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Add 3dZcat and 3dZeropad
Create nipype wrappers for the AFNI commands 3dZcat and 3dZeropad.
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‎nipype/interfaces/afni/__init__.py

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from .utils import (AFNItoNIFTI, Autobox, BrickStat, Calc, Copy,
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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,)
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Unifize, ZCutUp, GCOR, Zcat, Zeropad)

‎nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.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 ..preprocess import QwarpPlusMinus
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def test_QwarpPlusMinus_inputs():
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input_map = dict(args=dict(argstr='%s',
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),
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base_file=dict(argstr='-base %s',
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copyfile=False,
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mandatory=True,
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),
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blur=dict(argstr='-blur %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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ignore_exception=dict(nohash=True,
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usedefault=True,
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),
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minpatch=dict(argstr='-minpatch %d',
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),
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nopadWARP=dict(argstr='-nopadWARP',
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),
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noweight=dict(argstr='-noweight',
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),
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pblur=dict(argstr='-pblur %s',
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),
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source_file=dict(argstr='-source %s',
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copyfile=False,
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mandatory=True,
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),
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terminal_output=dict(nohash=True,
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),
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)
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inputs = QwarpPlusMinus.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_QwarpPlusMinus_outputs():
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output_map = dict(base_warp=dict(),
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source_warp=dict(),
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warped_base=dict(),
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warped_source=dict(),
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)
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outputs = QwarpPlusMinus.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/tests/test_auto_Unifize.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 Unifize
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def test_Unifize_inputs():
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input_map = dict(args=dict(argstr='%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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epi=dict(argstr='-EPI',
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requires=['no_duplo', 't2'],
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xor=['gm'],
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),
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gm=dict(argstr='-GM',
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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=-1,
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),
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no_duplo=dict(argstr='-noduplo',
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),
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out_file=dict(argstr='-prefix %s',
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name_source='in_file',
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),
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outputtype=dict(),
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scale_file=dict(argstr='-ssave %s',
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),
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t2=dict(argstr='-T2',
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),
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terminal_output=dict(nohash=True,
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),
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urad=dict(argstr='-Urad %s',
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),
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)
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inputs = Unifize.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_Unifize_outputs():
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output_map = dict(out_file=dict(),
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scale_file=dict(),
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)
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outputs = Unifize.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

