Java module file name fixes.

Author: chrisgorgo

nipype/interfaces/mipav/__init__.py

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

nipype/interfaces/mipav/developer.py

@@ -6,7 +6,7 @@
 import os
 
 
-class edu.jhu.bme.smile.demo.RandomVolInputSpec(CommandLineInputSpec):
+class 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")
@@ -22,11 +22,11 @@ class edu.jhu.bme.smile.demo.RandomVolInputSpec(CommandLineInputSpec):
     outExecution = traits.Str(desc="Execution Time", argstr="--outExecution %s")
 
 
-class edu.jhu.bme.smile.demo.RandomVolOutputSpec(TraitedSpec):
+class RandomVolOutputSpec(TraitedSpec):
     outRand1 = File(desc="Rand1", exists=True)
 
 
-class edu.jhu.bme.smile.demo.RandomVol(SEMLikeCommandLine):
+class RandomVol(SEMLikeCommandLine):
     """title: Random_Volume_Generator
 
 category: 
@@ -50,7 +50,7 @@ class edu.jhu.bme.smile.demo.RandomVol(SEMLikeCommandLine):
 
 """
 
-    input_spec = edu.jhu.bme.smile.demo.RandomVolInputSpec
-    output_spec = edu.jhu.bme.smile.demo.RandomVolOutputSpec
+    input_spec = RandomVolInputSpec
+    output_spec = 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

@@ -1,5 +1,6 @@
 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

nipype/interfaces/slicer/generate_classes.py

@@ -111,7 +111,7 @@ def generate_all_classes(modules_list=[], launcher=[]):
         print("=" * 80)
         print("Generating Definition for module {0}".format(module))
         print("^" * 80)
-        package, code = generate_class(module, launcher)
+        package, code, module = generate_class(module, launcher)
         cur_package = all_code
         module_name = package.strip().split(" ")[0].split(".")[-1]
         for package in package.strip().split(" ")[0].split(".")[:-1]:
@@ -126,8 +126,12 @@ def generate_all_classes(modules_list=[], launcher=[]):
     crawl_code_struct(all_code, os.getcwd())
 
 
-def generate_class(module, launcher):
+def generate_class(module, launcher, strip_module_name_prefix=True):
     dom = grab_xml(module, launcher)
+    if strip_module_name_prefix:
+        module_name = module.split(".")[-1]
+    else:
+        module_name = module
     inputTraits = []
     outputTraits = []
     outputs_filenames = {}
@@ -264,11 +268,11 @@ def generate_class(module, launcher):
                 inputTraits.append("%s = %s(%s%s)" % (name, type, parse_values(
                     values), parse_params(traitsParams)))
 
-    input_spec_code = "class " + module + "InputSpec(CommandLineInputSpec):\n"
+    input_spec_code = "class " + module_name + "InputSpec(CommandLineInputSpec):\n"
     for trait in inputTraits:
         input_spec_code += "    " + trait + "\n"
 
-    output_spec_code = "class " + module + "OutputSpec(TraitedSpec):\n"
+    output_spec_code = "class " + module_name + "OutputSpec(TraitedSpec):\n"
     if not outputTraits:
         output_spec_code += "    pass\n"
     else:
@@ -283,17 +287,17 @@ def generate_class(module, launcher):
     input_spec_code += "\n\n"
     output_spec_code += "\n\n"
 
-    template = """class %name%(SEMLikeCommandLine):
+    template = """class %module_name%(SEMLikeCommandLine):
     %class_str%
 
-    input_spec = %name%InputSpec
-    output_spec = %name%OutputSpec
+    input_spec = %module_name%InputSpec
+    output_spec = %module_name%OutputSpec
     _cmd = "%launcher% %name% "
     %output_filenames_code%\n"""
 
-    main_class = template.replace('%class_str%', class_string).replace("%name%", module).replace("%output_filenames_code%", output_filenames_code).replace("%launcher%", " ".join(launcher))
+    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))
 
-    return category, input_spec_code + output_spec_code + main_class
+    return category, input_spec_code + output_spec_code + main_class, module_name
 
 
 def grab_xml(module, launcher):