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test_immv_imcp.py 25.37 KiB
#!/usr/bin/env python
#
# test_immv_imcp.py -
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
from __future__ import print_function
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
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
from . import make_random_image
from . import make_dummy_file
from . import looks_like_image
from . import cleardir
real_print = print
def print(*args, **kwargs):
pass
def makeImage(filename):
return hash(make_random_image(filename).get_data().tobytes())
def checkImageHash(filename, datahash):
"""Checks that the given NIFTI image matches the given hash.
"""
img = nib.load(filename)
assert hash(img.get_data().tobytes()) == datahash
def checkFilesToExpect(files, outdir, outputType, datahashes):
exts = {
'NIFTI' : ['.nii'],
'NIFTI_PAIR' : ['.hdr', '.img'],
'NIFTI_GZ' : ['.nii.gz'],
'' : ['.nii.gz'],
}.get(outputType, None)
allFiles = []
if isinstance(files, str):
files = files.split()
for f in files:
f, fe = fslimage.splitExt(f)
fexts = exts
if fexts is None:
fexts = {
'.img' : ['.hdr', '.img'],
'.hdr' : ['.hdr', '.img'],
'.nii' : ['.nii'],
'.nii.gz' : ['.nii.gz']
}.get(fe, [])
# filename already has a different extension
elif fe != '' and fe not in fexts:
fexts = [fe]
for e in fexts:
expected = op.join(outdir, f + e)
allFiles.append(expected)
print(' ', expected)
assert op.exists(expected)
allThatExist = os.listdir(outdir)
allThatExist = [f for f in allThatExist if op.isfile(op.join(outdir, f))]
assert len(allThatExist) == len(allFiles)
for i, f in enumerate(files):
f = fslimage.addExt(op.join(outdir, f), mustExist=True)
if isinstance(datahashes, list):
if len(datahashes) > len(files):
diff = len(datahashes) - len(files)
h = datahashes[i + diff]
else:
h = datahashes[i]
else:
h = datahashes[op.basename(f)]
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))
imghash = hash(img.get_data().tobytes())
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])
imcp_args = [op.relpath(a, reldir) for a in imcp_args]
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:
real_print('indir: ', tindir)
real_print('outdir: ', 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):
#
# if not useDefaultExt:
#
# imcp src.img dest -> dest.img
# imcp src.img dest.nii -> dest.nii
#
# if defaultExt:
# imgp src.img dest -> dest.nii.gz
# imgp src.img dest.nii -> dest.nii.gz
#
# (files_to_create,
# [( imcp_args, files_which_should_exist),
# ...
# ]
# )
shouldPass = [
('file.img', [
('file file', 'file.img'),
('file file.img', 'file.img'),
('file file.hdr', 'file.img'),
('file .', 'file.img'),
('file.img file', 'file.img'),
('file.img file.img', 'file.img'),
('file.img file.hdr', 'file.img'),
('file.img .', 'file.img'),
('file.hdr file', 'file.img'),
('file.hdr file.img', 'file.img'),
('file.hdr file.hdr', 'file.img'),
('file.hdr .', 'file.img'),
]),
('file.img file.blob', [
('file file', 'file.img'),
('file file.img', 'file.img'),
('file file.hdr', 'file.img'),
('file .', 'file.img'),
('file.img file', 'file.img'),
('file.img file.img', 'file.img'),
('file.img file.hdr', 'file.img'),
('file.img .', 'file.img'),
('file.hdr file', 'file.img'),
('file.hdr file.img', 'file.img'),
('file.hdr file.hdr', 'file.img'),
('file.hdr .', 'file.img'),
]),
('file.img file.nii', [
('file.img file', 'file.img'),
('file.img file.img', 'file.img'),
('file.img file.hdr', 'file.img'),
('file.img .', 'file.img'),
('file.hdr file', 'file.img'),
('file.hdr file.img', 'file.img'),
('file.hdr file.hdr', 'file.img'),
('file.hdr .', 'file.img'),
('file.nii file', 'file.nii'),
('file.nii file.nii', 'file.nii'),
# TODO both img/nii files
]),
('file.nii', [
('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.gz', [
('file file', 'file.nii.gz'),
('file file.nii.gz', 'file.nii.gz'),
('file .', 'file.nii.gz'),
('file.nii.gz file', 'file.nii.gz'),
('file.nii.gz file.nii.gz', 'file.nii.gz'),
('file.nii.gz .', 'file.nii.gz'),
]),
('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'),
# TODO both
]),
('file.img file.nii file.nii.gz', [
('file.img file.nii file.nii.gz .', 'file.img file.nii file.nii.gz'),
('file.img .', 'file.img'),
('file.img .', 'file.img'),
('file.nii .', 'file.nii'),
('file.nii file.nii.gz .', 'file.nii file.nii.gz'),
]),
('001.img 002.img 003.img', [
('001 002 003 .', '001.img 002.img 003.img'),
('001.img 002.img 003.img .', '001.img 002.img 003.img'),
('001.hdr 002.hdr 003.hdr .', '001.img 002.img 003.img'),
('001.img 002 003 .', '001.img 002.img 003.img'),
('001.hdr 002 003 .', '001.img 002.img 003.img'),
('001.img 002.hdr 003.img .', '001.img 002.img 003.img'),
('001.hdr 002.img 003.hdr .', '001.img 002.img 003.img'),
('001 003 .', '001.img 003.img'),
('001.img 003.img .', '001.img 003.img'),
('001.hdr 003.hdr .', '001.img 003.img'),
('001.img 003 .', '001.img 003.img'),
('001.hdr 003 .', '001.img 003.img'),
('001.img 003.img .', '001.img 003.img'),
('001.hdr 003.hdr .', '001.img 003.img'),
]),
]
indir = tempfile.mkdtemp()
outdir = tempfile.mkdtemp()
try:
for files_to_create, tests in shouldPass:
files_to_create = files_to_create.split()
for imcp_args, should_exist in tests:
should_exist = should_exist.split()
imcp_args = imcp_args.split()
imcp_srcs = imcp_args[:-1]
imcp_dest = imcp_args[ -1]
hashes = {}
for fn in files_to_create:
if looks_like_image(fn):
hashes[fn] = makeImage(op.join(indir, fn))
else:
hashes[fn] = make_dummy_file(op.join(indir, fn))
print()
print('files_to_create: ', files_to_create)
print('imcp_srcs: ', imcp_srcs)
print('imcp_dest: ', imcp_dest)
print('should_exist: ', should_exist)
print('indir: ', os.listdir(indir))
for src in imcp_srcs:
print(' src: {}'.format(src))
src = op.join(indir, src)
if move: imcp.immv(src, op.join(outdir, imcp_dest), overwrite=True)
else: imcp.imcp(src, op.join(outdir, imcp_dest), overwrite=True)
print('indir after: ', os.listdir(indir))
print('outdir after: ', os.listdir(outdir))
# check file contents
checkFilesToExpect(should_exist,
outdir,
None,
hashes)
# 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 os.listdir(indir):
try: os.remove(op.join(indir, f))
except: pass
for f in os.listdir(outdir):
os.remove(op.join(outdir, f))
finally:
shutil.rmtree(indir)
shutil.rmtree(outdir)
def test_immv_shouldPass():
test_imcp_shouldPass(move=True)