Merge branch 'master' of git://github.com/nipy/nipype into fix/realign

Author: mgxd

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/ants/tests/test_auto_Registration.py

@@ -104,6 +104,8 @@ def test_Registration_inputs():
     use_estimate_learning_rate_once=dict(),
     use_histogram_matching=dict(usedefault=True,
     ),
+    verbose=dict(argstr='-v',
+    ),
     winsorize_lower_quantile=dict(argstr='%s',
     usedefault=True,
     ),

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
@@ -154,12 +190,9 @@ 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):
@@ -183,18 +216,19 @@ def _normalize_filenames(self):
     def _associated_file(in_file, out_name):
         """Based on MRIsBuildFileName in freesurfer/utils/mrisurf.c
 
+        If no path information is provided for out_name, use path and
+        hemisphere (if also unspecified) from in_file to determine the path
+        of the associated file.
         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))
+        return os.path.join(path, base)
 
 
 class FSScriptCommand(FSCommand):

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().vstring
 
 
 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_FSSurfaceCommand.py

@@ -0,0 +1,50 @@
+# AUTO-GENERATED by tools/checkspecs.py on 2017.04.21
+# Modified 2017.04.21 by Chris Markiewicz
+from __future__ import unicode_literals
+import pytest
+
+from ..base import FSSurfaceCommand
+from ... import freesurfer as fs
+from ...io import FreeSurferSource
+
+
+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
+
+
+@pytest.mark.skipif(fs.no_freesurfer(), reason="freesurfer is not installed")
+def test_associated_file():
+    fssrc = FreeSurferSource(subjects_dir=fs.Info.subjectsdir(),
+                             subject_id='fsaverage', hemi='lh')
+
+    fsavginfo = fssrc.run().outputs.get()
+
+    # Pairs of white/pial files in the same directories
+    for white, pial in [('lh.white', 'lh.pial'),
+                        ('./lh.white', './lh.pial'),
+                        (fsavginfo['white'], fsavginfo['pial'])]:
+
+        # Unspecified paths, possibly with missing hemisphere information,
+        # are equivalent to using the same directory and hemisphere
+        for name in ('pial', 'lh.pial', pial):
+            assert FSSurfaceCommand._associated_file(white, name) == pial
+
+        # With path information, no changes are made
+        for name in ('./pial', './lh.pial', fsavginfo['pial']):
+            assert FSSurfaceCommand._associated_file(white, name) == name

nipype/interfaces/freesurfer/tests/test_auto_FSSurfaceCommand.py

@@ -23,8 +23,6 @@ def test_MRIsExpand_inputs():
     mandatory=True,
     position=-3,
     ),
-    navgs=dict(argstr='-navgs %d %d',
-    ),
     nsurfaces=dict(argstr='-N %d',
     ),
     out_name=dict(argstr='%s',

nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py

@@ -1,13 +1,14 @@
 # -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
+from builtins import str
 import os
 
 import pytest
 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 +139,7 @@ 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:
@@ -154,3 +155,9 @@ def test_bbregister(create_files_in_directory):
                            '--reg {base}_bbreg_fsaverage.dat '
                            '--mov {full} --s fsaverage'.format(
                             full=filelist[0], base=base))
+
+def test_FSVersion():
+    """Check that FSVersion is a string that can be compared with LooseVersion
+    """
+    assert isinstance(freesurfer.preprocess.FSVersion, str)
+    assert LooseVersion(freesurfer.preprocess.FSVersion) >= LooseVersion("0")

nipype/interfaces/freesurfer/tests/test_preprocess.py

@@ -8,8 +8,10 @@
 from nipype.testing.fixtures import (create_files_in_directory_plus_dummy_file,
                                      create_surf_file_in_directory)
 
+from nipype.pipeline import engine as pe
+from nipype.interfaces import freesurfer as fs
 from nipype.interfaces.base import TraitError
-import nipype.interfaces.freesurfer as fs
+from nipype.interfaces.io import FreeSurferSource
 
 
 @pytest.mark.skipif(fs.no_freesurfer(), reason="freesurfer is not installed")
@@ -159,3 +161,52 @@ def test_surfshots(create_files_in_directory_plus_dummy_file):
         os.environ["DISPLAY"] = hold_display
     except KeyError:
         pass
+
+
+@pytest.mark.skipif(fs.no_freesurfer(), reason="freesurfer is not installed")
+def test_mrisexpand(tmpdir):
+    fssrc = FreeSurferSource(subjects_dir=fs.Info.subjectsdir(),
+                             subject_id='fsaverage', hemi='lh')
+
+    fsavginfo = fssrc.run().outputs.get()
+
+    # dt=60 to ensure very short runtime
+    expand_if = fs.MRIsExpand(in_file=fsavginfo['smoothwm'],
+                              out_name='expandtmp',
+                              distance=1,
+                              dt=60)
+
+    expand_nd = pe.Node(
+        fs.MRIsExpand(in_file=fsavginfo['smoothwm'],
+                      out_name='expandtmp',
+                      distance=1,
+                      dt=60),
+        name='expand_node')
+
+    # Interfaces should have same command line at instantiation
+    orig_cmdline = 'mris_expand -T 60 {} 1 expandtmp'.format(fsavginfo['smoothwm'])
+    assert expand_if.cmdline == orig_cmdline
+    assert expand_nd.interface.cmdline == orig_cmdline
+
+    # Run both interfaces
+    if_res = expand_if.run()
+    nd_res = expand_nd.run()
+
+    # Commandlines differ
+    node_cmdline = 'mris_expand -T 60 -pial {cwd}/lh.pial {cwd}/lh.smoothwm ' \
+        '1 expandtmp'.format(cwd=nd_res.runtime.cwd)
+    assert if_res.runtime.cmdline == orig_cmdline
+    assert nd_res.runtime.cmdline == node_cmdline
+
+    # Check output
+    if_out_file = if_res.outputs.get()['out_file']
+    nd_out_file = nd_res.outputs.get()['out_file']
+    # Same filename
+    assert op.basename(if_out_file) == op.basename(nd_out_file)
+    # Interface places output in source directory
+    assert op.dirname(if_out_file) == op.dirname(fsavginfo['smoothwm'])
+    # Node places output in working directory
+    assert op.dirname(nd_out_file) == nd_res.runtime.cwd
+
+    # Remove test surface
+    os.unlink(if_out_file)