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Commit f95277d9 authored by Paul McCarthy's avatar Paul McCarthy :mountain_bicyclist:
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TEST: New test_scripts sub-dir

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tests/test_imglob.py
+ 1
− 61
View file @ f95277d9
...@@ -5,14 +5,11 @@ ...@@ -5,14 +5,11 @@
# Author: Paul McCarthy <pauldmccarthy@gmail.com> # Author: Paul McCarthy <pauldmccarthy@gmail.com>
# #
import mock
import pytest import pytest
import fsl.scripts.imglob as imglob import fsl.scripts.imglob as imglob
from tests import testdir from . import testdir
from tests import CaptureStdout
def test_imglob_shouldPass(): def test_imglob_shouldPass():
...@@ -88,60 +85,3 @@ def test_imglob_shouldFail(): ...@@ -88,60 +85,3 @@ def test_imglob_shouldFail():
with pytest.raises(ValueError): with pytest.raises(ValueError):
imglob.imglob([], 'bag') imglob.imglob([], 'bag')
def test_imglob_script_shouldPass():
# (files to create, args, expected)
tests = [
('file.hdr file.img', 'file', 'file'),
('file.hdr file.img', '-extension file', 'file.hdr'),
('file.hdr file.img', '-extensions file', 'file.hdr file.img'),
('file.hdr file.img', 'file.hdr', 'file'),
('file.hdr file.img', ' -extension file.hdr', 'file.hdr'),
('file.hdr file.img', '-extensions file.hdr', 'file.hdr file.img'),
('file.hdr file.img', 'file.img', 'file'),
('file.hdr file.img', '-extension file.img', 'file.hdr'),
('file.hdr file.img', '-extensions file.img', 'file.hdr file.img'),
('file.hdr file.img', 'file.hdr file.img', 'file'),
('file.hdr file.img', '-extension file.hdr file.img', 'file.hdr'),
('file.hdr file.img', '-extensions file.hdr file.img', 'file.hdr file.img'),
('file.hdr file.img', 'file file.img', 'file'),
('file.hdr file.img', '-extension file file.img', 'file.hdr'),
('file.hdr file.img', '-extensions file file.img', 'file.hdr file.img'),
# no file or incomplete prefix
('file.hdr file.img', 'bag', ''),
('file.hdr file.img', '-extension bag', ''),
('file.hdr file.img', '-extensions bag', ''),
('file.hdr file.img', 'fi', ''),
('file.hdr file.img', '-extension fi', ''),
('file.hdr file.img', '-extensions fi', ''),
]
capture = CaptureStdout()
for to_create, args, expected in tests:
with testdir(to_create.split()) as td:
capture.reset()
with capture:
assert imglob.main(args.split()) == 0
assert capture.stdout.strip().split() == expected.split()
def test_imglob_script_shouldFail():
capture = CaptureStdout()
with capture:
assert imglob.main([]) != 0
assert capture.stdout.strip().lower().startswith('usage:')
with capture, mock.patch('sys.argv', ['imglob']):
assert imglob.main() != 0
assert capture.stdout.strip().lower().startswith('usage:')
tests/test_immv_imcp.py
+ 0
− 441
View file @ f95277d9
...@@ -10,26 +10,18 @@ from __future__ import print_function ...@@ -10,26 +10,18 @@ from __future__ import print_function
import os.path as op import os.path as op
import itertools as it
import subprocess as sp
import os import os
import shutil import shutil
import tempfile import tempfile
import pytest
import nibabel as nib import nibabel as nib
from fsl.utils.tempdir import tempdir
import fsl.utils.imcp as imcp import fsl.utils.imcp as imcp
import fsl.scripts.imcp as imcp_script
import fsl.scripts.immv as immv_script
import fsl.data.image as fslimage import fsl.data.image as fslimage
from . import make_random_image from . import make_random_image
from . import make_dummy_file from . import make_dummy_file
from . import looks_like_image from . import looks_like_image
from . import cleardir
real_print = print real_print = print
...@@ -111,415 +103,6 @@ def checkFilesToExpect(files, outdir, outputType, datahashes): ...@@ -111,415 +103,6 @@ def checkFilesToExpect(files, outdir, outputType, datahashes):
checkImageHash(f, h) checkImageHash(f, h)
def test_imcp_script_shouldPass(move=False):
# The imcp/immv scripts should honour the
# FSLOUTPUTTYPE env var. If it is unset
# or invalid - '' in this case), they
# should produce .nii.gz
outputTypes = ['NIFTI', 'NIFTI_PAIR', 'NIFTI_GZ', '']
reldirs = ['neutral', 'samedir', 'indir', 'outdir']
