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

@@ -555,6 +555,14 @@ class SeriesImage(SeriesImageBase):
         help_text="Reference to the object that has replaced this one.",
     )
 
+    def get_file_size(self):
+        try:
+            return self.image.size
+
+        # We catch this for when the image does not exist
+        except FileNotFoundError:
+            return 0
+
     def get_dicom_data(self):
         try:
             with pydicom.dcmread(self.image) as d:
@@ -562,6 +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:
@@ -586,6 +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")
@@ -1066,6 +1078,13 @@ class CaseDetail(models.Model):
         """Returns the correct question answers as a json string"""
         return json.dumps(self.question_answers)
 
+    def get_user_answers(self, user):
+        """Returns the users answers as a json string"""
+        try:
+            return UserReportAnswer.objects.get(question=self, user=user)
+        except UserReportAnswer.DoesNotExist:
+            return None
+
 class CasePrior(models.Model):
     case_detail = models.ForeignKey(CaseDetail, on_delete=models.CASCADE)
     prior_case = models.ForeignKey(Case, on_delete=models.CASCADE, related_name="prior_case")
@@ -1258,9 +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():
@@ -1295,7 +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":
@@ -1334,9 +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/collection_headers.html

@@ -1,5 +1,6 @@
 {% if request.user.is_authenticated %}
     <br/>Collection: {{collection.name}}-> <a href="{% url 'atlas:collection_detail' pk=collection.pk %}">Overview</a> /
+    <a href="{% url 'atlas:collection_history' collection.pk %}">History</a> /
     <a href="{% url 'atlas:collection_mark_overview' collection.pk %}">Mark</a> /
     <a href="{% url 'atlas:collection_scores_cid' collection.pk %}">Scores</a> /
     <a href="{% url 'atlas:exam_cids' collection.pk %}">Candidates</a> /

atlas/templates/atlas/collection_history.html

@@ -0,0 +1,20 @@
+{% extends 'atlas/exams.html' %}
+
+{% block content %}
+    <h2>{{collection.name}}</h2>
+
+    <h3>Users</h3>
+
+    <ul>
+        {% for userexam in userexams %}
+            <li>
+                <b><a href="{% url 'atlas:collection_history_user' collection.pk userexam.user_user.pk %}">{{userexam.get_user_name}}</a><b><br/>
+                Completed: {{userexam.completed}}<br/>
+                Started: {{userexam.start_time}}, Ended: {{userexam.end_time}}<br/>
+
+            </li>
+        {% endfor %}
+    </ul>
+
+
+{% endblock %}

atlas/templates/atlas/collection_history_user.html

@@ -0,0 +1,87 @@
+{% extends 'atlas/exams.html' %}
+
+{% block content %}
+    <h2>Collection: {{collection.name}}</h2>
+
+    <h3>User: {{user}}</h3>
+
+    <ul>
+        {% for casedetail, user_answer in user_answers %}
+            <li class="case">
+
+                <h4>{{forloop.counter}} / Case: {{casedetail.case.title}}</h4>
+                {% if not user_answer %}
+                    <span class="case-not-answered">Case not answered.</span>
+                {% else %}
+                    <div class="answer-block">
+                        {% for value, user_answer, correct_answer, answer_is_correct, automark in user_answer.get_correct_json_answers %}
+                            {% if not user_answer %}
+                                Not answered
+                            {% else %}
+                                <div class="{% if answer_is_correct %}
+                                                correct
+                                            {% else %}
+                                                incorrect
+                                            {% endif %}
+                                            {% if automark %}
+                                                automark
+                                            {% endif %}
+
+                                           ">
+                                    <h5>{{value.title}}</h5>
+                                    {{value.description}}
+                                    <div
+                                    >
+                                        Answer : {{user_answer}}
+
+                                        {% if not answer_is_correct %}
+                                            <br/>Correct answer: {{correct_answer}}
+                                        {% endif %}
+
+                                    </div>
+                                </div>
+                            {% endif %}
+
+                        {% endfor %}
+                    </div>
+                {% endif %}
+
+            </li>
+        {% endfor %}
+    </ul>
+
+
+{% endblock %}
+
+{% block css %}
+    {{ block.super }}
+    <style>
+        .correct {
+        }
+
+        .correct h5::after {
+            content: '✓';
+            color: green;
+        }
+
+        .incorrect h5::after {
+            content: '✗';
+            color: orange;
+        }
+
+        .incorrect.automark h5::after {
+            content: '✗';
+            color: red;
+        }
+
+        .answer-block>div {
+            padding-bottom: 10px;
+        }
+
+        .case:has(.case-not-answered) {
+            opacity: 0.5;
+        }
+
+
+    </style>
+{% endblock %}

