Merge f4c61a6 into eacd567

nipype/interfaces/afni/__init__.py

@@ -18,7 +18,7 @@
 from .utils import (
     ABoverlap, AFNItoNIFTI, Autobox, Axialize, BrickStat, Bucket, Calc, Cat,
     CatMatvec, CenterMass, ConvertDset, Copy, Dot, Edge3, Eval, FWHMx,
-    LocalBistat, MaskTool, Merge, Notes, NwarpApply, NwarpAdjust, NwarpCat,
-    OneDToolPy, Refit, Resample, TCat, TCatSubBrick, TStat, To3D, Unifize,
-    Undump, ZCutUp, GCOR, Zcat, Zeropad)
+    LocalBistat, Localstat, MaskTool, Merge, Notes, NwarpApply, NwarpAdjust,
+    NwarpCat, OneDToolPy, Refit, ReHo, Resample, TCat, TCatSubBrick, TStat,
+    To3D, Unifize, Undump, ZCutUp, GCOR, Zcat, Zeropad)
 from .model import (Deconvolve, Remlfit, Synthesize)

nipype/interfaces/afni/preprocess.py

@@ -1802,28 +1802,107 @@ class QualityIndex(CommandLine):
 
 class ROIStatsInputSpec(CommandLineInputSpec):
     in_file = File(
-        desc='input file to 3dROIstats',
+        desc='input dataset',
         argstr='%s',
-        position=-1,
+        position=-2,
         mandatory=True,
         exists=True)
-    mask = File(desc='input mask', argstr='-mask %s', position=3, exists=True)
+    mask_file = File(desc='input mask', argstr='-mask %s', exists=True)
     mask_f2short = traits.Bool(
         desc='Tells the program to convert a float mask to short integers, '
         'by simple rounding.',
-        argstr='-mask_f2short',
-        position=2)
-    quiet = traits.Bool(desc='execute quietly', argstr='-quiet', position=1)
+        argstr='-mask_f2short')
+    num_roi = traits.Int(
+        desc='Forces the assumption that the mask dataset\'s ROIs are '
+             'denoted by 1 to n inclusive.  Normally, the program '
+             'figures out the ROIs on its own.  This option is '
+             'useful if a) you are certain that the mask dataset '
+             'has no values outside the range [0 n], b) there may '
+             'be some ROIs missing between [1 n] in the mask data-'
+             'set and c) you want those columns in the output any-'
+             'way so the output lines up with the output from other '
+             'invocations of 3dROIstats.',
+        argstr='-numroi %s')
+    zerofill = traits.Str(
+        requires=['num_roi'],
+        desc='For ROI labels not found, use the provided string instead of '
+             'a \'0\' in the output file. Only active if `num_roi` is '
+             'enabled.',
+        argstr='-zerofill %s')
+    roisel = traits.File(
+        exists=True,
+        desc='Only considers ROIs denoted by values found in the specified '
+             'file. Note that the order of the ROIs as specified in the file '
+             'is not preserved. So an SEL.1D of \'2 8 20\' produces the same '
+             'output as \'8 20 2\'',
+        argstr='-roisel %s')
+    debug = traits.Bool(
+        desc='print debug information',
+        argstr='-debug')
+    quiet = traits.Bool(
+        desc='execute quietly',
+        argstr='-quiet')
+    nomeanout = traits.Bool(
+        desc='Do not include the (zero-inclusive) mean among computed stats',
+        argstr='-nomeanout')
+    nobriklab = traits.Bool(
+        desc='Do not print the sub-brick label next to its index',
+        argstr='-nobriklab')
+    format1D = traits.Bool(
+        xor=['format1DR'],
+        desc='Output results in a 1D format that includes commented labels',
+        argstr='-1Dformat')
+    format1DR = traits.Bool(
+        xor=['format1D'],
+        desc='Output results in a 1D format that includes uncommented '
+             'labels. May not work optimally with typical 1D functions, '
+             'but is useful for R functions.',
+        argstr='-1DRformat')
+    _stat_names = ['mean', 'sum', 'voxels', 'minmax', 'sigma', 'median',
+                   'mode', 'summary', 'zerominmax', 'zerosigma', 'zeromedian',
+                   'zeromode']
+    stat = InputMultiObject(
+        traits.Enum(_stat_names),
+        desc='statistics to compute. Options include: '
+             ' * mean       =   Compute the mean using only non_zero voxels.'
+             '                  Implies the opposite for the mean computed '
+             '                  by default.\n'
+             ' * median     =   Compute the median of nonzero voxels\n'
+             ' * mode       =   Compute the mode of nonzero voxels.'
+             '                  (integral valued sets only)\n'
+             ' * minmax     =   Compute the min/max of nonzero voxels\n'
+             ' * sum        =   Compute the sum using only nonzero voxels.\n'
+             ' * voxels     =   Compute the number of nonzero voxels\n'
+             ' * sigma      =   Compute the standard deviation of nonzero'
+             '                  voxels\n'
+             'Statistics that include zero-valued voxels:\n'
+             ' * zerominmax =   Compute the min/max of all voxels.\n'
+             ' * zerosigma  =   Compute the standard deviation of all'
+             '                  voxels.\n'
+             ' * zeromedian =   Compute the median of all voxels.\n'
+             ' * zeromode   =   Compute the mode of all voxels.\n'
+             ' * summary    =   Only output a summary line with the grand '
+             '                  mean across all briks in the input dataset.'
+             '                  This option cannot be used with nomeanout.\n'
+             'More that one option can be specified.',
+        argstr='%s...')
+    out_file = File(
+        name_template='%s_roistat.1D',
+        desc='output file',
+        keep_extension=False,
+        argstr='> %s',
+        name_source='in_file',
+        position=-1)
 
