From 4cc240dac5b6b07b475dd2997d22fda033d71c9c Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 29 Aug 2023 18:33:14 +0100
Subject: [PATCH] TEST: Don't set FSLOUTPUTTYPE in env
---
fsl/tests/test_scripts/test_immv_imcp.py | 136 +++++++++--------------
1 file changed, 53 insertions(+), 83 deletions(-)
diff --git a/fsl/tests/test_scripts/test_immv_imcp.py b/fsl/tests/test_scripts/test_immv_imcp.py
index 582a23d7c..276fa5759 100644
--- a/fsl/tests/test_scripts/test_immv_imcp.py
+++ b/fsl/tests/test_scripts/test_immv_imcp.py
@@ -6,9 +6,13 @@ import os.path as op
import itertools as it
import subprocess as sp
import os
+import glob
+import gzip
import shutil
import tempfile
+from unittest import mock
+
import pytest
import numpy as np
@@ -17,20 +21,12 @@ import nibabel as nib
from fsl.utils.tempdir import tempdir
import fsl.scripts.imcp as imcp_script
import fsl.scripts.immv as immv_script
+import fsl.data.image as fslimage
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):
@@ -234,80 +230,67 @@ def test_imcp_script_shouldPass(move=False):
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)))
+ with mock.patch.dict(os.environ, {'FSLOUTPUTTYPE' : outputType}):
- imcp_args = imcp_args.split()
+ for files_to_create, imcp_args, files_to_expect in tests:
- tindir = indir
- toutdir = outdir
+ imageHashes = []
- if reldir == 'neutral': reldir = startdir
- elif reldir == 'indir': reldir = tindir
- elif reldir == 'outdir': reldir = toutdir
- elif reldir == 'samedir':
- reldir = tindir
- toutdir = tindir
+ for i, fname in enumerate(files_to_create.split()):
+ imageHashes.append(makeImage(op.join(indir, fname)))
- if not move:
+ imcp_args = imcp_args.split()
- infiles = os.listdir(tindir)
+ tindir = indir
+ toutdir = outdir
- files_to_expect = files_to_expect + ' ' + \
- ' '.join(infiles)
+ if reldir == 'neutral': reldir = startdir
+ elif reldir == 'indir': reldir = tindir
+ elif reldir == 'outdir': reldir = toutdir
+ elif reldir == 'samedir':
+ reldir = tindir
+ toutdir = tindir
- for inf in infiles:
- img = nib.load(op.join(tindir, inf),
- mmap=False)
- imghash = hash(np.asanyarray(img.dataobj).tobytes())
- img = None
- imageHashes.append(imghash)
+ if not move:
- print('adj files_to_expect: ', files_to_expect)
+ infiles = os.listdir(tindir)
- os.chdir(reldir)
+ files_to_expect = files_to_expect + ' ' + \
+ ' '.join(infiles)
- imcp_args[:-1] = [op.join(tindir, a) for a in imcp_args[:-1]]
- imcp_args[ -1] = op.join(toutdir, imcp_args[-1])
+ for inf in infiles:
+ img = nib.load(op.join(tindir, inf),
+ mmap=False)
+ imghash = hash(np.asanyarray(img.dataobj).tobytes())
+ img = None
+ imageHashes.append(imghash)
- for i, a in enumerate(imcp_args):
- if op.splitdrive(a)[0] == op.splitdrive(reldir)[0]:
- imcp_args[i] = op.relpath(a, reldir)
+ os.chdir(reldir)
- print('indir before: ', os.listdir(tindir))
- print('outdir before: ', os.listdir(toutdir))
+ imcp_args[:-1] = [op.join(tindir, a) for a in imcp_args[:-1]]
+ imcp_args[ -1] = op.join(toutdir, imcp_args[-1])
- if move: result = immv_script.main(imcp_args)
- else: result = imcp_script.main(imcp_args)
+ 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 after: ', os.listdir(tindir))
- print('outdir after: ', os.listdir(toutdir))
+ if move: result = immv_script.main(imcp_args)
+ else: result = imcp_script.main(imcp_args)
- assert result == 0
+ assert result == 0
- checkFilesToExpect(
- files_to_expect, toutdir, outputType, imageHashes)
+ 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
+ # 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)
+ cleardir(indir)
+ cleardir(outdir)
finally:
os.chdir(startdir)
@@ -397,18 +380,9 @@ def test_imcp_script_shouldFail(move=False):
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())
@@ -430,7 +404,6 @@ def test_imcp_script_shouldFail(move=False):
else: assert imcp_script.main(['wa']) != 0
-
def test_immv_script_shouldPass():
test_imcp_script_shouldPass(move=True)
@@ -440,27 +413,24 @@ 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')
-
+ ihash = makeImage('file.nii.gz')
result = imcp_script.main(['file.nii', 'dest'])
assert result == 0
assert op.exists('dest.nii.gz')
-
+ checkImageHash('dest.nii.gz', ihash)
def test_immv_badExt():
with tempdir():
- with open('file.nii.gz', 'wt') as f:
- f.write('1')
-
+ ihash = makeImage('file.nii.gz')
result = immv_script.main(['file.nii', 'dest'])
assert result == 0
assert op.exists('dest.nii.gz')
+ checkImageHash('dest.nii.gz', ihash)
+
--
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