from functools import lru_cache import glob import os import shutil import zipfile from pathlib import Path import magic from dicom.models import Coordinate, Dicom, Project from django.core.files import File from django.core.files.uploadedfile import InMemoryUploadedFile, TemporaryUploadedFile from utils.generators import generate_charset from typing import List, Union from django.conf import settings import pydicom def process_files( files: List[Union[TemporaryUploadedFile, InMemoryUploadedFile]], user, slug=None ): if slug: project = Project.objects.get(slug=slug) else: project = Project.objects.create(user=user) for file in files: content_type = magic.from_file(file.temporary_file_path()) if content_type == "DICOM medical imaging data": Dicom.objects.create(file=file, project=project, user=user) elif "Zip" in content_type: dit_path = f"tmp/{generate_charset(10)}" os.mkdir(dit_path) with zipfile.ZipFile(file.temporary_file_path(), "r") as zip_ref: zip_ref.extractall(dit_path) files = glob.glob(dit_path + "/**/*", recursive=True) for file_in_d in files: if not os.path.isdir(file_in_d): content_type = magic.from_file(file_in_d) if content_type == "DICOM medical imaging data": path = Path(file_in_d) with path.open(mode="rb") as f: Dicom.objects.create( file=File(f, name=file_in_d.split("/")[-1]), project=project, user=user, ) shutil.rmtree(dit_path) return project def create_coordinate(coordinates, obj): for coordinate in coordinates: Coordinate.objects.create( x=coordinate["x"], y=coordinate["y"], shape=obj, ) def get_bbox(project_id, points, image_range): project: Project = Project.objects.get(slug=project_id) #print(Dicom.objects.all()) files = project.files.all() bbox_data = [] for file_number in range(image_range[0], image_range[1]+1): print(points[0]['x']) bbox_data.append( pydicom.dcmread( files[file_number].file.path).pixel_array[int(points[0]['x']):int(points[1]['x']), int(points[0]['y']):int(points[1]['y'])].tolist()) print(pydicom.dcmread(files[file_number].file.path).pixel_array) print(bbox_data) #print(project.files.all(), "files", project) return [] @lru_cache(512) def generate_3d_point_cloud(project_slug: str): project = Project.objects.get(slug=project_slug) point_clouds = [] for fileindex, file in enumerate(project.files.all()[::3]): print(fileindex) pixel_array = pydicom.dcmread( file.file.path ).pixel_array for iindex, i in enumerate(pixel_array[::3]): for jindex, j in enumerate(i[::3]): if j <= 240: pass #point_clouds.append({'x': jindex, 'y': iindex, 'z': fileindex, 'value': 0}) else: point_clouds.append([jindex, iindex, fileindex, j]) return point_clouds