diff --git a/Code/Mantid/MantidPlot/CMakeLists.txt b/Code/Mantid/MantidPlot/CMakeLists.txt
index 8195878f55aa36f349321ff13d4f98e076e86ed0..579a47f0ddb063e1c48c8f968d7842f4452b4b29 100644
--- a/Code/Mantid/MantidPlot/CMakeLists.txt
+++ b/Code/Mantid/MantidPlot/CMakeLists.txt
@@ -810,6 +810,11 @@ add_custom_command ( TARGET MantidPlot POST_BUILD
                        ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/${CMAKE_CFG_INTDIR}/ipython_plugin
 )
 
+###########################################################################
+# Documentation targets
+###########################################################################
+add_subdirectory( docs )
+
 ###########################################################################
 # MantidPlot Python Unit Tests
 ###########################################################################
diff --git a/Code/Mantid/MantidPlot/docs/CMakeLists.txt b/Code/Mantid/MantidPlot/docs/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f14056d397c99b18cca3db17ff33573bd25c618f
--- /dev/null
+++ b/Code/Mantid/MantidPlot/docs/CMakeLists.txt
@@ -0,0 +1,4 @@
+###########################################################################
+# Add each directory
+###########################################################################
+add_subdirectory( python )
diff --git a/Code/Mantid/MantidPlot/docs/python/CMakeLists.txt b/Code/Mantid/MantidPlot/docs/python/CMakeLists.txt
index 203801a22be84951d17719633dc2e7db13466152..97f439486007aefc5fef70c15afca42181325b66 100644
--- a/Code/Mantid/MantidPlot/docs/python/CMakeLists.txt
+++ b/Code/Mantid/MantidPlot/docs/python/CMakeLists.txt
@@ -6,30 +6,41 @@
 find_package ( Sphinx )
 
 if ( SPHINX_FOUND )
-  # Fill in the config file and autogen file
-  configure_file ( conf.py.in conf.py @ONLY ) 
+  # Fill in the config file and autogen file with build information
+  configure_file ( source/conf.py.in source/conf.py @ONLY ) 
   configure_file ( autogen_api.py.in autogen_api.py @ONLY ) 
-
-  # These files need to be relative to the conf.py file
-  add_custom_command ( OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/index.rst
-    COMMAND ${CMAKE_COMMAND} ARGS -E copy 
-      ${CMAKE_CURRENT_SOURCE_DIR}/index.rst ${CMAKE_CURRENT_BINARY_DIR}/index.rst
-    COMMAND ${CMAKE_COMMAND} ARGS -E copy_directory 
-      ${CMAKE_CURRENT_SOURCE_DIR}/api ${CMAKE_CURRENT_BINARY_DIR}/api
-    COMMAND ${CMAKE_COMMAND} ARGS -E copy_directory 
-      ${CMAKE_CURRENT_SOURCE_DIR}/_static ${CMAKE_CURRENT_BINARY_DIR}/_static
-    COMMAND ${CMAKE_COMMAND} ARGS -E copy_directory 
-      ${CMAKE_CURRENT_SOURCE_DIR}/_templates ${CMAKE_CURRENT_BINARY_DIR}/_templates
-    DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/conf.py
+  configure_file ( runsphinx.py.in runsphinx.py @ONLY )
+  
+  # Sphinx seems to require the config file to be next to the rest of the source 
+  # files meaning we need to copy everything over to the build directory
+  set ( SPHINX_SOURCE
+    source/index.rst
+    source/api/mantid.rst
+    source/api/mantidplot.rst
+    source/_templates/indexcontent.html
+    source/_templates/indexsidebar.html
+    source/_templates/layout.html
   )
+  
+  # The destination for the copied files
+  set ( SPHINX_CONF_DIR ${CMAKE_CURRENT_BINARY_DIR} )
+  set ( SPHINX_CONF_FILES )
+  foreach( file ${SPHINX_SOURCE} )
+    set ( out_file ${SPHINX_CONF_DIR}/${file} )
+    add_custom_command ( OUTPUT ${out_file}
+      COMMAND ${CMAKE_COMMAND} ARGS -E copy_if_different ${CMAKE_CURRENT_SOURCE_DIR}/${file} ${out_file}
+      DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/${file}
+    )
+  set ( SPHINX_CONF_FILES ${SPHINX_CONF_FILES} ${out_file} )
+  endforeach()  
 