 
 class ROIStatsOutputSpec(TraitedSpec):
-    stats = File(desc='output tab separated values file', exists=True)
+    out_file = File(desc='output tab-separated values file', exists=True)
 
 
 class ROIStats(AFNICommandBase):
     """Display statistics over masked regions
 
-    For complete details, see the `3dROIstats Documentation.
+    For complete details, see the `3dROIstats Documentation
     <https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dROIstats.html>`_
 
     Examples
@@ -1832,10 +1911,11 @@ class ROIStats(AFNICommandBase):
     >>> from nipype.interfaces import afni
     >>> roistats = afni.ROIStats()
     >>> roistats.inputs.in_file = 'functional.nii'
-    >>> roistats.inputs.mask = 'skeleton_mask.nii.gz'
-    >>> roistats.inputs.quiet = True
+    >>> roistats.inputs.mask_file = 'skeleton_mask.nii.gz'
+    >>> roistats.inputs.stat = ['mean', 'median', 'voxels']
+    >>> roistats.inputs.nomeanout = True
     >>> roistats.cmdline
-    '3dROIstats -quiet -mask skeleton_mask.nii.gz functional.nii'
+    '3dROIstats -quiet -mask skeleton_mask.nii.gz -nzmean -nzmedian -nzvoxels -nomeanout functional.nii > func_roistat.1D'
     >>> res = roistats.run()  # doctest: +SKIP
 
     """
@@ -1844,14 +1924,26 @@ class ROIStats(AFNICommandBase):
     input_spec = ROIStatsInputSpec
     output_spec = ROIStatsOutputSpec
 
-    def aggregate_outputs(self, runtime=None, needed_outputs=None):
-        outputs = self._outputs()
-        output_filename = 'roi_stats.csv'
-        with open(output_filename, 'w') as f:
-            f.write(runtime.stdout)
+    def _format_arg(self, name, spec, value):
 
-        outputs.stats = os.path.abspath(output_filename)
-        return outputs
+        _stat_dict  =   {
+                            'mean': '-nzmean',
+                            'median': '-nzmedian',
+                            'mode': '-nzmode',
+                            'minmax': '-nzminmax',
+                            'sigma': '-nzsigma',
+                            'voxels': '-nzvoxels',
+                            'sum': '-nzsum',
+                            'summary': '-summary',
+                            'zerominmax': '-minmax',
+                            'zeromedian': '-median',
+                            'zerosigma': '-sigma',
+                            'zeromode': '-mode'
+                        }
+        if name == 'stat':
+            value = [_stat_dict[v] for v in value]
+
+        return super(ROIStats, self)._format_arg(name, spec, value)
 
 
 class RetroicorInputSpec(AFNICommandInputSpec):

