improve dicom uploading

atlas/api.py

@@ -66,11 +66,17 @@ def upload_dicom(request, files: List[UploadedFile] = File(...)):
     return {"uploaded": uploaded, "duplicates": duplicate}
 
 
-@router.get("/clear_dicoms", auth=django_auth)
+@router.post("/clear_dicoms", auth=django_auth)
 def clear_dicoms(request):
-    dicoms = UncategorisedDicom.objects.filter(user=request.user)
+
+    if "selection" in request.POST:
+        dicoms = UncategorisedDicom.objects.filter(series_instance_uid__in=request.POST.getlist("selection"))
+
+    else:
+        dicoms = UncategorisedDicom.objects.filter(user=request.user)
 
     dicoms.delete()
+    print(dicoms)
 
     return True
 
@@ -90,7 +96,12 @@ def uncategorised_dicoms(request):
 
 
 def import_dicoms_helper(request, case_id: int | None = None):
-    dicoms = UncategorisedDicom.objects.filter(user=request.user)
+    #dicoms = UncategorisedDicom.objects.filter(user=request.user)
+    if "selection" in request.POST:
+        dicoms = UncategorisedDicom.objects.filter(series_instance_uid__in=request.POST.getlist("selection"))
+
+    else:
+        dicoms = UncategorisedDicom.objects.filter(user=request.user)
 
     data = defaultdict(list)
     for d in dicoms:
@@ -136,12 +147,12 @@ def import_dicoms_helper(request, case_id: int | None = None):
     return series_list
 
 
-@router.get("/import_dicoms", auth=django_auth, response=List[SeriesSchema])
+@router.post("/import_dicoms", auth=django_auth, response=List[SeriesSchema])
 def import_dicoms(request):
     return import_dicoms_helper(request)
 
 
-@router.get("/import_dicoms/{case_id}", auth=django_auth, response=List[SeriesSchema])
+@router.post("/import_dicoms/{case_id}", auth=django_auth, response=List[SeriesSchema])
 def import_dicoms_case(request, case_id: int):
     return import_dicoms_helper(request, case_id=case_id)
 

atlas/forms.py

@@ -223,7 +223,7 @@ class SeriesForm(ModelForm):
 
     class Meta:
         model = Series
-        exclude = ["author"]
+        exclude = ["author", "series_instance_uid"]
 
         widgets = {
             "examination": autocomplete.ModelSelect2(

atlas/migrations/0017_series_created_at_series_updated_at.py

@@ -0,0 +1,25 @@
+# Generated by Django 4.1.4 on 2023-10-23 08:53
+
+from django.db import migrations, models
+import django.utils.timezone
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0016_remove_uncategoriseddicom_is_dicom'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='series',
+            name='created_at',
+            field=models.DateTimeField(auto_now_add=True, default=django.utils.timezone.now),
+            preserve_default=False,
+        ),
+        migrations.AddField(
+            model_name='series',
+            name='updated_at',
+            field=models.DateTimeField(auto_now=True),
+        ),
+    ]

atlas/migrations/0018_rename_created_at_series_created_date_and_more.py

@@ -0,0 +1,23 @@
+# Generated by Django 4.1.4 on 2023-10-23 09:00
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0017_series_created_at_series_updated_at'),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name='series',
+            old_name='created_at',
+            new_name='created_date',
+        ),
+        migrations.RenameField(
+            model_name='series',
+            old_name='updated_at',
+            new_name='modified_date',
+        ),
+    ]

atlas/migrations/0019_uncategoriseddicom_series_instance_uid.py

@@ -0,0 +1,19 @@
+# Generated by Django 4.1.4 on 2023-10-23 10:45
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0018_rename_created_at_series_created_date_and_more'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='uncategoriseddicom',
+            name='series_instance_uid',
+            field=models.CharField(default='test', max_length=255),
+            preserve_default=False,
+        ),
+    ]

