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Feb 15, 2017
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BF: Supports reading TRK (version 1) #512

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fe3c9a5
BF: Supports reading TRK (version 1)
MarcCote Feb 13, 2017
9ead3a8
RF: refactor testing for trk header values
matthew-brett Feb 14, 2017
fcd7376
Revert to using direct import for the six module
MarcCote Feb 15, 2017
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87 changes: 57 additions & 30 deletions nibabel/streamlines/tests/test_trk.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
import os
import sys
import copy
import unittest
import numpy as np
Expand Down Expand Up @@ -99,68 +100,94 @@ def test_load_complex_file(self):
trk = TrkFile.load(DATA['complex_trk_fname'], lazy_load=lazy_load)
assert_tractogram_equal(trk.tractogram, DATA['complex_tractogram'])

def trk_with_bytes(self, trk_key='simple_trk_fname', endian='<'):
""" Return example trk file bytes and struct view onto bytes """
with open(DATA[trk_key], 'rb') as fobj:
trk_bytes = fobj.read()
dt = trk_module.header_2_dtype.newbyteorder(endian)
trk_struct = np.ndarray((1,), dt, buffer=trk_bytes)
trk_struct.flags.writeable = True
return trk_struct, trk_bytes

def test_load_file_with_wrong_information(self):
trk_file = open(DATA['simple_trk_fname'], 'rb').read()

# Simulate a TRK file where `count` was not provided.
count = np.array(0, dtype="int32").tostring()
new_trk_file = trk_file[:1000-12] + count + trk_file[1000-8:]
trk = TrkFile.load(BytesIO(new_trk_file), lazy_load=False)
trk_struct, trk_bytes = self.trk_with_bytes()
trk_struct[Field.NB_STREAMLINES] = 0
trk = TrkFile.load(BytesIO(trk_bytes), lazy_load=False)
assert_tractogram_equal(trk.tractogram, DATA['simple_tractogram'])

# Simulate a TRK where `vox_to_ras` is not recorded (i.e. all zeros).
vox_to_ras = np.zeros((4, 4), dtype=np.float32).tostring()
new_trk_file = trk_file[:440] + vox_to_ras + trk_file[440+64:]
trk_struct, trk_bytes = self.trk_with_bytes()
trk_struct[Field.VOXEL_TO_RASMM] = np.zeros((4, 4))
with clear_and_catch_warnings(record=True, modules=[trk_module]) as w:
trk = TrkFile.load(BytesIO(new_trk_file))
trk = TrkFile.load(BytesIO(trk_bytes))
assert_equal(len(w), 1)
assert_true(issubclass(w[0].category, HeaderWarning))
assert_true("identity" in str(w[0].message))
assert_array_equal(trk.affine, np.eye(4))

# Simulate a TRK where `vox_to_ras` is invalid.
vox_to_ras = np.zeros((4, 4), dtype=np.float32)
vox_to_ras[3, 3] = 1
vox_to_ras = vox_to_ras.tostring()
new_trk_file = trk_file[:440] + vox_to_ras + trk_file[440+64:]
trk_struct, trk_bytes = self.trk_with_bytes()
trk_struct[Field.VOXEL_TO_RASMM] = np.diag([0, 0, 0, 1])
with clear_and_catch_warnings(record=True, modules=[trk_module]) as w:
assert_raises(HeaderError, TrkFile.load, BytesIO(new_trk_file))
assert_raises(HeaderError, TrkFile.load, BytesIO(trk_bytes))

# Simulate a TRK file where `voxel_order` was not provided.
voxel_order = np.zeros(1, dtype="|S3").tostring()
new_trk_file = trk_file[:948] + voxel_order + trk_file[948+3:]
trk_struct, trk_bytes = self.trk_with_bytes()
trk_struct[Field.VOXEL_ORDER] = b''
with clear_and_catch_warnings(record=True, modules=[trk_module]) as w:
TrkFile.load(BytesIO(new_trk_file))
TrkFile.load(BytesIO(trk_bytes))
assert_equal(len(w), 1)
assert_true(issubclass(w[0].category, HeaderWarning))
assert_true("LPS" in str(w[0].message))

# Simulate a TRK file with an unsupported version.
version = np.int32(123).tostring()
new_trk_file = trk_file[:992] + version + trk_file[992+4:]
assert_raises(HeaderError, TrkFile.load, BytesIO(new_trk_file))
trk_struct, trk_bytes = self.trk_with_bytes()
trk_struct['version'] = 123
assert_raises(HeaderError, TrkFile.load, BytesIO(trk_bytes))

