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test_nifti1.py
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# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
#
# See COPYING file distributed along with the NiBabel package for the
# copyright and license terms.
#
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
''' Tests for nifti reading package '''
from __future__ import division, print_function, absolute_import
import os
import warnings
import struct
import six
import numpy as np
from nibabel import nifti1 as nifti1
from nibabel.affines import from_matvec
from nibabel.casting import type_info, have_binary128
from nibabel.eulerangles import euler2mat
from io import BytesIO
from nibabel.nifti1 import (load, Nifti1Header, Nifti1PairHeader, Nifti1Image,
Nifti1Pair, Nifti1Extension, Nifti1DicomExtension,
Nifti1Extensions, data_type_codes, extension_codes,
slice_order_codes)
from nibabel.spatialimages import HeaderDataError
from nibabel.tmpdirs import InTemporaryDirectory
from ..freesurfer import load as mghload
from .test_arraywriters import rt_err_estimate, IUINT_TYPES
from .test_helpers import bytesio_filemap, bytesio_round_trip
from .nibabel_data import get_nibabel_data, needs_nibabel_data
from numpy.testing import (assert_array_equal, assert_array_almost_equal,
assert_almost_equal)
from nose.tools import (assert_true, assert_false, assert_equal,
assert_raises)
from ..testing import (
clear_and_catch_warnings,
data_path,
runif_extra_has,
suppress_warnings,
)
from . import test_analyze as tana
from . import test_spm99analyze as tspm
header_file = os.path.join(data_path, 'nifti1.hdr')
image_file = os.path.join(data_path, 'example4d.nii.gz')
from nibabel.pydicom_compat import pydicom, dicom_test
# Example transformation matrix
R = [[0, -1, 0], [1, 0, 0], [0, 0, 1]] # rotation matrix
Z = [2.0, 3.0, 4.0] # zooms
T = [20, 30, 40] # translations
A = np.eye(4)
A[:3, :3] = np.array(R) * Z # broadcasting does the job
A[:3, 3] = T
class TestNifti1PairHeader(tana.TestAnalyzeHeader, tspm.HeaderScalingMixin):
header_class = Nifti1PairHeader
example_file = header_file
quat_dtype = np.float32
supported_np_types = tana.TestAnalyzeHeader.supported_np_types.union((
np.int8,
np.uint16,
np.uint32,
np.int64,
np.uint64,
np.complex128))
if have_binary128():
supported_np_types = supported_np_types.union((
np.longdouble,
np.longcomplex))
tana.add_intp(supported_np_types)
def test_empty(self):
tana.TestAnalyzeHeader.test_empty(self)
hdr = self.header_class()
assert_equal(hdr['magic'], hdr.pair_magic)
assert_equal(hdr['scl_slope'], 1)
assert_equal(hdr['vox_offset'], 0)
def test_from_eg_file(self):
hdr = self.header_class.from_fileobj(open(self.example_file, 'rb'))
assert_equal(hdr.endianness, '<')
assert_equal(hdr['magic'], hdr.pair_magic)
assert_equal(hdr['sizeof_hdr'], self.sizeof_hdr)
def test_data_scaling(self):
# Test scaling in header
super(TestNifti1PairHeader, self).test_data_scaling()
hdr = self.header_class()
data = np.arange(0, 3, 0.5).reshape((1, 2, 3))
hdr.set_data_shape(data.shape)
hdr.set_data_dtype(np.float32)
S = BytesIO()
# Writing to float dtype with scaling gives slope, intercept as (1, 0)
hdr.data_to_fileobj(data, S, rescale=True)
assert_array_equal(hdr.get_slope_inter(), (1, 0))
rdata = hdr.data_from_fileobj(S)
assert_array_almost_equal(data, rdata)
# Writing to integer datatype with scaling gives non-identity scaling
hdr.set_data_dtype(np.int8)
hdr.set_slope_inter(1, 0)
hdr.data_to_fileobj(data, S, rescale=True)
assert_false(np.allclose(hdr.get_slope_inter(), (1, 0)))
rdata = hdr.data_from_fileobj(S)
assert_array_almost_equal(data, rdata)
# Without scaling does rounding, doesn't alter scaling
hdr.set_slope_inter(1, 0)
with np.errstate(invalid='ignore'):
hdr.data_to_fileobj(data, S, rescale=False)
assert_array_equal(hdr.get_slope_inter(), (1, 0))
rdata = hdr.data_from_fileobj(S)
assert_array_almost_equal(np.round(data), rdata)
def test_big_scaling(self):
# Test that upcasting works for huge scalefactors
# See tests for apply_read_scaling in test_volumeutils
hdr = self.header_class()
hdr.set_data_shape((2, 1, 1))
hdr.set_data_dtype(np.int16)
sio = BytesIO()
dtt = np.float32
# This will generate a huge scalefactor
finf = type_info(dtt)
data = np.array([finf['min'], finf['max']], dtype=dtt)[:, None, None]
hdr.data_to_fileobj(data, sio)
data_back = hdr.data_from_fileobj(sio)
assert_true(np.allclose(data, data_back))
def test_slope_inter(self):
hdr = self.header_class()
nan, inf, minf = np.nan, np.inf, -np.inf
HDE = HeaderDataError
assert_equal(hdr.get_slope_inter(), (1.0, 0.0))
