Merge branch 'master' into enh/ETSConfigTookit

Author: Oscar Esteban

CHANGES

@@ -2,6 +2,7 @@ Next release
 ============
 
 * FIX: Prevent crash when tvtk is loaded - ETS_TOOLKIT=null (https://github.com/nipy/nipype/pull/973)
+* ENH: Added interfaces of AFNI (https://github.com/nipy/nipype/pull/1360)
 * ENH: Added support for PETPVC (https://github.com/nipy/nipype/pull/1335)
 * ENH: Merge S3DataSink into DataSink, added AWS documentation (https://github.com/nipy/nipype/pull/1316)
 * TST: Cache APT in CircleCI (https://github.com/nipy/nipype/pull/1333)

nipype/interfaces/afni/__init__.py

@@ -12,5 +12,5 @@
                          Fourier, Allineate, Maskave, SkullStrip, TCat, Fim,
                          BlurInMask, Autobox, TCorrMap, Bandpass, Retroicor,
                          TCorrelate, TCorr1D, BrickStat, ROIStats, AutoTcorrelate,
-                         AFNItoNIFTI, Eval, Means)
+                         AFNItoNIFTI, Eval, Means, Hist)
 from .svm import (SVMTest, SVMTrain)

nipype/interfaces/afni/preprocess.py

@@ -10,17 +10,17 @@
 """
 
 import os
+import os.path as op
 import re
 from warnings import warn
 
-from .base import AFNICommand, AFNICommandInputSpec, AFNICommandOutputSpec
+from .base import AFNICommand, AFNICommandInputSpec, AFNICommandOutputSpec, Info, no_afni
 from ..base import CommandLineInputSpec, CommandLine, OutputMultiPath
 from ..base import (Directory, TraitedSpec,
                     traits, isdefined, File, InputMultiPath, Undefined)
 from ...utils.filemanip import (load_json, save_json, split_filename)
 from ...utils.filemanip import fname_presuffix
 
-
 class To3DInputSpec(AFNICommandInputSpec):
     out_file = File(name_template="%s", desc='output image file name',
                     argstr='-prefix %s', name_source=["in_folder"])
@@ -1234,9 +1234,7 @@ class SkullStrip(AFNICommand):
     output_spec = AFNICommandOutputSpec
 
     def __init__(self, **inputs):
-        from .base import Info, no_afni
         super(SkullStrip, self).__init__(**inputs)
-
         if not no_afni():
             v = Info.version()
 
