Added human order sorting for FLAMEO outputs, fixed abspath for Cluster

outputs.

Author: chrisgorgo

nipype/interfaces/fsl/model.py

@@ -26,6 +26,7 @@
 from nipype.utils.filemanip import (
     list_to_filename, filename_to_list, fname_presuffix)
 from nibabel import load
+from nipype.utils.misc import human_order_sorted
 
 warn = warnings.warn
 warnings.filterwarnings('always', category=UserWarning)
@@ -734,51 +735,51 @@ def _list_outputs(self):
         outputs = self._outputs().get()
         pth = os.path.join(os.getcwd(), self.inputs.log_dir)
 
-        pes = glob(os.path.join(pth, 'pe[0-9]*.*'))
+        pes = human_order_sorted(glob(os.path.join(pth, 'pe[0-9]*.*')))
         assert len(pes) >= 1, 'No pe volumes generated by FSL Estimate'
         outputs['pes'] = pes
 
-        res4d = glob(os.path.join(pth, 'res4d.*'))
+        res4d = human_order_sorted(glob(os.path.join(pth, 'res4d.*')))
         assert len(res4d) == 1, 'No residual volume generated by FSL Estimate'
         outputs['res4d'] = res4d[0]
 
-        copes = glob(os.path.join(pth, 'cope[0-9]*.*'))
+        copes = human_order_sorted(glob(os.path.join(pth, 'cope[0-9]*.*')))
         assert len(copes) >= 1, 'No cope volumes generated by FSL CEstimate'
         outputs['copes'] = copes
 
-        var_copes = glob(os.path.join(pth, 'varcope[0-9]*.*'))
+        var_copes = human_order_sorted(glob(os.path.join(pth, 'varcope[0-9]*.*')))
         assert len(
             var_copes) >= 1, 'No varcope volumes generated by FSL CEstimate'
         outputs['var_copes'] = var_copes
 
-        zstats = glob(os.path.join(pth, 'zstat[0-9]*.*'))
+        zstats = human_order_sorted(glob(os.path.join(pth, 'zstat[0-9]*.*')))
         assert len(zstats) >= 1, 'No zstat volumes generated by FSL CEstimate'
         outputs['zstats'] = zstats
 
 
         if isdefined(self.inputs.f_con_file):
-            zfstats = glob(os.path.join(pth, 'zfstat[0-9]*.*'))
+            zfstats = human_order_sorted(glob(os.path.join(pth, 'zfstat[0-9]*.*')))
             assert len(zfstats) >= 1, 'No zfstat volumes generated by FSL CEstimate'
             outputs['zfstats'] = zfstats          
 
-            fstats = glob(os.path.join(pth, 'fstat[0-9]*.*'))          
+            fstats = human_order_sorted(glob(os.path.join(pth, 'fstat[0-9]*.*')))          
             assert len(fstats) >= 1, 'No fstat volumes generated by FSL CEstimate'
             outputs['fstats'] = fstats
 
-        tstats = glob(os.path.join(pth, 'tstat[0-9]*.*'))
+        tstats = human_order_sorted(glob(os.path.join(pth, 'tstat[0-9]*.*')))
         assert len(tstats) >= 1, 'No tstat volumes generated by FSL CEstimate'
         outputs['tstats'] = tstats
 
-        mrefs = glob(os.path.join(pth, 'mean_random_effects_var[0-9]*.*'))
+        mrefs = human_order_sorted(glob(os.path.join(pth, 'mean_random_effects_var[0-9]*.*')))
         assert len(
             mrefs) >= 1, 'No mean random effects volumes generated by FLAMEO'
         outputs['mrefvars'] = mrefs
 
-        tdof = glob(os.path.join(pth, 'tdof_t[0-9]*.*'))
+        tdof = human_order_sorted(glob(os.path.join(pth, 'tdof_t[0-9]*.*')))
         assert len(tdof) >= 1, 'No T dof volumes generated by FLAMEO'
         outputs['tdof'] = tdof
 
-        weights = glob(os.path.join(pth, 'weights[0-9]*.*'))
+        weights = human_order_sorted(glob(os.path.join(pth, 'weights[0-9]*.*')))
         assert len(weights) >= 1, 'No weight volumes generated by FLAMEO'
         outputs['weights'] = weights
 
@@ -1486,7 +1487,7 @@ def _list_outputs(self):
                                                           suffix='_' + suffix,
                                                           change_ext=change_ext)
                 else:
-                    outputs[outkey] = os.pardir.abspath(inval)
+                    outputs[outkey] = os.path.abspath(inval)
         return outputs
 
     def _format_arg(self, name, spec, value):

nipype/utils/misc.py

@@ -9,6 +9,17 @@
 import numpy as np
 from textwrap import dedent
 import sys
+import re
+
+def human_order_sorted(l):
+    """Sorts string in human order (i.e. 'stat10' will go after 'stat2')"""
+    def atoi(text):
+        return int(text) if text.isdigit() else text
+
+    def natural_keys(text):
+        return [ atoi(c) for c in re.split('(\d+)', text) ]
+
+    return sorted(l, key=natural_keys)
 
 def trim(docstring, marker=None):
     if not docstring: