start migration to dv3d

atlas/forms.py

@@ -175,7 +175,7 @@ class StructureForm(ModelForm):
 class SeriesFindingForm(ModelForm):
     class Meta:
         model = SeriesFinding
-        exclude = ["series", "annotation_json", "viewport_json", "current_image_id_index"]
+        exclude = ["series", "annotation_json", "viewport_json", "current_image_id_index", "annotation_json_3d", "viewer_state_3d"]
 
         widgets = {
             "findings": autocomplete.ModelSelect2Multiple(

atlas/migrations/0070_seriesfinding_annotation_json_3d_and_more.py

@@ -0,0 +1,23 @@
+# Generated by Django 5.1.4 on 2025-06-09 10:05
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0069_caseprior_prior_visibility'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='seriesfinding',
+            name='annotation_json_3d',
+            field=models.JSONField(default=dict),
+        ),
+        migrations.AddField(
+            model_name='seriesfinding',
+            name='viewer_state_3d',
+            field=models.JSONField(default=dict),
+        ),
+    ]

atlas/models.py

@@ -628,6 +628,8 @@ class SeriesFinding(FindingBase):
 
     def __str__(self) -> str:
         findings = self.findings.all().values_list("name")
+        if self.series is None:
+            return f"SeriesFinding: {findings}/{self.description} (no series)"
         return f"SeriesFinding: {self.series.id}/{findings}/{self.description}"
 
 @reversion.register

atlas/templates/atlas/series_viewer.html

@@ -3,8 +3,8 @@
 <div>{{ series.modality}}, {{ series.examination }}, {{ series.plane }}, {{ series.contrast }}</div>
 <div>Description: {{series.description}}</div>
 
-        Associated case:
+Associated case:
-    {% for case in series.case.all %}
+{% for case in series.case.all %}
     <span id="case-link-{{ case.pk }}" class="case-item">
         <a href="{% url 'atlas:case_detail' pk=case.pk %}">{{case}}</a>
         {% if can_edit %}
@@ -17,7 +17,7 @@
             </button>
         {% endif %}
     </span>
-    {% empty %}
+{% empty %}
     This series is not associated with any cases.
     {% if can_edit %}
         <details>
@@ -37,12 +37,18 @@
             <div id="add-series-to-case-result"></div>
         </details>
     {% endif %}
-    {% endfor %}
+{% endfor %}
 
 {% with image_url_array_and_count=series.get_image_url_array_and_count %}
     <div id="single-dicom-viewer" class="dicom-viewer" data-images="{{ image_url_array_and_count.0 }}" data-annotations=''>
     </div>
 
+    <div id="root" class="dicom-viewer-root" data-images="{{ image_url_array_and_count.0 }}"
+      style="width: 1000px; height: 600px; box-sizing: border-box; background: #222;"
+data-auto-cache-stack=true
+    ></div>
+
+
     {% if can_edit %}
         {% if editing_finding < 1 %}
             <button id="add-finding-button">Add finding</button>
@@ -80,6 +86,11 @@
             <div class="finding-box">
                 <button id="finding-{{finding.pk}}" class="view-finding-button" data-annotationjson={{finding.annotation_json}}
                         data-viewportjson={{finding.viewport_json}} data-findingid={{finding.id}} data-currentimageid={{finding.current_image_id_index}}>Click to view</button>
+                
+                {% if finding.viewer_state_3d %}
+                <button id="finding-{{finding.pk}}-3d" class="view-finding-button-3d" data-annotationjson3d='{{finding.annotation_json_3d}}' data-viewerstatejson='{{finding.viewer_state_3d}}'>Click to view 3D</button>
+                {% endif %}
+                    
                 <span class="view-finding-details">
                     Finding(s): {% for f in finding.findings.all %}{{f.get_link}}{% endfor %}<br />
                     Structure(s): {% for s in finding.structures.all %}{{s.get_link}}{% endfor %}<br />
@@ -95,6 +106,11 @@
                     <pre>{{finding.viewport_json}}</pre>
                             <h4>Image ID</h4>
                     <pre>{{finding.current_image_id_index}}</pre>
+
+                            <h4>3D Annotation JSON</h4>
+                    <pre>{{finding.annotation_json_3d}}</pre>
+                            <h4>Viewer State</h4>
+                    <pre>{{finding.viewer_state_3d}}</pre>
                         </div>
                     {% endif %}
                 </span>
@@ -124,8 +140,8 @@
 
