-#!/usr/bin/env python\r
-# -*- coding: utf-8 -*-\r
-\r
-'''\r
-HOOKE - A force spectroscopy review & analysis tool\r
-\r
-(C) 2008 Massimo Sandal\r
-\r
-Copyright (C) 2008 Massimo Sandal (University of Bologna, Italy).\r
-\r
-This program is released under the GNU General Public License version 2.\r
-'''\r
-\r
-from .libhooke import HOOKE_VERSION, WX_GOOD\r
-\r
-import os\r
-\r
-import wxversion\r
-wxversion.select(WX_GOOD)\r
-import wx\r
-import wxmpl\r
-from wx.lib.newevent import NewEvent\r
-\r
-import matplotlib.numerix as nx\r
-import scipy as sp\r
-\r
-from threading import Thread\r
-import Queue\r
-\r
-from .hooke_cli import HookeCli\r
-from .libhooke import HookeConfig, ClickedPoint\r
-from . import libhookecurve as lhc\r
-\r
-#import file versions, just to know with what we're working...\r
-from hooke_cli import __version__ as hookecli_version\r
-\r
-global __version__\r
-global events_from_gui\r
-global config\r
-global CLI_PLUGINS\r
-global GUI_PLUGINS\r
-global LOADED_PLUGINS\r
-global PLOTMANIP_PLUGINS\r
-global FILE_DRIVERS\r
-\r
-__version__=HOOKE_VERSION[0]\r
-__release_name__=HOOKE_VERSION[1]\r
-\r
-events_from_gui=Queue.Queue() #GUI ---> CLI COMMUNICATION\r
-\r
-print 'Starting Hooke.'\r
-#CONFIGURATION FILE PARSING\r
-config_obj=HookeConfig()\r
-config=config_obj.load_config('hooke.conf')\r
-\r
-#IMPORTING PLUGINS\r
-\r
-CLI_PLUGINS=[]\r
-GUI_PLUGINS=[]\r
-PLOTMANIP_PLUGINS=[]\r
-LOADED_PLUGINS=[]\r
-\r
-plugin_commands_namespaces=[]\r
-plugin_gui_namespaces=[]\r
-for plugin_name in config['plugins']:\r
- try:\r
- hooke_module=__import__('hooke.plugin.'+plugin_name)\r
- plugin = getattr(hooke_module.plugin, plugin_name)\r
- try:\r
- #take Command plugin classes\r
- commands = getattr(plugin, plugin_name+'Commands')\r
- CLI_PLUGINS.append(commands)\r
- plugin_commands_namespaces.append(dir(commands))\r
- except:\r
- pass\r
- try:\r
- #take Gui plugin classes\r
- gui = getattr(plugin, plugin_name+'Gui')\r
- GUI_PLUGINS.append(gui)\r
- plugin_gui_namespaces.append(dir(gui))\r
- except:\r
- pass\r
- except ImportError:\r
- print 'Cannot find plugin ',plugin_name\r
- else:\r
- LOADED_PLUGINS.append(plugin_name)\r
- print 'Imported plugin ',plugin_name\r
-\r
-#eliminate names common to all namespaces\r
-for i,namespace in enumerate(plugin_commands_namespaces):\r
- plugin_commands_namespaces[i] = \\r
- filter(lambda item : not (item.startswith('__')\r
- or item == '_plug_init'),\r
- namespace)\r
-#check for conflicts in namespaces between plugins\r
-#FIXME: only in commands now, because I don't have Gui plugins to check\r
-#FIXME: how to check for plugin-defined variables (self.stuff) ??\r
-plugin_commands_names=[]\r
-whatplugin_defines=[]\r
-plugin_gui_names=[]\r
-for namespace,plugin_name in zip(plugin_commands_namespaces, config['plugins']):\r
- for item in namespace:\r
- if item in plugin_commands_names:\r
- i=plugin_commands_names.index(item) #we exploit the fact index gives the *first* occurrence of a name...\r
- print 'Error. Plugin %s defines a function %s already defined by %s!' \\r
- % (plugin_name, item, whatplugin_defines[i])\r
- print 'This should not happen. Please disable one or both plugins and contact the plugin authors to solve the conflict.'\r
- print 'Hooke cannot continue.'\r
- exit()\r
- else:\r
- plugin_commands_names.append(item)\r
- whatplugin_defines.append(plugin_name)\r
-\r
-\r
-config['loaded_plugins']=LOADED_PLUGINS #FIXME: kludge -this should be global but not in config!\r
-#IMPORTING DRIVERS\r
-#FIXME: code duplication\r
-FILE_DRIVERS=[]\r
-LOADED_DRIVERS=[]\r
-for driver_name in config['drivers']:\r
- try:\r
- hooke_module=__import__('hooke.driver.'+driver_name)\r
- driver = getattr(hooke_module.driver, driver_name)\r
- try:\r
- FILE_DRIVERS.append(getattr(driver, driver_name+'Driver'))\r
- except:\r
- pass\r
- except ImportError:\r
- print 'Cannot find driver ',driver_name\r
- else:\r
- LOADED_DRIVERS.append(driver_name)\r
- print 'Imported driver ',driver_name\r
-config['loaded_drivers']=LOADED_DRIVERS\r
-\r
-#LIST OF CUSTOM WX EVENTS FOR CLI ---> GUI COMMUNICATION\r
-#FIXME: do they need to be here?\r