+  set ( SPHINX_HTML_BUILD ${CMAKE_CURRENT_BINARY_DIR}/../../../python-sphinx/html )
   # Sphinx is run as '${SPHINX_EXECUTABLE} -b sourcedir builddir'
-  set ( OUTPUT_DIR ${CMAKE_CURRENT_BINARY_DIR}/../../../python-sphinx/html )
   add_custom_target ( python-sphinx 
-    COMMAND python autogen_api.py
-    COMMAND ${SPHINX_EXECUTABLE} -b html ${CMAKE_CURRENT_BINARY_DIR} ${OUTPUT_DIR}
-    DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/index.rst
+    COMMAND ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/MantidPlot -xq autogen_api.py
+    COMMAND ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/MantidPlot -xq runsphinx.py
+    DEPENDS ${SPHINX_CONF_FILES}
     COMMENT "Build Python Sphinx API documentation"
-    )
+  )
 
 endif ()
diff --git a/Code/Mantid/MantidPlot/docs/python/autogen_api.py.in b/Code/Mantid/MantidPlot/docs/python/autogen_api.py.in
index fdb134dfe36bf70c17daf26b55329050de08f6d7..5a7857910f28bcba64231bf757dce42adabf86c1 100755
--- a/Code/Mantid/MantidPlot/docs/python/autogen_api.py.in
+++ b/Code/Mantid/MantidPlot/docs/python/autogen_api.py.in
@@ -5,9 +5,8 @@ import sys
 import os
 import inspect
 
-# Append the path to the mantid library
+# Append the path to the mantid/mantidplot library
 sys.path.append("@CMAKE_RUNTIME_OUTPUT_DIRECTORY@")
-import mantid
 
 #------------------------------------------------------------------------------
 
@@ -27,7 +26,6 @@ class ClassAPIWriter(object):
     :inherited-members:
 
 """
-    
     def __init__(self, cls, outputdir, extension):
         if not inspect.isclass(cls):
             raise TypeError("Expected class type, found %s" % str(type(cls)))
@@ -41,6 +39,11 @@ class ClassAPIWriter(object):
         
         # FQL name could contain '_cmodule' aswell, strip this off
         modname = self._cls.__module__
+
+        # Hack for replaceing qti reference with mantidplot ref
+        if 'qti' in modname:
+            modname = modname.replace('_qti','mantidplot')
+        # Build up the module name and don't reference the "private" modules
         pieces = modname.split('.')
         fqlmod = ''
         for p in pieces:
@@ -55,26 +58,89 @@ class ClassAPIWriter(object):
         
     def filename(self):
         return self._filename
+        
+class FunctionAPIWriter(object):
+    """Writes a Sphinx documentation file
+       for a given function
+    """
+    
+    _doc_template = \
+"""%(title)s
+%(underline)s
 
-if __name__ == '__main__':
-    extension = '.rst'
-    apidir = os.path.join(os.path.dirname(__file__), 'api')
-    output_dir = os.path.join(apidir,'generated')
-    if not os.path.exists(output_dir):
-        os.mkdir(output_dir)
+.. module:`%(modulename)s`
+
+.. autofunction:: %(modulename)s.%(function)s
+
+"""
+    
+    def __init__(self, func, outputdir, extension):
+        if not inspect.isfunction(func):
+            raise TypeError("Expected function type, found %s" % str(type(cls)))
+        self._filename = os.path.join(outputdir, func.__name__ + extension)
+        self._func = func
+        
+    def write(self):
+        rstfile = open(self._filename, 'w')
+        funcname = self._func.__name__
+        underline = '='*len(funcname) # Sphinx doesn't like the title underline being incorrect
+        # FQL name could contain '_cmodule' aswell, strip this off
+        modname = self._func.__module__
+        # Hack for replaceing qti reference with mantidplot ref
+        if 'qti' in modname:
+            modname = modname.replace('_qti','mantidplot')
+        
+        # Write the file
+        rstfile.write(self._doc_template % {'title':funcname, 'underline':underline,\
+					    'modulename':modname,'function':funcname})
+        rstfile.close()
+        
+    def filename(self):
+        return self._filename
+
+
+def generate_api_doc(module, indexfilename):
+    """Write the sphinx doc files for a given module
+    
+        @param module - The module object
+        @param indexfilename - A file that will contain an index list of the given files
+    """
     
-    indexfilename = os.path.join(apidir, 'autogen.txt')
     indexfile = open(indexfilename, 'w')
     indexfile.write(".. AUTO-GENERATED FILE -- DO NOT EDIT!\n\n")
     indexfile.write(".. toctree::\n\n")
 