# Test tuples have the following structure (each
# item is a string which will be split on spaces):
#
# (files_to_create, imcp_args, files_to_expect)
#
# The files_to_expect is a list of
# prefixes - the suffix(es) is(are)
# determined by the current outputType
#
# If multiple files are being copied, the
# files_to_create and files_to_expect lists
# have to be in the same order.
tests = [
('a.nii', 'a b', 'b'),
('a.nii', 'a.nii b', 'b'),
('a.nii', 'a b.nii', 'b'),
('a.nii', 'a.nii b.nii', 'b'),
('a.nii', 'a .', 'a'),
('a.nii', 'a.nii .', 'a'),
('a.nii', 'a b.hdr', 'b'),
('a.nii', 'a b.img', 'b'),
('a.nii', 'a b.nii.gz', 'b'),
('a.nii', 'a.nii b.hdr', 'b'),
('a.nii', 'a.nii b.img', 'b'),
('a.nii', 'a.nii b.nii.gz', 'b'),
('a.nii.gz', 'a b', 'b'),
('a.nii.gz', 'a.nii.gz b', 'b'),
('a.nii.gz', 'a b.nii.gz', 'b'),
('a.nii.gz', 'a.nii.gz b.nii.gz', 'b'),
('a.nii.gz', 'a .', 'a'),
('a.nii.gz', 'a.nii.gz .', 'a'),
('a.nii.gz', 'a b.hdr', 'b'),
('a.nii.gz', 'a b.img', 'b'),
('a.nii.gz', 'a b.nii', 'b'),
('a.nii.gz', 'a.nii.gz b.hdr', 'b'),
('a.nii.gz', 'a.nii.gz b.img', 'b'),
('a.nii.gz', 'a.nii.gz b.nii', 'b'),
('a.img', 'a b', 'b'),
('a.img', 'a b.img', 'b'),
('a.img', 'a b.hdr', 'b'),
('a.img', 'a .', 'a'),
('a.img', 'a.img b', 'b'),
('a.img', 'a.img b.img', 'b'),
('a.img', 'a.img b.hdr', 'b'),
('a.img', 'a.img .', 'a'),
('a.img', 'a.hdr b', 'b'),
('a.img', 'a.hdr b.img', 'b'),
('a.img', 'a.hdr b.hdr', 'b'),
('a.img', 'a.hdr .', 'a'),
('a.img', 'a b.nii', 'b'),
('a.img', 'a b.nii.gz', 'b'),
('a.img', 'a .', 'a'),
('a.img', 'a.hdr b.nii', 'b'),
('a.img', 'a.hdr b.nii.gz', 'b'),
('a.img', 'a.hdr .', 'a'),
('a.img', 'a.img b.nii', 'b'),
('a.img', 'a.img b.nii.gz', 'b'),
('a.img', 'a.img .', 'a'),
('a.nii b.nii', 'a b .', 'a b'),
('a.nii b.nii', 'a b.nii .', 'a b'),
('a.nii b.nii', 'a.nii b .', 'a b'),
('a.nii b.nii', 'a.nii b.nii .', 'a b'),
('a.img b.img', 'a b .', 'a b'),
('a.img b.img', 'a b.img .', 'a b'),
('a.img b.img', 'a b.hdr .', 'a b'),
('a.img b.img', 'a.img b .', 'a b'),
('a.img b.img', 'a.img b.img .', 'a b'),
('a.img b.img', 'a.img b.hdr .', 'a b'),
('a.img b.img', 'a.hdr b .', 'a b'),
('a.img b.img', 'a.hdr b.img .', 'a b'),
('a.img b.img', 'a.hdr b.hdr .', 'a b'),
('a.nii.gz b.nii.gz', 'a b .', 'a b'),
('a.nii.gz b.nii.gz', 'a b.nii.gz .', 'a b'),
('a.nii.gz b.nii.gz', 'a.nii.gz b .', 'a b'),
('a.nii.gz b.nii.gz', 'a.nii.gz b.nii.gz .', 'a b'),
# Heterogenous inputs
('a.nii b.nii.gz', 'a b .', 'a b'),
('a.nii b.nii.gz', 'a b.nii.gz .', 'a b'),
('a.nii b.nii.gz', 'a.nii b .', 'a b'),
('a.nii b.nii.gz', 'a.nii b.nii.gz .', 'a b'),
('a.nii b.img', 'a b .', 'a b'),
('a.nii b.img', 'a b.img .', 'a b'),
('a.nii b.img', 'a b.hdr .', 'a b'),
('a.nii b.img', 'a.nii b .', 'a b'),
('a.nii b.img', 'a.nii b.img .', 'a b'),
('a.nii b.img', 'a.nii b.hdr .', 'a b'),
('a.img b.nii', 'a b .', 'a b'),
('a.img b.nii', 'a b.nii .', 'a b'),
('a.img b.nii', 'a.img b .', 'a b'),
('a.img b.nii', 'a.img b.nii .', 'a b'),
('a.img b.nii', 'a.hdr b .', 'a b'),
('a.img b.nii', 'a.hdr b.nii .', 'a b'),
# Duplicate inputs
('a.img', 'a a .', 'a'),
('a.img', 'a a.img .', 'a'),
('a.img', 'a a.hdr .', 'a'),
('a.img', 'a.img a .', 'a'),
('a.img', 'a.img a.img .', 'a'),
('a.img', 'a.img a.hdr .', 'a'),
('a.img', 'a.hdr a .', 'a'),
('a.img', 'a.hdr a.img .', 'a'),
('a.img', 'a.hdr a.hdr .', 'a'),
('a.img b.img', 'a a b b .', 'a b'),
('a.img b.img', 'a a b b.img .', 'a b'),
('a.img b.img', 'a a b b.hdr .', 'a b'),
('a.img b.img', 'a a b.img b .', 'a b'),
('a.img b.img', 'a a b.img b.img .', 'a b'),
('a.img b.img', 'a a b.img b.hdr .', 'a b'),
('a.img b.img', 'a a.img b b .', 'a b'),
('a.img b.img', 'a a.img b b.img .', 'a b'),
('a.img b.img', 'a a.img b b.hdr .', 'a b'),
('a.img b.img', 'a a.img b.img b .', 'a b'),
('a.img b.img', 'a a.img b.img b.img .', 'a b'),
