#!/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
from . import testdir
def make_dummy_file(path):
with open(path, 'wt') as f:
f.write('{}\n'.format(op.basename(path)))
def make_dummy_image_file(path):
if path.endswith('.nii'): paths = [path]
elif path.endswith('.nii.gz'): paths = [path]
elif path.endswith('.img'): paths = [path, path[:-4] + '.hdr']
elif path.endswith('.hdr'): paths = [path, path[:-4] + '.img']
elif path.endswith('.img.gz'): paths = [path, path[:-7] + '.hdr.gz']
elif path.endswith('.hdr.gz'): paths = [path, path[:-7] + '.img.gz']
else: raise RuntimeError()
for path in paths:
make_dummy_file(path)
def cleardir(dir):
for f in os.listdir(dir):
f = op.join(dir, f)
if op.isfile(f):
os.remove(f)
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:
path = op.join(*path.split('/'))
if output is not None:
output = op.join(*output.split('/'))
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:
path = op.join(*path.split('/'))
if output is not None:
output = op.join(*output.split('/'))
assert fslpath.shallowest(path, suffixes) == output
def test_allFiles():
create = [
'a/1',
'a/2',
'a/b/1',
'a/b/2',
'a/b/c/1',
'a/b/d/1',
]
create = [op.join(*c.split('/')) for c in create]
with testdir(create) as td:
assert (sorted(fslpath.allFiles('.')) ==
sorted([op.join('.', c) for c in create]))
assert (sorted(fslpath.allFiles(td)) ==
sorted([op.join(td, c) for c in create]))
def test_hasExt():
tests = [
('file.nii', ['.nii', '.gz'], True),
('file.nii.gz', ['.nii'], False),
('file.nii.gz', ['.nii', '.gz'], True),
('file.nii.gz', ['.nii.gz'], True),
('file.txt', ['.nii', '.gz'], False),
]
for path, aexts, expected in tests:
assert fslpath.hasExt(path, aexts) == expected
def test_addExt_imageFiles_mustExist_shouldPass():
"""Tests the addExt function where the path exists, and the inputs
are valid.
"""
groups = fslimage.FILE_GROUPS
allowedExts = fslimage.ALLOWED_EXTENSIONS
# (files_to_create, path, expected)
tests = [
# Single files
('file.nii', 'file', '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.img', 'file', 'file.hdr'),
('file.img', 'file.hdr', 'file.hdr'),
('file.img', 'file.img', 'file.img'),
('file.img.gz', 'file', 'file.hdr.gz'),
('file.img.gz', 'file.hdr.gz', 'file.hdr.gz'),
('file.img.gz', 'file.img.gz', 'file.img.gz'),
# Multiple suffixes should be handled
('file.blob.nii', 'file.blob', 'file.blob.nii'),
('file.blob.nii', 'file.blob.nii', 'file.blob.nii'),
('file.blob.nii.gz', 'file.blob', 'file.blob.nii.gz'),
('file.blob.nii.gz', 'file.blob.nii.gz', 'file.blob.nii.gz'),
('file.blob.img', 'file.blob', 'file.blob.hdr'),
('file.blob.hdr', 'file.blob.hdr', 'file.blob.hdr'),
('file.blob.img', 'file.blob.img', 'file.blob.img'),
('file.blob.img.gz', 'file.blob', 'file.blob.hdr.gz'),
('file.blob.hdr.gz', 'file.blob.hdr.gz', 'file.blob.hdr.gz'),
('file.blob.img.gz', 'file.blob.img.gz', 'file.blob.img.gz'),
# Even if that suffix is a itself supported
# suffix (as long as the path is unambiguous)
('file.img.nii', 'file.img.nii', 'file.img.nii'),
('file.img.nii.gz', 'file.img.nii.gz', 'file.img.nii.gz'),
('file.img.hdr', 'file.img.hdr', 'file.img.hdr'),
('file.img.img', 'file.img.img', 'file.img.img'),
('file.img.hdr.gz', 'file.img.hdr.gz', 'file.img.hdr.gz'),
('file.img.img.gz', 'file.img.img.gz', 'file.img.img.gz'),
# Multiple files exist, but prefix is unambiguous
('file.nii file.nii.gz', 'file.nii', 'file.nii'),
('file.nii file.nii.gz', 'file.nii.gz', 'file.nii.gz'),
('file1.nii file2.nii.gz', 'file1', 'file1.nii'),
('file1.nii file2.nii.gz', 'file1.nii', 'file1.nii'),
('file1.nii file2.nii.gz', 'file2', 'file2.nii.gz'),
('file1.nii file2.nii.gz', 'file2.nii.gz', 'file2.nii.gz'),
('file.nii file.img', 'file.nii', 'file.nii'),
('file.nii file.img', 'file.img', 'file.img'),
('file.nii file.img', 'file.hdr', 'file.hdr'),
('file.img.gz file.img', 'file.img', 'file.img'),
('file.img.gz file.img', 'file.hdr', 'file.hdr'),
('file.img.gz file.img', 'file.img.gz', 'file.img.gz'),
('file.img.gz file.img', 'file.hdr.gz', 'file.hdr.gz'),
('file1.img.gz file2.img', 'file2', 'file2.hdr'),
('file1.img.gz file2.img', 'file2.img', 'file2.img'),
('file1.img.gz file2.img', 'file2.hdr', 'file2.hdr'),
('file1.img.gz file2.img', 'file1', 'file1.hdr.gz'),
('file1.img.gz file2.img', 'file1.img.gz', 'file1.img.gz'),
('file1.img.gz file2.img', 'file1.hdr.gz', 'file1.hdr.gz'),
('file1.nii file2.img', 'file1', 'file1.nii'),
('file1.nii file2.img', 'file1.nii', 'file1.nii'),
