Esempio n. 1
0
    def render_left_side(self,selectAllCompares=False):
        
        ### create the left side
        if self.leftAreaFrame != None:
            self.leftAreaFrame.destroy()
        
        self.leftAreaFrame = tk.Frame(self.master,height=self.canvasHeight)
        self.leftAreaFrame["bg"] = self.bgcolor
        self.leftAreaFrame.pack(side = tk.RIGHT,expand=tk.Y)

        ## to be carried out everytime the left are frame is rendered
        if self.controller.homeDir:
            fileList = get_fcs_file_names(self.controller.homeDir)
            imgNames = get_img_file_names(self.controller.homeDir) 
            if self.log.log['selectedFile'] == None:
                self.log.log['selectedFile'] = fileList[0]
                
            fileStates = [tk.NORMAL for i in fileList]
            fileStates[fileList.index(self.log.log['selectedFile'])] = tk.ACTIVE

        ## data processing
        if self.log.log['currentState'] == 'Data Processing':
            self.dataProcessingLeft = DataProcessingLeft(self.leftAreaFrame,fileList,fileStates,bg=self.bgcolor,fg=self.fgcolor,subsampleStates=self.subsampleStates,
                                                         selectedTransformCmd=self.set_selected_transform,subsampleFn=self.set_subsample,  
                                                         selectedCompCmd=self.set_selected_compensation,selectedCompensation=self.selectedCompensation,
                                                         selectedTransform = self.selectedTransform,uploadBtnFn=None,uploadFcsFn=self.controller.load_additional_fcs_files,
                                                         rmBtnFn=self.rm_selected_file,fileSelectorResponse=self.file_selector_response)
            self.dataProcessingLeft.pack(side=tk.TOP)

        ## quality assurance 
        elif self.log.log['currentState'] == 'Quality Assurance':
            self.qualityAssuranceLeft = QualityAssuranceLeft(self.leftAreaFrame,imgNames,fileList,fileStates,fileSelectorResponse=self.file_selector_response,
                                                             bg=self.bgcolor,fg=self.fgcolor,viewSelectedCmd=self.show_selected_image,  
                                                             contbtnFn=self.qa_to_model,returnBtnFn=self.close_image_viewer,viewAllFn=self.handle_view_all)
            self.qualityAssuranceLeft.pack(side=tk.TOP)
        
        ## results navigation
        elif self.log.log['currentState'] == 'Results Navigation':
            modelNames = get_models_run(self.controller.homeDir) 
            channelList = self.model.get_file_channel_list(self.log.log['selectedFile'])
            model = None

            # get file specific indices 
            try:
                self.statModel,self.statModelClasses = self.model.load_model_results_pickle(self.log.log['selectedModel'])
                channelsSelected = self.log.log['resultsChannels']
                fileSpecificIndices = [channelList.index(i) for i in channelsSelected]
            except:
                fileSpecificIndices = None
                self.statModel = None
                self.statModelClasses = None
                channelsSelected = None

            if self.log.log['componentStates'] != None:
                componentStates = self.log.log['componentStates']
            else:
                componentStates = None

            self.resultsNavigationLeft = ResultsNavigationLeft(self.leftAreaFrame,channelList,self.resultsMode,fileList,fileStates,self.statModel,
                                                               selectedInds = fileSpecificIndices,fileSelectorResponse=self.file_selector_response,
                                                               bg=self.bgcolor,fg=self.fgcolor,viewSelectedCmd=self.show_selected_image,
                                                               contbtnFn=self.qa_to_model,componentStates = componentStates,viewAllFn=self.handle_view_all,
                                                               returnBtnFn=self.close_image_viewer,rerenderFn=self.handle_results_navigation_figures)
            self.resultsNavigationLeft.pack(side=tk.TOP)

        self.messageBoard = tk.Canvas(self.leftAreaFrame,width=0.3*self.w,height=self.canvasHeight)
        self.messageBoard.configure(background = self.bgcolor)
        self.messageBoard.pack(side=tk.LEFT,expand=tk.Y)
Esempio n. 2
0
class View:
    def __init__(self,master,controller,model):
        self.master = master
        self.controller = controller
        self.log = self.controller.log
        self.model = model
        self.messageBoard = None
        self.centerAreaFrame = None
        self.leftAreaFrame = None
        self.dataProcessingSettings = None
        self.topAreaFrame = None
        self.stateBar = None
        self.stateList = ['Data Processing', 'Quality Assurance', 'Model', 'Results Navigation']
        self.bgcolor = self.master.cget("bg") #"#DDDDFF"  
        self.fgcolor = "#FFFF99" #"#CCCC66"
        self.lineNumber = 0
        
