image findings will now save and reload stack index

atlas/api.py

@@ -29,7 +29,6 @@ from loguru import logger
 router = Router()
 
 
-
 class SeriesSchema(ModelSchema):
     case_id: List[int] = []
 
@@ -59,6 +58,7 @@ def upload_dicom(request, files: List[UploadedFile] = File(...)):
     uploaded = []
     duplicate = []
     failed = []
+    duplicate_series = set()
     for file in files:
         # data = file.read()
         try:
@@ -67,26 +67,41 @@ def upload_dicom(request, files: List[UploadedFile] = File(...)):
             ud.save()
 
             uploaded.append((file.name, ud.image_blake3_hash))
-        except DuplicateDicom:
+        except DuplicateDicom as e:
             duplicate.append((file.name, ud.image_blake3_hash))
+
+            duplicate_series.add(e.duplicate.get_series().get_absolute_url())
+            print(duplicate_series)
             pass
         except InvalidDicomError:
             failed.append(file.name)
 
-    return {"uploaded": uploaded, "duplicates": duplicate, "failed": failed}
+    return {
+        "uploaded": uploaded,
+        "duplicates": duplicate,
+        "failed": failed,
+        "duplicate_series": list(duplicate_series),
+    }
+
 
 @router.post("/generate_image_hash", auth=django_auth)
-def generate_image_hash(request, id:int):
+def generate_image_hash(request, id: int):
     s = SeriesImage.objects.get(pk=id)
     s.generate_hashes()
 
-    return {"md5": s.image_md5_hash, "blake3": s.image_blake3_hash, "is_dicom": s.is_dicom}
+    return {
+        "md5": s.image_md5_hash,
+        "blake3": s.image_blake3_hash,
+        "is_dicom": s.is_dicom,
+    }
+
 
 @router.post("/clear_dicoms", auth=django_auth)
 def clear_dicoms(request):
-
     if "selection" in request.POST:
-        dicoms = UncategorisedDicom.objects.filter(series_instance_uid__in=request.POST.getlist("selection"))
+        dicoms = UncategorisedDicom.objects.filter(
+            series_instance_uid__in=request.POST.getlist("selection")
+        )
 
     else:
         dicoms = UncategorisedDicom.objects.filter(user=request.user)
@@ -110,15 +125,17 @@ def uncategorised_dicoms(request):
 
     return data
 
+
 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"))
+        dicoms = UncategorisedDicom.objects.filter(
+            series_instance_uid__in=request.POST.getlist("selection")
+        )
 
     else:
         dicoms = UncategorisedDicom.objects.filter(user=request.user)
 
-    
     if "order-series" in request.POST:
         order = request.POST["order-series"]
     else:
@@ -136,7 +153,9 @@ def import_dicoms_helper(request, case_id: int | None = None):
         tags = data[series_uid][0][1]
 
         # Check if series with the id already exists (in which case we just add to htat)
-        if Series.objects.filter(series_instance_uid=tags["SeriesInstanceUID"]).exists():
+        if Series.objects.filter(
+            series_instance_uid=tags["SeriesInstanceUID"]
+        ).exists():
             series = Series.objects.get(series_instance_uid=tags["SeriesInstanceUID"])
         else:
             series = Series(
@@ -146,16 +165,16 @@ def import_dicoms_helper(request, case_id: int | None = None):
             )
 
             if tags["StudyDescription"]:
-                examination, created = Examination.objects.get_or_create(examination=tags["StudyDescription"])
+                examination, created = Examination.objects.get_or_create(
+                    examination=tags["StudyDescription"]
+                )
                 if created:
                     examination.modality = modality
                     examination.save()
                 series.examination = examination
 
-
             series.save()
 
-
             match order:
                 case "order-series-instance-number":
                     series.order_by_dicom("InstanceNumber")
@@ -188,12 +207,18 @@ def import_dicoms_helper(request, case_id: int | None = None):
     return series_list
 
