after merge fixes

config/api_router.py

@@ -5,6 +5,7 @@ from dicom.api.views import (
     CreateRoiApi,
     CreateRulerApi,
     DeleteDicomProjectApi,
+    GeneratePatology,
     ListCreateDicomApi,
     ListCreateProjectApi,
     ListUpdateDicomImageNumberApi,
@@ -15,8 +16,6 @@ from dicom.api.views import (
     RetrieveUpdateDeleteRoiApi,
     RetrieveUpdateDeleteRulerApi,
     SmartFileUploadApi,
-    GeneratePatology,
-    GeneratePointCloud
 )
 from django.urls import include, path
 from rest_framework_simplejwt.views import TokenObtainPairView, TokenRefreshView
@@ -123,12 +122,11 @@ urlpatterns = [
         ),
     ),
     path(
-        'generate/',
+        "generate/",
         include(
             [
-                path('patology', GeneratePatology.as_view(), name='generate_patology'),
+                path("patology", GeneratePatology.as_view(), name="generate_patology"),
-                path('point_cloud', GeneratePointCloud.as_view(), name='generate_patology')
             ]
         ),
-    )
+    ),
 ]

config/settings/local.py

@@ -13,7 +13,13 @@ SECRET_KEY = env(
     default="XgO9NMQfMY5CNeVNh98WrKRXiQZnvtPzHJrF9ROPhAFLVEG1FvDD2ZRKTdJKVu8p",
 )
 # https://docs.djangoproject.com/en/dev/ref/settings/#allowed-hosts
-ALLOWED_HOSTS = ["localhost", "0.0.0.0", "127.0.0.1", "dev.akarpov.ru"]
+ALLOWED_HOSTS = [
+    "localhost",
+    "0.0.0.0",
+    "127.0.0.1",
+    "dev.akarpov.ru",
+    "dev2.akarpov.ru",
+]
 
 # CACHES
 # ------------------------------------------------------------------------------

image_markuper/dicom/api/serializers.py

@@ -181,3 +181,9 @@ class ProjectSerializer(serializers.ModelSerializer):
     class Meta:
         model = Project
         fields = ["files", "slug", "created"]
+
+
+class PatologyGenerateSerializer(serializers.Serializer):
+    project_slug = serializers.CharField()
+    points = serializers.ListField(child=CoordinateSerializer())
+    depth = serializers.ListField(child=serializers.IntegerField())

image_markuper/dicom/api/views.py

@@ -6,7 +6,7 @@ from rest_framework.parsers import FormParser, MultiPartParser
 from rest_framework.response import Response
 
 from ..models import Circle, Dicom, Project, Roi
-from ..services import generate_3d_point_cloud, get_bbox, process_files
+from ..services import process_files
 from .serializers import (
     BaseShapeLayerSerializer,
     BaseShapeSerializer,
@@ -15,13 +15,12 @@ from .serializers import (
     FreeHandSerializer,
     ListDicomSerializer,
     ListProjectSerializer,
-    PointCloudSerializer,
+    PatologyGenerateSerializer,
     ProjectSerializer,
     RoiSerializer,
     RulerSerializer,
     SmartFileUploadSerializer,
     create_coordinate,
-    PatologyGenerateSerializer
 )
 
 
@@ -224,17 +223,6 @@ class GeneratePatology(generics.CreateAPIView):
     serializer_class = PatologyGenerateSerializer
 
     def create(self, request, *args, **kwargs):
-        data = self.get_serializer(request.data).data
+        # data = self.get_serializer(request.data).data
-        bbox = get_bbox(data['project_slug'], data['points'], data['depth'])
+        # bbox = get_bbox(data["project_slug"], data["points"], data["depth"])
         return Response(data={}, status=200)
-
-
-class GeneratePointCloud(generics.CreateAPIView):
-    serializer_class = PointCloudSerializer
-
-    def create(self, request, *args, **kwargs):
-        print(request.data)
-        data = request.data
-        point_cloud = generate_3d_point_cloud(data['project_slug'])
-        print(point_cloud[0:5])
-        return Response(data={'voxels': point_cloud}, status=200)

