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added support for boolean flags in nipype_cmd #1213

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Merged
merged 2 commits into from
Sep 12, 2015
Merged

added support for boolean flags in nipype_cmd #1213

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f03dec0
added support for boolean flags
chrisgorgo Sep 12, 2015
13edf84
fixed tests
chrisgorgo Sep 12, 2015
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26 changes: 15 additions & 11 deletions nipype/utils/nipype_cmd.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
import argparse
import inspect
import sys
from nipype.interfaces.base import Interface, InputMultiPath
from nipype.interfaces.base import Interface, InputMultiPath, traits
from nipype.utils.misc import str2bool

def listClasses(module=None):
Expand All @@ -24,6 +24,9 @@ def add_options(parser=None, module=None, function=None):
for name, spec in sorted(interface.inputs.traits(transient=None).items()):
desc = "\n".join(interface._get_trait_desc(inputs, name, spec))[len(name)+2:]
args = {}

if spec.is_trait_type(traits.Bool):
args["action"] = 'store_true'

if hasattr(spec, "mandatory") and spec.mandatory:
if spec.is_trait_type(InputMultiPath):
Expand All @@ -43,16 +46,17 @@ def run_instance(interface, options):
for input_name, _ in interface.inputs.items():
if getattr(options, input_name) != None:
value = getattr(options, input_name)
#traits cannot cast from string to float or int
try:
value = float(value)
except:
pass
#try to cast string input to boolean
try:
value = str2bool(value)
except:
pass
if not isinstance(value, bool):
#traits cannot cast from string to float or int
try:
value = float(value)
except:
pass
#try to cast string input to boolean
try:
value = str2bool(value)
except:
pass
try:
setattr(interface.inputs, input_name,
value)
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4 changes: 2 additions & 2 deletions nipype/utils/tests/test_cmd.py
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Original file line number Diff line number Diff line change
Expand Up @@ -88,7 +88,7 @@ def test_run_4d_realign_without_arguments(self):
self.assertEqual(stderr.getvalue(),
"""usage: nipype_cmd nipype.interfaces.nipy FmriRealign4d [-h]
[--between_loops [BETWEEN_LOOPS [BETWEEN_LOOPS ...]]]
[--ignore_exception IGNORE_EXCEPTION]
[--ignore_exception]
[--loops [LOOPS [LOOPS ...]]]
[--slice_order SLICE_ORDER]
[--speedup [SPEEDUP [SPEEDUP ...]]]
Expand All @@ -113,4 +113,4 @@ def test_run_4d_realign_help(self):
self.assertTrue("Run FmriRealign4d" in stdout.getvalue())

if __name__ == '__main__':
unittest.main()
unittest.main()