/usr/lib/python2.7/dist-packages/dipy/tests/test_scripts.py is in python-dipy 0.10.1-1.
This file is owned by root:root, with mode 0o644.
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# vi: set ft=python sts=4 ts=4 sw=4 et:
""" Test scripts
Run scripts and check outputs
"""
from __future__ import division, print_function, absolute_import
import os
import shutil
from os.path import (dirname, join as pjoin, abspath)
from nose.tools import assert_true, assert_false, assert_equal
import numpy.testing as nt
import nibabel as nib
from nibabel.tmpdirs import InTemporaryDirectory
from dipy.data import get_data
# Quickbundles command-line requires matplotlib:
try:
import matplotlib
no_mpl = False
except ImportError:
no_mpl = True
from .scriptrunner import ScriptRunner
runner = ScriptRunner(
script_sdir = 'bin',
debug_print_var = 'NIPY_DEBUG_PRINT')
run_command = runner.run_command
DATA_PATH = abspath(pjoin(dirname(__file__), 'data'))
def test_dipy_peak_extraction():
# test dipy_peak_extraction script
cmd = 'dipy_peak_extraction'
code, stdout, stderr = run_command(cmd, check_code=False)
assert_equal(code, 2)
def test_dipy_fit_tensor():
# test dipy_fit_tensor script
cmd = 'dipy_fit_tensor'
code, stdout, stderr = run_command(cmd, check_code=False)
assert_equal(code, 2)
def test_dipy_sh_estimate():
# test dipy_sh_estimate script
cmd = 'dipy_sh_estimate'
code, stdout, stderr = run_command(cmd, check_code=False)
assert_equal(code, 2)
def assert_image_shape_affine(filename, shape, affine):
assert_true(os.path.isfile(filename))
image = nib.load(filename)
assert_equal(image.shape, shape)
nt.assert_array_almost_equal(image.get_affine(), affine)
def test_dipy_fit_tensor_again():
with InTemporaryDirectory():
dwi, bval, bvec = get_data("small_25")
# Copy data to tmp directory
shutil.copyfile(dwi, "small_25.nii.gz")
shutil.copyfile(bval, "small_25.bval")
shutil.copyfile(bvec, "small_25.bvec")
# Call script
cmd = ["dipy_fit_tensor", "--mask=none", "small_25.nii.gz"]
out = run_command(cmd)
assert_equal(out[0], 0)
# Get expected values
img = nib.load("small_25.nii.gz")
affine = img.get_affine()
shape = img.shape[:-1]
# Check expected outputs
assert_image_shape_affine("small_25_fa.nii.gz", shape, affine)
assert_image_shape_affine("small_25_t2di.nii.gz", shape, affine)
assert_image_shape_affine("small_25_dirFA.nii.gz", shape, affine)
assert_image_shape_affine("small_25_ad.nii.gz", shape, affine)
assert_image_shape_affine("small_25_md.nii.gz", shape, affine)
assert_image_shape_affine("small_25_rd.nii.gz", shape, affine)
with InTemporaryDirectory():
dwi, bval, bvec = get_data("small_25")
# Copy data to tmp directory
shutil.copyfile(dwi, "small_25.nii.gz")
shutil.copyfile(bval, "small_25.bval")
shutil.copyfile(bvec, "small_25.bvec")
# Call script
cmd = ["dipy_fit_tensor", "--save-tensor", "--mask=none", "small_25.nii.gz"]
out = run_command(cmd)
assert_equal(out[0], 0)
# Get expected values
img = nib.load("small_25.nii.gz")
affine = img.get_affine()
shape = img.shape[:-1]
# Check expected outputs
assert_image_shape_affine("small_25_fa.nii.gz", shape, affine)
assert_image_shape_affine("small_25_t2di.nii.gz", shape, affine)
assert_image_shape_affine("small_25_dirFA.nii.gz", shape, affine)
assert_image_shape_affine("small_25_ad.nii.gz", shape, affine)
assert_image_shape_affine("small_25_md.nii.gz", shape, affine)
assert_image_shape_affine("small_25_rd.nii.gz", shape, affine)
# small_25_tensor saves the tensor as a symmetric matrix following
# the nifti standard.
ten_shape = shape + (1, 6)
assert_image_shape_affine("small_25_tensor.nii.gz", ten_shape,
affine)
@nt.dec.skipif(no_mpl)
def test_qb_commandline():
with InTemporaryDirectory():
tracks_file = get_data('fornix')
cmd = ["dipy_quickbundles", tracks_file, '--pkl_file', 'mypickle.pkl',
'--out_file', 'tracks300.trk']
out = run_command(cmd)
assert_equal(out[0], 0)
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