def from_fileobj(klass, fileobj, endianness=None, check=True):
if fileobj.mode == 'rb':
fileobj = FileHolder(fileobj._name).get_prepare_fileobj(mode='r')
header_dict = klass.file_to_dict(fileobj.fobj)
endianness = klass.guessed_endian(header_dict)
return klass(header_dict=header_dict, endianness=endianness)
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 filespec_to_file_map(klass, filespec):
''' Method reimplemented from nibabel.spatialimages because it does not
allow enforce_extensions in types_filenames() to be False.
This is needed because MGH's compressed format is not filename.mgh.gz,
but it is filename.mgz.. types_filenames() removes the .mgz and gives
an error because it then doesn't find the file 'filename' in the system
'''
try:
filenames = types_filenames(
filespec,
klass.files_types,
trailing_suffixes=klass._compressed_exts,
enforce_extensions=False)
except TypesFilenamesError:
raise ImageFileError('Filespec "%s" does not look right for '
'class %s ' % (filespec, klass))
file_map = {}
for key, fname in filenames.items():
file_map[key] = FileHolder(filename=fname)
return file_map
def test_gifti_round_trip():
# From section 14.4 in GIFTI Surface Data Format Version 1.0
# (with some adaptations)
test_data = b'''<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE GIFTI SYSTEM "http://www.nitrc.org/frs/download.php/1594/gifti.dtd">
<GIFTI
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:noNamespaceSchemaLocation="http://www.nitrc.org/frs/download.php/1303/GIFTI_Caret.xsd"
Version="1.0"
NumberOfDataArrays="2">
<MetaData>
<MD>
<Name><![CDATA[date]]></Name>
<Value><![CDATA[Thu Nov 15 09:05:22 2007]]></Value>
</MD>
</MetaData>
<LabelTable/>
<DataArray Intent="NIFTI_INTENT_POINTSET"
DataType="NIFTI_TYPE_FLOAT32"
ArrayIndexingOrder="RowMajorOrder"
Dimensionality="2"
Dim0="4"
Dim1="3"
Encoding="ASCII"
Endian="LittleEndian"
ExternalFileName=""
ExternalFileOffset="">
<CoordinateSystemTransformMatrix>
<DataSpace><![CDATA[NIFTI_XFORM_TALAIRACH]]></DataSpace>
<TransformedSpace><![CDATA[NIFTI_XFORM_TALAIRACH]]></TransformedSpace>
<MatrixData>
1.000000 0.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.000000 1.000000
</MatrixData>
</CoordinateSystemTransformMatrix>
<Data>
10.5 0 0
0 20.5 0
0 0 30.5
0 0 0
</Data>
</DataArray>
<DataArray Intent="NIFTI_INTENT_TRIANGLE"
DataType="NIFTI_TYPE_INT32"
ArrayIndexingOrder="RowMajorOrder"
Dimensionality="2"
Dim0="4"
Dim1="3"
Encoding="ASCII"
Endian="LittleEndian"
ExternalFileName="" ExternalFileOffset="">
<Data>
0 1 2
1 2 3
0 1 3
0 2 3
</Data>
</DataArray>
</GIFTI>'''
exp_verts = np.zeros((4, 3))
exp_verts[0, 0] = 10.5
exp_verts[1, 1] = 20.5
exp_verts[2, 2] = 30.5
exp_faces = np.asarray([[0, 1, 2], [1, 2, 3], [0, 1, 3], [0, 2, 3]],
dtype=np.int32)
def _check_gifti(gio):
vertices = gio.get_arrays_from_intent('NIFTI_INTENT_POINTSET')[0].data
faces = gio.get_arrays_from_intent('NIFTI_INTENT_TRIANGLE')[0].data
assert_array_equal(vertices, exp_verts)
assert_array_equal(faces, exp_faces)
bio = BytesIO()
fmap = dict(image=FileHolder(fileobj=bio))
bio.write(test_data)
bio.seek(0)
gio = GiftiImage.from_file_map(fmap)
_check_gifti(gio)
# Write and read again
bio.seek(0)
gio.to_file_map(fmap)
bio.seek(0)
gio2 = GiftiImage.from_file_map(fmap)
_check_gifti(gio2)
def filespec_to_file_map(klass, filespec):
""" Check for compressed .mgz format, then .mgh format """
if splitext(filespec)[1] == '.mgz':
return dict(image=FileHolder(filename=filespec))
return super(MGHImage, klass).filespec_to_file_map(filespec)