        # data processing variables 
        self.selectedTransform = 'option 1'
        self.selectedCompensation = 'option 1'
        self.subsampleStates = None

        # results navigation variables
        self.resultsMode = 'model select'
        self.selectedResultsChannel1 = None
        self.selectedResultsChannel2 = None
        self.selectedComponents = None

        ## change the window title (default is Tk) 
        self.master.wm_title(self.controller.appName)

        ## set area to screen size
        self.set_area_to_screen_size()
  
        ### create status bar
        self.status = StatusBar(self.master,self.controller)

        ### create the top area
        self.topArea = tk.Frame(self.master)
        self.topArea.pack(fill=tk.X,side=tk.TOP)
        self.topArea.config(bg=self.bgcolor)

        ### create frame pieces
        self.render_menus()
        self.render_rt_side()
        self.render_main_canvas()
        self.render_left_side()
      
    def set_area_to_screen_size(self):
        self.w,self.h = float(self.master.winfo_screenwidth()),float(self.master.winfo_screenheight())

        ## check for dual screens 
        if self.w > 2000:
            self.w = self.w / 2.0

        #self.controller.root.overrideredirect(1) # if you also want to get rid of the titlebar 
        self.master.geometry("%dx%d+0+0"%(self.w,self.h))
    
    def set_state(self,state,progressbarMsg=None,img=None,comparisonStates=None,resultsNavMode=None):
        self.log.log['currentState'] = state

        ## save project
        if self.controller.homeDir:
            self.log.write()
            print 'saving project at', self.log.log['currentState']

        ## keep track of the highest state
        if self.stateList.__contains__(self.log.log['currentState']):
            if self.stateList.index(self.log.log['currentState']) > self.log.log['highestState']:
                self.log.log['highestState'] = self.stateList.index(self.log.log['currentState'])
        
        if self.log.log['currentState'] == 'Progressbar':
            self.render_main_canvas(canvasState='progressbar',progressbarMsg=progressbarMsg)
        elif self.log.log['currentState'] == 'configuration':
            self.render_main_canvas(canvasState='configuration')     
        elif self.log.log['currentState'] == 'projects menu':
            self.render_main_canvas(canvasState='projects menu')
        elif self.log.log['currentState'] == 'initial':
            self.render_main_canvas(canvasState='initial')
        elif self.log.log['currentState'] == 'Data Processing':
            self.render_main_canvas(canvasState='processing')
        elif self.log.log['currentState'] == 'Quality Assurance':
            self.render_main_canvas(canvasState='qa',img=img,comparisonStates=comparisonStates)
        elif self.log.log['currentState'] == 'Model':
            self.render_main_canvas(canvasState='model')
        elif self.log.log['currentState'] == 'Results Navigation':
            self.render_main_canvas(canvasState='results',resultsNavMode=None)
        else:
            print "ERROR: invalid state specified: %s" %state
        
        self.render_state()
        
    ##############################################################################
    #
    # image manipulation functions
    #
    ##############################################################################

    def render_state(self):
        if self.stateBar != None:
            self.stateBar.destroy()
            
        self.stateBar = Statebar(self.topArea,self.stateList,self.log.log['currentState'],handleTransition=self.handle_state_transition)
        self.stateBar.config(bg=self.bgcolor)
        self.stateBar.pack(side=tk.TOP,fill=tk.X,pady=2,padx=5)

    def mount_image(self,fileName,recreate=True):
        if fileName != "experiment_icon":
            fileName = os.path.join(self.controller.homeDir,'figs',fileName)
            if os.path.isfile(fileName+".png") == False:
                print "ERROR: Bad specified image file name"
                self.i = PhotoImage(file = fileName + ".gif")
            else:
                self.i = PhotoImage(file = fileName + ".gif")
        else:
            self.i = PhotoImage(file = fileName + ".gif")

        imageX = 0.5*self.canvasWidth
        imageY = 0.45*self.canvasHeight
        self.canvas.delete("image")
        self.canvas.pack(fill=tk.BOTH,side=tk.TOP,anchor=tk.N)
        self.canvas.create_image(imageX,imageY,image=self.i,tags="image")
        self.canvas.config(bg=self.bgcolor)

    def unmount_image(self):
        self.canvas.delete(image)

