fix a number of things

atlas/forms.py

@@ -583,8 +583,10 @@ class SelfReviewForm(ModelForm):
         widgets = {"user_exam": HiddenInput(), "case": HiddenInput()}
 
     def __init__(self, *args, **kwargs):
-        user_exam_id = kwargs.pop("user_exam_id")
+        if "user_exam_id" in kwargs:
-        case_id = kwargs.pop("case_id")
+            user_exam_id = kwargs.pop("user_exam_id")
+        if "case_id" in kwargs:
+            case_id = kwargs.pop("case_id")
 
         ModelForm.__init__(self, *args, **kwargs)
         super(SelfReviewForm, self).__init__(*args, **kwargs)

atlas/migrations/0008_remove_case_scrapped_case_archive.py

@@ -0,0 +1,22 @@
+# Generated by Django 4.1.4 on 2023-08-07 08:14
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0007_selfreview'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='case',
+            name='scrapped',
+        ),
+        migrations.AddField(
+            model_name='case',
+            name='archive',
+            field=models.BooleanField(default=False, help_text='Case has been archived, this will remain on the system but will not be shown'),
+        ),
+    ]

atlas/models.py

@@ -13,6 +13,7 @@ from django.utils import timezone
 
 
 import pydicom
+import pydicom.multival
 
 from django.core.files.storage import FileSystemStorage
 from django.conf import settings
@@ -272,8 +273,9 @@ class Case(models.Model):
         related_name="atlas_edited_cases",
     )
 
-    scrapped = models.BooleanField(
+    archive = models.BooleanField(
-        default=False, help_text="Question has been scrapped and will not be shown"
+        default=False,
+        help_text="Case has been archived, this will remain on the system but will not be shown",
     )
 
     open_access = models.BooleanField(
@@ -325,6 +327,30 @@ class Case(models.Model):
         examinations = [series.get_examination() for series in self.series.all()]
         return f"{self.pk}:{self.title} {'/'.join([str(c) for c in self.condition.all()])} [{', '.join(examinations)}]"
 
+    def get_case_dicom_json(self):
+        series_json = []
+        for series in self.series.all():
+            series_json.append(series.get_series_dicom_json())
+
+            print(series_json)
+
+        return {
+            "studies": [
+                {
+                    "StudyInstanceUID": "1.3.6.1.4.1.14519.5.2.1.6279.6001.298806137288633453246975630178",
+                    "StudyDate": "20000101",
+                    "StudyTime": "",
+                    "PatientName": "",
+                    "PatientID": "LIDC-IDRI-0001",
+                    "AccessionNumber": "",
+                    "PatientAge": "",
+                    "PatientSex": "",
+                    "series": series_json,
+                }
+            ]
+        }
+        pass
+
 
 class SeriesImage(SeriesImageBase):
     image = models.FileField(upload_to=image_directory_path)
@@ -332,6 +358,50 @@ class SeriesImage(SeriesImageBase):
         "Series", related_name="images", on_delete=models.SET_NULL, null=True
     )
 
+    def get_image_dicom_json(self):
+        try:
+            with pydicom.dcmread(self.image) as ds:
+                to_keep = [
+                    "Columns",
+                    "Rows",
+                    "InstanceNumber",
+                    "SOPClassUID",
+                    "PhotometricInterpretation",
+                    "BitsAllocated",
+                    "BitsStored",
+                    "PixelRepresentation",
+                    "SamplesPerPixel",
+                    "PixelSpacing",
+                    "HighBit",
+                    "ImageOrientationPatient",
+                    "ImagePositionPatient",
+                    "FrameOfReferenceUID",
+                    "ImageType",
+                    "Modality",
+                    "SOPInstanceUID",
+                    "SeriesInstanceUID",
+                    "StudyInstanceUID",
+                    "WindowCenter",
+                    "WindowWidth",
+                    "SeriesDate",
+                ]
+
+                d = {}
+
+                for key in to_keep:
+                    val = ds[key].value
+
+                    if type(val) == pydicom.multival.MultiValue:
+                        d[key] = list(val)
+                    else:
+                        d[key] = val
+
+
+
+                return {"metadata": d, "url": self.image.url}
+        except FileNotFoundError:
+            return []
+
 
 class SeriesFinding(models.Model):
     series = models.ForeignKey(
@@ -411,6 +481,23 @@ class Series(SeriesBase):
             "<a href='{}'>{}</a>", self.get_absolute_url(), self.get_full_str()
         )
 
