def get_comparisons_from_session(
label_session: LabelSession) -> List[Tuple[ImageSlice, ImageSlice]]:
comparisons = []
for el in label_session.elements:
comparisons.append((ImageSlice(el.image_1_name, el.slice_1_index,
SliceType[el.slice_1_type]),
ImageSlice(el.image_2_name, el.slice_2_index,
SliceType[el.slice_2_type])))
return comparisons
def test_sample_comparisons_max_not_enough(self):
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)
]
with self.assertRaises(AssertionError):
comparisons = sampling.sample_comparisons(slices, 100, 2)
def test_sample_comparisons_self_compare(self):
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 = sampling.sample_comparisons(slices, 3, None)
for co in comparisons:
self.assertNotEqual(co[0], co[1])
def test_sample_comparisons_length(self):
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 = sampling.sample_comparisons(slices, 3, None)
comparison_count = len(comparisons)
self.assertEqual(comparison_count, 3)
def test_get_slices_from_session_categorical_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)
]
sessions.create_categorical_slice_session(db.session, 'session1', 'prompt', dataset, ['l1', 'l2', 'l3'], slices)
label_session = sessions.get_session_by_id(db.session, 1)
check_slices = sampling.get_slices_from_session(label_session)
self.assertEqual(check_slices, slices)
def test_create_categorical_slice_session_elements_length(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)
]
sessions.create_categorical_slice_session(db.session, 'session1',
'test_prompt', dataset,
['l1', 'l2', 'l3'], slices)
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, 4)
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 get_slices_from_session(label_session: LabelSession) -> List[ImageSlice]:
if label_session.session_type == LabelSessionType.CATEGORICAL_SLICE.name:
slices = [ImageSlice(el.image_1_name, el.slice_1_index, SliceType[el.slice_1_type])
for el in label_session.elements]
elif label_session.session_type == LabelSessionType.COMPARISON_SLICE.name:
comparisons = get_comparisons_from_session(label_session)
slices = [co[0] for co in comparisons] + [co[1] for co in comparisons]
slices = set(slices)
slices = sorted(slices, key=lambda sl: sl.image_name + sl.slice_type.name + str(sl.slice_index))
elif label_session.session_type == LabelSessionType.SORT_SLICE.name:
slices = [ImageSlice(el.image_1_name, el.slice_1_index, SliceType[el.slice_1_type])
for el in label_session.elements if not el.is_comparison()]
else:
raise ValueError('Invalid session type {}'.format(label_session.session_type))
return slices
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 sample_slices(dataset: Dataset, slice_type: SliceType, image_count: int, slice_count: int,
min_slice_percent: int, max_slice_percent: int) -> List[ImageSlice]:
images = random.sample(backend.get_images(dataset), image_count)
slices: List[ImageSlice] = []
for i in range(slice_count):
im: DataImage = random.choice(images)
im_slice_max = get_volume_width(im.path, slice_type)
slice_min = int(im_slice_max * (min_slice_percent / 100))
slice_max = int(im_slice_max * (max_slice_percent / 100))
if slice_min == slice_max:
sl = slice_max
else:
sl = random.randrange(slice_min, slice_max)
slices.append(ImageSlice(im.name, sl, slice_type))
slices = list(set(slices)) # Remove duplicates
return slices
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_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')
def get_comparison_from_element(el: SessionElement) -> Tuple[ImageSlice, ImageSlice]:
return (ImageSlice(el.image_1_name, el.slice_1_index, SliceType[el.slice_1_type]),
ImageSlice(el.image_2_name, el.slice_2_index, SliceType[el.slice_2_type]))