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_metadata():
nvpair = GiftiNVPairs('key', 'value')
md = GiftiMetaData(nvpair=nvpair)
assert_equal(md.data[0].name, 'key')
assert_equal(md.data[0].value, 'value')
# Test deprecation
with clear_and_catch_warnings() as w:
warnings.filterwarnings('always', category=DeprecationWarning)
assert_equal(md.get_metadata(), dict(key='value'))
assert_equal(len(w), 1)
assert_equal(len(GiftiDataArray().get_metadata()), 0)
assert_equal(len(w), 2)
def test_metadata():
nvpair = GiftiNVPairs('key', 'value')
md = GiftiMetaData(nvpair=nvpair)
assert_equal(md.data[0].name, 'key')
assert_equal(md.data[0].value, 'value')
# Test deprecation
with clear_and_catch_warnings() as w:
warnings.filterwarnings('always', category=DeprecationWarning)
assert_equal(md.get_metadata(), dict(key='value'))
assert_equal(len(w), 1)
assert_equal(len(GiftiDataArray().get_metadata()), 0)
assert_equal(len(w), 2)
def test_metadata():
# Test deprecation
with clear_and_catch_warnings() as w:
warnings.filterwarnings('once', category=DeprecationWarning)
assert_equal(len(GiftiDataArray().get_metadata()), 0)
# Test deprecation
with clear_and_catch_warnings() as w:
warnings.filterwarnings('once', category=DeprecationWarning)
assert_equal(len(GiftiMetaData().get_metadata()), 0)
def test_dataarray_init():
# Test non-default dataarray initialization
gda = GiftiDataArray # shortcut
assert_equal(gda(None).data, None)
arr = np.arange(12, dtype=np.float32).reshape((3, 4))
assert_array_equal(gda(arr).data, arr)
# Intents
assert_raises(KeyError, gda, intent=1) # Invalid code
assert_raises(KeyError, gda, intent='not an intent') # Invalid string
assert_equal(gda(intent=2).intent, 2)
assert_equal(gda(intent='correlation').intent, 2)
assert_equal(gda(intent='NIFTI_INTENT_CORREL').intent, 2)
# Datatype
assert_equal(gda(datatype=2).datatype, 2)
assert_equal(gda(datatype='uint8').datatype, 2)
assert_raises(KeyError, gda, datatype='not_datatype')
# Float32 datatype comes from array if datatype not set
assert_equal(gda(arr).datatype, 16)
# Can be overriden by init
assert_equal(gda(arr, datatype='uint8').datatype, 2)
# Encoding
assert_equal(gda(encoding=1).encoding, 1)
assert_equal(gda(encoding='ASCII').encoding, 1)
assert_equal(gda(encoding='GIFTI_ENCODING_ASCII').encoding, 1)
assert_raises(KeyError, gda, encoding='not an encoding')
# Endian
assert_equal(gda(endian=1).endian, 1)
assert_equal(gda(endian='big').endian, 1)
assert_equal(gda(endian='GIFTI_ENDIAN_BIG').endian, 1)
assert_raises(KeyError, gda, endian='not endian code')
# CoordSys
aff = np.diag([2, 3, 4, 1])
cs = GiftiCoordSystem(1, 2, aff)
da = gda(coordsys=cs)
assert_equal(da.coordsys.dataspace, 1)
assert_equal(da.coordsys.xformspace, 2)
assert_array_equal(da.coordsys.xform, aff)
# Ordering
assert_equal(gda(ordering=2).ind_ord, 2)
assert_equal(gda(ordering='F').ind_ord, 2)
assert_equal(gda(ordering='ColumnMajorOrder').ind_ord, 2)
assert_raises(KeyError, gda, ordering='not an ordering')
# metadata
meta_dict = dict(one=1, two=2)
assert_equal(
gda(meta=GiftiMetaData.from_dict(meta_dict)).meta.metadata, meta_dict)
assert_equal(gda(meta=meta_dict).meta.metadata, meta_dict)
assert_equal(gda(meta=None).meta.metadata, {})
# ext_fname and ext_offset
assert_equal(gda(ext_fname='foo').ext_fname, 'foo')
assert_equal(gda(ext_offset=12).ext_offset, 12)
def test_dataarray_init():
# Test non-default dataarray initialization
gda = GiftiDataArray # shortcut
assert_equal(gda(None).data, None)
arr = np.arange(12, dtype=np.float32).reshape((3, 4))
assert_array_equal(gda(arr).data, arr)
# Intents
assert_raises(KeyError, gda, intent=1) # Invalid code
assert_raises(KeyError, gda, intent='not an intent') # Invalid string
assert_equal(gda(intent=2).intent, 2)
