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start removing lots of print

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This commit is contained in:
Ross
2025-06-30 10:39:42 +01:00
parent afa3b0c0ef
commit bc26209f07
14 changed files with 328 additions and 406 deletions
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anatomy/api.py
-2
View File
@@ -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
-1
View File
@@ -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
-2
View File
@@ -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
-17
View File
@@ -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
+23 -37
View File
@@ -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)
for d in dicoms:
# Group dicoms by SeriesInstanceUID, but don't keep all tags in memory
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))
series_list = []
for series_uid in data:
# Hmm probably not a good idea to blinding create a modality...
if series_uid not in series_map:
# Get or create Series and related objects as needed
try:
modality = Modality.objects.get(short_code=tags["Modality"])
except Modality.DoesNotExist:
modality = Modality.objects.create(short_code=tags["Modality"], modality=tags["Modality"])
tags = data[series_uid][0][1]
series_tags = tags # Save the first tag for this series
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
pass
series = Series.objects.get(series_instance_uid=series_uid)
if 'series' not in locals():
series = Series.objects.get(series_instance_uid=tags["SeriesInstanceUID"])
# We might only want to add the author during creation....
# Add author and case if needed
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()
dicom.delete()
d.delete() # Remove UncategorisedDicom immediately
# 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_list
return [(series, series.get_link()) for series in series_map.values()]
@router.post(
atlas/forms.py
-10
View File
@@ -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
-10
View File
@@ -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
-5
View File
@@ -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
+3 -1
View File
@@ -90,6 +90,8 @@
<p><a href="{% url 'atlas:series_view' %}?case=null&sort=-modified_date">View orphan series</a></p>
<script>
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"]'));
@@ -153,6 +155,7 @@ document.getElementById('import-dicoms-sequential-button').addEventListener('cli
}
statusDiv.innerHTML += "<div>All done.</div>";
});
}
</script>
{% endblock %}
@@ -221,4 +224,3 @@ document.getElementById('import-dicoms-sequential-button').addEventListener('cli
</style>
{% endblock css %}
atlas/tests/test_atlas_models.py
-1
View File
@@ -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
-7
View File
@@ -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
+1 -11
View File
@@ -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)
for i in slices:
print(map[i.SliceLocation])
return slices
#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
-1
View File
@@ -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:
rad/static/dv3d/index.js
+146 -146
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