diff --git a/tests/test_imglob.py b/tests/test_imglob.py
index 333fbd104c8599dda439543ee9d0d339df126cfd..9a8e838d1321fd45c91c1d94188700067423097f 100644
--- a/tests/test_imglob.py
+++ b/tests/test_imglob.py
@@ -5,14 +5,11 @@
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
-import mock
import pytest
import fsl.scripts.imglob as imglob
-from tests import testdir
-from tests import CaptureStdout
-
+from . import testdir
def test_imglob_shouldPass():
@@ -88,60 +85,3 @@ def test_imglob_shouldFail():
with pytest.raises(ValueError):
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:')
diff --git a/tests/test_immv_imcp.py b/tests/test_immv_imcp.py
index 215b4dc4062245786d4b37af190d626928cefc1c..dd1273d78e162a3ee96638cfba4b12850d1b080f 100644
--- a/tests/test_immv_imcp.py
+++ b/tests/test_immv_imcp.py
@@ -10,26 +10,18 @@ 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
-from fsl.utils.tempdir import tempdir
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
@@ -111,415 +103,6 @@ def checkFilesToExpect(files, outdir, outputType, datahashes):
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):
@@ -731,27 +314,3 @@ def test_imcp_shouldPass(move=False):
def test_immv_shouldPass():
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')
diff --git a/tests/test_scripts/__init__.py b/tests/test_scripts/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/tests/test_atlasq_list_summary.py b/tests/test_scripts/test_atlasq_list_summary.py
similarity index 100%
rename from tests/test_atlasq_list_summary.py
rename to tests/test_scripts/test_atlasq_list_summary.py
diff --git a/tests/test_atlasq_ohi.py b/tests/test_scripts/test_atlasq_ohi.py
similarity index 100%
rename from tests/test_atlasq_ohi.py
rename to tests/test_scripts/test_atlasq_ohi.py
diff --git a/tests/test_atlasq_query.py b/tests/test_scripts/test_atlasq_query.py
similarity index 100%
rename from tests/test_atlasq_query.py
rename to tests/test_scripts/test_atlasq_query.py
diff --git a/tests/test_fsl_ents.py b/tests/test_scripts/test_fsl_ents.py
similarity index 100%
rename from tests/test_fsl_ents.py
rename to tests/test_scripts/test_fsl_ents.py
diff --git a/tests/test_scripts/test_imglob.py b/tests/test_scripts/test_imglob.py
new file mode 100644
index 0000000000000000000000000000000000000000..0f8e934509ce68359d17a8a8794bbaaa47f1a691
--- /dev/null
+++ b/tests/test_scripts/test_imglob.py
@@ -0,0 +1,65 @@
+#!/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:')
diff --git a/tests/test_scripts/test_immv_imcp.py b/tests/test_scripts/test_immv_imcp.py
new file mode 100644
index 0000000000000000000000000000000000000000..607a7da5d761d69c824f5d85f27751b8bf5a395d
--- /dev/null
+++ b/tests/test_scripts/test_immv_imcp.py
@@ -0,0 +1,465 @@
+#!/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')