def write_mesh(cor, tri, filename):
from nibabel.gifti import GiftiImage, GiftiDataArray
nimg = GiftiImage()
intent = 'NIFTI_INTENT_POINTSET'
nimg.add_gifti_data_array(GiftiDataArray.from_array(cor,intent))
intent = 'NIFTI_INTENT_TRIANGLE'
nimg.add_gifti_data_array(GiftiDataArray.from_array(tri,intent))
gifti.write(nimg, filename)
def write_mesh(cor, tri, filename):
from nibabel.gifti import GiftiImage, GiftiDataArray
nimg = GiftiImage()
intent = 'NIFTI_INTENT_POINTSET'
nimg.add_gifti_data_array(GiftiDataArray.from_array(cor, intent))
intent = 'NIFTI_INTENT_TRIANGLE'
nimg.add_gifti_data_array(GiftiDataArray.from_array(tri, intent))
gifti.write(nimg, filename)
def test_dataarray_from_array():
with clear_and_catch_warnings() as w:
warnings.filterwarnings('always', category=DeprecationWarning)
da = GiftiDataArray.from_array(np.ones((3, 4)))
assert_equal(len(w), 1)
for dt_code in data_type_codes.value_set():
data_type = data_type_codes.type[dt_code]
if data_type is np.void: # not supported
continue
arr = np.zeros((10, 3), dtype=data_type)
da = GiftiDataArray.from_array(arr, 'triangle')
assert_equal(da.datatype, data_type_codes[arr.dtype])
bs_arr = arr.byteswap().newbyteorder()
da = GiftiDataArray.from_array(bs_arr, 'triangle')
assert_equal(da.datatype, data_type_codes[arr.dtype])
def test_dataarray_from_array():
with clear_and_catch_warnings() as w:
warnings.filterwarnings('always', category=DeprecationWarning)
da = GiftiDataArray.from_array(np.ones((3, 4)))
assert_equal(len(w), 1)
for dt_code in data_type_codes.value_set():
data_type = data_type_codes.type[dt_code]
if data_type is np.void: # not supported
continue
arr = np.zeros((10, 3), dtype=data_type)
da = GiftiDataArray.from_array(arr, 'triangle')
assert_equal(da.datatype, data_type_codes[arr.dtype])
bs_arr = arr.byteswap().newbyteorder()
da = GiftiDataArray.from_array(bs_arr, 'triangle')
assert_equal(da.datatype, data_type_codes[arr.dtype])
def extract_sub_mesh_with_files(input_mesh, center_node, radius,
output_mesh=None):
from nibabel import gifti
from nibabel.gifti import GiftiImage, GiftiDataArray
from pyhrf.tools._io import read_mesh
cor, tri, coord_sys = read_mesh(input_mesh)
sub_cor, sub_tri = extract_sub_mesh(cor, tri, center_node, radius)
#nimg = GiftiImage_fromTriangles(sub_cor, sub_tri)
nimg = GiftiImage()
intent = 'NIFTI_INTENT_POINTSET'
nimg.add_gifti_data_array(GiftiDataArray.from_array(sub_cor,intent))
intent = 'NIFTI_INTENT_TRIANGLE'
nimg.add_gifti_data_array(GiftiDataArray.from_array(sub_tri,intent))
if output_mesh is None:
output_mesh = non_existent_file(add_suffix(input_mesh, '_sub'))
pyhrf.verbose(1, 'Saving extracted mesh to %s' %output_mesh)
gifti.write(nimg, output_mesh)
return sub_cor, sub_tri, coord_sys
def test_dataarray():
for dt_code in data_type_codes.value_set():
data_type = data_type_codes.type[dt_code]
if data_type is np.void: # not supported
continue
arr = np.zeros((10, 3), dtype=data_type)
da = GiftiDataArray.from_array(arr, 'triangle')
assert_equal(da.datatype, data_type_codes[arr.dtype])
bs_arr = arr.byteswap().newbyteorder()
da = GiftiDataArray.from_array(bs_arr, 'triangle')
assert_equal(da.datatype, data_type_codes[arr.dtype])
# Smoke test on deprecated functions
da = GiftiDataArray.from_array(np.ones((1, )), 'triangle')
with clear_and_catch_warnings() as w:
warnings.filterwarnings('always', category=DeprecationWarning)
assert_true(isinstance(da.to_xml_open(), string_types))
assert_equal(len(w), 1)
with clear_and_catch_warnings() as w:
warnings.filterwarnings('once', category=DeprecationWarning)
assert_true(isinstance(da.to_xml_close(), string_types))
assert_equal(len(w), 1)
def test_dataarray():
for dt_code in data_type_codes.value_set():
data_type = data_type_codes.type[dt_code]
if data_type is np.void: # not supported
continue
arr = np.zeros((10, 3), dtype=data_type)
da = GiftiDataArray.from_array(arr, 'triangle')
assert_equal(da.datatype, data_type_codes[arr.dtype])
bs_arr = arr.byteswap().newbyteorder()
da = GiftiDataArray.from_array(bs_arr, 'triangle')
assert_equal(da.datatype, data_type_codes[arr.dtype])
# Smoke test on deprecated functions
da = GiftiDataArray.from_array(np.ones((1,)), 'triangle')
with clear_and_catch_warnings() as w:
warnings.filterwarnings('always', category=DeprecationWarning)
assert_true(isinstance(da.to_xml_open(), string_types))
assert_equal(len(w), 1)
with clear_and_catch_warnings() as w:
warnings.filterwarnings('once', category=DeprecationWarning)
assert_true(isinstance(da.to_xml_close(), string_types))
assert_equal(len(w), 1)
def extract_sub_mesh_with_files(input_mesh,
center_node,
radius,
output_mesh=None):
from nibabel import gifti
from nibabel.gifti import GiftiImage, GiftiDataArray
from pyhrf.tools._io import read_mesh
cor, tri, coord_sys = read_mesh(input_mesh)
sub_cor, sub_tri = extract_sub_mesh(cor, tri, center_node, radius)
#nimg = GiftiImage_fromTriangles(sub_cor, sub_tri)
nimg = GiftiImage()
intent = 'NIFTI_INTENT_POINTSET'
nimg.add_gifti_data_array(GiftiDataArray.from_array(sub_cor, intent))
intent = 'NIFTI_INTENT_TRIANGLE'
nimg.add_gifti_data_array(GiftiDataArray.from_array(sub_tri, intent))
if output_mesh is None:
output_mesh = non_existent_file(add_suffix(input_mesh, '_sub'))
logger.info('Saving extracted mesh to %s', output_mesh)
gifti.write(nimg, output_mesh)
return sub_cor, sub_tri, coord_sys