('a.img b.img', 'a a.img b.img b.hdr .', 'a b'),
('a.img b.img', 'a a.hdr b b .', 'a b'),
('a.img b.img', 'a a.hdr b b.img .', 'a b'),
('a.img b.img', 'a a.hdr b b.hdr .', 'a b'),
('a.img b.img', 'a a.hdr b.img b .', 'a b'),
('a.img b.img', 'a a.hdr b.img b.img .', 'a b'),
('a.img b.img', 'a a.hdr b.img b.hdr .', 'a b'),
('a.img b.img', 'a.img a b b .', 'a b'),
('a.img b.img', 'a.img a b b.img .', 'a b'),
('a.img b.img', 'a.img a b b.hdr .', 'a b'),
('a.img b.img', 'a.img a b.img b .', 'a b'),
('a.img b.img', 'a.img a b.img b.img .', 'a b'),
('a.img b.img', 'a.img a b.img b.hdr .', 'a b'),
('a.img b.img', 'a.img a.img b b .', 'a b'),
('a.img b.img', 'a.img a.img b b.img .', 'a b'),
('a.img b.img', 'a.img a.img b b.hdr .', 'a b'),
('a.img b.img', 'a.img a.img b.img b .', 'a b'),
('a.img b.img', 'a.img a.img b.img b.img .', 'a b'),
('a.img b.img', 'a.img a.img b.img b.hdr .', 'a b'),
('a.img b.img', 'a.img a.hdr b b .', 'a b'),
('a.img b.img', 'a.img a.hdr b b.img .', 'a b'),
('a.img b.img', 'a.img a.hdr b b.hdr .', 'a b'),
('a.img b.img', 'a.img a.hdr b.img b .', 'a b'),
('a.img b.img', 'a.img a.hdr b.img b.img .', 'a b'),
('a.img b.img', 'a.img a.hdr b.img b.hdr .', 'a b'),
('a.img b.img', 'a.hdr a b b .', 'a b'),
('a.img b.img', 'a.hdr a b b.img .', 'a b'),
('a.img b.img', 'a.hdr a b b.hdr .', 'a b'),
('a.img b.img', 'a.hdr a b.img b .', 'a b'),
('a.img b.img', 'a.hdr a b.img b.img .', 'a b'),
('a.img b.img', 'a.hdr a b.img b.hdr .', 'a b'),
('a.img b.img', 'a.hdr a.img b b .', 'a b'),
('a.img b.img', 'a.hdr a.img b b.img .', 'a b'),
('a.img b.img', 'a.hdr a.img b b.hdr .', 'a b'),
('a.img b.img', 'a.hdr a.img b.img b .', 'a b'),
('a.img b.img', 'a.hdr a.img b.img b.img .', 'a b'),
('a.img b.img', 'a.hdr a.img b.img b.hdr .', 'a b'),
('a.img b.img', 'a.hdr a.hdr b b .', 'a b'),
('a.img b.img', 'a.hdr a.hdr b b.img .', 'a b'),
('a.img b.img', 'a.hdr a.hdr b b.hdr .', 'a b'),
('a.img b.img', 'a.hdr a.hdr b.img b .', 'a b'),
('a.img b.img', 'a.hdr a.hdr b.img b.img .', 'a b'),
('a.img b.img', 'a.hdr a.hdr b.img b.hdr .', 'a b'),
# Inputs which cause the destination
# to be overwritten - this should be
# ok, the destination should be the
# last specified input. The order of
# files_to_create has to match the
# imcp_args order, otherwise my bodgy
# checkFilesToExpect function will
# break.
('a.nii a.img', 'a.nii a.img .', 'a'),
('a.img a.nii', 'a.img a.nii .', 'a'),
('a.nii a.img a.nii.gz', 'a.nii a.img a.nii.gz .', 'a'),
('a.nii a.nii.gz a.img ', 'a.nii a.nii.gz a.img .', 'a'),
('a.img a.nii.gz a.nii ', 'a.img a.nii.gz a.nii .', 'a'),
('a.img a.nii a.nii.gz', 'a.img a.nii a.nii.gz .', 'a'),
('a.nii.gz a.img a.nii ', 'a.nii.gz a.img a.nii .', 'a'),
('a.nii.gz a.nii a.img ', 'a.nii.gz a.nii a.img .', 'a'),
]
indir = tempfile.mkdtemp()
outdir = tempfile.mkdtemp()
startdir = os.getcwd()
try:
for outputType, reldir in it.product(outputTypes, reldirs):
os.environ['FSLOUTPUTTYPE'] = outputType
for files_to_create, imcp_args, files_to_expect in tests:
imageHashes = []
print()
print('files_to_create: ', files_to_create)
print('imcp_args: ', imcp_args)
print('files_to_expect: ', files_to_expect)
for i, fname in enumerate(files_to_create.split()):
imageHashes.append(makeImage(op.join(indir, fname)))
imcp_args = imcp_args.split()
tindir = indir
toutdir = outdir
if reldir == 'neutral': reldir = startdir
elif reldir == 'indir': reldir = tindir
elif reldir == 'outdir': reldir = toutdir
elif reldir == 'samedir':
reldir = tindir
toutdir = tindir
if not move:
infiles = os.listdir(tindir)
files_to_expect = files_to_expect + ' ' + \
' '.join(infiles)
for inf in infiles:
img = nib.load(op.join(tindir, inf),
mmap=False)
imghash = hash(img.get_data().tobytes())
img = None
imageHashes.append(imghash)
