basic support for bulk series uploading

atlas/api.py

@@ -0,0 +1,137 @@
+from collections import defaultdict
+from typing import List
+from django.shortcuts import get_object_or_404
+from ninja import ModelSchema, Router, Schema, Field
+
+# from .decorators import user_is_author_or_rapid_checker
+from django.core.exceptions import PermissionDenied
+
+from generic.decorators import check_user_in_group
+from generic.constants import Group
+
+from ninja.security import django_auth
+
+from ninja import NinjaAPI, File
+from ninja.files import UploadedFile
+
+from generic.models import Modality
+
+from .models import Case, DuplicateDicom, Series, SeriesImage, UncategorisedDicom
+
+
+router = Router()
+
+class SeriesSchema(ModelSchema):
+    case_id: List[int] = []
+
+    class Config:
+        model = Series
+        model_fields = ["id", "modality", "examination", "series_instance_uid", "author"]
+
+    @staticmethod
+    def resolve_case_id(obj):
+        return [i.id for i in obj.case.all()]
+
+
+@router.post("/upload_dicom", auth=django_auth)
+def upload_dicom(request, files: List[UploadedFile] = File(...)):
+    uploaded = []
+    duplicate = []
+    for file in files:
+        # data = file.read()
+        try:
+            ud = UncategorisedDicom(image=file, user=request.user)
+
+            ud.save()
+
+            uploaded.append(ud)
+        except DuplicateDicom:
+            duplicate.append(ud)
+            pass
+
+    return {"uploaded": len(uploaded), "duplicates": len(duplicate)}
+
+
+@router.get("/clear_dicoms", auth=django_auth)
+def clear_dicoms(request):
+    dicoms = UncategorisedDicom.objects.filter(user=request.user)
+
+    dicoms.delete()
+
+    return True
+
+
+@router.get("/uncategorised_dicoms", auth=django_auth)
+def uncategorised_dicoms(request):
+    dicoms = UncategorisedDicom.objects.filter(user=request.user)
+
+    data = defaultdict(list)
+    for d in dicoms:
+        tags = d.get_basic_dicom_tags()
+
+        data[tags["SeriesInstanceUID"]].append(tags)
+
+    return data
+
+
+@router.get("/import_dicoms", auth=django_auth)
+def import_dicoms(request):
+    dicoms = UncategorisedDicom.objects.filter(user=request.user)
+
+    data = defaultdict(list)
+    for d in dicoms:
+        tags = d.get_basic_dicom_tags()
+
+        data[tags["SeriesInstanceUID"]].append((d, tags))
+
+    for series_uid in data:
+
+        modality = get_object_or_404(Modality, short_code=tags["Modality"])
+        tags = data[series_uid][0][1]
+
+        # Check if series with the id already exists (in which case we just add to htat)
+        try:
+            series = Series.objects.get(series_instance_uid=tags["SeriesInstanceUID"])
+        except Series.DoesNotExist:
+            series = Series(
+                modality=modality,
+                description=tags["SeriesDescription"],
+                series_instance_uid=tags["SeriesInstanceUID"],
+            )
+            series.save()
+
+        # We might only want to add the author during creation....
+        series.author.add(request.user)
+
+        for dicom, dicom_tags in data[series_uid]:
+            series_image = SeriesImage(image=dicom.image, series=series)
+            series_image.save()
+
+            dicom.delete()
+
+    return {}
+
+@router.get("/orphan_series", auth=django_auth, response=List[SeriesSchema])
+def orphan_series(request):
+    #print(request.user.series.filter(case=None))
+    return request.user.series.filter(case=None)
+
+
+@router.get("/series_remove_duplicate_images", auth=django_auth)
+def series_remove_duplicate_images(request, series_id: int):
+
+    series = get_object_or_404(Series, pk=series_id)
+
+    img_ids = set()
+    dupes = set()
+    for series_image in series.images.all():
+        if series_image.image_md5_hash in img_ids:
+            dupes.add(series_image.id)
+        img_ids.add(series_image.image_md5_hash)
+
+    if dupes:
+        SeriesImage.objects.filter(id__in=dupes).delete()
+
+    return len(dupes)
+
+