-list_of_events={}\r
-\r
-plot_graph, EVT_PLOT = NewEvent()\r
-list_of_events['plot_graph']=plot_graph\r
-\r
-plot_contact, EVT_PLOT_CONTACT = NewEvent()\r
-list_of_events['plot_contact']=plot_contact\r
-\r
-measure_points, EVT_MEASURE_POINTS = NewEvent()\r
-list_of_events['measure_points']=measure_points\r
-\r
-export_image, EVT_EXPORT_IMAGE = NewEvent()\r
-list_of_events['export_image']=export_image\r
-\r
-close_plot, EVT_CLOSE_PLOT = NewEvent()\r
-list_of_events['close_plot'] = close_plot\r
-\r
-show_plots, EVT_SHOW_PLOTS = NewEvent()\r
-list_of_events['show_plots'] = show_plots\r
-\r
-get_displayed_plot, EVT_GET_DISPLAYED_PLOT = NewEvent()\r
-list_of_events['get_displayed_plot'] = get_displayed_plot\r
-#------------\r
-\r
-class CliThread(Thread):\r
-\r
- def __init__(self,frame,list_of_events):\r
- Thread.__init__(self)\r
-\r
- #here we have to put temporary references to pass to the cli object.\r
- self.frame=frame\r
- self.list_of_events=list_of_events\r
-\r
- self.debug=0 #to be used in the future\r
-\r
- def run(self):\r
- print '\n\nThis is Hooke, version',__version__ , __release_name__\r
- print\r
- print '(c) Massimo Sandal & others, 2006-2008. Released under the GNU Lesser General Public License Version 3'\r
- print 'Hooke is Free software.'\r
- print '----'\r
- print ''\r
-\r
- def make_command_class(*bases):\r
- #FIXME: perhaps redundant\r
- return type(HookeCli)("HookeCliPlugged", bases + (HookeCli,), {})\r
- cli = make_command_class(*CLI_PLUGINS)(self.frame,self.list_of_events,events_from_gui,config,FILE_DRIVERS)\r
- cli.cmdloop()\r
-\r
-'''\r
-GUI CODE\r
-\r
-FIXME: put it in a separate module in the future?\r
-'''\r
-class MainMenuBar(wx.MenuBar):\r
- '''\r
- Creates the menu bar\r
- '''\r
- def __init__(self):\r
- wx.MenuBar.__init__(self)\r
- '''the menu description. the key of the menu is XX&Menu, where XX is a number telling\r
- the order of the menus on the menubar.\r
- &Menu is the Menu text\r
- the corresponding argument is ('&Item', 'itemname'), where &Item is the item text and itemname\r
- the inner reference to use in the self.menu_items dictionary.\r
-\r
- See create_menus() to see how it works\r
-\r
- Note: the mechanism on page 124 of "wxPython in Action" is less awkward, maybe, but I want\r
- binding to be performed later. Perhaps I'm wrong :)\r
- ''' \r
-\r
- self.menu_desc={'00&File':[('&Open playlist','openplaymenu'),('&Exit','exitmenu')], \r
- '01&Edit':[('&Export text...','exporttextmenu'),('&Export image...','exportimagemenu')],\r
- '02&Help':[('&About Hooke','aboutmenu')]}\r
- self.create_menus()\r
-\r
- def create_menus(self):\r
- '''\r
- Smartish routine to create the menu from the self.menu_desc dictionary\r
- Hope it's a workable solution for the future.\r
- '''\r
- self.menus=[] #the menu objects to append to the menubar\r
- self.menu_items={} #the single menu items dictionary, to bind to events\r
-\r
- names=self.menu_desc.keys() #we gotta sort, because iterating keys goes in odd order\r
- names.sort()\r
-\r
- for name in names:\r
- self.menus.append(wx.Menu())\r
- for menu_item in self.menu_desc[name]:\r
- self.menu_items[menu_item[1]]=self.menus[-1].Append(-1, menu_item[0])\r
-\r
- for menu,name in zip(self.menus,names):\r
- self.Append(menu,name[2:])\r
-\r
-class MainPanel(wx.Panel):\r
- def __init__(self,parent,id): \r
-\r
- wx.Panel.__init__(self,parent,id)\r
- self.splitter = wx.SplitterWindow(self)\r
-\r
-ID_FRAME=100 \r
-class MainWindow(wx.Frame):\r
- '''we make a frame inheriting wx.Frame and setting up things on the init'''\r
- def __init__(self,parent,id,title):\r
-\r
- #-----------------------------\r
- #WX WIDGETS INITIALIZATION\r
-\r
- wx.Frame.__init__(self,parent,ID_FRAME,title,size=(800,600),style=wx.DEFAULT_FRAME_STYLE|wx.NO_FULL_REPAINT_ON_RESIZE)\r
-\r
- self.mainpanel=MainPanel(self,-1)\r
- self.cpanels=[]\r
-\r
- self.cpanels.append(wx.Panel(self.mainpanel.splitter,-1))\r
- self.cpanels.append(wx.Panel(self.mainpanel.splitter,-1))\r
-\r
- self.statusbar=wx.StatusBar(self,-1)\r
- self.SetStatusBar(self.statusbar)\r
-\r
- self.mainmenubar=MainMenuBar()\r
- self.SetMenuBar(self.mainmenubar)\r