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>
 
@@ -102,7 +112,7 @@
 
 
             {% if image.image %}
-                [{{image.image.size|filesizeformat}}]
+                [{{image.get_file_size|filesizeformat}}]
             {% endif %}
 
             {{image.image_md5_hash}} ({{image.is_dicom}}) {{image.image_blake3_hash}}
@@ -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/urls.py

@@ -85,6 +85,17 @@ urlpatterns = [
         views.GenericExamViews.exam_cids,
         name="exam_cids",
     ),
+    path(
+        "collection/<int:exam_id>/history",
+        views.collection_history,
+        name="collection_history",
+    ),
+    path(
+        "collection/<int:exam_id>/history/<int:user_pk>/user",
+        views.collection_history_user,
+        name="collection_history_user",
+    ),
+
     path(
         "collection/<int:pk>/user_status",
         views.GenericExamViews.exam_user_status,

atlas/views.py

@@ -246,6 +246,7 @@ def question_schema_detail(request, pk: int):
         {"question_schema": question_schema, "example_form": example_form},
     )
 
+
 @login_required
 # @user_is_atlas_editor
 def question_schema_schemas(request):
@@ -259,6 +260,7 @@ def question_schema_schemas(request):
         },
     )
 
+
 @login_required
 # @user_is_atlas_editor
 def condition_detail(request, pk):
@@ -857,14 +859,17 @@ class QuestionSchemaCreate(LoginRequiredMixin, CreateView):
     model = QuestionSchema
     form_class = QuestionSchemaForm
 
+
 class QuestionSchemaUpdate(LoginRequiredMixin, UpdateView):
     model = QuestionSchema
     form_class = QuestionSchemaForm
 
+
 class QuestionSchemaDelete(AuthorOrCheckerRequiredMixin, DeleteView):
     model = QuestionSchema
     template_name = "confirm_delete.html"
 
+
 class FindingUpdate(RevisionMixin, LoginRequiredMixin, UpdateView):
     model = Finding
     form_class = FindingForm
@@ -1272,7 +1277,6 @@ def series_order_dicom(request, pk):
 @login_required
 def image_diff(request):
     if request.htmx:
-
         image_ids = request.POST.getlist("image-id")
 
         if len(image_ids) == 2:
@@ -1381,6 +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)
@@ -1404,6 +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})
 
@@ -1596,6 +1602,58 @@ def collection_detail(request, pk):
     )
 
 
+@user_is_collection_author_or_atlas_editor
+def collection_history(request, exam_id: int):
+    """An overview page that shows who has attempted / finised the collection"""
+    collection = get_object_or_404(CaseCollection, pk=exam_id)
+
+    casedetails = CaseDetail.objects.filter(collection=collection).order_by(
+        "sort_order"
+    )
+
+    userexams = collection.get_cid_user_exams()
+
+    print(userexams)
+
+    return render(
+        request,
+        "atlas/collection_history.html",
+        {
+            "collection": collection,
+            "casesdetails": casedetails,
+            "can_edit": True,
+            "userexams": userexams,
+        },
+    )
+
+
+@user_is_collection_author_or_atlas_editor
+def collection_history_user(request, exam_id: int, user_pk: int):
+    collection = get_object_or_404(CaseCollection, pk=exam_id)
+
+    user = get_object_or_404(User, pk=user_pk)
+
+    casedetails = CaseDetail.objects.filter(
+        collection=collection,
+    ).order_by("sort_order")
+
+    print(user)
+    print(casedetails)
+
+    user_answers = [(casedetail, casedetail.get_user_answers(user)) for casedetail in casedetails]
+
+    return render(
+        request,
+        "atlas/collection_history_user.html",
+        {
+            "collection": collection,
+            "user": user,
+            "casedetails": casedetails,
+            "user_answers": user_answers,
+        },
+    )
+
+
 def collection_take_start(request, pk):
     """The starting page for taking / reviewing a case collection
 