-    print "Generating API docs"
-    for name, member in inspect.getmembers(mantid):
+    print "Generating %s API docs" % module.__name__
+    for name, member in inspect.getmembers(module):
+	if name.startswith("_"): continue
         if inspect.isclass(member):
             apiwriter = ClassAPIWriter(member, output_dir, extension)
+        elif inspect.isfunction(member):
+            apiwriter = FunctionAPIWriter(member, output_dir, extension)
         else:
             continue
         apiwriter.write()
         indexfile.write("   generated/" + os.path.basename(apiwriter.filename()) + "\n")
     indexfile.close()
-    print "Completed autogenerating API docs"
+    print "Done generating API %s docs" % module.__name__
+
+if __name__ == '__main__':
+    extension = '.rst'
+    apidir = os.path.join(os.path.dirname(__file__), 'source','api')
+    output_dir = os.path.join(apidir,'generated')
+    if not os.path.exists(output_dir):
+        os.mkdir(output_dir)
+
+    import mantid
+    indexfilename = os.path.join(apidir, 'automantid.txt')
+    generate_api_doc(mantid, indexfilename)
+    try:
+        import mantidplot
+        indexfilename = os.path.join(apidir, 'automantidplot.txt')
+        generate_api_doc(mantidplot, indexfilename)
+    except:
+        import warnings
+        warnings.warn("Unable to import mantidplot. No api documentation will be generated for MantidPlot")
+
+
+    
diff --git a/Code/Mantid/MantidPlot/docs/python/runsphinx.py.in b/Code/Mantid/MantidPlot/docs/python/runsphinx.py.in
new file mode 100644
index 0000000000000000000000000000000000000000..228a0545d8d3033b226a0386fa905af77a244640
--- /dev/null
+++ b/Code/Mantid/MantidPlot/docs/python/runsphinx.py.in
@@ -0,0 +1,21 @@
+"""We need to run Sphinx inside MantidPlot to document the internal
+   module. This script calls the sphinx entry point with the necessary 
+   arguments
+"""
+
+__requires__ = 'Sphinx==1.1.2'
+import sys
+import os
+from pkg_resources import load_entry_point
+
+mantidplot = "@CMAKE_RUNTIME_OUTPUT_DIRECTORY@/MantidPlot"
+builder = "html"
+src_dir = "@CMAKE_CURRENT_BINARY_DIR@/source"
+output_dir = "@CMAKE_CURRENT_BINARY_DIR@/../../../python-sphinx/" + builder
+argv = [mantidplot,'-b', builder, src_dir, output_dir]
+
+if __name__ == '__main__':
+    sys.exit(
+        load_entry_point('Sphinx==1.1.2', 'console_scripts', 'sphinx-build')(argv)
+    )
+
diff --git a/Code/Mantid/MantidPlot/docs/python/source/_static/Mantid.png b/Code/Mantid/MantidPlot/docs/python/source/_static/Mantid.png
new file mode 100644
index 0000000000000000000000000000000000000000..4423c49d05e87efedd4c75432e0aaae44d84b01c
Binary files /dev/null and b/Code/Mantid/MantidPlot/docs/python/source/_static/Mantid.png differ
diff --git a/Code/Mantid/MantidPlot/docs/python/source/_static/Mantid_Logo_Transparent.png b/Code/Mantid/MantidPlot/docs/python/source/_static/Mantid_Logo_Transparent.png
new file mode 100644
index 0000000000000000000000000000000000000000..247578ebf7aded4b1ea8ff48ab198cfb4224c1c8
Binary files /dev/null and b/Code/Mantid/MantidPlot/docs/python/source/_static/Mantid_Logo_Transparent.png differ
diff --git a/Code/Mantid/MantidPlot/docs/python/source/_templates/indexcontent.html b/Code/Mantid/MantidPlot/docs/python/source/_templates/indexcontent.html
new file mode 100644
index 0000000000000000000000000000000000000000..f2322b6fd654dd02978a8ec3f8149cff2337946b
--- /dev/null
+++ b/Code/Mantid/MantidPlot/docs/python/source/_templates/indexcontent.html
@@ -0,0 +1,45 @@
+{% extends "defindex.html" %}
+{% block tables %}
+
+  <p><strong>Contents:</strong></p>
+  <table class="contentstable" align="center"><tr>
+    <td width="50%">
+      <p class="biglink"><a class="biglink" href="http://www.mantidproject.org/Python_in_Mantid_Training">Introductary training</a><br/>
+         <span class="linkdescr">An introduction to Python in Mantid</span></p>
+    </td><td width="50%">
+      <p class="biglink"><a class="biglink" href="{{ pathto("api/mantid") }}">Mantid Framework Reference</a><br/>
+         <span class="linkdescr">Documents the classes and functions of the Mantid framework</span></p>
+      <p class="biglink"><a class="biglink" href="{{ pathto("api/mantidplot") }}">MantidPlot Reference</a><br/>
+         <span class="linkdescr">Documents the classes and functions of MantidPlot</span></p>
+    </td></tr>
+  </table>
+
+  <p><strong>Indices and tables:</strong></p>
+  <table class="contentstable" align="center"><tr>
+    <td width="50%">
+      <p class="biglink"><a class="biglink" href="{{ pathto("py-modindex") }}">Module Index</a><br/>
+         <span class="linkdescr">quick access to all modules</span></p>
+      <p class="biglink"><a class="biglink" href="{{ pathto("genindex") }}">General Index</a><br/>
+         <span class="linkdescr">all functions, classes, terms</span></p>
+      <p class="biglink"><a class="biglink" href="{{ pathto("glossary") }}">Glossary</a><br/>
+         <span class="linkdescr">the most important terms explained</span></p>
+    </td><td width="50%">
+      <p class="biglink"><a class="biglink" href="{{ pathto("search") }}">Search page</a><br/>
+         <span class="linkdescr">search this documentation</span></p>
+      <p class="biglink"><a class="biglink" href="{{ pathto("contents") }}">Complete Table of Contents</a><br/>
+         <span class="linkdescr">lists all sections and subsections</span></p>
+    </td></tr>
+  </table>
+  
+   <p><strong>Useful links:</strong></p>
+  <table class="contentstable" align="center"><tr>
+    <td width="50%">
+      <p class="biglink"><a class="biglink" href="http://www.mantidproject.org" }}">Mantid project wiki</a><br/>
+         <span class="linkdescr">Mantid wiki</span></p>
+    </td><td width="50%">
+      <p class="biglink"><a class="biglink" href="http://docs.scipy.org/doc/numpy-1.5.x/user/" }}">Numpy Tutorial</a><br/>
+         <span class="linkdescr">An introduction to numpy</span></p>
+    </td></tr>
+  </table>
+
+{% endblock %}
diff --git a/Code/Mantid/MantidPlot/docs/python/source/_templates/indexsidebar.html b/Code/Mantid/MantidPlot/docs/python/source/_templates/indexsidebar.html
new file mode 100644
index 0000000000000000000000000000000000000000..309b5904044b5a57d60a73d1d27edccdb0749a96
--- /dev/null
+++ b/Code/Mantid/MantidPlot/docs/python/source/_templates/indexsidebar.html
@@ -0,0 +1,6 @@
+            <h3>Resources</h3>
+            <ul>
+              <li><a href="http://www.mantidproject.org/">Mantid wiki</a></li>
+              <li>&nbsp;</li>
+              <li><a href="http://docs.python.org/">Python manual</a></li>
+            </ul>
diff --git a/Code/Mantid/MantidPlot/docs/python/source/_templates/layout.html b/Code/Mantid/MantidPlot/docs/python/source/_templates/layout.html
new file mode 100644
index 0000000000000000000000000000000000000000..6240cc9016f391dacf5fc35610bfa5832d747447
--- /dev/null
+++ b/Code/Mantid/MantidPlot/docs/python/source/_templates/layout.html
@@ -0,0 +1,10 @@
+{% extends "default/layout.html" %}
+
+{%- block sidebarlogo %}
+{%- if logo %}
+         <p class="logo"><a href="{{ pathto(master_doc) }}">
+           <img class="logo" src="{{ pathto('_static/' + logo, 1) }}" alt="Logo" width=220 height=110/>
+         </a></p>
+{%- endif %}
+{%- endblock %}
+
diff --git a/Code/Mantid/MantidPlot/docs/python/source/api/mantid.rst b/Code/Mantid/MantidPlot/docs/python/source/api/mantid.rst
index 9c5886d1e2bc13387ee089f3b9619ba202886b81..0d8ad2910ee66d2a9f4fd631e41353dbb3d3b4ed 100644
--- a/Code/Mantid/MantidPlot/docs/python/source/api/mantid.rst
+++ b/Code/Mantid/MantidPlot/docs/python/source/api/mantid.rst
@@ -1,13 +1,9 @@
 .. _mantid:
 
