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ENH: Allow transform to be saved from AFNI 3dWarp #2642

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merged 3 commits into from
Jul 25, 2018
Merged

ENH: Allow transform to be saved from AFNI 3dWarp #2642

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1ef1821
add option to save transform
salma1601 Jul 18, 2018
50f8d81
update warp interface test
salma1601 Jul 19, 2018
3dc803c
address comments
salma1601 Jul 24, 2018
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34 changes: 30 additions & 4 deletions nipype/interfaces/afni/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
from ...utils.filemanip import (load_json, save_json, split_filename,
fname_presuffix)
from ..base import (CommandLineInputSpec, CommandLine, TraitedSpec, traits,
isdefined, File, InputMultiPath, Undefined, Str,
isdefined, File, InputMultiPath, Undefined, Str,
InputMultiObject)

from .base import (AFNICommandBase, AFNICommand, AFNICommandInputSpec,
Expand Down Expand Up @@ -2563,7 +2563,7 @@ class TProject(AFNICommand):
_cmd = '3dTproject'
input_spec = TProjectInputSpec
output_spec = AFNICommandOutputSpec


class TShiftInputSpec(AFNICommandInputSpec):
in_file = File(
Expand Down Expand Up @@ -2758,7 +2758,8 @@ class WarpInputSpec(AFNICommandInputSpec):
name_template='%s_warp',
desc='output image file name',
argstr='-prefix %s',
name_source='in_file')
name_source='in_file',
keep_extension=True)
tta2mni = traits.Bool(
desc='transform dataset from Talairach to MNI152', argstr='-tta2mni')
mni2tta = traits.Bool(
Expand Down Expand Up @@ -2789,6 +2790,13 @@ class WarpInputSpec(AFNICommandInputSpec):
argstr='-zpad %d')
verbose = traits.Bool(
desc='Print out some information along the way.', argstr='-verb')
save_warp = traits.Bool(
desc='save warp as .mat file', requires=['verbose'])


class WarpOutputSpec(TraitedSpec):
out_file = File(desc='Warped file.', exists=True)
warp_file = File(desc='warp transform .mat file')


class Warp(AFNICommand):
Expand Down Expand Up @@ -2820,7 +2828,25 @@ class Warp(AFNICommand):
"""
_cmd = '3dWarp'
input_spec = WarpInputSpec
output_spec = AFNICommandOutputSpec
output_spec = WarpOutputSpec

def _run_interface(self, runtime):
runtime = super(Warp, self)._run_interface(runtime)

if self.inputs.save_warp:
import numpy as np
warp_file = self._list_outputs()['warp_file']
np.savetxt(warp_file, [runtime.stdout], fmt=str('%s'))
return runtime

def _list_outputs(self):
outputs = super(Warp, self)._list_outputs()
if self.inputs.save_warp:
outputs['warp_file'] = fname_presuffix(outputs['out_file'],
suffix='_transform.mat',
use_ext=False)

return outputs


class QwarpPlusMinusInputSpec(CommandLineInputSpec):
Expand Down
7 changes: 6 additions & 1 deletion nipype/interfaces/afni/tests/test_auto_Warp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,10 +29,12 @@ def test_Warp_inputs():
oblique_parent=dict(argstr='-oblique_parent %s', ),
out_file=dict(
argstr='-prefix %s',
keep_extension=True,
name_source='in_file',
name_template='%s_warp',
),
outputtype=dict(),
save_warp=dict(requires=['verbose'], ),
tta2mni=dict(argstr='-tta2mni', ),
verbose=dict(argstr='-verb', ),
zpad=dict(argstr='-zpad %d', ),
Expand All @@ -43,7 +45,10 @@ def test_Warp_inputs():
for metakey, value in list(metadata.items()):
assert getattr(inputs.traits()[key], metakey) == value
def test_Warp_outputs():
output_map = dict(out_file=dict(), )
output_map = dict(
out_file=dict(),
warp_file=dict(),
)
outputs = Warp.output_spec()

for key, metadata in list(output_map.items()):
Expand Down