# Simulate a TRK file with a wrong hdr_size.
hdr_size = np.int32(1234).tostring()
new_trk_file = trk_file[:996] + hdr_size + trk_file[996+4:]
assert_raises(HeaderError, TrkFile.load, BytesIO(new_trk_file))
trk_struct, trk_bytes = self.trk_with_bytes()
trk_struct['hdr_size'] = 1234
assert_raises(HeaderError, TrkFile.load, BytesIO(trk_bytes))

# Simulate a TRK file with a wrong scalar_name.
trk_file = open(DATA['complex_trk_fname'], 'rb').read()
noise = np.int32(42).tostring()
new_trk_file = trk_file[:47] + noise + trk_file[47+4:]
assert_raises(HeaderError, TrkFile.load, BytesIO(new_trk_file))
trk_struct, trk_bytes = self.trk_with_bytes('complex_trk_fname')
trk_struct['scalar_name'][0, 0] = b'colors\x003\x004'
assert_raises(HeaderError, TrkFile.load, BytesIO(trk_bytes))

# Simulate a TRK file with a wrong property_name.
noise = np.int32(42).tostring()
new_trk_file = trk_file[:254] + noise + trk_file[254+4:]
assert_raises(HeaderError, TrkFile.load, BytesIO(new_trk_file))
trk_struct, trk_bytes = self.trk_with_bytes('complex_trk_fname')
trk_struct['property_name'][0, 0] = b'colors\x003\x004'
assert_raises(HeaderError, TrkFile.load, BytesIO(trk_bytes))

def test_load_trk_version_1(self):
# Simulate and test a TRK (version 1).
# First check that setting the RAS affine works in version 2.
trk_struct, trk_bytes = self.trk_with_bytes()
trk_struct[Field.VOXEL_TO_RASMM] = np.diag([2, 3, 4, 1])
trk = TrkFile.load(BytesIO(trk_bytes))
assert_array_equal(trk.affine, np.diag([2, 3, 4, 1]))
# Next check that affine assumed identity if version 1.
trk_struct['version'] = 1
with clear_and_catch_warnings(record=True, modules=[trk_module]) as w:
trk = TrkFile.load(BytesIO(trk_bytes))
assert_equal(len(w), 1)
assert_true(issubclass(w[0].category, HeaderWarning))
assert_true("identity" in str(w[0].message))
assert_array_equal(trk.affine, np.eye(4))
assert_array_equal(trk.header['version'], 1)

def test_load_complex_file_in_big_endian(self):
trk_file = open(DATA['complex_trk_big_endian_fname'], 'rb').read()
trk_struct, trk_bytes = self.trk_with_bytes(
'complex_trk_big_endian_fname', endian='>')
# We use hdr_size as an indicator of little vs big endian.
hdr_size_big_endian = np.array(1000, dtype=">i4").tostring()
assert_equal(trk_file[996:996+4], hdr_size_big_endian)
good_orders = '>' if sys.byteorder == 'little' else '>='
hdr_size = trk_struct['hdr_size']
assert_true(hdr_size.dtype.byteorder in good_orders)
assert_equal(hdr_size, 1000)

for lazy_load in [False, True]:
trk = TrkFile.load(DATA['complex_trk_big_endian_fname'],
Expand Down
65 changes: 22 additions & 43 deletions nibabel/streamlines/trk.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -26,36 +26,11 @@
MAX_NB_NAMED_SCALARS_PER_POINT = 10
MAX_NB_NAMED_PROPERTIES_PER_STREAMLINE = 10

# See http://docs.scipy.org/doc/numpy/reference/arrays.dtypes.html
header_1_dtd = [(Field.MAGIC_NUMBER, 'S6'),
(Field.DIMENSIONS, 'h', 3),
(Field.VOXEL_SIZES, 'f4', 3),
(Field.ORIGIN, 'f4', 3),
(Field.NB_SCALARS_PER_POINT, 'h'),
('scalar_name', 'S20', MAX_NB_NAMED_SCALARS_PER_POINT),
(Field.NB_PROPERTIES_PER_STREAMLINE, 'h'),
('property_name', 'S20',
MAX_NB_NAMED_PROPERTIES_PER_STREAMLINE),
('reserved', 'S508'),
(Field.VOXEL_ORDER, 'S4'),
('pad2', 'S4'),
('image_orientation_patient', 'f4', 6),
('pad1', 'S2'),
('invert_x', 'S1'),
('invert_y', 'S1'),
('invert_z', 'S1'),
('swap_xy', 'S1'),
('swap_yz', 'S1'),
('swap_zx', 'S1'),
(Field.NB_STREAMLINES, 'i4'),
('version', 'i4'),
('hdr_size', 'i4'),
]