-#################################
-  Mantid Python Class Reference
-#################################
+##################################
+  Mantid Framework class reference
+##################################
 
 .. module:: mantid
    
-Some lovely wording here...
-
-and probably more structure
-
-.. include:: autogen.txt
+.. include:: automantid.txt
diff --git a/Code/Mantid/MantidPlot/docs/python/source/api/mantidplot.rst b/Code/Mantid/MantidPlot/docs/python/source/api/mantidplot.rst
new file mode 100644
index 0000000000000000000000000000000000000000..65d22abaf5b4bd5b885640bff69b932873786577
--- /dev/null
+++ b/Code/Mantid/MantidPlot/docs/python/source/api/mantidplot.rst
@@ -0,0 +1,9 @@
+.. _mantidplot:
+
+##########################
+  MantidPlot API reference
+##########################
+
+.. module:: mantidplot
+   
+.. include:: automantidplot.txt
diff --git a/Code/Mantid/MantidPlot/docs/python/source/conf.py.in b/Code/Mantid/MantidPlot/docs/python/source/conf.py.in
index a3d52ad8d12e92470e732da10e9bdae7e8d4093f..b88a2f3af52677ce527d2d39c7aa2bed226730d6 100644
--- a/Code/Mantid/MantidPlot/docs/python/source/conf.py.in
+++ b/Code/Mantid/MantidPlot/docs/python/source/conf.py.in
@@ -107,14 +107,15 @@ html_theme = 'default'
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-#html_title = None
+html_title = "%s v%s Python Manual" % ("Mantid", version)
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
 #html_short_title = None
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = None
+
+html_logo = os.path.relpath('@CMAKE_HOME_DIRECTORY@/Images/Mantid_Logo_Transparent.png')
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
@@ -135,11 +136,15 @@ html_static_path = ['_static']
 #html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
+html_sidebars = {
+    'index':'indexsidebar.html'
+}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
-#html_additional_pages = {}
+html_additional_pages = {
+    'index':'indexcontent.html'
+}
 
