Merge https://github.com/nipy/nipype

Author: mgxd

CHANGES

@@ -1,4 +1,4 @@
-Next release
+Release 0.12.0-rc1 (April 20, 2016)
 ============
 
 * ENH: Added dcm2niix interface (https://github.com/nipy/nipype/pull/1435)

CONTRIBUTING.md

@@ -19,7 +19,7 @@
 
 When opening a new Issue, please take the following steps:
 
-1. Search GitHub and/or [Neurostars](neurostars.org) for your issue to avoid duplicate reports.
+1. Search GitHub and/or [Neurostars](http://neurostars.org) for your issue to avoid duplicate reports.
    Keyword searches for your error messages are most helpful.
 2. If possible, try updating to master and reproducing your issue,
    because we may have already fixed it.

doc/_templates/indexsidebar.html

@@ -2,7 +2,7 @@
 <h3>{{ _('Links') }}</h3>
 
 <ul>
-    <li>Docs: <a href="http://nipy.org/nipype">Stable</a> · <a href="http://www.mit.edu/~satra/nipype-nightly/">Nightly</a></li>
+    <li>Docs: <a href="http://nipy.org/nipype">Stable</a> · <a href="http://nipype.readthedocs.org/en/latest/">Dev</a></li>
     <li>Code: <a href="http://github.com/nipy/nipype">Github</a> · <a href="http://github.com/nipy/nipype/issues">Bugs-Requests</a></li>
     <li>Forum: <a href="http://neurostars.org/t/nipype">User</a> · <a href="http://projects.scipy.org/mailman/listinfo/nipy-devel">Developer</a></li>
     <li><a href="http://nipy.org/software/license/index.html"><img src="https://img.shields.io/pypi/l/nipype.svg" alt="License"></a> · <a href="about.html#funding">Funding</a></li>

nipype/info.py

@@ -10,7 +10,7 @@
 _version_major = 0
 _version_minor = 12
 _version_micro = 0
-_version_extra = '-dev'  # Remove -dev for release
+_version_extra = '-rc1'  # Remove -dev for release
 
 
 def get_nipype_gitversion():

nipype/interfaces/afni/preprocess.py

@@ -2178,7 +2178,7 @@ class FWHMxInputSpec(CommandLineInputSpec):
              'is not given, the program picks q=NT/30. -detrend disables -demed, and includes '
              '-unif.')
     demed = traits.Bool(
-        False, argstr='-demed', xorg=['detrend'],
+        False, argstr='-demed', xor=['detrend'],
         desc='If the input dataset has more than one sub-brick (e.g., has a time axis), then '
              'subtract the median of each voxel\'s time series before processing FWHM. This will '
              'tend to remove intrinsic spatial structure and leave behind the noise.')

nipype/interfaces/afni/tests/test_auto_FWHMx.py

@@ -20,7 +20,7 @@ def test_FWHMx_inputs():
     compat=dict(argstr='-compat',
     ),
     demed=dict(argstr='-demed',
-    xorg=['detrend'],
+    xor=['detrend'],
     ),
     detrend=dict(argstr='-detrend',
     usedefault=True,

nipype/interfaces/dipy/reconstruction.py

@@ -276,9 +276,9 @@ def _list_outputs(self):
 class CSDInputSpec(DipyBaseInterfaceInputSpec):
     in_mask = File(exists=True, desc=('input mask in which compute tensors'))
     response = File(exists=True, desc=('single fiber estimated response'))
-    sh_order = traits.Int(8, exists=True, usedefault=True,
+    sh_order = traits.Int(8, usedefault=True,
                           desc=('maximal shperical harmonics order'))
-    save_fods = traits.Bool(True, exists=True, usedefault=True,
+    save_fods = traits.Bool(True, usedefault=True,
                             desc=('save fODFs in file'))
     out_fods = File(desc=('fODFs output file name'))
 

nipype/interfaces/dipy/tests/test_auto_CSD.py

@@ -19,11 +19,9 @@ def test_CSD_inputs():
     out_fods=dict(),
     out_prefix=dict(),
     response=dict(),
-    save_fods=dict(exists=True,
-    usedefault=True,
+    save_fods=dict(usedefault=True,
     ),
-    sh_order=dict(exists=True,
-    usedefault=True,
+    sh_order=dict(usedefault=True,
     ),
     )
     inputs = CSD.input_spec()