for in_tup, exp_err, out_tup, raw_values in (
# Null scalings
((None, None), None, (None, None), (nan, nan)),
((nan, None), None, (None, None), (nan, nan)),
((None, nan), None, (None, None), (nan, nan)),
((nan, nan), None, (None, None), (nan, nan)),
# Can only be one null
((None, 0), HDE, (None, None), (nan, 0)),
((nan, 0), HDE, (None, None), (nan, 0)),
((1, None), HDE, (None, None), (1, nan)),
((1, nan), HDE, (None, None), (1, nan)),
# Bad slope plus anything generates an error
((0, 0), HDE, (None, None), (0, 0)),
((0, None), HDE, (None, None), (0, nan)),
((0, nan), HDE, (None, None), (0, nan)),
((0, inf), HDE, (None, None), (0, inf)),
((0, minf), HDE, (None, None), (0, minf)),
((inf, 0), HDE, (None, None), (inf, 0)),
((inf, None), HDE, (None, None), (inf, nan)),
((inf, nan), HDE, (None, None), (inf, nan)),
((inf, inf), HDE, (None, None), (inf, inf)),
((inf, minf), HDE, (None, None), (inf, minf)),
((minf, 0), HDE, (None, None), (minf, 0)),
((minf, None), HDE, (None, None), (minf, nan)),
((minf, nan), HDE, (None, None), (minf, nan)),
((minf, inf), HDE, (None, None), (minf, inf)),
((minf, minf), HDE, (None, None), (minf, minf)),
# Good slope and bad inter generates error for get_slope_inter
((2, None), HDE, HDE, (2, nan)),
((2, nan), HDE, HDE, (2, nan)),
((2, inf), HDE, HDE, (2, inf)),
((2, minf), HDE, HDE, (2, minf)),
# Good slope and inter - you guessed it
((2, 0), None, (2, 0), (2, 0)),
((2, 1), None, (2, 1), (2, 1))):
hdr = self.header_class()
if not exp_err is None:
assert_raises(exp_err, hdr.set_slope_inter, *in_tup)
in_list = [v if not v is None else np.nan for v in in_tup]
hdr['scl_slope'], hdr['scl_inter'] = in_list
else:
hdr.set_slope_inter(*in_tup)
if isinstance(out_tup, Exception):
assert_raises(out_tup, hdr.get_slope_inter)
else:
assert_equal(hdr.get_slope_inter(), out_tup)
# Check set survives through checking
hdr = self.header_class.from_header(hdr, check=True)
assert_equal(hdr.get_slope_inter(), out_tup)
assert_array_equal([hdr['scl_slope'], hdr['scl_inter']],
raw_values)
def test_nifti_qfac_checks(self):
# Test qfac is 1 or -1
hdr = self.header_class()
# 1, -1 OK
hdr['pixdim'][0] = 1
self.log_chk(hdr, 0)
hdr['pixdim'][0] = -1
self.log_chk(hdr, 0)
# 0 is not
hdr['pixdim'][0] = 0
fhdr, message, raiser = self.log_chk(hdr, 20)
assert_equal(fhdr['pixdim'][0], 1)
assert_equal(message,
'pixdim[0] (qfac) should be 1 '
'(default) or -1; setting qfac to 1')
def test_nifti_qsform_checks(self):
# qform, sform checks
HC = self.header_class
# qform, sform
hdr = HC()
hdr['qform_code'] = -1
fhdr, message, raiser = self.log_chk(hdr, 30)
assert_equal(fhdr['qform_code'], 0)
assert_equal(message,
'qform_code -1 not valid; setting to 0')
hdr = HC()
hdr['sform_code'] = -1
fhdr, message, raiser = self.log_chk(hdr, 30)
assert_equal(fhdr['sform_code'], 0)
assert_equal(message,
'sform_code -1 not valid; setting to 0')
def test_magic_offset_checks(self):
# magic and offset
HC = self.header_class
hdr = HC()
hdr['magic'] = 'ooh'
fhdr, message, raiser = self.log_chk(hdr, 45)
assert_equal(fhdr['magic'], b'ooh')
assert_equal(message,
'magic string "ooh" is not valid; '
'leaving as is, but future errors are likely')
# For pairs, any offset is OK, but should be divisible by 16
# Singles need offset of at least 352 (nifti1) or 540 (nifti2) bytes,
# with the divide by 16 rule
svo = hdr.single_vox_offset
for magic, ok, bad_spm in ((hdr.pair_magic, 32, 40),
(hdr.single_magic, svo + 32, svo + 40)):
hdr['magic'] = magic
hdr['vox_offset'] = 0
self.assert_no_log_err(hdr)
hdr['vox_offset'] = ok
self.assert_no_log_err(hdr)
hdr['vox_offset'] = bad_spm
fhdr, message, raiser = self.log_chk(hdr, 30)
assert_equal(fhdr['vox_offset'], bad_spm)
assert_equal(message,
'vox offset (={0:g}) not divisible by 16, '
'not SPM compatible; leaving at current '
'value'.format(bad_spm))
# Check minimum offset (if offset set)
hdr['magic'] = hdr.single_magic
hdr['vox_offset'] = 10
fhdr, message, raiser = self.log_chk(hdr, 40)
assert_equal(fhdr['vox_offset'], hdr.single_vox_offset)
assert_equal(message,
'vox offset 10 too low for single '
'file nifti1; setting to minimum value '
'of ' + str(hdr.single_vox_offset))
def test_freesurfer_large_vector_hack(self):
# For large vector images, Freesurfer appears to set dim[1] to -1 and
# then use glmin for the vector length (an i4)
HC = self.header_class
# The standard case
hdr = HC()
hdr.set_data_shape((2, 3, 4))
assert_equal(hdr.get_data_shape(), (2, 3, 4))
assert_equal(hdr['glmin'], 0)
# Just left of the freesurfer case
dim_type = hdr.template_dtype['dim'].base
glmin = hdr.template_dtype['glmin'].base