-\r
- self.controls=[]\r
- self.figures=[]\r
- self.axes=[]\r
-\r
- #This is our matplotlib plot\r
- self.controls.append(wxmpl.PlotPanel(self.cpanels[0],-1))\r
- self.controls.append(wxmpl.PlotPanel(self.cpanels[1],-1))\r
- #These are our figure and axes, so to have easy references\r
- #Also, we initialize\r
- self.figures=[control.get_figure() for control in self.controls]\r
- self.axes=[figure.gca() for figure in self.figures]\r
-\r
- for i in range(len(self.axes)):\r
- self.axes[i].xaxis.set_major_formatter(EngrFormatter())\r
- self.axes[i].yaxis.set_major_formatter(EngrFormatter(2))\r
-\r
-\r
- self.cpanels[1].Hide()\r
- self.mainpanel.splitter.Initialize(self.cpanels[0])\r
-\r
- self.sizer_dance() #place/size the widgets\r
-\r
- self.controls[0].SetSize(self.cpanels[0].GetSize())\r
- self.controls[1].SetSize(self.cpanels[1].GetSize())\r
-\r
- #resize the frame to properly draw on Windows\r
- frameSize=self.GetSize()\r
- frameSize.DecBy(1, 1)\r
- self.SetSize(frameSize)\r
- '''\r
- #if you need the exact same size as before DecBy, uncomment this block\r
- frameSize.IncBy(1, 1)\r
- self.SetSize(frameSize)\r
- '''\r
-\r
- #-------------------------------------------\r
- #NON-WX WIDGETS INITIALIZATION\r
-\r
- #Flags.\r
- self.click_plot=0\r
-\r
- #FIXME: These could become a single flag with different (string?) values\r
- #self.on_measure_distance=False\r
- #self.on_measure_force=False\r
-\r
- self.plot_fit=False\r
-\r
- #Number of points to be clicked\r
- self.num_of_points = 2\r
-\r
- #Data.\r
- '''\r
- self.current_x_ext=[[],[]]\r
- self.current_y_ext=[[],[]]\r
- self.current_x_ret=[[],[]]\r
- self.current_y_ret=[[],[]]\r
-\r
-\r
- self.current_x_unit=[None,None]\r
- self.current_y_unit=[None,None]\r
- '''\r
-\r
- #Initialize xaxes, yaxes\r
- #FIXME: should come from config\r
- self.current_xaxes=0\r
- self.current_yaxes=0\r
-\r
- #Other\r
-\r
-\r
- self.index_buffer=[]\r
-\r
- self.clicked_points=[]\r
-\r
- self.measure_set=None\r
-\r
- self.events_from_gui = events_from_gui\r
-\r
- '''\r
- This dictionary keeps all the flags and the relative functon names that\r
- have to be called when a point is clicked.\r
- That is:\r
- - if point is clicked AND foo_flag=True\r
- - foo()\r
-\r
- Conversely, foo_flag is True if a corresponding event is launched by the CLI.\r
-\r
- self.ClickedPoints() takes care of handling this\r
- '''\r
-\r
- self.click_flags_functions={'measure_points':[False, 'MeasurePoints']}\r
-\r
- #Binding of custom events from CLI --> GUI functions! \r
- #FIXME: Should use the self.Bind() syntax\r
- EVT_PLOT(self, self.PlotCurve)\r
- EVT_PLOT_CONTACT(self, self.PlotContact)\r
- EVT_GET_DISPLAYED_PLOT(self, self.OnGetDisplayedPlot)\r
- EVT_MEASURE_POINTS(self, self.OnMeasurePoints)\r
- EVT_EXPORT_IMAGE(self,self.ExportImage)\r
- EVT_CLOSE_PLOT(self, self.OnClosePlot)\r
- EVT_SHOW_PLOTS(self, self.OnShowPlots)\r
-\r
- #This event and control decide what happens when I click on the plot 0.\r
- wxmpl.EVT_POINT(self, self.controls[0].GetId(), self.ClickPoint0)\r
- wxmpl.EVT_POINT(self, self.controls[1].GetId(), self.ClickPoint1)\r
-\r
- #RUN PLUGIN-SPECIFIC INITIALIZATION\r
- #make sure we execute _plug_init() for every command line plugin we import\r
- for plugin_name in config['plugins']:\r
- try:\r
- hooke_module=__import__('hooke.plugin.'+plugin_name)\r
- plugin = getattr(hooke_module.plugin, plugin_name)\r
- try:\r
- eval('plugin.'+plugin_name+'Gui._plug_init(self)')\r
- pass\r
- except AttributeError:\r
- pass\r
- except ImportError:\r
- pass\r
-\r
-\r
-\r
- #WX-SPECIFIC FUNCTIONS\r
- def sizer_dance(self):\r
- '''\r
- adjust size and placement of wxpython widgets.\r
- '''\r
- self.splittersizer = wx.BoxSizer(wx.VERTICAL)\r
- self.splittersizer.Add(self.mainpanel.splitter, 1, wx.EXPAND)\r
-\r
- self.plot1sizer = wx.BoxSizer()\r
- self.plot1sizer.Add(self.controls[0], 1, wx.EXPAND)\r
-\r
- self.plot2sizer = wx.BoxSizer()\r
- self.plot2sizer.Add(self.controls[1], 1, wx.EXPAND)\r
-\r
- self.panelsizer=wx.BoxSizer()\r
- self.panelsizer.Add(self.mainpanel, -1, wx.EXPAND)\r
-\r
- self.cpanels[0].SetSizer(self.plot1sizer)\r
