def write(self, surface_obj, file_path):
image_metadata = GiftiMetaData().from_dict(
surface_obj.generic_metadata)
vertices_metadata = GiftiMetaData().from_dict(
surface_obj.vertices_metadata)
triangles_metadata = GiftiMetaData().from_dict(
surface_obj.triangles_metadata)
gifti_image = GiftiImage()
gifti_image.set_metadata(image_metadata)
data = GiftiDataArray(surface_obj.vertices,
datatype='NIFTI_TYPE_FLOAT32',
intent='NIFTI_INTENT_POINTSET')
data.meta = vertices_metadata
data.coordsys = surface_obj.vertices_coord_system
gifti_image.add_gifti_data_array(data)
data = GiftiDataArray(surface_obj.triangles,
datatype='NIFTI_TYPE_INT32',
intent='NIFTI_INTENT_TRIANGLE')
data.meta = triangles_metadata
data.coordsys = None
gifti_image.add_gifti_data_array(data)
nibabel.save(gifti_image, file_path)
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_data_array_round_trip():
# Test valid XML generated from new in-memory array
# See: https://github.com/nipy/nibabel/issues/469
verts = np.zeros((4, 3), np.float32)
verts[0, 0] = 10.5
verts[1, 1] = 20.5
verts[2, 2] = 30.5
vertices = GiftiDataArray(verts)
img = GiftiImage()
img.add_gifti_data_array(vertices)
bio = BytesIO()
fmap = dict(image=FileHolder(fileobj=bio))
bio.write(img.to_xml())
bio.seek(0)
gio = GiftiImage.from_file_map(fmap)
vertices = gio.darrays[0].data
assert_array_equal(vertices, verts)
def test_data_array_round_trip():
# Test valid XML generated from new in-memory array
# See: https://github.com/nipy/nibabel/issues/469
verts = np.zeros((4, 3), np.float32)
verts[0, 0] = 10.5
verts[1, 1] = 20.5
verts[2, 2] = 30.5
vertices = GiftiDataArray(verts)
img = GiftiImage()
img.add_gifti_data_array(vertices)
bio = BytesIO()
fmap = dict(image=FileHolder(fileobj=bio))
bio.write(img.to_xml())
bio.seek(0)
gio = GiftiImage.from_file_map(fmap)
vertices = gio.darrays[0].data
assert_array_equal(vertices, verts)
def test_gifti_image():
# Check that we're not modifying the default empty list in the default
# arguments.
gi = GiftiImage()
assert_equal(gi.darrays, [])
assert_equal(gi.meta.metadata, {})
assert_equal(gi.labeltable.labels, [])
arr = np.zeros((2, 3))
gi.darrays.append(arr)
# Now check we didn't overwrite the default arg
gi = GiftiImage()
assert_equal(gi.darrays, [])
# Test darrays / numDA
gi = GiftiImage()
assert_equal(gi.numDA, 0)
# Test from numpy numeric array
data = np.random.random((5, ))
da = GiftiDataArray(data)
gi.add_gifti_data_array(da)
assert_equal(gi.numDA, 1)
assert_array_equal(gi.darrays[0].data, data)
# Test removing
gi.remove_gifti_data_array(0)
assert_equal(gi.numDA, 0)
# Remove from empty
gi = GiftiImage()
gi.remove_gifti_data_array_by_intent(0)
assert_equal(gi.numDA, 0)
# Remove one
gi = GiftiImage()
da = GiftiDataArray(np.zeros((5, )), intent=0)
gi.add_gifti_data_array(da)
gi.remove_gifti_data_array_by_intent(3)
assert_equal(gi.numDA, 1, "data array should exist on 'missed' remove")
gi.remove_gifti_data_array_by_intent(da.intent)
assert_equal(gi.numDA, 0)
def test_gifti_image():