 
-@router.post("/import_dicoms", auth=django_auth, response=List[Tuple[ SeriesSchema, str ]])
+@router.post(
+    "/import_dicoms", auth=django_auth, response=List[Tuple[SeriesSchema, str]]
+)
 def import_dicoms(request):
     return import_dicoms_helper(request)
 
 
-@router.post("/import_dicoms/{case_id}", auth=django_auth, response=List[Tuple[ SeriesSchema, str ]])
+@router.post(
+    "/import_dicoms/{case_id}",
+    auth=django_auth,
+    response=List[Tuple[SeriesSchema, str]],
+)
 def import_dicoms_case(request, case_id: int):
     return import_dicoms_helper(request, case_id=case_id)
 
@@ -220,8 +245,9 @@ def series_remove_duplicate_images(request, series_id: int):
 
     return len(dupes)
 
+
 @router.get("/series_truncate/{series_id}/{start}/{end}/", auth=django_auth)
-def series_truncate(request, series_id: int, start: int, end:int):
+def series_truncate(request, series_id: int, start: int, end: int):
     print(start, end)
     series = get_object_or_404(Series, pk=series_id)
 
@@ -230,11 +256,11 @@ def series_truncate(request, series_id: int, start: int, end:int):
 
     images_removed = []
     for n, image in enumerate(series.get_images()):
-        if n >= start and n <=end:
+        if n >= start and n <= end:
             continue
         else:
             print(n, image)
-            image.removed=True
+            image.removed = True
             image.image = None
             image.save()
             images_removed.append(image.pk)
@@ -261,6 +287,7 @@ def check_image_hash(request, hash: str):
         data = {"status": "success", "id": False}
         return data
 
+
 @router.post("/check_image_hashes/", auth=django_auth)
 def check_images_hashes(request, hashes: List[str]):
     """Checks a list of image hashes and returns the series id / url if found
@@ -278,21 +305,28 @@ def check_images_hashes(request, hashes: List[str]):
             data = {
                 "id": series_image.pk,
                 "url": series_image.series.get_absolute_url(),
-                "type": "series"
+                "type": "series",
             }
         except SeriesImage.DoesNotExist:
             try:
-                uncategorised_dicom = UncategorisedDicom.objects.get(image_blake3_hash=hash)
+                uncategorised_dicom = UncategorisedDicom.objects.get(
-                data = { "id":uncategorised_dicom.pk, "url": reverse("atlas:user_uploads"), "type": "uncategorised"}
+                    image_blake3_hash=hash
+                )
+                data = {
+                    "id": uncategorised_dicom.pk,
+                    "url": reverse("atlas:user_uploads"),
+                    "type": "uncategorised",
+                }
             except UncategorisedDicom.DoesNotExist:
-                data = { "id": False, "url": False}
+                data = {"id": False, "url": False}
 
         hash_status[hash] = data
 
     return hash_status
 
-#@router.get("/generate_image_hash/{id}", auth=django_auth)
+
-#def generate_image_hash(request, id: int):
+# @router.get("/generate_image_hash/{id}", auth=django_auth)
+# def generate_image_hash(request, id: int):
 #        series_image = SeriesImage.objects.get(pk=id)
 #
 #        series_image.image_blake3_hash = ""
@@ -301,21 +335,22 @@ def check_images_hashes(request, hashes: List[str]):
 #
 #        print(series_image)
 
+
 @router.get("/view_dicom_tags/{hash}", auth=django_auth)
 def view_dicom_tags(request, hash: str):
-
     item = SeriesImage.objects.get(image_blake3_hash=hash)
     return item.get_dicom_json()
 
+
 @router.get("/series_split_by_dicom_tag/{series_id}/{dicom_tag}", auth=django_auth)
-def series_split_by_tag(request, series_id: int, dicom_tag:str):
+def series_split_by_tag(request, series_id: int, dicom_tag: str):
     series = get_object_or_404(Series, pk=series_id)
 
     if not series.check_user_can_edit(request.user):
         return {"status": "permission denied"}
 
     if dicom_tag.startswith("(") and dicom_tag.endswith(")"):
-        dicom_tag = tuple([hex(int(i.strip(),16)) for i in dicom_tag[1:-1].split(",")])
+        dicom_tag = tuple([hex(int(i.strip(), 16)) for i in dicom_tag[1:-1].split(",")])
 
     image_map = defaultdict(list)
 
