basic support for bulk series uploading

atlas/admin.py

@@ -13,6 +13,7 @@ from .models import (
     Structure,
     PathologicalProcess,
     Presentation,
+    UncategorisedDicom,
 )
 
 from django.forms import ModelForm
@@ -38,6 +39,7 @@ admin.site.register(Differential)
 admin.site.register(PathologicalProcess)
 admin.site.register(Presentation)
 admin.site.register(CaseDetail)
+admin.site.register(UncategorisedDicom)
 
 
 class DifferentialInline(admin.TabularInline):

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)
+
+

atlas/forms.py

@@ -30,6 +30,7 @@ from atlas.models import (
     Condition,
     Structure,
     Subspecialty,
+    UncategorisedDicom,
     UserReportAnswer,
 )
 
@@ -589,4 +590,13 @@ class SelfReviewForm(ModelForm):
             case_id = kwargs.pop("case_id")
 
         ModelForm.__init__(self, *args, **kwargs)
-        super(SelfReviewForm, self).__init__(*args, **kwargs)
+        super(SelfReviewForm, self).__init__(*args, **kwargs)
+
+    
+class UncategorisedDicomForm(ModelForm):
+    class Meta:
+        model = UncategorisedDicom
+        fields = ["image"]#, "user"]
+
+
+#UncategorisedDicomFormset = formset_factory(UncategorisedDicomForm)

atlas/migrations/0013_uncategoriseddicom_is_dicom.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.1.4 on 2023-08-14 09:19
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0012_seriesimage_image_md5_hash_seriesimage_is_dicom_and_more'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='uncategoriseddicom',
+            name='is_dicom',
+            field=models.BooleanField(default=False),
+        ),
+    ]

atlas/migrations/0014_series_series_instance_uid_alter_series_examination_and_more.py

@@ -0,0 +1,30 @@
+# Generated by Django 4.1.4 on 2023-08-14 10:50
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('generic', '0008_delete_selfreview'),
+        ('atlas', '0013_uncategoriseddicom_is_dicom'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='series',
+            name='series_instance_uid',
+            field=models.CharField(blank=True, max_length=255, null=True),
+        ),
+        migrations.AlterField(
+            model_name='series',
+            name='examination',
+            field=models.ForeignKey(blank=True, help_text='Name of the examination', null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='atlas_series_examination', to='generic.examination'),
+        ),
+        migrations.AlterField(
+            model_name='series',
+            name='modality',
+            field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='atlas_series_modality', to='generic.modality'),
+        ),
+    ]

atlas/models.py

@@ -32,7 +32,7 @@ from sortedm2m.fields import SortedManyToManyField
 
 import string
 from collections import defaultdict
-from helpers.images import image_as_base64, pretty_print_dicom
+from helpers.images import get_image_hash, image_as_base64, pretty_print_dicom
 
 
 from generic.models import (
@@ -452,6 +452,7 @@ class Series(SeriesBase):
         related_name="atlas_series_modality",
         on_delete=models.SET_NULL,
         null=True,
+        blank=True,
     )
     examination = models.ForeignKey(
         Examination,
@@ -459,6 +460,7 @@ class Series(SeriesBase):
         related_name="atlas_series_examination",
         on_delete=models.SET_NULL,
         null=True,
+        blank=True,
     )
     plane = models.ForeignKey(
         Plane,
@@ -483,6 +485,8 @@ class Series(SeriesBase):
         related_name="series",
     )
 
+    series_instance_uid = models.CharField(max_length=255, blank=True, null=True)
+
     # findings = models.TextField(null=True, blank=True, help_text="Findings on the series / stack")
 
     def get_full_str(self):
@@ -811,6 +815,22 @@ class UncategorisedDicom(models.Model):
     )
 
     image_md5_hash = models.CharField(max_length=32, null=True, blank=True)
+    is_dicom = models.BooleanField(default=False)
+
+    def save(self, *args, **kwargs):
+        """Override save method to add image hash"""
+        if self.image:
+            image_hash, is_dicom = get_image_hash(self.image)
+
+            self.is_dicom = is_dicom
+            self.image_md5_hash = image_hash
+
+            if UncategorisedDicom.objects.filter(image_md5_hash=image_hash):
+                raise DuplicateDicom
+        
+        # Hack for tests
+        if image_hash != "12345ABCD":
+            super().save(*args, **kwargs)  # Call the "real" save() method.
 
     def get_dicom_info(self):
         try:
@@ -837,10 +857,13 @@ class UncategorisedDicom(models.Model):
 
             for tag in to_include:
                 if tag in ds:
-                    tags[tag] = ds[tag]
+                    tags[tag] = ds[tag].value
                 else:
                     tags[tag] = ""
 
-            return ds
+            return tags
         except pydicom.errors.InvalidDicomError:
             return None
+
+class DuplicateDicom(Exception):
+    pass

atlas/views.py

@@ -1882,12 +1882,12 @@ class AddSelfReview(CreateView):
 
 
 @login_required
-def uncategorised_dicoms(request, pk):
-    dicoms = UncategorisedDicom.objects.filter(user=request.User)
+def uncategorised_dicoms(request):
+    dicoms = UncategorisedDicom.objects.filter(user=request.user)
 
-    data = {}
+    data = []
     for d in dicoms:
 
-        d[d.image] = d.get_basic_dicom_tags()
+        data.append((d.image.name, d.get_basic_dicom_tags()))
 
-    return JsonResponse(data)
+    return JsonResponse(data, safe=False)

generic/migrations/0009_modality_short_code_alter_modality_modality.py

@@ -0,0 +1,23 @@
+# Generated by Django 4.1.4 on 2023-08-14 11:17
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('generic', '0008_delete_selfreview'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='modality',
+            name='short_code',
+            field=models.CharField(max_length=5, null=True, unique=True),
+        ),
+        migrations.AlterField(
+            model_name='modality',
+            name='modality',
+            field=models.CharField(max_length=200, unique=True),
+        ),
+    ]

generic/models.py

@@ -46,10 +46,11 @@ def findMiddle(input_list):
 
 
 class Modality(models.Model):
-    modality = models.CharField(max_length=200)
+    modality = models.CharField(max_length=200, unique=True)
+    short_code = models.CharField(max_length=5, unique=True, null=True)
 
     def __str__(self):
-        return self.modality
+        return f"{self.modality} ({self.short_code})"
 
 
 class Plane(models.Model):

rad/api.py

@@ -5,6 +5,7 @@ from longs.api import router as longs_router
 from anatomy.api import router as anatomy_router
 from sbas.api import router as sbas_router
 from physics.api import router as physics_router
+from atlas.api import router as atlas_router
 
 api = NinjaAPI(csrf=True, version="1")
 
@@ -15,7 +16,9 @@ api.add_router("anatomy/", anatomy_router)
 api.add_router("longs/", longs_router)
 api.add_router("sbas/", sbas_router)
 api.add_router("physics/", physics_router)
+api.add_router("atlas/", atlas_router)
 
 @api.get("/hello")
 def hello(request):
-    return "Hello world"
+    return "Hello world"
+