+    def get_series_dicom_json(self):
+        instances = []
+
+        image: SeriesImage
+        for image in self.images.all():
+            instances.append(image.get_image_dicom_json())
+
+        series_json = {
+            "SeriesInstanceUID": "1.3.6.1.4.1.14519.5.2.1.6279.6001.179049373636438705059720603192",
+            "SeriesNumber": 3000566,
+            "Modality": "CT",
+            "SliceThickness": 2.5,
+            "instances": instances,
+        }
+
+        return series_json
+
 
 class CaseCollection(ExamCollectionGenericBase):
     app_name = "atlas"
@@ -522,10 +609,14 @@ class CaseCollection(ExamCollectionGenericBase):
 
         return False
 
-    def get_case_by_index(self, case_index:int, case_count=False) -> Case | Tuple[Case, int]:
+    def get_case_by_index(
+        self, case_index: int, case_count=False
+    ) -> Case | Tuple[Case, int]:
         # Seems to be a bug when case_number is 0 or 1 the same (first) object gets returned
         # forces a list fixes (but is likely inefficient)
-        cases = list(self.cases.all().order_by("casedetail__sort_order").prefetch_related())
+        cases = list(
+            self.cases.all().order_by("casedetail__sort_order").prefetch_related()
+        )
 
         try:
             case = cases[case_index]
@@ -534,10 +625,20 @@ class CaseCollection(ExamCollectionGenericBase):
             raise Http404(s)
 
         if case_count:
-            return case, len(cases) 
+            return case, len(cases)
         else:
             return case
 
+    def get_case_take_url(self, case):
+        cases = list(
+            self.cases.all().order_by("casedetail__sort_order").prefetch_related()
+        )
+
+        return reverse(
+            "atlas:collection_case_view_take_user",
+            kwargs={"pk": self.pk, "case_number": cases.index(case)},
+        )
+
 
 class CaseDetail(models.Model):
     case = models.ForeignKey(Case, on_delete=models.CASCADE)
@@ -617,9 +718,7 @@ class SelfReview(models.Model):
     review_update_date = models.DateTimeField(auto_now=True)
 
     def get_absolute_url(self):
-        return reverse(
+        return self.user_exam.exam.get_case_take_url(self.case)
-            "atlas:collection_take_overview_user", kwargs={"pk": self.user_exam.exam.pk}
-        )
 
     def get_display_block(self):
         html = """<div class='self-feedback-block'>
@@ -628,15 +727,27 @@ class SelfReview(models.Model):
         Findings: <span class="findings">{findings}</span><br/>
 
         Interpretation: <span class="interpretation">{interpretation}</span><br/>
-        <span class="date">Date: {date}</span><br/>
+        <span class="date">Date: {date}</span><br/><a href="{edit_url}">Edit</a>
         </div>
         
         """
 
+        edit_url = reverse(
+            "atlas:self_review_update",
+            kwargs={
+                "user_exam_id": self.user_exam.pk,
+                "case_id": self.case.pk,
+                "pk": self.pk,
+            },
+        )
+        # edit_url = "TEST"
+
         return format_html(
             html,
             comments=self.comments,
             findings=self.findings,
             interpretation=self.interpretation,
             date=self.review_date,
+            id=self.pk,
+            edit_url=edit_url,
         )

atlas/templates/atlas/collection_case_view_take.html

@@ -1,6 +1,7 @@
 {% extends 'atlas/base.html' %}
 
 {% block content %}
+    <span class="collection-name-blend">Collection: {{collection}}</span>
     <h2>Case {{case_number|add:1}}
 
         {% if show_title %}
@@ -75,6 +76,10 @@
         </p>
     {% endif %}
 
+    {% if collection.publish_results or cid_user_exam.completed %}
+        <a href="{% url 'atlas:add_self_review' cid_user_exam.id case.id %}"><button>Add self review</button></a>
+
+    {% endif %}
     <form method="POST" class="post-form">{% csrf_token %}
         {% if collection.collection_type == "REP" %}
             <div class="form-contents">
@@ -84,21 +89,22 @@
             </div>
             <p>
                 {% if completed %}
-                    <h4>Answer score: {{answer.score}}</h4>
-                    Answer feedback: {{answer.feedback|safe}}
-                    <br/>
 