@@ -324,7 +359,7 @@ def series_split_by_tag(request, series_id: int, dicom_tag:str):
         print(image)
         ds = image.get_dicom_data()
 
-        #print("2a", ds[dicom_tag])
+        # print("2a", ds[dicom_tag])
 
         if dicom_tag in ds:
             val = ds[dicom_tag].value
@@ -353,12 +388,11 @@ def series_split_by_tag(request, series_id: int, dicom_tag:str):
 
         new_series.append(series.pk)
 
-
     return new_series
 
 
 @router.get("/split_order_by_dicom_tag/{series_id}/{dicom_tag}", auth=django_auth)
-def series_order_by_tag(request, series_id: int, dicom_tag:str):
+def series_order_by_tag(request, series_id: int, dicom_tag: str):
     series = get_object_or_404(Series, pk=series_id)
 
     series.order_by_dicom(dicom_tag)

atlas/forms.py

@@ -143,7 +143,7 @@ class StructureForm(ModelForm):
 class SeriesFindingForm(ModelForm):
     class Meta:
         model = SeriesFinding
-        exclude = ["series", "annotation_json", "viewport_json"]
+        exclude = ["series", "annotation_json", "viewport_json", "current_image_id_index"]
 
         widgets = {
             "findings": autocomplete.ModelSelect2Multiple(

atlas/migrations/0060_seriesfinding_current_image_id_index.py

@@ -0,0 +1,18 @@
+# Generated by Django 5.0.2 on 2024-09-23 12:45
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0059_alter_casecollection_markers'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='seriesfinding',
+            name='current_image_id_index',
+            field=models.IntegerField(blank=True, null=True),
+        ),
+    ]

atlas/models.py

@@ -570,6 +570,9 @@ class SeriesImage(SeriesImageBase):
         except InvalidDicomError:
             return {}
 
+    def get_series(self):
+        return self.series
+
     # def get_image_dicom_json(self, image_index):
     #    try:
     #        with pydicom.dcmread(self.image) as ds:
@@ -594,6 +597,7 @@ class SeriesFinding(models.Model):
     conditions = models.ManyToManyField(Condition, blank=True)
     annotation_json = models.TextField(null=True, blank=True)
     viewport_json = models.TextField(null=True, blank=True)
+    current_image_id_index = models.IntegerField(null=True, blank=True)
 
     def __str__(self) -> str:
         findings = self.findings.all().values_list("name")
@@ -1273,9 +1277,12 @@ class UncategorisedDicom(models.Model):
 
     basic_dicom_tags = models.JSONField(null=True, blank=True)
 
-    def check_for_duplicates(self, image_hash):
+    def check_for_duplicates(self, image_hash=None|str):
         duplicate = None
 
+        if image_hash is None:
+            image_hash = self.image_blake3_hash
+
         if obj := UncategorisedDicom.objects.filter(
             image_blake3_hash=image_hash
         ).first():
@@ -1310,7 +1317,8 @@ class UncategorisedDicom(models.Model):
 
             if duplicate is not None:
                 if duplicate != self:
-                    raise DuplicateDicom
+                    raise DuplicateDicom(duplicate)
+
 
         # Hack for tests
         if image_blake3_hash != "1234":
@@ -1349,9 +1357,13 @@ class UncategorisedDicom(models.Model):
         except pydicom.errors.InvalidDicomError:
             return None
 
