add point cloud and patology generation

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