrieve all frames for this video in the correct order.
-        """
-        frame_model = self.get_frame_model()
-        return frame_model.objects.filter(video=self).order_by('frame_number')
-
-    def get_frame(self, frame_number):
-        """
-        Retrieve a specific frame for this video.
-        """
-        frame_model = self.get_frame_model()
-        return frame_model.objects.get(video=self, frame_number=frame_number)
-
-    def get_frame_range(self, start_frame_number:int, end_frame_number:int):
-        """
-        Expects numbers of start and stop frame.
-        Returns all frames of this video within the given range in ascending order.
-        """
-        frame_model = self.get_frame_model()
-        return frame_model.objects.filter(video=self, frame_number__gte=start_frame_number, frame_number__lte=end_frame_number).order_by('frame_number')
-
-    def _create_frame_object(self, frame_number, image_file):
-        frame_model = self.get_frame_model()
-        frame = frame_model(
-                video=self,
-                frame_number=frame_number,
-                suffix='jpg',
-            )
-        frame.image_file = image_file  # Temporary store the file-like object
-
-        return frame
-
-    def _bulk_create_frames(self, frames_to_create):
-        frame_model = self.get_frame_model()
-        with transaction.atomic():
-            frame_model.objects.bulk_create(frames_to_create)
-
-            # After the DB operation, save the ImageField for each object
-            for frame in frames_to_create:
-                frame_name = f"video_{self.id}_frame_{str(frame.frame_number).zfill(7)}.jpg"
-                frame.image.save(frame_name, frame.image_file)
-
-            # Clear the list for the next batch
-            frames_to_create = []
-
-    def set_examination_date_from_video_meta(self, video_meta=None):
-        if not video_meta:
-            video_meta = self.meta
-        date_str = video_meta['examination_date'] # e.g. 2020-01-01
-        if date_str:
-            self.date = date.fromisoformat(date_str)
-            self.save()
-
-    def extract_all_frames(self):
-        """
-        Extract all frames from the video and store them in the database.
-        Uses Django's bulk_create for more efficient database operations.
-        """
-        # Open the video file
-        video = cv2.VideoCapture(self.file.path)
-
-        # Initialize video properties
-        self.initialize_video_specs(video)
-
-        # Prepare for batch operation
-        frames_to_create = []
-
-        # Extract frames
-        for frame_number in tqdm(range(int(self.duration * self.fps))):
-            # Read the frame
-            success, image = video.read()
-            if not success:
-                break
-
-            # Convert the numpy array to a PIL Image object
-            pil_image = Image.fromarray(cv2.cvtColor(image, cv2.COLOR_BGR2RGB))
-
-            # Save the PIL Image to a buffer
-            buffer = io.BytesIO()
-            pil_image.save(buffer, format='JPEG')
-
-            # Create a file-like object from the byte data in the buffer
-            image_file = ContentFile(buffer.getvalue())
-
-            # Prepare Frame instance (don't save yet)
-            frame = self._create_frame_object(frame_number, image_file)
-            frames_to_create.append(frame)
-
-            # Perform bulk create when reaching BATCH_SIZE
-            if len(frames_to_create) >= BATCH_SIZE:
-                self._bulk_create_frames(frames_to_create)
-                frames_to_create = []
-
-
-        # Handle remaining frames
-        if frames_to_create:
-            self._bulk_create_frames(frames_to_create)
-            frames_to_create = []
-
-        # Close the video file
-        video.release()
-        self.set_frames_extracted(True)
-
-
-    def initialize_video_specs(self, video):
-        """
-        Initialize and save video metadata like framerate, dimensions, and duration.
-        """
-        self.fps = video.get(cv2.CAP_PROP_FPS)
-        self.width = int(video.get(cv2.CAP_PROP_FRAME_WIDTH))
-        self.height = int(video.get(cv2.CAP_PROP_FRAME_HEIGHT))
-        self.duration = video.get(cv2.CAP_PROP_FRAME_COUNT) / self.fps
-        self.save()