    ##############################################################################
    #
    # menu functions
    #
    ##############################################################################

    def render_menus(self):
        ## initialize menu and menu commands as none
        self.filemenu = None
        self.helpmenu = None
        self.actionmenu = None

        ## load appropriate menus
        print 'loading menu'
        self.menu = tk.Menu(self.master)
        self.master.config(menu=self.menu)
        
        ## file menu
        self.filemenu = tk.Menu(self.menu)
        self.menu.add_cascade(label="File", menu = self.filemenu)
        
        self.filemenu.add_command(label="Create new project", command = self.create_new_project)
        self.filemenu.add_command(label="Open existing project", command = self.open_existing_projects_menu)
        self.filemenu.add_command(label="Export project", command = self.callback)
        self.filemenu.add_command(label="View project logfile", command = self.callback)

        if self.log.log['currentState'] in ['Quality Assurance','Model','Results Navigation']:
            self.filemenu.add_command(label="Export image", command = self.controller.saveas_image)
        
        self.filemenu.add_separator()
        if self.log.log['currentState'] in ['Data Processing','Quality Assurance','Model Preparation','Results Navigation']:
            self.filemenu.add_command(label="Close current project", command = self.topArea.quit)
        
        self.filemenu.add_command(label="Exit", command = self.topArea.quit)

        ## view menu
        self.viewmenu = tk.Menu(self.master)
        self.menu.add_cascade(label="View", menu=self.viewmenu)
        self.viewmenu.add_command(label="Set the default screen resolution", command=self.set_default_screen_resolution)
       
        ## action menu
        if self.log.log['currentState'] in ['Data Processing','Quality Assurance','Model','Results Navigation']:
            self.actionmenu = tk.Menu(self.menu)
            self.menu.add_cascade(label="Action", menu = self.actionmenu)
            self.actionmenu.add_command(label="action1", command = self.callback)

            if self.log.log['currentState'] in ['Data Processing']:
                self.actionmenu.add_command(label="Load additional file", command = self.controller.load_additional_fcs_files)

        ## help menu
        self.helpmenu = tk.Menu(self.menu)
        self.menu.add_cascade(label="Help", menu = self.helpmenu)
        self.helpmenu.add_command(label="User Manual", command = self.controller.show_documentation)
        self.helpmenu.add_command(label="About...", command = self.callback)
    
    def render_rt_side(self):
        ### create the right side
        self.rightAreaFrame = tk.Frame(self.master)
        #self.rightAreaFrame.pack_propagate(0)
        self.rightAreaFrame["bg"] = self.bgcolor
        self.rightArea = tk.Canvas(self.rightAreaFrame, width = 0.02 * self.w, height = 0.95 * self.h)
        self.rightArea.configure(background = self.bgcolor)
        self.rightAreaFrame.pack(side = tk.RIGHT)
        self.rightArea.pack()

    ##############################################################################
    #
    # main canvas functions
    #
    ##############################################################################

    def open_existing_projects_menu(self):
        self.set_state('projects menu')

    def open_existing_project(self):
        selectedProject = self.existingProjectsMenu.get_selected_project()
        if selectedProject != None:
            self.controller.projectID = selectedProject
            self.controller.homeDir = os.path.join(".","projects",self.controller.projectID)
            self.log.initialize(self.controller.projectID,self.controller.homeDir,load=True)
            self.controller.handle_subsampling()
            self.set_state(self.log.log['currentState'])
            print "the current state: ", self.log.log['currentState']
        else:
            self.display_warning("You must select an existing project first")

    def render_main_canvas(self,canvasState='initial',progressbarMsg=None,img=None,comparisonStates=None,useCurrentStates=False,resultsNavMode=None):