print('adj files_to_expect: ', files_to_expect)
os.chdir(reldir)
imcp_args[:-1] = [op.join(tindir, a) for a in imcp_args[:-1]]
imcp_args[ -1] = op.join(toutdir, imcp_args[-1])
for i, a in enumerate(imcp_args):
if op.splitdrive(a)[0] == op.splitdrive(reldir)[0]:
imcp_args[i] = op.relpath(a, reldir)
print('indir before: ', os.listdir(tindir))
print('outdir before: ', os.listdir(toutdir))
if move: result = immv_script.main(imcp_args)
else: result = imcp_script.main(imcp_args)
print('indir after: ', os.listdir(tindir))
print('outdir after: ', os.listdir(toutdir))
assert result == 0
checkFilesToExpect(
files_to_expect, toutdir, outputType, imageHashes)
# too hard if indir == outdir
if move and tindir != toutdir:
infiles = os.listdir(tindir)
infiles = [f for f in infiles if op.isfile(f)]
infiles = [f for f in infiles if op.isfile(f)]
assert len(infiles) == 0
cleardir(indir)
cleardir(outdir)
finally:
os.chdir(startdir)
shutil.rmtree(indir)
shutil.rmtree(outdir)
@pytest.mark.noroottest
def test_imcp_script_shouldFail(move=False):
# - len(srcs) > 1 and dest is not dir
# - input not readable
# - move=True and input not deleteable
# - ambiguous inputs
# - input is incomplete pair (e.g. .hdr
# without corresponding .img)
# a.img
# a.hdr
# a.nii
#
# FAIL: imcp a dest
# (files_to_create, imcp_args[, preproc])
tests = [
# non-existent input
('', 'a b'),
('a.img', 'b.img a'),
# dest is non-existent dir
('a.img', 'a.img non_existent_dir/'),
# len(srcs) > 1, but dest is not dir
('a.img b.img', 'a b c.img'),
# destination not writeable
('a.img b.img', 'a b ./readonly_dir', 'mkdir outdir/readonly_dir; chmod a-wx outdir/readonly_dir'),
('a.img', 'a b', 'mkdir outdir/b.nii.gz; chmod a-wx outdir/b.nii.gz'),
# input not readable
('a.img', 'a b', 'chmod a-rwx indir/a.img'),
# ambiguous input
('a.img a.nii', 'a b'),
# input is part of incomplete pair
('a.img', 'a b', 'rm indir/a.hdr'),
('a.img', 'a.img b', 'rm indir/a.hdr'),
('a.img', 'a.hdr b', 'rm indir/a.hdr'),
('a.img', 'a b', 'rm indir/a.img'),
('a.img', 'a.img b', 'rm indir/a.img'),
('a.img', 'a.hdr b', 'rm indir/a.img'),
]
if move:
tests = tests + [
# Input not deletable
('a.img', 'a b', 'chmod a-wx indir'),
('a.img', 'a b', 'chmod a-wx indir'),
('a.nii', 'a b', 'chmod a-wx indir')
]
indir = tempfile.mkdtemp()
outdir = tempfile.mkdtemp()
try:
for test in tests:
files_to_create = test[0]
imcp_args = test[1]
if len(test) == 3: preproc = test[2]
else: preproc = None
files_to_create = files_to_create.split()
imcp_args = imcp_args .split()
for fname in files_to_create:
makeImage(op.join(indir, fname))
imcp_args[:-1] = [op.join(indir, a) for a in imcp_args[:-1]]
imcp_args[ -1] = op.join(outdir, imcp_args[-1])
if preproc is not None:
for cmd in preproc.split(';'):
cmd = cmd.replace('indir', indir).replace('outdir', outdir)
sp.call(cmd.split())
print('calling {} {}'.format('immv' if move else 'imcp',
' '.join(imcp_args)))
print('indir before: {}'.format(os.listdir(indir)))
print('out dir before: {}'.format(os.listdir(outdir)))
if move: result = immv_script.main(imcp_args)
else: result = imcp_script.main(imcp_args)
print('indir after: {}'.format(os.listdir(indir)))
print('out dir after: {}'.format(os.listdir(outdir)))
assert result != 0
sp.call('chmod u+rwx {}'.format(indir) .split())
sp.call('chmod u+rwx {}'.format(outdir).split())
cleardir(indir)
cleardir(outdir)
finally:
shutil.rmtree(indir)
shutil.rmtree(outdir)
# Other failure cases
if move: assert immv_script.main() != 0
else: assert imcp_script.main() != 0
if move: assert immv_script.main([]) != 0
else: assert imcp_script.main([]) != 0
if move: assert immv_script.main(['wa']) != 0
else: assert imcp_script.main(['wa']) != 0
def test_immv_script_shouldPass():
test_imcp_script_shouldPass(move=True)
@pytest.mark.noroottest
def test_immv_script_shouldFail():