too_big = int(np.iinfo(dim_type).max) + 1
hdr.set_data_shape((too_big - 1, 1, 1))
assert_equal(hdr.get_data_shape(), (too_big - 1, 1, 1))
# The freesurfer case
full_shape = (too_big, 1, 1, 1, 1, 1, 1)
for dim in range(3, 8):
# First element in 'dim' field is number of dimensions
expected_dim = np.array([dim, -1, 1, 1, 1, 1, 1, 1])
with suppress_warnings():
hdr.set_data_shape(full_shape[:dim])
assert_equal(hdr.get_data_shape(), full_shape[:dim])
assert_array_equal(hdr['dim'], expected_dim)
assert_equal(hdr['glmin'], too_big)
# Allow the fourth dimension to vary
with suppress_warnings():
hdr.set_data_shape((too_big, 1, 1, 4))
assert_equal(hdr.get_data_shape(), (too_big, 1, 1, 4))
assert_array_equal(hdr['dim'][:5], np.array([4, -1, 1, 1, 4]))
# This only works when the first 3 dimensions are -1, 1, 1
assert_raises(HeaderDataError, hdr.set_data_shape, (too_big,))
assert_raises(HeaderDataError, hdr.set_data_shape, (too_big, 1))
assert_raises(HeaderDataError, hdr.set_data_shape, (too_big, 1, 2))
assert_raises(HeaderDataError, hdr.set_data_shape, (too_big, 2, 1))
assert_raises(HeaderDataError, hdr.set_data_shape, (1, too_big))
assert_raises(HeaderDataError, hdr.set_data_shape, (1, too_big, 1))
assert_raises(HeaderDataError, hdr.set_data_shape, (1, 1, too_big))
assert_raises(HeaderDataError, hdr.set_data_shape, (1, 1, 1, too_big))
# Outside range of glmin raises error
far_too_big = int(np.iinfo(glmin).max) + 1
with suppress_warnings():
hdr.set_data_shape((far_too_big - 1, 1, 1))
assert_equal(hdr.get_data_shape(), (far_too_big - 1, 1, 1))
assert_raises(HeaderDataError, hdr.set_data_shape, (far_too_big, 1, 1))
# glmin of zero raises error (implausible vector length)
hdr.set_data_shape((-1, 1, 1))
hdr['glmin'] = 0
assert_raises(HeaderDataError, hdr.get_data_shape)
# Lists or tuples or arrays will work for setting shape
for shape in ((too_big - 1, 1, 1), (too_big, 1, 1)):
for constructor in (list, tuple, np.array):
with suppress_warnings():
hdr.set_data_shape(constructor(shape))
assert_equal(hdr.get_data_shape(), shape)
@needs_nibabel_data('nitest-freesurfer')
def test_freesurfer_ico7_hack(self):
HC = self.header_class
hdr = HC()
full_shape = (163842, 1, 1, 1, 1, 1, 1)
# Test that using ico7 shape automatically uses factored dimensions
for dim in range(3, 8):
expected_dim = np.array([dim, 27307, 1, 6, 1, 1, 1, 1])
hdr.set_data_shape(full_shape[:dim])
assert_equal(hdr.get_data_shape(), full_shape[:dim])
assert_array_equal(hdr._structarr['dim'], expected_dim)
# Only works on dimensions >= 3
assert_raises(HeaderDataError, hdr.set_data_shape, full_shape[:1])
assert_raises(HeaderDataError, hdr.set_data_shape, full_shape[:2])
# Bad shapes
assert_raises(HeaderDataError, hdr.set_data_shape, (163842, 2, 1))
assert_raises(HeaderDataError, hdr.set_data_shape, (163842, 1, 2))
assert_raises(HeaderDataError, hdr.set_data_shape, (1, 163842, 1))
assert_raises(HeaderDataError, hdr.set_data_shape, (1, 1, 163842))
assert_raises(HeaderDataError, hdr.set_data_shape, (1, 1, 1, 163842))
# Test consistency of data in .mgh and mri_convert produced .nii
nitest_path = os.path.join(get_nibabel_data(), 'nitest-freesurfer')
mgh = mghload(os.path.join(nitest_path, 'fsaverage', 'surf',
'lh.orig.avg.area.mgh'))
nii = load(os.path.join(nitest_path, 'derivative', 'fsaverage', 'surf',
'lh.orig.avg.area.nii'))
assert_equal(mgh.shape, nii.shape)
assert_array_equal(mgh.get_data(), nii.get_data())
assert_array_equal(nii.header._structarr['dim'][1:4],
np.array([27307, 1, 6]))
# Test writing produces consistent nii files
with InTemporaryDirectory():
nii.to_filename('test.nii')
nii2 = load('test.nii')
assert_equal(nii.shape, nii2.shape)
assert_array_equal(nii.get_data(), nii2.get_data())
assert_array_equal(nii.get_affine(), nii2.get_affine())
def test_qform_sform(self):
HC = self.header_class
hdr = HC()
assert_array_equal(hdr.get_qform(), np.eye(4))
empty_sform = np.zeros((4, 4))
empty_sform[-1, -1] = 1
assert_array_equal(hdr.get_sform(), empty_sform)
assert_equal(hdr.get_qform(coded=True), (None, 0))
assert_equal(hdr.get_sform(coded=True), (None, 0))
# Affines with no shears
nice_aff = np.diag([2, 3, 4, 1])
another_aff = np.diag([3, 4, 5, 1])
# Affine with shears
nasty_aff = from_matvec(np.arange(9).reshape((3, 3)), [9, 10, 11])
nasty_aff[0, 0] = 1 # Make full rank
fixed_aff = unshear_44(nasty_aff)
assert_false(np.allclose(fixed_aff, nasty_aff))
for in_meth, out_meth in ((hdr.set_qform, hdr.get_qform),
(hdr.set_sform, hdr.get_sform)):
in_meth(nice_aff, 2)
aff, code = out_meth(coded=True)
assert_array_equal(aff, nice_aff)
assert_equal(code, 2)