+    def get_series(self):
+        return self.series
+
 
 class DuplicateDicom(Exception):
-    pass
+    def __init__(self, duplicate):
+        self.duplicate = duplicate
 
 
 class Resource(models.Model, AuthorMixin):

atlas/templates/atlas/new_uploads.html

@@ -41,6 +41,7 @@
             <ul id="uploaded-files"></ul>
             <h5>Duplicates</h5>
             <ul id="duplicate-files"></ul>
+            <ul id="duplicate-series"></ul>
             <h5>Failed</h5>
             <ul id="failed-files"></ul>
         </div>
@@ -78,6 +79,7 @@
     <script>
         window.to_upload = [];
         window.upload_count = 1;
+        window.duplicate_series = new Set()
 
         function* chunks(arr, n) {
             for (let i = 0; i < arr.length; i += n) {
@@ -149,6 +151,7 @@
                             item.textContent = JSON.parse(xhr.response)["duplicates"][i];
                             $("#duplicate-files").append(item);
                         }
+                        window.duplicate_series.add(...JSON.parse(xhr.response)["duplicate_series"]);
 
                         for (let i = 0; i < JSON.parse(xhr.response)["failed"].length; i++) {
                             let item = document.createElement("li");
@@ -162,6 +165,14 @@
                     }
                     if (current_chunk + 1 == total_chunks) {
                         $("#loading").hide();
+
+                        window.duplicate_series.forEach((element) => {
+                            let item = document.createElement("a");
+                            item.href = element;
+                            item.textContent = element;
+                            $("#duplicate-series").append(item, "<br/>");
+                        });
+                        //$("#duplicate-series").append([...window.duplicate_series].join("<br/>"));  
                         alert("Uploading complete")
                     }
                 }

atlas/templates/atlas/series_viewer.html

@@ -1,3 +1,5 @@
+{% load crispy_forms_tags %}
+
 <div>{{ series.modality}}, {{ series.examination }}, {{ series.plane }}, {{ series.contrast }}</div>
 <div>Description: {{series.description}}</div>
 
@@ -22,13 +24,7 @@
         <div class="hide" id="hidden-form">
             <form method="post" id="series_finding_form">
                 {% csrf_token %}
-                {{series_finding_form.management_form}}
+                {{series_finding_form|crispy}}
-                <div>
-                    <div>Description: {{ series_finding_form.description }}</div>
-                    <div>Findings: {{ series_finding_form.findings }}</div>
-                    <div>Structures: {{ series_finding_form.structures }}</div>
-                    <div>Conditions: {{ series_finding_form.conditions }}</div>
-                </div>
                 <input type="submit" value="Submit">
                 <button id="cancel-add-finding-button">Cancel</button>
             </form>
@@ -45,14 +41,28 @@
         {% for finding in series.findings.all %}
             <div class="finding-box">
                 <button class="view-finding-button" data-annotationjson={{finding.annotation_json}}
-                        data-viewportjson={{finding.viewport_json}} data-findingid={{finding.id}}>Click to view</button>
+                        data-viewportjson={{finding.viewport_json}} data-findingid={{finding.id}} data-currentimageid={{finding.current_image_id_index}}>Click to view</button>
                 <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 />
                     Condition(s): {% for s in finding.conditions.all %}{{s.get_link}}{% endfor %}<br />
                     Description: {{finding.description}}<br />
+                    
+                {% if request.user.is_superuser %}
+                <span _="on click toggle .hidden on next .extra-details">+</span>    
+                <div class="hidden extra-details">
+                    <h4>Annotation JSON</h4>
+                    <pre>{{finding.annotation_json}}</pre>
+                    <h4>Viewport JSON</h4>
+                    <pre>{{finding.viewport_json}}</pre>
+                    <h4>Image ID</h4>
+                    <pre>{{finding.current_image_id_index}}</pre>
+                </div>
+                {% endif %}
                 </span>
                 <a href="{% url 'atlas:series_edit_finding' pk=series.pk finding_pk=finding.pk %}" class="edit-finding-link">Edit</a>
+                
+                    
                 <a href="{% url 'atlas:delete_finding' pk=finding.pk %}" class="delete-finding-link">Delete</a>
             </div>
 
