#!/usr/bin/env python
#
# test_fsl_utils_path.py - Tests functions in the fsl.utils.path module.
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
from __future__ import print_function
import os
import os.path as op
import shutil
import tempfile
import pytest
import fsl.utils.path as fslpath
import fsl.data.image as fslimage
def test_addExt_exists_shouldPass(testdir):
"""Tests the addExt function where the path exists, and the inputs
are valid.
"""
groups = fslimage.FILE_GROUPS
allowedExts = fslimage.ALLOWED_EXTENSIONS
tests = [
('compressed', 'compressed.nii.gz'),
('compressed.nii.gz', 'compressed.nii.gz'),
('uncompressed', 'uncompressed.nii'),
('uncompressed.nii', 'uncompressed.nii'),
('img_hdr_pair', 'img_hdr_pair.img'),
('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.gz', 'compressed_img_hdr_pair.hdr.gz'),
('compressed_img_hdr_pair.img.gz', 'compressed_img_hdr_pair.img.gz'),
]
for test in tests:
prefix = op.join(testdir, 'nifti_formats', test[0])
output = op.join(testdir, 'nifti_formats', test[1])
assert fslpath.addExt(prefix,
allowedExts,
mustExist=True,
fileGroups=groups) == output
def test_addExt_exists_shouldFail(testdir):
"""Tests the addExt function with inputs that should cause it to raise an
error.
"""
groups = fslimage.FILE_GROUPS
allowedExts = fslimage.ALLOWED_EXTENSIONS
shouldFail = [
# For tests of length 1, allowedExts/replacements are set from above
#
# For tests of length 2, replacements is set from above, allowedExts
# is set from the tuple (unless False)
#
# For tests of length 3, replacements and allowedExts are set
# from the tuple (unless False)
('compressed', []),
('compressed', ['.badsuf']),
('img_hdr_pair'),
('img_hdr_pair', []),
('ambiguous'),
('ambiguous', []),
('ambiguous', False, {'.hdr' : ['.img']}),
('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'),
]
for test in shouldFail:
prefix = op.join(testdir, 'nifti_formats', test[0])
allowed = allowedExts
group = groups
if len(test) >= 2:
if not (test[1] == False):
allowed = test[1]
if len(test) == 3:
if not (test[2] == False):
group = test[2]
with pytest.raises(fslpath.PathError):
fslpath.addExt(prefix,
allowed,
mustExist=True,
fileGroups=group)
def test_addExt_noExist(testdir):
allowedExts = fslimage.ALLOWED_EXTENSIONS
# Prefix, output, defaultExt, allowedExts
tests = [
('blah', 'blahblah', 'blah'),
('blah', 'blah.blah', '.blah'),
('blah', None, None),
('blah.nii', None, None, ['blah']),
('blah.nii', 'blah.nii', 'blah'),
('blah', 'blah.nii', '.nii'),
('blah', 'blah.nii', '.nii', []),
('blah.nii.gz', 'blah.nii.gz', 'blah'),
('blah', 'blah.nii', '.nii'),
('blah', 'blah.nii', '.nii', []),
]
for test in tests:
prefix = test[0]
output = test[1]
if len(test) >= 3: default = test[2]
else: default = None
if len(test) >= 4: allowed = test[3]
else: allowed = allowedExts
assert fslpath.addExt(prefix,
allowed,
defaultExt=default,
mustExist=False) == output
def test_removeExt():