nipype/interfaces/afni/tests/test_auto_Localstat.py

@@ -0,0 +1,71 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..utils import Localstat
+
+
+def test_Localstat_inputs():
+    input_map = dict(
+        args=dict(argstr='%s', ),
+        automask=dict(argstr='-automask', ),
+        environ=dict(
+            nohash=True,
+            usedefault=True,
+        ),
+        grid_rmode=dict(
+            argstr='-grid_rmode %s',
+            requires=['reduce_restore_grid'],
+        ),
+        in_file=dict(
+            argstr='%s',
+            mandatory=True,
+            position=-1,
+        ),
+        mask_file=dict(argstr='-mask %s', ),
+        neighborhood=dict(
+            argstr="-nbhd '%s(%s)'",
+            mandatory=True,
+        ),
+        nonmask=dict(argstr='-use_nonmask', ),
+        num_threads=dict(
+            nohash=True,
+            usedefault=True,
+        ),
+        out_file=dict(
+            argstr='-prefix %s',
+            keep_extension=True,
+            name_source='in_file',
+            name_template='%s_localstat',
+            position=0,
+        ),
+        outputtype=dict(),
+        overwrite=dict(argstr='-overwrite', ),
+        quiet=dict(argstr='-quiet', ),
+        reduce_grid=dict(
+            argstr='-reduce_grid %s',
+            xor=['reduce_restore_grid', 'reduce_max_vox'],
+        ),
+        reduce_max_vox=dict(
+            argstr='-reduce_max_vox %s',
+            xor=['reduce_restore_grid', 'reduce_grid'],
+        ),
+        reduce_restore_grid=dict(
+            argstr='-reduce_restore_grid %s',
+            xor=['reduce_max_vox', 'reduce_grid'],
+        ),
+        stat=dict(
+            argstr='-stat %s...',
+            mandatory=True,
+        ),
+    )
+    inputs = Localstat.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+def test_Localstat_outputs():
+    output_map = dict(out_file=dict(), )
+    outputs = Localstat.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/interfaces/afni/tests/test_auto_ROIStats.py

@@ -6,26 +6,42 @@
 def test_ROIStats_inputs():
     input_map = dict(
         args=dict(argstr='%s', ),
+        debug=dict(argstr='-debug', ),
         environ=dict(
             nohash=True,
             usedefault=True,
         ),
+        format1D=dict(
+            argstr='-1Dformat',
+            xor=['format1DR'],
+        ),
+        format1DR=dict(
+            argstr='-1DRformat',
+            xor=['format1D'],
+        ),
         in_file=dict(
             argstr='%s',
             mandatory=True,
-            position=-1,
+            position=-2,
         ),
-        mask=dict(
-            argstr='-mask %s',
-            position=3,
-        ),
-        mask_f2short=dict(
-            argstr='-mask_f2short',
-            position=2,
+        mask_f2short=dict(argstr='-mask_f2short', ),
+        mask_file=dict(argstr='-mask %s', ),
+        nobriklab=dict(argstr='-nobriklab', ),
+        nomeanout=dict(argstr='-nomeanout', ),
+        num_roi=dict(argstr='-numroi %s', ),
+        out_file=dict(
+            argstr='> %s',
+            keep_extension=False,
+            name_source='in_file',
+            name_template='%s_roistat.1D',
+            position=-1,
         ),
-        quiet=dict(
-            argstr='-quiet',
-            position=1,
+        quiet=dict(argstr='-quiet', ),
+        roisel=dict(argstr='-roisel %s', ),
+        stat=dict(argstr='%s...', ),
+        zerofill=dict(
+            argstr='-zerofill %s',
+            requires=['num_roi'],
         ),
     )
     inputs = ROIStats.input_spec()
@@ -34,7 +50,7 @@ def test_ROIStats_inputs():
         for metakey, value in list(metadata.items()):
             assert getattr(inputs.traits()[key], metakey) == value
 def test_ROIStats_outputs():
-    output_map = dict(stats=dict(), )
+    output_map = dict(out_file=dict(), )
     outputs = ROIStats.output_spec()
 
     for key, metadata in list(output_map.items()):

nipype/interfaces/afni/tests/test_auto_ReHo.py

@@ -0,0 +1,56 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..utils import ReHo
+
+
+def test_ReHo_inputs():
+    input_map = dict(
+        args=dict(argstr='%s', ),
+        chi_sq=dict(argstr='-chi_sq', ),
+        ellipsoid=dict(
+            argstr='-neigh_X %s -neigh_Y %s -neigh_Z %s',
+            xor=['sphere', 'neighborhood'],
+        ),
+        environ=dict(
+            nohash=True,
+            usedefault=True,
+        ),
+        in_file=dict(
+            argstr='-inset %s',
+            mandatory=True,
+            position=1,
+        ),
+        label_set=dict(argstr='-in_rois %s', ),
+        mask=dict(argstr='-mask %s', ),
+        neighborhood=dict(
+            argstr='-nneigh %s',
+            xor=['sphere', 'ellipsoid'],
+        ),
+        out_file=dict(
+            argstr='-prefix %s',
+            keep_extension=True,
+            name_source='in_file',
+            name_template='%s_localstat',
+            position=0,
+        ),
+        overwrite=dict(argstr='-overwrite', ),
+        sphere=dict(
+            argstr='-neigh_RAD %s',
+            xor=['neighborhood', 'ellipsoid'],
+        ),
+    )
+    inputs = ReHo.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+def test_ReHo_outputs():
+    output_map = dict(
+        out_file=dict(),
+        out_vals=dict(),
+    )
+    outputs = ReHo.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value