.

atlas/admin.py

@@ -1,5 +1,5 @@
 from django.contrib import admin
-from .models import Case, Series, SeriesImage
+from .models import Case, Series, SeriesImage, Condition
 
 import tagulous.admin
 
@@ -11,13 +11,13 @@ from django.forms.widgets import RadioSelect
 from tinymce.widgets import TinyMCE
 
 # from generic.models import Examination, Sign, Site, Condition
-from generic.models import Examination, Sign, Condition
+from generic.models import Examination, Sign
 
 # Register your models here.
 # admin.site.register(Examination)
 # admin.site.register(Site)
 admin.site.register(SeriesImage)
-
+admin.site.register(Condition)
 
 
 class AtlasAdminForm(ModelForm):
@@ -37,10 +37,11 @@ class AtlasAdminForm(ModelForm):
             # "normal": RadioSelect(
             # choices=[(True, 'Yes'),
             #     (False, 'No')])
-            "findings" : TinyMCE(attrs={'cols': 80, 'rows': 30}),
+            "findings": TinyMCE(attrs={"cols": 80, "rows": 30}),
-            "mark_scheme" : TinyMCE(attrs={'cols': 80, 'rows': 30}),
+            "mark_scheme": TinyMCE(attrs={"cols": 80, "rows": 30}),
         }
 
+
 class AtlasAdmin(VersionAdmin):
     form = AtlasAdminForm
 
@@ -55,4 +56,5 @@ admin.site.register(Case, AtlasAdmin)
 class SeriesAdmin(VersionAdmin):
     pass
 
+
 admin.site.register(Series, SeriesAdmin)

atlas/migrations/0004_auto_20211125_2216.py

@@ -0,0 +1,26 @@
+# Generated by Django 3.2.8 on 2021-11-25 22:16
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0003_rename_subpecialty_case_subspecialty'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='Condition',
+            fields=[
+                ('id', models.BigAutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(max_length=255)),
+                ('synonym', models.ManyToManyField(blank=True, related_name='_atlas_condition_synonym_+', to='atlas.Condition')),
+            ],
+        ),
+        migrations.AlterField(
+            model_name='case',
+            name='condition',
+            field=models.ManyToManyField(blank=True, to='atlas.Condition'),
+        ),
+    ]

atlas/models.py

@@ -28,7 +28,15 @@ from helpers.images import image_as_base64, pretty_print_dicom
 
 from anatomy.models import Modality
 
-from generic.models import Examination, Condition, Sign, ExamBase, Plane, Contrast, QuestionNote
+from generic.models import (
+    Examination,
+    Condition,
+    Sign,
+    ExamBase,
+    Plane,
+    Contrast,
+    QuestionNote,
+)
 
 # from generic.models import Examination, Site, Condition, Sign
 
@@ -66,20 +74,26 @@ def findMiddle(input_list):
         return (input_list[int(middle)], input_list[int(middle - 1)])
 
 
+class Condition(models.Model):
+    name = models.CharField(max_length=255)
+
+    synonym = models.ManyToManyField("self", blank=True)
+
+
 @reversion.register
 class Case(models.Model):
     class SubspecialtyChoices(models.TextChoices):
-        BREAST = 'BR', _('Breast')
+        BREAST = "BR", _("Breast")
-        CARDIAC = 'CA', _('Cardiac')
+        CARDIAC = "CA", _("Cardiac")
-        GASTRO = 'GI', _('Gastrointestinal and hepatobiliary')
+        GASTRO = "GI", _("Gastrointestinal and hepatobiliary")
-        HEADNECK = 'HN', _('Head and Neck')
+        HEADNECK = "HN", _("Head and Neck")
-        MSK = 'MS', _('Musculoskeletal')
+        MSK = "MS", _("Musculoskeletal")
-        NEURO = 'NE', _('Neuroradiology')
+        NEURO = "NE", _("Neuroradiology")
-        OBSGYN = 'OG', _('Obstectric and Gynaecological')
+        OBSGYN = "OG", _("Obstectric and Gynaecological")
-        PAED = 'PA', _('Paediatric')
+        PAED = "PA", _("Paediatric")
-        URO = 'UR', _('Uroradiology')
+        URO = "UR", _("Uroradiology")
-        VASC = 'VA', _('Vascular')
+        VASC = "VA", _("Vascular")
-        HAEMONC = 'HA', _('Haemotology and Oncology')
+        HAEMONC = "HA", _("Haemotology and Oncology")
 
     title = models.CharField(max_length=255, help_text="Title of the case", default="")
     # author = models.ForeignKey('auth.User', on_delete=models.CASCADE)
@@ -95,11 +109,7 @@ class Case(models.Model):
 
     subspecialty = models.CharField(max_length=2, choices=SubspecialtyChoices.choices)
 
