def test_create_comparison_slice_session_elements_metadata(self):
dataset = backend.get_dataset('dataset1')
comparisons = [(ImageSlice('img1.nii.gz', 0, SliceType.SAGITTAL),
ImageSlice('img3', 1, SliceType.CORONAL)),
(ImageSlice('img2.nii', 0, SliceType.SAGITTAL),
ImageSlice('img3', 1, SliceType.AXIAL)),
(ImageSlice('img2.nii', 255, SliceType.CORONAL),
ImageSlice('img1.nii.gz', 100, SliceType.AXIAL))]
sessions.create_comparison_slice_session(db.session, 'session1',
'test_prompt', dataset,
['l1', 'l2', 'l3'],
comparisons)
label_session = sessions.get_session_by_id(db.session, 1)
session_elements = label_session.elements
self.assertEqual(session_elements[0].image_1_name, 'img1.nii.gz')
self.assertEqual(session_elements[0].image_2_name, 'img3')
self.assertEqual(session_elements[1].slice_1_index, 0)
self.assertEqual(session_elements[1].slice_2_index, 1)
self.assertEqual(session_elements[2].slice_1_type,
SliceType.CORONAL.name)
self.assertEqual(session_elements[2].slice_2_type,
SliceType.AXIAL.name)
def test_create_comparison_slice_session_metadata(self):
dataset = backend.get_dataset('dataset1')
sessions.create_comparison_slice_session(db.session, 'session1',
'test_prompt', dataset,
['l1', 'l2', 'l3'], [])
label_session = sessions.get_session_by_id(db.session, 1)
self.assertEqual(label_session.session_name, 'session1')
self.assertEqual(label_session.session_type,
LabelSessionType.COMPARISON_SLICE.name)
self.assertEqual(label_session.prompt, 'test_prompt')
self.assertEqual(label_session.dataset, 'dataset1')
self.assertEqual(label_session.label_values_str, 'l1,l2,l3')
def create_comparison_session(dataset_name: str):
dataset = backend.get_dataset(dataset_name)
if dataset is None:
abort(400)
current_sessions = sessions.get_sessions(db.session, dataset)
label_session_count = len(current_sessions)
images = backend.get_images(dataset)
total_image_count = len(images)
form = CreateComparisonSessionForm(meta={'csrf': False})
comparison_sessions = sessions.get_sessions(db.session, dataset, LabelSessionType.COMPARISON_SLICE)
for sess in comparison_sessions:
form.comparisons.choices.append((str(sess.id), sess.session_name))
form.image_count.validators = [
ComparisonNumberRange(min=1, max=total_image_count,
message='Must be between %(min)s and %(max)s (the dataset size).')
]
if form.validate_on_submit():
if form.session_name.data in [se.session_name for se in current_sessions]:
form.session_name.errors.append('Session name already in use.')
elif form.comparisons.data == 'create' and form.min_slice_percent.data >= form.max_slice_percent.data:
form.max_slice_percent.errors.append('Max must be greater than min.')
else:
slice_type = backend.SliceType[form.slice_type.data]
if form.comparisons.data == 'create':
slices = sampling.sample_slices(dataset, slice_type, form.image_count.data, form.slice_count.data,
form.min_slice_percent.data, form.max_slice_percent.data)
if form.comparison_count.data is None:
comparisons = sampling.all_comparisons(slices)
else:
comparisons = sampling.sample_comparisons(slices, form.comparison_count.data,
form.max_comparisons_per_slice.data)
else:
from_session = sessions.get_session_by_id(db.session, int(form.comparisons.data))
comparisons = sampling.get_comparisons_from_session(from_session)
label_values = [v.strip() for v in form.label_values.data.split(',')]
sessions.create_comparison_slice_session(db.session, form.session_name.data, form.prompt.data,
dataset, label_values, comparisons)
return redirect(url_for('dataset_overview', dataset_name=dataset.name))
return render_template('create_comparison_session.html',
dataset=dataset,
label_session_count=label_session_count,
total_image_count=total_image_count,
form=form)
def test_get_ranking_contains_slices(self):
dataset = backend.get_dataset('dataset1')
comparisons = [
(ImageSlice('img1.nii.gz', 0, SliceType.SAGITTAL), ImageSlice('img3', 1, SliceType.CORONAL)),
(ImageSlice('img2.nii', 0, SliceType.SAGITTAL), ImageSlice('img3', 1, SliceType.AXIAL)),
(ImageSlice('img2.nii', 255, SliceType.CORONAL), ImageSlice('img1.nii.gz', 100, SliceType.AXIAL))
]
sessions.create_comparison_slice_session(db.session, 'session1', 'prompt', dataset,
['l1', 'l2'], comparisons)
label_session = sessions.get_session_by_id(db.session, 1)
ranked_slices = ranking.rank_slices(label_session)
check_slices = sampling.get_slices_from_session(label_session)
self.assertEqual(set(ranked_slices), set(check_slices))
def test_create_comparison_slice_session_elements_length(self):
