Merge remote-tracking branch 'nipy/master'

Author: tsalo

CHANGES

@@ -1,6 +1,24 @@
 Upcoming Release
 =====================
 
+* ENH: AFNI motion parameter support for FrameWiseDisplacement (https://github.com/nipy/nipype/pull/1840)
+* ENH: Add ANTs KellyKapowski interface (https://github.com/nipy/nipype/pull/1845)
+* FIX: AFNI interface bug setting OMP_NUM_THREADS to 1 (https://github.com/nipy/nipype/pull/1728)
+* FIX: Select Eddy run command at runtime (https://github.com/nipy/nipype/pull/1871)
+* FIX: Increase FLIRT's flexibility with apply_xfm (https://github.com/nipy/nipype/pull/1875)
+* DOC: Update FSL preprocess docstrings (https://github.com/nipy/nipype/pull/1881)
+* ENH: Support GIFTI outputs in SampleToSurface (https://github.com/nipy/nipype/pull/1886)
+* FIX: Configparser differences between PY2 and PY3 (https://github.com/nipy/nipype/pull/1890)
+* ENH: Add mris_expand interface (https://github.com/nipy/nipype/pull/1893)
+* FIX: Split over-eager globs in FreeSurferSource (https://github.com/nipy/nipype/pull/1894)
+* FIX: Store undefined by default so that xor checks don't trip (https://github.com/nipy/nipype/pull/1903)
+* FIX: Gantt chart generator PY3 compatibility (https://github.com/nipy/nipype/pull/1907)
+* FIX: Add DOF and --fsl-dof options to BBRegister (https://github.com/nipy/nipype/pull/1917)
+* ENH: Auto-derive input_names in Function (https://github.com/nipy/nipype/pull/1918)
+* FIX: Minor fixes for NonSteadyStateDetector (https://github.com/nipy/nipype/pull/1926)
+* DOC: Add duecredit references for AFNI and FSL (https://github.com/nipy/nipype/pull/1930)
+* ENH: Added zenodo (https://zenodo.org/) file (https://github.com/nipy/nipype/pull/1924)
+* ENH: Disable symlinks on CIFS filesystems (https://github.com/nipy/nipype/pull/1941)
 * ENH: Sphinx extension to plot workflows (https://github.com/nipy/nipype/pull/1896)
 * ENH: Added non-steady state detector for EPI data (https://github.com/nipy/nipype/pull/1839)
 * ENH: Enable new BBRegister init options for FSv6+ (https://github.com/nipy/nipype/pull/1811)

nipype/interfaces/ants/registration.py

@@ -378,6 +378,8 @@ class RegistrationInputSpec(ANTSCommandInputSpec):
     winsorize_lower_quantile = traits.Range(
         low=0.0, high=1.0, value=0.0, argstr='%s', usedefault=True, desc="The Lower quantile to clip image ranges")
 
+    verbose = traits.Bool(argstr='-v', default=False)
+
 
 class RegistrationOutputSpec(TraitedSpec):
     forward_transforms = traits.List(

nipype/interfaces/dcm2nii.py

@@ -309,7 +309,10 @@ def _parse_stdout(self, stdout):
                 else:
                     pass
                 if out_file:
-                    files.append(out_file + ".nii.gz")
+                    if self.inputs.compress == 'n':
+                        files.append(out_file + ".nii")
+                    else:
+                        files.append(out_file + ".nii.gz")
                     if self.inputs.bids_format:
                         bids.append(out_file + ".json")
                     continue

nipype/interfaces/freesurfer/__init__.py

@@ -21,7 +21,7 @@
                     MRIFill, MRIsInflate, Sphere, FixTopology, EulerNumber,
                     RemoveIntersection, MakeSurfaces, Curvature, CurvatureStats,
                     Jacobian, MRIsCalc, VolumeMask, ParcellationStats, Contrast,
-                    RelabelHypointensities, Aparc2Aseg, Apas2Aseg, MRIsExpand)
+                    RelabelHypointensities, Aparc2Aseg, Apas2Aseg, MRIsExpand, MRIsCombine)
 from .longitudinal import (RobustTemplate, FuseSegmentations)
 from .registration import (MPRtoMNI305, RegisterAVItoTalairach, EMRegister, Register,
                            Paint)

nipype/interfaces/freesurfer/base.py

@@ -17,16 +17,17 @@
 from __future__ import print_function, division, unicode_literals, absolute_import
 from builtins import open, object, str
 
-
 import os
 
+from ... import LooseVersion
 from ...utils.filemanip import fname_presuffix
 from ..base import (CommandLine, Directory,
                     CommandLineInputSpec, isdefined,
                     traits, TraitedSpec, File)
 
 __docformat__ = 'restructuredtext'
 
+
 class Info(object):
     """ Freesurfer subject directory and version information.
 