@@ -195,6 +205,7 @@
         })
 
         $("#add-finding-button").click(() => {
+            $("#hidden-form").show()
             dicom_element = $(".cornerstone-element").get(0);
             cornerstoneTools.globalImageIdSpecificToolStateManager.clear(dicom_element);
             cornerstone.reset(dicom_element);
@@ -202,7 +213,6 @@
             //$("#finding-form").empty().append(
             //    $("#hidden-form form").clone()
             //);
-            $("#hidden-form").show()
 
         });
         $("#cancel-add-finding-button").click((e) => {
@@ -225,7 +235,9 @@
                 dicom_element = $(".cornerstone-element").get(0);
                 annotationjson = JSON.parse(e.currentTarget.dataset.annotationjson);
                 viewport = JSON.parse(e.currentTarget.dataset.viewportjson);
-                loadAnnotationAndViewportOnElement(annotationjson, viewport, dicom_element);
+                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);
 
 
             });
@@ -249,17 +261,26 @@
         {% endif %}
     });
 
-    function loadAnnotationAndViewportOnElement(annotation, viewport, dicom_element) {
+    function loadAnnotationAndViewportOnElement(annotation, viewport, dicom_element, current_image_id_index) {
         cornerstoneTools.globalImageIdSpecificToolStateManager.clear(dicom_element);
         cornerstone.getEnabledElement(dicom_element).viewport = viewport
         cornerstoneTools.globalImageIdSpecificToolStateManager.restoreToolState(
             annotation);
         console.log("annotation", annotation)
         console.log("viewport", viewport)
+
         //cornerstone.getEnabledElement(dicom_element).toolStateManager.restoreToolState(annotationjson)
         cornerstone.resize(dicom_element);
+        current_image_id_index = parseInt(current_image_id_index);
 
-        dicomViewer.getNextAnnotationImage(dicom_element);
+        console.log(current_image_id_index, Number.isInteger(current_image_id_index))
+        if (Number.isInteger(current_image_id_index)) {
+            console.log("loading stack index")
+            dicomViewer.loadStackIndex(current_image_id_index, dicom_element);
+        } else {
+            console.log("loading next annotation image")
+            dicomViewer.getNextAnnotationImage(dicom_element);
+        }
 
     }
 
@@ -276,6 +297,7 @@
                 description: $('#id_description').val(),
                 series: {{ series.pk }},
                 //annotation_json: JSON.stringify(c.toolStateManager.saveToolState()),
+                current_image_id_index: c.toolStateManager.toolState.stack.data[0].currentImageIdIndex,
                 annotation_json: JSON.stringify(cornerstoneTools.globalImageIdSpecificToolStateManager
                         .saveToolState()),
                 viewport_json: JSON.stringify(c.viewport),

atlas/views.py

@@ -1385,6 +1385,7 @@ def create_series_findings(request):
         description = request.POST.get("description")
         annotation_json = request.POST.get("annotation_json")
         viewport_json = request.POST.get("viewport_json")
+        current_image_id_index = int(request.POST.get("current_image_id_index"))
 
         series = Series.objects.get(pk=series_id)
         findings = Finding.objects.filter(pk__in=findings_ids)
@@ -1408,6 +1409,7 @@ def create_series_findings(request):
         sf.findings.set(findings)
         sf.structures.set(structures)
         sf.conditions.set(conditions)
+        sf.current_image_id_index = current_image_id_index
         sf.save()
         return JsonResponse({"success": True})
 

generic/migrations/0018_alter_supervisor_user.py

@@ -0,0 +1,21 @@
+# Generated by Django 5.0.2 on 2024-09-23 12:45
+
+import django.db.models.deletion
+from django.conf import settings
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('generic', '0017_cidusergroup_open_access_userusergroup_open_access_and_more'),
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='supervisor',
+            name='user',
+            field=models.OneToOneField(blank=True, help_text='If the supervisor has an account on the test system it can be associated here', null=True, on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL),
+        ),
+    ]