test_imcp_script_shouldFail(move=True)
def test_imcp_shouldPass(move=False): def test_imcp_shouldPass(move=False):
...@@ -731,27 +314,3 @@ def test_imcp_shouldPass(move=False): ...@@ -731,27 +314,3 @@ def test_imcp_shouldPass(move=False):
def test_immv_shouldPass(): def test_immv_shouldPass():
test_imcp_shouldPass(move=True) test_imcp_shouldPass(move=True)
def test_imcp_badExt():
with tempdir():
with open('file.nii.gz', 'wt') as f:
f.write('1')
result = imcp_script.main(['file.nii', 'dest'])
assert result == 0
assert op.exists('dest.nii.gz')
def test_immv_badExt():
with tempdir():
with open('file.nii.gz', 'wt') as f:
f.write('1')
result = immv_script.main(['file.nii', 'dest'])
assert result == 0
assert op.exists('dest.nii.gz')
tests/test_scripts/__init__.py 0 → 100644
+ 0
− 0
View file @ f95277d9
tests/test_atlasq_ohi.py → tests/test_scripts/test_atlasq_ohi.py
+ 0
− 0
View file @ f95277d9
File moved
tests/test_fsl_ents.py → tests/test_scripts/test_fsl_ents.py
+ 0
− 0
View file @ f95277d9
File moved
tests/test_scripts/test_imglob.py 0 → 100644
+ 65
− 0
View file @ f95277d9
#!/usr/bin/env python
import mock
import fsl.scripts.imglob as imglob
from .. import testdir
from .. import CaptureStdout
def test_imglob_script_shouldPass():
# (files to create, args, expected)
tests = [
('file.hdr file.img', 'file', 'file'),
('file.hdr file.img', '-extension file', 'file.hdr'),
('file.hdr file.img', '-extensions file', 'file.hdr file.img'),
('file.hdr file.img', 'file.hdr', 'file'),
('file.hdr file.img', ' -extension file.hdr', 'file.hdr'),
('file.hdr file.img', '-extensions file.hdr', 'file.hdr file.img'),
('file.hdr file.img', 'file.img', 'file'),
('file.hdr file.img', '-extension file.img', 'file.hdr'),
('file.hdr file.img', '-extensions file.img', 'file.hdr file.img'),
('file.hdr file.img', 'file.hdr file.img', 'file'),
('file.hdr file.img', '-extension file.hdr file.img', 'file.hdr'),
('file.hdr file.img', '-extensions file.hdr file.img', 'file.hdr file.img'),
('file.hdr file.img', 'file file.img', 'file'),
('file.hdr file.img', '-extension file file.img', 'file.hdr'),
('file.hdr file.img', '-extensions file file.img', 'file.hdr file.img'),
# no file or incomplete prefix
('file.hdr file.img', 'bag', ''),
('file.hdr file.img', '-extension bag', ''),
('file.hdr file.img', '-extensions bag', ''),
('file.hdr file.img', 'fi', ''),
('file.hdr file.img', '-extension fi', ''),
('file.hdr file.img', '-extensions fi', ''),
]
capture = CaptureStdout()
for to_create, args, expected in tests:
with testdir(to_create.split()) as td:
capture.reset()
with capture:
assert imglob.main(args.split()) == 0
assert capture.stdout.strip().split() == expected.split()
def test_imglob_script_shouldFail():
capture = CaptureStdout()
with capture:
assert imglob.main([]) != 0
assert capture.stdout.strip().lower().startswith('usage:')
with capture, mock.patch('sys.argv', ['imglob']):
assert imglob.main() != 0
assert capture.stdout.strip().lower().startswith('usage:')
tests/test_scripts/test_immv_imcp.py 0 → 100644
+ 465
− 0
View file @ f95277d9
#!/usr/bin/env python
import os.path as op
import itertools as it
import subprocess as sp
import os
import shutil
import tempfile
import pytest
import nibabel as nib
from fsl.utils.tempdir import tempdir
import fsl.scripts.imcp as imcp_script
import fsl.scripts.immv as immv_script
from .. import cleardir
from ..test_immv_imcp import makeImage, checkImageHash, checkFilesToExpect
real_print = print
def print(*args, **kwargs):
pass
def test_imcp_script_shouldPass(move=False):
# The imcp/immv scripts should honour the
# FSLOUTPUTTYPE env var. If it is unset
# or invalid - '' in this case), they
# should produce .nii.gz
outputTypes = ['NIFTI', 'NIFTI_PAIR', 'NIFTI_GZ', '']
reldirs = ['neutral', 'samedir', 'indir', 'outdir']
# Test tuples have the following structure (each
# item is a string which will be split on spaces):
#
# (files_to_create, imcp_args, files_to_expect)
#
# The files_to_expect is a list of
# prefixes - the suffix(es) is(are)
# determined by the current outputType
#
# If multiple files are being copied, the
# files_to_create and files_to_expect lists
# have to be in the same order.
tests = [
('a.nii', 'a b', 'b'),
('a.nii', 'a.nii b', 'b'),
('a.nii', 'a b.nii', 'b'),
('a.nii', 'a.nii b.nii', 'b'),
('a.nii', 'a .', 'a'),
('a.nii', 'a.nii .', 'a'),
('a.nii', 'a b.hdr', 'b'),
('a.nii', 'a b.img', 'b'),
('a.nii', 'a b.nii.gz', 'b'),
('a.nii', 'a.nii b.hdr', 'b'),
('a.nii', 'a.nii b.img', 'b'),
('a.nii', 'a.nii b.nii.gz', 'b'),
('a.nii.gz', 'a b', 'b'),
('a.nii.gz', 'a.nii.gz b', 'b'),
('a.nii.gz', 'a b.nii.gz', 'b'),
('a.nii.gz', 'a.nii.gz b.nii.gz', 'b'),
('a.nii.gz', 'a .', 'a'),
('a.nii.gz', 'a.nii.gz .', 'a'),
('a.nii.gz', 'a b.hdr', 'b'),
('a.nii.gz', 'a b.img', 'b'),
('a.nii.gz', 'a b.nii', 'b'),
('a.nii.gz', 'a.nii.gz b.hdr', 'b'),
('a.nii.gz', 'a.nii.gz b.img', 'b'),
('a.nii.gz', 'a.nii.gz b.nii', 'b'),
('a.img', 'a b', 'b'),
('a.img', 'a b.img', 'b'),
('a.img', 'a b.hdr', 'b'),
('a.img', 'a .', 'a'),
('a.img', 'a.img b', 'b'),
('a.img', 'a.img b.img', 'b'),
('a.img', 'a.img b.hdr', 'b'),
('a.img', 'a.img .', 'a'),
('a.img', 'a.hdr b', 'b'),
('a.img', 'a.hdr b.img', 'b'),
('a.img', 'a.hdr b.hdr', 'b'),
('a.img', 'a.hdr .', 'a'),
('a.img', 'a b.nii', 'b'),
('a.img', 'a b.nii.gz', 'b'),
('a.img', 'a .', 'a'),
('a.img', 'a.hdr b.nii', 'b'),
('a.img', 'a.hdr b.nii.gz', 'b'),
('a.img', 'a.hdr .', 'a'),
('a.img', 'a.img b.nii', 'b'),
('a.img', 'a.img b.nii.gz', 'b'),
('a.img', 'a.img .', 'a'),
('a.nii b.nii', 'a b .', 'a b'),
('a.nii b.nii', 'a b.nii .', 'a b'),
('a.nii b.nii', 'a.nii b .', 'a b'),
('a.nii b.nii', 'a.nii b.nii .', 'a b'),
('a.img b.img', 'a b .', 'a b'),
('a.img b.img', 'a b.img .', 'a b'),
('a.img b.img', 'a b.hdr .', 'a b'),
('a.img b.img', 'a.img b .', 'a b'),
('a.img b.img', 'a.img b.img .', 'a b'),
('a.img b.img', 'a.img b.hdr .', 'a b'),
('a.img b.img', 'a.hdr b .', 'a b'),
('a.img b.img', 'a.hdr b.img .', 'a b'),
('a.img b.img', 'a.hdr b.hdr .', 'a b'),
('a.nii.gz b.nii.gz', 'a b .', 'a b'),
('a.nii.gz b.nii.gz', 'a b.nii.gz .', 'a b'),
('a.nii.gz b.nii.gz', 'a.nii.gz b .', 'a b'),
('a.nii.gz b.nii.gz', 'a.nii.gz b.nii.gz .', 'a b'),
# Heterogenous inputs
('a.nii b.nii.gz', 'a b .', 'a b'),
('a.nii b.nii.gz', 'a b.nii.gz .', 'a b'),
('a.nii b.nii.gz', 'a.nii b .', 'a b'),
('a.nii b.nii.gz', 'a.nii b.nii.gz .', 'a b'),
('a.nii b.img', 'a b .', 'a b'),
('a.nii b.img', 'a b.img .', 'a b'),
('a.nii b.img', 'a b.hdr .', 'a b'),
('a.nii b.img', 'a.nii b .', 'a b'),
('a.nii b.img', 'a.nii b.img .', 'a b'),
('a.nii b.img', 'a.nii b.hdr .', 'a b'),
('a.img b.nii', 'a b .', 'a b'),
('a.img b.nii', 'a b.nii .', 'a b'),
('a.img b.nii', 'a.img b .', 'a b'),
('a.img b.nii', 'a.img b.nii .', 'a b'),
('a.img b.nii', 'a.hdr b .', 'a b'),
('a.img b.nii', 'a.hdr b.nii .', 'a b'),
# Duplicate inputs
('a.img', 'a a .', 'a'),
('a.img', 'a a.img .', 'a'),
('a.img', 'a a.hdr .', 'a'),
('a.img', 'a.img a .', 'a'),
('a.img', 'a.img a.img .', 'a'),
('a.img', 'a.img a.hdr .', 'a'),
('a.img', 'a.hdr a .', 'a'),
('a.img', 'a.hdr a.img .', 'a'),
('a.img', 'a.hdr a.hdr .', 'a'),
('a.img b.img', 'a a b b .', 'a b'),
('a.img b.img', 'a a b b.img .', 'a b'),
('a.img b.img', 'a a b b.hdr .', 'a b'),
('a.img b.img', 'a a b.img b .', 'a b'),
('a.img b.img', 'a a b.img b.img .', 'a b'),
('a.img b.img', 'a a b.img b.hdr .', 'a b'),
('a.img b.img', 'a a.img b b .', 'a b'),
('a.img b.img', 'a a.img b b.img .', 'a b'),
('a.img b.img', 'a a.img b b.hdr .', 'a b'),
('a.img b.img', 'a a.img b.img b .', 'a b'),
('a.img b.img', 'a a.img b.img b.img .', 'a b'),
('a.img b.img', 'a a.img b.img b.hdr .', 'a b'),
('a.img b.img', 'a a.hdr b b .', 'a b'),
('a.img b.img', 'a a.hdr b b.img .', 'a b'),