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@@ -1441,3 +1441,165 @@ def _run_interface(self, runtime):
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def _list_outputs(self):
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return {'out': getattr(self, '_gcor')}
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class ZcatInputSpec(AFNICommandInputSpec):
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in_files = InputMultiPath(
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File(
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desc='input files to 3dZcat',
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exists=True),
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argstr='%s',
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position=-1,
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mandatory=True,
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copyfile=False)
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out_file = File(
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name_template='zcat',
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desc='output dataset prefix name (default \'zcat\')',
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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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verb = traits.Bool(
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desc='print out some verbositiness as the program proceeds.',
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argstr='-verb')
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fscale = traits.Bool(
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desc='Force scaling of the output to the maximum integer '
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'range. This only has effect if the output datum is '
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'byte or short (either forced or defaulted). This '
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'option is sometimes necessary to eliminate '
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'unpleasant truncation artifacts.',
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argstr='-fscale',
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xor=['nscale'])
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nscale = traits.Bool(
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desc='Don\'t do any scaling on output to byte or short '
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'datasets. This may be especially useful when '
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'operating on mask datasets whose output values '
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'are only 0\'s and 1\'s.',
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argstr='-nscale',
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xor=['fscale'])
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class Zcat(AFNICommand):
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"""Copies an image of one type to an image of the same
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or different type using 3dZcat command
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For complete details, see the `3dZcat Documentation.
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<https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dZcat.html>`_
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Examples
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========
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>>> from nipype.interfaces import afni
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>>> zcat = afni.Zcat()
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>>> zcat.inputs.in_files = ['functional2.nii', 'functional3.nii']
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>>> zcat.inputs.out_file = 'cat_functional.nii'
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>>> zcat.cmdline # doctest: +ALLOW_UNICODE
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'3dZcat -prefix cat_functional.nii functional2.nii functional3.nii'
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>>> res = zcat.run() # doctest: +SKIP
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"""
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_cmd = '3dZcat'
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input_spec = ZcatInputSpec
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output_spec = AFNICommandOutputSpec
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class ZeropadInputSpec(AFNICommandInputSpec):
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in_files = File(
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desc='input dataset',
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argstr='%s',
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position=-1,
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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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name_template='zeropad',
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desc='output dataset prefix name (default \'zeropad\')',
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argstr='-prefix %s')
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I = traits.Int(
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desc='adds \'n\' planes of zero at the Inferior edge',
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argstr='-I %i',
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xor=['master'])
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S = traits.Int(
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desc='adds \'n\' planes of zero at the Superior edge',
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argstr='-S %i',
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xor=['master'])
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A = traits.Int(
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desc='adds \'n\' planes of zero at the Anterior edge',
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argstr='-A %i',
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xor=['master'])
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P = traits.Int(
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desc='adds \'n\' planes of zero at the Posterior edge',
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argstr='-P %i',
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xor=['master'])
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L = traits.Int(
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desc='adds \'n\' planes of zero at the Left edge',
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argstr='-L %i',
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xor=['master'])
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R = traits.Int(
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desc='adds \'n\' planes of zero at the Right edge',
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argstr='-R %i',
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xor=['master'])
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z = traits.Int(
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desc='adds \'n\' planes of zero on EACH of the '
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'dataset z-axis (slice-direction) faces',
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argstr='-z %i',
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xor=['master'])
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RL = traits.Int(desc='specify that planes should be added or cut '
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'symmetrically to make the resulting volume have'
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'N slices in the right-left direction',
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argstr='-RL %i',
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xor=['master'])
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AP = traits.Int(desc='specify that planes should be added or cut '
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'symmetrically to make the resulting volume have'
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'N slices in the anterior-posterior direction',
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argstr='-AP %i',
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xor=['master'])
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IS = traits.Int(desc='specify that planes should be added or cut '
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'symmetrically to make the resulting volume have'
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'N slices in the inferior-superior direction',
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argstr='-IS %i',
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xor=['master'])
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mm = traits.Bool(desc='pad counts \'n\' are in mm instead of slices, '
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'where each \'n\' is an integer and at least \'n\' '
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'mm of slices will be added/removed; e.g., n = 3 '
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'and slice thickness = 2.5 mm ==> 2 slices added',
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argstr='-mm',
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xor=['master'])
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master = traits.File(desc='match the volume described in dataset '
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'\'mset\', where mset must have the same '
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'orientation and grid spacing as dataset to be '
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'padded. the goal of -master is to make the '
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'output dataset from 3dZeropad match the '
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'spatial \'extents\' of mset by adding or '
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'subtracting slices as needed. You can\'t use '
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'-I,-S,..., or -mm with -master',
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argstr='-master %s',
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xor=['I', 'S', 'A', 'P', 'L', 'R', 'z',
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'RL', 'AP', 'IS', 'mm'])
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class Zeropad(AFNICommand):
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"""Adds planes of zeros to a dataset (i.e., pads it out).
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For complete details, see the `3dZeropad Documentation.
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<https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dZeropad.html>`_
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Examples
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========
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>>> from nipype.interfaces import afni
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>>> zeropad = afni.Zeropad()
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>>> zeropad.inputs.in_files = 'functional.nii'
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>>> zeropad.inputs.out_file = 'pad_functional.nii'
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>>> zeropad.inputs.I = 10
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>>> zeropad.inputs.S = 10
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>>> zeropad.inputs.A = 10
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>>> zeropad.inputs.P = 10
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>>> zeropad.inputs.R = 10
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>>> zeropad.inputs.L = 10
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>>> zeropad.cmdline # doctest: +ALLOW_UNICODE
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'3dZeropad -A 10 -I 10 -L 10 -P 10 -R 10 -S 10 -prefix pad_functional.nii functional.nii'
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>>> res = zeropad.run() # doctest: +SKIP
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"""
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_cmd = '3dZeropad'
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input_spec = ZeropadInputSpec
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output_spec = AFNICommandOutputSpec

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