image_markuper/dicom/services.py

@@ -1,4 +1,3 @@
-from functools import lru_cache
 import glob
 import os
 import shutil
@@ -6,18 +5,18 @@ import zipfile
 from pathlib import Path
 
 import magic
+import numpy as np
+import pydicom
 from dicom.models import Coordinate, Dicom, Project
 from django.core.files import File
 from django.core.files.uploadedfile import InMemoryUploadedFile, TemporaryUploadedFile
+from skimage import measure
+from stl import mesh
 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
+    files: list[TemporaryUploadedFile | InMemoryUploadedFile], user, slug=None
 ):
     if slug:
         project = Project.objects.get(slug=slug)
@@ -60,35 +59,56 @@ def create_coordinate(coordinates, obj):
 
 def get_bbox(project_id, points, image_range):
     project: Project = Project.objects.get(slug=project_id)
-    #print(Dicom.objects.all())
+    # print(Dicom.objects.all())
     files = project.files.all()
     bbox_data = []
-    for file_number in range(image_range[0], image_range[1]+1):
+    for file_number in range(image_range[0], image_range[1] + 1):
-        print(points[0]['x'])
+        print(points[0]["x"])
         bbox_data.append(
-            pydicom.dcmread(
+            pydicom.dcmread(files[file_number].file.path)
-                files[file_number].file.path).pixel_array[int(points[0]['x']):int(points[1]['x']), int(points[0]['y']):int(points[1]['y'])].tolist())
+            .pixel_array[
+                int(points[0]["x"]) : int(points[1]["x"]),  # noqa
+                int(points[0]["y"]) : int(points[1]["y"]),  # noqa
+            ]
+            .tolist()
+        )
         print(pydicom.dcmread(files[file_number].file.path).pixel_array)
     print(bbox_data)
-    #print(project.files.all(), "files", project)
+    # 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]):
+    for file_index, file in enumerate(project.files.all()[::10]):
-        print(fileindex)
+        print(file_index)
-        pixel_array = pydicom.dcmread(
+        pixel_array = pydicom.dcmread(file.file.path).pixel_array
-                file.file.path
+        for iindex, i in enumerate(pixel_array[::10]):
-            ).pixel_array
+            for jindex, j in enumerate(i[::10]):
-        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})
+                    # point_clouds.append({'x': jindex, 'y': iindex, 'z': fileindex, 'value': 0})
                 else:
-                    point_clouds.append([jindex, iindex, fileindex, j])
+                    point_clouds.append([jindex, iindex, file_index, j])
     return point_clouds
+
+
+def generate_3d_model(project: Project, thr=800) -> str:
+    image = []
+    for file in project.files.all():
+        image.append(pydicom.dcmread(file.file.path).pixel_array)
+
+    p = np.array(image).transpose(2, 1, 0)
+    verts, faces, normals, values = measure.marching_cubes(p, thr, step_size=1)
+
+    solid = mesh.Mesh(np.zeros(faces.shape[0], dtype=mesh.Mesh.dtype))
+    for i, f in enumerate(faces):
+        for j in range(3):
+            solid.vectors[i][j] = verts[f[j], :]
+
+    pth = f"/tmp/{generate_charset(4)}.stl"
+    solid.save(pth)
+    return pth

image_markuper/dicom/tasks.py

@@ -0,0 +1,9 @@
+from celery import shared_task
+from dicom.models import Project
+from dicom.services import generate_3d_model
+
+
+@shared_task()
+def process_dicom(pk: int):
+    generate_3d_model(Project.objects.get(pk=pk))
+    return pk

requirements/base.txt

@@ -25,5 +25,9 @@ django-cors-headers==3.13.0 # https://github.com/adamchainz/django-cors-headers
 djangorestframework-simplejwt==5.2.2
 # DRF-spectacular for api documentation
 drf-spectacular==0.24.2  # https://github.com/tfranzel/drf-spectacular
-numpy==1.23.4
+
+
 pydicom==2.3.0
+numpy==1.23.4
+numpy-stl==2.17.1
+scikit-image==0.19.3