('a.img b.img', 'a a.hdr b b.hdr .', 'a b'),
('a.img b.img', 'a a.hdr b.img b .', 'a b'),
('a.img b.img', 'a a.hdr b.img b.img .', 'a b'),
('a.img b.img', 'a a.hdr b.img b.hdr .', 'a b'),
('a.img b.img', 'a.img a b b .', 'a b'),
('a.img b.img', 'a.img a b b.img .', 'a b'),
('a.img b.img', 'a.img a b b.hdr .', 'a b'),
('a.img b.img', 'a.img a b.img b .', 'a b'),
('a.img b.img', 'a.img a b.img b.img .', 'a b'),
('a.img b.img', 'a.img a b.img b.hdr .', 'a b'),
('a.img b.img', 'a.img a.img b b .', 'a b'),
('a.img b.img', 'a.img a.img b b.img .', 'a b'),
('a.img b.img', 'a.img a.img b b.hdr .', 'a b'),
('a.img b.img', 'a.img a.img b.img b .', 'a b'),
('a.img b.img', 'a.img a.img b.img b.img .', 'a b'),
('a.img b.img', 'a.img a.img b.img b.hdr .', 'a b'),
('a.img b.img', 'a.img a.hdr b b .', 'a b'),
('a.img b.img', 'a.img a.hdr b b.img .', 'a b'),
('a.img b.img', 'a.img a.hdr b b.hdr .', 'a b'),
('a.img b.img', 'a.img a.hdr b.img b .', 'a b'),
('a.img b.img', 'a.img a.hdr b.img b.img .', 'a b'),
('a.img b.img', 'a.img a.hdr b.img b.hdr .', 'a b'),
('a.img b.img', 'a.hdr a b b .', 'a b'),
('a.img b.img', 'a.hdr a b b.img .', 'a b'),
('a.img b.img', 'a.hdr a b b.hdr .', 'a b'),
('a.img b.img', 'a.hdr a b.img b .', 'a b'),
('a.img b.img', 'a.hdr a b.img b.img .', 'a b'),
('a.img b.img', 'a.hdr a b.img b.hdr .', 'a b'),
('a.img b.img', 'a.hdr a.img b b .', 'a b'),
('a.img b.img', 'a.hdr a.img b b.img .', 'a b'),
('a.img b.img', 'a.hdr a.img b b.hdr .', 'a b'),
('a.img b.img', 'a.hdr a.img b.img b .', 'a b'),
('a.img b.img', 'a.hdr a.img b.img b.img .', 'a b'),
('a.img b.img', 'a.hdr a.img b.img b.hdr .', 'a b'),
('a.img b.img', 'a.hdr a.hdr b b .', 'a b'),
('a.img b.img', 'a.hdr a.hdr b b.img .', 'a b'),
('a.img b.img', 'a.hdr a.hdr b b.hdr .', 'a b'),
('a.img b.img', 'a.hdr a.hdr b.img b .', 'a b'),
('a.img b.img', 'a.hdr a.hdr b.img b.img .', 'a b'),
('a.img b.img', 'a.hdr a.hdr b.img b.hdr .', 'a b'),
# Inputs which cause the destination
# to be overwritten - this should be
# ok, the destination should be the
# last specified input. The order of
# files_to_create has to match the
# imcp_args order, otherwise my bodgy
# checkFilesToExpect function will
# break.
('a.nii a.img', 'a.nii a.img .', 'a'),
('a.img a.nii', 'a.img a.nii .', 'a'),
('a.nii a.img a.nii.gz', 'a.nii a.img a.nii.gz .', 'a'),
('a.nii a.nii.gz a.img ', 'a.nii a.nii.gz a.img .', 'a'),
('a.img a.nii.gz a.nii ', 'a.img a.nii.gz a.nii .', 'a'),
('a.img a.nii a.nii.gz', 'a.img a.nii a.nii.gz .', 'a'),
('a.nii.gz a.img a.nii ', 'a.nii.gz a.img a.nii .', 'a'),
('a.nii.gz a.nii a.img ', 'a.nii.gz a.nii a.img .', 'a'),
]
indir = tempfile.mkdtemp()
outdir = tempfile.mkdtemp()
startdir = os.getcwd()
try:
for outputType, reldir in it.product(outputTypes, reldirs):
os.environ['FSLOUTPUTTYPE'] = outputType
for files_to_create, imcp_args, files_to_expect in tests:
imageHashes = []
print()
print('files_to_create: ', files_to_create)
print('imcp_args: ', imcp_args)
print('files_to_expect: ', files_to_expect)
for i, fname in enumerate(files_to_create.split()):
imageHashes.append(makeImage(op.join(indir, fname)))
imcp_args = imcp_args.split()
tindir = indir
toutdir = outdir
if reldir == 'neutral': reldir = startdir
elif reldir == 'indir': reldir = tindir
elif reldir == 'outdir': reldir = toutdir
elif reldir == 'samedir':
reldir = tindir
toutdir = tindir
if not move:
infiles = os.listdir(tindir)
files_to_expect = files_to_expect + ' ' + \
' '.join(infiles)
for inf in infiles:
img = nib.load(op.join(tindir, inf),
mmap=False)
imghash = hash(img.get_data().tobytes())
img = None
imageHashes.append(imghash)
print('adj files_to_expect: ', files_to_expect)
os.chdir(reldir)
imcp_args[:-1] = [op.join(tindir, a) for a in imcp_args[:-1]]
imcp_args[ -1] = op.join(toutdir, imcp_args[-1])
for i, a in enumerate(imcp_args):
if op.splitdrive(a)[0] == op.splitdrive(reldir)[0]:
imcp_args[i] = op.relpath(a, reldir)
print('indir before: ', os.listdir(tindir))
