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https://github.com/leaders-of-digital-9-task/backend.git
synced 2024-11-10 20:16:37 +03:00
after merge fixes
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parent
adccb5cf94
commit
1e19f7edd0
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@ -5,6 +5,7 @@ from dicom.api.views import (
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CreateRoiApi,
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CreateRulerApi,
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DeleteDicomProjectApi,
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GeneratePatology,
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ListCreateDicomApi,
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ListCreateProjectApi,
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ListUpdateDicomImageNumberApi,
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@ -15,8 +16,6 @@ from dicom.api.views import (
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RetrieveUpdateDeleteRoiApi,
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RetrieveUpdateDeleteRulerApi,
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SmartFileUploadApi,
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GeneratePatology,
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GeneratePointCloud
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)
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from django.urls import include, path
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from rest_framework_simplejwt.views import TokenObtainPairView, TokenRefreshView
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@ -123,12 +122,11 @@ urlpatterns = [
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),
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),
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path(
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'generate/',
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"generate/",
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include(
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[
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path('patology', GeneratePatology.as_view(), name='generate_patology'),
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path('point_cloud', GeneratePointCloud.as_view(), name='generate_patology')
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path("patology", GeneratePatology.as_view(), name="generate_patology"),
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]
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),
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)
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),
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]
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@ -13,7 +13,13 @@ SECRET_KEY = env(
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default="XgO9NMQfMY5CNeVNh98WrKRXiQZnvtPzHJrF9ROPhAFLVEG1FvDD2ZRKTdJKVu8p",
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)
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# https://docs.djangoproject.com/en/dev/ref/settings/#allowed-hosts
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ALLOWED_HOSTS = ["localhost", "0.0.0.0", "127.0.0.1", "dev.akarpov.ru"]
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ALLOWED_HOSTS = [
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"localhost",
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"0.0.0.0",
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"127.0.0.1",
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"dev.akarpov.ru",
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"dev2.akarpov.ru",
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]
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# CACHES
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# ------------------------------------------------------------------------------
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@ -181,3 +181,9 @@ class ProjectSerializer(serializers.ModelSerializer):
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class Meta:
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model = Project
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fields = ["files", "slug", "created"]
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class PatologyGenerateSerializer(serializers.Serializer):
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project_slug = serializers.CharField()
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points = serializers.ListField(child=CoordinateSerializer())
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depth = serializers.ListField(child=serializers.IntegerField())
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@ -6,7 +6,7 @@ from rest_framework.parsers import FormParser, MultiPartParser
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from rest_framework.response import Response
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from ..models import Circle, Dicom, Project, Roi
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from ..services import generate_3d_point_cloud, get_bbox, process_files
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from ..services import process_files
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from .serializers import (
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BaseShapeLayerSerializer,
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BaseShapeSerializer,
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@ -15,13 +15,12 @@ from .serializers import (
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FreeHandSerializer,
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ListDicomSerializer,
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ListProjectSerializer,
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PointCloudSerializer,
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PatologyGenerateSerializer,
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ProjectSerializer,
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RoiSerializer,
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RulerSerializer,
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SmartFileUploadSerializer,
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create_coordinate,
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PatologyGenerateSerializer
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)
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@ -224,17 +223,6 @@ class GeneratePatology(generics.CreateAPIView):
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serializer_class = PatologyGenerateSerializer
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def create(self, request, *args, **kwargs):
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data = self.get_serializer(request.data).data
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bbox = get_bbox(data['project_slug'], data['points'], data['depth'])
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# data = self.get_serializer(request.data).data
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# bbox = get_bbox(data["project_slug"], data["points"], data["depth"])
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return Response(data={}, status=200)
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class GeneratePointCloud(generics.CreateAPIView):
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serializer_class = PointCloudSerializer
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def create(self, request, *args, **kwargs):
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print(request.data)
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data = request.data
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point_cloud = generate_3d_point_cloud(data['project_slug'])
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print(point_cloud[0:5])
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return Response(data={'voxels': point_cloud}, status=200)
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@ -1,4 +1,3 @@
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from functools import lru_cache
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import glob
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import os
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import shutil
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@ -6,18 +5,18 @@ import zipfile
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from pathlib import Path
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import magic