# Version 2 adds a 4x4 matrix giving the affine transformtation going
# Version 2 adds a 4x4 matrix giving the affine transformation going
# from voxel coordinates in the referenced 3D voxel matrix, to xyz
# coordinates (axes L->R, P->A, I->S). If (0 based) value [3, 3] from
# this matrix is 0, this means the matrix is not recorded.
# See http://docs.scipy.org/doc/numpy/reference/arrays.dtypes.html
header_2_dtd = [(Field.MAGIC_NUMBER, 'S6'),
(Field.DIMENSIONS, 'h', 3),
(Field.VOXEL_SIZES, 'f4', 3),
Expand Down Expand Up @@ -83,7 +58,6 @@
]

# Full header numpy dtypes
header_1_dtype = np.dtype(header_1_dtd)
header_2_dtype = np.dtype(header_2_dtd)


Expand Down Expand Up @@ -341,8 +315,8 @@ def load(cls, fileobj, lazy_load=False):
data_per_point_slice = {}
if hdr[Field.NB_SCALARS_PER_POINT] > 0:
cpt = 0
for scalar_name in hdr['scalar_name']:
scalar_name, nb_scalars = decode_value_from_name(scalar_name)
for scalar_field in hdr['scalar_name']:
scalar_name, nb_scalars = decode_value_from_name(scalar_field)

if nb_scalars == 0:
continue
Expand All @@ -358,8 +332,8 @@ def load(cls, fileobj, lazy_load=False):
data_per_streamline_slice = {}
if hdr[Field.NB_PROPERTIES_PER_STREAMLINE] > 0:
cpt = 0
for property_name in hdr['property_name']:
results = decode_value_from_name(property_name)
for property_field in hdr['property_name']:
results = decode_value_from_name(property_field)
property_name, nb_properties = results

if nb_properties == 0:
Expand Down Expand Up @@ -584,8 +558,8 @@ def _read_header(fileobj):
TrkFile.HEADER_SIZE))

if header_rec['version'] == 1:
header_rec = np.fromstring(string=header_str,
dtype=header_1_dtype)
# There is no 4x4 matrix for voxel to RAS transformation.
header_rec[Field.VOXEL_TO_RASMM] = np.zeros((4, 4))
elif header_rec['version'] == 2:
pass # Nothing more to do.
else:
Expand Down Expand Up @@ -724,12 +698,17 @@ def __str__(self):
hdr_field = getattr(Field, attr)
if hdr_field in vars:
vars[attr] = vars[hdr_field]
vars['scalar_names'] = '\n '.join([asstr(s)
for s in vars['scalar_name']
if len(s) > 0])
vars['property_names'] = "\n ".join([asstr(s)
for s in vars['property_name']
if len(s) > 0])

nb_scalars = self.header[Field.NB_SCALARS_PER_POINT]
scalar_names = [asstr(s)
for s in vars['scalar_name'][:nb_scalars]
if len(s) > 0]
vars['scalar_names'] = '\n '.join(scalar_names)
nb_properties = self.header[Field.NB_PROPERTIES_PER_STREAMLINE]
property_names = [asstr(s)
for s in vars['property_name'][:nb_properties]
if len(s) > 0]
vars['property_names'] = "\n ".join(property_names)
# Make all byte strings into strings
# Fixes recursion error on Python 3.3
vars = dict((k, asstr(v) if hasattr(v, 'decode') else v)
Expand All @@ -739,11 +718,11 @@ def __str__(self):
v.{version}
dim: {DIMENSIONS}
voxel_sizes: {VOXEL_SIZES}
orgin: {ORIGIN}
origin: {ORIGIN}
nb_scalars: {NB_SCALARS_PER_POINT}
scalar_name:\n {scalar_names}
scalar_names:\n {scalar_names}
nb_properties: {NB_PROPERTIES_PER_STREAMLINE}
property_name:\n {property_names}
property_names:\n {property_names}
vox_to_world:\n{VOXEL_TO_RASMM}
voxel_order: {VOXEL_ORDER}
image_orientation_patient: {image_orientation_patient}
Expand Down