Merge pull request #1205 from chrisfilo/fix/spm

reduce number of SPM calls

Author: chrisgorgo

nipype/interfaces/base.py

@@ -925,34 +925,36 @@ def _check_version_requirements(self, trait_object, raise_exception=True):
         """ Raises an exception on version mismatch
         """
         unavailable_traits = []
-        version = LooseVersion(str(self.version))
-        if not version:
-            return
         # check minimum version
         check = dict(min_ver=lambda t: t is not None)
         names = trait_object.trait_names(**check)
-        for name in names:
-            min_ver = LooseVersion(str(trait_object.traits()[name].min_ver))
-            if min_ver > version:
-                unavailable_traits.append(name)
-                if not isdefined(getattr(trait_object, name)):
-                    continue
-                if raise_exception:
-                    raise Exception('Trait %s (%s) (version %s < required %s)' %
-                                    (name, self.__class__.__name__,
-                                     version, min_ver))
-        check = dict(max_ver=lambda t: t is not None)
-        names = trait_object.trait_names(**check)
-        for name in names:
-            max_ver = LooseVersion(str(trait_object.traits()[name].max_ver))
-            if max_ver < version:
-                unavailable_traits.append(name)
-                if not isdefined(getattr(trait_object, name)):
-                    continue
-                if raise_exception:
-                    raise Exception('Trait %s (%s) (version %s > required %s)' %
-                                    (name, self.__class__.__name__,
-                                     version, max_ver))
+        
+        if names:
+            version = LooseVersion(str(self.version))
+            if not version:
+                return
+            for name in names:
+                min_ver = LooseVersion(str(trait_object.traits()[name].min_ver))
+                if min_ver > version:
+                    unavailable_traits.append(name)
+                    if not isdefined(getattr(trait_object, name)):
+                        continue
+                    if raise_exception:
+                        raise Exception('Trait %s (%s) (version %s < required %s)' %
+                                        (name, self.__class__.__name__,
+                                         version, min_ver))
+            check = dict(max_ver=lambda t: t is not None)
+            names = trait_object.trait_names(**check)
+            for name in names:
+                max_ver = LooseVersion(str(trait_object.traits()[name].max_ver))
+                if max_ver < version:
+                    unavailable_traits.append(name)
+                    if not isdefined(getattr(trait_object, name)):
+                        continue
+                    if raise_exception:
+                        raise Exception('Trait %s (%s) (version %s > required %s)' %
+                                        (name, self.__class__.__name__,
+                                         version, max_ver))
         return unavailable_traits
 
     def _run_wrapper(self, runtime):

nipype/interfaces/spm/preprocess.py

@@ -763,16 +763,19 @@ class Segment(SPMCommand):
 
     """
 
-    _local_version = SPMCommand().version
-    if _local_version and '12.' in _local_version:
-        _jobtype = 'tools'
-        _jobname = 'oldseg'
-    else:
-        _jobtype = 'spatial'
-        _jobname = 'preproc'
-
     input_spec = SegmentInputSpec
     output_spec = SegmentOutputSpec
+    
+    def __init__(self, **inputs):
+        _local_version = SPMCommand().version
+        if _local_version and '12.' in _local_version:
+            self._jobtype = 'tools'
+            self._jobname = 'oldseg'
+        else:
+            self._jobtype = 'spatial'
+            self._jobname = 'preproc'
+        
+        SPMCommand.__init__(self, **inputs)
 
     def _format_arg(self, opt, spec, val):
         """Convert input to appropriate format for spm
@@ -891,13 +894,17 @@ class NewSegment(SPMCommand):
 
     input_spec = NewSegmentInputSpec
     output_spec = NewSegmentOutputSpec
-    _local_version = SPMCommand().version
-    if _local_version and '12.' in _local_version:
-        _jobtype = 'spatial'
-        _jobname = 'preproc'
-    else:
-        _jobtype = 'tools'
-        _jobname = 'preproc8'
+        
+    def __init__(self, **inputs):
+        _local_version = SPMCommand().version
+        if _local_version and '12.' in _local_version:
+            self._jobtype = 'spatial'
+            self._jobname = 'preproc'
+        else:
+            self._jobtype = 'tools'
+            self._jobname = 'preproc8'
+        
+        SPMCommand.__init__(self, **inputs)
 
     def _format_arg(self, opt, spec, val):
         """Convert input to appropriate format for spm

nipype/interfaces/spm/tests/test_preprocess.py

@@ -106,20 +106,20 @@ def test_normalize12_list_outputs():
 @skipif(no_spm)
 def test_segment():
     if spm.Info.version()['name'] == "SPM12":
-        yield assert_equal, spm.Segment._jobtype, 'tools'
-        yield assert_equal, spm.Segment._jobname, 'oldseg'
+        yield assert_equal, spm.Segment()._jobtype, 'tools'
+        yield assert_equal, spm.Segment()._jobname, 'oldseg'
     else:
-        yield assert_equal, spm.Segment._jobtype, 'spatial'
-        yield assert_equal, spm.Segment._jobname, 'preproc'
+        yield assert_equal, spm.Segment()._jobtype, 'spatial'
+        yield assert_equal, spm.Segment()._jobname, 'preproc'
 
 @skipif(no_spm)
 def test_newsegment():
     if spm.Info.version()['name'] == "SPM12":
-        yield assert_equal, spm.NewSegment._jobtype, 'spatial'
-        yield assert_equal, spm.NewSegment._jobname, 'preproc'
+        yield assert_equal, spm.NewSegment()._jobtype, 'spatial'
+        yield assert_equal, spm.NewSegment()._jobname, 'preproc'
     else:
-        yield assert_equal, spm.NewSegment._jobtype, 'tools'
-        yield assert_equal, spm.NewSegment._jobname, 'preproc8'
+        yield assert_equal, spm.NewSegment()._jobtype, 'tools'
+        yield assert_equal, spm.NewSegment()._jobname, 'preproc8'
 
 
 def test_smooth():

nipype/testing/data/pyscript.m

@@ -1,6 +1,14 @@
 fprintf(1,'Executing %s at %s:\n',mfilename,datestr(now));
 ver,
-try,a=1;
+try,
+if isempty(which('spm')),
+throw(MException('SPMCheck:NotFound','SPM not in matlab path'));
+end;
+spm_path = spm('dir');
+[name, version] = spm('ver');
+fprintf(1, 'NIPYPE path:%s|name:%s|release:%s', spm_path, name, version);
+exit;
+        
 ,catch ME,
 fprintf(2,'MATLAB code threw an exception:\n');
 fprintf(2,'%s\n',ME.message);