('file1.nii file2.img', 'file2', 'file2.hdr'),
('file1.nii file2.img', 'file2.hdr', 'file2.hdr'),
('file1.nii file2.img', 'file2.img', 'file2.img'),
('file1.img file2.img', 'file1', 'file1.hdr'),
('file1.img file2.img', 'file1.hdr', 'file1.hdr'),
('file1.img file2.img', 'file1.img', 'file1.img'),
('file1.img file2.img', 'file2', 'file2.hdr'),
('file1.img file2.img', 'file2.hdr', 'file2.hdr'),
('file1.img file2.img', 'file2.img', 'file2.img'),
]
workdir = tempfile.mkdtemp()
try:
for files_to_create, prefix, expected in tests:
files_to_create = files_to_create.split()
for f in files_to_create:
make_dummy_image_file(op.join(workdir, f))
print('files_to_create: ', files_to_create)
print('workdir: ', os.listdir(workdir))
print('prefix: ', prefix)
print('expected: ', expected)
result = fslpath.addExt(op.join(workdir, prefix),
allowedExts,
mustExist=True,
fileGroups=groups)
print('result: ', result)
assert result == op.join(workdir, expected)
cleardir(workdir)
finally:
shutil.rmtree(workdir)
def test_addExt_otherFiles_mustExist_shouldPass():
workdir = tempfile.mkdtemp()
# (files_to_create, path, allowedExts, filegroups, expected)
tests = [
# allowedExts is None, fileGroups is None
('file.a', 'file.a', '', [], 'file.a'),
('file.a file.b', 'file.a', '', [], 'file.a'),
('file.a file.b', 'file.b', '', [], 'file.b'),
# fileGroups is None
('file.a', 'file', '.a', [], 'file.a'),
('file.a', 'file.a', '.a', [], 'file.a'),
('file.a file.b', 'file', '.a', [], 'file.a'),
('file.a file.b', 'file.a', '.a', [], 'file.a'),
('file.a file.b', 'file.b', '.a .b', [], 'file.b'),
('file1.a file2.b', 'file1', '.a .b', [], 'file1.a'),
('file1.a file2.b', 'file1.a', '.a .b', [], 'file1.a'),
('file1.a file2.b', 'file2.b', '.a .b', [], 'file2.b'),
('file1.a file2.b', 'file2.b', '.a .b', [], 'file2.b'),
('file.a file.b', 'file', '.a .b', ['.a .b'], 'file.a'),
('file.a file.b', 'file', '.a .b', ['.b .a'], 'file.b'),
('file.a file.b', 'file.a', '.a .b', ['.a .b'], 'file.a'),
('file.a file.b', 'file.b', '.a .b', ['.a .b'], 'file.b'),
('file.a file.b', 'file.a', '.a .b', ['.b .a'], 'file.a'),
('file.a file.b', 'file.b', '.a .b', ['.b .a'], 'file.b'),
('file.a file.b file.c file.d', 'file', '.a .b', ['.a .b'], 'file.a'),
('file.a file.b file.c file.d', 'file', '.a .b', ['.b .a'], 'file.b'),
('file.a file.b file.c file.d', 'file.a', '.a .b', ['.a .b'], 'file.a'),
('file.a file.b file.c file.d', 'file.b', '.a .b', ['.a .b'], 'file.b'),
('file1.a file1.b file2.a file2.b', 'file1', '.a .b', ['.a .b'], 'file1.a'),
('file1.a file1.b file2.a file2.b', 'file1.a', '.a .b', ['.a .b'], 'file1.a'),
('file1.a file1.b file2.a file2.b', 'file1.b', '.a .b', ['.a .b'], 'file1.b'),
('file1.a file1.b file2.a file2.b', 'file2', '.a .b', ['.a .b'], 'file2.a'),
('file1.a file1.b file2.a file2.b', 'file2.a', '.a .b', ['.a .b'], 'file2.a'),
('file1.a file1.b file2.a file2.b', 'file2.b', '.a .b', ['.a .b'], 'file2.b'),
('file1.a file1.b file2.c file2.d', 'file1', '.a .b .c .d', ['.a .b', '.c .d'], 'file1.a'),
('file1.a file1.b file2.c file2.d', 'file1.a', '.a .b .c .d', ['.a .b', '.c .d'], 'file1.a'),
('file1.a file1.b file2.c file2.d', 'file1.b', '.a .b .c .d', ['.a .b', '.c .d'], 'file1.b'),
('file1.a file1.b file2.c file2.d', 'file2', '.a .b .c .d', ['.a .b', '.c .d'], 'file2.c'),
('file1.a file1.b file2.c file2.d', 'file2.c', '.a .b .c .d', ['.a .b', '.c .d'], 'file2.c'),
('file1.a file1.b file2.c file2.d', 'file2.d', '.a .b .c .d', ['.a .b', '.c .d'], 'file2.d'),
]
try:
for files_to_create, prefix, allowedExts, fileGroups, expected in tests:
files_to_create = files_to_create.split()
allowedExts = allowedExts.split()
fileGroups = [g.split() for g in fileGroups]
if len(allowedExts) == 0: allowedExts = None
if len(fileGroups) == 0: fileGroups = None
for f in files_to_create:
make_dummy_file(op.join(workdir, f))
print('files_to_create: ', files_to_create)
print('prefix: ', prefix)
print('allowedExts: ', allowedExts)
print('fileGroups: ', fileGroups)
print('workdir: ', os.listdir(workdir))
print('expected: ', expected)
result = fslpath.addExt(op.join(workdir, prefix),
allowedExts=allowedExts,
mustExist=True,
fileGroups=fileGroups)
print('result: ', result)
assert result == op.join(workdir, expected)
cleardir(workdir)
finally:
shutil.rmtree(workdir)
def test_addExt_imageFiles_mustExist_shouldFail():
"""Tests the addExt function with inputs that should cause it to raise an
error.
