sty: mipav commit white space fixes and one test script

Author: satra

examples/smri_cbs_skullstripping.py

@@ -5,7 +5,7 @@
 import nipype.interfaces.fsl as fsl
 import nipype.interfaces.camino2trackvis as cam2trk
 import nipype.algorithms.misc as misc
-import os  
+import os
 from nipype.interfaces.mipav.developer import JistIntensityMp2rageMasking, MedicAlgorithmSPECTRE2010
 
 wf = pe.Workflow("skullstripping")

nipype/interfaces/base.py

@@ -994,13 +994,13 @@ def run(self, **inputs):
                         raise Exception('Error: Xvfb did not start')
                     old_displaynum = os.environ['DISPLAY']
                     runtime.environ['DISPLAY'] = ':%s' % vdisplay_num
-    
+
             runtime = self._run_interface(runtime)
-            
+
             if self._redirect_x:
                 xvfb_proc.kill()
                 xvfb_proc.wait()
-            
+
             outputs = self.aggregate_outputs(runtime)
             runtime.endTime = dt.isoformat(dt.utcnow())
             timediff = parseutc(runtime.endTime) - parseutc(runtime.startTime)

nipype/interfaces/mipav/generate_classes.py

@@ -15,7 +15,7 @@
                      'de.mpg.cbs.jist.brain.JistBrainMp2rageSkullStripping',
                      'de.mpg.cbs.jist.brain.JistBrainPartialVolumeFilter',
                      'de.mpg.cbs.jist.brain.JistBrainMp2rageDuraEstimation']
-    
+
     modules_from_chris = ['edu.jhu.ece.iacl.plugins.segmentation.skull_strip.MedicAlgorithmSPECTRE2010',
                          'edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmMipavReorient',
                          'edu.jhu.ece.iacl.plugins.utilities.math.MedicAlgorithmImageCalculator',
@@ -24,14 +24,14 @@
                          'edu.jhu.ece.iacl.plugins.utilities.volume.MedicAlgorithmThresholdToBinaryMask',
                          #'de.mpg.cbs.jist.cortex.JistCortexFullCRUISE', # waiting for http://www.nitrc.org/tracker/index.php?func=detail&aid=7236&group_id=228&atid=942 to be fixed
                          'de.mpg.cbs.jist.cortex.JistCortexSurfaceMeshInflation']
-    
+
     modules_from_julia = ['de.mpg.cbs.jist.intensity.JistIntensityMp2rageMasking',
                           'edu.jhu.ece.iacl.plugins.segmentation.skull_strip.MedicAlgorithmSPECTRE2010']
-    
+
     modules_from_leonie = ['edu.jhu.ece.iacl.plugins.classification.MedicAlgorithmLesionToads']
-    
+
     modules_from_yasinyazici = ['edu.jhu.ece.iacl.plugins.classification.MedicAlgorithmN3']
-    
+
     modules_list = list(set(modules_list).union(modules_from_chris).union(modules_from_leonie).union(modules_from_julia).union(modules_from_yasinyazici).union(modules_list))
 
     generate_all_classes(modules_list=modules_list,launcher=["java edu.jhu.ece.iacl.jist.cli.run" ], redirect_x=True, mipav_hacks=True)

nipype/interfaces/slicer/generate_classes.py

@@ -269,15 +269,15 @@ def generate_class(module, launcher, strip_module_name_prefix=True, redirect_x =
             else:  # For all other parameter types, they are implicitly only input types
                 inputTraits.append("%s = %s(%s%s)" % (name, type, parse_values(
                     values), parse_params(traitsParams)))
-                
+
     if mipav_hacks:
         blacklisted_inputs = ["maxMemoryUsage"]
         inputTraits = [trait for trait in inputTraits if trait.split()[0] not in blacklisted_inputs]
-        
+
         compulsory_inputs = ['xDefaultMem = traits.Int(desc="Set default maximum heap size", argstr="-xDefaultMem %d")',
                              'xMaxProcess = traits.Int(1, desc="Set default maximum number of processes.", argstr="-xMaxProcess %d", usedefault=True)']
         inputTraits += compulsory_inputs
-            
+
 
     input_spec_code = "class " + module_name + "InputSpec(CommandLineInputSpec):\n"
     for trait in inputTraits:
@@ -306,7 +306,7 @@ def generate_class(module, launcher, strip_module_name_prefix=True, redirect_x =
     _cmd = "%launcher% %name% "
     %output_filenames_code%\n"""
     template += "    _redirect_x = True\n"
-    
+
 
     main_class = template.replace('%class_str%', class_string).replace("%module_name%", module_name).replace("%name%", module).replace("%output_filenames_code%", output_filenames_code).replace("%launcher%", " ".join(launcher))
 
@@ -334,9 +334,9 @@ def grab_xml(module, launcher, mipav_hacks=False):
                 replace_closing_tag = False
             else:
                 new_xml += line + "\n"
-                
+
         xmlReturnValue = new_xml
-        
+
         #workaround for a JIST bug https://www.nitrc.org/tracker/index.php?func=detail&aid=7233&group_id=228&atid=942
         if xmlReturnValue.strip().endswith("XML"):
             xmlReturnValue = xmlReturnValue.strip()[:-3]

nipype/testing/data/pyscript.m

@@ -1,14 +1,6 @@
 fprintf(1,'Executing %s at %s:\n',mfilename,datestr(now));
 ver,
-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;
-        
+try,a=1;
 ,catch ME,
 fprintf(2,'MATLAB code threw an exception:\n');
 fprintf(2,'%s\n',ME.message);