From a5b31bd45a54c317957910d0679b694dfa432de6 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Sat, 7 Jul 2018 12:54:18 +0100
Subject: [PATCH] TEST: Unit tests for _FileOrThing
---
tests/__init__.py | 5 ++++
tests/test_wrappers.py | 19 ++++++++----
tests/test_wrapperutils.py | 61 ++++++++++++++++++++++++++++++++++----
3 files changed, 74 insertions(+), 11 deletions(-)
diff --git a/tests/__init__.py b/tests/__init__.py
index 1106e3059..eb16fa95a 100644
--- a/tests/__init__.py
+++ b/tests/__init__.py
@@ -203,6 +203,11 @@ def cleardir(dir, pat=None):
elif op.isdir(f): shutil.rmtree(f)
+def checkdir(dir, *expfiles):
+ for f in expfiles:
+ assert op.exists(op.join(dir, f))
+
+
def random_voxels(shape, nvoxels=1):
randVoxels = np.vstack(
[np.random.randint(0, s, nvoxels) for s in shape[:3]]).T
diff --git a/tests/test_wrappers.py b/tests/test_wrappers.py
index 1e366a166..5dcca79c1 100644
--- a/tests/test_wrappers.py
+++ b/tests/test_wrappers.py
@@ -15,14 +15,23 @@ import fsl.utils.run as run
from . import mockFSLDIR
-def checkResult(cmd, base, args):
+def checkResult(cmd, base, args, stripdir=None):
"""We can't control the order in which command line args are generated,
so we need to test all possible orderings.
- :arg cmd: Generated command
- :arg base: Beginning of expected command
- :arg args: Sequence of expected arguments
+ :arg cmd: Generated command
+ :arg base: Beginning of expected command
+ :arg args: Sequence of expected arguments
+ :arg stripdir: Sequence of indices indicating arguments
+ for whihc any leading directory should be ignored.
"""
+
+ if stripdir is not None:
+ cmd = list(cmd.split())
+ for si in stripdir:
+ cmd[si] = op.basename(cmd[si])
+ cmd = ' '.join(cmd)
+
permutations = it.permutations(args, len(args))
possible = [' '.join([base] + list(p)) for p in permutations]
@@ -34,7 +43,7 @@ def test_bet():
bet = op.join(fsldir, 'bin', 'bet')
result = fw.bet('input', 'output', mask=True, c=(10, 20, 30))
expected = (bet + ' input output', ('-m', '-c 10 20 30'))
- assert checkResult(result.output[0], *expected)
+ assert checkResult(result.output[0], *expected, stripdir=[2])
def test_robustfov():
diff --git a/tests/test_wrapperutils.py b/tests/test_wrapperutils.py
index 43341f91b..90cfc7ff9 100644
--- a/tests/test_wrapperutils.py
+++ b/tests/test_wrapperutils.py
@@ -25,7 +25,7 @@ import fsl.data.image as fslimage
import fsl.wrappers.wrapperutils as wutils
-from . import mockFSLDIR, cleardir
+from . import mockFSLDIR, cleardir, checkdir
from .test_run import mock_submit
@@ -311,10 +311,6 @@ def test_fileOrImage():
def test_fileOrImage_outprefix():
- import logging
- logging.basicConfig()
- logging.getLogger('fsl.wrappers').setLevel(logging.DEBUG)
-
@wutils.fileOrImage('img', outprefix='output_base')
def basefunc(img, output_base):
img = nib.load(img).get_data()
@@ -325,6 +321,7 @@ def test_fileOrImage_outprefix():
nib.save(out1, '{}_times5.nii.gz' .format(output_base))
nib.save(out2, '{}_times10.nii.gz'.format(output_base))
+
with tempdir.tempdir() as td:
img = nib.nifti1.Nifti1Image(np.array([[1, 2], [3, 4]]), np.eye(4))
exp1 = img.get_data() * 5
@@ -395,12 +392,64 @@ def test_fileOrImage_outprefix_differentTypes():
cleardir(td, 'myout*')
+def test_fileOrImage_outprefix_directory():
+
+ import logging
+ logging.basicConfig()
+ logging.getLogger('fsl.wrappers').setLevel(logging.DEBUG)
+
+ @wutils.fileOrImage('img', outprefix='outpref')
+ def func(img, outpref):
+ img = nib.load(img)
+ img2 = nib.nifti1.Nifti1Image(img.get_data() * 2, np.eye(4))
+ img4 = nib.nifti1.Nifti1Image(img.get_data() * 4, np.eye(4))
+ outdir = op.abspath('{}_imgs'.format(outpref))
-# test directory
+ os.mkdir(outdir)
+ nib.save(img2, op.join(outdir, 'img2.nii.gz'))
+ nib.save(img4, op.join(outdir, 'img4.nii.gz'))
+ with tempdir.tempdir() as td:
+ img = nib.nifti1.Nifti1Image(np.array([[1, 2], [3, 4]]), np.eye(4))
+ exp2 = img.get_data() * 2
+ exp4 = img.get_data() * 4
+
+ res = func(img, 'myout')
+ assert len(res) == 0
+ checkdir(td,
+ op.join('myout_imgs', 'img2.nii.gz'),
+ op.join('myout_imgs', 'img4.nii.gz'))
+ cleardir(td, 'myout*')
+ res = func(img, 'myout', myout_imgs=wutils.LOAD)
+ assert len(res) == 2
+ assert np.all(res['myout_imgs/img2'].get_data() == exp2)
+ assert np.all(res['myout_imgs/img4'].get_data() == exp4)
+
+ res = func(img, 'myout', **{'myout_imgs/img2' : wutils.LOAD})
+ assert len(res) == 1
+ assert np.all(res['myout_imgs/img2'].get_data() == exp2)
+
+ res = func(img, 'myout', **{'myout_imgs/img' : wutils.LOAD})
+ assert len(res) == 2
+ assert np.all(res['myout_imgs/img2'].get_data() == exp2)
+ assert np.all(res['myout_imgs/img4'].get_data() == exp4)
+
+ os.mkdir('foo')
+ res = func(img, 'foo/myout')
+ assert len(res) == 0
+ checkdir(td,
+ op.join('foo', 'myout_imgs', 'img2.nii.gz'),
+ op.join('foo', 'myout_imgs', 'img4.nii.gz'))
+ cleardir(td, 'foo')
+
+ os.mkdir('foo')
+ res = func(img, 'foo/myout', **{'foo/myout' : wutils.LOAD})
+ assert len(res) == 2
+ assert np.all(res['foo/myout_imgs/img2'].get_data() == exp2)
+ assert np.all(res['foo/myout_imgs/img4'].get_data() == exp4)
def test_chained_fileOrImageAndArray():
--
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