-                    {% if self_review %}
+                    {% if collection.self_review %}
-                        <h4>Self Feedback</h4>
+                        {% if self_review %}
+                            <h4>Self Feedback</h4>
 
-                        {% for review in self_review %}
+                            {% for review in self_review %}
-                            {{review.get_display_block}}
+                                {{review.get_display_block}}
 
-                        {% endfor %}
+                            {% endfor %}
+                        {% endif %}
+                    {% else %}
+                        <h4>Answer score: {{answer.score}}</h4>
+                        Answer feedback: {{answer.feedback|safe}}
+                        <br/>
                     {% endif %}
 
-
-
                 {% endif %}
             </p>
 
@@ -117,10 +123,6 @@
         <br />
         <button type="submit" name="finish" class="save btn btn-default">Overview</button>
         <button type="submit" id="goto-button" value="test" name="goto" class="hide">goto</button>
-        {% if collection.publish_results or cid_user_exam.completed %}
-            <a href="{% url 'atlas:add_self_review' cid_user_exam.id case.id %}">Add self review</a>
-
-        {% endif %}
     </form>
     <style>
         label {

atlas/templates/atlas/collection_take_overview.html

@@ -15,8 +15,8 @@
     {{answer_count}} out of {{collection_length}} cases answered. Click to go to case.
     <div class="sba-finish-list">
         <ul>
-            {% for question, answer in question_answer_tuples %}
+            {% for question, answer, self_review in question_answer_tuples %}
-                <li> <span {% if not collection.review_only and not answer %}class="unanswered"{% endif %}>
+                <li> <span class="{% if not collection.review_only and not answer %}unanswered{% endif %}">
                     <a href="
                              {% if cid is not None %}
                                  {% url 'atlas:collection_case_view_take' pk=collection.id case_number=forloop.counter0 cid=cid passcode=passcode %}
@@ -24,7 +24,7 @@
                                  {% url 'atlas:collection_case_view_take_user' pk=collection.id case_number=forloop.counter0 %}
                              {% endif %}
                             ">
-                        Case: {{forloop.counter}}
+                        Case: {{forloop.counter}}{% if self_review %} <span class="self-review-complete" title="You have reviewed this case."> <i class="bi-card-checklist"></i></span>{% endif %}
                     </a>
                     <br/>
                     {% if not collection.review_only  %}

atlas/templates/atlas/collection_take_start.html

@@ -22,6 +22,9 @@
                 <button>Start</button>
             {% endif %}
         </a>
+            {% if cid_exam.completed %}
+                <a href="{% url 'atlas:collection_take_overview_user' pk=collection.pk %}"><button>Overview</button></a>
+            {% endif %}
     {% else %}
         Enter your CID and passcode in the below boxes.<br />
         <p><input id="cid-box" type="text" value="Candidate ID"></p>

atlas/templates/atlas/index.html

@@ -1,4 +1,8 @@
 {% extends 'atlas/base.html' %}
 
 {% block content %}
+<h2>Atlas</h2>
+
+<a href="{% url 'atlas:user_collections' %}">Available collections</a>
+
 {% endblock %}

atlas/templates/atlas/selfreview_form.html

@@ -33,4 +33,5 @@
         </div> {% endcomment %}
         <input type="submit" value="Submit">
     </form>
+    {% if review %}<br/><a href="{% url 'atlas:self_review_delete' user_exam.id case.id review.id %}"><button>Delete review</button></a>{% endif %}
 {% endblock %}

atlas/templates/atlas/user_collections.html

@@ -0,0 +1,16 @@
+{% extends 'atlas/base.html' %}
+
+{% block content %}
+<h2>Collections</h2>
+
+    
+    <ul>
+    {% for collection in collections %}
+    <li>
+        <a href="{% url 'atlas:collection_take_start' collection.pk %}">{{collection}} {{collelction.is_complete}}</a>
+    </li>
+        
+    {% endfor %}
+    </ul>
+        
+{% endblock %}

atlas/urls.py

@@ -8,21 +8,32 @@ from . import views
 app_name = "atlas"
 