- self.cpanels[1].SetSizer(self.plot2sizer)\r
-\r
- self.mainpanel.SetSizer(self.splittersizer)\r
- self.SetSizer(self.panelsizer)\r
-\r
- def binding_dance(self):\r
- self.Bind(wx.EVT_MENU, self.OnOpenPlayMenu, self.menubar.menu_items['openplaymenu'])\r
- self.Bind(wx.EVT_MENU, self.OnExitMenu, self.menubar.menu_items['exitmenu'])\r
- self.Bind(wx.EVT_MENU, self.OnExportText, self.menubar.menu_items['exporttextmenu'])\r
- self.Bind(wx.EVT_MENU, self.OnExportImage, self.menubar.menu_items['exportimagemenu'])\r
- self.Bind(wx.EVT_MENU, self.OnAboutMenu, self.menubar.menu_items['aboutmenu'])\r
-\r
- # DOUBLE PLOT MANAGEMENT\r
- #----------------------\r
- def show_both(self):\r
- '''\r
- Shows both plots.\r
- '''\r
- self.mainpanel.splitter.SplitHorizontally(self.cpanels[0],self.cpanels[1])\r
- self.mainpanel.splitter.SetSashGravity(0.5)\r
- self.mainpanel.splitter.SetSashPosition(300) #FIXME: we should get it and restore it\r
- self.mainpanel.splitter.UpdateSize()\r
-\r
- def close_plot(self,plot):\r
- '''\r
- Closes one plot - only if it's open\r
- '''\r
- if not self.cpanels[plot].IsShown():\r
- return\r
- if plot != 0:\r
- self.current_plot_dest = 0\r
- else:\r
- self.current_plot_dest = 1\r
- self.cpanels[plot].Hide()\r
- self.mainpanel.splitter.Unsplit(self.cpanels[plot])\r
- self.mainpanel.splitter.UpdateSize()\r
-\r
-\r
- def OnClosePlot(self,event):\r
- self.close_plot(event.to_close) \r
-\r
- def OnShowPlots(self,event):\r
- self.show_both()\r
-\r
-\r
- #FILE MENU FUNCTIONS\r
- #--------------------\r
- def OnOpenPlayMenu(self, event):\r
- pass \r
-\r
- def OnExitMenu(self,event):\r
- pass\r
-\r
- def OnExportText(self,event):\r
- pass\r
-\r
- def OnExportImage(self,event):\r
- pass\r
-\r
- def OnAboutMenu(self,event):\r
- pass\r
-\r
- #PLOT INTERACTION \r
- #---------------- \r
- def PlotCurve(self,event):\r
- '''\r
- plots the current ext,ret curve.\r
- '''\r
- dest=0\r
-\r
- #FIXME: BAD kludge following. There should be a well made plot queue mechanism, with replacements etc.\r
- #---\r
- #If we have only one plot in the event, we already have one in self.plots and this is a secondary plot,\r
- #do not erase self.plots but append the new plot to it.\r
- if len(event.plots) == 1 and event.plots[0].destination != 0 and len(self.plots) == 1:\r
- self.plots.append(event.plots[0])\r
- #if we already have two plots and a new secondary plot comes, we substitute the previous\r
- if len(event.plots) == 1 and event.plots[0].destination != 0 and len(self.plots) > 1:\r
- self.plots[1] = event.plots[0]\r
- else:\r
- self.plots = event.plots\r
-\r
- #FIXME. Should be in PlotObject, somehow\r
- c=0\r
- for plot in self.plots:\r
- if self.plots[c].styles==[]:\r
- self.plots[c].styles=[None for item in plot.vectors] \r
- if self.plots[c].colors==[]:\r
- self.plots[c].colors=[None for item in plot.vectors] \r
-\r
- for plot in self.plots:\r
- '''\r
- MAIN LOOP FOR ALL PLOTS (now only 2 are allowed but...)\r
- '''\r
- if 'destination' in dir(plot):\r
- dest=plot.destination\r
-\r
- #if the requested panel is not shown, show it\r
- if not ( self.cpanels[dest].IsShown() ):\r
- self.show_both()\r
-\r
- self.axes[dest].hold(False)\r
- self.current_vectors=plot.vectors\r
- self.current_title=plot.title\r
- self.current_plot_dest=dest #let's try this way to take into account the destination plot...\r
-\r
- c=0\r
-\r
- if len(plot.colors)==0:\r
- plot.colors=[None] * len(plot.vectors)\r
- if len(plot.styles)==0:\r
- plot.styles=[None] * len(plot.vectors) \r
-\r
- for vectors_to_plot in self.current_vectors: \r
- if plot.styles[c]=='scatter':\r
- if plot.colors[c]==None:\r
- self.axes[dest].scatter(vectors_to_plot[0], vectors_to_plot[1])\r
- else:\r
- self.axes[dest].scatter(vectors_to_plot[0], vectors_to_plot[1],color=plot.colors[c])\r
- else:\r
- if plot.colors[c]==None:\r
- self.axes[dest].plot(vectors_to_plot[0], vectors_to_plot[1])\r
- else:\r
- self.axes[dest].plot(vectors_to_plot[0], vectors_to_plot[1], color=plot.colors[c])\r
- self.axes[dest].hold(True)\r
- c+=1\r
-\r
- '''\r
- for vectors_to_plot in self.current_vectors:\r
- if len(vectors_to_plot)==2: #3d plots are to come...\r