print('outdir before: ', os.listdir(toutdir))
if move: result = immv_script.main(imcp_args)
else: result = imcp_script.main(imcp_args)
print('indir after: ', os.listdir(tindir))
print('outdir after: ', os.listdir(toutdir))
assert result == 0
checkFilesToExpect(
files_to_expect, toutdir, outputType, imageHashes)
# too hard if indir == outdir
if move and tindir != toutdir:
infiles = os.listdir(tindir)
infiles = [f for f in infiles if op.isfile(f)]
infiles = [f for f in infiles if op.isfile(f)]
assert len(infiles) == 0
cleardir(indir)
cleardir(outdir)
finally:
os.chdir(startdir)
shutil.rmtree(indir)
shutil.rmtree(outdir)
@pytest.mark.noroottest
def test_imcp_script_shouldFail(move=False):
# - len(srcs) > 1 and dest is not dir
# - input not readable
# - move=True and input not deleteable
# - ambiguous inputs
# - input is incomplete pair (e.g. .hdr
# without corresponding .img)
# a.img
# a.hdr
# a.nii
#
# FAIL: imcp a dest
# (files_to_create, imcp_args[, preproc])
tests = [
# non-existent input
('', 'a b'),
('a.img', 'b.img a'),
# dest is non-existent dir
('a.img', 'a.img non_existent_dir/'),
# len(srcs) > 1, but dest is not dir
('a.img b.img', 'a b c.img'),
# destination not writeable
('a.img b.img', 'a b ./readonly_dir', 'mkdir outdir/readonly_dir; chmod a-wx outdir/readonly_dir'),
('a.img', 'a b', 'mkdir outdir/b.nii.gz; chmod a-wx outdir/b.nii.gz'),
# input not readable
('a.img', 'a b', 'chmod a-rwx indir/a.img'),
# ambiguous input
('a.img a.nii', 'a b'),
# input is part of incomplete pair
('a.img', 'a b', 'rm indir/a.hdr'),
('a.img', 'a.img b', 'rm indir/a.hdr'),
('a.img', 'a.hdr b', 'rm indir/a.hdr'),
('a.img', 'a b', 'rm indir/a.img'),
('a.img', 'a.img b', 'rm indir/a.img'),
('a.img', 'a.hdr b', 'rm indir/a.img'),
]
if move:
tests = tests + [
# Input not deletable
('a.img', 'a b', 'chmod a-wx indir'),
('a.img', 'a b', 'chmod a-wx indir'),
('a.nii', 'a b', 'chmod a-wx indir')
]
indir = tempfile.mkdtemp()
outdir = tempfile.mkdtemp()
try:
for test in tests:
files_to_create = test[0]
imcp_args = test[1]
if len(test) == 3: preproc = test[2]
else: preproc = None
files_to_create = files_to_create.split()
imcp_args = imcp_args .split()
for fname in files_to_create:
makeImage(op.join(indir, fname))
imcp_args[:-1] = [op.join(indir, a) for a in imcp_args[:-1]]
imcp_args[ -1] = op.join(outdir, imcp_args[-1])
if preproc is not None:
for cmd in preproc.split(';'):
cmd = cmd.replace('indir', indir).replace('outdir', outdir)
sp.call(cmd.split())
print('calling {} {}'.format('immv' if move else 'imcp',
' '.join(imcp_args)))
print('indir before: {}'.format(os.listdir(indir)))
print('out dir before: {}'.format(os.listdir(outdir)))
if move: result = immv_script.main(imcp_args)
else: result = imcp_script.main(imcp_args)
print('indir after: {}'.format(os.listdir(indir)))
print('out dir after: {}'.format(os.listdir(outdir)))
assert result != 0
sp.call('chmod u+rwx {}'.format(indir) .split())
sp.call('chmod u+rwx {}'.format(outdir).split())
cleardir(indir)
cleardir(outdir)
finally:
shutil.rmtree(indir)
shutil.rmtree(outdir)
# Other failure cases
if move: assert immv_script.main() != 0
else: assert imcp_script.main() != 0
if move: assert immv_script.main([]) != 0
else: assert imcp_script.main([]) != 0
if move: assert immv_script.main(['wa']) != 0
else: assert imcp_script.main(['wa']) != 0
def test_immv_script_shouldPass():
test_imcp_script_shouldPass(move=True)
@pytest.mark.noroottest
def test_immv_script_shouldFail():
test_imcp_script_shouldFail(move=True)
def test_imcp_badExt():
with tempdir():
with open('file.nii.gz', 'wt') as f:
f.write('1')
result = imcp_script.main(['file.nii', 'dest'])
assert result == 0
assert op.exists('dest.nii.gz')
def test_immv_badExt():
with tempdir():
with open('file.nii.gz', 'wt') as f:
f.write('1')
result = immv_script.main(['file.nii', 'dest'])
assert result == 0
assert op.exists('dest.nii.gz')
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