OPEN - task 790: Add MIPAV support

http://github.com/nipy/nipype/issues/issue/790

Author: chrisgorgo

nipype/interfaces/mipav/__init__.py

@@ -0,0 +1 @@
+from developer import edu.jhu.bme.smile.demo.RandomVol

nipype/interfaces/mipav/developer.py

@@ -0,0 +1,56 @@
+# -*- coding: utf8 -*-
+"""Autogenerated file - DO NOT EDIT
+If you spot a bug, please report it on the mailing list and/or change the generator."""
+
+from nipype.interfaces.base import CommandLine, CommandLineInputSpec, SEMLikeCommandLine, TraitedSpec, File, Directory, traits, isdefined, InputMultiPath, OutputMultiPath
+import os
+
+
+class edu.jhu.bme.smile.demo.RandomVolInputSpec(CommandLineInputSpec):
+    maxMemoryUsage = traits.Int(desc="Maximum Memory Allowed (in MegaBytes). Increase or decrease this depending on java virtual machine heap size requirements.", argstr="--maxMemoryUsage %d")
+    inSize = traits.Int(desc="Size of Volume in X direction", argstr="--inSize %d")
+    inSize2 = traits.Int(desc="Size of Volume in Y direction", argstr="--inSize2 %d")
+    inSize3 = traits.Int(desc="Size of Volume in Z direction", argstr="--inSize3 %d")
+    inSize4 = traits.Int(desc="Size of Volume in t direction", argstr="--inSize4 %d")
+    inStandard = traits.Int(desc="Standard Deviation for Normal Distribution", argstr="--inStandard %d")
+    inLambda = traits.Float(desc="Lambda Value for Exponential Distribution", argstr="--inLambda %f")
+    inMaximum = traits.Int(desc="Maximum Value", argstr="--inMaximum %d")
+    inMinimum = traits.Int(desc="Minimum Value", argstr="--inMinimum %d")
+    inField = traits.Enum(""Uniform"", ""Normal"", ""Exponential"", desc="Field", argstr="--inField %s")
+    xPrefExt = traits.Enum("nrrd", desc="Output File Type", argstr="--xPrefExt %s")
+    outRand1 = traits.Either(traits.Bool, File(), hash_files=False, desc="Rand1", argstr="--outRand1 %s")
+    outExecution = traits.Str(desc="Execution Time", argstr="--outExecution %s")
+
+
+class edu.jhu.bme.smile.demo.RandomVolOutputSpec(TraitedSpec):
+    outRand1 = File(desc="Rand1", exists=True)
+
+
+class edu.jhu.bme.smile.demo.RandomVol(SEMLikeCommandLine):
+    """title: Random_Volume_Generator
+
+category: 
+Developer Tools
+
+
+description: 
+Generate a random scalar volume.
+
+
+
+version: 1.11.RC
+
+documentation-url: 
+http://www.nitrc.org/projects/jist/
+
+
+contributor: 
+
+
+
+"""
+
+    input_spec = edu.jhu.bme.smile.demo.RandomVolInputSpec
+    output_spec = edu.jhu.bme.smile.demo.RandomVolOutputSpec
+    _cmd = "java edu.jhu.ece.iacl.jist.cli.run edu.jhu.bme.smile.demo.RandomVol "
+    _outputs_filenames = {'outRand1':'outRand1.nii'}

nipype/interfaces/mipav/generate_classes.py

@@ -0,0 +1,18 @@
+from nipype.interfaces.slicer.generate_classes import generate_all_classes
+
+if __name__ == "__main__":
+    ## NOTE:  For now either the launcher needs to be found on the default path, or
+    ##        every tool in the modules list must be found on the default path
+    ##        AND calling the module with --xml must be supported and compliant.
+    modules_list = ['edu.jhu.bme.smile.demo.RandomVol']
+
+    ## SlicerExecutionModel compliant tools that are usually statically built, and don't need the Slicer3 --launcher
+    generate_all_classes(modules_list=modules_list,launcher=["java edu.jhu.ece.iacl.jist.cli.run" ])
+    ## Tools compliant with SlicerExecutionModel called from the Slicer environment (for shared lib compatibility)
+    #launcher = ['/home/raid3/gorgolewski/software/slicer/Slicer', '--launch']
+    #generate_all_classes(modules_list=modules_list, launcher=launcher)
+    #generate_all_classes(modules_list=['BRAINSABC'], launcher=[] )])
+    ## Tools compliant with SlicerExecutionModel called from the Slicer environment (for shared lib compatibility)
+    #launcher = ['/home/raid3/gorgolewski/software/slicer/Slicer', '--launch']
+    #generate_all_classes(modules_list=modules_list, launcher=launcher)
+    #generate_all_classes(modules_list=['BRAINSABC'], launcher=[] )

nipype/interfaces/slicer/generate_classes.py

@@ -304,6 +304,9 @@ def grab_xml(module, launcher):
     final_command = " ".join(command_list)
     xmlReturnValue = subprocess.Popen(
         final_command, stdout=subprocess.PIPE, shell=True).communicate()[0]
+    #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]
     return xml.dom.minidom.parseString(xmlReturnValue)
 #        if ret.runtime.returncode == 0:
 #            return xml.dom.minidom.parseString(ret.runtime.stdout)