- if len(plot.styles) > 0 and plot.styles[c] == 'scatter':\r
- self.axes[dest].scatter(vectors_to_plot[0],vectors_to_plot[1])\r
- elif len(plot.styles) > 0 and plot.styles[c] == 'scatter_red':\r
- self.axes[dest].scatter(vectors_to_plot[0],vectors_to_plot[1],color='red')\r
- else:\r
- self.axes[dest].plot(vectors_to_plot[0],vectors_to_plot[1])\r
-\r
- self.axes[dest].hold(True)\r
- c+=1\r
- else:\r
- pass\r
- ''' \r
- #FIXME: tackles only 2d plots\r
- self.axes[dest].set_xlabel(plot.units[0])\r
- self.axes[dest].set_ylabel(plot.units[1])\r
-\r
- #FIXME: set smaller fonts\r
- self.axes[dest].set_title(plot.title)\r
-\r
- if plot.xaxes: \r
- #swap X axis\r
- xlim=self.axes[dest].get_xlim()\r
- self.axes[dest].set_xlim((xlim[1],xlim[0])) \r
- if plot.yaxes:\r
- #swap Y axis\r
- ylim=self.axes[dest].get_ylim() \r
- self.axes[dest].set_ylim((ylim[1],ylim[0])) \r
-\r
- for i in range(len(self.axes)):\r
- self.axes[i].xaxis.set_major_formatter(EngrFormatter())\r
- self.axes[i].yaxis.set_major_formatter(EngrFormatter(2))\r
-\r
-\r
- self.controls[dest].draw()\r
-\r
-\r
- def PlotContact(self,event):\r
- '''\r
- plots the contact point\r
- DEPRECATED!\r
- '''\r
- self.axes[0].hold(True)\r
- self.current_contact_index=event.contact_index\r
-\r
- #now we fake a clicked point \r
- self.clicked_points.append(ClickedPoint())\r
- self.clicked_points[-1].absolute_coords=self.current_x_ret[dest][self.current_contact_index], self.current_y_ret[dest][self.current_contact_index]\r
- self.clicked_points[-1].is_marker=True \r
-\r
- self._replot()\r
- self.clicked_points=[]\r
-\r
- def OnMeasurePoints(self,event):\r
- '''\r
- trigger flags to measure N points\r
- '''\r
- self.click_flags_functions['measure_points'][0]=True\r
- if 'num_of_points' in dir(event):\r
- self.num_of_points=event.num_of_points\r
- if 'set' in dir(event): \r
- self.measure_set=event.set \r
-\r
- def ClickPoint0(self,event):\r
- self.current_plot_dest=0\r
- self.ClickPoint(event)\r
- def ClickPoint1(self,event):\r
- self.current_plot_dest=1\r
- self.ClickPoint(event)\r
-\r
- def ClickPoint(self,event):\r
- '''\r
- this function decides what to do when we receive a left click on the axes.\r
- We trigger other functions:\r
- - the action chosen by the CLI sends an event\r
- - the event raises a flag : self.click_flags_functions['foo'][0]\r
- - the raised flag wants the function in self.click_flags_functions[1] to be called after a click\r
- '''\r
- for key, value in self.click_flags_functions.items():\r
- if value[0]:\r
- eval('self.'+value[1]+'(event)')\r
-\r
-\r
-\r
- def MeasurePoints(self,event,current_set=1):\r
- dest=self.current_plot_dest\r
- try:\r
- current_set=self.measure_set\r
- except AttributeError:\r
- pass\r
-\r
- #find the current plot matching the clicked destination\r
- plot=self._plot_of_dest()\r
- if len(plot.vectors)-1 < current_set: #what happens if current_set is 1 and we have only 1 vector?\r
- current_set=current_set-len(plot.vectors)\r
-\r
- xvector=plot.vectors[current_set][0]\r
- yvector=plot.vectors[current_set][1]\r
-\r
- self.clicked_points.append(ClickedPoint()) \r
- self.clicked_points[-1].absolute_coords=event.xdata, event.ydata\r
- self.clicked_points[-1].find_graph_coords(xvector,yvector)\r
- self.clicked_points[-1].is_marker=True \r
- self.clicked_points[-1].is_line_edge=True\r
- self.clicked_points[-1].dest=dest \r
-\r
- self._replot()\r
-\r
- if len(self.clicked_points)==self.num_of_points:\r
- self.events_from_gui.put(self.clicked_points)\r
- #restore to default state:\r
- self.clicked_points=[]\r
- self.click_flags_functions['measure_points'][0]=False \r
-\r
-\r
- def OnGetDisplayedPlot(self,event):\r
- if 'dest' in dir(event):\r
- self.GetDisplayedPlot(event.dest)\r
- else:\r
- self.GetDisplayedPlot(self.current_plot_dest)\r
-\r
- def GetDisplayedPlot(self,dest):\r
- '''\r
- returns to the CLI the currently displayed plot for the given destination\r
- '''\r
- displayed_plot=self._plot_of_dest(dest)\r
- events_from_gui.put(displayed_plot)\r
-\r
- def ExportImage(self,event):\r
- '''\r
- exports an image as a file.\r
- Current supported file formats: png, eps\r
