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Merge remote-tracking branch 'nipy/master'
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‎nipype/interfaces/afni/__init__.py

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Original file line numberDiff line numberDiff line change
@@ -17,7 +17,7 @@
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Seg, SkullStrip, TCorr1D, TCorrMap, TCorrelate,
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TShift, Volreg, Warp, QwarpPlusMinus)
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from .svm import (SVMTest, SVMTrain)
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from .utils import (AFNItoNIFTI, Autobox, BrickStat, Calc, Copy,
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from .utils import (AFNItoNIFTI, Autobox, BrickStat, Calc, Copy, Edge3,
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Eval, FWHMx,
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MaskTool, Merge, Notes, Refit, Resample, TCat, TStat, To3D,
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Unifize, ZCutUp, GCOR, Zcat, Zeropad)

‎nipype/interfaces/afni/tests/test_auto_Edge3.py

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# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
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from __future__ import unicode_literals
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from ..utils import Edge3
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def test_Edge3_inputs():
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input_map = dict(args=dict(argstr='%s',
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),
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datum=dict(argstr='-datum %s',
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),
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environ=dict(nohash=True,
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usedefault=True,
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),
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fscale=dict(argstr='-fscale',
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xor=['gscale', 'nscale', 'scale_floats'],
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),
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gscale=dict(argstr='-gscale',
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xor=['fscale', 'nscale', 'scale_floats'],
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),
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ignore_exception=dict(nohash=True,
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usedefault=True,
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),
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in_file=dict(argstr='-input %s',
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copyfile=False,
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mandatory=True,
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position=0,
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),
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nscale=dict(argstr='-nscale',
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xor=['fscale', 'gscale', 'scale_floats'],
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),
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out_file=dict(argstr='-prefix %s',
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position=-1,
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),
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outputtype=dict(),
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scale_floats=dict(argstr='-scale_floats %f',
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xor=['fscale', 'gscale', 'nscale'],
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),
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terminal_output=dict(nohash=True,
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),
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verbose=dict(argstr='-verbose',
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),
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)
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inputs = Edge3.input_spec()
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for key, metadata in list(input_map.items()):
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for metakey, value in list(metadata.items()):
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assert getattr(inputs.traits()[key], metakey) == value
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def test_Edge3_outputs():
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output_map = dict(out_file=dict(),
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)
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outputs = Edge3.output_spec()
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for key, metadata in list(output_map.items()):
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for metakey, value in list(metadata.items()):
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assert getattr(outputs.traits()[key], metakey) == value