assert_array_equal(out_meth(), nice_aff) # non coded
# Affine may be passed if code == 0, and will get set into header,
# but the returned affine with 'coded=True' will be None.
in_meth(another_aff, 0)
assert_equal(out_meth(coded=True), (None, 0)) # coded -> None
assert_array_almost_equal(out_meth(), another_aff) # else -> input
# Default qform code when previous == 0 is 2
in_meth(nice_aff)
aff, code = out_meth(coded=True)
assert_equal(code, 2)
# Unless code was non-zero before
in_meth(nice_aff, 1)
in_meth(nice_aff)
aff, code = out_meth(coded=True)
assert_equal(code, 1)
# Can set code without modifying affine, by passing affine=None
assert_array_equal(aff, nice_aff) # affine same as before
in_meth(None, 3)
aff, code = out_meth(coded=True)
assert_array_equal(aff, nice_aff) # affine same as before
assert_equal(code, 3)
# affine is None on its own, or with code==0, resets code to 0
in_meth(None, 0)
assert_equal(out_meth(coded=True), (None, 0))
in_meth(None)
assert_equal(out_meth(coded=True), (None, 0))
# List works as input
in_meth(nice_aff.tolist())
assert_array_equal(out_meth(), nice_aff)
# Qform specifics
# inexact set (with shears) is OK
hdr.set_qform(nasty_aff, 1)
assert_array_almost_equal(hdr.get_qform(), fixed_aff)
# Unless allow_shears is False
assert_raises(HeaderDataError, hdr.set_qform, nasty_aff, 1, False)
# Reset sform, give qform a code, to test sform
hdr.set_sform(None)
hdr.set_qform(nice_aff, 1)
# Check sform unchanged by setting qform
assert_equal(hdr.get_sform(coded=True), (None, 0))
# Setting does change the sform ouput
hdr.set_sform(nasty_aff, 1)
aff, code = hdr.get_sform(coded=True)
assert_array_equal(aff, nasty_aff)
assert_equal(code, 1)
def test_datatypes(self):
hdr = self.header_class()
for code in data_type_codes.value_set():
dt = data_type_codes.type[code]
if dt == np.void:
continue
hdr.set_data_dtype(code)
(assert_equal,
hdr.get_data_dtype(),
data_type_codes.dtype[code])
# Check that checks also see new datatypes
hdr.set_data_dtype(np.complex128)
hdr.check_fix()
def test_quaternion(self):
hdr = self.header_class()
hdr['quatern_b'] = 0
hdr['quatern_c'] = 0
hdr['quatern_d'] = 0
assert_true(np.allclose(hdr.get_qform_quaternion(), [1.0, 0, 0, 0]))
hdr['quatern_b'] = 1
hdr['quatern_c'] = 0
hdr['quatern_d'] = 0
assert_true(np.allclose(hdr.get_qform_quaternion(), [0, 1, 0, 0]))
# Check threshold set correctly for float32
hdr['quatern_b'] = 1 + np.finfo(self.quat_dtype).eps
assert_array_almost_equal(hdr.get_qform_quaternion(), [0, 1, 0, 0])
def test_qform(self):
# Test roundtrip case
ehdr = self.header_class()
ehdr.set_qform(A)
qA = ehdr.get_qform()
assert_true, np.allclose(A, qA, atol=1e-5)
assert_true, np.allclose(Z, ehdr['pixdim'][1:4])
xfas = nifti1.xform_codes
assert_true, ehdr['qform_code'] == xfas['aligned']
ehdr.set_qform(A, 'scanner')
assert_true, ehdr['qform_code'] == xfas['scanner']
ehdr.set_qform(A, xfas['aligned'])
assert_true, ehdr['qform_code'] == xfas['aligned']
# Test pixdims[1,2,3] are checked for negatives
for dims in ((-1, 1, 1), (1, -1, 1), (1, 1, -1)):
ehdr['pixdim'][1:4] = dims
assert_raises(HeaderDataError, ehdr.get_qform)
def test_sform(self):
# Test roundtrip case
ehdr = self.header_class()
ehdr.set_sform(A)
sA = ehdr.get_sform()
assert_true, np.allclose(A, sA, atol=1e-5)
xfas = nifti1.xform_codes
assert_true, ehdr['sform_code'] == xfas['aligned']
ehdr.set_sform(A, 'scanner')
assert_true, ehdr['sform_code'] == xfas['scanner']
ehdr.set_sform(A, xfas['aligned'])
assert_true, ehdr['sform_code'] == xfas['aligned']
def test_dim_info(self):
ehdr = self.header_class()
assert_true(ehdr.get_dim_info() == (None, None, None))
for info in ((0, 2, 1),
(None, None, None),
(0, 2, None),
(0, None, None),
(None, 2, 1),
(None, None, 1),
):
ehdr.set_dim_info(*info)
assert_true(ehdr.get_dim_info() == info)
def test_slice_times(self):
hdr = self.header_class()
# error if slice dimension not specified
assert_raises(HeaderDataError, hdr.get_slice_times)
hdr.set_dim_info(slice=2)
# error if slice dimension outside shape
assert_raises(HeaderDataError, hdr.get_slice_times)
hdr.set_data_shape((1, 1, 7))
# error if slice duration not set
assert_raises(HeaderDataError, hdr.get_slice_times)
hdr.set_slice_duration(0.1)
