MAINT: ensure interface _cmd only includes executable

nipype/interfaces/afni/preprocess.py

@@ -2953,107 +2953,6 @@ def _list_outputs(self):
         return outputs
 
 
-class QwarpPlusMinusInputSpec(CommandLineInputSpec):
-    source_file = File(
-        desc=
-        'Source image (opposite phase encoding direction than base image).',
-        argstr='-source %s',
-        mandatory=True,
-        exists=True,
-        copyfile=False)
-    base_file = File(
-        desc=
-        'Base image (opposite phase encoding direction than source image).',
-        argstr='-base %s',
-        mandatory=True,
-        exists=True,
-        copyfile=False)
-    pblur = traits.List(
-        traits.Float(),
-        desc='The fraction of the patch size that'
-        'is used for the progressive blur by providing a '
-        'value between 0 and 0.25.  If you provide TWO '
-        'values, the first fraction is used for '
-        'progressively blurring the base image and the '
-        'second for the source image.',
-        argstr='-pblur %s',
-        minlen=1,
-        maxlen=2)
-    blur = traits.List(
-        traits.Float(),
-        desc="Gaussian blur the input images by (FWHM) voxels "
-        "before doing the alignment (the output dataset "
-        "will not be blurred). The default is 2.345 (for "
-        "no good reason). Optionally, you can provide 2 "
-        "values, and then the first one is applied to the "
-        "base volume, the second to the source volume. A "
-        "negative blur radius means to use 3D median "
-        "filtering, rather than Gaussian blurring.  This "
-        "type of filtering will better preserve edges, "
-        "which can be important in alignment.",
-        argstr='-blur %s',
-        minlen=1,
-        maxlen=2)
-    noweight = traits.Bool(
-        desc='If you want a binary weight (the old default), use this option.'
-        'That is, each voxel in the base volume automask will be'
-        'weighted the same in the computation of the cost functional.',
-        argstr='-noweight')
-    minpatch = traits.Int(
-        desc="Set the minimum patch size for warp searching to 'mm' voxels.",
-        argstr='-minpatch %d')
-    nopadWARP = traits.Bool(
-        desc='If for some reason you require the warp volume to'
-        'match the base volume, then use this option to have the output'
-        'WARP dataset(s) truncated.',
-        argstr='-nopadWARP')
-
-
-class QwarpPlusMinusOutputSpec(TraitedSpec):
-    warped_source = File(desc='Undistorted source file.', exists=True)
-    warped_base = File(desc='Undistorted base file.', exists=True)
-    source_warp = File(
-        desc="Field suceptibility correction warp (in 'mm') for source image.",
-        exists=True)
-    base_warp = File(
-        desc="Field suceptibility correction warp (in 'mm') for base image.",
-        exists=True)
-
-
-class QwarpPlusMinus(CommandLine):
-    """A version of 3dQwarp for performing field susceptibility correction
-    using two images with opposing phase encoding directions.
-
-    For complete details, see the `3dQwarp Documentation.
-    <https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dQwarp.html>`_
-
-    Examples
-    ========
-
-    >>> from nipype.interfaces import afni
-    >>> qwarp = afni.QwarpPlusMinus()
-    >>> qwarp.inputs.source_file = 'sub-01_dir-LR_epi.nii.gz'
-    >>> qwarp.inputs.nopadWARP = True
-    >>> qwarp.inputs.base_file = 'sub-01_dir-RL_epi.nii.gz'
-    >>> qwarp.cmdline
-    '3dQwarp -prefix Qwarp.nii.gz -plusminus -base sub-01_dir-RL_epi.nii.gz -nopadWARP -source sub-01_dir-LR_epi.nii.gz'
-    >>> res = warp.run()  # doctest: +SKIP
-
-    """
-    _cmd = '3dQwarp -prefix Qwarp.nii.gz -plusminus'
-    input_spec = QwarpPlusMinusInputSpec
-    output_spec = QwarpPlusMinusOutputSpec
-
-    def _list_outputs(self):
-        outputs = self.output_spec().get()
-        outputs['warped_source'] = os.path.abspath("Qwarp_PLUS.nii.gz")
-        outputs['warped_base'] = os.path.abspath("Qwarp_MINUS.nii.gz")
-        outputs['source_warp'] = os.path.abspath("Qwarp_PLUS_WARP.nii.gz")
-        outputs['base_warp'] = os.path.abspath("Qwarp_MINUS_WARP.nii.gz")
-
-        return outputs
-
-
 class QwarpInputSpec(AFNICommandInputSpec):
     in_file = File(
         desc=
@@ -3722,3 +3621,54 @@ def _list_outputs(self):
     def _gen_filename(self, name):
         if name == 'out_file':
             return self._gen_fname(self.inputs.source_file, suffix='_QW')
+
+
+class QwarpPlusMinusInputSpec(QwarpInputSpec):
+    source_file = File(
+        desc='Source image (opposite phase encoding direction than base image)',
+        argstr='-source %s',
+        exists=True,
+        deprecated='1.1.2',
+        new_name='in_file',
+        copyfile=False)
+    out_file = File(
+        argstr='-prefix %s',
+        value='Qwarp.nii.gz',
+        position=0,
+        usedefault=True,
+        desc="Output file")
+    plusminus = traits.Bool(
+        True,
+        usedefault=True,
+        position=1,
+        desc='Normally, the warp displacements dis(x) are defined to match'
+        'base(x) to source(x+dis(x)).  With this option, the match'
+        'is between base(x-dis(x)) and source(x+dis(x)) -- the two'
+        'images \'meet in the middle\'. For more info, view Qwarp` interface',
+        argstr='-plusminus',
+        xor=['duplo', 'allsave', 'iwarp'])
+
+
+class QwarpPlusMinus(Qwarp):
+    """A version of 3dQwarp for performing field susceptibility correction
+    using two images with opposing phase encoding directions.
+
+    For complete details, see the `3dQwarp Documentation.
+    <https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dQwarp.html>`_
+
+    Examples
+    ========
+
+    >>> from nipype.interfaces import afni
+    >>> qwarp = afni.QwarpPlusMinus()
+    >>> qwarp.inputs.in_file = 'sub-01_dir-LR_epi.nii.gz'
+    >>> qwarp.inputs.nopadWARP = True
+    >>> qwarp.inputs.base_file = 'sub-01_dir-RL_epi.nii.gz'
+    >>> qwarp.cmdline
+    '3dQwarp -prefix Qwarp.nii.gz -plusminus -base sub-01_dir-RL_epi.nii.gz \
+    -source sub-01_dir-LR_epi.nii.gz -nopadWARP'
+    >>> res = warp.run()  # doctest: +SKIP
+
+    """
+
+    input_spec = QwarpPlusMinusInputSpec