"""
fileGroups = fslimage.FILE_GROUPS
allowedExts = fslimage.ALLOWED_EXTENSIONS
# All of these should raise an error
# (files_to_create, path)
tests = [
# Invalid path
('', 'file.img'),
('file.hdr file.img', 'blob'),
('file.hdr.gz file.img.gz', 'file.img'),
('file.hdr file.img', 'file1'),
('file.hdr file.img', 'file1.im'),
('file.hdr file.img', 'filehdr'),
('file.hdr file.img', 'fileimg'),
('filehdr fileimg', 'file.hdr'),
('filehdr fileimg', 'file.img'),
('file.hdr fileimg', 'filehdr'),
('file.hdr fileimg', 'file.img'),
('filehdr file.img', 'fileimg'),
('filehdr file.img', 'file.hdr'),
# Unsupported type/invalid path
('file.blob', 'file'),
('file.blob', 'file.img'),
('file.blob', 'file.nii'),
('file.blob', 'file.blob'),
# Ambiguous path
('file.hdr file.img file.nii', 'file'),
('file.hdr file.img file.hdr.gz file.img.gz', 'file'),
# Incomplete file pairs
('file.hdr', 'file.img'),
('file.img', 'file.hdr'),
('file1.hdr file2.img', 'file1.img'),
('file1.hdr file2.img', 'file2.hdr'),
# Stupid file names
('file.img.nii.gz', 'file.img'),
('file.img.nii', 'file.img'),
('file.img.img', 'file.img'),
('file.img.img.gz', 'file.img'),
]
workdir = tempfile.mkdtemp()
try:
for files_to_create, prefix in tests:
cleardir(workdir)
files_to_create = files_to_create.split()
for f in files_to_create:
make_dummy_file(op.join(workdir, f))
print('files_to_create: ', files_to_create)
print('prefix: ', prefix)
print('workdir: ', os.listdir(workdir))
with pytest.raises(fslpath.PathError):
result = fslpath.addExt(op.join(workdir, prefix),
allowedExts=allowedExts,
mustExist=True,
fileGroups=fileGroups)
print('result: ', result)
finally:
shutil.rmtree(workdir)
def test_addExt_otherFiles_mustExist_shouldFail():
workdir = tempfile.mkdtemp()
# Invalid path
# Unsupported suffix
# (files_to_create, path, allowedExts, fileGroups)
tests = [
# Invalid path
('', 'file.a', '', []),
('file.b', 'file.a', '.a', []),
('file.b', 'file.a', '.a', []),
# No supported extensions/ambiguous
('file.a', 'file', '', []),
('file.a file.b', 'file', '', []),
('file.a file.b', 'file', '.a .b', []),
# Weird group
('file.a file.b', 'file', '.a .b', ['.a']),
# Multiple groups, ambiguous path
('file.a file.b file.c file.d', 'file', '.a .b .c .d', ['.a .b', '.c .d']),
]
try:
for files_to_create, prefix, allowedExts, fileGroups in tests:
cleardir(workdir)
files_to_create = files_to_create.split()
allowedExts = allowedExts.split()
fileGroups = [g.split() for g in fileGroups]
if len(allowedExts) == 0: allowedExts = None
if len(fileGroups) == 0: fileGroups = None
for f in files_to_create:
make_dummy_file(op.join(workdir, f))
print('files_to_create: ', files_to_create)
print('prefix: ', prefix)
print('workdir: ', os.listdir(workdir))
with pytest.raises(fslpath.PathError):
result = fslpath.addExt(op.join(workdir, prefix),
allowedExts=allowedExts,
mustExist=True,
fileGroups=fileGroups)
print('result: ', result)
finally:
shutil.rmtree(workdir)
pass
def test_addExt_noExist():
