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 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