# We need a function to print out the Nones and floating point
# values in a predictable way, for the tests below.
_stringer = lambda val: val is not None and '%2.1f' % val or None
_print_me = lambda s: list(map(_stringer, s))
# The following examples are from the nifti1.h documentation.
hdr['slice_code'] = slice_order_codes['sequential increasing']
assert_equal(_print_me(hdr.get_slice_times()),
['0.0', '0.1', '0.2', '0.3', '0.4', '0.5', '0.6'])
hdr['slice_start'] = 1
hdr['slice_end'] = 5
assert_equal(_print_me(hdr.get_slice_times()),
[None, '0.0', '0.1', '0.2', '0.3', '0.4', None])
hdr['slice_code'] = slice_order_codes['sequential decreasing']
assert_equal(_print_me(hdr.get_slice_times()),
[None, '0.4', '0.3', '0.2', '0.1', '0.0', None])
hdr['slice_code'] = slice_order_codes['alternating increasing']
assert_equal(_print_me(hdr.get_slice_times()),
[None, '0.0', '0.3', '0.1', '0.4', '0.2', None])
hdr['slice_code'] = slice_order_codes['alternating decreasing']
assert_equal(_print_me(hdr.get_slice_times()),
[None, '0.2', '0.4', '0.1', '0.3', '0.0', None])
hdr['slice_code'] = slice_order_codes['alternating increasing 2']
assert_equal(_print_me(hdr.get_slice_times()),
[None, '0.2', '0.0', '0.3', '0.1', '0.4', None])
hdr['slice_code'] = slice_order_codes['alternating decreasing 2']
assert_equal(_print_me(hdr.get_slice_times()),
[None, '0.4', '0.1', '0.3', '0.0', '0.2', None])
# test set
hdr = self.header_class()
hdr.set_dim_info(slice=2)
# need slice dim to correspond with shape
times = [None, 0.2, 0.4, 0.1, 0.3, 0.0, None]
assert_raises(HeaderDataError, hdr.set_slice_times, times)
hdr.set_data_shape([1, 1, 7])
assert_raises(HeaderDataError, hdr.set_slice_times,
times[:-1]) # wrong length
assert_raises(HeaderDataError, hdr.set_slice_times,
(None,) * len(times)) # all None
n_mid_times = times[:]
n_mid_times[3] = None
assert_raises(HeaderDataError, hdr.set_slice_times,
n_mid_times) # None in middle
funny_times = times[:]
funny_times[3] = 0.05
assert_raises(HeaderDataError, hdr.set_slice_times,
funny_times) # can't get single slice duration
hdr.set_slice_times(times)
assert_equal(hdr.get_value_label('slice_code'),
'alternating decreasing')
assert_equal(hdr['slice_start'], 1)
assert_equal(hdr['slice_end'], 5)
assert_array_almost_equal(hdr['slice_duration'], 0.1)
# Ambiguous case
hdr2 = self.header_class()
hdr2.set_dim_info(slice=2)
hdr2.set_slice_duration(0.1)
hdr2.set_data_shape((1, 1, 2))
with clear_and_catch_warnings() as w:
warnings.simplefilter("always")
hdr2.set_slice_times([0.1, 0])
assert len(w) == 1
# but always must be choosing sequential one first
assert_equal(hdr2.get_value_label('slice_code'), 'sequential decreasing')
# and the other direction
hdr2.set_slice_times([0, 0.1])
assert_equal(hdr2.get_value_label('slice_code'), 'sequential increasing')
def test_intents(self):
ehdr = self.header_class()
ehdr.set_intent('t test', (10,), name='some score')
assert_equal(ehdr.get_intent(),
('t test', (10.0,), 'some score'))
# unknown intent name or code - unknown name will fail even when
# allow_unknown=True
assert_raises(KeyError, ehdr.set_intent, 'no intention')
assert_raises(KeyError, ehdr.set_intent, 'no intention',
allow_unknown=True)
assert_raises(KeyError, ehdr.set_intent, 32767)
# too many parameters
assert_raises(HeaderDataError, ehdr.set_intent, 't test', (10, 10))
# too few parameters
assert_raises(HeaderDataError, ehdr.set_intent, 'f test', (10,))
# check unset parameters are set to 0, and name to ''
ehdr.set_intent('t test')
assert_equal((ehdr['intent_p1'], ehdr['intent_p2'], ehdr['intent_p3']),
(0, 0, 0))
assert_equal(ehdr['intent_name'], b'')
ehdr.set_intent('t test', (10,))
assert_equal((ehdr['intent_p2'], ehdr['intent_p3']), (0, 0))
# store intent that is not in nifti1.intent_codes recoder
ehdr.set_intent(9999, allow_unknown=True)
assert_equal(ehdr.get_intent(), ('unknown code 9999', (), ''))
assert_equal(ehdr.get_intent('code'), (9999, (), ''))
ehdr.set_intent(9999, name='custom intent', allow_unknown=True)
assert_equal(ehdr.get_intent(),
('unknown code 9999', (), 'custom intent'))
assert_equal(ehdr.get_intent('code'), (9999, (), 'custom intent'))
# store unknown intent with parameters. set_intent will set the
# parameters, but get_intent won't return them
ehdr.set_intent(code=9999, params=(1, 2, 3), allow_unknown=True)
assert_equal(ehdr.get_intent(), ('unknown code 9999', (), ''))
assert_equal(ehdr.get_intent('code'), (9999, (), ''))
# unknown intent requires either zero, or three, parameters
assert_raises(HeaderDataError, ehdr.set_intent, 999, (1,),
allow_unknown=True)
assert_raises(HeaderDataError, ehdr.set_intent, 999, (1,2),
allow_unknown=True)
def test_set_slice_times(self):
hdr = self.header_class()
hdr.set_dim_info(slice=2)
hdr.set_data_shape([1, 1, 7])
hdr.set_slice_duration(0.1)
times = [0] * 6
assert_raises(HeaderDataError, hdr.set_slice_times, times)
times = [None] * 7
assert_raises(HeaderDataError, hdr.set_slice_times, times)
times = [None, 0, 1, None, 3, 4, None]
assert_raises(HeaderDataError, hdr.set_slice_times, times)
times = [None, 0, 1, 2.1, 3, 4, None]
assert_raises(HeaderDataError, hdr.set_slice_times, times)