allowedExts = fslimage.ALLOWED_EXTENSIONS
# When mustExist=False, the addExt
# function does not consult fileGroups.
# So we are not bothering with them
# here.
# Prefix, defaultExt, allowedExts, expected
tests = [
# If the prefix already has a supported extension,
# it should be returned unchanged.
('file.img', None, allowedExts, 'file.img'),
('file.hdr', None, allowedExts, 'file.hdr'),
('file.nii', None, allowedExts, 'file.nii'),
('file.nii.gz', None, allowedExts, 'file.nii.gz'),
('file.img.gz', None, allowedExts, 'file.img.gz'),
('file.hdr.gz', None, allowedExts, 'file.hdr.gz'),
('file.blob.img', '.img', allowedExts, 'file.blob.img'),
('file.blob.img', '.img', None, 'file.blob.img'),
# If the file does not have a prefix,
# it should be given the default prefix
('file', 'img', allowedExts, 'fileimg'),
('file', '.img', allowedExts, 'file.img'),
('file', 'img', None, 'fileimg'),
('file', '.img', None, 'file.img'),
# Unrecognised prefixes should be ignored
('file.blob', 'img', allowedExts, 'file.blobimg'),
('file.blob', '.img', allowedExts, 'file.blob.img'),
('file.blob', 'img', None, 'file.blobimg'),
('file.blob', '.img', None, 'file.blob.img'),
# If no defaultExt or allowedExts, the
# prefix should be returned unchanged
('file', None, None, 'file'),
('file.blob', None, None, 'file.blob'),
]
for prefix, defaultExt, allowedExts, expected in tests:
assert fslpath.addExt(prefix,
allowedExts,
defaultExt=defaultExt,
mustExist=False) == expected
def test_addExt_unambiguous():
allowedExts = fslimage.ALLOWED_EXTENSIONS
fileGroups = fslimage.FILE_GROUPS
# files to create, prefix, file groups, allowedExts, defaultExt, expected,
tests = [
('file.img file.hdr', 'file.img', None, None, None, 'file.img'),
('file.img file.hdr', 'file.hdr', None, None, None, 'file.hdr'),
('file.img file.hdr', 'file.hdr', None, None, None, 'file.hdr'),
('file.img file.hdr', 'file', None, None, '.hdr', 'file.hdr'),
('file.img file.hdr', 'file', None, None, '.img', 'file.img'),
('file.img file.hdr', 'file', None, allowedExts, None, 'file.hdr file.img'),
('file.img file.hdr', 'file.img', None, allowedExts, None, 'file.img'),
('file.img file.hdr', 'file', fileGroups, allowedExts, None, 'file.hdr file.img'),
('file.img file.hdr', 'file.img', fileGroups, allowedExts, None, 'file.img'),
('file.img file.hdr', 'file', None, allowedExts, '.img', 'file.hdr file.img'),
('file.img file.hdr', 'file.img', None, allowedExts, '.img', 'file.img'),
('file.img file.hdr', 'file', fileGroups, allowedExts, '.img', 'file.hdr file.img'),
('file.img file.hdr', 'file.img', fileGroups, allowedExts, '.img', 'file.img'),
]
for create, prefix, groups, exts, defaultExt, expected in tests:
create = create .split()
expected = expected.split()
with testdir(create) as td:
result = fslpath.addExt(prefix,
allowedExts=exts,
fileGroups=groups,
defaultExt=defaultExt,
unambiguous=False)
assert sorted(expected) == sorted(result)
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_getFileGroup_imageFiles_shouldPass():
allowedExts = fslimage.ALLOWED_EXTENSIONS
groups = fslimage.FILE_GROUPS
# [(files_to_create, path, files_to_expect [, unambiguous]),
# ...
# ]
#
tests = [
('file.hdr file.img', 'file', 'file.hdr file.img'),
('file.hdr file.img', 'file.img', 'file.hdr file.img'),
('file.hdr file.img', 'file.hdr', 'file.hdr file.img'),
('file.hdr.gz file.img.gz', 'file', 'file.hdr.gz file.img.gz'),
('file.hdr.gz file.img.gz', 'file.img.gz', 'file.hdr.gz file.img.gz'),
('file.hdr.gz file.img.gz', 'file.hdr.gz', 'file.hdr.gz file.img.gz'),
('file.hdr file.img file.hdr.gz file.img.gz', 'file.hdr', 'file.hdr file.img'),
('file.hdr file.img file.hdr.gz file.img.gz', 'file.img', 'file.hdr file.img'),
('file.hdr file.img file.hdr.gz file.img.gz', 'file.hdr.gz', 'file.hdr.gz file.img.gz'),
('file.hdr file.img file.hdr.gz file.img.gz', 'file.hdr.gz', 'file.hdr.gz file.img.gz'),
('file.hdr file.img file.nii', 'file.img', 'file.hdr file.img'),
('file.hdr file.img file.nii', 'file.hdr', 'file.hdr file.img'),
('file.hdr file.img file.blob', 'file', 'file.hdr file.img'),
('file.hdr file.img file.blob', 'file.hdr', 'file.hdr file.img'),
('file.hdr file.img file.blob', 'file.img', 'file.hdr file.img'),
('file.nii', 'file', 'file.nii'),
('file.nii', 'file.nii', 'file.nii'),
('file.nii file.hdr file.img', 'file.nii', 'file.nii'),
('file.nii file.blob', 'file', 'file.nii'),
('file.nii file.blob', 'file.nii', 'file.nii'),
# The unambiguous arg defaults to
# False, so paths to incomplete
# file groups should still work.
('file.hdr', 'file', 'file.hdr'),
('file.hdr', 'file.hdr', 'file.hdr'),
