def test(self):
ref_anat = os.path.join(self._tmp_dir, 'ref_anat.nii.gz')
generate_cross_image((10, 10, 10), (1.0, 1.0, 1.0), ref_anat)
output_path = os.path.join(self._tmp_dir, 'outpout.trk')
tracts_path = _generate_streamlines(self._tmp_dir, (0.0, 0.0, 0.0))
self.call(main, tracts_path, ref_anat, output_path, '--gnc', '--fnc')
created = nib.streamlines.load(output_path).streamlines.data
self.assertEqual(8 * 5, len(created), 'Wrong number of points')
tracts_path = _generate_streamlines(self._tmp_dir, (-0.5, -0.5, -0.5))
self.call(main, tracts_path, ref_anat, output_path, '-f', '--gnc',
'--fnc')
created = nib.streamlines.load(output_path).streamlines.data
self.assertEqual(8 * 5, len(created), 'Wrong number of points')
tracts_path = _generate_streamlines(self._tmp_dir, (0.0, 0.0, 0.0))
self.call(main, tracts_path, ref_anat, output_path, '-f', '--gnnc',
'--nfnc')
created = nib.streamlines.load(output_path).streamlines.data
self.assertEqual(8 * 5, len(created), 'Wrong number of points')
tracts_path = _generate_streamlines(self._tmp_dir, (-0.5, -0.5, -0.5))
self.call(main, tracts_path, ref_anat, output_path, '-f', '--gnnc',
'--nfnc')
created = nib.streamlines.load(output_path).streamlines.data
self.assertEqual(5 * 4, len(created), 'Wrong number of points')
def test(self):
image_path = os.path.join(self._tmp_dir, 'input_image.nii.gz')
generate_cross_image((10, 10, 10), (1.0, 1.0, 1.0), image_path)
with RedirectStdOut() as output:
self.call(main, image_path)
self.assertTrue(len(output) == 1, 'Should have 1 line')
self.assertTrue(
int(output[0]) == 22, 'There should be 8 + 7 + 7 non-zero voxels')
output_path = os.path.join(self._tmp_dir, 'stats.txt')
self.call(main, image_path, '-o' + output_path)
with open(output_path, 'r') as f:
lines = f.readlines()
self.assertTrue(len(lines) == 1, 'Should have 1 line')
self.assertTrue(
int(lines[0]) == 22,
'There should be 8 + 7 + 7 non-zero voxels')
self.call(main, image_path, '-o' + output_path, '--stats')
with open(output_path, 'r') as f:
lines = f.readlines()
self.assertTrue(len(lines) == 2, 'Should have 2 lines')
self.assertTrue(
int(lines[1]) == 22,
'There should be 8 + 7 + 7 non-zero voxels')
self.call(main, image_path, '-o' + output_path, '--stats', id=42)
with open(output_path, 'r') as f:
lines = f.readlines()
self.assertTrue(len(lines) == 3, 'Should have 3 lines')
self.assertTrue(lines[2] == "42 22",
'Third lihe should == "42 22"')
def test(self):
image_path = os.path.join(self._tmp_dir, 'input_image.nii.gz')
output_path = os.path.join(self._tmp_dir, 'outpout_image.nii.gz')
bbox_path = os.path.join(self._tmp_dir, 'bbox.pkl')
generate_cross_image((10, 10, 10), (0.5, 0.5, 0.5), image_path)
# Crop without bbox should create the bbox file
self.call(main, image_path, output_path, output_bbox=bbox_path)
self.assertTrue(
os.path.exists(bbox_path), 'The bbox file should exist.')
with open(bbox_path, 'r') as bbox_file:
wbbox = pickle.load(bbox_file)
if list(wbbox.minimums) != [0.5, 0.5, 0.5]\
or list(wbbox.maximums) != [4.5, 4.5, 4.5]\
or wbbox.voxel_size != (0.5, 0.5, 0.5):
self.fail('Bad values in bbox')
created = nib.load(output_path)
self.assertEqual((8, 8, 8), created.get_data().shape,
'Bad shape for cropped image.')
