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Afni suffix #367

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merged 5 commits into from
Apr 26, 2012
Merged

Afni suffix #367

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1c849f3
fixing what I messed up
Apr 26, 2012
fe4fd56
test/fixs
Apr 26, 2012
4e4ebfa
Merge branch 'master' into afni_suffix
Apr 26, 2012
565c5be
this is the nth time that I change this...
Apr 26, 2012
1647b70
AFNITraitedSpec for Calc
Apr 26, 2012
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145 changes: 84 additions & 61 deletions nipype/interfaces/afni/preprocess.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -167,10 +167,11 @@ def _gen_filename(self, name):

def _list_outputs(self):
outputs = self.output_spec().get()
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
if not isdefined(outputs['out_file']):
if not isdefined(self.inputs.out_file):
outputs['out_file'] = self._gen_fname(self.inputs.in_file,
suffix = self.inputs.suffix)
else:
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
return outputs


Expand Down Expand Up @@ -309,10 +310,11 @@ def _gen_filename(self, name):

def _list_outputs(self):
outputs = self.output_spec().get()
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
if not isdefined(outputs['out_file']):
outputs['out_file'] = self._gen_fname(
self.inputs.in_file, suffix=self.inputs.suffix)
if not isdefined(self.inputs.out_file):
outputs['out_file'] = self._gen_fname(self.inputs.in_file,
suffix = self.inputs.suffix)
else:
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
return outputs


Expand Down Expand Up @@ -369,10 +371,11 @@ def _gen_filename(self, name):

def _list_outputs(self):
outputs = self.output_spec().get()
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
if not isdefined(outputs['out_file']):
outputs['out_file'] = self._gen_fname(
self.inputs.in_file, suffix=self.inputs.suffix)
if not isdefined(self.inputs.out_file):
outputs['out_file'] = self._gen_fname(self.inputs.in_file,
suffix = self.inputs.suffix)
else:
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
return outputs


Expand Down Expand Up @@ -428,10 +431,11 @@ def _gen_filename(self, name):

def _list_outputs(self):
outputs = self.output_spec().get()
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
if not isdefined(outputs['out_file']):
outputs['out_file'] = self._gen_fname(
self.inputs.in_file, suffix=self.inputs.suffix)
if not isdefined(self.inputs.out_file):
outputs['out_file'] = self._gen_fname(self.inputs.in_file,
suffix = self.inputs.suffix)
else:
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
return outputs


Expand Down Expand Up @@ -485,10 +489,11 @@ def _gen_filename(self, name):

def _list_outputs(self):
outputs = self.output_spec().get()
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
if not isdefined(outputs['out_file']):
outputs['out_file'] = self._gen_fname(
self.inputs.in_file, suffix=self.inputs.suffix)
if not isdefined(self.inputs.out_file):
outputs['out_file'] = self._gen_fname(self.inputs.in_file,
suffix = self.inputs.suffix)
else:
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
return outputs


Expand Down Expand Up @@ -542,10 +547,11 @@ def _gen_filename(self, name):

def _list_outputs(self):
outputs = self.output_spec().get()
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
if not isdefined(outputs['out_file']):
outputs['out_file'] = self._gen_fname(
self.inputs.in_file, suffix=self.inputs.suffix)
if not isdefined(self.inputs.out_file):
outputs['out_file'] = self._gen_fname(self.inputs.in_file,
suffix = self.inputs.suffix)
else:
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
return outputs


Expand Down Expand Up @@ -621,15 +627,17 @@ def _gen_filename(self, name):

def _list_outputs(self):
outputs = self.output_spec().get()

outputs['out_file'] = os.path.abspath(self.inputs.out_file)
if not isdefined(outputs['out_file']):
if not isdefined(self.inputs.out_file):
outputs['out_file'] = self._gen_fname(
self.inputs.in_file, suffix=self.inputs.mask_suffix)
outputs['brain_file'] = os.path.abspath(self.inputs.apply_mask)
if not isdefined(outputs['brain_file']):
else:
outputs['out_file'] = os.path.abspath(self.inputs.out_file)

if not isdefined(self.inputs.apply_mask):
outputs['brain_file'] = self._gen_fname(
self.inputs.in_file, suffix=self.inputs.apply_suffix)
else:
outputs['brain_file'] = os.path.abspath(self.inputs.apply_mask)
return outputs