allowedExts = fslimage.ALLOWED_EXTENSIONS
# If len(test) == 2, allowedExts is set from above
# Otherwise, it is set from the test tuple
tests = [
('blah', 'blah'),
('blah.blah', 'blah.blah'),
('blah.blah', 'blah', ['.blah']),
('blah.blah', 'blah.', ['blah']),
('blah.nii', 'blah'),
('blah.nii.gz', 'blah'),
('blah.img', 'blah'),
('blah.hdr', 'blah'),
('blah.img.gz', 'blah'),
('blah.nii.gz', 'blah.nii.gz', []),
('blah.nii.gz', 'blah.nii', ['.gz']),
('blah.nii.gz', 'blah.nii.gz', ['.nii']),
('blah.nii.gz', 'blah', ['.nii.gz']),
('blah.nii.gz', 'blah.', ['nii.gz']),
]
for test in tests:
path = test[0]
output = test[1]
if len(test) == 2: allowed = allowedExts
else: allowed = test[2]
assert fslpath.removeExt(path, allowed) == output
def test_getExt():
allowedExts = fslimage.ALLOWED_EXTENSIONS
# len(test) == 2 -> allowedExts set from above
# Otherwise, allowedExts set from test tuple
tests = [
('blah.blah', '.blah', None),
('blah.blah', '.blah', ['.blah']),
('blah.blah', 'blah', ['blah']),
('blah', '', None),
('blah.nii', '.nii', None),
('blah.nii.gz', '.gz', None),
('blah.nii', '.nii'),
('blah.nii.gz', '.nii.gz'),
('blah.hdr', '.hdr'),
('blah.img', '.img'),
('blah.img.gz', '.img.gz'),
('blah', ''),
('blah.blah', ''),
('blah.blah', '', ['bla']),
('blah.nii.gz', '', ['.nii']),
]
for test in tests:
filename = test[0]
output = test[1]
if len(test) == 2: allowed = allowedExts
else: allowed = test[2]
print(filename, '==', output)
assert fslpath.getExt(filename, allowed) == output
def test_splitExt():
allowedExts = fslimage.ALLOWED_EXTENSIONS
# len(test) == 2 -> allowedExts set from above
# Otherwise, allowedExts set from test tuple
tests = [
('blah', ('blah', '')),
('blah.blah', ('blah.blah', '')),
('blah.blah', ('blah', '.blah'), ['.blah']),
('blah.blah', ('blah.', 'blah'), ['blah']),
('blah.nii', ('blah', '.nii')),
('blah.nii.gz', ('blah', '.nii.gz')),
('blah.img', ('blah', '.img')),
('blah.hdr', ('blah', '.hdr')),
('blah.img.gz', ('blah', '.img.gz')),
('blah.nii.gz', ('blah.nii.gz', ''), []),
('blah.nii.gz', ('blah.nii', '.gz'), ['.gz']),
('blah.nii.gz', ('blah.nii.gz', ''), ['.nii']),
('blah.nii.gz', ('blah', '.nii.gz'), ['.nii.gz']),
('blah.nii.gz', ('blah.', 'nii.gz'), ['nii.gz']),
('blah.blah', ('blah', '.blah'), None),
('blah.blah', ('blah', '.blah'), ['.blah']),
('blah.blah', ('blah.', 'blah'), ['blah']),
('blah', ('blah', ''), None),
('blah.nii', ('blah', '.nii'), None),
('blah.nii.gz', ('blah.nii', '.gz'), None),
('blah.nii', ('blah', '.nii')),
('blah.nii.gz', ('blah', '.nii.gz')),
('blah.hdr', ('blah', '.hdr')),
('blah.img', ('blah', '.img')),
('blah.img.gz', ('blah', '.img.gz')),
('blah', ('blah', '')),
('blah.blah', ('blah.blah', '')),
('blah.blah', ('blah.blah', ''), ['bla']),
('blah.nii.gz', ('blah.nii.gz', ''), ['.nii']),
]
for test in tests:
filename = test[0]
outbase, outext = test[1]
if len(test) == 2: allowed = allowedExts
else: allowed = test[2]