 # If false, no module index is generated.
 #html_domain_indices = True
@@ -168,7 +173,7 @@ html_use_index = True
 #html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'Mantiddoc'
+htmlhelp_basename = 'mantid'
 
 
 # -- Options for LaTeX output --------------------------------------------------
diff --git a/Code/Mantid/MantidPlot/docs/python/source/index.rst b/Code/Mantid/MantidPlot/docs/python/source/index.rst
index 03da8571917fddc9c4799c2d6346a6453d1189d5..4b858d036e5684870055de55eeddb6a13f33fbb6 100644
--- a/Code/Mantid/MantidPlot/docs/python/source/index.rst
+++ b/Code/Mantid/MantidPlot/docs/python/source/index.rst
@@ -16,6 +16,7 @@ Contents
    :maxdepth: 1
 
    api/mantid.rst
+   api/mantidplot.rst
 
 Indices and tables
 ==================
diff --git a/Code/Mantid/MantidPlot/mantidplot.py b/Code/Mantid/MantidPlot/mantidplot.py
index 0ca9973f9a16a3e711da7807f320c72ad05d9d09..0177ed9f7a020b1082f863e27df9859494203cf7 100644
--- a/Code/Mantid/MantidPlot/mantidplot.py
+++ b/Code/Mantid/MantidPlot/mantidplot.py
@@ -21,7 +21,7 @@ from _qti import PlotSymbol, ImageSymbol, ArrowMarker, ImageMarker
 #-------------------------- Mantid Python access functions----------------
 # Grab a few Mantid things so that we can recognise workspace variables
 # While we have 2 APIs we need to figure out which to use so add a little bit of indirection
-def get_analysis_data_service():
+def _get_analysis_data_service():
     """Returns an object that can be used to get a workspace by name from Mantid
     
     Returns:
@@ -44,7 +44,7 @@ def workspace(name):
     Args:
         name: The name of the workspace in the Analysis Data Service.
     """
-    return get_analysis_data_service()[name]
+    return _get_analysis_data_service()[name]
 
 def table(name):
     """Get a handle on a table.
@@ -217,8 +217,7 @@ def stemPlot(source, index, power=None, startPoint=None, endPoint=None):
     Args:
         source: A reference to a workspace or a table.
         index: For a table, the column number or name. For a workspace, the workspace index.
-        power: The stem unit as a power of 10. If not provided, a dialog will appear with a
-            suggested value.
+        power: The stem unit as a power of 10. If not provided, a dialog will appear with a suggested value.
         startPoint: The first point (row or bin) to use (Default: the first one).
         endPoint: The last point (row or bin) to use (Default: the last one).
         
@@ -457,26 +456,17 @@ def plotSlice(source, label="", xydim=None, slicepoint=None,
         
     Optional Keyword Args:
         label :: label for the window title
-        xydim :: indexes or names of the dimensions to plot,
-            as an (X,Y) list or tuple.
-            See SliceViewer::setXYDim()
-        slicepoint :: list with the slice point in each dimension. Must be the 
-            same length as the number of dimensions of the workspace.
-            See SliceViewer::setSlicePoint()
-        colormin :: value of the minimum color in the scale
-            See SliceViewer::setColorScaleMin()
-        colormax :: value of the maximum color in the scale
-            See SliceViewer::setColorScaleMax()
-        colorscalelog :: value of the maximum color in the scale
-            See SliceViewer::setColorScaleLog()
-        limits :: list with the (xleft, xright, ybottom, ytop) limits
-            to the view to show.
-            See SliceViewer::setXYLimits()
+        xydim :: indexes or names of the dimensions to plot, as an (X,Y) list or tuple. See SliceViewer::setXYDim()
+        slicepoint :: list with the slice point in each dimension.  Must be the same length as the number of dimensions of the workspace. See SliceViewer::setSlicePoint()
+        colormin :: value of the minimum color in the scale. See SliceViewer::setColorScaleMin()
+        colormax :: value of the maximum color in the scale. See SliceViewer::setColorScaleMax()
+        colorscalelog :: value of the maximum color in the scale. See SliceViewer::setColorScaleLog()
+        limits :: list with the (xleft, xright, ybottom, ytop) limits to the view to show. See SliceViewer::setXYLimits()
         
     Returns:
         a (list of) handle(s) to the SliceViewerWindow widgets that were open.
-            Use SliceViewerWindow.getSlicer() to get access to the functions of the
-            SliceViewer, e.g. setting the view and slice point.
+        Use SliceViewerWindow.getSlicer() to get access to the functions of the
+        SliceViewer, e.g. setting the view and slice point.
     """ 
     workspace_names = __getWorkspaceNames(source)
     try:
@@ -563,10 +553,6 @@ Layer.Right = _qti.GraphOptions.Right
 Layer.Bottom = _qti.GraphOptions.Bottom
 Layer.Top = _qti.GraphOptions.Top
 