# Unambigiuous paths, when
# unambiguous = True,
# should be ok.
('file.hdr file.img file.nii', 'file.nii', 'file.nii', True),
('file.hdr file.img file.nii', 'file.hdr', 'file.hdr file.img', True),
('file.hdr file.img file.nii', 'file.img', 'file.hdr file.img', True),
]
# TODO You need to add passing tests for unambiguous=True
workdir = tempfile.mkdtemp()
try:
for test in tests:
files_to_create = test[0]
path = test[1]
files_to_expect = test[2]
if len(test) == 4: unambiguous = test[3]
else: unambiguous = False
files_to_create = files_to_create.split()
files_to_expect = files_to_expect.split()
for fn in files_to_create:
with open(op.join(workdir, fn), 'wt') as f:
f.write('{}\n'.format(fn))
print()
print('files_to_create: ', files_to_create)
print('path: ', path)
print('files_to_expect: ', files_to_expect)
fullPaths = fslpath.getFileGroup(
op.join(workdir, path),
allowedExts=allowedExts,
fileGroups=groups,
fullPaths=True,
unambiguous=unambiguous)
exts = fslpath.getFileGroup(
op.join(workdir, path),
allowedExts=allowedExts,
fileGroups=groups,
fullPaths=False,
unambiguous=unambiguous)
assert sorted(fullPaths) == sorted([op.join(workdir, e) for e in files_to_expect])
assert sorted(exts) == sorted([fslpath.getExt(e, allowedExts) for e in files_to_expect])
cleardir(workdir)
finally:
shutil.rmtree(workdir)
def test_getFileGroup_otherFiles_shouldPass():
# (files_to_create, allowedExts, fileGroups, path, files_to_expect [, unambiguous])
tests = [
# allowedExts is None - incomplete paths are not allowed
('file.a', '', '', 'file.a', 'file.a'),
('file.a file.b', '', '', 'file.a', 'file.a'),
('file.a file.b', '', '', 'file.b', 'file.b'),
('file.a file.b', '', ['.a .b'], 'file.a', 'file.a file.b'),
('file.a file.b', '', ['.a .b'], 'file.b', 'file.a file.b'),
('file.a file.b file.c', '', ['.a .b .c'], 'file.a', 'file.a file.b file.c'),
('file.a file.b file.c', '', ['.a .b .c'], 'file.b', 'file.a file.b file.c'),
('file.a file.b file.c', '', ['.a .b .c'], 'file.c', 'file.a file.b file.c'),
('file.a file.b file.c file.d', '', ['.a .b', '.c .d'], 'file.a', 'file.a file.b'),
('file.a file.b file.c file.d', '', ['.a .b', '.c .d'], 'file.b', 'file.a file.b'),
('file.a file.b file.c file.d', '', ['.a .b', '.c .d'], 'file.c', 'file.c file.d'),
('file.a file.b file.c file.d', '', ['.a .b', '.c .d'], 'file.d', 'file.c file.d'),
# allowedExts != None - incomplete paths
# allowed, but must be unambiguous
('file.a', '.a', '', 'file', 'file.a'),
('file.a', '.a', '', 'file.a', 'file.a'),
('file.a file.b', '.a .b', '', 'file.a', 'file.a'),
('file.a file.b', '.a .b', '', 'file.b', 'file.b'),
('file1.a file2.b', '.a .b', '', 'file1', 'file1.a'),
('file1.a file2.b', '.a .b', '', 'file1.a', 'file1.a'),
('file1.a file2.b', '.a .b', '', 'file2', 'file2.b'),
('file1.a file2.b', '.a .b', '', 'file2.b', 'file2.b'),
('file.a file.b', '.a .b', ['.a .b'], 'file', 'file.a file.b'),
('file.a file.b', '.a .b', ['.a .b'], 'file.a', 'file.a file.b'),
('file.a file.b', '.a .b', ['.a .b'], 'file.b', 'file.a file.b'),
('file.a file.b file.c', '.a .b .c', ['.a .b .c'], 'file', 'file.a file.b file.c'),
('file.a file.b file.c', '.a .b .c', ['.a .b .c'], 'file.a', 'file.a file.b file.c'),
('file.a file.b file.c', '.a .b .c', ['.a .b .c'], 'file.b', 'file.a file.b file.c'),
('file.a file.b file.c', '.a .b .c', ['.a .b .c'], 'file.c', 'file.a file.b file.c'),
('file.a file.b file.c file.d', '.a .b .c .d', ['.a .b', '.c .d'], 'file.a', 'file.a file.b'),
('file.a file.b file.c file.d', '.a .b .c .d', ['.a .b', '.c .d'], 'file.b', 'file.a file.b'),
('file.a file.b file.c file.d', '.a .b .c .d', ['.a .b', '.c .d'], 'file.c', 'file.c file.d'),
('file.a file.b file.c file.d', '.a .b .c .d', ['.a .b', '.c .d'], 'file.d', 'file.c file.d'),
('file1.a file1.b file2.c file2.d', '.a .b .c .d', ['.a .b', '.c .d'], 'file1', 'file1.a file1.b'),
('file1.a file1.b file2.c file2.d', '.a .b .c .d', ['.a .b', '.c .d'], 'file1.a', 'file1.a file1.b'),
('file1.a file1.b file2.c file2.d', '.a .b .c .d', ['.a .b', '.c .d'], 'file1.b', 'file1.a file1.b'),
('file1.a file1.b file2.c file2.d', '.a .b .c .d', ['.a .b', '.c .d'], 'file2', 'file2.c file2.d'),
('file1.a file1.b file2.c file2.d', '.a .b .c .d', ['.a .b', '.c .d'], 'file2.c', 'file2.c file2.d'),
('file1.a file1.b file2.c file2.d', '.a .b .c .d', ['.a .b', '.c .d'], 'file2.d', 'file2.c file2.d'),
# incomplete group should be ok when
# unambiguous = False (the default)
('file.a', '.a .b', ['.a .b'], 'file', 'file.a'),
('file.a', '.a .b', ['.a .b'], 'file.a', 'file.a'),
# Unambiguous/complete group should
# be ok when unambiguous = True
('file.a file.b file.c', '.a .b .c', ['.a .b'], 'file.a', 'file.a file.b', True),
