Merge remote-tracking branch 'nipy/master'

Author: tsalo

nipype/interfaces/afni/tests/test_auto_Autobox.py

@@ -20,6 +20,7 @@ def test_Autobox_inputs():
     ),
     out_file=dict(argstr='-prefix %s',
     name_source='in_file',
+    name_template='%s_autobox',
     ),
     outputtype=dict(),
     padding=dict(argstr='-npad %d',

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

@@ -216,18 +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

@@ -38,7 +38,7 @@
 
 # Keeping this to avoid breaking external programs that depend on it, but
 # this should not be used internally
-FSVersion = Info.looseversion()
+FSVersion = Info.looseversion().vstring
 
 
 class ParseDICOMDirInputSpec(FSTraitedSpec):

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

@@ -151,6 +151,9 @@ def test_ReconAll_outputs():
     ),
     filled=dict(loc='mri',
     ),
+    graymid=dict(altkey=['graymid', 'midthickness'],
+    loc='surf',
+    ),
     inflated=dict(loc='surf',
     ),
     jacobian_white=dict(loc='surf',

nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py

@@ -1,6 +1,7 @@
 # -*- 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
@@ -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)