endoreg_db/models/data_file/frame.py

@@ -1,45 +0,0 @@
-from endoreg_db.models.annotation.image_classification import ImageClassificationAnnotation
-from endoreg_db.models.label.label import Label
-from .base_classes import AbstractFrame
-from django.db import models
-
-class Frame(AbstractFrame):
-    video = models.ForeignKey("Video", on_delete=models.CASCADE, related_name="frames")
-
-class LegacyFrame(AbstractFrame):
-    video = models.ForeignKey("LegacyVideo", on_delete=models.CASCADE, related_name='frames')
-    image = models.ImageField(upload_to="legacy_frames", blank=True, null=True)
-    suffix = models.CharField(max_length=255)
-    # ImageClassificationAnnotation has a foreign key to this model (related name: image_classification_annotations)
-
-    class Meta:
-        unique_together = ('video', 'frame_number')
-        indexes = [
-            models.Index(fields=['video', 'frame_number']),
-        ]
-
-    def get_classification_annotations(self):
-        """
-        Get all image classification annotations for this frame.
-        """
-        return ImageClassificationAnnotation.objects.filter(legacy_frame=self)
-
-    def get_classification_annotations_by_label(self, label:Label):
-        """
-        Get all image classification annotations for this frame with the given label.
-        """
-        return ImageClassificationAnnotation.objects.filter(legacy_frame=self, label=label)
-
-    def get_classification_annotations_by_value(self, value:bool):
-        """
-        Get all image classification annotations for this frame with the given value.
-        """
-        return ImageClassificationAnnotation.objects.filter(legacy_frame=self, value=value)
-
-    def get_classification_annotations_by_label_and_value(self, label:Label, value:bool):
-        """
-        Get all image classification annotations for this frame with the given label and value.
-        """
-        return ImageClassificationAnnotation.objects.filter(legacy_frame=self, label=label, value=value)
-
-    

endoreg_db/models/data_file/import_classes/__init__.py

@@ -1,32 +0,0 @@
-import os
-from pathlib import Path
-
-from .raw_video import RawVideoFile
-from .raw_pdf import RawPdfFile
-
-# FileImporter class
-# This class is used to import data from a file into the database.
-# Expects a directory containing files to import.
-# creates correct import file object depending on file type
-
-# FileImporter class
-# This class is used to import data from a file into the database by creating objects for the files.
-# main method is import_files which expects a path to a directory containing files to import.
-# creates correct import file object depending on file type by checking the file extension
-
-class FileImporter:
-    def __init__(self, directory):
-        self.directory = directory
-
-    def import_files(self):
-        directory_path = Path(self.directory)
-        for file in directory_path.iterdir():
-            if file.is_file():
-                if file.suffix.lower() in ['.mov', '.mp4']:
-                    RawVideoFile.create_from_file(file)
-                else:
-                    raise ValueError(f"File type {file.suffix} not supported")
-            else:
-                raise ValueError(f"{file} is not a file")
-            
-        

endoreg_db/models/data_file/import_classes/processing_functions/__init__.py

@@ -1,35 +0,0 @@
-from .video import (
-    get_videos_scheduled_for_frame_extraction, 
-    extract_frames_from_video,
-    extract_frames_from_videos,
-
-    get_videos_scheduled_for_ocr,
-    videos_scheduled_for_ocr_preflight,
-    perform_ocr_on_video,
-    perform_ocr_on_videos,
-
-    videos_scheduled_for_initial_prediction_preflight,
-    get_videos_scheduled_for_initial_prediction,
-    get_multilabel_model,
-    get_multilabel_classifier,
-    get_crops,
-    perform_initial_prediction_on_video,
-    perform_initial_prediction_on_videos,
-
-    videos_scheduled_for_prediction_import_preflight,
-    get_videos_scheduled_for_prediction_import,
-    import_predictions_for_video,
-    import_predictions_for_videos,
-    
-
-    delete_frames_preflight,
-    get_videos_scheduled_for_frame_deletion,
-    delete_frames_for_video,
-    delete_frames,
-)
-
-from .pdf import (
-    get_pdf_files_scheduled_for_processing,
-    process_pdf_file,
-    process_pdf_files,
-)

endoreg_db/models/data_file/import_classes/processing_functions/pdf.py

@@ -1,28 +0,0 @@
-from ..raw_pdf import RawPdfFile
-from logging import getLogger
-#
-# # setup logging to pdf_import.log
-logger = getLogger('examination_pdf_import')
-
-def get_pdf_files_scheduled_for_processing():
-    reports = RawPdfFile.objects.filter(
-        state_report_processing_required=True
-    )
-    return reports
-
-def process_pdf_file(report:RawPdfFile):
-    if report.update(save=True, verbose=True):
-        logger.info(f"Report {report} processed successfully")
-        return True
-    else:
-        logger.error(f"Report {report} processing failed")
-        return False
-
-
-def process_pdf_files():
-    reports = get_pdf_files_scheduled_for_processing()
-    for report in reports:
-        process_pdf_file(report)
-    
-
-