('file.a file.b file.c', '.a .b .c', ['.a .b'], 'file.b', 'file.a file.b', True),
('file.a file.b file.c', '.a .b .c', ['.a .b'], 'file.c', 'file.c', True),
]
workdir = tempfile.mkdtemp()
try:
for test in tests:
files_to_create = test[0]
allowedExts = test[1]
fileGroups = test[2]
path = test[3]
files_to_expect = test[4]
if len(test) == 6: unambiguous = test[5]
else: unambiguous = False
files_to_create = files_to_create.split()
allowedExts = allowedExts.split()
fileGroups = [g.split() for g in fileGroups]
files_to_expect = files_to_expect.split()
if len(allowedExts) == 0: allowedExts = None
if len(fileGroups) == 0: fileGroups = None
for fn in files_to_create:
with open(op.join(workdir, fn), 'wt') as f:
f.write('{}\n'.format(fn))
print()
print('files_to_create: ', files_to_create)
print('path: ', path)
print('allowedExts: ', allowedExts)
print('fileGroups: ', fileGroups)
print('files_to_expect: ', files_to_expect)
fullPaths = fslpath.getFileGroup(
op.join(workdir, path),
allowedExts=allowedExts,
fileGroups=fileGroups,
fullPaths=True,
unambiguous=unambiguous)
exts = fslpath.getFileGroup(
op.join(workdir, path),
allowedExts=allowedExts,
fileGroups=fileGroups,
fullPaths=False,
unambiguous=unambiguous)
assert sorted(fullPaths) == sorted([op.join(workdir, e) for e in files_to_expect])
assert sorted(exts) == sorted([fslpath.getExt(e, allowedExts) for e in files_to_expect])
cleardir(workdir)
finally:
shutil.rmtree(workdir)
def test_getFileGroup_shouldFail():
# All of these tests should raise an error
allowedExts = ' '.join(fslimage.ALLOWED_EXTENSIONS)
fileGroups = [' '.join(g) for g in fslimage.FILE_GROUPS]
# (files_to_create, path, allowedExts, fileGroups[, unambiguous])
tests = [
# Unsupported extension
('file.a', 'file.a', '.b', []),
# Incomplete path, and allowedExts is None
('file.a', 'file', '', []),
# non existent path
('file.a', 'file.b', '.a', []),
# ambigiuous
('file.a file.b file.c file.d', 'file', '.a .b .c .d', ['.a .b', '.c .d']),
# Incomplete group, when unambiguous is set to True
('file.a', 'file', '.a .b', ['.a .b'], True),
('file.a', 'file.a', '.a .b', ['.a .b'], True),
('file.hdr', 'file', allowedExts, fileGroups, True),
('file.hdr', 'file.hdr', allowedExts, fileGroups, True),
('file.img', 'file', allowedExts, fileGroups, True),
('file.img', 'file.img', allowedExts, fileGroups, True),
# Part of more than one group, when unambiguous is True
('file.a file.b file.c', 'file.a', '.a .b', ['.a .b', '.a .c'], True),
]
workdir = tempfile.mkdtemp()
try:
for test in tests:
files_to_create = test[0]
path = test[1]
allowedExts = test[2]
fileGroups = test[3]
if len(test) > 4: unambiguous = test[4]
else: unambiguous = False
files_to_create = files_to_create.split()
allowedExts = allowedExts.split()
fileGroups = [g.split() for g in fileGroups]
if len(allowedExts) == 0: allowedExts = None
if len(fileGroups) == 0: fileGroups = None
for fn in files_to_create:
with open(op.join(workdir, fn), 'wt') as f:
f.write('{}\n'.format(fn))
print()
print('files_to_create: ', files_to_create)
print('path: ', path)
print('allowedExts: ', allowedExts)
print('fileGroups: ', fileGroups)
with pytest.raises(fslpath.PathError):
fullPaths = fslpath.getFileGroup(
op.join(workdir, path),
allowedExts=allowedExts,
fileGroups=fileGroups,
fullPaths=True,
unambiguous=unambiguous)
print('fullPaths: ', fullPaths)
with pytest.raises(fslpath.PathError):
exts = fslpath.getFileGroup(
op.join(workdir, path),
allowedExts=allowedExts,
fileGroups=fileGroups,
fullPaths=False,
unambiguous=unambiguous)
print('exts: ', exts)
cleardir(workdir)
finally:
shutil.rmtree(workdir)
def test_removeDuplicates_imageFiles_shouldPass():
allowedExts = fslimage.ALLOWED_EXTENSIONS
groups = fslimage.FILE_GROUPS
# [(files_to_create,
# [(paths, expected),
# ...
# ]),
# ...
# ]
allTests = [
('file.hdr file.img', [
('file', 'file.hdr'),
('file file', 'file.hdr'),
('file file.hdr', 'file.hdr'),
('file file.img', 'file.hdr'),
('file.hdr file', 'file.hdr'),
('file.hdr file.hdr', 'file.hdr'),
('file.hdr file.img', 'file.hdr'),
('file.img file', 'file.hdr'),
('file.img file.hdr', 'file.hdr'),
('file.img file.img', 'file.hdr'),
('file.hdr', 'file.hdr'),
('file.img', 'file.hdr'),
('file.hdr file.img', 'file.hdr'),
('file.img file.hdr', 'file.hdr'),
]),
('file.hdr file.img file.blob', [
('file', 'file.hdr'),
('file.hdr', 'file.hdr'),
('file.img', 'file.hdr'),
('file.hdr file.img', 'file.hdr'),
('file.img file.hdr', 'file.hdr'),
]),
('file.hdr file.img file.nii', [
('file.hdr', 'file.hdr'),
('file.img', 'file.hdr'),
('file.hdr file.nii', 'file.hdr file.nii'),