dataset = backend.get_dataset('dataset1')
comparisons = [(ImageSlice('img1.nii.gz', 0, SliceType.SAGITTAL),
ImageSlice('img3', 1, SliceType.CORONAL)),
(ImageSlice('img2.nii', 0, SliceType.SAGITTAL),
ImageSlice('img3', 1, SliceType.AXIAL)),
(ImageSlice('img2.nii', 255, SliceType.CORONAL),
ImageSlice('img1.nii.gz', 100, SliceType.AXIAL))]
sessions.create_comparison_slice_session(db.session, 'session1',
'test_prompt', dataset,
['l1', 'l2', 'l3'],
comparisons)
label_session = sessions.get_session_by_id(db.session, 1)
session_elements = label_session.elements
session_element_count = len(session_elements)
self.assertEqual(session_element_count, 3)
def test_get_comparisons_from_session(self):
dataset = backend.get_dataset('dataset1')
slices = [
ImageSlice('img1.nii.gz', 0, SliceType.SAGITTAL),
ImageSlice('img1.nii.gz', 100, SliceType.SAGITTAL),
ImageSlice('img2.nii', 1, SliceType.CORONAL),
ImageSlice('img3', 255, SliceType.AXIAL)
]
comparisons = [(slices[0], slices[1]), (slices[2], slices[0]),
(slices[3], slices[1])]
sessions.create_comparison_slice_session(db.session, 'session1',
'prompt', dataset,
['l1', 'l2', 'l3'],
comparisons)
label_session = sessions.get_session_by_id(db.session, 1)
check_comparisons = sampling.get_comparisons_from_session(
label_session)
self.assertEqual(check_comparisons, comparisons)
def test_get_slices_from_session_comparison_slice(self):
dataset = backend.get_dataset('dataset1')
slices = [
ImageSlice('img1.nii.gz', 0, SliceType.SAGITTAL),
ImageSlice('img1.nii.gz', 100, SliceType.SAGITTAL),
ImageSlice('img2.nii', 1, SliceType.CORONAL),
ImageSlice('img3', 255, SliceType.AXIAL)
]
comparisons = [(slices[0], slices[1]), (slices[2], slices[0]),
(slices[3], slices[1])]
sessions.create_comparison_slice_session(db.session, 'session1',
'prompt', dataset,
['l1', 'l2', 'l3'],
comparisons)
label_session = sessions.get_session_by_id(db.session, 1)
check_slices = sampling.get_slices_from_session(label_session)
# Note: Result from get_slices_by_session is sorted, so this relies on slices being defined in order above
self.assertEqual(check_slices, slices)
def test_get_sessions_by_type_length(self):
dataset = backend.get_dataset('dataset1')
sessions.create_categorical_image_session(db.session, 'session1',
'prompt', dataset,
['l1', 'l2', 'l3'])
sessions.create_categorical_image_session(db.session, 'session2',
'prompt', dataset,
['l1', 'l2', 'l3'])
sessions.create_categorical_slice_session(db.session, 'session3',
'prompt', dataset,
['l1', 'l2', 'l3'], [])
sessions.create_categorical_slice_session(db.session, 'session4',
'prompt', dataset,
['l1', 'l2', 'l3'], [])
sessions.create_comparison_slice_session(db.session, 'session5',
'prompt', dataset,
['l1', 'l2'], [])
sessions.create_categorical_image_session(db.session, 'session6',
'prompt', dataset,
['l1', 'l2', 'l3'])
sessions.create_categorical_image_session(db.session, 'session7',
'prompt', dataset,
['l1', 'l2', 'l3'])
categorical_image_sessions = sessions.get_sessions(
db.session, dataset, LabelSessionType.CATEGORICAL_IMAGE)
categorical_image_session_count = len(categorical_image_sessions)
categorical_slice_sessions = sessions.get_sessions(
db.session, dataset, LabelSessionType.CATEGORICAL_SLICE)
categorical_slice_session_count = len(categorical_slice_sessions)
comparison_slice_sessions = sessions.get_sessions(
db.session, dataset, LabelSessionType.COMPARISON_SLICE)
comparison_slice_session_count = len(comparison_slice_sessions)
self.assertEqual(categorical_image_session_count, 4)
self.assertEqual(categorical_slice_session_count, 2)
self.assertEqual(comparison_slice_session_count, 1)
def test_export_session_json_elements_metadata(self):
dataset = backend.get_dataset('dataset1')
comparisons = [(ImageSlice('img1.nii.gz', 0, SliceType.SAGITTAL),
ImageSlice('img3', 1, SliceType.CORONAL)),
(ImageSlice('img2.nii', 0, SliceType.SAGITTAL),
ImageSlice('img3', 1, SliceType.AXIAL)),
(ImageSlice('img2.nii', 255, SliceType.CORONAL),
ImageSlice('img1.nii.gz', 100, SliceType.AXIAL))]
sessions.create_comparison_slice_session(db.session, 'session1',
'test_prompt', dataset,
['l1', 'l2', 'l3'],
comparisons)
label_session = sessions.get_session_by_id(db.session, 1)
session_json = sessions.export_session_json(label_session)
elements_json = session_json['elements']
self.assertEqual(elements_json[0],
'0,img1.nii.gz,SAGITTAL,0,img3,CORONAL,1')
self.assertEqual(elements_json[1],
'1,img2.nii,SAGITTAL,0,img3,AXIAL,1')
self.assertEqual(elements_json[2],
'2,img2.nii,CORONAL,255,img1.nii.gz,AXIAL,100')