 
 <div>Author: {{ series.get_author_display }}</div>
-    {% if can_edit %}
+{% if can_edit %}
-<details>
+    <details>
         <summary>Series info</summary>
         <div>
             <a href="{% url 'atlas:series_anonymise_dicom' pk=series.pk %}"
@@ -171,8 +187,8 @@
 
         <p>Total image size: {{series.get_total_image_size|filesizeformat}}</p>
         <p><a href="{% url 'atlas:series_download' pk=series.pk %}">Download images</a></p>
-</details>
+    </details>
-<span id="diff-controls">show <span id="diff-show-all" _="on click
+    <span id="diff-controls">show <span id="diff-show-all" _="on click
                                                               log '1'
                                                               for row in .diff.rows
                                                               show row
@@ -284,6 +300,17 @@
             cornerstone.resize(dicom_element, true);
 
         });
+        $(".view-finding-button-3d").each((n, el) => {
+            $(el).click((e) => {
+                dicom_element = $(".cornerstone-element").get(0);
+                annotationjson3d = JSON.parse(e.currentTarget.dataset.annotationjson3d);
+                viewer_state_json = JSON.parse(e.currentTarget.dataset.viewerstatejson);
+                console.log("Loading 3D annotation and viewer state", annotationjson3d, viewer_state_json);
+                importAnnotations_root(annotationjson3d);
+                importViewerState_root(viewer_state_json);
+                $(el).addClass("active");
+            });
+        });
 
         $(".view-finding-button").each((n, el) => {
             $(el).click((e) => {
@@ -293,6 +320,11 @@
                 current_image_id_index = e.currentTarget.dataset.currentimageid;
                 console.log(e.currentTarget, current_image_id_index)
                 loadAnnotationAndViewportOnElement(annotationjson, viewport, dicom_element, current_image_id_index);
+
+                importLegacyViewport_root(viewport)
+                importLegacyAnnotations_root(annotationjson);
+                jumpToSliceByImageId_root(0, current_image_id_index);
+                console.log("Loaded annotation and viewport on element", dicom_element, annotationjson, viewport, current_image_id_index);
                 $(el).addClass("active");
 
 
@@ -368,6 +400,8 @@
                 annotation_json: JSON.stringify(cornerstoneTools.globalImageIdSpecificToolStateManager
                         .saveToolState()),
                 viewport_json: JSON.stringify(c.viewport),
+                annotation_json_3d: window.exportAnnotations_root(),
+                viewer_state_3d: window.exportViewerState_root(),
                 findings: JSON.stringify($('#finding-form select[name="findings"]').find(":selected")
                         .map((i, el) => {
                             return $(el).val()

atlas/templates/atlas/series_viewer_test.html

@@ -0,0 +1,74 @@
+{% load static %}
+<!doctype html>
+<html lang="en">
+  <head>
+    <meta charset="UTF-8" />
+    <link rel="icon" type="image/svg+xml" href="/vite.svg" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>Vite + React + TS</title>
+  </head>
+  <body>
+{% with image_url_array_and_count=series.get_image_url_array_and_count %}
+{% comment %}     <div id="single-dicom-viewer" class="dicom-viewer" data-images="{{ image_url_array_and_count.0 }}" data-annotations=''>
+    </div> {% endcomment %}
+
+    <div id="root" class="dicom-viewer-root" data-images="{{ image_url_array_and_count.0 }}"
+      style="width: 1000px; height: 600px; box-sizing: border-box; background: #222;"
+    ></div>
+
+{% endwith %}
+        <script type="module" src="{% static 'dv3d/index-DCNn6AQH.js' %}" defer="defer" type="module"></script>
+
+<input type="file" id="dicomInput" multiple />
+<button onclick="sendToViewer()">Send to Viewer</button>
+<button onclick="testLoadWadouriStack()">Test Load wadouri Stack</button>
+<script>
+function sendToViewer() {
+  const files = document.getElementById('dicomInput').files;
+  if (window.loadDicomStackFromFiles) {
+    window.loadDicomStackFromFiles(files);
+  } else {
+    alert("Viewer API not ready");
+  }
+}
+
+
+function testLoadWadouriStack() {
+  const urls = [
+    "https://www.penracourses.org.uk/media/atlas/dicom/IMG_757_XQQyovo.dcm",
+    "https://www.penracourses.org.uk/media/atlas/dicom/IMG_766_8fWI0Qc.dcm",
+    "https://www.penracourses.org.uk/media/atlas/dicom/IMG_774_c8IpxUu.dcm",
+    "https://www.penracourses.org.uk/media/atlas/dicom/IMG_758_6WKI7ws.dcm",
+    "https://www.penracourses.org.uk/media/atlas/dicom/IMG_767_TduVOb8.dcm",
+    "https://www.penracourses.org.uk/media/atlas/dicom/IMG_775_7zWneQ0.dcm",
+    "https://www.penracourses.org.uk/media/atlas/dicom/IMG_759_BtKzgS5.dcm",
+    "https://www.penracourses.org.uk/media/atlas/dicom/IMG_768_RdvtM8K.dcm",
+    "https://www.penracourses.org.uk/media/atlas/dicom/IMG_776_LhVY3Ty.dcm",
+    "https://www.penracourses.org.uk/media/atlas/dicom/IMG_760_a8CiR4J.dcm",
+    "https://www.penracourses.org.uk/media/atlas/dicom/IMG_769_YHyJ1l6.dcm",
+    "https://www.penracourses.org.uk/media/atlas/dicom/IMG_777_8IFYJmL.dcm",
+    "https://www.penracourses.org.uk/media/atlas/dicom/IMG_761_vyvO1EN.dcm",
+    "https://www.penracourses.org.uk/media/atlas/dicom/IMG_770_vQwi4LW.dcm",
+    "https://www.penracourses.org.uk/media/atlas/dicom/IMG_778_BwGAMOR.dcm",
+    "https://www.penracourses.org.uk/media/atlas/dicom/IMG_762_DhSgQsm.dcm",
+    "https://www.penracourses.org.uk/media/atlas/dicom/IMG_771_xifitCl.dcm",
+    "https://www.penracourses.org.uk/media/atlas/dicom/IMG_779_LyA1zYn.dcm",
+    "https://www.penracourses.org.uk/media/atlas/dicom/IMG_763_aVjff3H.dcm",
+    "https://www.penracourses.org.uk/media/atlas/dicom/IMG_772_cDQZtxQ.dcm",
+    "https://www.penracourses.org.uk/media/atlas/dicom/IMG_780_qaZqsqg.dcm",
+    "https://www.penracourses.org.uk/media/atlas/dicom/IMG_764_dDoeldL.dcm",
+    "https://www.penracourses.org.uk/media/atlas/dicom/IMG_773_93Hvedg.dcm",
+    "https://www.penracourses.org.uk/media/atlas/dicom/IMG_781_bEx9Owg.dcm",
+    "https://www.penracourses.org.uk/media/atlas/dicom/IMG_765_qmd5mYJ.dcm"
+  ];
+  const wadouriList = urls.map(url => "wadouri:" + url);
+  if (window.loadDicomStackFromWadouriList) {
+    window.loadDicomStackFromWadouriList(wadouriList);
+  } else {
+    alert("Viewer API not ready");
+  }
+}
+</script>
+
+  </body>
+</html>