('file.img file.nii', 'file.hdr file.nii'),
('file.hdr file.img', 'file.hdr'),
('file.img file.hdr', 'file.hdr'),
('file.img file.hdr', 'file.hdr'),
('file.hdr file.img file.nii', 'file.hdr file.nii'),
('file.img file.hdr file.nii', 'file.hdr file.nii'),
('file.img file.hdr file.nii', 'file.hdr file.nii'),
]),
('001.hdr 001.img 002.hdr 002.img 003.hdr 003.img', [
('001 002 003', '001.hdr 002.hdr 003.hdr'),
('001.hdr 002.hdr 003.hdr', '001.hdr 002.hdr 003.hdr'),
('001.img 002.img 003.img', '001.hdr 002.hdr 003.hdr'),
('001.hdr 001.img 002.hdr 002.img 003.img', '001.hdr 002.hdr 003.hdr'),
('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.hdr 002.hdr 003.hdr'),
])
]
workdir = tempfile.mkdtemp()
try:
for files_to_create, tests in allTests:
files_to_create = files_to_create.split()
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 = paths.split()
expected = expected.split()
print()
print('files_to_create: ', files_to_create)
print('paths: ', paths)
print('expected: ', expected)
paths = [op.join(workdir, p) for p in paths]
result = fslpath.removeDuplicates(paths, allowedExts, groups)
print('result: ', result)
assert result == [op.join(workdir, e) for e in expected]
cleardir(workdir)
finally:
shutil.rmtree(workdir)
def test_removeDuplicates_otherFiles_shouldPass():
# files_to_create, paths, allowedExts, fileGroups, expected
tests = [
# allowedExts is None, but paths are unambiguouos
('file.a file.b', 'file.a file.b', '', [], 'file.a file.b'),
# Retured path should be the first in the group
('file.a file.b', 'file.a file.b', '', ['.a .b'], 'file.a'),
('file.a file.b', 'file.a file.b', '', ['.b .a'], 'file.b'),
('file.a file.b file.c', 'file.a file.b file.c', '', ['.a .b'], 'file.a file.c'),
('file.a file.b file.c', 'file.a file.b file.c', '', ['.b .a'], 'file.b file.c'),
('file.a file.b file.c', 'file.a file.b file.c', '', ['.a .b .c'], 'file.a'),
('file.a file.b file.c', 'file.a file.b file.c', '', ['.a .b .c'], 'file.a'),
('file.a file.b file.c', 'file.a file.b file.c', '', ['.a .b .c'], 'file.a'),
('file.a file.b file.c file.d', 'file.a file.b file.c file.d', '', ['.a .b', '.c .d'], 'file.a file.c'),
('file1.a file1.b file2.a file2.b', 'file1.a file1.b file2.a file2.b', '', ['.a .b'], 'file1.a file2.a'),
# Incomplete paths (but are unambiguouos because of allowedExts)
('file.a' , 'file', '.a', [], 'file.a'),
('file.a' , 'file.a', '.a', [], 'file.a'),
('file.a file.b', 'file.a', '.a', [], 'file.a'),
('file.a file.b', 'file.a file.b', '.a .b', [], 'file.a file.b'),
('file.a file.b', 'file', '.a .b', ['.a .b'], 'file.a'),
('file.a file.b', 'file file', '.a .b', ['.a .b'], 'file.a'),
('file.a file.b', 'file file.a file.b', '.a .b', ['.a .b'], 'file.a'),
('file1.a file1.b file2.a file2.b', 'file1 file1.a file2 file2.a', '.a .b', ['.a .b'], 'file1.a file2.a'),
('file1.a file1.b file2.a file2.b', 'file1 file2', '.a .b', ['.a .b'], 'file1.a file2.a'),
('file1.a file1.b file2.a file2.b', 'file1 file1.a file2', '.a .b', ['.a .b'], 'file1.a file2.a'),
# no file groups - should still work
('file1.a file1.b file2.a file2.b', 'file1.a', '', [], 'file1.a'),
('file1.a file1.b file2.a file2.b', 'file1.a file1.b', '', [], 'file1.a file1.b'),
('file1.a file1.b file2.a file2.b', 'file1.a file2.a', '', [], 'file1.a file2.a'),
]
workdir = tempfile.mkdtemp()
try:
for files_to_create, paths, allowedExts, fileGroups, expected in tests:
files_to_create = files_to_create.split()
paths = paths.split()
allowedExts = allowedExts.split()
fileGroups = [g.split() for g in fileGroups]
expected = expected.split()
if len(allowedExts) == 0: allowedExts = None
if len(fileGroups) == 0: fileGroups = None
for f in files_to_create:
make_dummy_file(op.join(workdir, f))
print('files_to_create: {}'.format(files_to_create))
print('paths: {}'.format(paths))
print('allowedExts: {}'.format(allowedExts))
print('fileGroups: {}'.format(fileGroups))
print('workdir: {}'.format(os.listdir(workdir)))
print('expected: {}'.format(expected))
result = fslpath.removeDuplicates([op.join(workdir, p) for p in paths],
allowedExts=allowedExts,
fileGroups=fileGroups)
print('result: {}'.format(result))
assert result == [op.join(workdir, e) for e in expected]
cleardir(workdir)
finally:
shutil.rmtree(workdir)
def test_removeDuplicates_shouldFail():
# (files_to_create, paths, allowedExts, fileGroups)
tests = [
# Invalid path(s)
('', 'file.a', '', []),
('file.a', 'file.b', '', []),
('file.a', 'file.b file.c', '', []),
('file.a', 'file', '', []),
('file.a', 'file.b', '.a .b', ['.a .b']),
# Unsupported extension
('file.a', 'file.a', '.b', []),
