def test_can_extract_hagmann_density(self): global f_cmtk f_cmtk.set_spacing('mm') import nibabel roi_img = nibabel.load("%s/CMTK_roi.nii.gz" % IMAGES_DIR) wm_img = nibabel.load("%s/CMTK_wm_1mm.nii.gz" % IMAGES_DIR) my_connectome = fibers.generate_connectome(f_cmtk, roi_img) fibers.extract_hagmann_density(my_connectome, roi_img, wm_img) for i,j in my_connectome.edges_iter(): assert my_connectome[i][j]['hagmann_density'] > 0
def test_can_extract_hagmann_density(self): global f_cmtk f_cmtk.set_spacing('mm') import nibabel roi_img = nibabel.load("%s/CMTK_roi.nii.gz" % IMAGES_DIR) wm_img = nibabel.load("%s/CMTK_wm_1mm.nii.gz" % IMAGES_DIR) my_connectome = fibers.generate_connectome(f_cmtk, roi_img) fibers.extract_hagmann_density(my_connectome, roi_img, wm_img) for i, j in my_connectome.edges_iter(): assert my_connectome[i][j]['hagmann_density'] > 0
def test_can_get_cmat_for_key(self): global f_cmtk f_cmtk.set_spacing('mm') import nibabel roi_img = nibabel.load("%s/CMTK_roi.nii.gz" % IMAGES_DIR) my_connectome = fibers.generate_connectome(f_cmtk, roi_img) fiber_cmat = fibers.cmat_for_key(my_connectome, 'number_of_fibers') for i,j in my_connectome.edges_iter(): expected_fibers = my_connectome[i][j]['number_of_fibers'] assert fiber_cmat[i-1][j-1] == expected_fibers assert fiber_cmat[j-1][i-1] == expected_fibers
def test_can_get_cmat_for_key(self): global f_cmtk f_cmtk.set_spacing('mm') import nibabel roi_img = nibabel.load("%s/CMTK_roi.nii.gz" % IMAGES_DIR) my_connectome = fibers.generate_connectome(f_cmtk, roi_img) fiber_cmat = fibers.cmat_for_key(my_connectome, 'number_of_fibers') for i, j in my_connectome.edges_iter(): expected_fibers = my_connectome[i][j]['number_of_fibers'] assert fiber_cmat[i - 1][j - 1] == expected_fibers assert fiber_cmat[j - 1][i - 1] == expected_fibers
def test_can_map_vertices_to_roi(self): global f_cmtk f_cmtk.set_spacing('mm') import nibabel roi_img = nibabel.load("%s/CMTK_roi.nii.gz" % IMAGES_DIR) my_connectome = fibers.generate_connectome(f_cmtk, roi_img) import networkx expected_connectome = networkx.read_gpickle( "%s/CMTK_connectome_scale33.gpickle" % FIBERS_DIR) for i,j in my_connectome.edges_iter(): assert my_connectome[i][j]['number_of_fibers'] == \ expected_connectome[i][j]['number_of_fibers'] assert rms(my_connectome[i][j]['fiber_length_mean'], expected_connectome[i][j]['fiber_length_mean']) < 10**-4
def test_can_map_vertices_to_roi(self): global f_cmtk f_cmtk.set_spacing('mm') import nibabel roi_img = nibabel.load("%s/CMTK_roi.nii.gz" % IMAGES_DIR) my_connectome = fibers.generate_connectome(f_cmtk, roi_img) import networkx expected_connectome = networkx.read_gpickle( "%s/CMTK_connectome_scale33.gpickle" % FIBERS_DIR) for i, j in my_connectome.edges_iter(): assert my_connectome[i][j]['number_of_fibers'] == \ expected_connectome[i][j]['number_of_fibers'] assert rms(my_connectome[i][j]['fiber_length_mean'], expected_connectome[i][j]['fiber_length_mean']) < 10**-4
def test_can_extract_scalars(self): global f_cmtk f_cmtk.set_spacing('mm') import nibabel roi_img = nibabel.load("%s/CMTK_roi.nii.gz" % IMAGES_DIR) my_connectome = fibers.generate_connectome(f_cmtk, roi_img) fa_img = nibabel.load("%s/CMTK_fa.nii.gz" % IMAGES_DIR) fibers.extract_scalars(f_cmtk, my_connectome, fa_img, 'fa', scale_factor=[2.,2.,2.]) import networkx expected_connectome = networkx.read_gpickle( "%s/CMTK_connectome_scale33.gpickle" % FIBERS_DIR) for i,j in my_connectome.edges_iter(): print i, j assert rms(my_connectome[i][j]['fa_mean'], expected_connectome[i][j]['fa_mean']) < 10**-4
def test_can_extract_scalars(self): global f_cmtk f_cmtk.set_spacing('mm') import nibabel roi_img = nibabel.load("%s/CMTK_roi.nii.gz" % IMAGES_DIR) my_connectome = fibers.generate_connectome(f_cmtk, roi_img) fa_img = nibabel.load("%s/CMTK_fa.nii.gz" % IMAGES_DIR) fibers.extract_scalars(f_cmtk, my_connectome, fa_img, 'fa', scale_factor=[2., 2., 2.]) import networkx expected_connectome = networkx.read_gpickle( "%s/CMTK_connectome_scale33.gpickle" % FIBERS_DIR) for i, j in my_connectome.edges_iter(): print i, j assert rms(my_connectome[i][j]['fa_mean'], expected_connectome[i][j]['fa_mean']) < 10**-4