Fix tutorials (continuation of #1036)

doc/devel/cmd_interface_devel.rst

@@ -80,7 +80,7 @@ symbols. For an input defined in InputSpec to be included into the executed
 commandline ``argstr`` has to be included. Additionally inside the main
 interface class you need to specify the name of the executable by assigning it
 to the ``_cmd`` field. Also the main interface class needs to inherit from
-:class:`nipype.interfaces.base.CommandLine`:
+:class:`CommandLine <nipype.interfaces.base.core.CommandLine>`:
 
 .. testcode::
 

doc/devel/matlab_example1.py

@@ -0,0 +1,47 @@
+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).
+        mlab = MatlabCommand(script=script, mfile=True)
+        result = mlab.run()
+        return result.runtime
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        outputs['out_file'] = os.path.abspath(self.inputs.out_file)
+        return outputs

doc/devel/matlab_example2.py

@@ -0,0 +1,54 @@
+from nipype.interfaces.base import traits
+from nipype.interfaces.base import TraitedSpec
+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(TraitedSpec):
+    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

doc/devel/matlab_interface_devel.rst

@@ -4,127 +4,30 @@
 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 and
+output 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

doc/index.rst

@@ -2,6 +2,7 @@
 
  * -  .. image:: images/nipype_architecture_overview2.png
          :width: 100 %
+
    -  .. container::
 
         Current neuroimaging software offer users an incredible opportunity to

doc/users/function_interface.rst

@@ -146,6 +146,6 @@ the string would be
 Unlike when using a function object, this input can be set like any other,
 meaning that you could write a function that outputs different function
 strings depending on some run-time contingencies, and connect that output
-the the ``function_str`` input of a downstream Function interface.
+the ``function_str`` input of a downstream Function interface.
 
 .. include:: ../links_names.txt