start removing lots of print

anatomy/api.py

@@ -113,8 +113,6 @@ def get_exam_user_status_cid_user(request, exam_id: int, cid: int):
     if not exam.check_user_can_edit(request.user):
         raise HttpError(HTTPStatus.UNAUTHORIZED,"Exam author required")
 
-    print(exam_id, cid)
-
     return exam.exam_user_status.filter(cid_user_exam__cid_user__cid=cid)
 
 @router.get('/exam/{exam_id}/user_status/{user_id}/user', response=List[ExamStatusSchema])

anatomy/models.py

@@ -492,7 +492,6 @@ class Exam(ExamBase):
         return answer
 
     def get_question_user_user_answer(self, question_index, user):
-        print(user)
         question = self.get_question_by_index(question_index)
         answer = UserAnswer.objects.filter(question=question, user=user.pk, exam=self)
 

anatomy/tests/test_anatomy_exams.py

@@ -194,8 +194,6 @@ def test_exams(db, client):
         exam.save()
 
         res = client.get(exam_metadata["url"])
-        print("PRE ERRER", exam_metadata["url"])
-        print(res.content)
         assert res.status_code == 404
 
         exam.active = True

anatomy/views.py

@@ -646,22 +646,6 @@ class AnatomyQuestionUpdate(UpdateQuestionMixin):
         context = self.get_context_data(form=form)
         #formset = context["answer_formset"]
         return super().form_valid(form)
-        ## logger.debug(formset.is_valid())
-        #if formset.is_valid():
-        #    response = super().form_valid(form)
-        #    formset.instance = self.object
-        #    formset.save()
-
-        #    # restore exam orders
-        #    #for exam in self.object.exams.all():
-        #    #    if exam in exam_orders and self.object in exam_orders[exam]:
-        #    #        print(exam_orders[exam])
-        #    #        exam.exam_questions.set(exam_orders[exam])
-        #    #        exam.save()
-
-        #    return response
-        #else:
-        #    return super().form_invalid(form)
 
 
 class QuestionClone(AnatomyQuestionCreateBase):
@@ -797,7 +781,6 @@ def question_save_annotation(request, pk):
         question = get_object_or_404(AnatomyQuestion, pk=pk)
 
         question.image_annotations = request.POST.get("annotation")
-        print(question.image_annotations)
 
         question.save()
         data = {"status": "success"}

atlas/api.py

@@ -128,15 +128,10 @@ def uncategorised_dicoms(request):
 
 
 def import_dicoms_helper(request, case_id: int | None = None):
-    # TODO: move this out of the api (would be better with HTMX)
-
-
-    # dicoms = UncategorisedDicom.objects.filter(user=request.user)
     if "selection" in request.POST:
         dicoms = UncategorisedDicom.objects.filter(
             series_instance_uid__in=request.POST.getlist("selection")
         )
-
     else:
         dicoms = UncategorisedDicom.objects.filter(user=request.user)
 
@@ -145,33 +140,30 @@ def import_dicoms_helper(request, case_id: int | None = None):
     else:
         order = None
 
-    data = defaultdict(list)
+    # Group dicoms by SeriesInstanceUID, but don't keep all tags in memory
-    for d in dicoms:
+    series_map = {}
+    for d in dicoms.iterator():  # Use iterator() to avoid loading all at once
         tags = d.basic_dicom_tags
+        series_uid = tags["SeriesInstanceUID"]
 
-        data[tags["SeriesInstanceUID"]].append((d, tags))
+        if series_uid not in series_map:
-
+            # Get or create Series and related objects as needed
-    series_list = []
-    for series_uid in data:
-        # Hmm probably not a good idea to blinding create a modality...
             try:
                 modality = Modality.objects.get(short_code=tags["Modality"])
             except Modality.DoesNotExist:
                 modality = Modality.objects.create(short_code=tags["Modality"], modality=tags["Modality"])
 