atlas/migrations/0020_alter_uncategoriseddicom_series_instance_uid.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.1.4 on 2023-10-23 10:46
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0019_uncategoriseddicom_series_instance_uid'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='uncategoriseddicom',
+            name='series_instance_uid',
+            field=models.CharField(default='', max_length=255),
+        ),
+    ]

atlas/migrations/0021_alter_uncategoriseddicom_series_instance_uid.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.1.4 on 2023-10-23 10:51
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0020_alter_uncategoriseddicom_series_instance_uid'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='uncategoriseddicom',
+            name='series_instance_uid',
+            field=models.CharField(default='', max_length=255, null=True),
+        ),
+    ]

atlas/migrations/0022_alter_uncategoriseddicom_series_and_more.py

@@ -0,0 +1,24 @@
+# Generated by Django 4.1.4 on 2023-10-23 11:07
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0021_alter_uncategoriseddicom_series_instance_uid'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='uncategoriseddicom',
+            name='series',
+            field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='imported_dicoms', to='atlas.series'),
+        ),
+        migrations.AlterField(
+            model_name='uncategoriseddicom',
+            name='series_instance_uid',
+            field=models.CharField(blank=True, max_length=255, null=True),
+        ),
+    ]

atlas/models.py

@@ -811,9 +811,11 @@ class UncategorisedDicom(models.Model):
     )
 
     series = models.ForeignKey(
-        "Series", related_name="imported_dicoms", on_delete=models.SET_NULL, null=True
+        "Series", related_name="imported_dicoms", on_delete=models.SET_NULL, null=True, blank=True
     )
 
+    series_instance_uid = models.CharField(max_length=255, blank=True, null=True)
+
     image_md5_hash = models.CharField(max_length=32, null=True, blank=True)
 
     def check_for_duplicates(self, image_hash):
@@ -833,10 +835,14 @@ class UncategorisedDicom(models.Model):
     def save(self, *args, **kwargs):
         """Override save method to add image hash"""
         if self.image:
+
+            ds = self.get_dicom_info()
+
+            self.series_instance_uid = ds["SeriesInstanceUID"].value
+
             # if self.check_for_duplicates():
             #    return DuplicateDicom
-            image_hash = get_image_dicom_hash(self.image)
-
+            image_hash = get_image_dicom_hash(None, dataset=ds)
 
             self.image_md5_hash = image_hash
 

atlas/tables.py

@@ -110,6 +110,8 @@ class SeriesTable(tables.Table):
             "plane",
             "contrast",
             "author",
+            "created_date",
+            "modified_date",
         )
         sequence = ("view", "popup", "images", "case")
 

atlas/templates/atlas/case_display_block.html

@@ -1,5 +1,5 @@
 <div class="atlas {% if case.scrapped %}atlas-scrapped{% endif %}">
-    <div><a href="https://viewer.penracourses.org.uk/viewer/dicomjson?url=https://www.penracourses.org.uk{% url 'atlas:case_dicom_json' case.pk %}"">View case in OHIF</a></div>
+    <div><a href="https://viewer.penracourses.org.uk/viewer/dicomjson?url=https://www.penracourses.org.uk{% url 'atlas:case_dicom_json' case.pk %}">View case in OHIF</a></div>
 
     <div class="date">
         {{ case.created_date|date:"d/m/Y" }}
@@ -42,7 +42,10 @@
                 </span>
             </span>
         {% endfor %}
-        <a href="{% url 'atlas:series_id_create' pk=case.pk %}">Add new series</a><br />
+        <span>
+            <a href="{% url 'atlas:series_id_create' pk=case.pk %}">Add new series</a><br />
+            <a href="{% url 'atlas:user_uploads_case' case_id=case.pk %}">Import new uploads</a><br />
+        </span>
     </div>
     {% comment %} <p><b>Scrapped:</b> {{ case.scrapped }} <a
             href="{% url 'atlas:case_scrap' pk=case.pk %}">(toggle)</a> {% endcomment %}

