def test_get_values_below_labels_list_wrong_input():
omega = [80, 80, 80]
cube_a_seg = [[10, 60, 55], 11, 1]
cube_a_anat = [[10, 60, 55], 11, 1.5]
sky_a = cube_shape(omega,
center=cube_a_anat[0],
side_length=cube_a_anat[1],
foreground_intensity=cube_a_anat[2],
dtype=np.float32)
sky_s = cube_shape(omega,
center=cube_a_seg[0],
side_length=cube_a_seg[1],
foreground_intensity=cube_a_seg[2])
im_segm = nib.Nifti1Image(sky_s, affine=np.eye(4))
im_anat = nib.Nifti1Image(sky_a, affine=np.eye(4))
with assert_raises(IOError):
get_values_below_labels_list(im_segm, im_anat, [1, [2, 3], '3', '4'])
def values_below_labels(self,
segmentation_filename,
anatomy_filename,
labels=None):
"""
:param segmentation_filename:
:param anatomy_filename:
:param labels:
:return: pandas series with label names and corresponding vectors of labels values
"""
pfi_anat = connect_path_tail_head(self.pfo_in, anatomy_filename)
pfi_segm = connect_path_tail_head(self.pfo_in, segmentation_filename)
assert os.path.exists(pfi_anat)
assert os.path.exists(pfi_segm)
im_anat = nib.load(pfi_anat)
im_segm = nib.load(pfi_segm)
labels_list, labels_names = labels_query(
labels, segmentation_array=im_segm.get_data())
labels_values = get_values_below_labels_list(im_segm, im_anat,
labels_list)
return pa.Series(labels_values, index=labels_names)
def get_raw_MD(self):
labels_names_list = self.single_label_dict.keys()
labels_list = [self.single_label_dict[l][0] for l in labels_names_list]
im_segm = nib.load(
jph(self.pfo_subject, 'stereotaxic', 'segm',
'{0}_approved_round3.nii.gz'.format(self.subject_name)))
im_anat = nib.load(
jph(self.pfo_subject, 'stereotaxic', 'mod',
'{0}_MD.nii.gz'.format(self.subject_name)))
FA_values = get_values_below_labels_list(im_segm, im_anat, labels_list)
for i, (label_name,
label_id) in enumerate(zip(labels_names_list, labels_list)):
if i == 0:
pass
else:
fin = '{0}_MD_{1}_{2}'.format(
sj,
label_name.replace(' ', '').strip(), label_id)
np.save(jph(self.pfo_report, fin + '.npy'), FA_values[i])
np.savetxt(jph(self.pfo_report, fin + '.csv'),
FA_values[i],
delimiter=",")
def test_get_values_below_labels_list():
omega = [80, 80, 80]
cube_a_seg = [[10, 60, 55], 11, 1]
cube_b_seg = [[50, 55, 42], 15, 2]
cube_c_seg = [[25, 20, 20], 13, 3]
cube_d_seg = [[55, 16, 9], 7, 4]
cube_a_anat = [[10, 60, 55], 11, 1.5]
cube_b_anat = [[50, 55, 42], 15, 2.5]
cube_c_anat = [[25, 20, 20], 13, 3.5]
cube_d_anat = [[55, 16, 9], 7, 4.5]
sky_s = cube_shape(omega,
center=cube_a_seg[0],
side_length=cube_a_seg[1],
foreground_intensity=cube_a_seg[2])
sky_s += cube_shape(omega,
center=cube_b_seg[0],
side_length=cube_b_seg[1],
foreground_intensity=cube_b_seg[2])
sky_s += cube_shape(omega,
center=cube_c_seg[0],
side_length=cube_c_seg[1],
foreground_intensity=cube_c_seg[2])
sky_s += cube_shape(omega,
center=cube_d_seg[0],
side_length=cube_d_seg[1],
foreground_intensity=cube_d_seg[2])
sky_a = cube_shape(omega,
center=cube_a_anat[0],
side_length=cube_a_anat[1],
foreground_intensity=cube_a_anat[2],
dtype=np.float32)
sky_a += cube_shape(omega,
center=cube_b_anat[0],
side_length=cube_b_anat[1],
foreground_intensity=cube_b_anat[2],
dtype=np.float32)
sky_a += cube_shape(omega,
center=cube_c_anat[0],
side_length=cube_c_anat[1],
foreground_intensity=cube_c_anat[2],
dtype=np.float32)
sky_a += cube_shape(omega,
center=cube_d_anat[0],
side_length=cube_d_anat[1],
foreground_intensity=cube_d_anat[2],
dtype=np.float32)
im_segm = nib.Nifti1Image(sky_s, affine=np.eye(4))
im_anat = nib.Nifti1Image(sky_a, affine=np.eye(4))
assert im_segm.shape == im_anat.shape
labels_list = [[1, 2], [3, 4], 4]
vals_below = get_values_below_labels_list(im_segm, im_anat, labels_list)
assert_array_equal(vals_below[0],
np.array([
1.5,
] * (11**3) + [2.5] * (15**3)))
assert_array_equal(vals_below[1],
np.array([
3.5,
] * (13**3) + [4.5] * (7**3)))
assert_array_equal(vals_below[2], np.array([4.5] * (7**3)))