-
+            series_tags = tags  # Save the first tag for this series
-        tags = data[series_uid][0][1]
-
             try:
                 with transaction.atomic():
                     series, created = Series.objects.get_or_create(
-                    series_instance_uid=tags["SeriesInstanceUID"],
+                        series_instance_uid=series_uid,
                         defaults={
                             "modality": modality,
-                        "description": tags["SeriesDescription"],
+                            "description": tags.get("SeriesDescription", ""),
                         }
                     )
-                if created and tags["StudyDescription"]:
+                    if created and tags.get("StudyDescription"):
                         examination, created_exam = Examination.objects.get_or_create(
                             examination=tags["StudyDescription"]
                         )
@@ -181,37 +173,33 @@ def import_dicoms_helper(request, case_id: int | None = None):
                         series.examination = examination
                         series.save()
             except IntegrityError:
-            # If a race condition still occurs, fetch the existing series
+                series = Series.objects.get(series_instance_uid=series_uid)
-            pass
 
-
+            # Add author and case if needed
-        if 'series' not in locals():
-            series = Series.objects.get(series_instance_uid=tags["SeriesInstanceUID"])
-
-
-        # We might only want to add the author during creation....
             series.author.add(request.user)
-
             if case_id is not None:
                 case_object = get_object_or_404(Case, pk=case_id)
                 try:
                     series.case.add(case_object)
                 except IntegrityError:
-                # The relation already exists, safe to ignore
                     pass
 
-        for dicom, dicom_tags in data[series_uid]:
+            series_map[series_uid] = series
+        else:
+            series = series_map[series_uid]
+
+        # Create and save SeriesImage immediately
         series_image = SeriesImage(
-                image=dicom.image,
+            image=d.image,
             series=series,
             is_dicom=True,
-                image_blake3_hash=dicom.image_blake3_hash,
+            image_blake3_hash=d.image_blake3_hash,
         )
         series_image.save()
-            # dicom.image.delete()
+        d.delete()  # Remove UncategorisedDicom immediately
-
-            dicom.delete()
 
+    # Optionally, re-order series if needed
+    for series in series_map.values():
         match order:
             case "order-series-instance-number":
                 series.order_by_dicom("InstanceNumber")
@@ -220,9 +208,7 @@ def import_dicoms_helper(request, case_id: int | None = None):
             case _:
                 pass
 
-        series_list.append((series, series.get_link()))
+    return [(series, series.get_link()) for series in series_map.values()]
-
-    return series_list
 
 
 @router.post(

atlas/forms.py

@@ -84,9 +84,6 @@ class CaseSelect(Select):
     def create_option(self, *args, **kwargs):
         option = super().create_option(*args, **kwargs)
 
-        print(option)
-
-
         return option
 
     def get_context(self, name: str, value, attrs) -> dict[str, Any]:
@@ -694,7 +691,6 @@ class CidReportAnswerMarkForm(ModelForm):
 #
 #    def __init__(self, *args, user, **kwargs):
 #        super(AddCollectionToCaseForm, self).__init__(*args, **kwargs)
-#        print("INIT", args, kwargs)
 #
 #        if not user.groups.filter(name="atlas_editor").exists():
 #            queryset = CaseCollection.objects.filter(author__id=user.id)
@@ -736,7 +732,6 @@ class AddCollectionToCaseForm(Form):
 
     def __init__(self, *args, user, **kwargs):
         super(AddCollectionToCaseForm, self).__init__(*args, **kwargs)
-        print("INIT", args, kwargs)
 
         if not user.groups.filter(name="atlas_editor").exists():
             queryset = CaseCollection.objects.filter(author__id=user.id)
@@ -752,21 +747,16 @@ class AddCollectionToCaseForm(Form):
         )
 
     def save(self, *args, **kwargs):
-        print("SAVE", args, kwargs)
         instance = super(AddCollectionToCaseForm, self).save(*args, **kwargs)
 
         # Here we save the modified project selection back into the database
         instance.casecollection_set.set(self.cleaned_data['casecollection'])
 
-        print(f"{instance=}")
-
         return instance
 
     def clean_casecollection(self):
         collection_set = self.cleaned_data["casecollection"]
 