# Check that we're not modifying the default empty list in the default
# arguments.
gi = GiftiImage()
assert_equal(gi.darrays, [])
assert_equal(gi.meta.metadata, {})
assert_equal(gi.labeltable.labels, [])
arr = np.zeros((2, 3))
gi.darrays.append(arr)
# Now check we didn't overwrite the default arg
gi = GiftiImage()
assert_equal(gi.darrays, [])
# Test darrays / numDA
gi = GiftiImage()
assert_equal(gi.numDA, 0)
# Test from numpy numeric array
data = np.random.random((5,))
da = GiftiDataArray(data)
gi.add_gifti_data_array(da)
assert_equal(gi.numDA, 1)
assert_array_equal(gi.darrays[0].data, data)
# Test removing
gi.remove_gifti_data_array(0)
assert_equal(gi.numDA, 0)
# Remove from empty
gi = GiftiImage()
gi.remove_gifti_data_array_by_intent(0)
assert_equal(gi.numDA, 0)
# Remove one
gi = GiftiImage()
da = GiftiDataArray(np.zeros((5,)), intent=0)
gi.add_gifti_data_array(da)
gi.remove_gifti_data_array_by_intent(3)
assert_equal(gi.numDA, 1, "data array should exist on 'missed' remove")
gi.remove_gifti_data_array_by_intent(da.intent)
assert_equal(gi.numDA, 0)
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 write(self, surface_obj, file_path):
image_metadata = GiftiMetaData().from_dict(surface_obj.generic_metadata)
vertices_metadata = GiftiMetaData().from_dict(surface_obj.vertices_metadata)
triangles_metadata = GiftiMetaData().from_dict(surface_obj.triangles_metadata)
gifti_image = GiftiImage()
gifti_image.set_metadata(image_metadata)
data = GiftiDataArray(
surface_obj.vertices, datatype='NIFTI_TYPE_FLOAT32', intent='NIFTI_INTENT_POINTSET')
data.meta = vertices_metadata
data.coordsys = surface_obj.vertices_coord_system
gifti_image.add_gifti_data_array(data)
data = GiftiDataArray(
surface_obj.triangles, datatype='NIFTI_TYPE_INT32', intent='NIFTI_INTENT_TRIANGLE')
data.meta = triangles_metadata
data.coordsys = None
gifti_image.add_gifti_data_array(data)
nibabel.save(gifti_image, file_path)
def test_gifti_image():
# Check that we're not modifying the default empty list in the default
# arguments.
gi = GiftiImage()
assert_equal(gi.darrays, [])
arr = np.zeros((2, 3))
gi.darrays.append(arr)
# Now check we didn't overwrite the default arg
gi = GiftiImage()
assert_equal(gi.darrays, [])
# Test darrays / numDA
gi = GiftiImage()
assert_equal(gi.numDA, 0)
da = GiftiDataArray(data='data')
gi.add_gifti_data_array(da)
assert_equal(gi.numDA, 1)
assert_equal(gi.darrays[0].data, 'data')
gi.remove_gifti_data_array(0)
assert_equal(gi.numDA, 0)
# Remove from empty
gi = GiftiImage()
gi.remove_gifti_data_array_by_intent(0)
assert_equal(gi.numDA, 0)
# Remove one
gi = GiftiImage()
da = GiftiDataArray(data='data')
gi.add_gifti_data_array(da)
gi.remove_gifti_data_array_by_intent(0)
assert_equal(gi.numDA, 1)
gi.darrays[0].intent = 0
gi.remove_gifti_data_array_by_intent(0)
assert_equal(gi.numDA, 0)
def test_gifti_image():
# Check that we're not modifying the default empty list in the default
# arguments.
gi = GiftiImage()
assert_equal(gi.darrays, [])
arr = np.zeros((2, 3))
gi.darrays.append(arr)
# Now check we didn't overwrite the default arg
gi = GiftiImage()
assert_equal(gi.darrays, [])
# Test darrays / numDA
gi = GiftiImage()
assert_equal(gi.numDA, 0)
da = GiftiDataArray(data='data')
gi.add_gifti_data_array(da)
assert_equal(gi.numDA, 1)
assert_equal(gi.darrays[0].data, 'data')
gi.remove_gifti_data_array(0)
assert_equal(gi.numDA, 0)
# Remove from empty
gi = GiftiImage()
gi.remove_gifti_data_array_by_intent(0)
assert_equal(gi.numDA, 0)
# Remove one
gi = GiftiImage()
da = GiftiDataArray(data='data')
gi.add_gifti_data_array(da)
gi.remove_gifti_data_array_by_intent(0)
assert_equal(gi.numDA, 1)
gi.darrays[0].intent = 0
gi.remove_gifti_data_array_by_intent(0)
assert_equal(gi.numDA, 0)
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
def write_gifti(self, surface, surface_path):
gifti_image = GiftiImage()
data_array = [0 for _ in xrange(2)]
data_array[0] = surface.vertices
data_array[1] = surface.triangles
image_metadata = GiftiMetaData().from_dict(surface.image_metadata)
vertices_metadata = GiftiMetaData().from_dict(surface.vertices_metadata)
triangles_metadata = GiftiMetaData().from_dict(surface.triangles_metadata)
# TODO We currently write metadata of the old surface
gifti_image.set_metadata(image_metadata)
data = GiftiDataArray(data_array[0], datatype='NIFTI_TYPE_FLOAT32', intent='NIFTI_INTENT_POINTSET')
data.meta = vertices_metadata
data.coordsys = surface.vertices_coord_system
gifti_image.add_gifti_data_array(data)
data = GiftiDataArray(data_array[1], datatype='NIFTI_TYPE_INT32', intent='NIFTI_INTENT_TRIANGLE')
data.meta = triangles_metadata
data.coordsys = None
gifti_image.add_gifti_data_array(data)
nibabel.save(gifti_image, surface_path)
