Add nipype_crash_search script

CHANGES

@@ -1,6 +1,7 @@
 Next release
 ============
 
+* ENH: Add nipype_crash_search command (https://github.com/nipy/nipype/pull/1422)
 * ENH: Created interface for BrainSuite Cortical Surface Extraction command line tools (https://github.com/nipy/nipype/pull/1305)
 * FIX: job execution on systems/approaches where locale is undefined (https://github.com/nipy/nipype/pull/1401)
 * FIX: Clean up byte/unicode issues using subprocess (https://github.com/nipy/nipype/pull/1394)
@@ -28,6 +29,7 @@ Next release
 * FIX: Correct linking/copying fallback behavior (https://github.com/nipy/nipype/pull/1391)
 * ENH: Nipype workflow and interfaces for FreeSurfer's recon-all (https://github.com/nipy/nipype/pull/1326)
 * FIX: Permit relative path for concatenated_file input to Concatenate() (https://github.com/nipy/nipype/pull/1411)
+* ENH: Makes ReconAll workflow backwards compatible with FreeSurfer 5.3.0 (https://github.com/nipy/nipype/pull/1434)
 
 Release 0.11.0 (September 15, 2015)
 ============

bin/nipype_crash_search.py

@@ -0,0 +1,76 @@
+#!/usr/bin/env python
+"""Search for tracebacks inside a folder of nipype crash
+log files that match a given regular expression.
+
+Examples:
+nipype_crash_search -d nipype/wd/log -r '.*subject123.*'
+"""
+import re
+import os.path as op
+from glob import glob
+
+from traits.trait_errors import TraitError
+from nipype.utils.filemanip import loadcrash
+
+
+def load_pklz_traceback(crash_filepath):
+    """ Return the traceback message in the given crash file."""
+    try:
+        data = loadcrash(crash_filepath)
+    except TraitError as te:
+        return str(te)
+    except:
+        raise
+    else:
+        return '\n'.join(data['traceback'])
+
+
+def iter_tracebacks(logdir):
+    """ Return an iterator over each file path and
+    traceback field inside `logdir`.
+    Parameters
+    ----------
+    logdir: str
+        Path to the log folder.
+
+    field: str
+        Field name to be read from the crash file.
+
+    Yields
+    ------
+    path_file: str
+
+    traceback: str
+    """
+    crash_files = sorted(glob(op.join(logdir, '*.pkl*')))
+
+    for cf in crash_files:
+        yield cf, load_pklz_traceback(cf)
+
+
+def display_crash_search(logdir, regex):
+    rex = re.compile(regex, re.IGNORECASE)
+    for file, trace in iter_tracebacks(logdir):
+        if rex.search(trace):
+            print("-" * len(file))
+            print(file)
+            print("-" * len(file))
+            print(trace)
+
+
+if __name__ == "__main__":
+    from argparse import ArgumentParser, RawTextHelpFormatter
+    defstr = ' (default %(default)s)'
+    parser = ArgumentParser(prog='nipype_crash_search',
+                            description=__doc__,
+                            formatter_class=RawTextHelpFormatter)
+    parser.add_argument('-l','--logdir', type=str, dest='logdir',
+                        action="store", default=None,
+                        help='The working directory log file.' + defstr)
+    parser.add_argument('-r', '--regex', dest='regex',
+                        default='*',
+                        help='Regular expression to be searched in each traceback.' + defstr)
+
+    args = parser.parse_args()
+
+    display_crash_search(args.logdir, args.regex)

doc/_templates/layout.html

@@ -14,6 +14,12 @@
   ga('create', 'UA-339450-7', 'nipy.org/nipype');
   ga('send', 'pageview');
 </script>
+<script>
+  ((window.gitter = {}).chat = {}).options = {
+    room: 'nipy/nipype'
+  };
+</script>
+<script src="https://sidecar.gitter.im/dist/sidecar.v1.js" async defer></script>
 {% endblock %}
 
 {% block header %}

doc/users/debug.rst

@@ -42,6 +42,9 @@ performance issues.
 #. All Nipype crashfiles can be inspected with the `nipype_display_crash`
    utility.
 
+#. The `nipype_crash_search` command allows you to search for regular expressions
+in the tracebacks of the Nipype crashfiles within a log folder.
+
 #. Nipype determines the hash of the input state of a node. If any input
    contains strings that represent files on the system path, the hash evaluation
    mechanism will determine the timestamp or content hash of each of those

nipype/interfaces/freesurfer/model.py

@@ -752,8 +752,9 @@ def _list_outputs(self):
 