        ### create the center
        if self.centerAreaFrame != None:
            self.centerAreaFrame.destroy()
            
        self.canvasWidth = 0.72 * self.w       # 0.72
        self.canvasHeight = 0.95 * self.h      # 0.85 remember to change them all
        self.controller.mainAreaWidth = self.canvasWidth
        self.controller.mainAreaHeight = self.canvasHeight
        self.textSpacing = 0.02* self.canvasHeight
        self.centerAreaFrame = tk.Frame(self.master,height=self.canvasHeight,width=self.canvasWidth)
        self.centerAreaFrame["bg"] = self.bgcolor
        self.centerAreaFrame.pack_propagate(0) # don't shrink
        self.centerAreaFrame.pack(side = tk.RIGHT)       
        self.canvas = tk.Canvas(self.centerAreaFrame,height=self.canvasHeight,width=self.canvasWidth)
        
        if canvasState != 'initial' and self.controller.homeDir != None:
            fileNames  = get_fcs_file_names(self.controller.homeDir)

        if canvasState == 'initial':
            self.mount_image("experiment_icon")
            print 'rendering main canvas -- initial'
            self.canvas.pack()
        elif canvasState == 'configuration':
            msg = "Your current screen geometry is %sx%s\nHere you may select another resolution\n\n"%(int(self.w), int(self.h))
            self.resolutionSelector = ResolutionSelector(self.centerAreaFrame,msg,bg=self.bgcolor,fg=self.fgcolor,command=self.change_default_screen_resolution)
        elif canvasState == 'progressbar':
            self.progressbar = Progressbar(self.centerAreaFrame,withLabel=progressbarMsg,bg=self.bgcolor,fg=self.fgcolor)
            self.progressbar.pack(side=tk.TOP,fill=tk.BOTH,pady=0.2*self.canvasHeight,anchor=tk.S)

        elif canvasState == 'processing':
            dataProcessing = True
            masterChannelList = self.model.get_master_channel_list()
            if useCurrentStates == False:
                self.set_selected_channel_states()
            self.dataProcessingSettings = DataProcessingSettings(self.centerAreaFrame,fileNames,masterChannelList,width=self.canvasWidth,
                                                                 bg=self.bgcolor,fg=self.fgcolor,showNameBtn=self.display_file_by_button,
                                                                 loadbtnFn=self.controller.load_additional_fcs_files,selectAllFn=self.handle_select_all_channels,
                                                                 channelStates=self.controller.log.log['processingChannels'],contbtnFn=self.processing_to_qa)
        elif canvasState == 'qa':
            imgNames = get_img_file_names(self.controller.homeDir)
            imgNames = [image[:-4] for image in imgNames]
            self.canvas = tk.Canvas(self.centerAreaFrame,height=self.canvasHeight,width=self.canvasWidth)

            if img != None:
                self.mount_image(img) # img
                self.canvas.pack(anchor=tk.N,side=tk.TOP)
            else:
                mode = 'view all'
                self.qualityAssuranceSettings = QualityAssuranceSettings(self.centerAreaFrame,mode,fileNames,imgNames,self.controller.homeDir,
                                                                         imgHandler = self.show_selected_image, width=self.canvasWidth,
                                                                         bg=self.bgcolor,fg=self.fgcolor,allStates=comparisonStates,
                                                                         contbtnFn=self.qa_to_model,selectAllCmd=None)
                self.qualityAssuranceSettings.pack()

        elif canvasState == 'model':
            self.modelSettings = ModelSettings(self.centerAreaFrame,fileNames,width=self.canvasWidth,
                                               bg=self.bgcolor,fg=self.fgcolor,runModelBtnFn=self.model_to_results_navigation,
                                               contbtnFn=self.model_to_results_navigation)
        elif canvasState == 'results':
            modelList = get_models_run(self.controller.homeDir)

            if self.resultsMode in ['model select']:
                self.resultsNavigationSettings = ResultsNavigationSettings(self.centerAreaFrame,modelList,self.resultsMode,width=self.canvasWidth,
                                                                           dblClickBtnFn=self.show_model_log,bg=self.bgcolor,fg=self.fgcolor,
                                                                           loadbtnFn=None,contBtnFn=self.handle_results_navigation_settings)
                self.resultsSelectCanvas = tk.Canvas(self.centerAreaFrame,width=0.5*self.canvasWidth,height=0.5*self.canvasHeight)
                self.resultsSelectCanvas.configure(background=self.bgcolor)
                self.resultsSelectCanvas.pack(side=tk.LEFT)