nipype/interfaces/freesurfer/model.py

@@ -654,7 +654,7 @@ class SegStatsInputSpec(FSTraitedSpec):
     wm_vol_from_surf = traits.Bool(argstr='--surf-wm-vol', desc='Compute wm volume from surf')
     cortex_vol_from_surf = traits.Bool(argstr='--surf-ctx-vol', desc='Compute cortex volume from surf')
     non_empty_only = traits.Bool(argstr='--nonempty', desc='Only report nonempty segmentations')
-    empty = traits.Bool(argstr="--empty", mandatory=False,
+    empty = traits.Bool(argstr="--empty",
                         desc="Report on segmentations listed in the color table")
     mask_file = File(exists=True, argstr='--mask %s',
                      desc='Mask volume (same size as seg')
@@ -690,7 +690,7 @@ class SegStatsInputSpec(FSTraitedSpec):
                              desc="Compute volume of total gray matter")
     euler = traits.Bool(argstr="--euler",
                         desc="Write out number of defect holes in orig.nofix based on the euler number")
-    in_intensity = File(argstr="--in %s --in-intensity-name %s", mandatory=False,
+    in_intensity = File(argstr="--in %s --in-intensity-name %s",
                         desc="Undocumented input norm.mgz file")
     intensity_units = traits.Enum('MR', argstr="--in-intensity-units %s",
                                   requires=["in_intensity"], desc="Intensity units")
@@ -1083,14 +1083,13 @@ class Label2LabelInputSpec(FSTraitedSpec):
     source_subject = traits.String(argstr="--srcsubject %s", mandatory=True,
                                    desc="Source subject name")
     # optional
-    out_file = File(argstr="--trglabel %s", mandatory=False,
+    out_file = File(argstr="--trglabel %s",
                     name_source=['source_label'], name_template='%s_converted',
                     hash_files=False, keep_extension=True,
                     desc="Target label")
     registration_method = traits.Enum('surface', 'volume', usedefault=True,
                                         argstr="--regmethod %s", desc="Registration method")
-    copy_inputs = traits.Bool(mandatory=False,
-                              desc="If running as a node, set this to True." +
+    copy_inputs = traits.Bool(desc="If running as a node, set this to True." +
                               "This will copy the input files to the node " +
                               "directory.")
 
@@ -1180,11 +1179,11 @@ class Label2AnnotInputSpec(FSTraitedSpec):
     orig = File(exists=True, mandatory=True,
                 desc="implicit {hemisphere}.orig")
     # optional
-    keep_max = traits.Bool(argstr="--maxstatwinner", mandatory=False,
+    keep_max = traits.Bool(argstr="--maxstatwinner",
                            desc="Keep label with highest 'stat' value")
-    verbose_off = traits.Bool(argstr="--noverbose", mandatory=False,
+    verbose_off = traits.Bool(argstr="--noverbose",
                               desc="Turn off overlap and stat override messages")
-    color_table = File(argstr="--ctab %s", mandatory=False, exists=True,
+    color_table = File(argstr="--ctab %s", exists=True,
                        desc="File that defines the structure names, their indices, and their color")
     copy_inputs = traits.Bool(desc="copy implicit inputs and create a temp subjects_dir")
 

nipype/interfaces/freesurfer/preprocess.py

@@ -1502,11 +1502,11 @@ class NormalizeInputSpec(FSTraitedSpec):
     # optional
     gradient = traits.Int(1, argstr="-g %d", usedefault=False,
                           desc="use max intensity/mm gradient g (default=1)")
-    mask = File(argstr="-mask %s", mandatory=False, exists=True,
+    mask = File(argstr="-mask %s",  exists=True,
                 desc="The input mask file for Normalize")
-    segmentation = File(argstr="-aseg %s", mandatory=False,
+    segmentation = File(argstr="-aseg %s",
                         exists=True, desc="The input segmentation for Normalize")
-    transform = File(exists=True, mandatory=False,
+    transform = File(exists=True,
                      desc="Tranform file from the header of the input file")
 