-
-
-
-
 #-----------------------------------------------------------------------------
 #--------------------------- "Private" functions -----------------------------
 #-----------------------------------------------------------------------------
@@ -604,7 +590,7 @@ def __getWorkspaceNames(source):
         else:
             ws_names.append(wspace.getName())
     elif isinstance(source,str):
-        w = get_analysis_data_service()[source]
+        w = _get_analysis_data_service()[source]
         if w != None:
             names = __getWorkspaceNames(w)
             for n in names:
diff --git a/Code/Mantid/MantidPlot/src/ApplicationWindow.cpp b/Code/Mantid/MantidPlot/src/ApplicationWindow.cpp
index f74e11d1f661ebb55322b4b3d2d83e5c6f92c12f..8e85e4513d436668d5ccf1aaadcb9da8c1e5d638 100644
--- a/Code/Mantid/MantidPlot/src/ApplicationWindow.cpp
+++ b/Code/Mantid/MantidPlot/src/ApplicationWindow.cpp
@@ -10008,7 +10008,7 @@ void ApplicationWindow::addFunctionCurve()
 
   Graph* g = plot->activeGraph();
   if ( g ) {
-    FunctionDialog* fd = functionDialog(g);
+    functionDialog(g);
   }
 }
 
@@ -14445,6 +14445,8 @@ void ApplicationWindow::parseCommandLineArguments(const QStringList& args)
     {
       exec = true;
       quit = true;
+      // Minimize ourselves
+      this->showMinimized();
     }
     else if (str.startsWith("-") || str.startsWith("--"))
     {
@@ -15935,13 +15937,20 @@ void ApplicationWindow::goToColumn()
   }
 }
 
-void ApplicationWindow::showScriptWindow(bool forceVisible)
+/**
+ * Show the script window, creating it if necessary
+ * @param forceVisible - If true the window is forced to visible rather than toggling
+ * @param quitting - If true then it is assumed MantidPlot will exit automatically so stdout redirect
+ * from scripts is disabled.
+ */
+void ApplicationWindow::showScriptWindow(bool forceVisible, bool quitting)
 {
   if( !scriptingWindow )
   {
     // MG 09/02/2010 : Removed parent from scripting window. If it has one then it doesn't respect the always on top 
     // flag, it is treated as a sub window of its parent
-    scriptingWindow = new ScriptingWindow(scriptingEnv(), NULL);
+    const bool capturePrint = !quitting;
+    scriptingWindow = new ScriptingWindow(scriptingEnv(),capturePrint, NULL);
     scriptingWindow->setObjectName("ScriptingWindow");
     scriptingWindow->setAttribute(Qt::WA_DeleteOnClose, false);
     connect(scriptingWindow, SIGNAL(closeMe()), this, SLOT(saveScriptWindowGeometry()));
@@ -15954,7 +15963,14 @@ void ApplicationWindow::showScriptWindow(bool forceVisible)
   {
     scriptingWindow->resize(d_script_win_size);
     scriptingWindow->move(d_script_win_pos);
-    scriptingWindow->show();
+    if( quitting )
+    {
+      scriptingWindow->showMinimized();
+    }
+    else
+    {
+      scriptingWindow->show();
+    }
     scriptingWindow->setFocus();
   }
   else 
@@ -16121,7 +16137,7 @@ ApplicationWindow * ApplicationWindow::loadScript(const QString& fn, bool execut
   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
   setScriptingLanguage("Python");
   restoreApplicationGeometry();
-  showScriptWindow();
+  showScriptWindow(false, quit);
   scriptingWindow->open(fn, false);
   QApplication::restoreOverrideCursor();
   if (execute)
diff --git a/Code/Mantid/MantidPlot/src/ApplicationWindow.h b/Code/Mantid/MantidPlot/src/ApplicationWindow.h
index 66c1d722f84b7c5d9828d2f97b711693c29248cc..67270d924aa4334207e9f91720d7f10dcfeb5e6c 100644
--- a/Code/Mantid/MantidPlot/src/ApplicationWindow.h
+++ b/Code/Mantid/MantidPlot/src/ApplicationWindow.h
@@ -728,7 +728,7 @@ public slots:
   //! Connected to the context menu signal from lv; it's called when there are no items selected in the list
   void showListViewPopupMenu(const QPoint &p);
 
-  void showScriptWindow(bool forceVisible = false);
+  void showScriptWindow(bool forceVisible = false, bool quitting = false);
   void saveScriptWindowGeometry();
   void showScriptInterpreter();
   bool testForIPython();
diff --git a/Code/Mantid/MantidPlot/src/PythonScript.cpp b/Code/Mantid/MantidPlot/src/PythonScript.cpp
index 86ab6dc7ff655f312d415c996ede0fd3c2332477..36613b596f5ed4310714bf17e6519d599af4b126 100644
--- a/Code/Mantid/MantidPlot/src/PythonScript.cpp
+++ b/Code/Mantid/MantidPlot/src/PythonScript.cpp
@@ -96,6 +96,12 @@ PythonScript::PythonScript(PythonScripting *env, const QString &code, QObject *c
   GILHolder gil;
   PyObject *pymodule = PyImport_AddModule("__main__");
   localDict = PyDict_Copy(PyModule_GetDict(pymodule));
+  if( QFileInfo(Name).exists() )
+  {
+    QString scriptPath = QFileInfo(Name).absoluteFilePath();
+    // Make sure the __file__ variable is set
+    PyDict_SetItem(localDict,PyString_FromString("__file__"), PyString_FromString(scriptPath.toAscii().data()));
+  }
   setQObject(Context, "self");
   updatePath(Name, true);
 