# Ambiguous
('file.a file.b', 'file', '.a .b', []),
('file.a file.b file.c', 'file file.c', '.a .b .c', ['.a .b']),
]
workdir = tempfile.mkdtemp()
try:
for files_to_create, path, allowedExts, fileGroups in tests:
cleardir(workdir)
files_to_create = files_to_create.split()
allowedExts = allowedExts.split()
fileGroups = [g.split() for g in fileGroups]
if len(allowedExts) == 0: allowedExts = None
if len(fileGroups) == 0: fileGroups = None
for fn in files_to_create:
with open(op.join(workdir, fn), 'wt') as f:
f.write('{}\n'.format(fn))
print()
print('files_to_create: ', files_to_create)
print('path: ', path)
print('allowedExts: ', allowedExts)
print('fileGroups: ', fileGroups)
with pytest.raises(fslpath.PathError):
result = fslpath.removeDuplicates(path,
allowedExts=allowedExts,
fileGroups=fileGroups)
print('result: ', result)
finally:
shutil.rmtree(workdir)
def test_uniquePrefix():
contents = """
100307.32k_fs_LR.wb.spec
100307.ArealDistortion_FS.32k_fs_LR.dscalar.nii
100307.ArealDistortion_MSMSulc.32k_fs_LR.dscalar.nii
100307.BA.32k_fs_LR.dlabel.nii
100307.L.ArealDistortion_FS.32k_fs_LR.shape.gii
100307.L.ArealDistortion_MSMSulc.32k_fs_LR.shape.gii
100307.L.BA.32k_fs_LR.label.gii
100307.L.MyelinMap.32k_fs_LR.func.gii
100307.L.MyelinMap_BC.32k_fs_LR.func.gii
100307.L.SmoothedMyelinMap.32k_fs_LR.func.gii
100307.L.SmoothedMyelinMap_BC.32k_fs_LR.func.gii
100307.L.aparc.32k_fs_LR.label.gii
100307.L.aparc.a2009s.32k_fs_LR.label.gii
100307.L.atlasroi.32k_fs_LR.shape.gii
100307.L.corrThickness.32k_fs_LR.shape.gii
100307.L.curvature.32k_fs_LR.shape.gii
100307.L.flat.32k_fs_LR.surf.gii
100307.L.inflated.32k_fs_LR.surf.gii
100307.L.midthickness.32k_fs_LR.surf.gii
100307.L.pial.32k_fs_LR.surf.gii
100307.L.sphere.32k_fs_LR.surf.gii
100307.L.sulc.32k_fs_LR.shape.gii
100307.L.thickness.32k_fs_LR.shape.gii
100307.L.very_inflated.32k_fs_LR.surf.gii
100307.L.white.32k_fs_LR.surf.gii
100307.MyelinMap.32k_fs_LR.dscalar.nii
100307.MyelinMap_BC.32k_fs_LR.dscalar.nii
100307.R.ArealDistortion_FS.32k_fs_LR.shape.gii
100307.R.ArealDistortion_MSMSulc.32k_fs_LR.shape.gii
100307.R.BA.32k_fs_LR.label.gii
100307.R.MyelinMap.32k_fs_LR.func.gii
100307.R.MyelinMap_BC.32k_fs_LR.func.gii
100307.R.SmoothedMyelinMap.32k_fs_LR.func.gii
100307.R.SmoothedMyelinMap_BC.32k_fs_LR.func.gii
100307.R.aparc.32k_fs_LR.label.gii
100307.R.aparc.a2009s.32k_fs_LR.label.gii
100307.R.atlasroi.32k_fs_LR.shape.gii
100307.R.corrThickness.32k_fs_LR.shape.gii
100307.R.curvature.32k_fs_LR.shape.gii
100307.R.flat.32k_fs_LR.surf.gii
100307.R.inflated.32k_fs_LR.surf.gii
100307.R.midthickness.32k_fs_LR.surf.gii
100307.R.pial.32k_fs_LR.surf.gii
100307.R.sphere.32k_fs_LR.surf.gii
100307.R.sulc.32k_fs_LR.shape.gii
100307.R.thickness.32k_fs_LR.shape.gii
100307.R.very_inflated.32k_fs_LR.surf.gii
100307.R.white.32k_fs_LR.surf.gii
100307.SmoothedMyelinMap.32k_fs_LR.dscalar.nii
100307.SmoothedMyelinMap_BC.32k_fs_LR.dscalar.nii
100307.aparc.32k_fs_LR.dlabel.nii
100307.aparc.a2009s.32k_fs_LR.dlabel.nii
100307.corrThickness.32k_fs_LR.dscalar.nii
100307.curvature.32k_fs_LR.dscalar.nii
100307.sulc.32k_fs_LR.dscalar.nii
100307.thickness.32k_fs_LR.dscalar.nii
""".split()
# (filename, expected_result)
tests = [
('100307.32k_fs_LR.wb.spec', '100307.3'),
('100307.ArealDistortion_FS.32k_fs_LR.dscalar.nii', '100307.ArealDistortion_F'),
('100307.L.ArealDistortion_FS.32k_fs_LR.shape.gii', '100307.L.ArealDistortion_F'),
('100307.L.flat.32k_fs_LR.surf.gii', '100307.L.f'),
('100307.R.flat.32k_fs_LR.surf.gii', '100307.R.f'),
('100307.MyelinMap.32k_fs_LR.dscalar.nii', '100307.MyelinMap.'),
('100307.SmoothedMyelinMap.32k_fs_LR.dscalar.nii', '100307.SmoothedMyelinMap.'),
('100307.sulc.32k_fs_LR.dscalar.nii', '100307.s'),
]
workdir = tempfile.mkdtemp()
try:
for fname in contents:
with open(op.join(workdir, fname), 'wt') as f:
f.write(fname)
for filename, expected in tests:
expected = op.join(workdir, expected)
result = fslpath.uniquePrefix(op.join(workdir, filename))
assert result == expected
# test that an error is raised on an invalid path
with pytest.raises(fslpath.PathError):
fslpath.uniquePrefix(op.join(workdir, 'not-a-valid-path'))
with pytest.raises(fslpath.PathError):
fslpath.uniquePrefix(op.join(workdir, '100307'))
finally:
shutil.rmtree(workdir)
def test_commonBase():
tests = [
('/',
['/a/b/c',
'/d/e',
'/f/g/h/i']),
('/a',
['/a/b/c',
'/a/d/e/f/g',
'/a/d/h/g/h/i']),
('a',
['a/b/c/d',
'a/e/f/g/h',
'a/i/j/k/'])
]
for exp, paths in tests:
assert fslpath.commonBase(paths) == exp
failtests = [
['a/b/c', 'd/e/f'],
['/a/b/c', 'd/e/f'],
['a', 'b/c/d']]
for ft in failtests:
with pytest.raises(fslpath.PathError):
fslpath.commonBase(ft)