-    condition = tagulous.models.TagField(
+    condition = models.ManyToManyField(Condition, blank=True)
-        to=Condition,
-        blank=True,
-        help_text='Associated condition. Will allow searching / filtering and tips / hints to be displayed. Conditions with spaces must be enclosed in quotes "..."',
-    )
 
     sign = tagulous.models.TagField(
         to=Sign, blank=True, help_text="Radiological signs in the question"
@@ -127,7 +137,7 @@ class Case(models.Model):
 
     notes = GenericRelation(QuestionNote)
 
-    #question_file = models.FileField(upload_to=question_file_directory_path, blank=True, null=True)
+    # question_file = models.FileField(upload_to=question_file_directory_path, blank=True, null=True)
 
     def get_absolute_url(self):
         return reverse("atlas:case_detail", kwargs={"pk": self.pk})
@@ -158,11 +168,19 @@ class Case(models.Model):
 
     def get_image_urls(self):
         return ",".join(
-            ["https://www.penracourses.org.uk{}".format(i.url) for i in self.get_images()]
+            [
+                "https://www.penracourses.org.uk{}".format(i.url)
+                for i in self.get_images()
+            ]
         )
 
     def get_image_url_array(self):
-        return json.dumps(["https://www.penracourses.org.uk{}".format(i.url) for i in self.get_images()])
+        return json.dumps(
+            [
+                "https://www.penracourses.org.uk{}".format(i.url)
+                for i in self.get_images()
+            ]
+        )
 
 
 class SeriesImage(models.Model):
@@ -174,20 +192,23 @@ class SeriesImage(models.Model):
     )
 
     class Meta:
-        ordering = ['position']
+        ordering = ["position"]
 
     def get_dicom_info(self):
         try:
             info = pretty_print_dicom(pydicom.read_file(self.image))
         except pydicom.errors.InvalidDicomError:
             info = "File is not a dicom."
-        return(info)
+        return info
 
 
 @reversion.register
 class Series(models.Model):
     modality = models.ForeignKey(
-        Modality, related_name="atlas_series_modality", on_delete=models.SET_NULL, null=True
+        Modality,
+        related_name="atlas_series_modality",
+        on_delete=models.SET_NULL,
+        null=True,
     )
     examination = models.ForeignKey(
         Examination,
@@ -227,15 +248,14 @@ class Series(models.Model):
         help_text="If a question should be freely available to browse", default=True
     )
 
-
     def __str__(self):
         if self.case:
             case_id = ", ".format([case.pk for case in self.case.all()])
-            #case_id = self.case.pk
+            # case_id = self.case.pk
         else:
             case_id = "None"
-        return "{}/{} : {} [{}]".format(self.pk,
+        return "{}/{} : {} [{}]".format(
-            self.get_examination(), self.description, case_id
+            self.pk, self.get_examination(), self.description, case_id
         )
 
     def get_author_objects(self):
@@ -295,7 +315,9 @@ class Series(models.Model):
             thumbnailer = get_thumbnailer(img)
             thumbnail = thumbnailer["exam-list"]
         except InvalidImageFormatError:
-            return format_html('<span title="{}">Invalid image url<span>', img), len(images)
+            return format_html('<span title="{}">Invalid image url<span>', img), len(
+                images
+            )
         return format_html('<img src="/media/{}" />', thumbnail), len(images)
 
     def get_block(self):
@@ -324,8 +346,6 @@ class Series(models.Model):
             i.save()
             n = n + 1
 
-
-
     def order_by_dicom(self, field="SliceLocation"):
         images = self.images.all()
 
@@ -334,7 +354,7 @@ class Series(models.Model):
         for i in images:
             files.append((i, pydicom.dcmread(i.image.path)))
 
-        #print("file count: {}".format(len(files)))
+        # print("file count: {}".format(len(files)))
 
         # skip files with no SliceLocation (eg scout views)
         slices = []
@@ -343,7 +363,7 @@ class Series(models.Model):
         for i, f in files:
             if hasattr(f, field):
                 slices.append(f)
-                #map[f.SliceLocation] = i
+                # map[f.SliceLocation] = i
                 map[f[field].value] = i
             else:
                 skipcount = skipcount + 1
@@ -353,8 +373,7 @@ class Series(models.Model):
         # ensure they are in the correct order
         slices = sorted(slices, key=lambda s: s[field].value)
 
-
+        # print(slices)
-        #print(slices)
         n = 1
         for f in slices:
             i = map[f[field].value]