@@ -675,6 +681,7 @@ void PythonScript::beginStdoutRedirect()
  */
 void PythonScript::endStdoutRedirect()
 {
+
   GILHolder gil; // Aqcuire the GIL
   PyDict_SetItemString(env()->sysDict(), "stdout", stdoutSave);
   Py_XDECREF(stdoutSave);
diff --git a/Code/Mantid/MantidPlot/src/PythonScripting.cpp b/Code/Mantid/MantidPlot/src/PythonScripting.cpp
index b81ab36990609df2ae18e30a740ce2c3d826f099..a34667d66c8ce9a30215168226acbab12b57f92a 100644
--- a/Code/Mantid/MantidPlot/src/PythonScripting.cpp
+++ b/Code/Mantid/MantidPlot/src/PythonScripting.cpp
@@ -184,7 +184,6 @@ bool PythonScripting::start()
 
     //Get the refresh protection flag
     Mantid::Kernel::ConfigService::Instance().getValue("pythonalgorithms.refresh.allowed", refresh_allowed);
-
     if( loadInitFile(mantidbin.absoluteFilePath("mantidplotrc.py")) )
     {
       d_initialized = true;
@@ -193,18 +192,22 @@ bool PythonScripting::start()
     {
       d_initialized = false;
     }
-    return d_initialized;
   }
   catch(std::exception & ex)
   {
     std::cerr << "Exception in PythonScripting.cpp: " << ex.what() << std::endl;
-    return false;
+    d_initialized = false;
   }
   catch(...)
   {
     std::cerr << "Exception in PythonScripting.cpp" << std::endl;
-    return false;
+    d_initialized = false;
   }
+  // Reset the stdout/err printers
+  PyDict_SetItemString(m_sys, "stdout",PyDict_GetItemString(m_sys, "__stdout__"));
+  PyDict_SetItemString(m_sys, "stderr",PyDict_GetItemString(m_sys, "__stderr__"));
+
+  return d_initialized;
 }
 
 /**
diff --git a/Code/Mantid/MantidPlot/src/ScriptManagerWidget.cpp b/Code/Mantid/MantidPlot/src/ScriptManagerWidget.cpp
index 051c9635e1d350e8ef5b94f1e9f0d350a26c661d..b4722275e3f10be34181ec2d48413fea2473a399 100644
--- a/Code/Mantid/MantidPlot/src/ScriptManagerWidget.cpp
+++ b/Code/Mantid/MantidPlot/src/ScriptManagerWidget.cpp
@@ -40,10 +40,10 @@
 /**
  * Constructor
  */
-ScriptManagerWidget::ScriptManagerWidget(ScriptingEnv *env, QWidget *parent, bool interpreter_mode)
+ScriptManagerWidget::ScriptManagerWidget(ScriptingEnv *env, QWidget *parent, bool interpreter_mode, bool capturePrint)
   : QTabWidget(parent), Scripted(env), m_last_dir(""), m_script_runners(),
     m_cursor_pos(), m_findrep_dlg(NULL), 
-    m_interpreter_mode(interpreter_mode)
+    m_interpreter_mode(interpreter_mode), m_recentScriptList(), m_capturePrint(capturePrint)
 {
   //Create actions for this widget
   initActions();
@@ -1062,11 +1062,18 @@ void ScriptManagerWidget::open(bool newtab, const QString & filename)
 Script * ScriptManagerWidget::createScriptRunner(ScriptEditor *editor)
 {
   Script *script = scriptingEnv()->newScript("", this, editor->fileName(), true,
-					     m_toggle_progress->isChecked());
-  // Connect the signals that print output and error messages to the formatting functions
-  connect(script, SIGNAL(print(const QString &)), this, SLOT(displayOutput(const QString &)));
-  connect(script, SIGNAL(error(const QString &, const QString&, int)), this, 
-	  SLOT(displayError(const QString &)));
+                                             m_toggle_progress->isChecked());
+  if( m_capturePrint )
+  {
+    // Connect the signals that print output and error messages to the formatting functions
+    connect(script, SIGNAL(print(const QString &)), this, SLOT(displayOutput(const QString &)));
+    connect(script, SIGNAL(error(const QString &, const QString&, int)), this,
+            SLOT(displayError(const QString &)));
+  }
+  else
+  {
+    script->redirectStdOut(false);
+  }
   if( editor )
   {
     connect(script, SIGNAL(keywordsChanged(const QStringList&)), editor, 
diff --git a/Code/Mantid/MantidPlot/src/ScriptManagerWidget.h b/Code/Mantid/MantidPlot/src/ScriptManagerWidget.h
index d03912a6695f971328682c96b3b9165e2d7e618d..8f1409f9d1a03dabd70079660475ecee9c4b11f1 100644
--- a/Code/Mantid/MantidPlot/src/ScriptManagerWidget.h
+++ b/Code/Mantid/MantidPlot/src/ScriptManagerWidget.h
@@ -62,7 +62,7 @@ class ScriptManagerWidget : public QTabWidget, Scripted
 