nipype/interfaces/afni/tests/test_auto_QwarpPlusMinus.py

@@ -5,25 +5,154 @@
 
 def test_QwarpPlusMinus_inputs():
     input_map = dict(
+        Qfinal=dict(argstr='-Qfinal', ),
+        Qonly=dict(argstr='-Qonly', ),
+        allineate=dict(argstr='-allineate', ),
+        allineate_opts=dict(
+            argstr='-allineate_opts %s',
+            requires=['allineate'],
+        ),
+        allsave=dict(
+            argstr='-allsave',
+            xor=['nopadWARP', 'duplo', 'plusminus'],
+        ),
         args=dict(argstr='%s', ),
+        ballopt=dict(
+            argstr='-ballopt',
+            xor=['workhard', 'boxopt'],
+        ),
         base_file=dict(
             argstr='-base %s',
             copyfile=False,
             mandatory=True,
         ),
+        baxopt=dict(
+            argstr='-boxopt',
+            xor=['workhard', 'ballopt'],
+        ),
         blur=dict(argstr='-blur %s', ),
+        duplo=dict(
+            argstr='-duplo',
+            xor=[
+                'gridlist', 'maxlev', 'inilev', 'iniwarp', 'plusminus',
+                'allsave'
+            ],
+        ),
+        emask=dict(
+            argstr='-emask %s',
+            copyfile=False,
+        ),
         environ=dict(
             nohash=True,
             usedefault=True,
         ),
+        expad=dict(
+            argstr='-expad %d',
+            xor=['nopadWARP'],
+        ),
+        gridlist=dict(
+            argstr='-gridlist %s',
+            copyfile=False,
+            xor=['duplo', 'plusminus'],
+        ),
+        hel=dict(
+            argstr='-hel',
+            xor=['nmi', 'mi', 'lpc', 'lpa', 'pear'],
+        ),
+        in_file=dict(
+            argstr='-source %s',
+            copyfile=False,
+            mandatory=True,
+        ),
+        inilev=dict(
+            argstr='-inilev %d',
+            xor=['duplo'],
+        ),
+        iniwarp=dict(
+            argstr='-iniwarp %s',
+            xor=['duplo'],
+        ),
+        iwarp=dict(
+            argstr='-iwarp',
+            xor=['plusminus'],
+        ),
+        lpa=dict(
+            argstr='-lpa',
+            xor=['nmi', 'mi', 'lpc', 'hel', 'pear'],
+        ),
+        lpc=dict(
+            argstr='-lpc',
+            position=-2,
+            xor=['nmi', 'mi', 'hel', 'lpa', 'pear'],
+        ),
+        maxlev=dict(
+            argstr='-maxlev %d',
+            position=-1,
+            xor=['duplo'],
+        ),
+        mi=dict(
+            argstr='-mi',
+            xor=['mi', 'hel', 'lpc', 'lpa', 'pear'],
+        ),
         minpatch=dict(argstr='-minpatch %d', ),
-        nopadWARP=dict(argstr='-nopadWARP', ),
+        nmi=dict(
+            argstr='-nmi',
+            xor=['nmi', 'hel', 'lpc', 'lpa', 'pear'],
+        ),
+        noXdis=dict(argstr='-noXdis', ),
+        noYdis=dict(argstr='-noYdis', ),
+        noZdis=dict(argstr='-noZdis', ),
+        noneg=dict(argstr='-noneg', ),
+        nopad=dict(argstr='-nopad', ),
+        nopadWARP=dict(
+            argstr='-nopadWARP',
+            xor=['allsave', 'expad'],
+        ),
+        nopenalty=dict(argstr='-nopenalty', ),
+        nowarp=dict(argstr='-nowarp', ),
         noweight=dict(argstr='-noweight', ),
+        num_threads=dict(