 urlpatterns = [
-    path("", views.CaseView.as_view(), name="index"),
+    path("", views.index, name="index"),
     path(
         "create/",
         RedirectView.as_view(pattern_name="atlas:case_create", permanent=False),
         name="create",
     ),
     path(
-        "add_self_review/<int:user_exam_id>/<int:case_id>",
+        "self_review/<int:user_exam_id>/<int:case_id>/add",
         views.AddSelfReview.as_view(),
         name="add_self_review",
     ),
+    path(
+        "self_review/<int:user_exam_id>/<int:case_id>/update/<int:pk>",
+        views.SelfReviewUpdate.as_view(),
+        name="self_review_update",
+    ),
+    path(
+        "self_review/<int:user_exam_id>/<int:case_id>/delete/<int:pk>",
+        views.SelfReviewDelete.as_view(),
+        name="self_review_delete",
+    ),
     path("author/<int:pk>/", views.author_detail, name="author_detail"),
     path("author/", views.author_list, name="author_list"),
     path("case/", views.CaseView.as_view(), name="case_view"),
     path("collection/", views.CollectionView.as_view(), name="collection_view"),
+    path("collection/user", views.user_collections, name="user_collections"),
     path(
         "collection/create",
         views.CaseCollectionCreate.as_view(),
@@ -125,6 +136,12 @@ urlpatterns = [
         views.GenericExamViews.exam_json_edit,
         name="exam_json_edit",
     ),
+    path(
+        "case/<int:pk>/dicom_json",
+        views.case_dicom_json,
+        name="case_dicom_json",
+    ),
+
     path("condition/", views.ConditionView.as_view(), name="condition_view"),
     path("categories/", views.categories_list, name="categories_list"),
     path("condition/<int:pk>", views.condition_detail, name="condition_detail"),

atlas/views.py

@@ -290,6 +290,13 @@ def author_list(request):
 
     return render(request, "atlas/author_list.html", {"authors": authors})
 
+def index(request):
+    return render(request, "atlas/index.html", {})
+
+def user_collections(request):
+    collections = request.user.user_casecollection_exams.all()
+
+    return render(request, "atlas/user_collections.html", {"collections": collections})
 
 class CaseDelete(RevisionMixin, AuthorOrCheckerRequiredMixin, DeleteView):
     model = Case
@@ -1325,12 +1332,13 @@ def collection_take_overview(
 
     question_answer_tuples = []
     answer_count = 0
-    for q in case_details:
+    for cd in case_details:
-        if q in answer_question_map and answer_question_map[q].answer:
+        self_review = cid_user_exam.selfreview_set.filter(case=cd.case)
-            question_answer_tuples.append((q, answer_question_map[q]))
+        if cd in answer_question_map and answer_question_map[cd].answer:
+            question_answer_tuples.append((cd, answer_question_map[cd], self_review))
             answer_count += 1
         else:
-            question_answer_tuples.append((q, None))
+            question_answer_tuples.append((cd, None, self_review))
 
     return render(
         request,
@@ -1347,6 +1355,7 @@ def collection_take_overview(
     )
 
 
+
 def collection_case_view_take_user(request, pk: int, case_number: int):
     return collection_case_view_take(request, pk, case_number)
 
@@ -1543,6 +1552,10 @@ def collection_case_view(request, pk, case_number):
         },
     )
 
+def case_dicom_json(request, pk):
+    case = get_object_or_404(Case, pk=pk)
+
+    return JsonResponse(case.get_case_dicom_json())
 
 @user_is_collection_author_or_atlas_editor
 def delete_collection_cid_answers(request, exam_id, cid):
@@ -1761,6 +1774,70 @@ class CollectionCloneMixin:
 class CollectionClone(CollectionCloneMixin, CaseCollectionCreate):
     """Clone exam view"""
 