‎nipype/interfaces/afni/utils.py

Lines changed: 93 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -394,6 +394,99 @@ class Copy(AFNICommand):
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output_spec = AFNICommandOutputSpec
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class Edge3InputSpec(AFNICommandInputSpec):
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in_file = File(
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desc='input file to 3dedge3',
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argstr='-input %s',
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position=0,
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mandatory=True,
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exists=True,
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copyfile=False)
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out_file = File(
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desc='output image file name',
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position=-1,
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argstr='-prefix %s')
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datum = traits.Enum(
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'byte','short','float',
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argstr='-datum %s',
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desc='specify data type for output. Valid types are \'byte\', '
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'\'short\' and \'float\'.')
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fscale = traits.Bool(
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desc='Force scaling of the output to the maximum integer range.',
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argstr='-fscale',
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xor=['gscale', 'nscale', 'scale_floats'])
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gscale = traits.Bool(
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desc='Same as \'-fscale\', but also forces each output sub-brick to '
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'to get the same scaling factor.',
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argstr='-gscale',
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xor=['fscale', 'nscale', 'scale_floats'])
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nscale = traits.Bool(
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desc='Don\'t do any scaling on output to byte or short datasets.',
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argstr='-nscale',
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xor=['fscale', 'gscale', 'scale_floats'])
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scale_floats = traits.Float(
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desc='Multiply input by VAL, but only if the input datum is '
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'float. This is needed when the input dataset '
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'has a small range, like 0 to 2.0 for instance. '
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'With such a range, very few edges are detected due to '
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'what I suspect to be truncation problems. '
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'Multiplying such a dataset by 10000 fixes the problem '
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'and the scaling is undone at the output.',
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argstr='-scale_floats %f',
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xor=['fscale', 'gscale', 'nscale'])
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verbose = traits.Bool(
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desc='Print out some information along the way.',
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argstr='-verbose')
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class Edge3(AFNICommand):
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"""Does 3D Edge detection using the library 3DEdge
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by Gregoire Malandain ([email protected]).
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For complete details, see the `3dedge3 Documentation.
447+
<https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dedge3.html>`_
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references_ = [{'entry': BibTeX('@article{Deriche1987,'
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'author={R. Deriche},'
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'title={Optimal edge detection using recursive filtering},'
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'journal={International Journal of Computer Vision},'
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'volume={2},',
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'pages={167-187},'
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'year={1987},'
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'}'),
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'tags': ['method'],
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},
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{'entry': BibTeX('@article{MongaDericheMalandainCocquerez1991,'
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'author={O. Monga, R. Deriche, G. Malandain, J.P. Cocquerez},'
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'title={Recursive filtering and edge tracking: two primary tools for 3D edge detection},'
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'journal={Image and vision computing},'
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'volume={9},',
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'pages={203-214},'
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'year={1991},'
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'}'),
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'tags': ['method'],
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},
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]
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Examples
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========
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>>> from nipype.interfaces import afni
475+
>>> edge3 = afni.Edge3()
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>>> edge3.inputs.in_file = 'functional.nii'
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>>> edge3.inputs.out_file = 'edges.nii'
478+
>>> edge3.inputs.datum = 'byte'
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>>> edge3.cmdline # doctest: +ALLOW_UNICODE
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'3dedge3 -input functional.nii -datum byte -prefix edges.nii'
481+
>>> res = edge3.run() # doctest: +SKIP
482+
483+
"""
484+
485+
_cmd = '3dedge3'
486+
input_spec = Edge3InputSpec
487+
output_spec = AFNICommandOutputSpec
488+
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397490
class EvalInputSpec(AFNICommandInputSpec):
398491
in_file_a = File(
399492
desc='input file to 1deval',

‎nipype/interfaces/base.py

Lines changed: 33 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1381,6 +1381,35 @@ def _get_ram_mb(pid, pyfunc=False):
13811381
return mem_mb
13821382

13831383

1384+
def _canonicalize_env(env):
1385+
"""Windows requires that environment be dicts with bytes as keys and values
1386+
This function converts any unicode entries for Windows only, returning the
1387+
dictionary untouched in other environments.
1388+
1389+
Parameters
1390+
----------
1391+
env : dict
1392+
environment dictionary with unicode or bytes keys and values
1393+
1394+
Returns
1395+
-------
1396+
env : dict
1397+
Windows: environment dictionary with bytes keys and values
1398+
Other: untouched input ``env``
1399+
"""
1400+
if os.name != 'nt':
1401+
return env
1402+
1403+
out_env = {}
1404+
for key, val in env:
1405+
if not isinstance(key, bytes):
1406+
key = key.encode('utf-8')
1407+
if not isinstance(val, bytes):
1408+
val = key.encode('utf-8')
1409+
out_env[key] = val
1410+
return out_env
1411+
1412+
13841413
# Get max resources used for process
13851414
def get_max_resources_used(pid, mem_mb, num_threads, pyfunc=False):
13861415
"""Function to get the RAM and threads usage of a process
@@ -1435,6 +1464,8 @@ def run_command(runtime, output=None, timeout=0.01, redirect_x=False):
14351464
raise RuntimeError('Xvfb was not found, X redirection aborted')
14361465
cmdline = 'xvfb-run -a ' + cmdline
14371466

1467+
env = _canonicalize_env(runtime.environ)
1468+
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default_encoding = locale.getdefaultlocale()[1]
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if default_encoding is None:
14401471
default_encoding = 'UTF-8'
@@ -1449,14 +1480,14 @@ def run_command(runtime, output=None, timeout=0.01, redirect_x=False):
14491480
stderr=stderr,
14501481
shell=True,
14511482
cwd=runtime.cwd,
1452-
env=runtime.environ)
1483+
env=env)
14531484
else:
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proc = subprocess.Popen(cmdline,
14551486
stdout=PIPE,
14561487
stderr=PIPE,
14571488
shell=True,
14581489
cwd=runtime.cwd,
1459-
env=runtime.environ)
1490+
env=env)
14601491
result = {}
14611492
errfile = os.path.join(runtime.cwd, 'stderr.nipype')
14621493
outfile = os.path.join(runtime.cwd, 'stdout.nipype')

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