- (matplotlib docs say that jpeg should be supported too, but with .jpg it doesn't work for me!)\r
- '''\r
- #dest=self.current_plot_dest\r
- dest=event.dest\r
- filename=event.name\r
- self.figures[dest].savefig(filename)\r
-\r
- '''\r
- def _find_nearest_point(self, mypoint, dataset=1):\r
-\r
- #Given a clicked point on the plot, finds the nearest point in the dataset (in X) that\r
- #corresponds to the clicked point.\r
-\r
- dest=self.current_plot_dest\r
-\r
- xvector=plot.vectors[dataset][0]\r
- yvector=plot.vectors[dataset][1]\r
-\r
- #Ye Olde sorting algorithm...\r
- #FIXME: is there a better solution?\r
- index=0\r
- best_index=0\r
- best_diff=10^9 #hope we never go over this magic number :(\r
- for point in xvector:\r
- diff=abs(point-mypoint)\r
- if diff<best_diff:\r
- best_index=index\r
- best_diff=diff\r
- index+=1\r
-\r
- return best_index,xvector[best_index],yvector[best_index]\r
- ''' \r
-\r
- def _plot_of_dest(self,dest=None):\r
- '''\r
- returns the plot that has the current destination\r
- '''\r
- if dest==None:\r
- dest=self.current_plot_dest\r
- try:\r
- plot=None\r
- for aplot in self.plots:\r
- if aplot.destination == dest:\r
- plot=aplot\r
- return plot\r
- except:\r
- print "No curve available"\r
- return None\r
-\r
- def _replot(self):\r
- '''\r
- this routine is needed for a fresh clean-and-replot of interface\r
- otherwise, refreshing works very badly :(\r
-\r
- thanks to Ken McIvor, wxmpl author!\r
- '''\r
- dest=self.current_plot_dest\r
- #we get current zoom limits\r
- xlim=self.axes[dest].get_xlim()\r
- ylim=self.axes[dest].get_ylim() \r
- #clear axes\r
- self.axes[dest].cla()\r
-\r
- #Plot curve: \r
- #find the current plot matching the clicked destination\r
- plot=self._plot_of_dest()\r
- #plot all superimposed plots \r
- c=0 \r
- if len(plot.colors)==0:\r
- plot.colors=[None] * len(plot.vectors)\r
- if len(plot.styles)==0:\r
- plot.styles=[None] * len(plot.vectors) \r
- for plotset in plot.vectors: \r
- if plot.styles[c]=='scatter':\r
- if plot.colors[c]==None:\r
- self.axes[dest].scatter(plotset[0], plotset[1])\r
- else:\r
- self.axes[dest].scatter(plotset[0], plotset[1],color=plot.colors[c])\r
- else:\r
- if plot.colors[c]==None:\r
- self.axes[dest].plot(plotset[0], plotset[1])\r
- else:\r
- self.axes[dest].plot(plotset[0], plotset[1], color=plot.colors[c])\r
- ''' \r
- if len(plot.styles) > 0 and plot.styles[c]=='scatter':\r
- self.axes[dest].scatter(plotset[0], plotset[1],color=plot.colors[c])\r
- elif len(plot.styles) > 0 and plot.styles[c] == 'scatter_red':\r
- self.axes[dest].scatter(plotset[0],plotset[1],color='red')\r
- else:\r
- self.axes[dest].plot(plotset[0], plotset[1])\r
- '''\r
- c+=1\r
- #plot points we have clicked\r
- for item in self.clicked_points:\r
- if item.is_marker:\r
- if item.graph_coords==(None,None): #if we have no graph coords, we display absolute coords\r
- self.axes[dest].scatter([item.absolute_coords[0]],[item.absolute_coords[1]])\r
- else:\r
- self.axes[dest].scatter([item.graph_coords[0]],[item.graph_coords[1]]) \r
-\r
- if self.plot_fit:\r
- print 'DEBUGGING WARNING: use of self.plot_fit is deprecated!'\r
- self.axes[dest].plot(self.plot_fit[0],self.plot_fit[1])\r
-\r
- self.axes[dest].hold(True) \r
- #set old axes again\r
- self.axes[dest].set_xlim(xlim)\r
- self.axes[dest].set_ylim(ylim)\r
- #set title and names again...\r
- self.axes[dest].set_title(self.current_title) \r
- self.axes[dest].set_xlabel(plot.units[0])\r
- self.axes[dest].set_ylabel(plot.units[1])\r
- #and redraw!\r
- self.controls[dest].draw()\r
-\r
-\r
-class MySplashScreen(wx.SplashScreen):\r
- """\r
- Create a splash screen widget.\r
- That's just a fancy addition... every serious application has a splash screen!\r
- """\r
- def __init__(self, frame):\r
- # This is a recipe to a the screen.\r
- # Modify the following variables as necessary.\r
- #aBitmap = wx.Image(name = "wxPyWiki.jpg").ConvertToBitmap()\r
- aBitmap=wx.Image(name=os.path.join(\r
- config['install']['docpath'],\r
- 'hooke.jpg')).ConvertToBitmap()\r
- splashStyle = wx.SPLASH_CENTRE_ON_SCREEN | wx.SPLASH_TIMEOUT\r
- splashDuration = 2000 # milliseconds\r
- splashCallback = None\r
- # Call the constructor with the above arguments in exactly the\r
- # following order.\r
- wx.SplashScreen.__init__(self, aBitmap, splashStyle,\r
- splashDuration, None, -1)\r
- wx.EVT_CLOSE(self, self.OnExit)\r
- self.frame=frame\r
- wx.Yield()\r
-\r
- def OnExit(self, evt):\r
- self.Hide()\r
-\r
- self.frame.Show()\r
- # The program will freeze without this line.\r
- evt.Skip() # Make sure the default handler runs too...\r
-\r
-\r
-#------------------------------------------------------------------------------\r
-\r
-def main():\r
- app=wx.PySimpleApp()\r
-\r
- def make_gui_class(*bases):\r
- return type(MainWindow)("MainWindowPlugged", bases + (MainWindow,), {})\r
-\r
- main_frame = make_gui_class(*GUI_PLUGINS)(None, -1, ('Hooke '+__version__))\r
-\r
- #FIXME. The frame.Show() is called by the splashscreen here! Ugly as hell.\r
-\r
- mysplash=MySplashScreen(main_frame)\r
- mysplash.Show()\r
-\r
- my_cmdline=CliThread(main_frame, list_of_events)\r
- my_cmdline.start()\r
-\r
- app.MainLoop()\r
-\r
-if __name__ == '__main__':\r
- main()\r
+# Copyright (C) 2008-2010 Fabrizio Benedetti
+# Massimo Sandal <devicerandom@gmail.com>
+# Rolf Schmidt <rschmidt@alcor.concordia.ca>
+# W. Trevor King <wking@drexel.edu>
+#
+# This file is part of Hooke.
+#
+# Hooke is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Lesser General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# Hooke is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General
+# Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with Hooke. If not, see
+# <http://www.gnu.org/licenses/>.
+
+"""Hooke - A force spectroscopy review & analysis tool.
+"""
+
+if False: # Queue pickle error debugging code
+ """The Hooke class is passed back from the CommandEngine process
+ to the main process via a :class:`multiprocessing.queues.Queue`,
+ which uses :mod:`pickle` for serialization. There are a number of
+ objects that are unpicklable, and the error messages are not
+ always helpful. This block of code hooks you into the Queue's
+ _feed method so you can print out useful tidbits to help find the
+ particular object that is gumming up the pickle works.
+ """
+ import multiprocessing.queues
+ import sys
+ feed = multiprocessing.queues.Queue._feed
+ def new_feed (buffer, notempty, send, writelock, close):
+ def s(obj):
+ print 'SEND:', obj, dir(obj)
+ for a in dir(obj):
+ attr = getattr(obj, a)
+ #print ' ', a, attr, type(attr)
+ if obj.__class__.__name__ == 'Hooke':
+ # Set suspect attributes to None until you resolve the
+ # PicklingError. Then fix whatever is breaking the
+ # pickling.
+ #obj.commands = None
+ #obj.drivers = None
+ #obj.plugins = None
+ #obj.ui = None
+ pass
+ sys.stdout.flush()
+ send(obj)
+ feed(buffer, notempty, s, writelock, close)
+ multiprocessing.queues.Queue._feed = staticmethod(new_feed)
+
+from ConfigParser import NoSectionError
+import logging
+import logging.config
+import multiprocessing
+import optparse
+import os.path
+import Queue
+import unittest
+import StringIO
+import sys
+
+from . import version
+from . import engine
+from . import config as config_mod
+from . import playlist
+from . import plugin as plugin_mod
+from . import driver as driver_mod
+from . import ui
+
+
+class Hooke (object):
+ def __init__(self, config=None, debug=0):
+ self.debug = debug
+ default_settings = (config_mod.DEFAULT_SETTINGS
+ + plugin_mod.default_settings()
+ + driver_mod.default_settings()
+ + ui.default_settings())
+ if config == None:
+ config = config_mod.HookeConfigParser(
+ paths=config_mod.DEFAULT_PATHS,
+ default_settings=default_settings)
+ config.read()
+ self.config = config
+ self.load_log()
+ self.load_plugins()
+ self.load_drivers()
+ self.load_ui()
+ self.engine = engine.CommandEngine()
+ self.playlists = playlist.NoteIndexList()
+
+ def load_log(self):
+ config_file = StringIO.StringIO()
+ self.config.write(config_file)
+ logging.config.fileConfig(StringIO.StringIO(config_file.getvalue()))
+ # Don't attach the logger because it contains an unpicklable
+ # thread.lock. Instead, grab it directly every time you need it.
+ #self.log = logging.getLogger('hooke')
+
+ def load_plugins(self):
+ self.plugins = plugin_mod.load_graph(
+ plugin_mod.PLUGIN_GRAPH, self.config, include_section='plugins')
+ self.configure_plugins()
+ self.commands = []
+ for plugin in self.plugins:
+ self.commands.extend(plugin.commands())
+ self.command_by_name = dict(
+ [(c.name, c) for c in self.commands])
+
+ def load_drivers(self):
+ self.drivers = plugin_mod.load_graph(
+ driver_mod.DRIVER_GRAPH, self.config, include_section='drivers')
+ self.configure_drivers()
+
+ def load_ui(self):
+ self.ui = ui.load_ui(self.config)
+ self.configure_ui()
+
+ def configure_plugins(self):
+ for plugin in self.plugins:
+ self._configure_item(plugin)
+
+ def configure_drivers(self):
+ for driver in self.drivers:
+ self._configure_item(driver)
+
+ def configure_ui(self):
+ self._configure_item(self.ui)
+
+ def _configure_item(self, item):
+ conditions = self.config.items('conditions')
+ try:
+ item.config = dict(self.config.items(item.setting_section))
+ except NoSectionError:
+ item.config = {}
+ for key,value in conditions:
+ if key not in item.config:
+ item.config[key] = value
+
+ def close(self, save_config=False):
+ if save_config == True:
+ self.config.write() # Does not preserve original comments
+
+ def run_command(self, command, arguments):
+ """Run the command named `command` with `arguments` using
+ :meth:`~hooke.engine.CommandEngine.run_command`.
+
+ Allows for running commands without spawning another process
+ as in :class:`HookeRunner`.
+ """
+ self.engine.run_command(self, command, arguments)
+
+
+class HookeRunner (object):
+ def run(self, hooke):
+ """Run Hooke's main execution loop.
+
+ Spawns a :class:`hooke.engine.CommandEngine` subprocess and
+ then runs the UI, rejoining the `CommandEngine` process after
+ the UI exits.
+ """
+ ui_to_command,command_to_ui,command = self._setup_run(hooke)
+ try:
+ hooke.ui.run(hooke.commands, ui_to_command, command_to_ui)
+ finally:
+ hooke = self._cleanup_run(ui_to_command, command_to_ui, command)
+ return hooke
+
+ def run_lines(self, hooke, lines):
+ """Run the pre-set commands `lines` with the "command line" UI.
+
+ Allows for non-interactive sessions that are otherwise
+ equivalent to :meth:'.run'.
+ """
+ cmdline = ui.load_ui(hooke.config, 'command line')
+ ui_to_command,command_to_ui,command = self._setup_run(hooke)
+ try:
+ cmdline.run_lines(
+ hooke.commands, ui_to_command, command_to_ui, lines)
+ finally:
+ hooke = self._cleanup_run(ui_to_command, command_to_ui, command)
+ return hooke
+
+ def _setup_run(self, hooke):
+ ui_to_command = multiprocessing.Queue()
+ command_to_ui = multiprocessing.Queue()
+ manager = multiprocessing.Manager()
+ command = multiprocessing.Process(name='command engine',
+ target=hooke.engine.run, args=(hooke, ui_to_command, command_to_ui))
+ command.start()
+ hooke.engine = None # no more need for the UI-side version.
+ return (ui_to_command, command_to_ui, command)
+
+ def _cleanup_run(self, ui_to_command, command_to_ui, command):
+ log = logging.getLogger('hooke')
+ log.debug('cleanup sending CloseEngine')
+ ui_to_command.put(engine.CloseEngine())
+ hooke = None
+ while not isinstance(hooke, Hooke):
+ log.debug('cleanup waiting for Hooke instance from the engine.')
+ hooke = command_to_ui.get(block=True)
+ log.debug('cleanup got %s instance' % type(hooke))
+ command.join()
+ return hooke
+
+
+def main():
+ p = optparse.OptionParser()
+ p.add_option(
+ '--version', dest='version', default=False, action='store_true',
+ help="Print Hooke's version information and exit.")
+ p.add_option(
+ '-s', '--script', dest='script', metavar='FILE',
+ help='Script of command line Hooke commands to run.')
+ p.add_option(
+ '-c', '--command', dest='commands', metavar='COMMAND',
+ action='append', default=[],
+ help='Add a command line Hooke command to run.')
+ p.add_option(
+ '-p', '--persist', dest='persist', action='store_true', default=False,
+ help="Don't exit after running a script or commands.")
+ p.add_option(
+ '--save-config', dest='save_config',
+ action='store_true', default=False,
+ help="Automatically save a changed configuration on exit.")
+ p.add_option(
+ '--debug', dest='debug', action='store_true', default=False,
+ help="Enable debug logging.")
+ options,arguments = p.parse_args()
+ if len(arguments) > 0:
+ print >> sys.stderr, 'More than 0 arguments to %s: %s' \
+ % (sys.argv[0], arguments)
+ p.print_help(sys.stderr)
+ sys.exit(1)
+
+ hooke = Hooke(debug=__debug__)
+ runner = HookeRunner()
+
+ if options.version == True:
+ print version()
+ sys.exit(0)
+ if options.debug == True:
+ hooke.config.set(
+ section='handler_hand1', option='level', value='NOTSET')
+ hooke.load_log()
+ if options.script != None:
+ with open(os.path.expanduser(options.script), 'r') as f:
+ options.commands.extend(f.readlines())
+ if len(options.commands) > 0:
+ try:
+ hooke = runner.run_lines(hooke, options.commands)
+ finally:
+ if options.persist == False:
+ hooke.close(save_config=options.save_config)
+ sys.exit(0)
+
+ try:
+ hooke = runner.run(hooke)
+ finally:
+ hooke.close(save_config=options.save_config)
projects / hooke.git / blobdiff