atlas/templates/atlas/series_form.html

@@ -411,7 +411,7 @@
     {{ form.media }}
 {% endblock %}
 {% block content %}
-    <h2>Add Series</h2>
+    <h2>Series Form</h2>
     This form will create a image set that can be associated with a atlas question. If the question has already been created
     it can be linked below.
     <form action="" method="post" enctype="multipart/form-data" id="atlas-form">

atlas/templates/atlas/user_uploads.html

@@ -2,46 +2,55 @@
 
 {% block content %}
     <h2>Uploaded dicoms</h2>
+    Click to select cases to import. If no cases are selected all will be seleced/imported.
 
 
     {% if series_list %}
-        <ul>
-            {% for series, n, tags in series_list %}
-                <li>
-                    {{series}} [{{n}} images] <br/>
-                    {{tags}}
-                </li>
-            {% endfor %}
-        </ul>
+            <ul id="series-list">
+                {% for series, n, tags in series_list %}
+                    <li _="
+                    on click toggle .selected on me 
+                    then set i to the first <input/> in me
+                    then set i.checked to not i.checked" >
+                        {{series}} [{{n}} images] <br/>
+                        {{tags}}
+                        <input class="hidden" type="checkbox" name="selection" value="{{ series }}">
+                    </li>
+                {% endfor %}
+            </ul>
 
-        {% if case %}
-            <p>Importing into case {{case}}</p>
-        {% endif %}
+            {% if case %}
+                <p>Importing into case {{case}}</p>
+            {% endif %}
 
-        <button
-            hx-get="{% url 'api-1:clear_dicoms' %}"
-            hx-confirm="This will clear all uploads that have not been imported into series, Continue?"
-        >Delete Uploads</button>
-        {% if case %}
-        <button
-            hx-get="{% url 'api-1:import_dicoms_case' case.id %}"
-            hx-target=".imported"
-        >Import</button>
+            <button id="delete-uploads-button"
+                    hx-post="{% url 'api-1:clear_dicoms' %}"
+                    hx-include="[name='selection']"
+                    hx-confirm="This will clear selected uploads, Continue?"
+                    title="Deleted selected uploads"
+            >Delete Uploads</button>
+            {% if case %}
+                <button id="import-dicoms-case-button"
+                        hx-post="{% url 'api-1:import_dicoms_case' case.id %}"
+                        hx-target=".imported"
+                        hx-include=".selected"
+                >Import into case</button>
 
-        {% else %}
-        <button
-            hx-get="{% url 'api-1:import_dicoms' %}"
-            hx-target=".imported"
-        >Import</button>
-        {% endif %}
+            {% else %}
+                <button id="import-dicoms-button"
+                        hx-post="{% url 'api-1:import_dicoms' %}"
+                        hx-target=".imported"
+                        hx-include=".selected"
+                >Import</button>
+            {% endif %}
 
-        <div class="imported">
+            <div class="imported">
 
-        </div>
+            </div>
     {% else %}
         No uploads awaiting importing have been found.
     {% endif %}
 
-    <p><a href="{% url 'atlas:series_view' %}?case=null">View orphan series</a></p>
+    <p><a href="{% url 'atlas:series_view' %}?case=null&sort=-modified_date">View orphan series</a></p>
 
 {% endblock %}

atlas/urls.py

@@ -35,7 +35,7 @@ urlpatterns = [
     path("collection/", views.CollectionView.as_view(), name="collection_view"),
     path("collection/user", views.user_collections, name="user_collections"),
     path("uploads", views.user_uploads, name="user_uploads"),
-    path("uploads/case/<int:case_id>", views.user_uploads, name="user_uploads"),
+    path("uploads/case/<int:case_id>", views.user_uploads, name="user_uploads_case"),
     path(
         "collection/create",
         views.CaseCollectionCreate.as_view(),