From 8037259ed97a242560dcab6299a8112c4bbb8746 Mon Sep 17 00:00:00 2001
From: "W. Trevor King" <wking@drexel.edu>
Date: Fri, 18 Jun 2010 09:19:05 -0400
Subject: [PATCH] Hack merge illysam's hooke.py into hooke/ui/gui/__init__.py

---
 hooke.py                 | 1396 --------------------------------------
 hooke/ui/gui/__init__.py | 1386 +++++++++++++++++++++++++++++++++++++
 2 files changed, 1386 insertions(+), 1396 deletions(-)
 delete mode 100644 hooke.py

diff --git a/hooke.py b/hooke.py
deleted file mode 100644
index 43b7510..0000000
--- a/hooke.py
+++ /dev/null
@@ -1,1396 +0,0 @@
-#!/usr/bin/env python
-
-'''
-HOOKE - A force spectroscopy review & analysis tool
-
-Copyright 2008 by Massimo Sandal (University of Bologna, Italy)
-Copyright 2010 by Rolf Schmidt (Concordia University, Canada)
-
-This program is released under the GNU General Public License version 2.
-'''
-
-import lib.libhooke as lh
-import wxversion
-wxversion.select(lh.WX_GOOD)
-
-from configobj import ConfigObj
-import copy
-import os.path
-import platform
-import shutil
-import time
-
-import wx.html
-import wx.lib.agw.aui as aui
-import wx.lib.evtmgr as evtmgr
-import wx.propgrid as wxpg
-
-from matplotlib.ticker import FuncFormatter
-
-from configobj import __version__ as configobj_version
-from matplotlib import __version__ as mpl_version
-from numpy import __version__ as numpy_version
-from scipy import __version__ as scipy_version
-from sys import version as python_version
-from wx import __version__ as wx_version
-from wx.propgrid import PROPGRID_MAJOR
-from wx.propgrid import PROPGRID_MINOR
-from wx.propgrid import PROPGRID_RELEASE
-
-try:
-    from agw import cubecolourdialog as CCD
-except ImportError: # if it's not there locally, try the wxPython lib.
-    import wx.lib.agw.cubecolourdialog as CCD
-
-#set the Hooke directory
-lh.hookeDir = os.path.abspath(os.path.dirname(__file__))
-from config.config import config
-import drivers
-import lib.clickedpoint
-import lib.curve
-import lib.delta
-import lib.playlist
-import lib.plotmanipulator
-import lib.prettyformat
-import panels.commands
-import panels.note
-import panels.perspectives
-import panels.playlist
-import panels.plot
-import panels.propertyeditor
-import panels.results
-import plugins
-
-global __version__
-global __codename__
-global __releasedate__
-__version__ = lh.HOOKE_VERSION[0]
-__codename__ = lh.HOOKE_VERSION[1]
-__releasedate__ = lh.HOOKE_VERSION[2]
-__release_name__ = lh.HOOKE_VERSION[1]
-
-ID_About = wx.NewId()
-ID_Next = wx.NewId()
-ID_Previous = wx.NewId()
-
-ID_ViewAssistant = wx.NewId()
-ID_ViewCommands = wx.NewId()
-ID_ViewFolders = wx.NewId()
-ID_ViewNote = wx.NewId()
-ID_ViewOutput = wx.NewId()
-ID_ViewPlaylists = wx.NewId()
-ID_ViewProperties = wx.NewId()
-ID_ViewResults = wx.NewId()
-
-ID_DeletePerspective = wx.NewId()
-ID_SavePerspective = wx.NewId()
-
-ID_FirstPerspective = ID_SavePerspective + 1000
-#I hope we'll never have more than 1000 perspectives
-ID_FirstPlot = ID_SavePerspective + 2000
-
-class Hooke(wx.App):
-
-    def OnInit(self):
-        self.SetAppName('Hooke')
-        self.SetVendorName('')
-
-        window_height = config['main']['height']
-        window_left= config['main']['left']
-        window_top = config['main']['top']
-        window_width = config['main']['width']
-
-        #sometimes, the ini file gets confused and sets 'left'
-        #and 'top' to large negative numbers
-        #let's catch and fix this
-        #keep small negative numbers, the user might want those
-        if window_left < -window_width:
-            window_left = 0
-        if window_top < -window_height:
-            window_top = 0
-        window_position = (window_left, window_top)
-        window_size = (window_width, window_height)
-
-        #setup the splashscreen
-        if config['splashscreen']['show']:
-            filename = lh.get_file_path('hooke.jpg', ['resources'])
-            if os.path.isfile(filename):
-                bitmap = wx.Image(filename).ConvertToBitmap()
-                splashStyle = wx.SPLASH_CENTRE_ON_SCREEN|wx.SPLASH_TIMEOUT
-                splashDuration = config['splashscreen']['duration']
-                wx.SplashScreen(bitmap, splashStyle, splashDuration, None, -1)
-                wx.Yield()
-                '''
-                we need for the splash screen to disappear
-                for whatever reason splashDuration and sleep do not correspond to each other
-                at least not on Windows
-                maybe it's because duration is in milliseconds and sleep in seconds
-                thus we need to increase the sleep time a bit
-                a factor of 1.2 seems to work quite well
-                '''
-                sleepFactor = 1.2
-                time.sleep(sleepFactor * splashDuration / 1000)
-
-        plugin_objects = []
-        for plugin in config['plugins']:
-            if config['plugins'][plugin]:
-                filename = ''.join([plugin, '.py'])
-                path = lh.get_file_path(filename, ['plugins'])
-                if os.path.isfile(path):
-                    #get the corresponding filename and path
-                    plugin_name = ''.join(['plugins.', plugin])
-                    #import the module
-                    __import__(plugin_name)
-                    #get the file that contains the plugin
-                    class_file = getattr(plugins, plugin)
-                    #get the class that contains the commands
-                    class_object = getattr(class_file, plugin + 'Commands')
-                    plugin_objects.append(class_object)
-
-        def make_command_class(*bases):
-            #create metaclass with plugins and plotmanipulators
-            return type(HookeFrame)("HookeFramePlugged", bases + (HookeFrame,), {})
-        frame = make_command_class(*plugin_objects)(parent=None, id=wx.ID_ANY, title='Hooke', pos=window_position, size=window_size)
-        frame.Show(True)
-        self.SetTopWindow(frame)
-
-        return True
-
-    def OnExit(self):
-        return True
-
-
-class HookeFrame(wx.Frame):
-
-    def __init__(self, parent, id=-1, title='', pos=wx.DefaultPosition, size=wx.DefaultSize, style=wx.DEFAULT_FRAME_STYLE|wx.SUNKEN_BORDER|wx.CLIP_CHILDREN):
-        #call parent constructor
-        wx.Frame.__init__(self, parent, id, title, pos, size, style)
-        self.config = config
-        self.CreateApplicationIcon()
-        #self.configs contains: {the name of the Commands file: corresponding ConfigObj}
-        self.configs = {}
-        #self.displayed_plot holds the currently displayed plot
-        self.displayed_plot = None
-        #self.playlists contains: {the name of the playlist: [playlist, tabIndex, plotID]}
-        self.playlists = {}
-        #list of all plotmanipulators
-        self.plotmanipulators = []
-        #self.plugins contains: {the name of the plugin: [caption, function]}
-        self.plugins = {}
-        #self.results_str contains the type of results we want to display
-        self.results_str = 'wlc'
-
-        #tell FrameManager to manage this frame
-        self._mgr = aui.AuiManager()
-        self._mgr.SetManagedWindow(self)
-        #set the gradient style
-        self._mgr.GetArtProvider().SetMetric(aui.AUI_DOCKART_GRADIENT_TYPE, aui.AUI_GRADIENT_NONE)
-        #set transparent drag
-        self._mgr.SetFlags(self._mgr.GetFlags() ^ aui.AUI_MGR_TRANSPARENT_DRAG)
-
-        # set up default notebook style
-        self._notebook_style = aui.AUI_NB_DEFAULT_STYLE | aui.AUI_NB_TAB_EXTERNAL_MOVE | wx.NO_BORDER
-        self._notebook_theme = 0
-
-        #holds the perspectives: {name, perspective_str}
-        self._perspectives = {}
-
-        # min size for the frame itself isn't completely done.
-        # see the end up FrameManager::Update() for the test
-        # code. For now, just hard code a frame minimum size
-        self.SetMinSize(wx.Size(500, 500))
-        #define the list of active drivers
-        self.drivers = []
-        for driver in self.config['drivers']:
-            if self.config['drivers'][driver]:
-                #get the corresponding filename and path
-                filename = ''.join([driver, '.py'])
-                path = lh.get_file_path(filename, ['drivers'])
-                #the driver is active for driver[1] == 1
-                if os.path.isfile(path):
-                    #driver files are located in the 'drivers' subfolder
-                    driver_name = ''.join(['drivers.', driver])
-                    __import__(driver_name)
-                    class_file = getattr(drivers, driver)
-                    for command in dir(class_file):
-                        if command.endswith('Driver'):
-                            self.drivers.append(getattr(class_file, command))
-        #import all active plugins and plotmanips
-        #add 'core.ini' to self.configs (this is not a plugin and thus must be imported separately)
-        ini_path = lh.get_file_path('core.ini', ['plugins'])
-        plugin_config = ConfigObj(ini_path)
-        #self.config.merge(plugin_config)
-        self.configs['core'] = plugin_config
-        #existing_commands contains: {command: plugin}
-        existing_commands = {}
-        #make sure we execute _plug_init() for every command line plugin we import
-        for plugin in self.config['plugins']:
-            if self.config['plugins'][plugin]:
-                filename = ''.join([plugin, '.py'])
-                path = lh.get_file_path(filename, ['plugins'])
-                if os.path.isfile(path):
-                    #get the corresponding filename and path
-                    plugin_name = ''.join(['plugins.', plugin])
-                    try:
-                        #import the module
-                        module = __import__(plugin_name)
-                        #prepare the ini file for inclusion
-                        ini_path = path.replace('.py', '.ini')
-                        #include ini file
-                        plugin_config = ConfigObj(ini_path)
-                        #self.config.merge(plugin_config)
-                        self.configs[plugin] = plugin_config
-                        #add to plugins
-                        commands = eval('dir(module.' + plugin+ '.' + plugin + 'Commands)')
-                        #keep only commands (ie names that start with 'do_')
-                        commands = [command for command in commands if command.startswith('do_')]
-                        if commands:
-                            for command in commands:
-                                if existing_commands.has_key(command):
-                                    message_str = 'Adding "' + command + '" in plugin "' + plugin + '".\n\n'
-                                    message_str += '"' + command + '" already exists in "' + str(existing_commands[command]) + '".\n\n'
-                                    message_str += 'Only "' + command + '" in "' + str(existing_commands[command]) + '" will work.\n\n'
-                                    message_str += 'Please rename one of the commands in the source code and restart Hooke or disable one of the plugins.'
-                                    dialog = wx.MessageDialog(self, message_str, 'Warning', wx.OK|wx.ICON_WARNING|wx.CENTER)
-                                    dialog.ShowModal()
-                                    dialog.Destroy()
-                                existing_commands[command] = plugin
-                            self.plugins[plugin] = commands
-                        try:
-                            #initialize the plugin
-                            eval('module.' + plugin+ '.' + plugin + 'Commands._plug_init(self)')
-                        except AttributeError:
-                            pass
-                    except ImportError:
-                        pass
-        #add commands from hooke.py i.e. 'core' commands
-        commands = dir(HookeFrame)
-        commands = [command for command in commands if command.startswith('do_')]
-        if commands:
-            self.plugins['core'] = commands
-        #create panels here
-        self.panelAssistant = self.CreatePanelAssistant()
-        self.panelCommands = self.CreatePanelCommands()
-        self.panelFolders = self.CreatePanelFolders()
-        self.panelPlaylists = self.CreatePanelPlaylists()
-        self.panelProperties = self.CreatePanelProperties()
-        self.panelNote = self.CreatePanelNote()
-        self.panelOutput = self.CreatePanelOutput()
-        self.panelResults = self.CreatePanelResults()
-        self.plotNotebook = self.CreateNotebook()
-
-        # add panes
-        self._mgr.AddPane(self.panelFolders, aui.AuiPaneInfo().Name('Folders').Caption('Folders').Left().CloseButton(True).MaximizeButton(False))
-        self._mgr.AddPane(self.panelPlaylists, aui.AuiPaneInfo().Name('Playlists').Caption('Playlists').Left().CloseButton(True).MaximizeButton(False))
-        self._mgr.AddPane(self.panelNote, aui.AuiPaneInfo().Name('Note').Caption('Note').Left().CloseButton(True).MaximizeButton(False))
-        self._mgr.AddPane(self.plotNotebook, aui.AuiPaneInfo().Name('Plots').CenterPane().PaneBorder(False))
-        self._mgr.AddPane(self.panelCommands, aui.AuiPaneInfo().Name('Commands').Caption('Settings and commands').Right().CloseButton(True).MaximizeButton(False))
-        self._mgr.AddPane(self.panelProperties, aui.AuiPaneInfo().Name('Properties').Caption('Properties').Right().CloseButton(True).MaximizeButton(False))
-        self._mgr.AddPane(self.panelAssistant, aui.AuiPaneInfo().Name('Assistant').Caption('Assistant').Right().CloseButton(True).MaximizeButton(False))
-        self._mgr.AddPane(self.panelOutput, aui.AuiPaneInfo().Name('Output').Caption('Output').Bottom().CloseButton(True).MaximizeButton(False))
-        self._mgr.AddPane(self.panelResults, aui.AuiPaneInfo().Name('Results').Caption('Results').Bottom().CloseButton(True).MaximizeButton(False))
-        #self._mgr.AddPane(self.textCtrlCommandLine, aui.AuiPaneInfo().Name('CommandLine').CaptionVisible(False).Fixed().Bottom().Layer(2).CloseButton(False).MaximizeButton(False))
-        #self._mgr.AddPane(panelBottom, aui.AuiPaneInfo().Name("panelCommandLine").Bottom().Position(1).CloseButton(False).MaximizeButton(False))
-
-        # add the toolbars to the manager
-        #self.toolbar=self.CreateToolBar()
-        self.toolbarNavigation=self.CreateToolBarNavigation()
-        #self._mgr.AddPane(self.toolbar, aui.AuiPaneInfo().Name('toolbar').Caption('Toolbar').ToolbarPane().Top().Layer(1).Row(1).LeftDockable(False).RightDockable(False))
-        self._mgr.AddPane(self.toolbarNavigation, aui.AuiPaneInfo().Name('toolbarNavigation').Caption('Navigation').ToolbarPane().Top().Layer(1).Row(1).LeftDockable(False).RightDockable(False))
-        # "commit" all changes made to FrameManager
-        self._mgr.Update()
-        #create the menubar after the panes so that the default perspective
-        #is created with all panes open
-        self.CreateMenuBar()
-        self.statusbar = self.CreateStatusbar()
-        self._BindEvents()
-
-        name = self.config['perspectives']['active']
-        menu_item = self.GetPerspectiveMenuItem(name)
-        if menu_item is not None:
-            self.OnRestorePerspective(menu_item)
-            #TODO: config setting to remember playlists from last session
-        self.playlists = self.panelPlaylists.Playlists
-        #initialize the commands tree
-        self.panelCommands.Initialize(self.plugins)
-        for command in dir(self):
-            if command.startswith('plotmanip_'):
-                self.plotmanipulators.append(lib.plotmanipulator.Plotmanipulator(method=getattr(self, command), command=command))
-
-        #load default list, if possible
-        self.do_loadlist(self.GetStringFromConfig('core', 'preferences', 'playlist'))
-
-    def _BindEvents(self):
-        #TODO: figure out if we can use the eventManager for menu ranges
-        #and events of 'self' without raising an assertion fail error
-        self.Bind(wx.EVT_ERASE_BACKGROUND, self.OnEraseBackground)
-        self.Bind(wx.EVT_SIZE, self.OnSize)
-        self.Bind(wx.EVT_CLOSE, self.OnClose)
-        # Show How To Use The Closing Panes Event
-        self.Bind(aui.EVT_AUI_PANE_CLOSE, self.OnPaneClose)
-        self.Bind(aui.EVT_AUINOTEBOOK_PAGE_CLOSE, self.OnNotebookPageClose)
-        #menu
-        evtmgr.eventManager.Register(self.OnAbout, wx.EVT_MENU, win=self, id=wx.ID_ABOUT)
-        evtmgr.eventManager.Register(self.OnClose, wx.EVT_MENU, win=self, id=wx.ID_EXIT)
-        #view
-        self.Bind(wx.EVT_MENU_RANGE, self.OnView, id=ID_ViewAssistant, id2=ID_ViewResults)
-        #perspectives
-        self.Bind(wx.EVT_MENU, self.OnDeletePerspective, id=ID_DeletePerspective)
-        self.Bind(wx.EVT_MENU, self.OnSavePerspective, id=ID_SavePerspective)
-        self.Bind(wx.EVT_MENU_RANGE, self.OnRestorePerspective, id=ID_FirstPerspective, id2=ID_FirstPerspective+1000)
-        #toolbar
-        evtmgr.eventManager.Register(self.OnNext, wx.EVT_TOOL, win=self, id=ID_Next)
-        evtmgr.eventManager.Register(self.OnPrevious, wx.EVT_TOOL, win=self, id=ID_Previous)
-        #self.Bind(.EVT_AUITOOLBAR_TOOL_DROPDOWN, self.OnDropDownToolbarItem, id=ID_DropDownToolbarItem)
-        #dir control
-        treeCtrl = self.panelFolders.GetTreeCtrl()
-        #tree.Bind(wx.EVT_LEFT_UP, self.OnDirCtrl1LeftUp)
-        #tree.Bind(wx.EVT_LEFT_DOWN, self.OnGenericDirCtrl1LeftDown)
-        treeCtrl.Bind(wx.EVT_LEFT_DCLICK, self.OnDirCtrlLeftDclick)
-        #playlist tree
-        self.panelPlaylists.PlaylistsTree.Bind(wx.EVT_LEFT_DOWN, self.OnPlaylistsLeftDown)
-        self.panelPlaylists.PlaylistsTree.Bind(wx.EVT_LEFT_DCLICK, self.OnPlaylistsLeftDclick)
-        #commands tree
-        evtmgr.eventManager.Register(self.OnExecute, wx.EVT_BUTTON, self.panelCommands.ExecuteButton)
-        evtmgr.eventManager.Register(self.OnTreeCtrlCommandsSelectionChanged, wx.EVT_TREE_SEL_CHANGED, self.panelCommands.CommandsTree)
-        evtmgr.eventManager.Register(self.OnTreeCtrlItemActivated, wx.EVT_TREE_ITEM_ACTIVATED, self.panelCommands.CommandsTree)
-        evtmgr.eventManager.Register(self.OnUpdateNote, wx.EVT_BUTTON, self.panelNote.UpdateButton)
-        #property editor
-        self.panelProperties.pg.Bind(wxpg.EVT_PG_CHANGED, self.OnPropGridChanged)
-        #results panel
-        self.panelResults.results_list.OnCheckItem = self.OnResultsCheck
-
-    def _GetActiveFileIndex(self):
-        lib.playlist.Playlist = self.GetActivePlaylist()
-        #get the selected item from the tree
-        selected_item = self.panelPlaylists.PlaylistsTree.GetSelection()
-        #test if a playlist or a curve was double-clicked
-        if self.panelPlaylists.PlaylistsTree.ItemHasChildren(selected_item):
-            return -1
-        else:
-            count = 0
-            selected_item = self.panelPlaylists.PlaylistsTree.GetPrevSibling(selected_item)
-            while selected_item.IsOk():
-                count += 1
-                selected_item = self.panelPlaylists.PlaylistsTree.GetPrevSibling(selected_item)
-            return count
-
-    def _GetPlaylistTab(self, name):
-        for index, page in enumerate(self.plotNotebook._tabs._pages):
-            if page.caption == name:
-                return index
-        return -1
-
-    def _GetUniquePlaylistName(self, name):
-        playlist_name = name
-        count = 1
-        while playlist_name in self.playlists:
-            playlist_name = ''.join([name, str(count)])
-            count += 1
-        return playlist_name
-
-    def _RestorePerspective(self, name):
-        self._mgr.LoadPerspective(self._perspectives[name])
-        self.config['perspectives']['active'] = name
-        self._mgr.Update()
-        all_panes = self._mgr.GetAllPanes()
-        for pane in all_panes:
-            if not pane.name.startswith('toolbar'):
-                if pane.name == 'Assistant':
-                    self.MenuBar.FindItemById(ID_ViewAssistant).Check(pane.window.IsShown())
-                if pane.name == 'Folders':
-                    self.MenuBar.FindItemById(ID_ViewFolders).Check(pane.window.IsShown())
-                if pane.name == 'Playlists':
-                    self.MenuBar.FindItemById(ID_ViewPlaylists).Check(pane.window.IsShown())
-                if pane.name == 'Commands':
-                    self.MenuBar.FindItemById(ID_ViewCommands).Check(pane.window.IsShown())
-                if pane.name == 'Note':
-                    self.MenuBar.FindItemById(ID_ViewNote).Check(pane.window.IsShown())
-                if pane.name == 'Properties':
-                    self.MenuBar.FindItemById(ID_ViewProperties).Check(pane.window.IsShown())
-                if pane.name == 'Output':
-                    self.MenuBar.FindItemById(ID_ViewOutput).Check(pane.window.IsShown())
-                if pane.name == 'Results':
-                    self.MenuBar.FindItemById(ID_ViewResults).Check(pane.window.IsShown())
-
-    def _SavePerspectiveToFile(self, name, perspective):
-        filename = ''.join([name, '.txt'])
-        filename = lh.get_file_path(filename, ['perspectives'])
-        perspectivesFile = open(filename, 'w')
-        perspectivesFile.write(perspective)
-        perspectivesFile.close()
-
-    def _UnbindEvents(self):
-        #menu
-        evtmgr.eventManager.DeregisterListener(self.OnAbout)
-        evtmgr.eventManager.DeregisterListener(self.OnClose)
-        #toolbar
-        evtmgr.eventManager.DeregisterListener(self.OnNext)
-        evtmgr.eventManager.DeregisterListener(self.OnPrevious)
-        #commands tree
-        evtmgr.eventManager.DeregisterListener(self.OnExecute)
-        evtmgr.eventManager.DeregisterListener(self.OnTreeCtrlCommandsSelectionChanged)
-        evtmgr.eventManager.DeregisterListener(self.OnTreeCtrlItemActivated)
-        evtmgr.eventManager.DeregisterListener(self.OnUpdateNote)
-
-    def AddPlaylist(self, playlist=None, name='Untitled'):
-        if playlist and playlist.count > 0:
-            playlist.name = self._GetUniquePlaylistName(name)
-            playlist.reset()
-            self.AddToPlaylists(playlist)
-
-    def AddPlaylistFromFiles(self, files=[], name='Untitled'):
-        if files:
-            playlist = lib.playlist.Playlist(self, self.drivers)
-            for item in files:
-                playlist.add_curve(item)
-        if playlist.count > 0:
-            playlist.name = self._GetUniquePlaylistName(name)
-            playlist.reset()
-            self.AddTayliss(playlist)
-
-    def AddToPlaylists(self, playlist):
-        if playlist.count > 0:
-            #setup the playlist in the Playlist tree
-            tree_root = self.panelPlaylists.PlaylistsTree.GetRootItem()
-            playlist_root = self.panelPlaylists.PlaylistsTree.AppendItem(tree_root, playlist.name, 0)
-            #add all files to the Playlist tree
-#            files = {}
-            hide_curve_extension = self.GetBoolFromConfig('core', 'preferences', 'hide_curve_extension')
-            for index, file_to_add in enumerate(playlist.files):
-                #optionally remove the extension from the name of the curve
-                if hide_curve_extension:
-                    file_to_add.name = lh.remove_extension(file_to_add.name)
-                file_ID = self.panelPlaylists.PlaylistsTree.AppendItem(playlist_root, file_to_add.name, 1)
-                if index == playlist.index:
-                    self.panelPlaylists.PlaylistsTree.SelectItem(file_ID)
-            playlist.reset()
-            #create the plot tab and add playlist to the dictionary
-            plotPanel = panels.plot.PlotPanel(self, ID_FirstPlot + len(self.playlists))
-            notebook_tab = self.plotNotebook.AddPage(plotPanel, playlist.name, True)
-            #tab_index = self.plotNotebook.GetSelection()
-            playlist.figure = plotPanel.get_figure()
-            self.playlists[playlist.name] = playlist
-            #self.playlists[playlist.name] = [playlist, figure]
-            self.panelPlaylists.PlaylistsTree.Expand(playlist_root)
-            self.statusbar.SetStatusText(playlist.get_status_string(), 0)
-            self.UpdateNote()
-            self.UpdatePlot()
-
-    def AppendToOutput(self, text):
-        self.panelOutput.AppendText(''.join([text, '\n']))
-
-    def AppliesPlotmanipulator(self, name):
-        '''
-        Returns True if the plotmanipulator 'name' is applied, False otherwise
-        name does not contain 'plotmanip_', just the name of the plotmanipulator (e.g. 'flatten')
-        '''
-        return self.GetBoolFromConfig('core', 'plotmanipulators', name)
-
-    def ApplyPlotmanipulators(self, plot, plot_file):
-        '''
-        Apply all active plotmanipulators.
-        '''
-        if plot is not None and plot_file is not None:
-            manipulated_plot = copy.deepcopy(plot)
-            for plotmanipulator in self.plotmanipulators:
-                if self.GetBoolFromConfig('core', 'plotmanipulators', plotmanipulator.name):
-                    manipulated_plot = plotmanipulator.method(manipulated_plot, plot_file)
-            return manipulated_plot
-
-    def CreateApplicationIcon(self):
-        iconFile = 'resources' + os.sep + 'microscope.ico'
-        icon = wx.Icon(iconFile, wx.BITMAP_TYPE_ICO)
-        self.SetIcon(icon)
-
-    def CreateCommandLine(self):
-        return wx.TextCtrl(self, -1, '', style=wx.NO_BORDER|wx.EXPAND)
-
-    def CreatePanelAssistant(self):
-        panel = wx.TextCtrl(self, -1, '', wx.Point(0, 0), wx.Size(150, 90), wx.NO_BORDER|wx.TE_MULTILINE)
-        panel.SetEditable(False)
-        return panel
-
-    def CreatePanelCommands(self):
-        return panels.commands.Commands(self)
-
-    def CreatePanelFolders(self):
-        #set file filters
-        filters = self.config['folders']['filters']
-        index = self.config['folders'].as_int('filterindex')
-        #set initial directory
-        folder = self.GetStringFromConfig('core', 'preferences', 'workdir')
-        return wx.GenericDirCtrl(self, -1, dir=folder, size=(200, 250), style=wx.DIRCTRL_SHOW_FILTERS, filter=filters, defaultFilter=index)
-
-    def CreatePanelNote(self):
-        return panels.note.Note(self)
-
-    def CreatePanelOutput(self):
-        return wx.TextCtrl(self, -1, '', wx.Point(0, 0), wx.Size(150, 90), wx.NO_BORDER|wx.TE_MULTILINE)
-
-    def CreatePanelPlaylists(self):
-        return panels.playlist.Playlists(self)
-
-    def CreatePanelProperties(self):
-        return panels.propertyeditor.PropertyEditor(self)
-
-    def CreatePanelResults(self):
-        return panels.results.Results(self)
-
-    def CreatePanelWelcome(self):
-        #TODO: move into panels.welcome
-        ctrl = wx.html.HtmlWindow(self, -1, wx.DefaultPosition, wx.Size(400, 300))
-        introStr = '<h1>Welcome to Hooke</h1>' + \
-                 '<h3>Features</h3>' + \
-                 '<ul>' + \
-                 '<li>View, annotate, measure force files</li>' + \
-                 '<li>Worm-like chain fit of force peaks</li>' + \
-                 '<li>Automatic convolution-based filtering of empty files</li>' + \
-                 '<li>Automatic fit and measurement of multiple force peaks</li>' + \
-                 '<li>Handles force-clamp force experiments (experimental)</li>' + \
-                 '<li>It is extensible by users by means of plugins and drivers</li>' + \
-                 '</ul>' + \
-                 '<p>See the <a href="http://code.google.com/p/hooke/wiki/DocumentationIndex">DocumentationIndex</a> for more information</p>'
-        ctrl.SetPage(introStr)
-        return ctrl
-
-    def CreateMenuBar(self):
-        menu_bar = wx.MenuBar()
-        self.SetMenuBar(menu_bar)
-        #file
-        file_menu = wx.Menu()
-        file_menu.Append(wx.ID_EXIT, 'Exit\tCtrl-Q')
-#        edit_menu.AppendSeparator();
-#        edit_menu.Append(ID_Config, 'Preferences')
-        #view
-        view_menu = wx.Menu()
-        view_menu.AppendCheckItem(ID_ViewFolders, 'Folders\tF5')
-        view_menu.AppendCheckItem(ID_ViewPlaylists, 'Playlists\tF6')
-        view_menu.AppendCheckItem(ID_ViewCommands, 'Commands\tF7')
-        view_menu.AppendCheckItem(ID_ViewProperties, 'Properties\tF8')
-        view_menu.AppendCheckItem(ID_ViewAssistant, 'Assistant\tF9')
-        view_menu.AppendCheckItem(ID_ViewResults, 'Results\tF10')
-        view_menu.AppendCheckItem(ID_ViewOutput, 'Output\tF11')
-        view_menu.AppendCheckItem(ID_ViewNote, 'Note\tF12')
-        #perspectives
-        perspectives_menu = wx.Menu()
-
-        #help
-        help_menu = wx.Menu()
-        help_menu.Append(wx.ID_ABOUT, 'About Hooke')
-        #put it all together
-        menu_bar.Append(file_menu, 'File')
-        menu_bar.Append(view_menu, 'View')
-        menu_bar.Append(perspectives_menu, "Perspectives")
-        self.UpdatePerspectivesMenu()
-        menu_bar.Append(help_menu, 'Help')
-
-    def CreateNotebook(self):
-        # create the notebook off-window to avoid flicker
-        client_size = self.GetClientSize()
-        ctrl = aui.AuiNotebook(self, -1, wx.Point(client_size.x, client_size.y), wx.Size(430, 200), self._notebook_style)
-        arts = [aui.AuiDefaultTabArt, aui.AuiSimpleTabArt, aui.VC71TabArt, aui.FF2TabArt, aui.VC8TabArt, aui.ChromeTabArt]
-        art = arts[self._notebook_theme]()
-        ctrl.SetArtProvider(art)
-        #uncomment if we find a nice icon
-        #page_bmp = wx.ArtProvider.GetBitmap(wx.ART_NORMAL_FILE, wx.ART_OTHER, wx.Size(16, 16))
-        ctrl.AddPage(self.CreatePanelWelcome(), "Welcome", False)
-        return ctrl
-
-    def CreateStatusbar(self):
-        statusbar = self.CreateStatusBar(2, wx.ST_SIZEGRIP)
-        statusbar.SetStatusWidths([-2, -3])
-        statusbar.SetStatusText('Ready', 0)
-        welcomeString=u'Welcome to Hooke (version '+__version__+', '+__release_name__+')!'
-        statusbar.SetStatusText(welcomeString, 1)
-        return statusbar
-
-    def CreateToolBarNavigation(self):
-        toolbar = wx.ToolBar(self, -1, wx.DefaultPosition, wx.DefaultSize, wx.TB_FLAT | wx.TB_NODIVIDER)
-        toolbar.SetToolBitmapSize(wx.Size(16,16))
-        toolbar_bmpBack = wx.ArtProvider_GetBitmap(wx.ART_GO_BACK, wx.ART_OTHER, wx.Size(16, 16))
-        toolbar_bmpForward = wx.ArtProvider_GetBitmap(wx.ART_GO_FORWARD, wx.ART_OTHER, wx.Size(16, 16))
-        toolbar.AddLabelTool(ID_Previous, 'Previous', toolbar_bmpBack, shortHelp='Previous curve')
-        toolbar.AddLabelTool(ID_Next, 'Next', toolbar_bmpForward, shortHelp='Next curve')
-        toolbar.Realize()
-        return toolbar
-
-    def DeleteFromPlaylists(self, name):
-        if name in self.playlists:
-            del self.playlists[name]
-        tree_root = self.panelPlaylists.PlaylistsTree.GetRootItem()
-        item, cookie = self.panelPlaylists.PlaylistsTree.GetFirstChild(tree_root)
-        while item.IsOk():
-            playlist_name = self.panelPlaylists.PlaylistsTree.GetItemText(item)
-            if playlist_name == name:
-                try:
-                    self.panelPlaylists.PlaylistsTree.Delete(item)
-                except:
-                    pass
-            item = self.panelPlaylists.PlaylistsTree.GetNextSibling(item)
-
-    def GetActiveFigure(self):
-        playlist_name = self.GetActivePlaylistName()
-        figure = self.playlists[playlist_name].figure
-        if figure is not None:
-            return figure
-        return None
-
-    def GetActiveFile(self):
-        playlist = self.GetActivePlaylist()
-        if playlist is not None:
-            return playlist.get_active_file()
-        return None
-
-    def GetActivePlaylist(self):
-        playlist_name = self.GetActivePlaylistName()
-        if playlist_name in self.playlists:
-            return self.playlists[playlist_name]
-        return None
-
-    def GetActivePlaylistName(self):
-        #get the selected item from the tree
-        selected_item = self.panelPlaylists.PlaylistsTree.GetSelection()
-        #test if a playlist or a curve was double-clicked
-        if self.panelPlaylists.PlaylistsTree.ItemHasChildren(selected_item):
-            playlist_item = selected_item
-        else:
-            #get the name of the playlist
-            playlist_item = self.panelPlaylists.PlaylistsTree.GetItemParent(selected_item)
-        #now we have a playlist
-        return self.panelPlaylists.PlaylistsTree.GetItemText(playlist_item)
-
-    def GetActivePlot(self):
-        playlist = self.GetActivePlaylist()
-        if playlist is not None:
-            return playlist.get_active_file().plot
-        return None
-
-    def GetDisplayedPlot(self):
-        plot = copy.deepcopy(self.displayed_plot)
-        #plot.curves = []
-        #plot.curves = copy.deepcopy(plot.curves)
-        return plot
-
-    def GetDisplayedPlotCorrected(self):
-        plot = copy.deepcopy(self.displayed_plot)
-        plot.curves = []
-        plot.curves = copy.deepcopy(plot.corrected_curves)
-        return plot
-
-    def GetDisplayedPlotRaw(self):
-        plot = copy.deepcopy(self.displayed_plot)
-        plot.curves = []
-        plot.curves = copy.deepcopy(plot.raw_curves)
-        return plot
-
-    def GetDockArt(self):
-        return self._mgr.GetArtProvider()
-
-    def GetBoolFromConfig(self, *args):
-        if len(args) == 2:
-            plugin = args[0]
-            section = args[0]
-            key = args[1]
-        elif len(args) == 3:
-            plugin = args[0]
-            section = args[1]
-            key = args[2]
-        if self.configs.has_key(plugin):
-            config = self.configs[plugin]
-            return config[section][key].as_bool('value')
-        return None
-
-    def GetColorFromConfig(self, *args):
-        if len(args) == 2:
-            plugin = args[0]
-            section = args[0]
-            key = args[1]
-        elif len(args) == 3:
-            plugin = args[0]
-            section = args[1]
-            key = args[2]
-        if self.configs.has_key(plugin):
-            config = self.configs[plugin]
-            color_tuple = eval(config[section][key]['value'])
-            color = [value / 255.0 for value in color_tuple]
-            return color
-        return None
-
-    def GetFloatFromConfig(self, *args):
-        if len(args) == 2:
-            plugin = args[0]
-            section = args[0]
-            key = args[1]
-        elif len(args) == 3:
-            plugin = args[0]
-            section = args[1]
-            key = args[2]
-        if self.configs.has_key(plugin):
-            config = self.configs[plugin]
-            return config[section][key].as_float('value')
-        return None
-
-    def GetIntFromConfig(self, *args):
-        if len(args) == 2:
-            plugin = args[0]
-            section = args[0]
-            key = args[1]
-        elif len(args) == 3:
-            plugin = args[0]
-            section = args[1]
-            key = args[2]
-        if self.configs.has_key(plugin):
-            config = self.configs[plugin]
-            return config[section][key].as_int('value')
-        return None
-
-    def GetStringFromConfig(self, *args):
-        if len(args) == 2:
-            plugin = args[0]
-            section = args[0]
-            key = args[1]
-        elif len(args) == 3:
-            plugin = args[0]
-            section = args[1]
-            key = args[2]
-        if self.configs.has_key(plugin):
-            config = self.configs[plugin]
-            return config[section][key]['value']
-        return None
-
-    def GetPlotmanipulator(self, name):
-        '''
-        Returns a plot manipulator function from its name
-        '''
-        for plotmanipulator in self.plotmanipulators:
-            if plotmanipulator.name == name:
-                return plotmanipulator
-        return None
-
-    def GetPerspectiveMenuItem(self, name):
-        if self._perspectives.has_key(name):
-            perspectives_list = [key for key, value in self._perspectives.iteritems()]
-            perspectives_list.sort()
-            index = perspectives_list.index(name)
-            perspective_Id = ID_FirstPerspective + index
-            menu_item = self.MenuBar.FindItemById(perspective_Id)
-            return menu_item
-        else:
-            return None
-
-    def HasPlotmanipulator(self, name):
-        '''
-        returns True if the plotmanipulator 'name' is loaded, False otherwise
-        '''
-        for plotmanipulator in self.plotmanipulators:
-            if plotmanipulator.command == name:
-                return True
-        return False
-
-    def OnAbout(self, event):
-        message = 'Hooke\n\n'+\
-            'A free, open source data analysis platform\n\n'+\
-            'Copyright 2006-2008 by Massimo Sandal\n'+\
-            'Copyright 2010 by Dr. Rolf Schmidt\n\n'+\
-            'Hooke is released under the GNU General Public License version 2.'
-        dialog = wx.MessageDialog(self, message, 'About Hooke', wx.OK | wx.ICON_INFORMATION)
-        dialog.ShowModal()
-        dialog.Destroy()
-
-    def OnClose(self, event):
-        #apply changes
-        self.config['main']['height'] = str(self.GetSize().GetHeight())
-        self.config['main']['left'] = str(self.GetPosition()[0])
-        self.config['main']['top'] = str(self.GetPosition()[1])
-        self.config['main']['width'] = str(self.GetSize().GetWidth())
-        #save the configuration file to 'config/hooke.ini'
-        self.config.write()
-        #save all plugin config files
-        for config in self.configs:
-            plugin_config = self.configs[config]
-            plugin_config.write()
-        self._UnbindEvents()
-        self._mgr.UnInit()
-        del self._mgr
-        self.Destroy()
-
-    def OnDeletePerspective(self, event):
-        dialog = panels.perspectives.Perspectives(self, -1, 'Delete perspective(s)')
-        dialog.CenterOnScreen()
-        dialog.ShowModal()
-        dialog.Destroy()
-        self.UpdatePerspectivesMenu()
-        #unfortunately, there is a bug in wxWidgets (Ticket #3258) that
-        #makes the radio item indicator in the menu disappear
-        #the code should be fine once this issue is fixed
-
-    def OnDirCtrlLeftDclick(self, event):
-        file_path = self.panelFolders.GetPath()
-        if os.path.isfile(file_path):
-            if file_path.endswith('.hkp'):
-                self.do_loadlist(file_path)
-        event.Skip()
-
-    def OnEraseBackground(self, event):
-        event.Skip()
-
-    def OnExecute(self, event):
-        item = self.panelCommands.CommandsTree.GetSelection()
-        if item.IsOk():
-            if not self.panelCommands.CommandsTree.ItemHasChildren(item):
-                item_text = self.panelCommands.CommandsTree.GetItemText(item)
-                command = ''.join(['self.do_', item_text, '()'])
-                #self.AppendToOutput(command + '\n')
-                exec(command)
-
-    def OnExit(self, event):
-        self.Close()
-
-    def OnNext(self, event):
-        '''
-        NEXT
-        Go to the next curve in the playlist.
-        If we are at the last curve, we come back to the first.
-        -----
-        Syntax: next, n
-        '''
-        selected_item = self.panelPlaylists.PlaylistsTree.GetSelection()
-        if self.panelPlaylists.PlaylistsTree.ItemHasChildren(selected_item):
-            #GetFirstChild returns a tuple
-            #we only need the first element
-            next_item = self.panelPlaylists.PlaylistsTree.GetFirstChild(selected_item)[0]
-        else:
-            next_item = self.panelPlaylists.PlaylistsTree.GetNextSibling(selected_item)
-            if not next_item.IsOk():
-                parent_item = self.panelPlaylists.PlaylistsTree.GetItemParent(selected_item)
-                #GetFirstChild returns a tuple
-                #we only need the first element
-                next_item = self.panelPlaylists.PlaylistsTree.GetFirstChild(parent_item)[0]
-        self.panelPlaylists.PlaylistsTree.SelectItem(next_item, True)
-        if not self.panelPlaylists.PlaylistsTree.ItemHasChildren(selected_item):
-            playlist = self.GetActivePlaylist()
-            if playlist.count > 1:
-                playlist.next()
-                self.statusbar.SetStatusText(playlist.get_status_string(), 0)
-                self.UpdateNote()
-                self.UpdatePlot()
-
-    def OnNotebookPageClose(self, event):
-        ctrl = event.GetEventObject()
-        playlist_name = ctrl.GetPageText(ctrl._curpage)
-        self.DeleteFromPlaylists(playlist_name)
-
-    def OnPaneClose(self, event):
-        event.Skip()
-
-    def OnPlaylistsLeftDclick(self, event):
-        if self.panelPlaylists.PlaylistsTree.Count > 0:
-            playlist_name = self.GetActivePlaylistName()
-            #if that playlist already exists
-            #we check if it is the active playlist (ie selected in panelPlaylists)
-            #and switch to it if necessary
-            if playlist_name in self.playlists:
-                index = self.plotNotebook.GetSelection()
-                current_playlist = self.plotNotebook.GetPageText(index)
-                if current_playlist != playlist_name:
-                    index = self._GetPlaylistTab(playlist_name)
-                    self.plotNotebook.SetSelection(index)
-                #if a curve was double-clicked
-                item = self.panelPlaylists.PlaylistsTree.GetSelection()
-                if not self.panelPlaylists.PlaylistsTree.ItemHasChildren(item):
-                    index = self._GetActiveFileIndex()
-                else:
-                    index = 0
-                if index >= 0:
-                    playlist = self.GetActivePlaylist()
-                    playlist.index = index
-                    self.statusbar.SetStatusText(playlist.get_status_string(), 0)
-                    self.UpdateNote()
-                    self.UpdatePlot()
-            #if you uncomment the following line, the tree will collapse/expand as well
-            #event.Skip()
-
-    def OnPlaylistsLeftDown(self, event):
-        hit_item, hit_flags = self.panelPlaylists.PlaylistsTree.HitTest(event.GetPosition())
-        if (hit_flags & wx.TREE_HITTEST_ONITEM) != 0:
-            self.panelPlaylists.PlaylistsTree.SelectItem(hit_item)
-            playlist_name = self.GetActivePlaylistName()
-            playlist = self.GetActivePlaylist()
-            #if a curve was clicked
-            item = self.panelPlaylists.PlaylistsTree.GetSelection()
-            if not self.panelPlaylists.PlaylistsTree.ItemHasChildren(item):
-                index = self._GetActiveFileIndex()
-                if index >= 0:
-                    playlist.index = index
-            self.playlists[playlist_name] = playlist
-        event.Skip()
-
-    def OnPrevious(self, event):
-        '''
-        PREVIOUS
-        Go to the previous curve in the playlist.
-        If we are at the first curve, we jump to the last.
-        -------
-        Syntax: previous, p
-        '''
-        #playlist = self.playlists[self.GetActivePlaylistName()][0]
-        #select the previous curve and tell the user if we wrapped around
-        #self.AppendToOutput(playlist.previous())
-        selected_item = self.panelPlaylists.PlaylistsTree.GetSelection()
-        if self.panelPlaylists.PlaylistsTree.ItemHasChildren(selected_item):
-            previous_item = self.panelPlaylists.PlaylistsTree.GetLastChild(selected_item)
-        else:
-            previous_item = self.panelPlaylists.PlaylistsTree.GetPrevSibling(selected_item)
-            if not previous_item.IsOk():
-                parent_item = self.panelPlaylists.PlaylistsTree.GetItemParent(selected_item)
-                previous_item = self.panelPlaylists.PlaylistsTree.GetLastChild(parent_item)
-        self.panelPlaylists.PlaylistsTree.SelectItem(previous_item, True)
-        playlist = self.GetActivePlaylist()
-        if playlist.count > 1:
-            playlist.previous()
-            self.statusbar.SetStatusText(playlist.get_status_string(), 0)
-            self.UpdateNote()
-            self.UpdatePlot()
-
-    def OnPropGridChanged (self, event):
-        prop = event.GetProperty()
-        if prop:
-            item_section = self.panelProperties.SelectedTreeItem
-            item_plugin = self.panelCommands.CommandsTree.GetItemParent(item_section)
-            plugin = self.panelCommands.CommandsTree.GetItemText(item_plugin)
-            config = self.configs[plugin]
-            property_section = self.panelCommands.CommandsTree.GetItemText(item_section)
-            property_key = prop.GetName()
-            property_value = prop.GetDisplayedString()
-
-            config[property_section][property_key]['value'] = property_value
-
-    def OnRestorePerspective(self, event):
-        name = self.MenuBar.FindItemById(event.GetId()).GetLabel()
-        self._RestorePerspective(name)
-
-    def OnResultsCheck(self, index, flag):
-        results = self.GetActivePlot().results
-        if results.has_key(self.results_str):
-            results[self.results_str].results[index].visible = flag
-            results[self.results_str].update()
-            self.UpdatePlot()
-
-    def OnSavePerspective(self, event):
-
-        def nameExists(name):
-            menu_position = self.MenuBar.FindMenu('Perspectives')
-            menu = self.MenuBar.GetMenu(menu_position)
-            for item in menu.GetMenuItems():
-                if item.GetText() == name:
-                    return True
-            return False
-
-        done = False
-        while not done:
-            dialog = wx.TextEntryDialog(self, 'Enter a name for the new perspective:', 'Save perspective')
-            dialog.SetValue('New perspective')
-            if dialog.ShowModal() != wx.ID_OK:
-                return
-            else:
-                name = dialog.GetValue()
-
-            if nameExists(name):
-                dialogConfirm = wx.MessageDialog(self, 'A file with this name already exists.\n\nDo you want to replace it?', 'Confirm', wx.YES_NO|wx.ICON_QUESTION|wx.CENTER)
-                if dialogConfirm.ShowModal() == wx.ID_YES:
-                    done = True
-            else:
-                done = True
-
-        perspective = self._mgr.SavePerspective()
-        self._SavePerspectiveToFile(name, perspective)
-        self.config['perspectives']['active'] = name
-        self.UpdatePerspectivesMenu()
-#        if nameExists(name):
-#            #check the corresponding menu item
-#            menu_item = self.GetPerspectiveMenuItem(name)
-#            #replace the perspectiveStr in _pespectives
-#            self._perspectives[name] = perspective
-#        else:
-#            #because we deal with radio items, we need to do some extra work
-#            #delete all menu items from the perspectives menu
-#            for item in self._perspectives_menu.GetMenuItems():
-#                self._perspectives_menu.DeleteItem(item)
-#            #recreate the perspectives menu
-#            self._perspectives_menu.Append(ID_SavePerspective, 'Save Perspective')
-#            self._perspectives_menu.Append(ID_DeletePerspective, 'Delete Perspective')
-#            self._perspectives_menu.AppendSeparator()
-#            #convert the perspectives dictionary into a list
-#            # the list contains:
-#            #[0]: name of the perspective
-#            #[1]: perspective
-#            perspectives_list = [key for key, value in self._perspectives.iteritems()]
-#            perspectives_list.append(name)
-#            perspectives_list.sort()
-#            #add all previous perspectives
-#            for index, item in enumerate(perspectives_list):
-#                menu_item = self._perspectives_menu.AppendRadioItem(ID_FirstPerspective + index, item)
-#                if item == name:
-#                    menu_item.Check()
-#            #add the new perspective to _perspectives
-#            self._perspectives[name] = perspective
-
-    def OnSize(self, event):
-        event.Skip()
-
-    def OnTreeCtrlCommandsSelectionChanged(self, event):
-        selected_item = event.GetItem()
-        if selected_item is not None:
-            plugin = ''
-            section = ''
-            #deregister/register the listener to avoid infinite loop
-            evtmgr.eventManager.DeregisterListener(self.OnTreeCtrlCommandsSelectionChanged)
-            self.panelCommands.CommandsTree.SelectItem(selected_item)
-            evtmgr.eventManager.Register(self.OnTreeCtrlCommandsSelectionChanged, wx.EVT_TREE_SEL_CHANGED, self.panelCommands.CommandsTree)
-            self.panelProperties.SelectedTreeItem = selected_item
-            #if a command was clicked
-            properties = []
-            if not self.panelCommands.CommandsTree.ItemHasChildren(selected_item):
-                item_plugin = self.panelCommands.CommandsTree.GetItemParent(selected_item)
-                plugin = self.panelCommands.CommandsTree.GetItemText(item_plugin)
-                if self.configs.has_key(plugin):
-                    #config = self.panelCommands.CommandsTree.GetPyData(item_plugin)
-                    config = self.configs[plugin]
-                    section = self.panelCommands.CommandsTree.GetItemText(selected_item)
-                    #display docstring in help window
-                    doc_string = eval('self.do_' + section + '.__doc__')
-                    if section in config:
-                        for option in config[section]:
-                            properties.append([option, config[section][option]])
-            else:
-                plugin = self.panelCommands.CommandsTree.GetItemText(selected_item)
-                if plugin != 'core':
-                    doc_string = eval('plugins.' + plugin + '.' + plugin + 'Commands.__doc__')
-                else:
-                    doc_string = 'The module "core" contains Hooke core functionality'
-            if doc_string is not None:
-                self.panelAssistant.ChangeValue(doc_string)
-            else:
-                self.panelAssistant.ChangeValue('')
-            panels.propertyeditor.PropertyEditor.Initialize(self.panelProperties, properties)
-            #save the currently selected command/plugin to the config file
-            self.config['command']['command'] = section
-            self.config['command']['plugin'] = plugin
-
-    def OnTreeCtrlItemActivated(self, event):
-        self.OnExecute(event)
-
-    def OnUpdateNote(self, event):
-        '''
-        Saves the note to the active file.
-        '''
-        active_file = self.GetActiveFile()
-        active_file.note = self.panelNote.Editor.GetValue()
-
-    def OnView(self, event):
-        menu_id = event.GetId()
-        menu_item = self.MenuBar.FindItemById(menu_id)
-        menu_label = menu_item.GetLabel()
-
-        pane = self._mgr.GetPane(menu_label)
-        pane.Show(not pane.IsShown())
-        #if we don't do the following, the Folders pane does not resize properly on hide/show
-        if pane.caption == 'Folders' and pane.IsShown() and pane.IsDocked():
-            #folders_size = pane.GetSize()
-            self.panelFolders.Fit()
-        self._mgr.Update()
-
-    def _clickize(self, xvector, yvector, index):
-        '''
-        Returns a ClickedPoint() object from an index and vectors of x, y coordinates
-        '''
-        point = lib.clickedpoint.ClickedPoint()
-        point.index = index
-        point.absolute_coords = xvector[index], yvector[index]
-        point.find_graph_coords(xvector, yvector)
-        return point
-
-    def _delta(self, message='Click 2 points', whatset=lh.RETRACTION):
-        '''
-        Calculates the difference between two clicked points
-        '''
-        clicked_points = self._measure_N_points(N=2, message=message, whatset=whatset)
-
-        plot = self.GetDisplayedPlotCorrected()
-        curve = plot.curves[whatset]
-
-        delta = lib.delta.Delta()
-        delta.point1.x = clicked_points[0].graph_coords[0]
-        delta.point1.y = clicked_points[0].graph_coords[1]
-        delta.point2.x = clicked_points[1].graph_coords[0]
-        delta.point2.y = clicked_points[1].graph_coords[1]
-        delta.units.x = curve.units.x
-        delta.units.y = curve.units.y
-
-        return delta
-
-    def _measure_N_points(self, N, message='', whatset=lh.RETRACTION):
-        '''
-        General helper function for N-points measurements
-        By default, measurements are done on the retraction
-        '''
-        if message:
-            dialog = wx.MessageDialog(None, message, 'Info', wx.OK)
-            dialog.ShowModal()
-
-        figure = self.GetActiveFigure()
-
-        xvector = self.displayed_plot.curves[whatset].x
-        yvector = self.displayed_plot.curves[whatset].y
-
-        clicked_points = figure.ginput(N, timeout=-1, show_clicks=True)
-
-        points = []
-        for clicked_point in clicked_points:
-            point = lib.clickedpoint.ClickedPoint()
-            point.absolute_coords = clicked_point[0], clicked_point[1]
-            point.dest = 0
-            #TODO: make this optional?
-            #so far, the clicked point is taken, not the corresponding data point
-            point.find_graph_coords(xvector, yvector)
-            point.is_line_edge = True
-            point.is_marker = True
-            points.append(point)
-        return points
-
-    def do_copylog(self):
-        '''
-        Copies all files in the current playlist that have a note to the destination folder.
-        destination: select folder where you want the files to be copied
-        use_LVDT_folder: when checked, the files will be copied to a folder called 'LVDT' in the destination folder (for MFP-1D files only)
-        '''
-        playlist = self.GetActivePlaylist()
-        if playlist is not None:
-            destination = self.GetStringFromConfig('core', 'copylog', 'destination')
-            if not os.path.isdir(destination):
-                os.makedirs(destination)
-            for current_file in playlist.files:
-                if current_file.note:
-                    shutil.copy(current_file.filename, destination)
-                    if current_file.driver.filetype == 'mfp1d':
-                        filename = current_file.filename.replace('deflection', 'LVDT', 1)
-                        path, name = os.path.split(filename)
-                        filename = os.path.join(path, 'lvdt', name)
-                        use_LVDT_folder = self.GetBoolFromConfig('core', 'copylog', 'use_LVDT_folder')
-                        if use_LVDT_folder:
-                            destination = os.path.join(destination, 'LVDT')
-                        shutil.copy(filename, destination)
-
-    def do_plotmanipulators(self):
-        '''
-        Please select the plotmanipulators you would like to use
-        and define the order in which they will be applied to the data.
-
-        Click 'Execute' to apply your changes.
-        '''
-        self.UpdatePlot()
-
-    def do_preferences(self):
-        '''
-        Please set general preferences for Hooke here.
-        hide_curve_extension: hides the extension of the force curve files.
-                              not recommended for 'picoforce' files
-        '''
-        pass
-
-    def do_test(self):
-        '''
-        Use this command for testing purposes. You find do_test in hooke.py.
-        '''
-        pass
-
-    def do_version(self):
-        '''
-        VERSION
-        ------
-        Prints the current version and codename, plus library version. Useful for debugging.
-        '''
-        self.AppendToOutput('Hooke ' + __version__ + ' (' + __codename__ + ')')
-        self.AppendToOutput('Released on: ' + __releasedate__)
-        self.AppendToOutput('---')
-        self.AppendToOutput('Python version: ' + python_version)
-        self.AppendToOutput('WxPython version: ' + wx_version)
-        self.AppendToOutput('Matplotlib version: ' + mpl_version)
-        self.AppendToOutput('SciPy version: ' + scipy_version)
-        self.AppendToOutput('NumPy version: ' + numpy_version)
-        self.AppendToOutput('ConfigObj version: ' + configobj_version)
-        self.AppendToOutput('wxPropertyGrid version: ' + '.'.join([str(PROPGRID_MAJOR), str(PROPGRID_MINOR), str(PROPGRID_RELEASE)]))
-        self.AppendToOutput('---')
-        self.AppendToOutput('Platform: ' + str(platform.uname()))
-        self.AppendToOutput('******************************')
-        self.AppendToOutput('Loaded plugins')
-        self.AppendToOutput('---')
-
-        #sort the plugins into alphabetical order
-        plugins_list = [key for key, value in self.plugins.iteritems()]
-        plugins_list.sort()
-        for plugin in plugins_list:
-            self.AppendToOutput(plugin)
-
-    def UpdateNote(self):
-        #update the note for the active file
-        active_file = self.GetActiveFile()
-        if active_file is not None:
-            self.panelNote.Editor.SetValue(active_file.note)
-
-    def UpdatePerspectivesMenu(self):
-        #add perspectives to menubar and _perspectives
-        perspectivesDirectory = os.path.join(lh.hookeDir, 'perspectives')
-        self._perspectives = {}
-        if os.path.isdir(perspectivesDirectory):
-            perspectiveFileNames = os.listdir(perspectivesDirectory)
-            for perspectiveFilename in perspectiveFileNames:
-                filename = lh.get_file_path(perspectiveFilename, ['perspectives'])
-                if os.path.isfile(filename):
-                    perspectiveFile = open(filename, 'rU')
-                    perspective = perspectiveFile.readline()
-                    perspectiveFile.close()
-                    if perspective:
-                        name, extension = os.path.splitext(perspectiveFilename)
-                        if extension == '.txt':
-                            self._perspectives[name] = perspective
-
-        #in case there are no perspectives
-        if not self._perspectives:
-            perspective = self._mgr.SavePerspective()
-            self._perspectives['Default'] = perspective
-            self._SavePerspectiveToFile('Default', perspective)
-
-        selected_perspective = self.config['perspectives']['active']
-        if not self._perspectives.has_key(selected_perspective):
-            self.config['perspectives']['active'] = 'Default'
-            selected_perspective = 'Default'
-
-        perspectives_list = [key for key, value in self._perspectives.iteritems()]
-        perspectives_list.sort()
-
-        #get the Perspectives menu
-        menu_position = self.MenuBar.FindMenu('Perspectives')
-        menu = self.MenuBar.GetMenu(menu_position)
-        #delete all menu items
-        for item in menu.GetMenuItems():
-            menu.DeleteItem(item)
-        #rebuild the menu by adding the standard menu items
-        menu.Append(ID_SavePerspective, 'Save Perspective')
-        menu.Append(ID_DeletePerspective, 'Delete Perspective')
-        menu.AppendSeparator()
-        #add all previous perspectives
-        for index, label in enumerate(perspectives_list):
-            menu_item = menu.AppendRadioItem(ID_FirstPerspective + index, label)
-            if label == selected_perspective:
-                self._RestorePerspective(label)
-                menu_item.Check(True)
-
-    def UpdatePlaylistsTreeSelection(self):
-        playlist = self.GetActivePlaylist()
-        if playlist is not None:
-            if playlist.index >= 0:
-                self.statusbar.SetStatusText(playlist.get_status_string(), 0)
-                self.UpdateNote()
-                self.UpdatePlot()
-
-    def UpdatePlot(self, plot=None):
-
-        def add_to_plot(curve, set_scale=True):
-            if curve.visible and curve.x and curve.y:
-                #get the index of the subplot to use as destination
-                destination = (curve.destination.column - 1) * number_of_rows + curve.destination.row - 1
-                #set all parameters for the plot
-                axes_list[destination].set_title(curve.title)
-                if set_scale:
-                    axes_list[destination].set_xlabel(curve.prefix.x + curve.units.x)
-                    axes_list[destination].set_ylabel(curve.prefix.y + curve.units.y)
-                    #set the formatting details for the scale
-                    formatter_x = lib.curve.PrefixFormatter(curve.decimals.x, curve.prefix.x, use_zero)
-                    formatter_y = lib.curve.PrefixFormatter(curve.decimals.y, curve.prefix.y, use_zero)
-                    axes_list[destination].xaxis.set_major_formatter(formatter_x)
-                    axes_list[destination].yaxis.set_major_formatter(formatter_y)
-                if curve.style == 'plot':
-                    axes_list[destination].plot(curve.x, curve.y, color=curve.color, label=curve.label, lw=curve.linewidth, zorder=1)
-                if curve.style == 'scatter':
-                    axes_list[destination].scatter(curve.x, curve.y, color=curve.color, label=curve.label, s=curve.size, zorder=2)
-                #add the legend if necessary
-                if curve.legend:
-                    axes_list[destination].legend()
-
-        if plot is None:
-            active_file = self.GetActiveFile()
-            if not active_file.driver:
-                #the first time we identify a file, the following need to be set
-                active_file.identify(self.drivers)
-                for curve in active_file.plot.curves:
-                    curve.decimals.x = self.GetIntFromConfig('core', 'preferences', 'x_decimals')
-                    curve.decimals.y = self.GetIntFromConfig('core', 'preferences', 'y_decimals')
-                    curve.legend = self.GetBoolFromConfig('core', 'preferences', 'legend')
-                    curve.prefix.x = self.GetStringFromConfig('core', 'preferences', 'x_prefix')
-                    curve.prefix.y = self.GetStringFromConfig('core', 'preferences', 'y_prefix')
-            if active_file.driver is None:
-                self.AppendToOutput('Invalid file: ' + active_file.filename)
-                return
-            self.displayed_plot = copy.deepcopy(active_file.plot)
-            #add raw curves to plot
-            self.displayed_plot.raw_curves = copy.deepcopy(self.displayed_plot.curves)
-            #apply all active plotmanipulators
-            self.displayed_plot = self.ApplyPlotmanipulators(self.displayed_plot, active_file)
-            #add corrected curves to plot
-            self.displayed_plot.corrected_curves = copy.deepcopy(self.displayed_plot.curves)
-        else:
-            active_file = None
-            self.displayed_plot = copy.deepcopy(plot)
-
-        figure = self.GetActiveFigure()
-        figure.clear()
-
-        #use '0' instead of e.g. '0.00' for scales
-        use_zero = self.GetBoolFromConfig('core', 'preferences', 'use_zero')
-        #optionally remove the extension from the title of the plot
-        hide_curve_extension = self.GetBoolFromConfig('core', 'preferences', 'hide_curve_extension')
-        if hide_curve_extension:
-            title = lh.remove_extension(self.displayed_plot.title)
-        else:
-            title = self.displayed_plot.title
-        figure.suptitle(title, fontsize=14)
-        #create the list of all axes necessary (rows and columns)
-        axes_list =[]
-        number_of_columns = max([curve.destination.column for curve in self.displayed_plot.curves])
-        number_of_rows = max([curve.destination.row for curve in self.displayed_plot.curves])
-        for index in range(number_of_rows * number_of_columns):
-            axes_list.append(figure.add_subplot(number_of_rows, number_of_columns, index + 1))
-
-        #add all curves to the corresponding plots
-        for curve in self.displayed_plot.curves:
-            add_to_plot(curve)
-
-        #make sure the titles of 'subplots' do not overlap with the axis labels of the 'main plot'
-        figure.subplots_adjust(hspace=0.3)
-
-        #display results
-        self.panelResults.ClearResults()
-        if self.displayed_plot.results.has_key(self.results_str):
-            for curve in self.displayed_plot.results[self.results_str].results:
-                add_to_plot(curve, set_scale=False)
-            self.panelResults.DisplayResults(self.displayed_plot.results[self.results_str])
-        else:
-            self.panelResults.ClearResults()
-        #refresh the plot
-        figure.canvas.draw()
-
-if __name__ == '__main__':
-
-    ## now, silence a deprecation warning for py2.3
-    import warnings
-    warnings.filterwarnings("ignore", "integer", DeprecationWarning, "wxPython.gdi")
-
-    redirect = True
-    if __debug__:
-        redirect=False
-
-    app = Hooke(redirect=redirect)
-
-    app.MainLoop()
diff --git a/hooke/ui/gui/__init__.py b/hooke/ui/gui/__init__.py
index 310902f..153b06d 100644
--- a/hooke/ui/gui/__init__.py
+++ b/hooke/ui/gui/__init__.py
@@ -3,6 +3,1392 @@
 """Defines :class:`GUI` providing a wxWindows interface to Hooke.
 """
 
+import lib.libhooke as lh
+import wxversion
+wxversion.select(lh.WX_GOOD)
+
+from configobj import ConfigObj
+import copy
+import os.path
+import platform
+import shutil
+import time
+
+import wx.html
+import wx.lib.agw.aui as aui
+import wx.lib.evtmgr as evtmgr
+import wx.propgrid as wxpg
+
+from matplotlib.ticker import FuncFormatter
+
+from configobj import __version__ as configobj_version
+from matplotlib import __version__ as mpl_version
+from numpy import __version__ as numpy_version
+from scipy import __version__ as scipy_version
+from sys import version as python_version
+from wx import __version__ as wx_version
+from wx.propgrid import PROPGRID_MAJOR
+from wx.propgrid import PROPGRID_MINOR
+from wx.propgrid import PROPGRID_RELEASE
+
+try:
+    from agw import cubecolourdialog as CCD
+except ImportError: # if it's not there locally, try the wxPython lib.
+    import wx.lib.agw.cubecolourdialog as CCD
+
+#set the Hooke directory
+lh.hookeDir = os.path.abspath(os.path.dirname(__file__))
+from config.config import config
+import drivers
+import lib.clickedpoint
+import lib.curve
+import lib.delta
+import lib.playlist
+import lib.plotmanipulator
+import lib.prettyformat
+import panels.commands
+import panels.note
+import panels.perspectives
+import panels.playlist
+import panels.plot
+import panels.propertyeditor
+import panels.results
+import plugins
+
+global __version__
+global __codename__
+global __releasedate__
+__version__ = lh.HOOKE_VERSION[0]
+__codename__ = lh.HOOKE_VERSION[1]
+__releasedate__ = lh.HOOKE_VERSION[2]
+__release_name__ = lh.HOOKE_VERSION[1]
+
+ID_About = wx.NewId()
+ID_Next = wx.NewId()
+ID_Previous = wx.NewId()
+
+ID_ViewAssistant = wx.NewId()
+ID_ViewCommands = wx.NewId()
+ID_ViewFolders = wx.NewId()
+ID_ViewNote = wx.NewId()
+ID_ViewOutput = wx.NewId()
+ID_ViewPlaylists = wx.NewId()
+ID_ViewProperties = wx.NewId()
+ID_ViewResults = wx.NewId()
+
+ID_DeletePerspective = wx.NewId()
+ID_SavePerspective = wx.NewId()
+
+ID_FirstPerspective = ID_SavePerspective + 1000
+#I hope we'll never have more than 1000 perspectives
+ID_FirstPlot = ID_SavePerspective + 2000
+
+class Hooke(wx.App):
+
+    def OnInit(self):
+        self.SetAppName('Hooke')
+        self.SetVendorName('')
+
+        window_height = config['main']['height']
+        window_left= config['main']['left']
+        window_top = config['main']['top']
+        window_width = config['main']['width']
+
+        #sometimes, the ini file gets confused and sets 'left'
+        #and 'top' to large negative numbers
+        #let's catch and fix this
+        #keep small negative numbers, the user might want those
+        if window_left < -window_width:
+            window_left = 0
+        if window_top < -window_height:
+            window_top = 0
+        window_position = (window_left, window_top)
+        window_size = (window_width, window_height)
+
+        #setup the splashscreen
+        if config['splashscreen']['show']:
+            filename = lh.get_file_path('hooke.jpg', ['resources'])
+            if os.path.isfile(filename):
+                bitmap = wx.Image(filename).ConvertToBitmap()
+                splashStyle = wx.SPLASH_CENTRE_ON_SCREEN|wx.SPLASH_TIMEOUT
+                splashDuration = config['splashscreen']['duration']
+                wx.SplashScreen(bitmap, splashStyle, splashDuration, None, -1)
+                wx.Yield()
+                '''
+                we need for the splash screen to disappear
+                for whatever reason splashDuration and sleep do not correspond to each other
+                at least not on Windows
+                maybe it's because duration is in milliseconds and sleep in seconds
+                thus we need to increase the sleep time a bit
+                a factor of 1.2 seems to work quite well
+                '''
+                sleepFactor = 1.2
+                time.sleep(sleepFactor * splashDuration / 1000)
+
+        plugin_objects = []
+        for plugin in config['plugins']:
+            if config['plugins'][plugin]:
+                filename = ''.join([plugin, '.py'])
+                path = lh.get_file_path(filename, ['plugins'])
+                if os.path.isfile(path):
+                    #get the corresponding filename and path
+                    plugin_name = ''.join(['plugins.', plugin])
+                    #import the module
+                    __import__(plugin_name)
+                    #get the file that contains the plugin
+                    class_file = getattr(plugins, plugin)
+                    #get the class that contains the commands
+                    class_object = getattr(class_file, plugin + 'Commands')
+                    plugin_objects.append(class_object)
+
+        def make_command_class(*bases):
+            #create metaclass with plugins and plotmanipulators
+            return type(HookeFrame)("HookeFramePlugged", bases + (HookeFrame,), {})
+        frame = make_command_class(*plugin_objects)(parent=None, id=wx.ID_ANY, title='Hooke', pos=window_position, size=window_size)
+        frame.Show(True)
+        self.SetTopWindow(frame)
+
+        return True
+
+    def OnExit(self):
+        return True
+
+
+class HookeFrame(wx.Frame):
+
+    def __init__(self, parent, id=-1, title='', pos=wx.DefaultPosition, size=wx.DefaultSize, style=wx.DEFAULT_FRAME_STYLE|wx.SUNKEN_BORDER|wx.CLIP_CHILDREN):
+        #call parent constructor
+        wx.Frame.__init__(self, parent, id, title, pos, size, style)
+        self.config = config
+        self.CreateApplicationIcon()
+        #self.configs contains: {the name of the Commands file: corresponding ConfigObj}
+        self.configs = {}
+        #self.displayed_plot holds the currently displayed plot
+        self.displayed_plot = None
+        #self.playlists contains: {the name of the playlist: [playlist, tabIndex, plotID]}
+        self.playlists = {}
+        #list of all plotmanipulators
+        self.plotmanipulators = []
+        #self.plugins contains: {the name of the plugin: [caption, function]}
+        self.plugins = {}
+        #self.results_str contains the type of results we want to display
+        self.results_str = 'wlc'
+
+        #tell FrameManager to manage this frame
+        self._mgr = aui.AuiManager()
+        self._mgr.SetManagedWindow(self)
+        #set the gradient style
+        self._mgr.GetArtProvider().SetMetric(aui.AUI_DOCKART_GRADIENT_TYPE, aui.AUI_GRADIENT_NONE)
+        #set transparent drag
+        self._mgr.SetFlags(self._mgr.GetFlags() ^ aui.AUI_MGR_TRANSPARENT_DRAG)
+
+        # set up default notebook style
+        self._notebook_style = aui.AUI_NB_DEFAULT_STYLE | aui.AUI_NB_TAB_EXTERNAL_MOVE | wx.NO_BORDER
+        self._notebook_theme = 0
+
+        #holds the perspectives: {name, perspective_str}
+        self._perspectives = {}
+
+        # min size for the frame itself isn't completely done.
+        # see the end up FrameManager::Update() for the test
+        # code. For now, just hard code a frame minimum size
+        self.SetMinSize(wx.Size(500, 500))
+        #define the list of active drivers
+        self.drivers = []
+        for driver in self.config['drivers']:
+            if self.config['drivers'][driver]:
+                #get the corresponding filename and path
+                filename = ''.join([driver, '.py'])
+                path = lh.get_file_path(filename, ['drivers'])
+                #the driver is active for driver[1] == 1
+                if os.path.isfile(path):
+                    #driver files are located in the 'drivers' subfolder
+                    driver_name = ''.join(['drivers.', driver])
+                    __import__(driver_name)
+                    class_file = getattr(drivers, driver)
+                    for command in dir(class_file):
+                        if command.endswith('Driver'):
+                            self.drivers.append(getattr(class_file, command))
+        #import all active plugins and plotmanips
+        #add 'core.ini' to self.configs (this is not a plugin and thus must be imported separately)
+        ini_path = lh.get_file_path('core.ini', ['plugins'])
+        plugin_config = ConfigObj(ini_path)
+        #self.config.merge(plugin_config)
+        self.configs['core'] = plugin_config
+        #existing_commands contains: {command: plugin}
+        existing_commands = {}
+        #make sure we execute _plug_init() for every command line plugin we import
+        for plugin in self.config['plugins']:
+            if self.config['plugins'][plugin]:
+                filename = ''.join([plugin, '.py'])
+                path = lh.get_file_path(filename, ['plugins'])
+                if os.path.isfile(path):
+                    #get the corresponding filename and path
+                    plugin_name = ''.join(['plugins.', plugin])
+                    try:
+                        #import the module
+                        module = __import__(plugin_name)
+                        #prepare the ini file for inclusion
+                        ini_path = path.replace('.py', '.ini')
+                        #include ini file
+                        plugin_config = ConfigObj(ini_path)
+                        #self.config.merge(plugin_config)
+                        self.configs[plugin] = plugin_config
+                        #add to plugins
+                        commands = eval('dir(module.' + plugin+ '.' + plugin + 'Commands)')
+                        #keep only commands (ie names that start with 'do_')
+                        commands = [command for command in commands if command.startswith('do_')]
+                        if commands:
+                            for command in commands:
+                                if existing_commands.has_key(command):
+                                    message_str = 'Adding "' + command + '" in plugin "' + plugin + '".\n\n'
+                                    message_str += '"' + command + '" already exists in "' + str(existing_commands[command]) + '".\n\n'
+                                    message_str += 'Only "' + command + '" in "' + str(existing_commands[command]) + '" will work.\n\n'
+                                    message_str += 'Please rename one of the commands in the source code and restart Hooke or disable one of the plugins.'
+                                    dialog = wx.MessageDialog(self, message_str, 'Warning', wx.OK|wx.ICON_WARNING|wx.CENTER)
+                                    dialog.ShowModal()
+                                    dialog.Destroy()
+                                existing_commands[command] = plugin
+                            self.plugins[plugin] = commands
+                        try:
+                            #initialize the plugin
+                            eval('module.' + plugin+ '.' + plugin + 'Commands._plug_init(self)')
+                        except AttributeError:
+                            pass
+                    except ImportError:
+                        pass
+        #add commands from hooke.py i.e. 'core' commands
+        commands = dir(HookeFrame)
+        commands = [command for command in commands if command.startswith('do_')]
+        if commands:
+            self.plugins['core'] = commands
+        #create panels here
+        self.panelAssistant = self.CreatePanelAssistant()
+        self.panelCommands = self.CreatePanelCommands()
+        self.panelFolders = self.CreatePanelFolders()
+        self.panelPlaylists = self.CreatePanelPlaylists()
+        self.panelProperties = self.CreatePanelProperties()
+        self.panelNote = self.CreatePanelNote()
+        self.panelOutput = self.CreatePanelOutput()
+        self.panelResults = self.CreatePanelResults()
+        self.plotNotebook = self.CreateNotebook()
+
+        # add panes
+        self._mgr.AddPane(self.panelFolders, aui.AuiPaneInfo().Name('Folders').Caption('Folders').Left().CloseButton(True).MaximizeButton(False))
+        self._mgr.AddPane(self.panelPlaylists, aui.AuiPaneInfo().Name('Playlists').Caption('Playlists').Left().CloseButton(True).MaximizeButton(False))
+        self._mgr.AddPane(self.panelNote, aui.AuiPaneInfo().Name('Note').Caption('Note').Left().CloseButton(True).MaximizeButton(False))
+        self._mgr.AddPane(self.plotNotebook, aui.AuiPaneInfo().Name('Plots').CenterPane().PaneBorder(False))
+        self._mgr.AddPane(self.panelCommands, aui.AuiPaneInfo().Name('Commands').Caption('Settings and commands').Right().CloseButton(True).MaximizeButton(False))
+        self._mgr.AddPane(self.panelProperties, aui.AuiPaneInfo().Name('Properties').Caption('Properties').Right().CloseButton(True).MaximizeButton(False))
+        self._mgr.AddPane(self.panelAssistant, aui.AuiPaneInfo().Name('Assistant').Caption('Assistant').Right().CloseButton(True).MaximizeButton(False))
+        self._mgr.AddPane(self.panelOutput, aui.AuiPaneInfo().Name('Output').Caption('Output').Bottom().CloseButton(True).MaximizeButton(False))
+        self._mgr.AddPane(self.panelResults, aui.AuiPaneInfo().Name('Results').Caption('Results').Bottom().CloseButton(True).MaximizeButton(False))
+        #self._mgr.AddPane(self.textCtrlCommandLine, aui.AuiPaneInfo().Name('CommandLine').CaptionVisible(False).Fixed().Bottom().Layer(2).CloseButton(False).MaximizeButton(False))
+        #self._mgr.AddPane(panelBottom, aui.AuiPaneInfo().Name("panelCommandLine").Bottom().Position(1).CloseButton(False).MaximizeButton(False))
+
+        # add the toolbars to the manager
+        #self.toolbar=self.CreateToolBar()
+        self.toolbarNavigation=self.CreateToolBarNavigation()
+        #self._mgr.AddPane(self.toolbar, aui.AuiPaneInfo().Name('toolbar').Caption('Toolbar').ToolbarPane().Top().Layer(1).Row(1).LeftDockable(False).RightDockable(False))
+        self._mgr.AddPane(self.toolbarNavigation, aui.AuiPaneInfo().Name('toolbarNavigation').Caption('Navigation').ToolbarPane().Top().Layer(1).Row(1).LeftDockable(False).RightDockable(False))
+        # "commit" all changes made to FrameManager
+        self._mgr.Update()
+        #create the menubar after the panes so that the default perspective
+        #is created with all panes open
+        self.CreateMenuBar()
+        self.statusbar = self.CreateStatusbar()
+        self._BindEvents()
+
+        name = self.config['perspectives']['active']
+        menu_item = self.GetPerspectiveMenuItem(name)
+        if menu_item is not None:
+            self.OnRestorePerspective(menu_item)
+            #TODO: config setting to remember playlists from last session
+        self.playlists = self.panelPlaylists.Playlists
+        #initialize the commands tree
+        self.panelCommands.Initialize(self.plugins)
+        for command in dir(self):
+            if command.startswith('plotmanip_'):
+                self.plotmanipulators.append(lib.plotmanipulator.Plotmanipulator(method=getattr(self, command), command=command))
+
+        #load default list, if possible
+        self.do_loadlist(self.GetStringFromConfig('core', 'preferences', 'playlist'))
+
+    def _BindEvents(self):
+        #TODO: figure out if we can use the eventManager for menu ranges
+        #and events of 'self' without raising an assertion fail error
+        self.Bind(wx.EVT_ERASE_BACKGROUND, self.OnEraseBackground)
+        self.Bind(wx.EVT_SIZE, self.OnSize)
+        self.Bind(wx.EVT_CLOSE, self.OnClose)
+        # Show How To Use The Closing Panes Event
+        self.Bind(aui.EVT_AUI_PANE_CLOSE, self.OnPaneClose)
+        self.Bind(aui.EVT_AUINOTEBOOK_PAGE_CLOSE, self.OnNotebookPageClose)
+        #menu
+        evtmgr.eventManager.Register(self.OnAbout, wx.EVT_MENU, win=self, id=wx.ID_ABOUT)
+        evtmgr.eventManager.Register(self.OnClose, wx.EVT_MENU, win=self, id=wx.ID_EXIT)
+        #view
+        self.Bind(wx.EVT_MENU_RANGE, self.OnView, id=ID_ViewAssistant, id2=ID_ViewResults)
+        #perspectives
+        self.Bind(wx.EVT_MENU, self.OnDeletePerspective, id=ID_DeletePerspective)
+        self.Bind(wx.EVT_MENU, self.OnSavePerspective, id=ID_SavePerspective)
+        self.Bind(wx.EVT_MENU_RANGE, self.OnRestorePerspective, id=ID_FirstPerspective, id2=ID_FirstPerspective+1000)
+        #toolbar
+        evtmgr.eventManager.Register(self.OnNext, wx.EVT_TOOL, win=self, id=ID_Next)
+        evtmgr.eventManager.Register(self.OnPrevious, wx.EVT_TOOL, win=self, id=ID_Previous)
+        #self.Bind(.EVT_AUITOOLBAR_TOOL_DROPDOWN, self.OnDropDownToolbarItem, id=ID_DropDownToolbarItem)
+        #dir control
+        treeCtrl = self.panelFolders.GetTreeCtrl()
+        #tree.Bind(wx.EVT_LEFT_UP, self.OnDirCtrl1LeftUp)
+        #tree.Bind(wx.EVT_LEFT_DOWN, self.OnGenericDirCtrl1LeftDown)
+        treeCtrl.Bind(wx.EVT_LEFT_DCLICK, self.OnDirCtrlLeftDclick)
+        #playlist tree
+        self.panelPlaylists.PlaylistsTree.Bind(wx.EVT_LEFT_DOWN, self.OnPlaylistsLeftDown)
+        self.panelPlaylists.PlaylistsTree.Bind(wx.EVT_LEFT_DCLICK, self.OnPlaylistsLeftDclick)
+        #commands tree
+        evtmgr.eventManager.Register(self.OnExecute, wx.EVT_BUTTON, self.panelCommands.ExecuteButton)
+        evtmgr.eventManager.Register(self.OnTreeCtrlCommandsSelectionChanged, wx.EVT_TREE_SEL_CHANGED, self.panelCommands.CommandsTree)
+        evtmgr.eventManager.Register(self.OnTreeCtrlItemActivated, wx.EVT_TREE_ITEM_ACTIVATED, self.panelCommands.CommandsTree)
+        evtmgr.eventManager.Register(self.OnUpdateNote, wx.EVT_BUTTON, self.panelNote.UpdateButton)
+        #property editor
+        self.panelProperties.pg.Bind(wxpg.EVT_PG_CHANGED, self.OnPropGridChanged)
+        #results panel
+        self.panelResults.results_list.OnCheckItem = self.OnResultsCheck
+
+    def _GetActiveFileIndex(self):
+        lib.playlist.Playlist = self.GetActivePlaylist()
+        #get the selected item from the tree
+        selected_item = self.panelPlaylists.PlaylistsTree.GetSelection()
+        #test if a playlist or a curve was double-clicked
+        if self.panelPlaylists.PlaylistsTree.ItemHasChildren(selected_item):
+            return -1
+        else:
+            count = 0
+            selected_item = self.panelPlaylists.PlaylistsTree.GetPrevSibling(selected_item)
+            while selected_item.IsOk():
+                count += 1
+                selected_item = self.panelPlaylists.PlaylistsTree.GetPrevSibling(selected_item)
+            return count
+
+    def _GetPlaylistTab(self, name):
+        for index, page in enumerate(self.plotNotebook._tabs._pages):
+            if page.caption == name:
+                return index
+        return -1
+
+    def _GetUniquePlaylistName(self, name):
+        playlist_name = name
+        count = 1
+        while playlist_name in self.playlists:
+            playlist_name = ''.join([name, str(count)])
+            count += 1
+        return playlist_name
+
+    def _RestorePerspective(self, name):
+        self._mgr.LoadPerspective(self._perspectives[name])
+        self.config['perspectives']['active'] = name
+        self._mgr.Update()
+        all_panes = self._mgr.GetAllPanes()
+        for pane in all_panes:
+            if not pane.name.startswith('toolbar'):
+                if pane.name == 'Assistant':
+                    self.MenuBar.FindItemById(ID_ViewAssistant).Check(pane.window.IsShown())
+                if pane.name == 'Folders':
+                    self.MenuBar.FindItemById(ID_ViewFolders).Check(pane.window.IsShown())
+                if pane.name == 'Playlists':
+                    self.MenuBar.FindItemById(ID_ViewPlaylists).Check(pane.window.IsShown())
+                if pane.name == 'Commands':
+                    self.MenuBar.FindItemById(ID_ViewCommands).Check(pane.window.IsShown())
+                if pane.name == 'Note':
+                    self.MenuBar.FindItemById(ID_ViewNote).Check(pane.window.IsShown())
+                if pane.name == 'Properties':
+                    self.MenuBar.FindItemById(ID_ViewProperties).Check(pane.window.IsShown())
+                if pane.name == 'Output':
+                    self.MenuBar.FindItemById(ID_ViewOutput).Check(pane.window.IsShown())
+                if pane.name == 'Results':
+                    self.MenuBar.FindItemById(ID_ViewResults).Check(pane.window.IsShown())
+
+    def _SavePerspectiveToFile(self, name, perspective):
+        filename = ''.join([name, '.txt'])
+        filename = lh.get_file_path(filename, ['perspectives'])
+        perspectivesFile = open(filename, 'w')
+        perspectivesFile.write(perspective)
+        perspectivesFile.close()
+
+    def _UnbindEvents(self):
+        #menu
+        evtmgr.eventManager.DeregisterListener(self.OnAbout)
+        evtmgr.eventManager.DeregisterListener(self.OnClose)
+        #toolbar
+        evtmgr.eventManager.DeregisterListener(self.OnNext)
+        evtmgr.eventManager.DeregisterListener(self.OnPrevious)
+        #commands tree
+        evtmgr.eventManager.DeregisterListener(self.OnExecute)
+        evtmgr.eventManager.DeregisterListener(self.OnTreeCtrlCommandsSelectionChanged)
+        evtmgr.eventManager.DeregisterListener(self.OnTreeCtrlItemActivated)
+        evtmgr.eventManager.DeregisterListener(self.OnUpdateNote)
+
+    def AddPlaylist(self, playlist=None, name='Untitled'):
+        if playlist and playlist.count > 0:
+            playlist.name = self._GetUniquePlaylistName(name)
+            playlist.reset()
+            self.AddToPlaylists(playlist)
+
+    def AddPlaylistFromFiles(self, files=[], name='Untitled'):
+        if files:
+            playlist = lib.playlist.Playlist(self, self.drivers)
+            for item in files:
+                playlist.add_curve(item)
+        if playlist.count > 0:
+            playlist.name = self._GetUniquePlaylistName(name)
+            playlist.reset()
+            self.AddTayliss(playlist)
+
+    def AddToPlaylists(self, playlist):
+        if playlist.count > 0:
+            #setup the playlist in the Playlist tree
+            tree_root = self.panelPlaylists.PlaylistsTree.GetRootItem()
+            playlist_root = self.panelPlaylists.PlaylistsTree.AppendItem(tree_root, playlist.name, 0)
+            #add all files to the Playlist tree
+#            files = {}
+            hide_curve_extension = self.GetBoolFromConfig('core', 'preferences', 'hide_curve_extension')
+            for index, file_to_add in enumerate(playlist.files):
+                #optionally remove the extension from the name of the curve
+                if hide_curve_extension:
+                    file_to_add.name = lh.remove_extension(file_to_add.name)
+                file_ID = self.panelPlaylists.PlaylistsTree.AppendItem(playlist_root, file_to_add.name, 1)
+                if index == playlist.index:
+                    self.panelPlaylists.PlaylistsTree.SelectItem(file_ID)
+            playlist.reset()
+            #create the plot tab and add playlist to the dictionary
+            plotPanel = panels.plot.PlotPanel(self, ID_FirstPlot + len(self.playlists))
+            notebook_tab = self.plotNotebook.AddPage(plotPanel, playlist.name, True)
+            #tab_index = self.plotNotebook.GetSelection()
+            playlist.figure = plotPanel.get_figure()
+            self.playlists[playlist.name] = playlist
+            #self.playlists[playlist.name] = [playlist, figure]
+            self.panelPlaylists.PlaylistsTree.Expand(playlist_root)
+            self.statusbar.SetStatusText(playlist.get_status_string(), 0)
+            self.UpdateNote()
+            self.UpdatePlot()
+
+    def AppendToOutput(self, text):
+        self.panelOutput.AppendText(''.join([text, '\n']))
+
+    def AppliesPlotmanipulator(self, name):
+        '''
+        Returns True if the plotmanipulator 'name' is applied, False otherwise
+        name does not contain 'plotmanip_', just the name of the plotmanipulator (e.g. 'flatten')
+        '''
+        return self.GetBoolFromConfig('core', 'plotmanipulators', name)
+
+    def ApplyPlotmanipulators(self, plot, plot_file):
+        '''
+        Apply all active plotmanipulators.
+        '''
+        if plot is not None and plot_file is not None:
+            manipulated_plot = copy.deepcopy(plot)
+            for plotmanipulator in self.plotmanipulators:
+                if self.GetBoolFromConfig('core', 'plotmanipulators', plotmanipulator.name):
+                    manipulated_plot = plotmanipulator.method(manipulated_plot, plot_file)
+            return manipulated_plot
+
+    def CreateApplicationIcon(self):
+        iconFile = 'resources' + os.sep + 'microscope.ico'
+        icon = wx.Icon(iconFile, wx.BITMAP_TYPE_ICO)
+        self.SetIcon(icon)
+
+    def CreateCommandLine(self):
+        return wx.TextCtrl(self, -1, '', style=wx.NO_BORDER|wx.EXPAND)
+
+    def CreatePanelAssistant(self):
+        panel = wx.TextCtrl(self, -1, '', wx.Point(0, 0), wx.Size(150, 90), wx.NO_BORDER|wx.TE_MULTILINE)
+        panel.SetEditable(False)
+        return panel
+
+    def CreatePanelCommands(self):
+        return panels.commands.Commands(self)
+
+    def CreatePanelFolders(self):
+        #set file filters
+        filters = self.config['folders']['filters']
+        index = self.config['folders'].as_int('filterindex')
+        #set initial directory
+        folder = self.GetStringFromConfig('core', 'preferences', 'workdir')
+        return wx.GenericDirCtrl(self, -1, dir=folder, size=(200, 250), style=wx.DIRCTRL_SHOW_FILTERS, filter=filters, defaultFilter=index)
+
+    def CreatePanelNote(self):
+        return panels.note.Note(self)
+
+    def CreatePanelOutput(self):
+        return wx.TextCtrl(self, -1, '', wx.Point(0, 0), wx.Size(150, 90), wx.NO_BORDER|wx.TE_MULTILINE)
+
+    def CreatePanelPlaylists(self):
+        return panels.playlist.Playlists(self)
+
+    def CreatePanelProperties(self):
+        return panels.propertyeditor.PropertyEditor(self)
+
+    def CreatePanelResults(self):
+        return panels.results.Results(self)
+
+    def CreatePanelWelcome(self):
+        #TODO: move into panels.welcome
+        ctrl = wx.html.HtmlWindow(self, -1, wx.DefaultPosition, wx.Size(400, 300))
+        introStr = '<h1>Welcome to Hooke</h1>' + \
+                 '<h3>Features</h3>' + \
+                 '<ul>' + \
+                 '<li>View, annotate, measure force files</li>' + \
+                 '<li>Worm-like chain fit of force peaks</li>' + \
+                 '<li>Automatic convolution-based filtering of empty files</li>' + \
+                 '<li>Automatic fit and measurement of multiple force peaks</li>' + \
+                 '<li>Handles force-clamp force experiments (experimental)</li>' + \
+                 '<li>It is extensible by users by means of plugins and drivers</li>' + \
+                 '</ul>' + \
+                 '<p>See the <a href="http://code.google.com/p/hooke/wiki/DocumentationIndex">DocumentationIndex</a> for more information</p>'
+        ctrl.SetPage(introStr)
+        return ctrl
+
+    def CreateMenuBar(self):
+        menu_bar = wx.MenuBar()
+        self.SetMenuBar(menu_bar)
+        #file
+        file_menu = wx.Menu()
+        file_menu.Append(wx.ID_EXIT, 'Exit\tCtrl-Q')
+#        edit_menu.AppendSeparator();
+#        edit_menu.Append(ID_Config, 'Preferences')
+        #view
+        view_menu = wx.Menu()
+        view_menu.AppendCheckItem(ID_ViewFolders, 'Folders\tF5')
+        view_menu.AppendCheckItem(ID_ViewPlaylists, 'Playlists\tF6')
+        view_menu.AppendCheckItem(ID_ViewCommands, 'Commands\tF7')
+        view_menu.AppendCheckItem(ID_ViewProperties, 'Properties\tF8')
+        view_menu.AppendCheckItem(ID_ViewAssistant, 'Assistant\tF9')
+        view_menu.AppendCheckItem(ID_ViewResults, 'Results\tF10')
+        view_menu.AppendCheckItem(ID_ViewOutput, 'Output\tF11')
+        view_menu.AppendCheckItem(ID_ViewNote, 'Note\tF12')
+        #perspectives
+        perspectives_menu = wx.Menu()
+
+        #help
+        help_menu = wx.Menu()
+        help_menu.Append(wx.ID_ABOUT, 'About Hooke')
+        #put it all together
+        menu_bar.Append(file_menu, 'File')
+        menu_bar.Append(view_menu, 'View')
+        menu_bar.Append(perspectives_menu, "Perspectives")
+        self.UpdatePerspectivesMenu()
+        menu_bar.Append(help_menu, 'Help')
+
+    def CreateNotebook(self):
+        # create the notebook off-window to avoid flicker
+        client_size = self.GetClientSize()
+        ctrl = aui.AuiNotebook(self, -1, wx.Point(client_size.x, client_size.y), wx.Size(430, 200), self._notebook_style)
+        arts = [aui.AuiDefaultTabArt, aui.AuiSimpleTabArt, aui.VC71TabArt, aui.FF2TabArt, aui.VC8TabArt, aui.ChromeTabArt]
+        art = arts[self._notebook_theme]()
+        ctrl.SetArtProvider(art)
+        #uncomment if we find a nice icon
+        #page_bmp = wx.ArtProvider.GetBitmap(wx.ART_NORMAL_FILE, wx.ART_OTHER, wx.Size(16, 16))
+        ctrl.AddPage(self.CreatePanelWelcome(), "Welcome", False)
+        return ctrl
+
+    def CreateStatusbar(self):
+        statusbar = self.CreateStatusBar(2, wx.ST_SIZEGRIP)
+        statusbar.SetStatusWidths([-2, -3])
+        statusbar.SetStatusText('Ready', 0)
+        welcomeString=u'Welcome to Hooke (version '+__version__+', '+__release_name__+')!'
+        statusbar.SetStatusText(welcomeString, 1)
+        return statusbar
+
+    def CreateToolBarNavigation(self):
+        toolbar = wx.ToolBar(self, -1, wx.DefaultPosition, wx.DefaultSize, wx.TB_FLAT | wx.TB_NODIVIDER)
+        toolbar.SetToolBitmapSize(wx.Size(16,16))
+        toolbar_bmpBack = wx.ArtProvider_GetBitmap(wx.ART_GO_BACK, wx.ART_OTHER, wx.Size(16, 16))
+        toolbar_bmpForward = wx.ArtProvider_GetBitmap(wx.ART_GO_FORWARD, wx.ART_OTHER, wx.Size(16, 16))
+        toolbar.AddLabelTool(ID_Previous, 'Previous', toolbar_bmpBack, shortHelp='Previous curve')
+        toolbar.AddLabelTool(ID_Next, 'Next', toolbar_bmpForward, shortHelp='Next curve')
+        toolbar.Realize()
+        return toolbar
+
+    def DeleteFromPlaylists(self, name):
+        if name in self.playlists:
+            del self.playlists[name]
+        tree_root = self.panelPlaylists.PlaylistsTree.GetRootItem()
+        item, cookie = self.panelPlaylists.PlaylistsTree.GetFirstChild(tree_root)
+        while item.IsOk():
+            playlist_name = self.panelPlaylists.PlaylistsTree.GetItemText(item)
+            if playlist_name == name:
+                try:
+                    self.panelPlaylists.PlaylistsTree.Delete(item)
+                except:
+                    pass
+            item = self.panelPlaylists.PlaylistsTree.GetNextSibling(item)
+
+    def GetActiveFigure(self):
+        playlist_name = self.GetActivePlaylistName()
+        figure = self.playlists[playlist_name].figure
+        if figure is not None:
+            return figure
+        return None
+
+    def GetActiveFile(self):
+        playlist = self.GetActivePlaylist()
+        if playlist is not None:
+            return playlist.get_active_file()
+        return None
+
+    def GetActivePlaylist(self):
+        playlist_name = self.GetActivePlaylistName()
+        if playlist_name in self.playlists:
+            return self.playlists[playlist_name]
+        return None
+
+    def GetActivePlaylistName(self):
+        #get the selected item from the tree
+        selected_item = self.panelPlaylists.PlaylistsTree.GetSelection()
+        #test if a playlist or a curve was double-clicked
+        if self.panelPlaylists.PlaylistsTree.ItemHasChildren(selected_item):
+            playlist_item = selected_item
+        else:
+            #get the name of the playlist
+            playlist_item = self.panelPlaylists.PlaylistsTree.GetItemParent(selected_item)
+        #now we have a playlist
+        return self.panelPlaylists.PlaylistsTree.GetItemText(playlist_item)
+
+    def GetActivePlot(self):
+        playlist = self.GetActivePlaylist()
+        if playlist is not None:
+            return playlist.get_active_file().plot
+        return None
+
+    def GetDisplayedPlot(self):
+        plot = copy.deepcopy(self.displayed_plot)
+        #plot.curves = []
+        #plot.curves = copy.deepcopy(plot.curves)
+        return plot
+
+    def GetDisplayedPlotCorrected(self):
+        plot = copy.deepcopy(self.displayed_plot)
+        plot.curves = []
+        plot.curves = copy.deepcopy(plot.corrected_curves)
+        return plot
+
+    def GetDisplayedPlotRaw(self):
+        plot = copy.deepcopy(self.displayed_plot)
+        plot.curves = []
+        plot.curves = copy.deepcopy(plot.raw_curves)
+        return plot
+
+    def GetDockArt(self):
+        return self._mgr.GetArtProvider()
+
+    def GetBoolFromConfig(self, *args):
+        if len(args) == 2:
+            plugin = args[0]
+            section = args[0]
+            key = args[1]
+        elif len(args) == 3:
+            plugin = args[0]
+            section = args[1]
+            key = args[2]
+        if self.configs.has_key(plugin):
+            config = self.configs[plugin]
+            return config[section][key].as_bool('value')
+        return None
+
+    def GetColorFromConfig(self, *args):
+        if len(args) == 2:
+            plugin = args[0]
+            section = args[0]
+            key = args[1]
+        elif len(args) == 3:
+            plugin = args[0]
+            section = args[1]
+            key = args[2]
+        if self.configs.has_key(plugin):
+            config = self.configs[plugin]
+            color_tuple = eval(config[section][key]['value'])
+            color = [value / 255.0 for value in color_tuple]
+            return color
+        return None
+
+    def GetFloatFromConfig(self, *args):
+        if len(args) == 2:
+            plugin = args[0]
+            section = args[0]
+            key = args[1]
+        elif len(args) == 3:
+            plugin = args[0]
+            section = args[1]
+            key = args[2]
+        if self.configs.has_key(plugin):
+            config = self.configs[plugin]
+            return config[section][key].as_float('value')
+        return None
+
+    def GetIntFromConfig(self, *args):
+        if len(args) == 2:
+            plugin = args[0]
+            section = args[0]
+            key = args[1]
+        elif len(args) == 3:
+            plugin = args[0]
+            section = args[1]
+            key = args[2]
+        if self.configs.has_key(plugin):
+            config = self.configs[plugin]
+            return config[section][key].as_int('value')
+        return None
+
+    def GetStringFromConfig(self, *args):
+        if len(args) == 2:
+            plugin = args[0]
+            section = args[0]
+            key = args[1]
+        elif len(args) == 3:
+            plugin = args[0]
+            section = args[1]
+            key = args[2]
+        if self.configs.has_key(plugin):
+            config = self.configs[plugin]
+            return config[section][key]['value']
+        return None
+
+    def GetPlotmanipulator(self, name):
+        '''
+        Returns a plot manipulator function from its name
+        '''
+        for plotmanipulator in self.plotmanipulators:
+            if plotmanipulator.name == name:
+                return plotmanipulator
+        return None
+
+    def GetPerspectiveMenuItem(self, name):
+        if self._perspectives.has_key(name):
+            perspectives_list = [key for key, value in self._perspectives.iteritems()]
+            perspectives_list.sort()
+            index = perspectives_list.index(name)
+            perspective_Id = ID_FirstPerspective + index
+            menu_item = self.MenuBar.FindItemById(perspective_Id)
+            return menu_item
+        else:
+            return None
+
+    def HasPlotmanipulator(self, name):
+        '''
+        returns True if the plotmanipulator 'name' is loaded, False otherwise
+        '''
+        for plotmanipulator in self.plotmanipulators:
+            if plotmanipulator.command == name:
+                return True
+        return False
+
+    def OnAbout(self, event):
+        message = 'Hooke\n\n'+\
+            'A free, open source data analysis platform\n\n'+\
+            'Copyright 2006-2008 by Massimo Sandal\n'+\
+            'Copyright 2010 by Dr. Rolf Schmidt\n\n'+\
+            'Hooke is released under the GNU General Public License version 2.'
+        dialog = wx.MessageDialog(self, message, 'About Hooke', wx.OK | wx.ICON_INFORMATION)
+        dialog.ShowModal()
+        dialog.Destroy()
+
+    def OnClose(self, event):
+        #apply changes
+        self.config['main']['height'] = str(self.GetSize().GetHeight())
+        self.config['main']['left'] = str(self.GetPosition()[0])
+        self.config['main']['top'] = str(self.GetPosition()[1])
+        self.config['main']['width'] = str(self.GetSize().GetWidth())
+        #save the configuration file to 'config/hooke.ini'
+        self.config.write()
+        #save all plugin config files
+        for config in self.configs:
+            plugin_config = self.configs[config]
+            plugin_config.write()
+        self._UnbindEvents()
+        self._mgr.UnInit()
+        del self._mgr
+        self.Destroy()
+
+    def OnDeletePerspective(self, event):
+        dialog = panels.perspectives.Perspectives(self, -1, 'Delete perspective(s)')
+        dialog.CenterOnScreen()
+        dialog.ShowModal()
+        dialog.Destroy()
+        self.UpdatePerspectivesMenu()
+        #unfortunately, there is a bug in wxWidgets (Ticket #3258) that
+        #makes the radio item indicator in the menu disappear
+        #the code should be fine once this issue is fixed
+
+    def OnDirCtrlLeftDclick(self, event):
+        file_path = self.panelFolders.GetPath()
+        if os.path.isfile(file_path):
+            if file_path.endswith('.hkp'):
+                self.do_loadlist(file_path)
+        event.Skip()
+
+    def OnEraseBackground(self, event):
+        event.Skip()
+
+    def OnExecute(self, event):
+        item = self.panelCommands.CommandsTree.GetSelection()
+        if item.IsOk():
+            if not self.panelCommands.CommandsTree.ItemHasChildren(item):
+                item_text = self.panelCommands.CommandsTree.GetItemText(item)
+                command = ''.join(['self.do_', item_text, '()'])
+                #self.AppendToOutput(command + '\n')
+                exec(command)
+
+    def OnExit(self, event):
+        self.Close()
+
+    def OnNext(self, event):
+        '''
+        NEXT
+        Go to the next curve in the playlist.
+        If we are at the last curve, we come back to the first.
+        -----
+        Syntax: next, n
+        '''
+        selected_item = self.panelPlaylists.PlaylistsTree.GetSelection()
+        if self.panelPlaylists.PlaylistsTree.ItemHasChildren(selected_item):
+            #GetFirstChild returns a tuple
+            #we only need the first element
+            next_item = self.panelPlaylists.PlaylistsTree.GetFirstChild(selected_item)[0]
+        else:
+            next_item = self.panelPlaylists.PlaylistsTree.GetNextSibling(selected_item)
+            if not next_item.IsOk():
+                parent_item = self.panelPlaylists.PlaylistsTree.GetItemParent(selected_item)
+                #GetFirstChild returns a tuple
+                #we only need the first element
+                next_item = self.panelPlaylists.PlaylistsTree.GetFirstChild(parent_item)[0]
+        self.panelPlaylists.PlaylistsTree.SelectItem(next_item, True)
+        if not self.panelPlaylists.PlaylistsTree.ItemHasChildren(selected_item):
+            playlist = self.GetActivePlaylist()
+            if playlist.count > 1:
+                playlist.next()
+                self.statusbar.SetStatusText(playlist.get_status_string(), 0)
+                self.UpdateNote()
+                self.UpdatePlot()
+
+    def OnNotebookPageClose(self, event):
+        ctrl = event.GetEventObject()
+        playlist_name = ctrl.GetPageText(ctrl._curpage)
+        self.DeleteFromPlaylists(playlist_name)
+
+    def OnPaneClose(self, event):
+        event.Skip()
+
+    def OnPlaylistsLeftDclick(self, event):
+        if self.panelPlaylists.PlaylistsTree.Count > 0:
+            playlist_name = self.GetActivePlaylistName()
+            #if that playlist already exists
+            #we check if it is the active playlist (ie selected in panelPlaylists)
+            #and switch to it if necessary
+            if playlist_name in self.playlists:
+                index = self.plotNotebook.GetSelection()
+                current_playlist = self.plotNotebook.GetPageText(index)
+                if current_playlist != playlist_name:
+                    index = self._GetPlaylistTab(playlist_name)
+                    self.plotNotebook.SetSelection(index)
+                #if a curve was double-clicked
+                item = self.panelPlaylists.PlaylistsTree.GetSelection()
+                if not self.panelPlaylists.PlaylistsTree.ItemHasChildren(item):
+                    index = self._GetActiveFileIndex()
+                else:
+                    index = 0
+                if index >= 0:
+                    playlist = self.GetActivePlaylist()
+                    playlist.index = index
+                    self.statusbar.SetStatusText(playlist.get_status_string(), 0)
+                    self.UpdateNote()
+                    self.UpdatePlot()
+            #if you uncomment the following line, the tree will collapse/expand as well
+            #event.Skip()
+
+    def OnPlaylistsLeftDown(self, event):
+        hit_item, hit_flags = self.panelPlaylists.PlaylistsTree.HitTest(event.GetPosition())
+        if (hit_flags & wx.TREE_HITTEST_ONITEM) != 0:
+            self.panelPlaylists.PlaylistsTree.SelectItem(hit_item)
+            playlist_name = self.GetActivePlaylistName()
+            playlist = self.GetActivePlaylist()
+            #if a curve was clicked
+            item = self.panelPlaylists.PlaylistsTree.GetSelection()
+            if not self.panelPlaylists.PlaylistsTree.ItemHasChildren(item):
+                index = self._GetActiveFileIndex()
+                if index >= 0:
+                    playlist.index = index
+            self.playlists[playlist_name] = playlist
+        event.Skip()
+
+    def OnPrevious(self, event):
+        '''
+        PREVIOUS
+        Go to the previous curve in the playlist.
+        If we are at the first curve, we jump to the last.
+        -------
+        Syntax: previous, p
+        '''
+        #playlist = self.playlists[self.GetActivePlaylistName()][0]
+        #select the previous curve and tell the user if we wrapped around
+        #self.AppendToOutput(playlist.previous())
+        selected_item = self.panelPlaylists.PlaylistsTree.GetSelection()
+        if self.panelPlaylists.PlaylistsTree.ItemHasChildren(selected_item):
+            previous_item = self.panelPlaylists.PlaylistsTree.GetLastChild(selected_item)
+        else:
+            previous_item = self.panelPlaylists.PlaylistsTree.GetPrevSibling(selected_item)
+            if not previous_item.IsOk():
+                parent_item = self.panelPlaylists.PlaylistsTree.GetItemParent(selected_item)
+                previous_item = self.panelPlaylists.PlaylistsTree.GetLastChild(parent_item)
+        self.panelPlaylists.PlaylistsTree.SelectItem(previous_item, True)
+        playlist = self.GetActivePlaylist()
+        if playlist.count > 1:
+            playlist.previous()
+            self.statusbar.SetStatusText(playlist.get_status_string(), 0)
+            self.UpdateNote()
+            self.UpdatePlot()
+
+    def OnPropGridChanged (self, event):
+        prop = event.GetProperty()
+        if prop:
+            item_section = self.panelProperties.SelectedTreeItem
+            item_plugin = self.panelCommands.CommandsTree.GetItemParent(item_section)
+            plugin = self.panelCommands.CommandsTree.GetItemText(item_plugin)
+            config = self.configs[plugin]
+            property_section = self.panelCommands.CommandsTree.GetItemText(item_section)
+            property_key = prop.GetName()
+            property_value = prop.GetDisplayedString()
+
+            config[property_section][property_key]['value'] = property_value
+
+    def OnRestorePerspective(self, event):
+        name = self.MenuBar.FindItemById(event.GetId()).GetLabel()
+        self._RestorePerspective(name)
+
+    def OnResultsCheck(self, index, flag):
+        results = self.GetActivePlot().results
+        if results.has_key(self.results_str):
+            results[self.results_str].results[index].visible = flag
+            results[self.results_str].update()
+            self.UpdatePlot()
+
+    def OnSavePerspective(self, event):
+
+        def nameExists(name):
+            menu_position = self.MenuBar.FindMenu('Perspectives')
+            menu = self.MenuBar.GetMenu(menu_position)
+            for item in menu.GetMenuItems():
+                if item.GetText() == name:
+                    return True
+            return False
+
+        done = False
+        while not done:
+            dialog = wx.TextEntryDialog(self, 'Enter a name for the new perspective:', 'Save perspective')
+            dialog.SetValue('New perspective')
+            if dialog.ShowModal() != wx.ID_OK:
+                return
+            else:
+                name = dialog.GetValue()
+
+            if nameExists(name):
+                dialogConfirm = wx.MessageDialog(self, 'A file with this name already exists.\n\nDo you want to replace it?', 'Confirm', wx.YES_NO|wx.ICON_QUESTION|wx.CENTER)
+                if dialogConfirm.ShowModal() == wx.ID_YES:
+                    done = True
+            else:
+                done = True
+
+        perspective = self._mgr.SavePerspective()
+        self._SavePerspectiveToFile(name, perspective)
+        self.config['perspectives']['active'] = name
+        self.UpdatePerspectivesMenu()
+#        if nameExists(name):
+#            #check the corresponding menu item
+#            menu_item = self.GetPerspectiveMenuItem(name)
+#            #replace the perspectiveStr in _pespectives
+#            self._perspectives[name] = perspective
+#        else:
+#            #because we deal with radio items, we need to do some extra work
+#            #delete all menu items from the perspectives menu
+#            for item in self._perspectives_menu.GetMenuItems():
+#                self._perspectives_menu.DeleteItem(item)
+#            #recreate the perspectives menu
+#            self._perspectives_menu.Append(ID_SavePerspective, 'Save Perspective')
+#            self._perspectives_menu.Append(ID_DeletePerspective, 'Delete Perspective')
+#            self._perspectives_menu.AppendSeparator()
+#            #convert the perspectives dictionary into a list
+#            # the list contains:
+#            #[0]: name of the perspective
+#            #[1]: perspective
+#            perspectives_list = [key for key, value in self._perspectives.iteritems()]
+#            perspectives_list.append(name)
+#            perspectives_list.sort()
+#            #add all previous perspectives
+#            for index, item in enumerate(perspectives_list):
+#                menu_item = self._perspectives_menu.AppendRadioItem(ID_FirstPerspective + index, item)
+#                if item == name:
+#                    menu_item.Check()
+#            #add the new perspective to _perspectives
+#            self._perspectives[name] = perspective
+
+    def OnSize(self, event):
+        event.Skip()
+
+    def OnTreeCtrlCommandsSelectionChanged(self, event):
+        selected_item = event.GetItem()
+        if selected_item is not None:
+            plugin = ''
+            section = ''
+            #deregister/register the listener to avoid infinite loop
+            evtmgr.eventManager.DeregisterListener(self.OnTreeCtrlCommandsSelectionChanged)
+            self.panelCommands.CommandsTree.SelectItem(selected_item)
+            evtmgr.eventManager.Register(self.OnTreeCtrlCommandsSelectionChanged, wx.EVT_TREE_SEL_CHANGED, self.panelCommands.CommandsTree)
+            self.panelProperties.SelectedTreeItem = selected_item
+            #if a command was clicked
+            properties = []
+            if not self.panelCommands.CommandsTree.ItemHasChildren(selected_item):
+                item_plugin = self.panelCommands.CommandsTree.GetItemParent(selected_item)
+                plugin = self.panelCommands.CommandsTree.GetItemText(item_plugin)
+                if self.configs.has_key(plugin):
+                    #config = self.panelCommands.CommandsTree.GetPyData(item_plugin)
+                    config = self.configs[plugin]
+                    section = self.panelCommands.CommandsTree.GetItemText(selected_item)
+                    #display docstring in help window
+                    doc_string = eval('self.do_' + section + '.__doc__')
+                    if section in config:
+                        for option in config[section]:
+                            properties.append([option, config[section][option]])
+            else:
+                plugin = self.panelCommands.CommandsTree.GetItemText(selected_item)
+                if plugin != 'core':
+                    doc_string = eval('plugins.' + plugin + '.' + plugin + 'Commands.__doc__')
+                else:
+                    doc_string = 'The module "core" contains Hooke core functionality'
+            if doc_string is not None:
+                self.panelAssistant.ChangeValue(doc_string)
+            else:
+                self.panelAssistant.ChangeValue('')
+            panels.propertyeditor.PropertyEditor.Initialize(self.panelProperties, properties)
+            #save the currently selected command/plugin to the config file
+            self.config['command']['command'] = section
+            self.config['command']['plugin'] = plugin
+
+    def OnTreeCtrlItemActivated(self, event):
+        self.OnExecute(event)
+
+    def OnUpdateNote(self, event):
+        '''
+        Saves the note to the active file.
+        '''
+        active_file = self.GetActiveFile()
+        active_file.note = self.panelNote.Editor.GetValue()
+
+    def OnView(self, event):
+        menu_id = event.GetId()
+        menu_item = self.MenuBar.FindItemById(menu_id)
+        menu_label = menu_item.GetLabel()
+
+        pane = self._mgr.GetPane(menu_label)
+        pane.Show(not pane.IsShown())
+        #if we don't do the following, the Folders pane does not resize properly on hide/show
+        if pane.caption == 'Folders' and pane.IsShown() and pane.IsDocked():
+            #folders_size = pane.GetSize()
+            self.panelFolders.Fit()
+        self._mgr.Update()
+
+    def _clickize(self, xvector, yvector, index):
+        '''
+        Returns a ClickedPoint() object from an index and vectors of x, y coordinates
+        '''
+        point = lib.clickedpoint.ClickedPoint()
+        point.index = index
+        point.absolute_coords = xvector[index], yvector[index]
+        point.find_graph_coords(xvector, yvector)
+        return point
+
+    def _delta(self, message='Click 2 points', whatset=lh.RETRACTION):
+        '''
+        Calculates the difference between two clicked points
+        '''
+        clicked_points = self._measure_N_points(N=2, message=message, whatset=whatset)
+
+        plot = self.GetDisplayedPlotCorrected()
+        curve = plot.curves[whatset]
+
+        delta = lib.delta.Delta()
+        delta.point1.x = clicked_points[0].graph_coords[0]
+        delta.point1.y = clicked_points[0].graph_coords[1]
+        delta.point2.x = clicked_points[1].graph_coords[0]
+        delta.point2.y = clicked_points[1].graph_coords[1]
+        delta.units.x = curve.units.x
+        delta.units.y = curve.units.y
+
+        return delta
+
+    def _measure_N_points(self, N, message='', whatset=lh.RETRACTION):
+        '''
+        General helper function for N-points measurements
+        By default, measurements are done on the retraction
+        '''
+        if message:
+            dialog = wx.MessageDialog(None, message, 'Info', wx.OK)
+            dialog.ShowModal()
+
+        figure = self.GetActiveFigure()
+
+        xvector = self.displayed_plot.curves[whatset].x
+        yvector = self.displayed_plot.curves[whatset].y
+
+        clicked_points = figure.ginput(N, timeout=-1, show_clicks=True)
+
+        points = []
+        for clicked_point in clicked_points:
+            point = lib.clickedpoint.ClickedPoint()
+            point.absolute_coords = clicked_point[0], clicked_point[1]
+            point.dest = 0
+            #TODO: make this optional?
+            #so far, the clicked point is taken, not the corresponding data point
+            point.find_graph_coords(xvector, yvector)
+            point.is_line_edge = True
+            point.is_marker = True
+            points.append(point)
+        return points
+
+    def do_copylog(self):
+        '''
+        Copies all files in the current playlist that have a note to the destination folder.
+        destination: select folder where you want the files to be copied
+        use_LVDT_folder: when checked, the files will be copied to a folder called 'LVDT' in the destination folder (for MFP-1D files only)
+        '''
+        playlist = self.GetActivePlaylist()
+        if playlist is not None:
+            destination = self.GetStringFromConfig('core', 'copylog', 'destination')
+            if not os.path.isdir(destination):
+                os.makedirs(destination)
+            for current_file in playlist.files:
+                if current_file.note:
+                    shutil.copy(current_file.filename, destination)
+                    if current_file.driver.filetype == 'mfp1d':
+                        filename = current_file.filename.replace('deflection', 'LVDT', 1)
+                        path, name = os.path.split(filename)
+                        filename = os.path.join(path, 'lvdt', name)
+                        use_LVDT_folder = self.GetBoolFromConfig('core', 'copylog', 'use_LVDT_folder')
+                        if use_LVDT_folder:
+                            destination = os.path.join(destination, 'LVDT')
+                        shutil.copy(filename, destination)
+
+    def do_plotmanipulators(self):
+        '''
+        Please select the plotmanipulators you would like to use
+        and define the order in which they will be applied to the data.
+
+        Click 'Execute' to apply your changes.
+        '''
+        self.UpdatePlot()
+
+    def do_preferences(self):
+        '''
+        Please set general preferences for Hooke here.
+        hide_curve_extension: hides the extension of the force curve files.
+                              not recommended for 'picoforce' files
+        '''
+        pass
+
+    def do_test(self):
+        '''
+        Use this command for testing purposes. You find do_test in hooke.py.
+        '''
+        pass
+
+    def do_version(self):
+        '''
+        VERSION
+        ------
+        Prints the current version and codename, plus library version. Useful for debugging.
+        '''
+        self.AppendToOutput('Hooke ' + __version__ + ' (' + __codename__ + ')')
+        self.AppendToOutput('Released on: ' + __releasedate__)
+        self.AppendToOutput('---')
+        self.AppendToOutput('Python version: ' + python_version)
+        self.AppendToOutput('WxPython version: ' + wx_version)
+        self.AppendToOutput('Matplotlib version: ' + mpl_version)
+        self.AppendToOutput('SciPy version: ' + scipy_version)
+        self.AppendToOutput('NumPy version: ' + numpy_version)
+        self.AppendToOutput('ConfigObj version: ' + configobj_version)
+        self.AppendToOutput('wxPropertyGrid version: ' + '.'.join([str(PROPGRID_MAJOR), str(PROPGRID_MINOR), str(PROPGRID_RELEASE)]))
+        self.AppendToOutput('---')
+        self.AppendToOutput('Platform: ' + str(platform.uname()))
+        self.AppendToOutput('******************************')
+        self.AppendToOutput('Loaded plugins')
+        self.AppendToOutput('---')
+
+        #sort the plugins into alphabetical order
+        plugins_list = [key for key, value in self.plugins.iteritems()]
+        plugins_list.sort()
+        for plugin in plugins_list:
+            self.AppendToOutput(plugin)
+
+    def UpdateNote(self):
+        #update the note for the active file
+        active_file = self.GetActiveFile()
+        if active_file is not None:
+            self.panelNote.Editor.SetValue(active_file.note)
+
+    def UpdatePerspectivesMenu(self):
+        #add perspectives to menubar and _perspectives
+        perspectivesDirectory = os.path.join(lh.hookeDir, 'perspectives')
+        self._perspectives = {}
+        if os.path.isdir(perspectivesDirectory):
+            perspectiveFileNames = os.listdir(perspectivesDirectory)
+            for perspectiveFilename in perspectiveFileNames:
+                filename = lh.get_file_path(perspectiveFilename, ['perspectives'])
+                if os.path.isfile(filename):
+                    perspectiveFile = open(filename, 'rU')
+                    perspective = perspectiveFile.readline()
+                    perspectiveFile.close()
+                    if perspective:
+                        name, extension = os.path.splitext(perspectiveFilename)
+                        if extension == '.txt':
+                            self._perspectives[name] = perspective
+
+        #in case there are no perspectives
+        if not self._perspectives:
+            perspective = self._mgr.SavePerspective()
+            self._perspectives['Default'] = perspective
+            self._SavePerspectiveToFile('Default', perspective)
+
+        selected_perspective = self.config['perspectives']['active']
+        if not self._perspectives.has_key(selected_perspective):
+            self.config['perspectives']['active'] = 'Default'
+            selected_perspective = 'Default'
+
+        perspectives_list = [key for key, value in self._perspectives.iteritems()]
+        perspectives_list.sort()
+
+        #get the Perspectives menu
+        menu_position = self.MenuBar.FindMenu('Perspectives')
+        menu = self.MenuBar.GetMenu(menu_position)
+        #delete all menu items
+        for item in menu.GetMenuItems():
+            menu.DeleteItem(item)
+        #rebuild the menu by adding the standard menu items
+        menu.Append(ID_SavePerspective, 'Save Perspective')
+        menu.Append(ID_DeletePerspective, 'Delete Perspective')
+        menu.AppendSeparator()
+        #add all previous perspectives
+        for index, label in enumerate(perspectives_list):
+            menu_item = menu.AppendRadioItem(ID_FirstPerspective + index, label)
+            if label == selected_perspective:
+                self._RestorePerspective(label)
+                menu_item.Check(True)
+
+    def UpdatePlaylistsTreeSelection(self):
+        playlist = self.GetActivePlaylist()
+        if playlist is not None:
+            if playlist.index >= 0:
+                self.statusbar.SetStatusText(playlist.get_status_string(), 0)
+                self.UpdateNote()
+                self.UpdatePlot()
+
+    def UpdatePlot(self, plot=None):
+
+        def add_to_plot(curve, set_scale=True):
+            if curve.visible and curve.x and curve.y:
+                #get the index of the subplot to use as destination
+                destination = (curve.destination.column - 1) * number_of_rows + curve.destination.row - 1
+                #set all parameters for the plot
+                axes_list[destination].set_title(curve.title)
+                if set_scale:
+                    axes_list[destination].set_xlabel(curve.prefix.x + curve.units.x)
+                    axes_list[destination].set_ylabel(curve.prefix.y + curve.units.y)
+                    #set the formatting details for the scale
+                    formatter_x = lib.curve.PrefixFormatter(curve.decimals.x, curve.prefix.x, use_zero)
+                    formatter_y = lib.curve.PrefixFormatter(curve.decimals.y, curve.prefix.y, use_zero)
+                    axes_list[destination].xaxis.set_major_formatter(formatter_x)
+                    axes_list[destination].yaxis.set_major_formatter(formatter_y)
+                if curve.style == 'plot':
+                    axes_list[destination].plot(curve.x, curve.y, color=curve.color, label=curve.label, lw=curve.linewidth, zorder=1)
+                if curve.style == 'scatter':
+                    axes_list[destination].scatter(curve.x, curve.y, color=curve.color, label=curve.label, s=curve.size, zorder=2)
+                #add the legend if necessary
+                if curve.legend:
+                    axes_list[destination].legend()
+
+        if plot is None:
+            active_file = self.GetActiveFile()
+            if not active_file.driver:
+                #the first time we identify a file, the following need to be set
+                active_file.identify(self.drivers)
+                for curve in active_file.plot.curves:
+                    curve.decimals.x = self.GetIntFromConfig('core', 'preferences', 'x_decimals')
+                    curve.decimals.y = self.GetIntFromConfig('core', 'preferences', 'y_decimals')
+                    curve.legend = self.GetBoolFromConfig('core', 'preferences', 'legend')
+                    curve.prefix.x = self.GetStringFromConfig('core', 'preferences', 'x_prefix')
+                    curve.prefix.y = self.GetStringFromConfig('core', 'preferences', 'y_prefix')
+            if active_file.driver is None:
+                self.AppendToOutput('Invalid file: ' + active_file.filename)
+                return
+            self.displayed_plot = copy.deepcopy(active_file.plot)
+            #add raw curves to plot
+            self.displayed_plot.raw_curves = copy.deepcopy(self.displayed_plot.curves)
+            #apply all active plotmanipulators
+            self.displayed_plot = self.ApplyPlotmanipulators(self.displayed_plot, active_file)
+            #add corrected curves to plot
+            self.displayed_plot.corrected_curves = copy.deepcopy(self.displayed_plot.curves)
+        else:
+            active_file = None
+            self.displayed_plot = copy.deepcopy(plot)
+
+        figure = self.GetActiveFigure()
+        figure.clear()
+
+        #use '0' instead of e.g. '0.00' for scales
+        use_zero = self.GetBoolFromConfig('core', 'preferences', 'use_zero')
+        #optionally remove the extension from the title of the plot
+        hide_curve_extension = self.GetBoolFromConfig('core', 'preferences', 'hide_curve_extension')
+        if hide_curve_extension:
+            title = lh.remove_extension(self.displayed_plot.title)
+        else:
+            title = self.displayed_plot.title
+        figure.suptitle(title, fontsize=14)
+        #create the list of all axes necessary (rows and columns)
+        axes_list =[]
+        number_of_columns = max([curve.destination.column for curve in self.displayed_plot.curves])
+        number_of_rows = max([curve.destination.row for curve in self.displayed_plot.curves])
+        for index in range(number_of_rows * number_of_columns):
+            axes_list.append(figure.add_subplot(number_of_rows, number_of_columns, index + 1))
+
+        #add all curves to the corresponding plots
+        for curve in self.displayed_plot.curves:
+            add_to_plot(curve)
+
+        #make sure the titles of 'subplots' do not overlap with the axis labels of the 'main plot'
+        figure.subplots_adjust(hspace=0.3)
+
+        #display results
+        self.panelResults.ClearResults()
+        if self.displayed_plot.results.has_key(self.results_str):
+            for curve in self.displayed_plot.results[self.results_str].results:
+                add_to_plot(curve, set_scale=False)
+            self.panelResults.DisplayResults(self.displayed_plot.results[self.results_str])
+        else:
+            self.panelResults.ClearResults()
+        #refresh the plot
+        figure.canvas.draw()
+
+if __name__ == '__main__':
+
+    ## now, silence a deprecation warning for py2.3
+    import warnings
+    warnings.filterwarnings("ignore", "integer", DeprecationWarning, "wxPython.gdi")
+
+    redirect = True
+    if __debug__:
+        redirect=False
+
+    app = Hooke(redirect=redirect)
+
+    app.MainLoop()
+
 from ..command import CommandExit, Exit, Command, Argument, StoreValue
 from ..interaction import Request, BooleanRequest, ReloadUserInterfaceConfig
 from ..ui import UserInterface, CommandMessage
-- 
2.26.2