print(filename, '==', (outbase, outext))
assert fslpath.splitExt(filename, allowed) == (outbase, outext)
def test_deepest():
# path, suffixes, output
tests = [
('/blah.feat/foo.ica/fum.gfeat/moo.ica', ['.feat'], '/blah.feat'),
('/blah.feat/foo.ica/fum.gfeat/moo.ica', ['.feat', '.gfeat'], '/blah.feat/foo.ica/fum.gfeat'),
('/blah.feat/foo.ica/fum.gfeat/moo.ica', ['.gfeat'], '/blah.feat/foo.ica/fum.gfeat'),
('/blah.feat/foo.ica/fum.gfeat/moo.ica', ['.ica'], '/blah.feat/foo.ica/fum.gfeat/moo.ica'),
('/blah.feat/foo.ica/fum.gfeat/moo.ica', ['.bob'], None),
('/blah.feat/foo.ica/fum.gfeat/moo.bob', ['.ica'], '/blah.feat/foo.ica'),
('/blah.feat/foo.ica/fum.gfeat/moo.bob', ['.bob'], '/blah.feat/foo.ica/fum.gfeat/moo.bob'),
( 'blah.feat/foo.ica/fum.gfeat/moo.ica', ['.feat'], 'blah.feat'),
( 'blah.feat/foo.ica/fum.gfeat/moo.ica', ['.feat', '.gfeat'], 'blah.feat/foo.ica/fum.gfeat'),
( 'blah.feat/foo.ica/fum.gfeat/moo.ica', ['.gfeat'], 'blah.feat/foo.ica/fum.gfeat'),
( 'blah.feat/foo.ica/fum.gfeat/moo.ica', ['.ica'], 'blah.feat/foo.ica/fum.gfeat/moo.ica'),
( 'blah.feat/foo.ica/fum.gfeat/moo.ica', ['.bob'], None),
( 'blah.feat/foo.ica/fum.gfeat/moo.bob', ['.ica'], 'blah.feat/foo.ica'),
( 'blah.feat/foo.ica/fum.gfeat/moo.bob', ['.ica', '.bob'], 'blah.feat/foo.ica/fum.gfeat/moo.bob'),
('/', [], None),
('', [], None),
('///', [], None),
('/', ['blah'], None),
('', ['blah'], None),
('///', ['blah'], None),
]
for path, suffixes, output in tests:
assert fslpath.deepest(path, suffixes) == output
def test_shallowest():
# path, suffixes, output
tests = [
('/blah.feat/foo.ica/fum.gfeat/moo.ica', ['.feat'], '/blah.feat'),
('/blah.feat/foo.ica/fum.gfeat/moo.ica', ['.feat', '.gfeat'], '/blah.feat'),
('/blah.feat/foo.ica/fum.gfeat/moo.ica', ['.gfeat'], '/blah.feat/foo.ica/fum.gfeat'),
('/blah.feat/foo.ica/fum.gfeat/moo.ica', ['.ica'], '/blah.feat/foo.ica'),
('/blah.feat/foo.ica/fum.gfeat/moo.ica', ['.bob'], None),
('/blah.feat/foo.ica/fum.gfeat/moo.bob', ['.ica'], '/blah.feat/foo.ica'),
('/blah.feat/foo.ica/fum.gfeat/moo.bob', ['.bob'], '/blah.feat/foo.ica/fum.gfeat/moo.bob'),
( 'blah.feat/foo.ica/fum.gfeat/moo.ica', ['.feat'], 'blah.feat'),
( 'blah.feat/foo.ica/fum.gfeat/moo.ica', ['.feat', '.gfeat'], 'blah.feat'),
( 'blah.feat/foo.ica/fum.gfeat/moo.ica', ['.gfeat'], 'blah.feat/foo.ica/fum.gfeat'),
( 'blah.feat/foo.ica/fum.gfeat/moo.ica', ['.ica'], 'blah.feat/foo.ica'),
( 'blah.feat/foo.ica/fum.gfeat/moo.ica', ['.bob'], None),
( 'blah.feat/foo.ica/fum.gfeat/moo.bob', ['.ica'], 'blah.feat/foo.ica'),
( 'blah.feat/foo.ica/fum.gfeat/moo.bob', ['.ica', '.bob'], 'blah.feat/foo.ica'),
(' blah.feat/foo.ica/fum.gfeat/moo.bob', ['.ica', '.bob'], 'blah.feat/foo.ica'),
('/', [], None),
('', [], None),
('///', [], None),
('/', ['blah'], None),
('', ['blah'], None),
('///', ['blah'], None),
]
for path, suffixes, output in tests:
assert fslpath.shallowest(path, suffixes) == output
def test_removeDuplicates():