 public:
   /// Constructor
-  ScriptManagerWidget(ScriptingEnv *env, QWidget *parent, bool interpreter_mode = false);
+  ScriptManagerWidget(ScriptingEnv *env, QWidget *parent, bool interpreter_mode = false, bool capturePrint = true);
   ///Destructor
   ~ScriptManagerWidget();
   ///Save settings applicable to the manager
@@ -244,6 +244,8 @@ private:
   bool m_interpreter_mode;
   ///list storing the recent scripts
   QStringList m_recentScriptList;
+  /// Flag to indicate whether stdout should be redirected
+  bool m_capturePrint;
   /// enum used for maximum of recent scripts size
   enum {MaxRecentScripts = 5};
 };
@@ -314,7 +316,6 @@ private:
 
   /// If a find is in progress
   bool m_find_inprogress;
-  
 };
 
 
diff --git a/Code/Mantid/MantidPlot/src/ScriptingWindow.cpp b/Code/Mantid/MantidPlot/src/ScriptingWindow.cpp
index bab4640a463961950eb1dc8fa4f2ecc9afc4d233..3fec164e2f09a2e467913004fbd53df51d8c1ac0 100755
--- a/Code/Mantid/MantidPlot/src/ScriptingWindow.cpp
+++ b/Code/Mantid/MantidPlot/src/ScriptingWindow.cpp
@@ -257,12 +257,13 @@ void ScriptOutputDock::resetFont()
  * @param parent :: The parent widget
  * @param flags :: Window flags passed to the base class
  */
-ScriptingWindow::ScriptingWindow(ScriptingEnv *env,QWidget *parent, Qt::WindowFlags flags) : 
+ScriptingWindow::ScriptingWindow(ScriptingEnv *env, bool capturePrint, QWidget *parent, Qt::WindowFlags flags) :
   QMainWindow(parent, flags), m_acceptClose(false)
 {
   setObjectName("MantidScriptWindow");
   // Sub-widgets
-  m_manager = new ScriptManagerWidget(env, this);
+  const bool interpreterMode(false);
+  m_manager = new ScriptManagerWidget(env, this, interpreterMode, capturePrint);
   setCentralWidget(m_manager);
   m_output_dock = new ScriptOutputDock(QString(), m_manager, this);
   m_output_dock->setScriptIsRunning(false);
@@ -279,7 +280,7 @@ ScriptingWindow::ScriptingWindow(ScriptingEnv *env,QWidget *parent, Qt::WindowFl
   QSettings settings;
   settings.beginGroup("/ScriptWindow");
   QString lastdir = settings.value("LastDirectoryVisited", "").toString();
-  // If nothgin, set the last directory to the Mantid scripts directory (if present)
+  // If nothing, set the last directory to the Mantid scripts directory (if present)
   if( lastdir.isEmpty() )
   {  
     lastdir = QString::fromStdString(Mantid::Kernel::ConfigService::Instance().getString("pythonscripts.directory"));
diff --git a/Code/Mantid/MantidPlot/src/ScriptingWindow.h b/Code/Mantid/MantidPlot/src/ScriptingWindow.h
index 4856996a4428c6117c469adf83b14521fbdd29f3..454279341aba33ced79ec47381cea7d202a405b7 100755
--- a/Code/Mantid/MantidPlot/src/ScriptingWindow.h
+++ b/Code/Mantid/MantidPlot/src/ScriptingWindow.h
@@ -107,13 +107,13 @@ class ScriptingWindow : public QMainWindow
 
 public:
   ///Constructor
-  ScriptingWindow(ScriptingEnv *env,QWidget *parent = 0, Qt::WindowFlags flags = 0);
+  ScriptingWindow(ScriptingEnv *env,bool capturePrint = true,QWidget *parent = 0, Qt::WindowFlags flags = 0);
   ///Destructor
   ~ScriptingWindow();
   /// Override the closeEvent
   void closeEvent(QCloseEvent *event);
   /// Override the showEvent
-  void showEvent(QShowEvent *event);		      
+  void showEvent(QShowEvent *event);
   /// Is a script running?
   bool isScriptRunning() const;
   ///Save the current state of the script window for next time
@@ -177,7 +177,6 @@ private:
   QAction *m_scripting_lang;
   /// Flag to define whether we should accept a close event
   bool m_acceptClose;
-  
 };
 
 #endif //SCRIPTINGWINDOW_H_