+            nohash=True,
+            usedefault=True,
+        ),
+        out_file=dict(
+            argstr='-prefix %s',
+            position=0,
+            usedefault=True,
+        ),
+        out_weight_file=dict(argstr='-wtprefix %s', ),
+        outputtype=dict(),
+        overwrite=dict(argstr='-overwrite', ),
         pblur=dict(argstr='-pblur %s', ),
+        pear=dict(argstr='-pear', ),
+        penfac=dict(argstr='-penfac %f', ),
+        plusminus=dict(
+            argstr='-plusminus',
+            position=1,
+            usedefault=True,
+            xor=['duplo', 'allsave', 'iwarp'],
+        ),
+        quiet=dict(
+            argstr='-quiet',
+            xor=['verb'],
+        ),
+        resample=dict(argstr='-resample', ),
         source_file=dict(
             argstr='-source %s',
             copyfile=False,
-            mandatory=True,
+            deprecated='1.1.2',
+            new_name='in_file',
+        ),
+        verb=dict(
+            argstr='-verb',
+            xor=['quiet'],
+        ),
+        wball=dict(argstr='-wball %s', ),
+        weight=dict(argstr='-weight %s', ),
+        wmask=dict(argstr='-wpass %s %f', ),
+        workhard=dict(
+            argstr='-workhard',
+            xor=['boxopt', 'ballopt'],
         ),
     )
     inputs = QwarpPlusMinus.input_spec()
@@ -37,6 +166,7 @@ def test_QwarpPlusMinus_outputs():
         source_warp=dict(),
         warped_base=dict(),
         warped_source=dict(),
+        weights=dict(),
     )
     outputs = QwarpPlusMinus.output_spec()
 

nipype/interfaces/elastix/registration.py

@@ -178,21 +178,36 @@ def _list_outputs(self):
         return outputs
 
 
-class AnalyzeWarpInputSpec(ElastixBaseInputSpec):
-    transform_file = File(
+class AnalyzeWarpInputSpec(ApplyWarpInputSpec):
+    points = traits.Enum(
+        'all',
+        usedefault=True,
+        position=0,
+        argstr='-def %s',
+        desc='transform all points from the input-image, which effectively'
+             ' generates a deformation field.')
+    jac = traits.Enum(
+        'all',
+        usedefault=True,
+        argstr='-jac %s',
+        desc='generate an image with the determinant of the spatial Jacobian')
+    jacmat = traits.Enum(
+        'all',
+        usedefault=True,
+        argstr='-jacmat %s',
+        desc='generate an image with the spatial Jacobian matrix at each voxel')
+    moving_image = File(
         exists=True,
-        mandatory=True,
-        argstr='-tp %s',
-        desc='transform-parameter file, only 1')
-
+        argstr='-in %s',
+        desc='input image to deform (not used)')
 
 class AnalyzeWarpOutputSpec(TraitedSpec):
     disp_field = File(desc='displacements field')
     jacdet_map = File(desc='det(Jacobian) map')
     jacmat_map = File(desc='Jacobian matrix map')
 
 
-class AnalyzeWarp(CommandLine):
+class AnalyzeWarp(ApplyWarp):
     """
     Use transformix to get details from the input transform (generate
     the corresponding deformation field, generate the determinant of the
@@ -210,7 +225,6 @@ class AnalyzeWarp(CommandLine):
 
     """
 
-    _cmd = 'transformix -def all -jac all -jacmat all'
     input_spec = AnalyzeWarpInputSpec
     output_spec = AnalyzeWarpOutputSpec