Expand Down Expand Up @@ -706,17 +714,20 @@ def _gen_filename(self, name):
def _list_outputs(self):
outputs = self.output_spec().get()

outputs['out_file'] = os.path.abspath(self.inputs.out_file)
if not isdefined(outputs['out_file']):

if not isdefined(self.inputs.out_file):
outputs['out_file'] = self._gen_fname(self.inputs.in_file,
suffix=self.inputs.suffix)
else:
outputs['out_file'] = os.path.abspath(self.inputs.out_file)

outputs['oned_file'] = os.path.abspath(self.inputs.oned_file)
if not isdefined(outputs['oned_file']):
if not isdefined(self.inputs.oned_file):
outputs['oned_file'] = fname_presuffix(
self.inputs.in_file,
suffix = '%s.1D'%self.inputs.suffix,
use_ext = False, newpath = os.getcwd())
else:
outputs['oned_file'] = os.path.abspath(self.inputs.oned_file)
return outputs


Expand Down Expand Up @@ -771,10 +782,11 @@ class Merge(AFNICommand):

def _list_outputs(self):
outputs = self.output_spec().get()
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
if not isdefined(outputs['out_file']):
if not isdefined(self.inputs.out_file):
outputs['out_file'] = self._gen_fname(self.inputs.in_files[0],
suffix=self.inputs.suffix)
else:
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
return outputs

def _gen_filename(self, name):
Expand Down Expand Up @@ -825,10 +837,11 @@ class Copy(AFNICommand):

def _list_outputs(self):
outputs = self.output_spec().get()
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
if not isdefined(outputs['out_file']):
if not isdefined(self.inputs.out_file):
outputs['out_file'] = self._gen_fname(self.inputs.in_file,
suffix=self.inputs.suffix)
else:
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
return outputs

def _gen_filename(self, name):
Expand Down Expand Up @@ -891,10 +904,11 @@ class Fourier(AFNICommand):

def _list_outputs(self):
outputs = self.output_spec().get()
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
if not isdefined(outputs['out_file']):
if not isdefined(self.inputs.out_file):
outputs['out_file'] = self._gen_fname(self.inputs.in_file,
suffix=self.inputs.suffix)
suffix = self.inputs.suffix)
else:
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
return outputs

def _gen_filename(self, name):
Expand Down Expand Up @@ -948,10 +962,11 @@ class ZCutUp(AFNICommand):

def _list_outputs(self):
outputs = self.output_spec().get()
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
if not isdefined(outputs['out_file']):
if not isdefined(self.inputs.out_file):
outputs['out_file'] = self._gen_fname(self.inputs.in_file,
suffix=self.inputs.suffix)
suffix = self.inputs.suffix)
else:
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
return outputs

def _gen_filename(self, name):
Expand Down Expand Up @@ -1005,10 +1020,11 @@ class Allineate(AFNICommand):

def _list_outputs(self):
outputs = self.output_spec().get()
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
if not isdefined(outputs['out_file']):
if not isdefined(self.inputs.out_file):
outputs['out_file'] = self._gen_fname(self.inputs.in_file,
suffix=self.inputs.suffix)
suffix = self.inputs.suffix)
else:
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
return outputs

def _gen_filename(self, name):
Expand Down Expand Up @@ -1069,10 +1085,11 @@ class Maskave(AFNICommand):

def _list_outputs(self):
outputs = self.output_spec().get()
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
if not isdefined(outputs['out_file']):
if not isdefined(self.inputs.out_file):
outputs['out_file'] = self._gen_fname(self.inputs.in_file,
suffix=self.inputs.suffix)
suffix = self.inputs.suffix)
else:
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
return outputs

