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Commit 2a8929a3 authored by Paul McCarthy's avatar Paul McCarthy :mountain_bicyclist:
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TEST: update wrapper tests ("output" -> "stdout"). New test for results 

attribute access. New test for fileOrText decorator
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tests/test_wrappers.py
+ 29
− 29
View file @ 2a8929a3
......@@ -48,7 +48,7 @@ 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, stripdir=[2])
assert checkResult(result.stdout[0], *expected, stripdir=[2])
def test_robustfov():
......@@ -56,7 +56,7 @@ def test_robustfov():
rfov = op.join(fsldir, 'bin', 'robustfov')
result = fw.robustfov('input', 'output', b=180)
expected = (rfov + ' -i input', ('-r output', '-b 180'))
assert checkResult(result.output[0], *expected)
assert checkResult(result.stdout[0], *expected)
def test_eddy_cuda():
......@@ -73,7 +73,7 @@ def test_eddy_cuda():
'--out=out',
'--dont_mask_output'))
assert checkResult(result.output[0], *expected)
assert checkResult(result.stdout[0], *expected)
def test_topup():
......@@ -81,7 +81,7 @@ def test_topup():
topup = op.join(fsldir, 'bin', 'topup')
result = fw.topup('imain', 'datain', minmet=1)
expected = topup + ' --imain=imain --datain=datain --minmet=1'
assert result.output[0] == expected
assert result.stdout[0] == expected
def test_flirt():
......@@ -90,7 +90,7 @@ def test_flirt():
result = fw.flirt('src', 'ref', usesqform=True, anglerep='euler')
expected = (flirt + ' -in src -ref ref',
('-usesqform', '-anglerep euler'))
assert checkResult(result.output[0], *expected)
assert checkResult(result.stdout[0], *expected)
def test_applyxfm():
......@@ -102,7 +102,7 @@ def test_applyxfm():
'-out out',
'-init mat',
'-interp trilinear'))
assert checkResult(result.output[0], *expected)
assert checkResult(result.stdout[0], *expected)
def test_applyxfm():
......@@ -113,7 +113,7 @@ def test_applyxfm():
expected = (applyxfm + ' src ref out mat',
('-fourdigit',
'-userprefix boo'))
assert checkResult(result.output[0], *expected)
assert checkResult(result.stdout[0], *expected)
def test_invxfm():
......@@ -121,7 +121,7 @@ def test_invxfm():
cnvxfm = op.join(fsldir, 'bin', 'convert_xfm')
result = fw.invxfm('mat', 'output')
expected = cnvxfm + ' -omat output -inverse mat'
assert result.output[0] == expected
assert result.stdout[0] == expected
def test_concatxfm():
......@@ -129,7 +129,7 @@ def test_concatxfm():
cnvxfm = op.join(fsldir, 'bin', 'convert_xfm')
result = fw.concatxfm('mat1', 'mat2', 'output')
expected = cnvxfm + ' -omat output -concat mat2 mat1'
assert result.output[0] == expected
assert result.stdout[0] == expected
def test_mcflirt():
......@@ -140,7 +140,7 @@ def test_mcflirt():
('-out output',
'-cost normcorr',
'-dof 12'))
assert checkResult(result.output[0], *expected)
assert checkResult(result.stdout[0], *expected)
def test_fnirt():
......@@ -153,7 +153,7 @@ def test_fnirt():
'--iout=iout',
'--fout=fout',
'--subsamp=8,6,4,2'))
assert checkResult(result.output[0], *expected)
assert checkResult(result.stdout[0], *expected)
def test_applywarp():
......@@ -162,7 +162,7 @@ def test_applywarp():
result = fw.applywarp('src', 'ref', 'out', warp='warp', abs=True, super=True)
expected = (applywarp + ' --in=src --ref=ref --out=out',
('--warp=warp', '--abs', '--super'))
assert checkResult(result.output[0], *expected)
assert checkResult(result.stdout[0], *expected)
def test_invwarp():
......@@ -172,7 +172,7 @@ def test_invwarp():
rel=True, noconstraint=True)
expected = (invwarp + ' --warp=warp --ref=ref --out=out',
('--rel', '--noconstraint'))
assert checkResult(result.output[0], *expected)