-        print(f"{collection_set=}")
-
         for col in collection_set:
             if col not in self.valid_collections:
                 raise ValidationError("Invalid collection")

atlas/models.py

@@ -1215,10 +1215,7 @@ class BaseReportAnswer(models.Model):
         if self.question.question_schema is None or not "properties" in self.question.question_schema:
             return []
         answers = []
-        print("1", self.json_answer)
-        print("2", self.question.question_answers)
         for name, value in self.question.question_schema["properties"].items():
-            print(name, value)
 
             try: 
                 user_answer = self.json_answer[name]
@@ -1229,11 +1226,8 @@ class BaseReportAnswer(models.Model):
             except KeyError: # If the schema has changed?
                 correct_answer = ""
 
-            print(correct_answer)
-
             match value:
                 case {"type": "string", "enum": _}:
-                    print("YES", value)
                     automark = True
                     answer_is_correct = user_answer == correct_answer
                 case {"type": "string"}:
@@ -1366,8 +1360,6 @@ class UncategorisedDicom(models.Model):
             # duplicate = obj
             return obj
 
-        print(image_hash)
-
         if obj := SeriesImage.objects.filter(image_blake3_hash=image_hash).first():
             duplicate = obj
 
@@ -1409,8 +1401,6 @@ class UncategorisedDicom(models.Model):
             ds = pydicom.dcmread(self.image)
             return ds
         except pydicom.errors.InvalidDicomError:
-            print("Error getting dicom dataset")
-            print(self.image)
             return {"SeriesInstanceUID": "1234"}
 
     def get_basic_dicom_tags(self, dataset=None):

atlas/tables.py

@@ -196,11 +196,6 @@ class PopupLinkColumn(tables.Column):
         return obj.get_thumbnail()[0]
 
 
-def create_link(test):
-    print(test)
-    return "Hello"
-
-
 class SeriesTable(tables.Table):
     edit = tables.LinkColumn(
         "atlas:series_update", text="Edit", args=[A("pk")], orderable=False

atlas/templates/atlas/user_uploads.html

@@ -69,12 +69,12 @@
                 title="Deleted selected uploads"
         >Delete Uploads</button>
 
-<button id="import-dicoms-sequential-button"
+        <button id="import-dicoms-sequential-button"
                 type="button"
                 class="btn btn-primary"
->Import {% if case %}into case{% endif %} (one at a time)</button>
+        >Import {% if case %}into case{% endif %} (one at a time)</button>
 
-<div id="import-status"></div>
+        <div id="import-status"></div>
 
         <div class="indicator"><div class="loader"></div>Loading...</div>
         <div id="import-status"></div>
@@ -89,8 +89,10 @@
 
     <p><a href="{% url 'atlas:series_view' %}?case=null&sort=-modified_date">View orphan series</a></p>
 
-<script>
+    <script>
-document.getElementById('import-dicoms-sequential-button').addEventListener('click', async function() {
+        const importButton = document.getElementById('import-dicoms-sequential-button');
+        if (importButton) {
+            document.getElementById('import-dicoms-sequential-button').addEventListener('click', async function() {
                 const checkboxes = Array.from(document.querySelectorAll('input[name="selection"]:checked'));
                 const allCheckboxes = Array.from(document.querySelectorAll('input[name="selection"]'));
     // Only include checkboxes that are not disabled (i.e., not already imported)
@@ -152,29 +154,30 @@ document.getElementById('import-dicoms-sequential-button').addEventListener('cli
                     }
                 }
                 statusDiv.innerHTML += "<div>All done.</div>";
-});
+            });
-</script>
+        }
+    </script>
 
 {% endblock %}
 
 
 {% block css %}
-<style>
+    <style>
-.indicator {
+        .indicator {
             display: none;
-}
+        }
 
-.indicator.htmx-request {
+        .indicator.htmx-request {
             display: block;
-}
+        }
 
-.loader {
+        .loader {
             width: 50px;
             aspect-ratio: 1;
             display: grid;
-}
+        }
-.loader::before,
+        .loader::before,
-.loader::after {    
+        .loader::after {
             content:"";
             grid-area: 1/1;
             --c:no-repeat radial-gradient(farthest-side,#25b09b 92%,#0000);
@@ -185,40 +188,39 @@ document.getElementById('import-dicoms-sequential-button').addEventListener('cli
                         var(--c) 0    50%;
             background-size: 12px 12px;
             animation: l12 1s infinite;
-}
+        }
-.loader::before {
+        .loader::before {
             margin: 4px;
             filter: hue-rotate(45deg);
             background-size: 8px 8px;
             animation-timing-function: linear
-}
+        }
 