            else:

                if self.selectedResultsChannel1 == None or self.selectedResultsChannel2 == None:
                    fileName = self.log.log['selectedFile']
                    imgDir = os.path.join(self.controller.homeDir,'figs',re.sub(fileName[:-4]+"\_","",self.log.log['selectedModel']))
                    imageHandler = self.show_selected_image
                    self.ibm = ImageButtonMagic(self.centerAreaFrame,imgDir,imageHandler)
                    self.ibm.config(bg=self.bgcolor)
                    self.ibm.pack()
                else:
                    ### get model
                    if not self.statModel:
                        self.statModel,self.modelClasses = self.model.load_model_results_pickle(self.log.log['selectedModel'])
                    try: self.statModel
                    except:
                        self.statModel = None
                        self.statModelClasses = None

                    self.mplCanvas = self.model.make_scatter_plot(self.log.log['selectedFile'],self.selectedResultsChannel1,
                                                                  self.selectedResultsChannel2,labels=self.statModelClasses,
                                                                  root=self.centerAreaFrame,width=self.canvasWidth,height=self.canvasHeight,getCanvas=True)
                    self.mplCanvas._tkcanvas.pack(fill=tk.BOTH,expand=1)

        elif canvasState == 'projects menu':
            existingProjects = get_project_names()
            self.existingProjectsMenu = ExistingProjectsMenu(self.centerAreaFrame,existingProjects,bg=self.bgcolor,fg=self.fgcolor,
                                                             command=self.open_existing_project,loadBtnFn=self.open_existing_project)
            self.existingProjectsMenu.pack()

        ### finally render the left side    
        self.render_left_side()

    def display_file_by_button(self,ind):
        fileList = get_fcs_file_names(self.controller.homeDir)
        if ind == 0:
            self.status.set("Does that look like a file to you?")
        else:
            self.status.set(fileList[ind-1])

    def handle_select_all_channels(self):
        self.set_state("Data Processing")

    def set_selected_channel_states(self):

        masterList = self.model.get_master_channel_list()
        fileList = get_fcs_file_names(self.controller.homeDir)

        ## create a list of list to represent the channel states (each list is one row) 
        channelStates = [ [0]+np.zeros(len(masterList),dtype=int).tolist()+[0,0,0] for c in range(len(fileList))]

        ## if applicable get selected channels  
        if self.dataProcessingSettings != None:
            selectedChannels = self.dataProcessingSettings.get_selected_channels()
            for row in range(len(selectedChannels)):
                for col in range(len(selectedChannels[0])):
                    state = selectedChannels[row][col]
                    if state != 0:
                        channelStates[row][col] = state

        ## check to see if select all was used  
        selectedRow = None
        if self.dataProcessingSettings != None:
            currentChannels = self.log.log['processingChannels']

            for row in range(len(selectedChannels)):
                stateSelected = selectedChannels[row][0]
                stateCurrent = currentChannels[row][0]
            
                if stateSelected != stateCurrent:
                    selectedRow = row

            if selectedRow != None:
                if currentChannels[selectedRow][0] == 1:
                    channelStates[selectedRow] = [0 for i in range(len(currentChannels[row]))]
                elif currentChannels[selectedRow][0] == 0:
                    channelStates[selectedRow] = [1 for i in range(len(currentChannels[row]))]

        ## ready unavailable channels for disabling (-1)
        for f in range(len(fileList)):
            file = fileList[f]
            channels = self.model.get_file_channel_list(file)
            masterIndices = [np.where(np.array(masterList) == ch)[0][0] for ch in channels]
            disabledChannels = list(set(range(len(masterList))).difference(set(masterIndices)))
            for c in range(len(masterList)):
                if c in disabledChannels:
                    channelStates[f][c+1] = -1
        
        self.controller.log.log['processingChannels'] = channelStates

    ##############################################################################
    #
    # messageboard, fileselector
    #
    ##############################################################################

    def render_left_side(self,selectAllCompares=False):
        
        ### create the left side
        if self.leftAreaFrame != None:
            self.leftAreaFrame.destroy()
        
        self.leftAreaFrame = tk.Frame(self.master,height=self.canvasHeight)
        self.leftAreaFrame["bg"] = self.bgcolor
        self.leftAreaFrame.pack(side = tk.RIGHT,expand=tk.Y)

