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Commit ddaa767

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Merge branch 'master' of github.com:nipy/nipype into add_antsMotionCorr
2 parents 1c57878 + b304510 commit ddaa767

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7 files changed

+261
-105
lines changed

7 files changed

+261
-105
lines changed

‎.travis.yml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -33,7 +33,7 @@ install:
3333
conda config --add channels conda-forge &&
3434
conda update --yes conda &&
3535
conda update --all -y python=$TRAVIS_PYTHON_VERSION &&
36-
conda install -y nipype icu==56.1 &&
36+
conda install -y nipype icu &&
3737
rm -r /home/travis/miniconda/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype* &&
3838
pip install -r requirements.txt &&
3939
pip install -e .[$NIPYPE_EXTRAS]; }

‎CHANGES‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -29,6 +29,7 @@ Upcoming release 0.13
2929
* ENH: Added support for custom job submission check in SLURM (https://github.com/nipy/nipype/pull/1582)
3030
* ENH: Added ANTs interface CreateJacobianDeterminantImage; replaces deprecated JacobianDeterminant
3131
(https://github.com/nipy/nipype/pull/1654)
32+
* ENH: Update ReconAll interface for FreeSurfer v6.0.0 (https://github.com/nipy/nipype/pull/1790)
3233

3334
Release 0.12.1 (August 3, 2016)
3435
===============================

‎nipype/algorithms/misc.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1271,9 +1271,9 @@ def split_rois(in_file, mask=None, roishape=None):
12711271
np.savez(iname, (nzels[0][first:last],))
12721272

12731273
if fill > 0:
1274-
droi = np.vstack((droi, np.zeros((fill, nvols), dtype=np.float32)))
1274+
droi = np.vstack((droi, np.zeros((int(fill), int(nvols)), dtype=np.float32)))
12751275
partialmsk = np.ones((roisize,), dtype=np.uint8)
1276-
partialmsk[-fill:] = 0
1276+
partialmsk[-int(fill):] = 0
12771277
partname = op.abspath('partialmask.nii.gz')
12781278
nb.Nifti1Image(partialmsk.reshape(roishape), None,
12791279
None).to_filename(partname)

‎nipype/algorithms/modelgen.py‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -655,12 +655,12 @@ def _gen_regress(self, i_onsets, i_durations, i_amplitudes, nscans):
655655
hrf = spm_hrf(dt * 1e-3)
656656
reg_scale = 1.0
657657
if self.inputs.scale_regressors:
658-
boxcar = np.zeros((50.0 * 1e3 / dt))
658+
boxcar = np.zeros(int(50.0 * 1e3 / dt))
659659
if self.inputs.stimuli_as_impulses:
660-
boxcar[1.0 * 1e3 / dt] = 1.0
660+
boxcar[int(1.0 * 1e3 / dt)] = 1.0
661661
reg_scale = float(TA / dt)
662662
else:
663-
boxcar[(1.0 * 1e3 / dt):(2.0 * 1e3 / dt)] = 1.0
663+
boxcar[int(1.0 * 1e3 / dt):int(2.0 * 1e3 / dt)] = 1.0
664664
if isdefined(self.inputs.model_hrf) and self.inputs.model_hrf:
665665
response = np.convolve(boxcar, hrf)
666666
reg_scale = 1.0 / response.max()

‎nipype/interfaces/freesurfer/preprocess.py‎

Lines changed: 202 additions & 98 deletions
Large diffs are not rendered by default.

‎nipype/utils/filemanip.py‎

Lines changed: 13 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -447,6 +447,19 @@ def list_to_filename(filelist):
447447
else:
448448
return filelist[0]
449449

450+
451+
def check_depends(targets, dependencies):
452+
"""Return true if all targets exist and are newer than all dependencies.
453+
454+
An OSError will be raised if there are missing dependencies.
455+
"""
456+
tgts = filename_to_list(targets)
457+
deps = filename_to_list(dependencies)
458+
return all(map(os.path.exists, tgts)) and \
459+
min(map(os.path.getmtime, tgts)) > \
460+
max(list(map(os.path.getmtime, deps)) + [0])
461+
462+
450463
def save_json(filename, data):
451464
"""Save data to a json file
452465

‎nipype/utils/tests/test_filemanip.py‎

Lines changed: 39 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,9 @@
55
from builtins import open
66

77
import os
8-
from tempfile import mkstemp
8+
import time
9+
from tempfile import mkstemp, mkdtemp
10+
import shutil
911
import warnings
1012

1113
import pytest
@@ -15,6 +17,7 @@
1517
hash_rename, check_forhash,
1618
copyfile, copyfiles,
1719
filename_to_list, list_to_filename,
20+
check_depends,
1821
split_filename, get_related_files)
1922

2023
import numpy as np
@@ -271,6 +274,41 @@ def test_list_to_filename(list, expected):
271274
assert x == expected
272275

273276

277+
def test_check_depends():
278+
def touch(fname):
279+
with open(fname, 'a'):
280+
os.utime(fname, None)
281+
282+
tmpdir = mkdtemp()
283+
284+
dependencies = [os.path.join(tmpdir, str(i)) for i in range(3)]
285+
targets = [os.path.join(tmpdir, str(i)) for i in range(3, 6)]
286+
287+
# Targets newer than dependencies
288+
for dep in dependencies:
289+
touch(dep)
290+
time.sleep(1)
291+
for tgt in targets:
292+
touch(tgt)
293+
assert check_depends(targets, dependencies)
294+
295+
# Targets older than newest dependency
296+
time.sleep(1)
297+
touch(dependencies[0])
298+
assert not check_depends(targets, dependencies)
299+
300+
# Missing dependency
301+
os.unlink(dependencies[0])
302+
try:
303+
check_depends(targets, dependencies)
304+
except OSError as e:
305+
pass
306+
else:
307+
assert False, "Should raise OSError on missing dependency"
308+
309+
shutil.rmtree(tmpdir)
310+
311+
274312
def test_json():
275313
# Simple roundtrip test of json files, just a sanity check.
276314
adict = dict(a='one', c='three', b='two')

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