@@ -2090,3 +2088,75 @@ class Means(AFNICommand):
     _cmd = '3dMean'
     input_spec = MeansInputSpec
     output_spec = AFNICommandOutputSpec
+
+
+class HistInputSpec(CommandLineInputSpec):
+    in_file = File(
+        desc='input file to 3dHist', argstr='-input %s', position=1, mandatory=True,
+        exists=True, copyfile=False)
+    out_file = File(
+        desc='Write histogram to niml file with this prefix', name_template='%s_hist',
+        keep_extension=False, argstr='-prefix %s', name_source=['in_file'])
+    showhist = traits.Bool(False, usedefault=True, desc='write a text visual histogram',
+                           argstr='-showhist')
+    out_show = File(
+        name_template="%s_hist.out", desc='output image file name', keep_extension=False,
+        argstr="> %s", name_source="in_file", position=-1)
+    mask = File(desc='matrix to align input file', argstr='-mask %s', exists=True)
+    nbin = traits.Int(desc='number of bins', argstr='-nbin %d')
+    max_value = traits.Float(argstr='-max %f', desc='maximum intensity value')
+    min_value = traits.Float(argstr='-min %f', desc='minimum intensity value')
+    bin_width = traits.Float(argstr='-binwidth %f', desc='bin width')
+
+class HistOutputSpec(TraitedSpec):
+    out_file = File(desc='output file', exists=True)
+    out_show = File(desc='output visual histogram')
+
+
+class Hist(CommandLine):
+    """Computes average of all voxels in the input dataset
+    which satisfy the criterion in the options list
+
+    For complete details, see the `3dHist Documentation.
+    <http://afni.nimh.nih.gov/pub/dist/doc/program_help/3dHist.html>`_
+
+    Examples
+    ========
+
+    >>> from nipype.interfaces import afni as afni
+    >>> hist = afni.Hist()
+    >>> hist.inputs.in_file = 'functional.nii'
+    >>> hist.cmdline
+    '3dHist -input functional.nii -prefix functional_hist'
+    >>> res = hist.run() # doctest: +SKIP
+
+    """
+
+    _cmd = '3dHist'
+    input_spec = HistInputSpec
+    output_spec = HistOutputSpec
+    _redirect_x = True
+
+    def __init__(self, **inputs):
+        super(Hist, self).__init__(**inputs)
+        if not no_afni():
+            version = Info.version()
+
+            # As of AFNI 16.0.00, redirect_x is not needed
+            if isinstance(version[0], int) and version[0] > 15:
+                self._redirect_x = False
+
+    def _parse_inputs(self, skip=None):
+        if not self.inputs.showhist:
+            if skip is None:
+                skip = []
+            skip += ['out_show']
+        return super(Hist, self)._parse_inputs(skip=skip)
+
+
+    def _list_outputs(self):
+        outputs = super(Hist, self)._list_outputs()
+        outputs['out_file'] += '.niml.hist'
+        if not self.inputs.showhist:
+            outputs['out_show'] = Undefined
+        return outputs

nipype/interfaces/afni/tests/test_auto_Hist.py

@@ -0,0 +1,62 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ....testing import assert_equal
+from ..preprocess import Hist
+
+
+def test_Hist_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    bin_width=dict(argstr='-binwidth %f',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='-input %s',
+    copyfile=False,
+    mandatory=True,
+    position=1,
+    ),
+    mask=dict(argstr='-mask %s',
+    ),
+    max_value=dict(argstr='-max %f',
+    ),
+    min_value=dict(argstr='-min %f',
+    ),
+    nbin=dict(argstr='-nbin %d',
+    ),
+    out_file=dict(argstr='-prefix %s',
+    keep_extension=False,
+    name_source=['in_file'],
+    name_template='%s_hist',
+    ),
+    out_show=dict(argstr='> %s',
+    keep_extension=False,
+    name_source='in_file',
+    name_template='%s_hist.out',
+    position=-1,
+    ),
+    showhist=dict(argstr='-showhist',
+    usedefault=True,
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = Hist.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+
+def test_Hist_outputs():
+    output_map = dict(out_file=dict(),
+    out_show=dict(),
+    )
+    outputs = Hist.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value

nipype/interfaces/ants/resampling.py

@@ -247,7 +247,7 @@ class ApplyTransformsInputSpec(ANTSCommandInputSpec):
                                                           traits.Float())
                                              )
     transforms = InputMultiPath(
-        File(exists=True), argstr='%s', mandatory=True, desc='transform files')
+        File(exists=True), argstr='%s', mandatory=True, desc='transform files: will be applied in reverse order. For example, the last specified transform will be applied first')
     invert_transform_flags = InputMultiPath(traits.Bool())
     default_value = traits.Float(0.0, argstr='--default-value %g', usedefault=True)
     print_out_composite_warp_file = traits.Bool(False, requires=["output_image"],
@@ -274,12 +274,12 @@ class ApplyTransforms(ANTSCommand):
     >>> at.inputs.output_image = 'deformed_moving1.nii'
     >>> at.inputs.interpolation = 'Linear'
     >>> at.inputs.default_value = 0
-    >>> at.inputs.transforms = ['trans.mat', 'ants_Warp.nii.gz']
+    >>> at.inputs.transforms = ['ants_Warp.nii.gz', 'trans.mat']
     >>> at.inputs.invert_transform_flags = [False, False]
     >>> at.cmdline
     'antsApplyTransforms --default-value 0 --dimensionality 3 --input moving1.nii --interpolation Linear \
---output deformed_moving1.nii --reference-image fixed1.nii --transform [ trans.mat, 0 ] \
---transform [ ants_Warp.nii.gz, 0 ]'
+--output deformed_moving1.nii --reference-image fixed1.nii --transform [ ants_Warp.nii.gz, 0 ] \
+--transform [ trans.mat, 0 ]'
 
     >>> at1 = ApplyTransforms()
     >>> at1.inputs.dimension = 3
@@ -289,12 +289,12 @@ class ApplyTransforms(ANTSCommand):
     >>> at1.inputs.interpolation = 'BSpline'
     >>> at1.inputs.interpolation_parameters = (5,)
     >>> at1.inputs.default_value = 0
-    >>> at1.inputs.transforms = ['trans.mat', 'ants_Warp.nii.gz']
+    >>> at1.inputs.transforms = ['ants_Warp.nii.gz', 'trans.mat']
     >>> at1.inputs.invert_transform_flags = [False, False]
     >>> at1.cmdline
     'antsApplyTransforms --default-value 0 --dimensionality 3 --input moving1.nii --interpolation BSpline[ 5 ] \
---output deformed_moving1.nii --reference-image fixed1.nii --transform [ trans.mat, 0 ] \
---transform [ ants_Warp.nii.gz, 0 ]'
+--output deformed_moving1.nii --reference-image fixed1.nii --transform [ ants_Warp.nii.gz, 0 ] \
+--transform [ trans.mat, 0 ]'
 
 
     """

nipype/interfaces/fsl/epi.py

@@ -589,7 +589,7 @@ class EpiRegInputSpec(FSLCommandInputSpec):
     no_fmapreg = traits.Bool(False, argstr='--nofmapreg',
                              desc='do not perform registration of fmap to T1 \
                         (use if fmap already registered)')
-    no_clean = traits.Bool(False, argstr='--noclean',
+    no_clean = traits.Bool(True, argstr='--noclean', usedefault=True,
                            desc='do not clean up intermediate files')
 
 
@@ -640,8 +640,8 @@ class EpiReg(FSLCommand):
     >>> epireg.inputs.pedir='y'
     >>> epireg.cmdline #doctest: +ELLIPSIS
     'epi_reg --echospacing=0.000670 --fmap=fieldmap_phase_fslprepared.nii \
---fmapmag=fieldmap_mag.nii --fmapmagbrain=fieldmap_mag_brain.nii --pedir=y \
---epi=epi.nii --t1=T1.nii --t1brain=T1_brain.nii --out=epi2struct'
+--fmapmag=fieldmap_mag.nii --fmapmagbrain=fieldmap_mag_brain.nii --noclean \
+--pedir=y --epi=epi.nii --t1=T1.nii --t1brain=T1_brain.nii --out=epi2struct'
     >>> epireg.run() # doctest: +SKIP
 
     """

nipype/interfaces/fsl/tests/test_auto_EpiReg.py

@@ -25,6 +25,7 @@ def test_EpiReg_inputs():
     usedefault=True,
     ),
     no_clean=dict(argstr='--noclean',
+    usedefault=True,
     ),
     no_fmapreg=dict(argstr='--nofmapreg',
     ),

nipype/pipeline/engine/utils.py

@@ -1021,7 +1021,7 @@ def export_graph(graph_in, base_dir=None, show=False, use_execgraph=False,
                                suffix='.dot',
                                use_ext=False,
                                newpath=base_dir)
-    nx.write_dot(pklgraph, outfname)
+    nx.drawing.nx_pydot.write_dot(pklgraph, outfname)
     logger.info('Creating dot file: %s' % outfname)
     cmd = 'dot -T%s -O %s' % (format, outfname)
     res = CommandLine(cmd, terminal_output='allatonce').run()