 
@@ -1551,9 +1551,9 @@ class CANormalizeInputSpec(FSTraitedSpec):
     transform = File(argstr='%s', exists=True, mandatory=True,
                      position=-2, desc="The tranform file in lta format")
     # optional
-    mask = File(argstr='-mask %s', exists=True, mandatory=False,
+    mask = File(argstr='-mask %s', exists=True,
                 desc="Specifies volume to use as mask")
-    control_points = File(argstr='-c %s', mandatory=False,
+    control_points = File(argstr='-c %s',
                           desc="File name for the output control points")
     long_file = File(argstr='-long %s',
                      desc='undocumented flag used in longitudinal processing')
@@ -1596,20 +1596,20 @@ class CARegisterInputSpec(FSTraitedSpecOpenMP):
     #required
     in_file = File(argstr='%s', exists=True, mandatory=True,
                    position=-3, desc="The input volume for CARegister")
-    out_file = File(argstr='%s', mandatory=False, position=-1,
+    out_file = File(argstr='%s',  position=-1,
                     genfile=True, desc="The output volume for CARegister")
-    template = File(argstr='%s', exists=True, mandatory=False,
+    template = File(argstr='%s', exists=True,
                     position=-2, desc="The template file in gca format")
     # optional
-    mask = File(argstr='-mask %s', exists=True, mandatory=False,
+    mask = File(argstr='-mask %s', exists=True,
                 desc="Specifies volume to use as mask")
-    invert_and_save = traits.Bool(argstr='-invert-and-save', mandatory=False, position=-4,
+    invert_and_save = traits.Bool(argstr='-invert-and-save',  position=-4,
                                   desc="Invert and save the .m3z multi-dimensional talaraich transform to x, y, and z .mgz files")
     no_big_ventricles = traits.Bool(
-        argstr='-nobigventricles', mandatory=False, desc="No big ventricles")
-    transform = File(argstr='-T %s', exists=True, mandatory=False,
+        argstr='-nobigventricles',  desc="No big ventricles")
+    transform = File(argstr='-T %s', exists=True,
                      desc="Specifies transform in lta format")
-    align = traits.String(argstr='-align-%s', mandatory=False,
+    align = traits.String(argstr='-align-%s',
                           desc="Specifies when to perform alignment")
     levels = traits.Int(
         argstr='-levels %d',
@@ -1675,17 +1675,18 @@ class CALabelInputSpec(FSTraitedSpecOpenMP):
     intensities = File(argstr="-r %s", exists=True,
                        desc="input label intensities file(used in longitudinal processing)")
     no_big_ventricles = traits.Bool(
-        argstr="-nobigventricles", mandatory=False, desc="No big ventricles")
-    align = traits.Bool(argstr="-align", mandatory=False, desc="Align CALabel")
+        argstr="-nobigventricles",  desc="No big ventricles")
+    align = traits.Bool(argstr="-align",  desc="Align CALabel")
     prior = traits.Float(argstr="-prior %.1f",
-                         mandatory=False, desc="Prior for CALabel")
+                          desc="Prior for CALabel")
     relabel_unlikely = traits.Tuple(traits.Int, traits.Float,
                                     argstr="-relabel_unlikely %d %.1f",
-                                    desc="Reclassify voxels at least some std devs from the mean using some size Gaussian window",
-                                    mandatory=False)
-    label = traits.File(argstr="-l %s", mandatory=False, exists=True,
+                                    desc=("Reclassify voxels at least some std"
+                                          " devs from the mean using some size"
+                                          " Gaussian window"))
+    label = traits.File(argstr="-l %s",  exists=True,
                         desc="Undocumented flag. Autorecon3 uses ../label/{hemisphere}.cortex.label as input file")
-    aseg = traits.File(argstr="-aseg %s", mandatory=False, exists=True,
+    aseg = traits.File(argstr="-aseg %s",  exists=True,
                        desc="Undocumented flag. Autorecon3 uses ../mri/aseg.presurf.mgz as input file")
 
 
@@ -1742,11 +1743,11 @@ class MRIsCALabelInputSpec(FSTraitedSpecOpenMP):
                     hash_files=False, name_template="%s.aparc.annot",
                     desc="Annotated surface output file")
     # optional
-    label = traits.File(argstr="-l %s", mandatory=False, exists=True,
+    label = traits.File(argstr="-l %s",  exists=True,
                         desc="Undocumented flag. Autorecon3 uses ../label/{hemisphere}.cortex.label as input file")
-    aseg = traits.File(argstr="-aseg %s", mandatory=False, exists=True,
+    aseg = traits.File(argstr="-aseg %s",  exists=True,
                        desc="Undocumented flag. Autorecon3 uses ../mri/aseg.presurf.mgz as input file")
-    seed = traits.Int(argstr="-seed %d", mandatory=False,
+    seed = traits.Int(argstr="-seed %d",
                       desc="")
     copy_inputs = traits.Bool(desc="Copies implicit inputs to node directory " +
                               "and creates a temp subjects_directory. " +
@@ -1835,8 +1836,7 @@ class SegmentCCInputSpec(FSTraitedSpec):
     subject_id = traits.String('subject_id', argstr="%s", mandatory=True,
                                position=-1, usedefault=True,
                                desc="Subject name")
-    copy_inputs = traits.Bool(mandatory=False,
-                              desc="If running as a node, set this to True." +
+    copy_inputs = traits.Bool(desc="If running as a node, set this to True." +
                               "This will copy the input files to the node " +
                               "directory.")
 
@@ -1979,10 +1979,10 @@ class EditWMwithAsegInputSpec(FSTraitedSpec):
                       desc="Input brain/T1 file")
     seg_file = File(argstr="%s", position=-2, mandatory=True, exists=True,
                     desc="Input presurf segmentation file")
-    out_file = File(argstr="%s", position=-1, mandtaory=True, exists=False,
+    out_file = File(argstr="%s", position=-1, mandatory=True, exists=False,
                     desc="File to be written as output")
     # optional
-    keep_in = traits.Bool(argstr="-keep-in", mandatory=False,
+    keep_in = traits.Bool(argstr="-keep-in",
                           desc="Keep edits as found in input volume")
 
 class EditWMwithAsegOutputSpec(TraitedSpec):