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import numpy as np
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import pydicom
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from dicom.models import Coordinate, Dicom, Project
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from django.core.files import File
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from django.core.files.uploadedfile import InMemoryUploadedFile, TemporaryUploadedFile
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from skimage import measure
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from stl import mesh
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from utils.generators import generate_charset
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from typing import List, Union
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from django.conf import settings
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import pydicom
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def process_files(
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files: List[Union[TemporaryUploadedFile, InMemoryUploadedFile]], user, slug=None
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files: list[TemporaryUploadedFile | InMemoryUploadedFile], user, slug=None
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):
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if slug:
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project = Project.objects.get(slug=slug)
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@ -60,35 +59,56 @@ def create_coordinate(coordinates, obj):
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def get_bbox(project_id, points, image_range):
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project: Project = Project.objects.get(slug=project_id)
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#print(Dicom.objects.all())
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# print(Dicom.objects.all())
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files = project.files.all()
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bbox_data = []
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for file_number in range(image_range[0], image_range[1]+1):
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print(points[0]['x'])
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for file_number in range(image_range[0], image_range[1] + 1):
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print(points[0]["x"])
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bbox_data.append(
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pydicom.dcmread(
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files[file_number].file.path).pixel_array[int(points[0]['x']):int(points[1]['x']), int(points[0]['y']):int(points[1]['y'])].tolist())
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pydicom.dcmread(files[file_number].file.path)
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.pixel_array[
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int(points[0]["x"]) : int(points[1]["x"]), # noqa
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int(points[0]["y"]) : int(points[1]["y"]), # noqa
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]
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.tolist()
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)
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print(pydicom.dcmread(files[file_number].file.path).pixel_array)
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print(bbox_data)
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#print(project.files.all(), "files", project)
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# print(project.files.all(), "files", project)
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return []
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@lru_cache(512)
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def generate_3d_point_cloud(project_slug: str):
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project = Project.objects.get(slug=project_slug)
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point_clouds = []
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for fileindex, file in enumerate(project.files.all()[::3]):
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print(fileindex)
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pixel_array = pydicom.dcmread(
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file.file.path
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).pixel_array
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for iindex, i in enumerate(pixel_array[::3]):
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for jindex, j in enumerate(i[::3]):
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for file_index, file in enumerate(project.files.all()[::10]):
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print(file_index)
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pixel_array = pydicom.dcmread(file.file.path).pixel_array
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for iindex, i in enumerate(pixel_array[::10]):
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for jindex, j in enumerate(i[::10]):
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if j <= 240:
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pass
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#point_clouds.append({'x': jindex, 'y': iindex, 'z': fileindex, 'value': 0})
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# point_clouds.append({'x': jindex, 'y': iindex, 'z': fileindex, 'value': 0})
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else:
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point_clouds.append([jindex, iindex, fileindex, j])
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point_clouds.append([jindex, iindex, file_index, j])
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return point_clouds
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def generate_3d_model(project: Project, thr=800) -> str:
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image = []
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for file in project.files.all():
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image.append(pydicom.dcmread(file.file.path).pixel_array)
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p = np.array(image).transpose(2, 1, 0)
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verts, faces, normals, values = measure.marching_cubes(p, thr, step_size=1)
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solid = mesh.Mesh(np.zeros(faces.shape[0], dtype=mesh.Mesh.dtype))
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for i, f in enumerate(faces):
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for j in range(3):
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solid.vectors[i][j] = verts[f[j], :]
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pth = f"/tmp/{generate_charset(4)}.stl"
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solid.save(pth)
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return pth
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9
image_markuper/dicom/tasks.py
Normal file
9
image_markuper/dicom/tasks.py
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from celery import shared_task
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from dicom.models import Project
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from dicom.services import generate_3d_model
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@shared_task()
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def process_dicom(pk: int):
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generate_3d_model(Project.objects.get(pk=pk))
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return pk
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@ -25,5 +25,9 @@ django-cors-headers==3.13.0 # https://github.com/adamchainz/django-cors-headers
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djangorestframework-simplejwt==5.2.2
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# DRF-spectacular for api documentation
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drf-spectacular==0.24.2 # https://github.com/tfranzel/drf-spectacular
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pydicom==2.3.0
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numpy==1.23.4
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pydicom==2.3.0
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numpy-stl==2.17.1
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scikit-image==0.19.3
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