times = [None, 0, 4, 3, 2, 1, None]
assert_raises(HeaderDataError, hdr.set_slice_times, times)
times = [0, 1, 2, 3, 4, 5, 6]
hdr.set_slice_times(times)
assert_equal(hdr['slice_code'], 1)
assert_equal(hdr['slice_start'], 0)
assert_equal(hdr['slice_end'], 6)
assert_equal(hdr['slice_duration'], 1.0)
times = [None, 0, 1, 2, 3, 4, None]
hdr.set_slice_times(times)
assert_equal(hdr['slice_code'], 1)
assert_equal(hdr['slice_start'], 1)
assert_equal(hdr['slice_end'], 5)
assert_equal(hdr['slice_duration'], 1.0)
times = [None, 0.4, 0.3, 0.2, 0.1, 0, None]
hdr.set_slice_times(times)
assert_true(np.allclose(hdr['slice_duration'], 0.1))
times = [None, 4, 3, 2, 1, 0, None]
hdr.set_slice_times(times)
assert_equal(hdr['slice_code'], 2)
times = [None, 0, 3, 1, 4, 2, None]
hdr.set_slice_times(times)
assert_equal(hdr['slice_code'], 3)
times = [None, 2, 4, 1, 3, 0, None]
hdr.set_slice_times(times)
assert_equal(hdr['slice_code'], 4)
times = [None, 2, 0, 3, 1, 4, None]
hdr.set_slice_times(times)
assert_equal(hdr['slice_code'], 5)
times = [None, 4, 1, 3, 0, 2, None]
hdr.set_slice_times(times)
assert_equal(hdr['slice_code'], 6)
def test_xyzt_units(self):
hdr = self.header_class()
assert_equal(hdr.get_xyzt_units(), ('unknown', 'unknown'))
hdr.set_xyzt_units('mm', 'sec')
assert_equal(hdr.get_xyzt_units(), ('mm', 'sec'))
hdr.set_xyzt_units()
assert_equal(hdr.get_xyzt_units(), ('unknown', 'unknown'))
def test_recoded_fields(self):
hdr = self.header_class()
assert_equal(hdr.get_value_label('qform_code'), 'unknown')
hdr['qform_code'] = 3
assert_equal(hdr.get_value_label('qform_code'), 'talairach')
assert_equal(hdr.get_value_label('sform_code'), 'unknown')
hdr['sform_code'] = 3
assert_equal(hdr.get_value_label('sform_code'), 'talairach')
assert_equal(hdr.get_value_label('intent_code'), 'none')
hdr.set_intent('t test', (10,), name='some score')
assert_equal(hdr.get_value_label('intent_code'), 't test')
assert_equal(hdr.get_value_label('slice_code'), 'unknown')
hdr['slice_code'] = 4 # alternating decreasing
assert_equal(hdr.get_value_label('slice_code'),
'alternating decreasing')
def unshear_44(affine):
RZS = affine[:3, :3]
zooms = np.sqrt(np.sum(RZS * RZS, axis=0))
R = RZS / zooms
P, S, Qs = np.linalg.svd(R)
PR = np.dot(P, Qs)
return from_matvec(PR * zooms, affine[:3, 3])
class TestNifti1SingleHeader(TestNifti1PairHeader):
header_class = Nifti1Header
def test_empty(self):
tana.TestAnalyzeHeader.test_empty(self)
hdr = self.header_class()
assert_equal(hdr['magic'], hdr.single_magic)
assert_equal(hdr['scl_slope'], 1)
assert_equal(hdr['vox_offset'], 0)
def test_binblock_is_file(self):
# Override test that binary string is the same as the file on disk; in
# the case of the single file version of the header, we need to append
# the extension string (4 0s)
hdr = self.header_class()
str_io = BytesIO()
hdr.write_to(str_io)
assert_equal(str_io.getvalue(), hdr.binaryblock + b'\x00' * 4)
def test_float128(self):
hdr = self.header_class()
# Allow for Windows visual studio where longdouble is float64
ld_dt = np.dtype(np.longdouble)
if have_binary128() or ld_dt == np.dtype(np.float64):
hdr.set_data_dtype(np.longdouble)
assert_equal(hdr.get_data_dtype(), ld_dt)
else:
assert_raises(HeaderDataError, hdr.set_data_dtype, np.longdouble)
class TestNifti1Pair(tana.TestAnalyzeImage, tspm.ImageScalingMixin):
# Run analyze-flavor spatialimage tests
image_class = Nifti1Pair
supported_np_types = TestNifti1PairHeader.supported_np_types
def test_none_qsform(self):
# Check that affine gets set to q/sform if header is None
img_klass = self.image_class
hdr_klass = img_klass.header_class
shape = (2, 3, 4)
data = np.arange(24).reshape(shape)
# With specified affine
aff = from_matvec(euler2mat(0.1, 0.2, 0.3), [11, 12, 13])
for hdr in (None, hdr_klass()):
img = img_klass(data, aff, hdr)
assert_almost_equal(img.affine, aff)
assert_almost_equal(img.header.get_sform(), aff)
assert_almost_equal(img.header.get_qform(), aff)
# Even if affine is default for empty header
hdr = hdr_klass()
hdr.set_data_shape(shape)
default_aff = hdr.get_best_affine()
img = img_klass(data, default_aff, None)
assert_almost_equal(img.header.get_sform(), default_aff)
assert_almost_equal(img.header.get_qform(), default_aff)
# If affine is None, s/qform not set
img = img_klass(data, None, None)
assert_almost_equal(img.header.get_sform(), np.diag([0, 0, 0, 1]))
assert_almost_equal(img.header.get_qform(), np.eye(4))
def _qform_rt(self, img):
# Round trip image after setting qform, sform codes
hdr = img.header
hdr['qform_code'] = 3
hdr['sform_code'] = 4
# Save / reload using bytes IO objects
for key, value in img.file_map.items():
value.fileobj = BytesIO()
img.to_file_map()
return img.from_file_map(img.file_map)
def test_qform_cycle(self):
# Qform load save cycle
img_klass = self.image_class
# None affine
img = img_klass(np.zeros((2, 3, 4)), None)
hdr_back = self._qform_rt(img).header
assert_equal(hdr_back['qform_code'], 3)
assert_equal(hdr_back['sform_code'], 4)
# Try non-None affine
img = img_klass(np.zeros((2, 3, 4)), np.eye(4))
hdr_back = self._qform_rt(img).header
assert_equal(hdr_back['qform_code'], 3)
assert_equal(hdr_back['sform_code'], 4)