allowedExts = fslimage.ALLOWED_EXTENSIONS
groups = fslimage.FILE_GROUPS
# [(files_to_create,
# [([paths], [expected]),
# ...
# ]),
# ...
# ]
allTests = [
(['file.hdr', 'file.img'], [
(['file'], ['file']),
(['file.hdr'], ['file.hdr']),
(['file.img'], ['file.img']),
(['file.hdr', 'file.img'], ['file.hdr']),
(['file.img', 'file.hdr'], ['file.img']),
]),
(['file.hdr', 'file.img', 'file.blob'], [
(['file'], ['file']),
(['file.hdr'], ['file.hdr']),
(['file.img'], ['file.img']),
(['file.hdr', 'file.img'], ['file.hdr']),
(['file.img', 'file.hdr'], ['file.img']),
]),
(['file.hdr', 'file.img', 'file.nii'], [
(['file'], ['file']),
(['file.hdr'], ['file.hdr']),
(['file.img'], ['file.img']),
(['file.hdr', 'file.img'], ['file.hdr']),
(['file.img', 'file.hdr'], ['file.img']),
]),
(['001.hdr', '001.img', '002.hdr', '002.img', '003.hdr', '003.img'], [
(['001', '002', '003'],
['001', '002', '003']),
(['001.hdr', '002.hdr', '003.hdr'],
['001.hdr', '002.hdr', '003.hdr']),
(['001.img', '002.img', '003.img'],
['001.img', '002.img', '003.img']),
(['001.hdr', '001.img', '002.hdr', '002.img', '003.img'],
['001.hdr', '002.hdr', '003.img']),
(['001.hdr', '001.img', '002.hdr', '002.img', '003.hdr', '003.img'],
['001.hdr', '002.hdr', '003.hdr']),
(['001.img', '001.hdr', '002.img', '002.hdr', '003.img', '003.hdr'],
['001.img', '002.img', '003.img']),
])
]
workdir = tempfile.mkdtemp()
try:
for files_to_create, tests in allTests:
for fn in files_to_create:
with open(op.join(workdir, fn), 'wt') as f:
f.write('{}\n'.format(fn))
for paths, expected in tests:
paths = [op.join(workdir, p) for p in paths]
result = fslpath.removeDuplicates(paths, allowedExts, groups)
assert result == [op.join(workdir, e) for e in expected]
for f in files_to_create:
os.remove(op.join(workdir, f))
finally:
shutil.rmtree(workdir)
def test_getFileGroup():
allowedExts = fslimage.ALLOWED_EXTENSIONS
groups = fslimage.FILE_GROUPS
# (files_to_create,
# [(path, expected),
# ...
# ]
# )
#
# expected == 'all' is equivalent to expected == files_to_create
allTests = [
(['file.hdr', 'file.img'], [
('file.hdr', 'all'),
('file.img', 'all')]),
(['file.hdr.gz', 'file.img.gz'], [
('file.hdr.gz', 'all'),
('file.img.gz', 'all')]),
(['file.hdr', 'file.img', 'file.nii'], [
('file.hdr', ['file.hdr', 'file.img']),
('file.img', ['file.hdr', 'file.img'])]),
(['file.hdr', 'file.img', 'file.blob'], [
('file.hdr', ['file.hdr', 'file.img']),
('file.img', ['file.hdr', 'file.img'])]),
(['file.hdr'], [
('file.hdr', ['file.hdr']),
('file.img', ['file.img'])]),
(['file.img'], [
('file.hdr', ['file.hdr']),
('file.img', ['file.img'])]),
]
workdir = tempfile.mkdtemp()
try:
for files_to_create, tests in allTests:
for fn in files_to_create:
with open(op.join(workdir, fn), 'wt') as f:
f.write('{}\n'.format(fn))
for path, expected in tests:
if expected == 'all':
expected = list(files_to_create)
fullPaths = fslpath.getFileGroup(
op.join(workdir, path),
allowedExts=allowedExts,
fileGroups=groups,
fullPaths=True)
exts = fslpath.getFileGroup(
op.join(workdir, path),
allowedExts=allowedExts,
fileGroups=groups,
fullPaths=False)
assert sorted(fullPaths) == sorted([op.join(workdir, e) for e in expected])
assert sorted(exts) == sorted([fslpath.getExt(e, allowedExts) for e in expected])
for f in files_to_create:
try: os.remove(op.join(workdir, f))
except: pass
finally:
shutil.rmtree(workdir)
def test_imcp_shouldPass(move=False):