assert checkResult(result.stdout[0], *expected)
def test_convertwarp():
......@@ -181,7 +181,7 @@ def test_convertwarp():
result = fw.convertwarp('out', 'ref', absout=True, jacobian='jacobian')
expected = (cnvwarp + ' --ref=ref --out=out',
('--absout', '--jacobian=jacobian'))
assert checkResult(result.output[0], *expected)
assert checkResult(result.stdout[0], *expected)
def test_fugue():
......@@ -193,7 +193,7 @@ def test_fugue():
'--warp=warp',
'--median',
'--dwell=10'))
assert checkResult(result.output[0], *expected)
assert checkResult(result.stdout[0], *expected)
......@@ -203,7 +203,7 @@ def test_sigloss():
result = fw.sigloss('input', 'sigloss', mask='mask', te=0.5)
expected = (sigloss + ' --in input --sigloss sigloss',
('--mask mask', '--te 0.5'))
assert checkResult(result.output[0], *expected)
assert checkResult(result.stdout[0], *expected)
def test_prelude():
......@@ -217,7 +217,7 @@ def test_prelude():
'--out=out',
'--labelslices',
'--start=5'))
assert checkResult(result.output[0], *expected)
assert checkResult(result.stdout[0], *expected)
def test_melodic():
......@@ -226,7 +226,7 @@ def test_melodic():
result = fw.melodic('input', dim=50, mask='mask', Oall=True)
expected = (melodic + ' --in=input',
('--dim=50', '--mask=mask', '--Oall'))
assert checkResult(result.output[0], *expected)
assert checkResult(result.stdout[0], *expected)
def test_fsl_regfilt():
......@@ -236,7 +236,7 @@ def test_fsl_regfilt():
filter=(1, 2, 3, 4), vn=True)
expected = (regfilt + ' --in=input --out=output --design=design',
('--filter=1,2,3,4', '--vn'))
assert checkResult(result.output[0], *expected)
assert checkResult(result.stdout[0], *expected)
......@@ -245,7 +245,7 @@ def test_fslreorient2std():
r2std = op.join(fsldir, 'bin', 'fslreorient2std')
result = fw.fslreorient2std('input', 'output')
expected = r2std + ' input output'
assert result.output[0] == expected
assert result.stdout[0] == expected
def test_fslroi():
......@@ -254,15 +254,15 @@ def test_fslroi():
result = fw.fslroi('input', 'output', 1, 10)
expected = fslroi + ' input output 1 10'
assert result.output[0] == expected
assert result.stdout[0] == expected
result = fw.fslroi('input', 'output', 1, 10, 2, 20, 3, 30)
expected = fslroi + ' input output 1 10 2 20 3 30'
assert result.output[0] == expected
assert result.stdout[0] == expected
result = fw.fslroi('input', 'output', 1, 10, 2, 20, 3, 30, 4, 40)
expected = fslroi + ' input output 1 10 2 20 3 30 4 40'
assert result.output[0] == expected
assert result.stdout[0] == expected
def test_slicer():
......@@ -270,7 +270,7 @@ def test_slicer():
slicer = op.join(fsldir, 'bin', 'slicer')
result = fw.slicer('input1', 'input2', i=(20, 100), x=(20, 'x.png'))
expected = slicer + ' input1 input2 -i 20 100 -x 20 x.png'
assert result.output[0] == expected
assert result.stdout[0] == expected
def test_cluster():
......@@ -280,7 +280,7 @@ def test_cluster():
fractional=True, osize='osize')
expected = (cluster + ' --in=input --thresh=thresh',
('--fractional', '--osize=osize'))
assert checkResult(result.output[0], *expected)
assert checkResult(result.stdout[0], *expected)
def test_fslmaths():
......@@ -300,7 +300,7 @@ def test_fslmaths():
'-inm inmim', '-bptf 1 10', 'output']
expected = ' '.join(expected)
assert result.output[0] == expected
assert result.stdout[0] == expected
# test LOAD output
with tempdir() as td, mockFSLDIR(bin=('fslmaths',)) as fsldir:
......@@ -328,12 +328,12 @@ def test_fast():
result = fw.fast('input', 'myseg', n_classes=3)
expected = [cmd, '-v', '--out=myseg', '--class=3', 'input']
assert result.output[0] == ' '.join(expected)
assert result.stdout[0] == ' '.join(expected)