# Modify affine in-place - does it hold?
img.affine[0, 0] = 9
img.to_file_map()
img_back = img.from_file_map(img.file_map)
exp_aff = np.diag([9, 1, 1, 1])
assert_array_equal(img_back.affine, exp_aff)
hdr_back = img.header
assert_array_equal(hdr_back.get_sform(), exp_aff)
assert_array_equal(hdr_back.get_qform(), exp_aff)
def test_header_update_affine(self):
# Test that updating occurs only if affine is not allclose
img = self.image_class(np.zeros((2, 3, 4)), np.eye(4))
hdr = img.header
aff = img.affine
aff[:] = np.diag([1.1, 1.1, 1.1, 1]) # inexact floats
hdr.set_qform(aff, 2)
hdr.set_sform(aff, 2)
img.update_header()
assert_equal(hdr['sform_code'], 2)
assert_equal(hdr['qform_code'], 2)
def test_set_qform(self):
img = self.image_class(np.zeros((2, 3, 4)),
np.diag([2.2, 3.3, 4.3, 1]))
hdr = img.header
new_affine = np.diag([1.1, 1.1, 1.1, 1])
# Affine is same as sform (best affine)
assert_array_almost_equal(img.affine, hdr.get_best_affine())
# Reset affine to something different again
aff_affine = np.diag([3.3, 4.5, 6.6, 1])
img.affine[:] = aff_affine
assert_array_almost_equal(img.affine, aff_affine)
# Set qform using new_affine
img.set_qform(new_affine, 1)
assert_array_almost_equal(img.get_qform(), new_affine)
assert_equal(hdr['qform_code'], 1)
# Image get is same as header get
assert_array_almost_equal(img.get_qform(), new_affine)
# Coded version of get gets same information
qaff, code = img.get_qform(coded=True)
assert_equal(code, 1)
assert_array_almost_equal(qaff, new_affine)
# Image affine now reset to best affine (which is sform)
assert_array_almost_equal(img.affine, hdr.get_best_affine())
# Reset image affine and try update_affine == False
img.affine[:] = aff_affine
img.set_qform(new_affine, 1, update_affine=False)
assert_array_almost_equal(img.affine, aff_affine)
# Clear qform using None, zooms unchanged
assert_array_almost_equal(hdr.get_zooms(), [1.1, 1.1, 1.1])
img.set_qform(None)
qaff, code = img.get_qform(coded=True)
assert_equal((qaff, code), (None, 0))
assert_array_almost_equal(hdr.get_zooms(), [1.1, 1.1, 1.1])
# Best affine similarly
assert_array_almost_equal(img.affine, hdr.get_best_affine())
# If sform is not set, qform should update affine
img.set_sform(None)
img.set_qform(new_affine, 1)
qaff, code = img.get_qform(coded=True)
assert_equal(code, 1)
assert_array_almost_equal(img.affine, new_affine)
new_affine[0, 1] = 2
# If affine has has shear, should raise Error if strip_shears=False
img.set_qform(new_affine, 2)
assert_raises(HeaderDataError, img.set_qform, new_affine, 2, False)
# Unexpected keyword raises error
assert_raises(TypeError, img.get_qform, strange=True)
# updating None affine, None header does not work, because None header
# results in setting the sform to default
img = self.image_class(np.zeros((2, 3, 4)), None)
new_affine = np.eye(4)
img.set_qform(new_affine, 2)
assert_array_almost_equal(img.affine, img.header.get_best_affine())
# Unless we unset the sform
img.set_sform(None, update_affine=True)
assert_array_almost_equal(img.affine, new_affine)
def test_set_sform(self):
orig_aff = np.diag([2.2, 3.3, 4.3, 1])
img = self.image_class(np.zeros((2, 3, 4)), orig_aff)
hdr = img.header
new_affine = np.diag([1.1, 1.1, 1.1, 1])
qform_affine = np.diag([1.2, 1.2, 1.2, 1])
# Reset image affine to something different again
aff_affine = np.diag([3.3, 4.5, 6.6, 1])
img.affine[:] = aff_affine
assert_array_almost_equal(img.affine, aff_affine)
# Sform, Qform codes are 'aligned', 'unknown' by default
assert_equal((hdr['sform_code'], hdr['qform_code']), (2, 0))
# Set sform using new_affine when qform is 0
img.set_sform(new_affine, 1)
assert_equal(hdr['sform_code'], 1)
assert_array_almost_equal(hdr.get_sform(), new_affine)
# Image get is same as header get
assert_array_almost_equal(img.get_sform(), new_affine)
# Coded version gives same result
saff, code = img.get_sform(coded=True)
assert_equal(code, 1)
assert_array_almost_equal(saff, new_affine)
# Because we've reset the sform with update_affine, the affine changes
assert_array_almost_equal(img.affine, hdr.get_best_affine())