     def _format_arg(self, name, spec, value):
         if name in ('summary_file', 'avgwf_txt_file'):
-            if not os.path.isabs(value):
-                value = os.path.join('.', value)
+            if not isinstance(value, bool):
+                if not os.path.isabs(value):
+                    value = os.path.join('.', value)
         if name in ['avgwf_txt_file', 'avgwf_file', 'sf_avg_file']:
             if isinstance(value, bool):
                 fname = self._list_outputs()[name]
@@ -779,7 +780,7 @@ class SegStatsReconAllInputSpec(SegStatsInputSpec):
     # implicit
     ribbon = traits.File(mandatory=True, exists=True,
                          desc="Input file mri/ribbon.mgz")
-    presurf_seg = File(mandatory=True, exists=True,
+    presurf_seg = File(exists=True,
                        desc="Input segmentation volume")
     transform = File(mandatory=True, exists=True,
                      desc="Input transform file")
@@ -795,6 +796,8 @@ class SegStatsReconAllInputSpec(SegStatsInputSpec):
                    desc="Input file must be <subject_id>/surf/lh.pial")
     rh_pial = File(mandatory=True, exists=True,
                    desc="Input file must be <subject_id>/surf/rh.pial")
+    aseg = File(exists=True,
+                desc="Mandatory implicit input in 5.3")
     copy_inputs = traits.Bool(desc="If running as a node, set this to True " +
                               "otherwise, this will copy the implicit inputs " +
                               "to the node directory.")
@@ -858,7 +861,7 @@ def run(self, **inputs):
             copy2subjdir(self, self.inputs.lh_white,
                          'surf', 'lh.white')
             copy2subjdir(self, self.inputs.rh_white,
-                         'Surf', 'Rh.White')
+                         'surf', 'rh.white')
             copy2subjdir(self, self.inputs.lh_pial,
                          'surf', 'lh.pial')
             copy2subjdir(self, self.inputs.rh_pial,
@@ -867,12 +870,13 @@ def run(self, **inputs):
                          'mri', 'ribbon.mgz')
             copy2subjdir(self, self.inputs.presurf_seg,
                          'mri', 'aseg.presurf.mgz')
+            copy2subjdir(self, self.inputs.aseg,
+                         'mri', 'aseg.mgz')
             copy2subjdir(self, self.inputs.transform,
                          os.path.join('mri', 'transforms'),
                          'talairach.xfm')
             copy2subjdir(self, self.inputs.in_intensity, 'mri')
-            if isdefined(self.inputs.brainmask_file):
-                copy2subjdir(self, self.inputs.brainmask_file, 'mri')
+            copy2subjdir(self, self.inputs.brainmask_file, 'mri')
         return super(SegStatsReconAll, self).run(**inputs)
 
 

nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py

@@ -19,6 +19,7 @@ def test_Aparc2Aseg_inputs():
     environ=dict(nohash=True,
     usedefault=True,
     ),
+    filled=dict(),
     hypo_wm=dict(argstr='--hypo-as-wm',
     mandatory=False,
     ),

nipype/interfaces/freesurfer/tests/test_auto_Curvature.py

@@ -19,6 +19,7 @@ def test_Curvature_inputs():
     usedefault=True,
     ),
     in_file=dict(argstr='%s',
+    copyfile=True,
     mandatory=True,
     position=-2,
     ),

nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py

@@ -35,6 +35,7 @@ def test_MakeSurfaces_inputs():
     in_orig=dict(argstr='-orig %s',
     mandatory=True,
     ),
+    in_white=dict(),
     in_wm=dict(mandatory=True,
     ),
     longitudinal=dict(argstr='-long',
@@ -66,6 +67,8 @@ def test_MakeSurfaces_inputs():
     subjects_dir=dict(),
     terminal_output=dict(nohash=True,
     ),
+    white=dict(argstr='-white %s',
+    ),
     white_only=dict(argstr='-whiteonly',
     mandatory=False,
     ),

nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py

@@ -10,6 +10,7 @@ def test_SegStatsReconAll_inputs():
     ),
     args=dict(argstr='%s',
     ),
+    aseg=dict(),
     avgwf_file=dict(argstr='--avgwfvol %s',
     ),
     avgwf_txt_file=dict(argstr='--avgwf %s',
@@ -85,8 +86,7 @@ def test_SegStatsReconAll_inputs():
     ),
     partial_volume_file=dict(argstr='--pv %s',
     ),
-    presurf_seg=dict(mandatory=True,
-    ),
+    presurf_seg=dict(),
     rh_orig_nofix=dict(mandatory=True,
     ),
     rh_pial=dict(mandatory=True,

nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py

@@ -6,6 +6,8 @@
 def test_VolumeMask_inputs():
     input_map = dict(args=dict(argstr='%s',
     ),
+    aseg=dict(xor=['in_aseg'],
+    ),
     copy_inputs=dict(mandatory=False,
     ),
     environ=dict(nohash=True,
@@ -16,6 +18,7 @@ def test_VolumeMask_inputs():
     ),
     in_aseg=dict(argstr='--aseg_name %s',
     mandatory=False,
+    xor=['aseg'],
     ),
     left_ribbonlabel=dict(argstr='--label_left_ribbon %d',
     mandatory=True,