result = fw.fast(('in1', 'in2', 'in3'), 'myseg', n_classes=3)
expected = [cmd, '-v', '--out=myseg', '--class=3', 'in1', 'in2', 'in3']
assert result.output[0] == ' '.join(expected)
assert result.stdout[0] == ' '.join(expected)
......@@ -348,4 +348,4 @@ def test_fsl_anat():
expected = [cmd, '-i', 't1', '-o', 'fsl_anat', '-t', 'T1',
'-s', '25']
assert result.output[0] == ' '.join(expected)
assert result.stdout[0] == ' '.join(expected)
tests/test_wrapperutils.py
+ 92
− 0
View file @ 2a8929a3
......@@ -8,6 +8,7 @@
import os.path as op
import os
import shlex
import pathlib
import textwrap
try: from unittest import mock
......@@ -353,6 +354,30 @@ def test_fileOrThing_sequence():
assert np.all(func(infiles[0], wutils.LOAD)['out'] == inputs[0])
def test_fileOrText():
@wutils.fileOrText('input', 'output')
def func(input, output):
data = open(input).read()
data = ''.join(['{}{}'.format(c, c) for c in data])
open(output, 'wt').write(data)
with tempdir.tempdir():
data = 'abcdefg'
exp = 'aabbccddeeffgg'
open('input.txt', 'wt').write(data)
func(pathlib.Path('input.txt'), pathlib.Path('output.txt'))
assert open('output.txt').read() == exp
func('abcdefg', pathlib.Path('output.txt'))
assert open('output.txt').read() == exp
assert func('12345', wutils.LOAD).output == '1122334455'
def test_fileOrThing_outprefix():
@wutils.fileOrImage('img', outprefix='output_base')
......@@ -496,6 +521,73 @@ def test_fileOrThing_outprefix_directory():
assert np.all(np.asanyarray(res[op.join('foo', 'myout_imgs', 'img4')].dataobj) == exp4)
def test_fileOrThing_results():
@wutils.fileOrArray('input', 'regular_output', outprefix='outpref')
def func(input, regular_output, outpref):
input = np.loadtxt(input)
regout = input * 2
prefouts = []
for i in range(3, 6):
prefouts.append(input * i)
np.savetxt(regular_output, regout)
for i, o in enumerate(prefouts):
np.savetxt('{}_{}.txt'.format(outpref, i), o)
return ('return', 'value')
input = np.random.randint(1, 10, (3, 3))
infile = 'input.txt'
exp = [input * i for i in range(2, 6)]
with tempdir.tempdir():
np.savetxt(infile, input)
result = func('input.txt', 'regout.txt', 'outpref')
assert len(result) == 0
assert result.stdout == ('return', 'value')
assert (np.loadtxt('regout.txt') == exp[0]).all()
for i in range(3):
assert (np.loadtxt('outpref_{}.txt'.format(i)) == exp[i+1]).all()
result = func(input, 'regout.txt', 'outpref')
assert len(result) == 0
assert result.stdout == ('return', 'value')
assert (np.loadtxt('regout.txt') == exp[0]).all()
for i in range(3):
assert (np.loadtxt('outpref_{}.txt'.format(i)) == exp[i+1]).all()
result = func(input, wutils.LOAD, 'outpref')
assert len(result) == 1
assert result.stdout == ('return', 'value')
assert (result .regular_output == exp[0]).all()
assert (result['regular_output'] == exp[0]).all()
for i in range(3):
assert (np.loadtxt('outpref_{}.txt'.format(i)) == exp[i+1]).all()
# todo outpref
result = func(input, wutils.LOAD, wutils.LOAD)
assert len(result) == 4
assert result.stdout == ('return', 'value')
assert (result .regular_output == exp[0]).all()
assert (result['regular_output'] == exp[0]).all()
assert (result .outpref_0 == exp[1]).all()
assert (result['outpref_0'] == exp[1]).all()
assert (result .outpref_1 == exp[2]).all()
assert (result['outpref_1'] == exp[2]).all()
assert (result .outpref_2 == exp[3]).all()
assert (result['outpref_2'] == exp[3]).all()
for i in range(3):
assert (np.loadtxt('outpref_{}.txt'.format(i)) == exp[i+1]).all()
def test_chained_fileOrImageAndArray():
@wutils.fileOrImage('image', 'outimage')
@wutils.fileOrArray('array', 'outarray')
......
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