backend/image_markuper/dicom/services.py

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