@@ -65,6 +66,41 @@ def version():
         fid.close()
         return version
 
+    @classmethod
+    def looseversion(cls):
+        """ Return a comparable version object
+
+        If no version found, use LooseVersion('0.0.0')
+        """
+        ver = cls.version()
+        if ver is None:
+            return LooseVersion('0.0.0')
+
+        vinfo = ver.rstrip().split('-')
+        try:
+            int(vinfo[-1], 16)
+        except ValueError:
+            githash = ''
+        else:
+            githash = '.' + vinfo[-1]
+
+        # As of FreeSurfer v6.0.0, the final component is a githash
+        if githash:
+            if vinfo[3] == 'dev':
+                # This will need updating when v6.0.1 comes out
+                vstr = '6.0.0-dev' + githash
+            elif vinfo[5][0] == 'v':
+                vstr = vinfo[5][1:]
+            else:
+                raise RuntimeError('Unknown version string: ' + ver)
+        # Retain pre-6.0.0 heuristics
+        elif 'dev' in ver:
+            vstr = vinfo[-1] + '-dev'
+        else:
+            vstr = ver.rstrip().split('-v')[-1]
+
+        return LooseVersion(vstr)
+
     @classmethod
     def subjectsdir(cls):
         """Check the global SUBJECTS_DIR
@@ -154,16 +190,49 @@ def _gen_fname(self, basename, fname=None, cwd=None, suffix='_fs',
 
     @property
     def version(self):
-        ver = Info.version()
-        if ver:
-            if 'dev' in ver:
-                return ver.rstrip().split('-')[-1] + '.dev'
-            else:
-                return ver.rstrip().split('-v')[-1]
+        ver = Info.looseversion()
+        if ver > LooseVersion("0.0.0"):
+            return ver.vstring
+
+
+class FSSurfaceCommand(FSCommand):
+    """Support for FreeSurfer surface-related functions.
+    For some functions, if the output file is not specified starting with
+    'lh.' or 'rh.', FreeSurfer prepends the prefix from the input file to the
+    output filename. Output out_file must be adjusted to accommodate this.
+    By including the full path in the filename, we can also avoid this behavior.
+    """
+    def _get_filecopy_info(self):
+        self._normalize_filenames()
+        return super(FSSurfaceCommand, self)._get_filecopy_info()
+
+    def _normalize_filenames(self):
+        """Filename normalization routine to perform only when run in Node
+        context
+        """
+        pass
+
+    @staticmethod
+    def _associated_file(in_file, out_name):
+        """Based on MRIsBuildFileName in freesurfer/utils/mrisurf.c
+
+        Use in_file prefix to indicate hemisphere for out_name, rather than
+        inspecting the surface data structure.
+        Also, output to in_file's directory if path information not provided
+        for out_name.
+        """
+        path, base = os.path.split(out_name)
+        if path == '':
+            path, in_file = os.path.split(in_file)
+            hemis = ('lh.', 'rh.')
+            if in_file[:3] in hemis and base[:3] not in hemis:
+                base = in_file[:3] + base
+        return os.path.abspath(os.path.join(path, base))
 
 
 class FSScriptCommand(FSCommand):
-    """ Support for Freesurfer script commands with log inputs.terminal_output """
+    """ Support for Freesurfer script commands with log inputs.terminal_output
+    """
     _terminal_output = 'file'
     _always_run = False
 

nipype/interfaces/freesurfer/preprocess.py

@@ -36,13 +36,9 @@
 __docformat__ = 'restructuredtext'
 iflogger = logging.getLogger('interface')
 
-FSVersion = "0"
-_ver = Info.version()
-if _ver:
-    if 'dev' in _ver:
-        FSVersion = _ver.rstrip().split('-')[-1] + '.dev'
-    else:
-        FSVersion = _ver.rstrip().split('-v')[-1]
+# Keeping this to avoid breaking external programs that depend on it, but
+# this should not be used internally
+FSVersion = Info.looseversion()
 
 
 class ParseDICOMDirInputSpec(FSTraitedSpec):
@@ -724,7 +720,7 @@ class ReconAll(CommandLine):
                         'mri/brainmask.auto.mgz',
                         'mri/brainmask.mgz'], []),
         ]
-    if LooseVersion(FSVersion) < LooseVersion("6.0.0"):
+    if Info.looseversion() < LooseVersion("6.0.0"):
         _autorecon2_steps = [
             ('gcareg', ['mri/transforms/talairach.lta'], []),
             ('canorm', ['mri/norm.mgz'], []),
@@ -1072,7 +1068,7 @@ class BBRegister(FSCommand):
     """
 
     _cmd = 'bbregister'
-    if FSVersion and LooseVersion(FSVersion) < LooseVersion("6.0.0"):
+    if LooseVersion('0.0.0') < Info.looseversion() < LooseVersion("6.0.0"):
         input_spec = BBRegisterInputSpec
     else:
         input_spec = BBRegisterInputSpec6

nipype/interfaces/freesurfer/tests/test_auto_FSSurfaceCommand.py

@@ -0,0 +1,24 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..base import FSSurfaceCommand
+
+
+def test_FSSurfaceCommand_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    subjects_dir=dict(),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = FSSurfaceCommand.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+

nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py

@@ -0,0 +1,42 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..utils import MRIsCombine
+
+
+def test_MRIsCombine_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_files=dict(argstr='--combinesurfs %s',
+    mandatory=True,
+    position=1,
+    ),
+    out_file=dict(argstr='%s',
+    genfile=True,
+    mandatory=True,
+    position=-1,
+    ),
+    subjects_dir=dict(),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = MRIsCombine.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_MRIsCombine_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = MRIsCombine.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/freesurfer/tests/test_preprocess.py