+class SelfReviewDelete(DeleteView):
+    model = SelfReview
+    template_name = "confirm_delete.html"
+    #success_url = reverse_lazy("atlas:finding_view")
+
+    def get_initial(self):
+        user_exam_id = self.kwargs["user_exam_id"]
+        case_id = self.kwargs["case_id"]
+        review_id = self.kwargs["pk"]
+
+        self.user_exam = get_object_or_404(CidUserExam, pk=user_exam_id)
+        self.case = get_object_or_404(Case, pk=case_id)
+        self.review = get_object_or_404(SelfReview, pk=review_id)
+        return {"user_exam": user_exam_id, "case": case_id, "review": review_id}
+
+    def get_context_data(self, **kwargs):
+        # This can also be accessed via view.**** in the template
+        context = super(SelfReviewDelete, self).get_context_data(**kwargs)
+        context["user_exam"] = self.user_exam
+        context["case"] = self.case
+        context["review"] = self.review
+        return context
+
+    def get_success_url(self) -> str:
+        return self.user_exam.exam.get_case_take_url(self.case)
+
+class SelfReviewUpdate(
+    UpdateView
+):
+    model = SelfReview
+    form_class = SelfReviewForm
+
+    def get_initial(self):
+        user_exam_id = self.kwargs["user_exam_id"]
+        case_id = self.kwargs["case_id"]
+        review_id = self.kwargs["pk"]
+
+        self.user_exam = get_object_or_404(CidUserExam, pk=user_exam_id)
+        self.case = get_object_or_404(Case, pk=case_id)
+        self.review = get_object_or_404(SelfReview, pk=review_id)
+        return {"user_exam": user_exam_id, "case": case_id, "review": review_id}
+
+    def get_context_data(self, **kwargs):
+        # This can also be accessed via view.**** in the template
+        context = super(SelfReviewUpdate, self).get_context_data(**kwargs)
+        context["user_exam"] = self.user_exam
+        context["case"] = self.case
+        context["review"] = self.review
+        return context
+
+    def get_success_url(self) -> str:
+        return self.user_exam.exam.get_case_take_url(self.case)
+
+    #def get_object(self):
+    #    return self.review
+    #    return
+    #def get_initial(self):
+    #    user_exam_id = self.kwargs["user_exam_id"]
+    #    case_id = self.kwargs["case_id"]
+
+    #    self.user_exam = get_object_or_404(CidUserExam, pk=user_exam_id)
+    #    self.case = get_object_or_404(Case, pk=case_id)
+    #    return {"user_exam": user_exam_id, "case": case_id}
+
 class AddSelfReview(CreateView):
     model = SelfReview
     form_class = SelfReviewForm
@@ -1789,6 +1866,10 @@ class AddSelfReview(CreateView):
         context["case"] = self.case
         return context
 
+    def get_success_url(self) -> str:
+        return self.user_exam.exam.get_case_take_url(self.case)
+        #return reverse("atlas:collection_take_overview_user", kwargs={"pk": self.user_exam.collection.id })
+
 #    def form_valid(self, form):
 #        model = form.save(commit=False)
 #

docker/docker-compose.yml

@@ -8,6 +8,7 @@ services:
     volumes:
       - ./rad/:/usr/src/rad/
       - ../rts/:/usr/src/rad/rts
+      - ../Viewers/platform/app/dist/:/usr/src/rad/viewer
       - ./backups:/usr/src/backups
       - ./media:/usr/src/media
       - ./static:/usr/src/static

rad/static/css/anatomy.css

@@ -1013,4 +1013,9 @@ h1, h2, h3, h4, h5, h6 {
 .self-feedback-block.data {
   opacity: 60%;
   font-size: small;
+}
+
+.collection-name-blend {
+  opacity: 70%;
+  font-size: small;
 }

rad/urls.py

@@ -164,6 +164,7 @@ if settings.DEBUG:
     #urlpatterns += static(settings.MEDIA_URL, document_root=settings.MEDIA_ROOT)
     urlpatterns += static(settings.STATIC_URL, document_root=settings.STATIC_ROOT)
     urlpatterns += static("/rts/", document_root="rts")
+    urlpatterns += static("/viewer/", document_root="viewer")
     import debug_toolbar
 
     urlpatterns = [

templates/base.html

@@ -17,6 +17,8 @@
     <link href="{% static 'css/widgets.css' %}" type="text/css" media="all" rel="stylesheet">
     <link rel="stylesheet" href="{% static 'css/dicomViewer.css' %}">
     <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/toastr.js/2.1.4/toastr.min.css" integrity="sha512-6S2HWzVFxruDlZxI3sXOZZ4/eJ8AcxkQH1+JjSe/ONCEqR9L4Ysq5JdT5ipqtzU7WHalNwzwBv+iE51gNHJNqQ==" crossorigin="anonymous" referrerpolicy="no-referrer" />
+    <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap-icons@1.10.5/font/bootstrap-icons.css">
+
 
 <link href="/static/css/widgets.css" type="text/css" media="all" rel="stylesheet">
 <link href="/static/admin/css/vendor/select2/select2.min.css" type="text/css" media="screen" rel="stylesheet">