allowedExts = fslimage.ALLOWED_EXTENSIONS
groups = fslimage.FILE_GROUPS
#
# (files_to_create,
# [( imcp_src, imcp_dest, files_which_should_exist),
# ( imcp_src, imcp_dest, [files_which_should_exist]),
# ([imcp_srcs], imcp_dest, files_which_should_exist),
# ([imcp_srcs], imcp_dest, [files_which_should_exist]),
# ...
# ]
# )
#
# if icmp_dest == '', it means to copy to the directory
# files_which_should_exist == 'all' is equivalent to files_which_should_exist == files_to_create
shouldPass = [
(['file.hdr', 'file.img'], [
('file', 'file', 'all'),
('file', 'file.img', 'all'),
('file', 'file.hdr', 'all'),
('file', '', 'all'),
('file.img', 'file', 'all'),
('file.img', 'file.img', 'all'),
('file.img', 'file.hdr', 'all'),
('file.img', '', 'all'),
('file.hdr', 'file', 'all'),
('file.hdr', 'file.img', 'all'),
('file.hdr', 'file.hdr', 'all'),
('file.hdr', '', 'all'),
]),
(['file.hdr', 'file.img', 'file.blob'], [
('file', 'file', ['file.hdr', 'file.img']),
('file', 'file.img', ['file.hdr', 'file.img']),
('file', 'file.hdr', ['file.hdr', 'file.img']),
('file', '', ['file.hdr', 'file.img']),
('file.img', 'file', ['file.hdr', 'file.img']),
('file.img', 'file.img', ['file.hdr', 'file.img']),
('file.img', 'file.hdr', ['file.hdr', 'file.img']),
('file.img', '', ['file.hdr', 'file.img']),
('file.hdr', 'file', ['file.hdr', 'file.img']),
('file.hdr', 'file.img', ['file.hdr', 'file.img']),
('file.hdr', 'file.hdr', ['file.hdr', 'file.img']),
('file.hdr', '', ['file.hdr', 'file.img']),
]),
(['file.hdr', 'file.img', 'file.nii'], [
('file.img', 'file', ['file.hdr', 'file.img']),
('file.img', 'file.img', ['file.hdr', 'file.img']),
('file.img', 'file.hdr', ['file.hdr', 'file.img']),
('file.img', '', ['file.hdr', 'file.img']),
('file.hdr', 'file', ['file.hdr', 'file.img']),
('file.hdr', 'file.img', ['file.hdr', 'file.img']),
('file.hdr', 'file.hdr', ['file.hdr', 'file.img']),
('file.hdr', '', ['file.hdr', 'file.img']),
('file.nii', 'file', 'file.nii'),
('file.nii', 'file.nii', 'file.nii'),
('file.nii', '', 'file.nii'),
]),
(['file.nii'], [
('file', 'file', 'all'),
('file', 'file.nii', 'all'),
('file', '', 'all'),
('file.nii', 'file', 'all'),
('file.nii', 'file.nii', 'all'),
('file.nii', '', 'all'),
]),
(['file.nii.gz'], [
('file', 'file', 'all'),
('file', 'file.nii.gz', 'all'),
('file', '', 'all'),
('file.nii.gz', 'file', 'all'),
('file.nii.gz', 'file.nii.gz', 'all'),
('file.nii.gz', '', 'all'),
]),
(['file.nii', 'file.blob'], [
('file', 'file', 'file.nii'),
('file', 'file.nii', 'file.nii'),
('file', '', 'file.nii'),
('file.nii', 'file', 'file.nii'),
('file.nii', 'file.nii', 'file.nii'),
('file.nii', '', 'file.nii'),
]),
(['file.nii', 'file.nii.gz'], [
('file.nii', 'file', 'file.nii'),
('file.nii', 'file.nii', 'file.nii'),
('file.nii', '', 'file.nii'),
('file.nii.gz', 'file', 'file.nii.gz'),
('file.nii.gz', 'file.nii.gz', 'file.nii.gz'),