@@ -7,7 +7,7 @@
 from nipype.testing.fixtures import create_files_in_directory
 
 from nipype.interfaces import freesurfer
-from nipype.interfaces.freesurfer.preprocess import FSVersion
+from nipype.interfaces.freesurfer import Info
 from nipype import LooseVersion
 
 
@@ -138,7 +138,7 @@ def test_bbregister(create_files_in_directory):
     bbr.inputs.contrast_type = 't2'
 
     # Check that 'init' is mandatory in FS < 6, but not in 6+
-    if LooseVersion(FSVersion) < LooseVersion("6.0.0"):
+    if Info.looseversion() < LooseVersion("6.0.0"):
         with pytest.raises(ValueError):
             bbr.cmdline
     else:

nipype/interfaces/freesurfer/utils.py

@@ -21,7 +21,7 @@
 from ...utils.filemanip import fname_presuffix, split_filename
 from ..base import (TraitedSpec, File, traits, OutputMultiPath, isdefined,
                     CommandLine, CommandLineInputSpec)
-from .base import (FSCommand, FSTraitedSpec,
+from .base import (FSCommand, FSTraitedSpec, FSSurfaceCommand,
                    FSScriptCommand, FSScriptOutputSpec,
                    FSTraitedSpecOpenMP, FSCommandOpenMP)
 __docformat__ = 'restructuredtext'
@@ -954,6 +954,77 @@ def _gen_outfilename(self):
         return name + ext + "_converted." + self.inputs.out_datatype
 
 
+class MRIsCombineInputSpec(FSTraitedSpec):
+    """
+    Uses Freesurfer's mris_convert to combine two surface files into one.
+    """
+    in_files = traits.List(File(Exists=True), maxlen=2, minlen=2,
+                           mandatory=True, position=1, argstr='--combinesurfs %s',
+                           desc='Two surfaces to be combined.')
+    out_file = File(argstr='%s', position=-1, genfile=True,
+                    mandatory=True,
+                    desc='Output filename. Combined surfaces from in_files.')
+
+
+class MRIsCombineOutputSpec(TraitedSpec):
+    """
+    Uses Freesurfer's mris_convert to combine two surface files into one.
+    """
+    out_file = File(exists=True, desc='Output filename. Combined surfaces from '
+                                      'in_files.')
+
+
+class MRIsCombine(FSSurfaceCommand):
+    """
+    Uses Freesurfer's mris_convert to combine two surface files into one.
+
+    For complete details, see the `mris_convert Documentation.
+    <https://surfer.nmr.mgh.harvard.edu/fswiki/mris_convert>`_
+
+    If given an out_file that does not begin with 'lh.' or 'rh.',
+    mris_convert will prepend 'lh.' to the file name.
+    To avoid this behavior, consider setting out_file = './<filename>', or
+    leaving out_file blank.
+
+    Example
+    -------
+
+    >>> import nipype.interfaces.freesurfer as fs
+    >>> mris = fs.MRIsCombine()
+    >>> mris.inputs.in_files = ['lh.pial', 'rh.pial']
+    >>> mris.inputs.out_file = 'bh.pial'
+    >>> mris.cmdline  # doctest: +ALLOW_UNICODE
+    'mris_convert --combinesurfs lh.pial rh.pial bh.pial'
+    >>> mris.run()  # doctest: +SKIP
+    """
+    _cmd = 'mris_convert'
+    input_spec = MRIsCombineInputSpec
+    output_spec = MRIsCombineOutputSpec
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        outputs['out_file'] = self._associated_file(self.inputs.in_files[0],
+                                                    self.inputs.out_file)
+        return outputs
+
+    @staticmethod
+    def _associated_file(in_file, out_name):
+        """Unlike the standard _associated_file, which uses the prefix from
+        in_file, in MRIsCombine, it uses 'lh.' as the prefix for the output
+        file no matter what the inputs are.
+        """
+        path, base = os.path.split(out_name)
+        if path == '':
+            hemis = ('lh.', 'rh.')
+            if base[:3] not in hemis:
+                base = 'lh.' + base
+        return os.path.abspath(os.path.join(path, base))
+
+    def _normalize_filenames(self):
+        if isdefined(self.inputs.out_file):
+            self.inputs.out_file = os.path.abspath(self.inputs.out_file)
+
+
 class MRITessellateInputSpec(FSTraitedSpec):
     """
     Uses Freesurfer's mri_tessellate to create surfaces by tessellating a given input volume