atlas/templates/atlas/seriesfinding_migration_status.html

@@ -0,0 +1,47 @@
+{% extends 'atlas/base.html' %}
+
+{% block content %}
+
+<h2>SeriesFinding Migration Status</h2>
+<table class="table table-bordered table-sm">
+    <thead>
+        <tr>
+            <th>ID</th>
+            <th>Description</th>
+            <th>Series</th>
+            <th>annotation_json_3d</th>
+            <th>viewer_state_3d</th>
+        </tr>
+    </thead>
+    <tbody>
+        {% for f in findings_status %}
+        <tr>
+            <td>{{ f.id }}</td>
+            <td>{{ f.str }}</td>
+            <td>
+                {% if f.series %}
+                    <a href="{% url 'atlas:series_detail' f.series.pk %}">{{ f.series }}</a>
+                {% else %}
+                    <span class="text-muted">None</span>
+                {% endif %}
+            </td>
+            <td>
+                {% if f.annotation_json_3d %}
+                    <span class="badge bg-success">Populated</span>
+                {% else %}
+                    <span class="badge bg-danger">Empty</span>
+                {% endif %}
+            </td>
+            <td>
+                {% if f.viewer_state_3d %}
+                    <span class="badge bg-success">Populated</span>
+                {% else %}
+                    <span class="badge bg-danger">Empty</span>
+                {% endif %}
+            </td>
+        </tr>
+        {% endfor %}
+    </tbody>
+</table>
+    
+{% endblock content %}

atlas/urls.py

@@ -266,6 +266,8 @@ urlpatterns = [
     ),
     path('series/<int:series_pk>/add-to-case/', views.add_series_to_case, name='add_series_to_case'),
     path('series/<int:series_pk>/<int:case_pk>/remove-from-case/', views.remove_series_from_case, name='remove_series_from_case'),
+    path('series_finding/<int:finding_id>/details/', views.series_finding_details, name='series_finding_details'),
+    path('series_finding/migration-status/', views.seriesfinding_migration_status, name='seriesfinding_migration_status'),
     path("uncategorised_dicoms/", views.uncategorised_dicoms, name="uncategorised_dicoms_view"),
     path("question_schema/", views.QuestionSchemaView.as_view(), name="question_schema_overview"),
     path("question_schema/<int:pk>", views.question_schema_detail, name="question_schema_detail"),
@@ -297,7 +299,6 @@ urlpatterns = [
     ),
     path("condition/create", views.ConditionCreate.as_view(), name="condition_create"),
     path("finding/", views.FindingView.as_view(), name="finding_view"),
-    path('series_finding/<int:finding_id>/details/', views.series_finding_details, name='series_finding_details'),
     path("finding/<int:pk>", views.finding_detail, name="finding_detail"),
     path(
         "finding/<int:pk>/delete", views.FindingDelete.as_view(), name="finding_delete"
@@ -323,6 +324,7 @@ urlpatterns = [
     path("series/<int:pk>/thumbnail", views.series_thumbnail, name="series_thumbnail"),
     # TODO: case context series viewing (so that we can view series in the context of a case)
     path("series/<int:pk>", views.series_detail, name="series_detail"),
+    path("series/<int:pk>/viewer", views.series_viewer, name="series_viewer"),
     path("series/<int:pk>/authors", views.SeriesAuthorUpdate.as_view(), name="series_authors"),
     path("series/<int:series_id>/finding/related", views.series_finding_related, name="series_finding_related"),
     path("series/", views.SeriesView.as_view(), name="series_view"),

atlas/views.py

@@ -231,6 +231,19 @@ def series_thumbnail(request, pk, fail_loudly=False):
 
     return HttpResponse(thumbnail)
 
+@login_required
+@user_is_author_or_atlas_series_checker_or_atlas_marker_or_open_access
+def series_viewer(request, pk, finding_pk=None):
+    series = get_object_or_404(Series, pk=pk)
+    context = {
+            "series": series,
+    }
+
+    return render(
+        request,
+        "atlas/series_viewer_test.html",
+        context,
+    )
 