        ## to be carried out everytime the left are frame is rendered
        if self.controller.homeDir:
            fileList = get_fcs_file_names(self.controller.homeDir)
            imgNames = get_img_file_names(self.controller.homeDir) 
            if self.log.log['selectedFile'] == None:
                self.log.log['selectedFile'] = fileList[0]
                
            fileStates = [tk.NORMAL for i in fileList]
            fileStates[fileList.index(self.log.log['selectedFile'])] = tk.ACTIVE

        ## data processing
        if self.log.log['currentState'] == 'Data Processing':
            self.dataProcessingLeft = DataProcessingLeft(self.leftAreaFrame,fileList,fileStates,bg=self.bgcolor,fg=self.fgcolor,subsampleStates=self.subsampleStates,
                                                         selectedTransformCmd=self.set_selected_transform,subsampleFn=self.set_subsample,  
                                                         selectedCompCmd=self.set_selected_compensation,selectedCompensation=self.selectedCompensation,
                                                         selectedTransform = self.selectedTransform,uploadBtnFn=None,uploadFcsFn=self.controller.load_additional_fcs_files,
                                                         rmBtnFn=self.rm_selected_file,fileSelectorResponse=self.file_selector_response)
            self.dataProcessingLeft.pack(side=tk.TOP)

        ## quality assurance 
        elif self.log.log['currentState'] == 'Quality Assurance':
            self.qualityAssuranceLeft = QualityAssuranceLeft(self.leftAreaFrame,imgNames,fileList,fileStates,fileSelectorResponse=self.file_selector_response,
                                                             bg=self.bgcolor,fg=self.fgcolor,viewSelectedCmd=self.show_selected_image,  
                                                             contbtnFn=self.qa_to_model,returnBtnFn=self.close_image_viewer,viewAllFn=self.handle_view_all)
            self.qualityAssuranceLeft.pack(side=tk.TOP)
        
        ## results navigation
        elif self.log.log['currentState'] == 'Results Navigation':
            modelNames = get_models_run(self.controller.homeDir) 
            channelList = self.model.get_file_channel_list(self.log.log['selectedFile'])
            model = None

            # get file specific indices 
            try:
                self.statModel,self.statModelClasses = self.model.load_model_results_pickle(self.log.log['selectedModel'])
                channelsSelected = self.log.log['resultsChannels']
                fileSpecificIndices = [channelList.index(i) for i in channelsSelected]
            except:
                fileSpecificIndices = None
                self.statModel = None
                self.statModelClasses = None
                channelsSelected = None

            if self.log.log['componentStates'] != None:
                componentStates = self.log.log['componentStates']
            else:
                componentStates = None

            self.resultsNavigationLeft = ResultsNavigationLeft(self.leftAreaFrame,channelList,self.resultsMode,fileList,fileStates,self.statModel,
                                                               selectedInds = fileSpecificIndices,fileSelectorResponse=self.file_selector_response,
                                                               bg=self.bgcolor,fg=self.fgcolor,viewSelectedCmd=self.show_selected_image,
                                                               contbtnFn=self.qa_to_model,componentStates = componentStates,viewAllFn=self.handle_view_all,
                                                               returnBtnFn=self.close_image_viewer,rerenderFn=self.handle_results_navigation_figures)
            self.resultsNavigationLeft.pack(side=tk.TOP)

        self.messageBoard = tk.Canvas(self.leftAreaFrame,width=0.3*self.w,height=self.canvasHeight)
        self.messageBoard.configure(background = self.bgcolor)
        self.messageBoard.pack(side=tk.LEFT,expand=tk.Y)

    ## this function is called from the fileselector widget
    def file_selector_response(self):
        if self.log.log['currentState'] == "Data Processing":
            self.lineNumber = 0
            self.log.log['selectedFile'] = self.dataProcessingLeft.get_selected_file()
            file = self.model.pyfcm_load_fcs_file(self.log.log['selectedFile'])

            n,d = np.shape(file)
            self.render_left_side()
            self.message_board_display("file - %s "%self.log.log['selectedFile'])
            self.message_board_display("observations -  %s "%n)
            self.message_board_display("dimensions -  %s "%d)
        else:
            print "resonse method not available yet"