('file.nii.gz', '', 'file.nii.gz'),
]),
(['file.hdr', 'file.img', 'file.nii', 'file.nii.gz'], [
(['file.img', 'file.nii', 'file.nii.gz'], '', 'all'),
('file.img', '', ['file.hdr', 'file.img']),
(['file.hdr', 'file.img'], '', ['file.hdr', 'file.img']),
('file.nii', '', 'file.nii'),
(['file.nii', 'file.nii.gz'], '', ['file.nii', 'file.nii.gz']),
]),
(['001.hdr', '001.img', '002.hdr', '002.img', '003.hdr', '003.img'], [
(['001', '002', '003'], '', 'all'),
(['001.img', '002.img', '003.img'], '', 'all'),
(['001.hdr', '002.hdr', '003.hdr'], '', 'all'),
(['001.img', '002', '003'], '', 'all'),
(['001.hdr', '002', '003'], '', 'all'),
(['001.img', '002.hdr', '003.img'], '', 'all'),
(['001.hdr', '002.img', '003.hdr'], '', 'all'),
(['001', '003'], '', ['001.hdr', '001.img', '003.hdr', '003.img']),
(['001.img', '003.img'], '', ['001.hdr', '001.img', '003.hdr', '003.img']),
(['001.hdr', '003.hdr'], '', ['001.hdr', '001.img', '003.hdr', '003.img']),
(['001.img', '003'], '', ['001.hdr', '001.img', '003.hdr', '003.img']),
(['001.hdr', '003'], '', ['001.hdr', '001.img', '003.hdr', '003.img']),
(['001.img', '003.img'], '', ['001.hdr', '001.img', '003.hdr', '003.img']),
(['001.hdr', '003.hdr'], '', ['001.hdr', '001.img', '003.hdr', '003.img']),
(['001.img', '001.hdr', '002.img', '002.hdr', '003.img', '003.hdr'], '', 'all'),
]),
]
indir = tempfile.mkdtemp()
outdir = tempfile.mkdtemp()
try:
for files_to_create, tests in shouldPass:
if not isinstance(files_to_create, list):
files_to_create = [files_to_create]
for imcp_src, imcp_dest, should_exist in tests:
if not isinstance(imcp_src, list): imcp_src = [imcp_src]
if should_exist == 'all': should_exist = list(files_to_create)
elif not isinstance(should_exist, list): should_exist = [should_exist]
imcp_dest = op.join(outdir, imcp_dest)
# Each input file contains
# its name in plain text,
# so we can verify that the
# files were correctly copied
for fn in files_to_create:
with open(op.join(indir, fn), 'wt') as f:
f.write('{}\n'.format(fn))
for src in imcp_src:
src = op.join(indir, src)
if move: fslpath.immv(src, imcp_dest, allowedExts=allowedExts, fileGroups=groups, overwrite=True)
else: fslpath.imcp(src, imcp_dest, allowedExts=allowedExts, fileGroups=groups, overwrite=True)
copied = os.listdir(outdir)
copied = [f for f in copied if op.isfile(op.join(outdir, f))]
assert sorted(copied) == sorted(should_exist)
# check file contents
for fn in should_exist:
with open(op.join(outdir, fn), 'rt') as f:
assert f.read() == '{}\n'.format(fn)
# If move, check that
# input files are gone
if move:
for f in should_exist:
assert not op.exists(op.join(indir, f))
for f in files_to_create:
try: os.remove(op.join(indir, f))
except: pass
for f in should_exist:
os.remove(op.join(outdir, f))
finally:
shutil.rmtree(indir)
shutil.rmtree(outdir)
def test_immv_shouldPass():
test_imcp_shouldPass(move=True)