 @login_required
 @user_is_author_or_atlas_series_checker_or_atlas_marker_or_open_access
@@ -1440,6 +1453,8 @@ def create_series_findings(request):
         annotation_json = request.POST.get("annotation_json")
         viewport_json = request.POST.get("viewport_json")
         current_image_id_index = request.POST.get("current_image_id_index")
+        annotation_json_3d = request.POST.get("annotation_json_3d")
+        viewer_state_3d = request.POST.get("viewer_state_3d")
 
         series = Series.objects.get(pk=series_id)
         findings = Finding.objects.filter(pk__in=findings_ids)
@@ -1464,6 +1479,8 @@ def create_series_findings(request):
         sf.structures.set(structures)
         sf.conditions.set(conditions)
         sf.current_image_id_index = current_image_id_index
+        sf.annotation_json_3d = annotation_json_3d
+        sf.viewer_state_3d = viewer_state_3d
         sf.save()
         return JsonResponse({"success": True})
 
@@ -3146,3 +3163,22 @@ def series_finding_related(request, series_id):
     series = get_object_or_404(Series, pk=series_id)
     findings = series.get_related_findings()
     return render(request, 'atlas/series_finding_related.html', {'series': series, 'findings': findings})
+
+def seriesfinding_migration_status(request):
+    """
+    View to list all SeriesFinding objects and their migration status.
+    Shows whether annotation_json_3d and viewer_state_3d are populated.
+    """
+    findings = SeriesFinding.objects.all().select_related()
+    findings_status = []
+    for finding in findings:
+        findings_status.append({
+            "id": finding.id,
+            "str": str(finding),
+            "annotation_json_3d": bool(finding.annotation_json_3d),
+            "viewer_state_3d": bool(finding.viewer_state_3d),
+            "series": finding.series
+        })
+    return render(request, "atlas/seriesfinding_migration_status.html", {
+        "findings_status": findings_status
+    })

generic/models.py

@@ -1998,6 +1998,9 @@ class FindingBase(models.Model):
     # This has been migrated to install the image id (not index)
     current_image_id_index = models.TextField(null=True, blank=True)
 
+    annotation_json_3d = models.JSONField(default=dict)
+    viewer_state_3d = models.JSONField(default=dict)
+
     # TODO add tags
     # tags = models.ManyToManyField(Tag, blank=True)
 

rad/static/dv3d/assets/index-BNYRLLy7.css

@@ -0,0 +1 @@
+html,body,#root{width:100vw;height:100vh;margin:0;padding:0;overflow:hidden;box-sizing:border-box}.dicom-viewer-root,#root{width:100vw;height:100vh;min-height:0;min-width:0;position:relative}.dicom-viewer-test-root{box-sizing:border-box;color:gray;display:block;font-family:system-ui,-apple-system,Segoe UI,Roboto,Helvetica Neue,Arial,Noto Sans,Liberation Sans,sans-serif,"Apple Color Emoji","Segoe UI Emoji",Segoe UI Symbol,"Noto Color Emoji";font-size:16px;font-weight:400;height:500px;line-height:24px;max-height:500px;overflow-x:auto;overflow-y:auto;text-align:start;text-size-adjust:100%;unicode-bidi:isolate;width:1296px;-webkit-tap-highlight-color:rgba(0,0,0,0)}.cornerstone-viewport,.cornerstone-canvas{cursor:inherit!important}

shorts/migrations/0009_questionfinding_annotation_json_3d_and_more.py

@@ -0,0 +1,23 @@
+# Generated by Django 5.1.4 on 2025-06-09 10:05
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('shorts', '0008_useranswer_candidate_feedback_answermarks'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='questionfinding',
+            name='annotation_json_3d',
+            field=models.JSONField(default=dict),
+        ),
+        migrations.AddField(
+            model_name='questionfinding',
+            name='viewer_state_3d',
+            field=models.JSONField(default=dict),
+        ),
+    ]

templates/base.html

@@ -70,6 +70,8 @@
         <script src="{% static 'js/cornerstone/cornerstoneWADOImageLoader.min.js' %}"></script>
         <script src="{% static 'js/cornerstone/cornerstone-base64-image-loader.umd.js' %}"></script>
         <script src="{% static 'js/anatomy.js' %}" defer="defer" type="module"></script>
+        <script src="{% static 'dv3d/index-DwrZLsZY.js' %}" type="module" defer="defer" type="module"></script>
+
         {% block js %}
         {% endblock %}
         <link rel="stylesheet" href="{% static 'css/anatomy.css' %}">