    #########################################################################
    # 
    # Results navigation handles
    #
    #########################################################################

    def handle_results_navigation_settings(self):
        selectedModel = self.resultsNavigationSettings.get_selected_model()
        fileList = get_fcs_file_names(self.controller.homeDir)
        fileName = None

        if selectedModel != None:
            for file in fileList:
                m = re.search(re.sub("[\.fcs|\.pickle]","",file),selectedModel)
                if m:
                    fileName = m.group(0)
        
        if selectedModel != None:
            self.log.log['selectedModel'] = selectedModel
            self.log.log['selectedFile'] = fileName + ".fcs"
            self.resultsMode = 'mixture components'
            self.set_state('Results Navigation')
        elif selectedModel == None:
            self.display_warning("You must select a model before navigating its results")

    def handle_results_navigation_figures(self):
        imageChannels = self.resultsNavigationLeft.get_image_channels()
        self.log.log['componentStates'] = self.resultsNavigationLeft.get_component_states()
        if not self.statModel:
            self.statModel,self.statModelClasses = self.model.load_model_results_pickle(self.log.log['selectedModel'])

        if imageChannels != None:
            self.selectedResultsChannel1 = imageChannels[0]
            self.selectedResultsChannel2 = imageChannels[1]
            self.log.log['resultsChannels'] = [imageChannels[0],imageChannels[1]]
            print "setting results channels to", self.log.log['resultsChannels']
            self.set_state('Results Navigation')
        else:
            self.display_warning("You must select a two channels file before viewing a plot")

    def handle_results_navigation_model_summary(self):
        print 'handling results naviation model summary'


    def show_model_log(self):
        selectedModel = self.resultsNavigationSettings.get_selected_model()
        fileList = get_fcs_file_names(self.controller.homeDir)
        fileName = None
        for file in fileList:
            m = re.search(re.sub("[\.fcs|\.pickle]","",file),selectedModel)
            if m:
                fileName = m.group(0)
        
        lineCount = 1
        whiteSpace = self.h / 70.0
        modelLogFile = self.log.read_model_log(selectedModel)
        self.resultsSelectCanvas.delete(tk.ALL)
        logKeys = modelLogFile.keys()
        logKeys.sort()

        for key in logKeys:
            item = modelLogFile[key]
            self.resultsSelectCanvas.create_text(0.05*self.w,lineCount*whiteSpace,text="%s - %s"%(key,item),fill="black",anchor=tk.W)
            lineCount+=1

        self.status.set("displaying results for %s"%selectedModel)

            
    #########################################################################
    # 
    #  Data processing handles
    #
    #########################################################################

    def rm_selected_file(self):
        
        if self.log.log['selectedFile'] == None:
            self.display_warning("You must select a file before removing it")
        else:
            selectedFile = os.path.join(self.controller.homeDir,'data',self.log.log['selectedFile'])
            self.controller.rm_fcs_file(selectedFile)
            self.log.log['selectedFile'] = None
            self.set_state("Data Processing")
    
    def set_selected_transform(self):
        self.selectedTransform = self.dataProcessingLeft.get_selected_transform()

    def set_selected_compensation(self):
        self.selectedCompensation = self.dataProcessingLeft.get_selected_compensation()

    def message_board_display(self,msg,align='left',withButton=False):
        if self.lineNumber == 0:
            self.render_left_side()

        whiteSpace = self.h / 100.0
        self.lineNumber+=1
        
        if self.lineNumber == 1:
            self.lineNumber+=1
            self.message_board_display("Project - %s"%self.controller.projectID,align='left')
            self.lineNumber+=1
            lineHeight = (self.lineNumber * whiteSpace) #+ (0.1 * whiteSpace)
            self.messageBoard.create_line((0,lineHeight),(0.3*self.w,lineHeight), fill="black")
            self.lineNumber+=2

        if align=='center':
            self.messageBoard.create_text(0.15*self.w,self.lineNumber*whiteSpace,text=msg,fill="black",tags="line"+str(self.lineNumber),anchor=tk.CENTER)
            self.lineNumber+=1
        elif align == 'left':
            self.messageBoard.create_text(0.008*self.w,self.lineNumber*whiteSpace,text=msg,fill="black",tags="line"+str(self.lineNumber),anchor=tk.W)
            self.lineNumber+=1
        else:
            print "ERROR: did not impliment other aligns besides center and left"