@@ -1630,23 +1688,29 @@ def collection_take_start(request, pk):
                 request, "atlas/collection_review_start.html", template_variables
             )
 
+
 @user_is_collection_author_or_atlas_editor
 def collection_case_priors(request, exam_id, case_id):
     case_detail = CaseDetail.objects.get(case=case_id, collection=exam_id)
 
-
     if request.htmx:
         if "remove" in request.POST:
-            p = CasePrior.objects.get(case_detail=case_detail, prior_case=request.POST["remove"])
+            p = CasePrior.objects.get(
+                case_detail=case_detail, prior_case=request.POST["remove"]
+            )
             p.delete()
             return HttpResponse(f"Case removed")
         elif "prior_case_id" in request.POST:
             prior_case = Case.objects.get(pk=request.POST["prior_case_id"])
-            p, created = CasePrior.objects.get_or_create(case_detail=case_detail, prior_case=prior_case)
+            p, created = CasePrior.objects.get_or_create(
-            p.relation_text=request.POST["relation"]
+                case_detail=case_detail, prior_case=prior_case
+            )
+            p.relation_text = request.POST["relation"]
 
             if not p.relation_text:
-                return HttpResponse("You need to enter text to describe the relationship between the cases")
+                return HttpResponse(
+                    "You need to enter text to describe the relationship between the cases"
+                )
 
             p.save()
 
@@ -1674,7 +1738,6 @@ def collection_case_priors(request, exam_id, case_id):
         else:
             available_priors.append((case, False, ""))
 
-
     form = PriorCaseForm()
 
     case_number, case_count = collection.get_index_of_case(
@@ -1684,14 +1747,13 @@ def collection_case_priors(request, exam_id, case_id):
     previous = collection.get_previous_case(case_detail.case)
     next = collection.get_next_case(case_detail.case)
 
-
     return render(
         request,
         "atlas/collection_case_priors.html",
         {
             "case_detail": case_detail,
             "form": form,
-            #"example_form": example_form,
+            # "example_form": example_form,
             "collection": collection,
             "case": case_detail.case,
             "previous": previous,
@@ -1703,6 +1765,7 @@ def collection_case_priors(request, exam_id, case_id):
         },
     )
 
+
 @user_is_collection_author_or_atlas_editor
 def collection_case_details(request, exam_id, case_id):
     case_detail = CaseDetail.objects.get(case=case_id, collection=exam_id)
@@ -1713,7 +1776,6 @@ def collection_case_details(request, exam_id, case_id):
         raise Http404("Collection not in question mode")
 
     if request.method == "POST":
-
         # Called if the user saves the correct answer form
         if request.POST.get("submit") == "answer":
             # answers = request.POST
@@ -1986,7 +2048,9 @@ def collection_take_overview(
             cid_user_exam.save()
 
             collection.exam_user_status.create(
-                cid_user_exam=cid_user_exam, status="submitted", extra="manual submission"
+                cid_user_exam=cid_user_exam,
+                status="submitted",
+                extra="manual submission",
             )
 
             return HttpResponse("True")
@@ -2012,7 +2076,9 @@ def collection_take_overview(
     answer_count = 0
     for cd in case_details:
         self_review = cid_user_exam.selfreview_set.filter(case=cd.case)
-        if cd in answer_question_map and (answer_question_map[cd].answer or answer_question_map[cd].json_answer):
+        if cd in answer_question_map and (
+            answer_question_map[cd].answer or answer_question_map[cd].json_answer
+        ):
             question_answer_tuples.append((cd, answer_question_map[cd], self_review))
             answer_count += 1
         else:
@@ -2192,8 +2258,6 @@ def collection_case_view_take(
         for series in prior.prior_case.get_series():
             series_to_load.append((series, True, prior.relation_text))
 