def _gen_filename(self, name):
Expand Down Expand Up @@ -1123,10 +1140,11 @@ class SkullStrip(AFNICommand):

def _list_outputs(self):
outputs = self.output_spec().get()
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
if not isdefined(outputs['out_file']):
if not isdefined(self.inputs.out_file):
outputs['out_file'] = self._gen_fname(self.inputs.in_file,
suffix=self.inputs.suffix)
suffix = self.inputs.suffix)
else:
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
return outputs

def _gen_filename(self, name):
Expand Down Expand Up @@ -1180,10 +1198,11 @@ class TCat(AFNICommand):

def _list_outputs(self):
outputs = self.output_spec().get()
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
if not isdefined(outputs['out_file']):
if not isdefined(self.inputs.out_file):
outputs['out_file'] = self._gen_fname(self.inputs.in_files[0],
suffix=self.inputs.suffix)
else:
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
return outputs

def _gen_filename(self, name):
Expand Down Expand Up @@ -1246,10 +1265,11 @@ class Fim(AFNICommand):

def _list_outputs(self):
outputs = self.output_spec().get()
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
if not isdefined(outputs['out_file']):
if not isdefined(self.inputs.out_file):
outputs['out_file'] = self._gen_fname(self.inputs.in_file,
suffix=self.inputs.suffix)
suffix = self.inputs.suffix)
else:
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
return outputs

def _gen_filename(self, name):
Expand Down Expand Up @@ -1317,10 +1337,12 @@ class TCorrelate(AFNICommand):

def _list_outputs(self):
outputs = self.output_spec().get()
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
if not isdefined(outputs['out_file']):

if not isdefined(self.inputs.out_file):
outputs['out_file'] = self._gen_fname(self.inputs.xset,
suffix=self.inputs.suffix)
else:
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
return outputs

def _gen_filename(self, name):
Expand Down Expand Up @@ -1491,7 +1513,7 @@ def aggregate_outputs(self, runtime=None, needed_outputs=None):
"""


class CalcInputSpec(CommandLineInputSpec):
class CalcInputSpec(AFNITraitedSpec):
in_file_a = File(desc='input file to 3dcalc',
argstr='-a %s', position=0, mandatory=True)
in_file_b = File(desc='operand file to 3dcalc',
Expand All @@ -1513,7 +1535,7 @@ class CalcOutputSpec(TraitedSpec):
out_file = File(desc=' output file', exists=True)


class Calc(CommandLine):
class Calc(AFNICommand):
"""This program does voxel-by-voxel arithmetic on 3D datasets

For complete details, see the `3dcalc Documentation.
Expand All @@ -1540,10 +1562,11 @@ class Calc(CommandLine):

def _list_outputs(self):
outputs = self.output_spec().get()
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
if not isdefined(outputs['out_file']):
if not isdefined(self.inputs.out_file):
outputs['out_file'] = self._gen_fname(self.inputs.in_file_a,
suffix=self.inputs.suffix)
else:
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
return outputs

def _gen_filename(self, name):
Expand Down
4 changes: 2 additions & 2 deletions nipype/interfaces/afni/tests/test_preprocess.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -132,7 +132,7 @@ def test_tcat():
input_map = dict(args = dict(argstr='%s',),
environ = dict(usedefault=True,),
ignore_exception = dict(usedefault=True,),
in_file = dict(argstr=' %s',mandatory=True,),
in_files = dict(argstr=' %s',mandatory=True,),
out_file = dict(argstr='-prefix %s',),
outputtype = dict(),
rlt = dict(argstr='-rlt%s',),
Expand Down Expand Up @@ -288,7 +288,7 @@ def test_merge():
doall = dict(argstr='-doall',),
environ = dict(usedefault=True,),
ignore_exception = dict(usedefault=True,),
in_file = dict(argstr='%s',mandatory=True,),
in_files = dict(argstr='%s',mandatory=True,),
other = dict(argstr='%s',),
out_file = dict(argstr='-prefix %s',genfile=True,),
outputtype = dict(),
Expand Down