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Commit 8bc789a8 authored by Paul McCarthy's avatar Paul McCarthy
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More path tests, and tests for fsl.data.image

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tests/test_fsl_utils_path.py
+ 12
− 10
View file @ 8bc789a8
......@@ -10,6 +10,7 @@ import os.path as op
import pytest
import fsl.utils.path as fslpath
import fsl.data.image as fslimage
def test_addExt_exists_shouldPass(testdir):
......@@ -17,9 +18,8 @@ def test_addExt_exists_shouldPass(testdir):
are valid.
"""
# If we have a .hdr/.img pair, the .img should take precedence
replacements = {'.hdr' : ['.img', '.img.gz']}
allowedExts = ['.hdr', '.img', '.nii', '.nii.gz', '.img.gz']
replacements = fslimage.REPLACEMENTS
allowedExts = fslimage.ALLOWED_EXTENSIONS
tests = [
('compressed', 'compressed.nii.gz'),
......@@ -30,7 +30,7 @@ def test_addExt_exists_shouldPass(testdir):
('img_hdr_pair.hdr', 'img_hdr_pair.hdr'),
('img_hdr_pair.img', 'img_hdr_pair.img'),
('compressed_img_hdr_pair', 'compressed_img_hdr_pair.img.gz'),
('compressed_img_hdr_pair.hdr', 'compressed_img_hdr_pair.hdr'),
('compressed_img_hdr_pair.hdr.gz', 'compressed_img_hdr_pair.hdr.gz'),
('compressed_img_hdr_pair.img.gz', 'compressed_img_hdr_pair.img.gz'),
]
......@@ -48,9 +48,9 @@ def test_addExt_exists_shouldFail(testdir):
"""Tests the addExt function with inputs that should cause it to raise an
error.
"""
replacements = {'.hdr' : ['.img', '.img.gz']}
allowedExts = ['.hdr', '.img', '.nii', '.nii.gz', '.img.gz']
replacements = fslimage.REPLACEMENTS
allowedExts = fslimage.ALLOWED_EXTENSIONS
shouldFail = [
......@@ -73,6 +73,8 @@ def test_addExt_exists_shouldFail(testdir):
('ambiguous', [], {'.hdr' : ['.img']}),
('ambiguous', False, {'.hdr' : ['.img.gz']}),
('ambiguous', [], {'.hdr' : ['.img.gz']}),
('ambiguous', False, {'.hdr' : ['.img', '.img.gz', '.nii']}),
('ambiguous', [], {'.hdr' : ['.img', '.img.gz', '.nii']}),
('badpath'),
('badpath.nii.gz'),
......@@ -101,7 +103,7 @@ def test_addExt_exists_shouldFail(testdir):
def test_addExt_noExist(testdir):
allowedExts = ['.hdr', '.img', '.nii', '.nii.gz', '.img.gz']
allowedExts = fslimage.ALLOWED_EXTENSIONS
# Prefix, output, defaultExt, allowedExts
tests = [
......@@ -136,7 +138,7 @@ def test_addExt_noExist(testdir):
def test_removeExt(testdir):
allowedExts = ['.hdr', '.img', '.nii', '.nii.gz', '.img.gz']
allowedExts = fslimage.ALLOWED_EXTENSIONS
# If len(test) == 2, allowedExts is set from above
# Otherwise, it is set from the test tuple
......@@ -170,7 +172,7 @@ def test_removeExt(testdir):
def test_getExt(testdir):
allowedExts = ['.hdr', '.img', '.nii', '.nii.gz', '.img.gz']
allowedExts = fslimage.ALLOWED_EXTENSIONS
# len(test) == 2 -> allowedExts set from above
# Otherwise, allowedExts set from test tuple
......
tests/test_image.py
+ 156
− 9
View file @ 8bc789a8
......@@ -6,13 +6,16 @@
#
import os.path as op
import logging
import pytest
import glob
import numpy as np
import nibabel as nib
import fsl.data.image as fslimage
import fsl.data.constants as constants
import fsl.data.image as fslimage
import fsl.utils.path as fslpath
# Need to test:
......@@ -25,13 +28,157 @@ import fsl.data.image as fslimage
def test_load(testdir):
assert testdir is not None
shouldPass = ['compressed',
'compressed.nii.gz',
'uncompressed',
'uncompressed.nii',
'img_hdr_pair',
'img_hdr_pair.img',
'img_hdr_pair.hdr',
'compressed_img_hdr_pair',
'compressed_img_hdr_pair.img.gz',
'compressed_img_hdr_pair.hdr.gz',
'ambiguous.nii',
'ambiguous.hdr',
'ambiguous.img',
'ambiguous.hdr.gz',
'ambiguous.img.gz']
shouldRaise = ['notexist',
'notexist.nii.gz',
'ambiguous']
fslimage.Image(op.join(testdir, 'nifti_formats', 'compressed'))
fslimage.Image(op.join(testdir, 'nifti_formats', 'compressed.nii.gz'))
fslimage.Image(op.join(testdir, 'nifti_formats', 'uncompressed'))
fslimage.Image(op.join(testdir, 'nifti_formats', 'uncompressed.nii'))
fslimage.Image(op.join(testdir, 'nifti_formats', 'img_hdr_pair'))
fslimage.Image(op.join(testdir, 'nifti_formats', 'img_hdr_pair.img'))
fslimage.Image(op.join(testdir, 'nifti_formats', 'img_hdr_pair.hdr'))
# Not raising an error means the test passes
for fname in shouldPass:
fslimage.Image(op.join(testdir, 'nifti_formats', fname))
# These should raise an error
for fname in shouldRaise:
with pytest.raises(fslpath.PathError):
print fname
fslimage.Image(op.join(testdir, 'nifti_formats', fname))
def test_Image_atts(testdir):
allowedExts = fslimage.ALLOWED_EXTENSIONS
# (file, dims, pixdims)
tests = [
('MNI152_T1_0.5mm', (364, 436, 364), (0.5, 0.5, 0.5), np.uint8),
('MNI152_T1_1mm', (182, 218, 182), (1.0, 1.0, 1.0), np.int16),
('MNI152_T1_2mm', (91, 109, 91), (2.0, 2.0, 2.0), np.int16),
('MNI152_T1_2mm_4D', (91, 109, 91, 5), (2.0, 2.0, 2.0, 1.0), np.int16),
(op.join('nifti2D', 'MNI152_T1_2mm_sliceXY'), (91, 109, 1), (2.0, 2.0, 2.0), np.int16),
(op.join('nifti2D', 'MNI152_T1_2mm_sliceXZ'), (91, 1, 91), (2.0, 2.0, 2.0), np.int16),
(op.join('nifti2D', 'MNI152_T1_2mm_sliceYZ'), (1, 109, 91), (2.0, 2.0, 2.0), np.int16)]
for path, dims, pixdims, dtype in tests:
path = op.abspath(op.join(testdir, path))
i = fslimage.Image(path)
assert tuple(i.shape) == tuple(dims)
assert tuple(i.pixdim) == tuple(pixdims)
assert tuple(i.nibImage.shape) == tuple(dims)
assert tuple(i.nibImage.header.get_zooms()) == tuple(pixdims)
assert i.dtype == dtype
assert i.name == op.basename(path)
assert i.dataSource == fslpath.addExt(path, allowedExts, mustExist=True)
def test_looksLikeImage():
# (file, expected)
tests = [
('blah', False),
('blah.moo', False),
('blah.nii', True),
('blah.nii.gz', True),
('blah.hdr', True),
('blah.img', True),
('blah.hdr.gz', True),
('blah.img.gz', True),
]
for path, expected in tests:
assert fslimage.looksLikeImage(path) == expected
def test_addExt(testdir):
default = fslimage.DEFAULT_EXTENSION
# (file, mustExist, expected)
tests = [
('blah', False, 'blah{}'.format(default)),
('blah.nii', False, 'blah.nii'),
('blah.nii.gz', False, 'blah.nii.gz'),
('blah.img', False, 'blah.img'),
('blah.hdr', False, 'blah.hdr'),
('blah.img.gz', False, 'blah.img.gz'),
('blah.hdr.gz', False, 'blah.hdr.gz'),
('compressed', True, 'compressed.nii.gz'),
('compressed.nii.gz', True, 'compressed.nii.gz'),
('uncompressed', True, 'uncompressed.nii'),
('uncompressed.nii', True, 'uncompressed.nii'),
('img_hdr_pair', True, 'img_hdr_pair.img'),
('img_hdr_pair.hdr', True, 'img_hdr_pair.hdr'),
('img_hdr_pair.img', True, 'img_hdr_pair.img'),
('compressed_img_hdr_pair', True, 'compressed_img_hdr_pair.img.gz'),
('compressed_img_hdr_pair.img.gz', True, 'compressed_img_hdr_pair.img.gz'),
('compressed_img_hdr_pair.hdr.gz', True, 'compressed_img_hdr_pair.hdr.gz'),
('ambiguous.nii', True, 'ambiguous.nii'),
('ambiguous.nii.gz', True, 'ambiguous.nii.gz'),
('ambiguous.img', True, 'ambiguous.img'),
('ambiguous.hdr', True, 'ambiguous.hdr'),
('ambiguous.img.gz', True, 'ambiguous.img.gz'),
('ambiguous.hdr.gz', True, 'ambiguous.hdr.gz')]
for path, mustExist, expected in tests:
if mustExist:
path = op.join(testdir, 'nifti_formats', path)
expected = op.join(testdir, 'nifti_formats', expected)
assert fslimage.addExt(path, mustExist) == expected
with pytest.raises(fslimage.PathError):
path = op.join(testdir, 'nifti_formats', 'ambiguous')
fslimage.addExt(path, mustExist=True)
def test_Image_orientation(testdir):
neuro = op.join(testdir, 'dtifit', 'neuro', 'dti_FA')
radio = op.join(testdir, 'dtifit', 'radio', 'dti_FA')
neuro = fslimage.Image(neuro)
radio = fslimage.Image(radio)
assert neuro.isNeurological()
assert not radio.isNeurological()
# Both images should have the
# same orientation in the
# world coordinate system
assert neuro.getOrientation(0, np.eye(4)) == constants.ORIENT_L2R
assert neuro.getOrientation(1, np.eye(4)) == constants.ORIENT_P2A
assert neuro.getOrientation(2, np.eye(4)) == constants.ORIENT_I2S
assert radio.getOrientation(0, np.eye(4)) == constants.ORIENT_L2R
assert radio.getOrientation(1, np.eye(4)) == constants.ORIENT_P2A
assert radio.getOrientation(2, np.eye(4)) == constants.ORIENT_I2S
# The radio image should be
# l/r flipped in the voxel
# coordinate system
assert neuro.getOrientation(0, neuro.worldToVoxMat) == constants.ORIENT_L2R
assert neuro.getOrientation(1, neuro.worldToVoxMat) == constants.ORIENT_P2A
assert neuro.getOrientation(2, neuro.worldToVoxMat) == constants.ORIENT_I2S
assert radio.getOrientation(0, radio.worldToVoxMat) == constants.ORIENT_R2L
assert radio.getOrientation(1, radio.worldToVoxMat) == constants.ORIENT_P2A
assert radio.getOrientation(2, radio.worldToVoxMat) == constants.ORIENT_I2S
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