-        
-
     previous = case_number > 0
     next = case_number < (case_count - 1)
 
@@ -2317,6 +2381,7 @@ def use_dates_as_descriptions(request, pk):
 
     return HttpResponse("Done")
 
+
 def collection_case_dicom_json(request, exam_id, case_id):
     case_detail = CaseDetail.objects.get(case=case_id, collection=exam_id)
 
@@ -2715,6 +2780,7 @@ class CaseCollectionAuthorUpdate(RevisionMixin, AuthorRequiredMixin, UpdateView)
         context["collection"] = context["object"]
         return context
 
+
 class ExamGroupsUpdate(ExamGroupsUpdateBase):
     model = CaseCollection
     form_class = ExamGroupsForm
@@ -2819,6 +2885,7 @@ def collection_question_schemas(request, exam_id: int):
         },
     )
 
+
 def collection_reset_answers(request, exam_id: int):
     if request.htmx:
         collection = get_object_or_404(CaseCollection, pk=exam_id)
@@ -2834,7 +2901,6 @@ def collection_reset_answers(request, exam_id: int):
             user_answers = case.userreportanswer_set.all()
             user_answers.delete()
 
-        
         # User statuses
         collection.exam_user_status.all().delete()
 
@@ -2842,6 +2908,5 @@ def collection_reset_answers(request, exam_id: int):
         collection.cid_users.all().delete()
         return HttpResponse("Success")
 
-
     else:
         raise Http404("Invalid request")

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),
+        ),
+    ]

generic/models.py

@@ -531,7 +531,7 @@ class SeriesBase(models.Model):
         size = 0
 
         for i in images:
-            size += i.image.size
+            size += i.get_file_size()
 
         return size
 
@@ -997,7 +997,6 @@ class ExamBase(ExamOrCollectionGenericBase):
 
         return User.objects.filter(pk__in=user_ids)
 
-
     def generate_user_report(self, user):
         exam_text = [f"Candidate {user.first_name} [{user.email}]"]
 
@@ -1478,6 +1477,12 @@ class CidUserExam(models.Model):
 
         return f"{self.exam} / {user}: {start_time} {end_time}"
 
+    def get_user_name(self) -> str:
+        if self.cid_user is None:
+            return self.user_user.username
+        else:
+            return "CID" + str(self.cid_user.cid)
+
 
 CID_GROUP_EXAMS = (
     ("SBAs", "sba_cid_user_groups"),
@@ -1504,7 +1509,6 @@ class BaseUserGroup(models.Model):
 
 
 class CidUserGroup(BaseUserGroup):
-
     def __str__(self) -> str:
         return str(self.name)
 

rad/views.py

@@ -747,7 +747,7 @@ def accounts_bulk_create_check(request):
         supervisor = Supervisor.objects.filter(email=user["supervisor_email"])
 
         if not supervisor:
-            return HttpResponse("Ok, supervisor will be created")
+            return HttpResponse("Ok, supervisor does not exist so will be created")
 
         if supervisor.count() > 1:
             return HttpResponse(format_html("<span class='error'>{}</span>", "More than one supervisor with that email"))
@@ -793,7 +793,7 @@ def accounts_bulk_create(request):
                         print(user)
                         user_dict = {
                             "username": user["email"],
-                            "first_name": user["email"],
+                            "first_name": user["first_name"],
                             "last_name": user["last_name"],
                             "email": user["email"],
                             "password": secrets.token_hex(nbytes=16),