assert_equal(gda(intent='correlation').intent, 2)
assert_equal(gda(intent='NIFTI_INTENT_CORREL').intent, 2)
# Datatype
assert_equal(gda(datatype=2).datatype, 2)
assert_equal(gda(datatype='uint8').datatype, 2)
assert_raises(KeyError, gda, datatype='not_datatype')
# Float32 datatype comes from array if datatype not set
assert_equal(gda(arr).datatype, 16)
# Can be overriden by init
assert_equal(gda(arr, datatype='uint8').datatype, 2)
# Encoding
assert_equal(gda(encoding=1).encoding, 1)
assert_equal(gda(encoding='ASCII').encoding, 1)
assert_equal(gda(encoding='GIFTI_ENCODING_ASCII').encoding, 1)
assert_raises(KeyError, gda, encoding='not an encoding')
# Endian
assert_equal(gda(endian=1).endian, 1)
assert_equal(gda(endian='big').endian, 1)
assert_equal(gda(endian='GIFTI_ENDIAN_BIG').endian, 1)
assert_raises(KeyError, gda, endian='not endian code')
# CoordSys
aff = np.diag([2, 3, 4, 1])
cs = GiftiCoordSystem(1, 2, aff)
da = gda(coordsys=cs)
assert_equal(da.coordsys.dataspace, 1)
assert_equal(da.coordsys.xformspace, 2)
assert_array_equal(da.coordsys.xform, aff)
# Ordering
assert_equal(gda(ordering=2).ind_ord, 2)
assert_equal(gda(ordering='F').ind_ord, 2)
assert_equal(gda(ordering='ColumnMajorOrder').ind_ord, 2)
assert_raises(KeyError, gda, ordering='not an ordering')
# metadata
meta_dict=dict(one=1, two=2)
assert_equal(gda(meta=GiftiMetaData.from_dict(meta_dict)).meta.metadata,
meta_dict)
assert_equal(gda(meta=meta_dict).meta.metadata, meta_dict)
assert_equal(gda(meta=None).meta.metadata, {})
# ext_fname and ext_offset
assert_equal(gda(ext_fname='foo').ext_fname, 'foo')
assert_equal(gda(ext_offset=12).ext_offset, 12)
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)
def ply2gii(in_file, metadata, out_file=None):
"""Convert from ply to GIfTI"""
from pathlib import Path
from numpy import eye
from nibabel.gifti import (
GiftiMetaData,
GiftiCoordSystem,
GiftiImage,
GiftiDataArray,
)
from pyntcloud import PyntCloud
in_file = Path(in_file)
surf = PyntCloud.from_file(str(in_file))
# Update centroid metadata
metadata.update(
zip(
("SurfaceCenterX", "SurfaceCenterY", "SurfaceCenterZ"),
["%.4f" % c for c in surf.centroid],
))
# Prepare data arrays
da = (
GiftiDataArray(
data=surf.xyz.astype("float32"),
datatype="NIFTI_TYPE_FLOAT32",
intent="NIFTI_INTENT_POINTSET",
meta=GiftiMetaData.from_dict(metadata),
coordsys=GiftiCoordSystem(xform=eye(4), xformspace=3),
),
GiftiDataArray(
data=surf.mesh.values,
datatype="NIFTI_TYPE_INT32",
intent="NIFTI_INTENT_TRIANGLE",
coordsys=None,
),
)
surfgii = GiftiImage(darrays=da)
if out_file is None:
out_file = fname_presuffix(in_file.name,
suffix=".gii",
use_ext=False,
newpath=str(Path.cwd()))
surfgii.to_filename(str(out_file))
return out_file
def ply2gii(in_file, metadata, out_file=None):
"""Convert from ply to GIfTI"""
from pathlib import Path
from numpy import eye
from nibabel.gifti import (
GiftiMetaData, GiftiCoordSystem, GiftiImage, GiftiDataArray,
)
from pyntcloud import PyntCloud
in_file = Path(in_file)
surf = PyntCloud.from_file(str(in_file))
# Update centroid metadata
metadata.update(
zip(('SurfaceCenterX', 'SurfaceCenterY', 'SurfaceCenterZ'),
['%.4f' % c for c in surf.centroid])
)
# Prepare data arrays
da = (
GiftiDataArray(
data=surf.xyz.astype('float32'),
datatype='NIFTI_TYPE_FLOAT32',
intent='NIFTI_INTENT_POINTSET',
meta=GiftiMetaData.from_dict(metadata),
coordsys=GiftiCoordSystem(xform=eye(4), xformspace=3)),
GiftiDataArray(
data=surf.mesh.values,
datatype='NIFTI_TYPE_INT32',
intent='NIFTI_INTENT_TRIANGLE',
coordsys=None))
surfgii = GiftiImage(darrays=da)
if out_file is None:
out_file = fname_presuffix(
in_file.name, suffix='.gii', use_ext=False, newpath=str(Path.cwd()))
surfgii.to_filename(str(out_file))
return out_file
