DOC Updated doc/devel/matlab_interface_devel.rst: remove invalid caracters in example, PEP8-ize examples, language.

Author: Mathieu Dubois

doc/devel/matlab_interface_devel.rst

@@ -4,127 +4,29 @@
 How to wrap a MATLAB script
 ===========================
 
-This is minimal script for wrapping MATLAB code. You should replace the MATLAB
-code template, and define approriate inputs and outputs.
-
 
 Example 1
 +++++++++
 
-.. testcode::
-
-	from nipype.interfaces.matlab import MatlabCommand
-	from nipype.interfaces.base import TraitedSpec, BaseInterface, BaseInterfaceInputSpec, File
-	import os
-	from string import Template
-
-	class ConmapTxt2MatInputSpec(BaseInterfaceInputSpec):
-	    in_file = File(exists=True, mandatory=True)
-	    out_file = File('cmatrix.mat', usedefault=True)
-
-	class ConmapTxt2MatOutputSpec(TraitedSpec):
-	    out_file = File(exists=True)
-
-	class ConmapTxt2Mat(BaseInterface):
-	    input_spec = ConmapTxt2MatInputSpec
-	    output_spec = ConmapTxt2MatOutputSpec
-
-	    def _run_interface(self, runtime):
-	        d = dict(in_file=self.inputs.in_file,
-	        out_file=self.inputs.out_file)
-	        #this is your MATLAB code template
-	        script = Template("""in_file = ‘$in_file';
-	out_file = ‘$out_file';
-	ConmapTxt2Mat(in_file, out_file);
-	exit;
-	""").substitute(d)
-
-	        # mfile = True  will create an .m file with your script and executed.
-		# Alternatively
-	        # mfile can be set to False which will cause the matlab code to be
-		# passed
-	        # as a commandline argument to the matlab executable
-		# (without creating any files).
-	        # This, however, is less reliable and harder to debug
-		# (code will be reduced to
-	        # a single line and stripped of any comments).
+This is a minimal script for wrapping MATLAB code. You should replace the MATLAB
+code template, and define approriate inputs and outputs.
 
-	        mlab = MatlabCommand(script=script, mfile=True)
-		result = mlab.run()
-	        return result.runtime
+.. literalinclude:: matlab_example1.py
 
-	    def _list_outputs(self):
-	        outputs = self._outputs().get()
-	        outputs['out_file'] = os.path.abspath(self.inputs.out_file)
-	        return outputs
+.. admonition:: Example source code
 
+  You can download :download:`the source code of this example <matlab_example1.py>`.
 
 Example 2
 +++++++++
 
-By subclassing **MatlabCommand** for your main class, and **MatlabInputSpec** for your input and output spec, you gain access to some useful MATLAB hooks
-
-.. testcode::
-
-	import os
-        from nipype.interfaces.base import File, traits
-        from nipype.interfaces.matlab import MatlabCommand, MatlabInputSpec
-
-
-        class HelloWorldInputSpec( MatlabInputSpec):
-            name = traits.Str( mandatory = True,
-                               desc = 'Name of person to say hello to')
-
-    	class HelloWorldOutputSpec( MatlabInputSpec):
-            matlab_output = traits.Str( )
-
-        class HelloWorld( MatlabCommand):
-            """ Basic Hello World that displays Hello <name> in MATLAB
-
-            Returns
-            -------
-
-            matlab_output : capture of matlab output which may be
-                            parsed by user to get computation results
-
-	    Examples
-	    --------
-
-            >>> hello = HelloWorld()
-            >>> hello.inputs.name = 'hello_world'
-            >>> out = hello.run()
-            >>> print out.outputs.matlab_output
-            """
-            input_spec = HelloWorldInputSpec
-            output_spec = HelloWorldOutputSpec
-
-	    def _my_script(self):
-        	"""This is where you implement your script"""
-        	script = """
-        	disp('Hello %s Python')
-        	two = 1 + 1
-        	"""%(self.inputs.name)
-        	return script
-
-
-    	    def run(self, **inputs):
-        	## inject your script
-        	self.inputs.script =  self._my_script()
-        	results = super(MatlabCommand, self).run( **inputs)
-        	stdout = results.runtime.stdout
-        	# attach stdout to outputs to access matlab results
-        	results.outputs.matlab_output = stdout
-        	return results
-
-
-            def _list_outputs(self):
-                outputs = self._outputs().get()
-                return outputs
-
-
-
+By subclassing :class:`nipype.interfaces.matlab.MatlabCommand` for your main class, and :class:`nipype.interfaces.matlab.MatlabInputSpec` for your input spec, you gain access to some useful MATLAB hooks
 
+.. literalinclude:: matlab_example2.py
 
+.. admonition:: Example source code
 
+  You can download :download:`the source code of this example <matlab_example2.py>`.
 
+.. include:: ../links_names.txt