# Crop with a modified bbox
wbbox.maximums = np.array([4.0, 4.0, 4.0])
with open(bbox_path, 'w') as bbox_file:
pickle.dump(wbbox, bbox_file)
self.call(main, image_path, output_path, '-f', input_bbox=bbox_path)
created = nib.load(output_path)
self.assertEqual((7, 7, 7), created.get_data().shape,
'Bad shape for cropped image.')
def test(self):
image_path = os.path.join(self._tmp_dir, 'image.nii.gz')
mask_path = os.path.join(self._tmp_dir, 'mask.nii.gz')
output_path = os.path.join(self._tmp_dir, 'histogram.png')
s = 5
shape = (s, s, s)
spacing = (1.0, 1.0, 1.0)
generate_cross_image(shape, spacing, image_path)
generate_half_mask(shape, spacing, mask_path)
# 5*5*2 (50) voxels in mask. 49==0 and 1==1 in this ROI
self.call(main, image_path, mask_path, output_path, label='test')
self.compare_images(output_path,
self.fetch('GT', 'plot_histogram.png'))
def test(self):
spacing = (1.0, 1.0, 1.0)
tracts_path = generate_streamlines(self._tmp_dir, spacing)
image_path = os.path.join(self._tmp_dir, 'input.nii.gz')
output_path = os.path.join(self._tmp_dir, 'output.nii.gz')
generate_cross_image((10, 10, 10), spacing, image_path)
self.call(main, tracts_path, image_path, output_path,
tp='trackvis')
self.assertTrue(_check(nib.load(output_path).get_data(), 1),
'Wrong voxels values')
self.call(main, tracts_path, image_path, output_path, '-f',
tp='trackvis', binary=42)
self.assertTrue(_check(nib.load(output_path).get_data(), 42),
'Wrong voxels values')
def test(self):
def check(img, expected_spacing, expected_shape):
self.assertEqual(list(expected_spacing),
list(img.header['pixdim'][1:4]),
'Bad spacing')
self.assertEqual(expected_shape, img.shape, 'Bad shape')
input_path = os.path.join(self._tmp_dir, 'input_image.nii.gz')
output_path = os.path.join(self._tmp_dir, 'outpout_image.nii.gz')
generate_cross_image((10, 10, 10), (0.5, 0.7, 0.7), input_path, float)
self.call(main, input_path, output_path,
'--iso_min', interp='quad')
check(nib.load(output_path), (0.5, 0.5, 0.5), (10, 14, 14))
generate_cross_image((10, 10, 10), (0.5, 0.5, 0.5), input_path)
self.call(main, input_path, output_path, '-f', resolution=1.0)
check(nib.load(output_path), (1.0, 1.0, 1.0), (5, 5, 5))
reference_path = os.path.join(self._tmp_dir, 'reference_image.nii.gz')
generate_cross_image((10, 10, 10), (1.0, 1.0, 1.0), reference_path)
self.call(main, input_path, output_path, '-f', ref=reference_path)
check(nib.load(output_path), (1.0, 1.0, 1.0), (5, 5, 5))
generate_cross_image(
(20, 20, 20), (0.25, 0.25, 0.25), reference_path)
self.call(main, input_path, output_path,
'--enforce_dimensions', '-f', ref=reference_path)
im = nib.load(output_path)
check(im, (0.25, 0.25, 0.25), (20, 20, 20))
data = im.get_data()
self.assertTrue((data[2:18, 10, 10] == 1).all(),
'Wrong data on X axis')
self.assertTrue((data[10, 2:18, 10] == 1).all(),
'Wrong data on Y axis')
self.assertTrue((data[10, 10, 2:18] == 1).all(),
'Wrong data on Z axis')
def test(self):
image1 = os.path.join(self._tmp_dir, 'image1.nii.gz')
generate_cross_image((10, 10, 10), (1.0, 1.0, 1.0), image1)
image2 = os.path.join(self._tmp_dir, 'image2.nii.gz')
generate_cross_image((10, 10, 10), (1.0, 1.0, 1.0), image2)
image_float = os.path.join(self._tmp_dir, 'image3.nii.gz')
generate_cross_image((10, 10, 10), (1.0, 1.0, 1.0),
image_float,
dtype=float)
image_small = os.path.join(self._tmp_dir, 'image2.nii.gz')
generate_cross_image((10, 10, 10), (1.0, 1.0, 1.0), image_small)
output_path = os.path.join(self._tmp_dir, 'outpout_image.nii.gz')
self.call(main, image1, image2, output_path)
data = nib.load(output_path).get_data()
if not ((data[1:9, 5, 5] == 2).all() and
(data[5, 1:9, 5] == 2).all() and (data[5, 5, 1:9] == 2).all()):
self.fail('All voxels in the cross should == 2')
self.assertRaises(TypeError, self.call, image1, image_float,
output_path)
self.assertRaises(TypeError, self.call, image1, image_small,
output_path)