Merge remote-tracking branch 'origin/point-cloud-and-patology-generation'

# Conflicts:
#	image_markuper/dicom/api/serializers.py

config/api_router.py

@@ -15,6 +15,8 @@ from dicom.api.views import (
     RetrieveUpdateDeleteRoiApi,
     RetrieveUpdateDeleteRulerApi,
     SmartFileUploadApi,
+    GeneratePatology,
+    GeneratePointCloud
 )
 from django.urls import include, path
 from rest_framework_simplejwt.views import TokenObtainPairView, TokenRefreshView
@@ -120,4 +122,13 @@ urlpatterns = [
             ]
         ),
     ),
+    path(
+        'generate/',
+        include(
+            [
+                path('patology', GeneratePatology.as_view(), name='generate_patology'),
+                path('point_cloud', GeneratePointCloud.as_view(), name='generate_patology')
+            ]
+        ),
+    )
 ]

config/settings/base.py

@@ -299,7 +299,7 @@ SPECTACULAR_SETTINGS = {
     "SERVE_PERMISSIONS": ["rest_framework.permissions.AllowAny"],
     "SERVERS": [
         {"url": "https://dev.akarpov.ru", "description": "Development server"},
-        {"url": "https//127.0.0.1:8000", "description": "Development server"},
+        {"url": "http://127.0.0.1:8000", "description": "Development server"},
     ],
 }
 

image_markuper/dicom/api/serializers.py

@@ -181,6 +181,3 @@ class ProjectSerializer(serializers.ModelSerializer):
     class Meta:
         model = Project
         fields = ["files", "slug", "created"]
-
-    def create(self, validated_data):
-        return Project.objects.create(user=self.context["request"].user)

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 process_files
+from ..services import generate_3d_point_cloud, get_bbox, process_files
 from .serializers import (
     BaseShapeLayerSerializer,
     BaseShapeSerializer,
@@ -15,11 +15,13 @@ from .serializers import (
     FreeHandSerializer,
     ListDicomSerializer,
     ListProjectSerializer,
+    PointCloudSerializer,
     ProjectSerializer,
     RoiSerializer,
     RulerSerializer,
     SmartFileUploadSerializer,
     create_coordinate,
+    PatologyGenerateSerializer
 )
 
 
@@ -216,3 +218,23 @@ class RetrieveUpdateDeleteProjectApi(generics.RetrieveUpdateDestroyAPIView):
     queryset = Project.objects.all()
 
     lookup_field = "slug"
+
+
+class GeneratePatology(generics.CreateAPIView):
+    serializer_class = PatologyGenerateSerializer
+
+    def create(self, request, *args, **kwargs):
+        data = self.get_serializer(request.data).data
+        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

@@ -1,3 +1,4 @@
+from functools import lru_cache
 import glob
 import os
 import shutil
@@ -9,10 +10,14 @@ 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[TemporaryUploadedFile | InMemoryUploadedFile], user, slug=None
+    files: List[Union[TemporaryUploadedFile, InMemoryUploadedFile]], user, slug=None
 ):
     if slug:
         project = Project.objects.get(slug=slug)
@@ -23,7 +28,7 @@ def process_files(
         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)}"
+            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)
@@ -51,3 +56,39 @@ def create_coordinate(coordinates, obj):
             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

requirements/base.txt

@@ -25,3 +25,5 @@ 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