# Reset image affine and try update_affine == False
img.affine[:] = aff_affine
img.set_sform(new_affine, 1, update_affine=False)
assert_array_almost_equal(img.affine, aff_affine)
# zooms do not get updated when qform is 0
assert_array_almost_equal(img.get_qform(), orig_aff)
assert_array_almost_equal(hdr.get_zooms(), [2.2, 3.3, 4.3])
img.set_qform(None)
assert_array_almost_equal(hdr.get_zooms(), [2.2, 3.3, 4.3])
# Set sform using new_affine when qform is set
img.set_qform(qform_affine, 1)
img.set_sform(new_affine, 1)
saff, code = img.get_sform(coded=True)
assert_equal(code, 1)
assert_array_almost_equal(saff, new_affine)
assert_array_almost_equal(img.affine, new_affine)
# zooms follow qform
assert_array_almost_equal(hdr.get_zooms(), [1.2, 1.2, 1.2])
# Clear sform using None, best_affine should fall back on qform
img.set_sform(None)
assert_equal(hdr['sform_code'], 0)
assert_equal(hdr['qform_code'], 1)
# Sform holds previous affine from last set
assert_array_almost_equal(hdr.get_sform(), saff)
# Image affine follows qform
assert_array_almost_equal(img.affine, qform_affine)
assert_array_almost_equal(hdr.get_best_affine(), img.affine)
# Unexpected keyword raises error
assert_raises(TypeError, img.get_sform, strange=True)
# updating None affine should also work
img = self.image_class(np.zeros((2, 3, 4)), None)
new_affine = np.eye(4)
img.set_sform(new_affine, 2)
assert_array_almost_equal(img.affine, new_affine)
def test_sqform_code_type(self):
# make sure get_s/qform returns codes as integers
img = self.image_class(np.zeros((2, 3, 4)), None)
assert isinstance(img.get_sform(coded=True)[1], six.integer_types)
assert isinstance(img.get_qform(coded=True)[1], six.integer_types)
img.set_sform(None, 3)
img.set_qform(None, 3)
assert isinstance(img.get_sform(coded=True)[1], six.integer_types)
assert isinstance(img.get_qform(coded=True)[1], six.integer_types)
img.set_sform(None, 2.0)
img.set_qform(None, 4.0)
assert isinstance(img.get_sform(coded=True)[1], six.integer_types)
assert isinstance(img.get_qform(coded=True)[1], six.integer_types)
img.set_sform(None, img.get_sform(coded=True)[1])
img.set_qform(None, img.get_qform(coded=True)[1])
def test_hdr_diff(self):
# Check an offset beyond data does not raise an error
img = self.image_class(np.zeros((2, 3, 4)), np.eye(4))
ext = dict(img.files_types)['image']
hdr_len = len(img.header.binaryblock)
img.header['vox_offset'] = hdr_len + 400
with InTemporaryDirectory():
img.to_filename('another_file' + ext)
def test_load_save(self):
IC = self.image_class
img_ext = IC.files_types[0][1]
shape = (2, 4, 6)
npt = np.float32
data = np.arange(np.prod(shape), dtype=npt).reshape(shape)
affine = np.diag([1, 2, 3, 1])
img = IC(data, affine)
assert_equal(img.header.get_data_offset(), 0)
assert_equal(img.shape, shape)
img.set_data_dtype(npt)
img2 = bytesio_round_trip(img)
assert_array_equal(img2.get_data(), data)
with InTemporaryDirectory() as tmpdir:
for ext in ('', '.gz', '.bz2'):
fname = os.path.join(tmpdir, 'test' + img_ext + ext)
img.to_filename(fname)
img3 = IC.load(fname)
assert_true(isinstance(img3, img.__class__))
assert_array_equal(img3.get_data(), data)
assert_equal(img3.header, img.header)
assert_true(isinstance(img3.get_data(),
np.memmap if ext == '' else np.ndarray))
# del to avoid windows errors of form 'The process cannot
# access the file because it is being used'
del img3
def test_load_pixdims(self):
# Make sure load preserves separate qform, pixdims, sform
IC = self.image_class
HC = IC.header_class
arr = np.arange(24).reshape((2, 3, 4))
qaff = np.diag([2, 3, 4, 1])
saff = np.diag([5, 6, 7, 1])
hdr = HC()
hdr.set_qform(qaff)
assert_array_equal(hdr.get_qform(), qaff)
hdr.set_sform(saff)
assert_array_equal(hdr.get_sform(), saff)
simg = IC(arr, None, hdr)
img_hdr = simg.header
# Check qform, sform, pixdims are the same
assert_array_equal(img_hdr.get_qform(), qaff)
assert_array_equal(img_hdr.get_sform(), saff)
assert_array_equal(img_hdr.get_zooms(), [2, 3, 4])
# Save to stringio
re_simg = bytesio_round_trip(simg)
assert_array_equal(re_simg.get_data(), arr)
# Check qform, sform, pixdims are the same