-@keyframes l12 { 
+        @keyframes l12 {
             100%{transform: rotate(.5turn)}
-}
+        }
 
-#series-list {
+        #series-list {
             user-select: none;
             cursor: pointer;
-}
+        }
 
-#series-list li {
+        #series-list li {
-}
+        }
-#series-list .selected {
+        #series-list .selected {
             color: white;
             border: 1px solid #52057b;
             user-select: none;
             margin: -1px;
 
-}
+        }
-.series-block-popup-link {
+        .series-block-popup-link {
             float: right;
-}
+        }
-#series-list li.imported {
+        #series-list li.imported {
             border-color: #e6ffe6;
             opacity: 0.7;
-}
+        }
-</style>
+    </style>
 
 {% endblock css %}
-    

atlas/tests/test_atlas_models.py

@@ -37,7 +37,6 @@ def test_condition_tree_structure(db):
     assert len(child2.get_parents()) == 1
     assert parent in child2.get_parents()
 
-    print(parent.get_descendents())
 
 #@pytest.fixture
 #def create_basic_user(db, django_user_model):

generic/models.py

@@ -568,7 +568,6 @@ class SeriesBase(models.Model):
             n = n + 1
 
     def order_by_dicom(self, field="SliceLocation"):
-        print(f"Ordering by dicom field {field}")
         images = self.images.filter(removed=False)
 
 
@@ -577,9 +576,6 @@ class SeriesBase(models.Model):
         for i in images:
             files.append((i, pydicom.dcmread(i.image.path)))
 
-        print("images to order")
-        print(files)
-
         # print("file count: {}".format(len(files)))
 
         # skip files with no SliceLocation (eg scout views)
@@ -594,8 +590,6 @@ class SeriesBase(models.Model):
             else:
                 skipcount = skipcount + 1
 
-        print("skipped, no {}: {}".format(field, skipcount))
-
         if not slices:
             return
 
@@ -607,7 +601,6 @@ class SeriesBase(models.Model):
         for f in slices:
             i = map[f[field].value]
             i.position = n
-            print(f"Setting position {n} for {i}")
             i.save()
             n = n + 1
 

helpers/images.py

@@ -93,38 +93,29 @@ def get_dicom_order(path):
     files = []
 
     for fname in glob.glob(path, recursive=False):
-        print("loading: {}".format(fname))
         files.append((fname, pydicom.dcmread(fname)))
 
-    print("file count: {}".format(len(files)))
-
     # skip files with no SliceLocation (eg scout views)
     slices = []
     map = {}
     skipcount = 0
     for fname, f in files:
-        print(dir(f))
-        print(fname)
         if hasattr(f, 'SliceLocation'):
             slices.append(f)
             map[f.SliceLocation] = fname
         else:
             skipcount = skipcount + 1
 
-    print("skipped, no SliceLocation: {}".format(skipcount))
 
     # ensure they are in the correct order
     slices = sorted(slices, key=lambda s: s.SliceLocation)
 
-    #print(slices)
+    return slices
-    for i in slices:
-        print(map[i.SliceLocation])
 
 #get_dicom_order("/home/ross/Downloads/DICOM HEAD/STD4/SER1/*.dcm")
 
 def pretty_print_dicom(dataset, indent=0):
     l = print_dicom(dataset, indent)
-    print(l)
     return "".join(l)
 
 
@@ -183,7 +174,6 @@ def get_image_dicom_hash(img, dataset=None, hash_type="md5", direct_pixel_data=T
             hasher.update(dataset.PixelData)
         except AttributeError as e:
             print("Error getting pixel data hash from dataset")
-            print(dataset)
             raise InvalidDicomError("Error getting pixel data hash from dataset")
 
     else:

manage.py

@@ -11,7 +11,6 @@ if __name__ == "__main__":
     if os.environ.get('RUN_MAIN'):
         if settings.DEBUG_CONTAINER:
             import debugpy
-            print("DEBUG LISTEN")
             debugpy.listen(("0.0.0.0", 3459))
 
     try: