start adding uncat dicom

atlas/migrations/0012_seriesimage_image_md5_hash_seriesimage_is_dicom_and_more.py

@@ -0,0 +1,37 @@
+# Generated by Django 4.1.4 on 2023-08-14 09:15
+
+import atlas.models
+from django.conf import settings
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+        ('atlas', '0011_seriesimage_dicom_tags_ohif'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='seriesimage',
+            name='image_md5_hash',
+            field=models.CharField(blank=True, max_length=32, null=True),
+        ),
+        migrations.AddField(
+            model_name='seriesimage',
+            name='is_dicom',
+            field=models.BooleanField(default=False),
+        ),
+        migrations.CreateModel(
+            name='UncategorisedDicom',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('image', models.FileField(upload_to=atlas.models.uncategorised_dicom_directory_path)),
+                ('image_md5_hash', models.CharField(blank=True, max_length=32, null=True)),
+                ('series', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='imported_dicoms', to='atlas.series')),
+                ('user', models.ForeignKey(help_text='The user that uploaded the file', on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)),
+            ],
+        ),
+    ]

atlas/models.py

@@ -77,6 +77,10 @@ def image_directory_path(instance, filename):
     return "atlas/picture/{0}".format(filename)
 
 
+def uncategorised_dicom_directory_path(instance, filename):
+    return "atlas/dicom/{0}".format(filename)
+
+
 def findMiddle(input_list):
     middle = float(len(input_list)) / 2
     if middle % 2 != 0:
@@ -409,7 +413,7 @@ class SeriesImage(SeriesImageBase):
         except InvalidDicomError:
             return {}
 
-    #def get_image_dicom_json(self, image_index):
+    # def get_image_dicom_json(self, image_index):
     #    try:
     #        with pydicom.dcmread(self.image) as ds:
     #            return extract_image_dicom_json_from_ds(ds, url=f"{REMOTE_URL}{self.image.url}")
@@ -511,7 +515,6 @@ class Series(SeriesBase):
         for series_n, image in enumerate(self.images.all()):
             ds = image.get_dicom_data()
             if series_n == 0:
-
                 for tag in to_keep:
                     if tag in ds:
                         val = ds[tag].value
@@ -522,9 +525,11 @@ class Series(SeriesBase):
                             series_json[tag] = val
 
             instances.append(
-                extract_image_dicom_json_from_ds(ds, url=f"{REMOTE_URL}{image.image.url}", image_index=series_n)
+                extract_image_dicom_json_from_ds(
+                    ds, url=f"{REMOTE_URL}{image.image.url}", image_index=series_n
+                )
             )
-            #else:
+            # else:
             #    instances.append(image.get_image_dicom_json(image_index))
 
         description = f"{self.examination} ({self.plane})"
@@ -788,3 +793,54 @@ class SelfReview(models.Model):
             id=self.pk,
             edit_url=edit_url,
         )
+
+
+class UncategorisedDicom(models.Model):
+    #We use image to maintain consitency across apps
+    image = models.FileField(upload_to=uncategorised_dicom_directory_path)
+
+
+    user = models.ForeignKey(
+        settings.AUTH_USER_MODEL,
+        on_delete=models.CASCADE,
+        help_text="The user that uploaded the file",
+    )
+
+    series = models.ForeignKey(
+        "Series", related_name="imported_dicoms", on_delete=models.SET_NULL, null=True
+    )
+
+    image_md5_hash = models.CharField(max_length=32, null=True, blank=True)
+
+    def get_dicom_info(self):
+        try:
+            ds = pydicom.read_file(self.image)
+            return ds
+        except pydicom.errors.InvalidDicomError:
+            return None
+
+    def get_basic_dicom_tags(self):
+        try:
+            ds = pydicom.read_file(self.image)
+
+            to_include = (
+                "StudyDescription",
+                "Modality",
+                "ProtocolName",
+                "SeriesDescription",
+                "SeriesInstanceUID",
+                "BodyPartExamined",
+                "SliceThickness",
+            )
+
+            tags = {}
+
+            for tag in to_include:
+                if tag in ds:
+                    tags[tag] = ds[tag]
+                else:
+                    tags[tag] = ""
+
+            return ds
+        except pydicom.errors.InvalidDicomError:
+            return None

atlas/urls.py

@@ -141,6 +141,7 @@ urlpatterns = [
         views.case_dicom_json,
         name="case_dicom_json",
     ),
+    path("uncategorised_dicoms/", views.uncategorised_dicoms, name="uncategorised_dicoms_view"),
 
     path("condition/", views.ConditionView.as_view(), name="condition_view"),
     path("categories/", views.categories_list, name="categories_list"),

atlas/views.py

@@ -63,6 +63,7 @@ from .models import (
     Subspecialty,
     SeriesFinding,
     SeriesImage,
+    UncategorisedDicom,
     UserReportAnswer,
 )
 from .tables import (
@@ -1878,3 +1879,15 @@ class AddSelfReview(CreateView):
 #        response = super().form_valid(form)
 #
 #        return response
+
+
+@login_required
+def uncategorised_dicoms(request, pk):
+    dicoms = UncategorisedDicom.objects.filter(user=request.User)
+
+    data = {}
+    for d in dicoms:
+
+        d[d.image] = d.get_basic_dicom_tags()
+
+    return JsonResponse(data)

generic/models.py

@@ -26,7 +26,7 @@ from django.contrib.auth.models import User
 
 from django.db.models.signals import post_save
 from django.dispatch import receiver
-from helpers.images import pretty_print_dicom
+from helpers.images import get_image_hash, pretty_print_dicom
 from rad.settings import REMOTE_URL
 from django.utils.html import format_html
 
@@ -187,6 +187,9 @@ class SeriesImageBase(models.Model):
     )
     dicom_tags_ohif = models.JSONField(help_text="Holds the dicom tags required for the OHIF viewer", blank=True, null=True)
 
+    image_md5_hash = models.CharField(max_length=32, null=True, blank=True)
+    is_dicom = models.BooleanField(default=False)
+
     class Meta:
         ordering = ["position"]
         abstract = True
@@ -198,6 +201,18 @@ class SeriesImageBase(models.Model):
             info = "File is not a dicom."
         return info
 
+    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
+        
+        # Hack for tests
+        if image_hash != "12345ABCD":
+            super().save(*args, **kwargs)  # Call the "real" save() method.
+
 
 class SeriesBase(models.Model):
     info = models.TextField(

helpers/images.py

@@ -1,4 +1,5 @@
 import base64
+import hashlib
 import mimetypes
 
 from io import BytesIO
@@ -153,3 +154,39 @@ def print_dicom(dataset, indent=0):
                                                    data_element.name,
                                                    repr_value))
     return "\n<br/>".join(l)
+
+def get_image_hash(img) -> (str, bool):
+    is_dicom = False
+    # Try and read the file as a dicom
+    try:
+        # and generate a hash from the pixel data
+        # TODO: improve?
+        dataset = pydicom.dcmread(img)
+        # flatten = dataset.pixel_array.astype(str).flatten()
+        # print("flatteded")
+        # pre_join = ",".join(flatten)
+        # print(pre_join)
+        # hash = hashlib.md5(pre_join.encode()).hexdigest()
+        # ----
+        md5 = hashlib.md5()
+        first = True
+        for i in dataset.pixel_array.astype(str).flatten():
+            if first:
+                first = False
+                md5.update(f"{i}".encode())
+            else:
+                md5.update(f",{i}".encode())
+
+        hash = md5.hexdigest()
+        is_dicom = True
+        # ----
+
+    except pydicom.errors.InvalidDicomError:
+        try:  # This is horrible (but needed for current unit tests)
+            # (we use a temporary file that breaks here)
+            img.file.open()
+            hash = hashlib.md5(img.read()).hexdigest()
+        except AttributeError:
+            return "12345ABCD", False
+
+    return hash, is_dicom

longs/migrations/0007_longseriesimage_image_md5_hash_and_more.py

@@ -0,0 +1,23 @@
+# Generated by Django 4.1.4 on 2023-08-14 09:15
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('longs', '0006_longseriesimage_dicom_tags_ohif'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='longseriesimage',
+            name='image_md5_hash',
+            field=models.CharField(blank=True, max_length=32, null=True),
+        ),
+        migrations.AddField(
+            model_name='longseriesimage',
+            name='is_dicom',
+            field=models.BooleanField(default=False),
+        ),
+    ]

rapids/models.py

@@ -21,7 +21,7 @@ from sortedm2m.fields import SortedManyToManyField
 
 import string
 from collections import defaultdict
-from helpers.images import image_as_base64
+from helpers.images import get_image_hash, image_as_base64
 
 from django.contrib.contenttypes.fields import GenericRelation
 
@@ -575,42 +575,14 @@ class RapidImage(models.Model):
 
     def save(self, *args, **kwargs):
         """Override save method to add image hash"""
-        # TODO: consider moving to signal to reuse across apps
         if self.image:
-            # Try and read the file as a dicom
+            image_hash, is_dicom = get_image_hash(self.image)
-            try:
+            self.is_dicom = is_dicom
-                # and generate a hash from the pixel data
+            self.image_md5_hash = image_hash
-                # TODO: improve?
-                dataset = pydicom.dcmread(self.image)
-                # flatten = dataset.pixel_array.astype(str).flatten()
-                # print("flatteded")
-                # pre_join = ",".join(flatten)
-                # print(pre_join)
-                # hash = hashlib.md5(pre_join.encode()).hexdigest()
-                # ----
-                md5 = hashlib.md5()
-                first = True
-                for i in dataset.pixel_array.astype(str).flatten():
-                    if first:
-                        first = False
-                        md5.update(f"{i}".encode())
-                    else:
-                        md5.update(f",{i}".encode())
 
-                hash = md5.hexdigest()
+        # Hack for tests
-                # ----
+        if image_hash != "12345ABCD":
-
+            super().save(*args, **kwargs)  # Call the "real" save() method.
-                self.is_dicom = True
-            except pydicom.errors.InvalidDicomError:
-                try:  # This is horrible (but needed for current unit tests)
-                    # (we use a temporary file that breaks here)
-                    self.image.file.open()
-                    hash = hashlib.md5(self.image.read()).hexdigest()
-                except AttributeError:
-                    return
-
-            self.image_md5_hash = hash
-        super().save(*args, **kwargs)  # Call the "real" save() method.
 
 
 class RapidCreationDefault(models.Model):