    def show_fcs_file_names(self):
        self.lineNumber = 0
        for fileName in os.listdir(os.path.join(self.controller.homeDir,"data")):
            if re.search("\.fcs",fileName):
                self.message_board_display("file - %s"%fileName,align='left', withButton=True)

    def show_selected_image(self):
        
        if self.log.log['currentState'] == 'Quality Assurance':
            img = self.qualityAssuranceLeft.get_selected_image()
        
            if img == None:
                img = self.qualityAssuranceSettings.ibm.selectedImg
                img = os.path.split(img)[-1]
                img = re.sub('\_thumb','',img)[:-4]

            self.set_state('Quality Assurance',img=img)

        elif self.log.log['currentState'] == 'Results Navigation':
            print 'should be handling generatino of image'
            fileChannels = self.model.get_file_channel_list(self.log.log['selectedFile'])

            img = self.ibm.selectedImg
            img = os.path.split(img)[-1]
            img = re.sub('\_thumb','',img)[:-4]

            # get the channels from file name
            imageChannels = []
            for chan in fileChannels:
                if re.search(chan,img):
                    imageChannels.append(chan)

            self.log.log['componentStates'] = self.resultsNavigationLeft.get_component_states()
            if not self.statModel:
                self.statModel,self.statModelClasses = self.model.load_model_results_pickle(self.log.log['selectedModel'])
            
            if imageChannels != None:
                self.selectedResultsChannel1 = imageChannels[0]
                self.selectedResultsChannel2 = imageChannels[1]
                self.log.log['resultsChannels'] = [imageChannels[0],imageChannels[1]]
                print "setting results channels to", self.log.log['resultsChannels']
                self.set_state('Results Navigation')

    def set_subsample(self):
        if self.dataProcessingLeft.get_subsample() != 'All Data':
            ss = re.sub("\s","",self.dataProcessingLeft.get_subsample())
        else:
            ss = self.dataProcessingLeft.get_subsample()
        self.log.log['subsample'] = ss
        subsamples = ['All Data','1e3','1e4','5e4']                 # make sure this matches in dataprocessingleft
        self.subsampleStates = [tk.NORMAL for st in range(len(subsamples))]
        if subsamples.__contains__(self.log.log['subsample']) == True:
            self.subsampleStates[subsamples.index(self.log.log['subsample'])] = tk.ACTIVE

    def create_new_project(self):
        tkMessageBox.showinfo(self.controller.appName,"Load a *.fcs file ")       
        fcsFileName = askopenfilename()  
        self.controller.create_new_project(fcsFileName)

        if self.controller.homeDir != None:
            self.set_state("Data Processing")

    #########################################################################
    # 
    #  Reuseable handles
    #
    #########################################################################

    def handle_view_all(self):
        if self.log.log['currentState'] == "Quality Assurance":
            self.set_state('Quality Assurance')

        if self.log.log['currentState'] == "Results Navigation":
            self.selectedResultsChannel1 = None
            self.selectedResultsChannel2 = None
            self.log.log['resultsChannels'] = None
            self.set_state('Results Navigation')

    def close_image_viewer(self):
        self.set_state(self.log.log['currentState'])

    def select_all_comparisons(self):
        if self.log.log['currentState'] == 'Quality Assurance':
            selectState = self.qualityAssuranceSettings.get_select_all_state()
        elif self.log.log['currentState'] == 'Results Navigation':
            selectState = self.resultsNavigationSettings.get_select_all_state()
        
        imgNames = get_img_file_names(self.controller.homeDir)
        imgNames = [image[:-4] for image in imgNames]
    
        if selectState[0] == 1:
            comparisonStates = [tk.ACTIVE for i in imgNames]
        else:
            comparisonStates = None
    
        self.set_state(self.log.log['currentState'],comparisonStates=comparisonStates)

    
    ##############################################################################
    #
    # model handles
    #
    ##############################################################################

    def run_selected_model(self):
        modelSelectedLong = self.modelSettings.get_selected_model()
        self.set_state('Progressbar',progressbarMsg="Running '%s'..."%modelSelectedLong)

        fileList = get_fcs_file_names(self.controller.homeDir)
        
        if modelSelectedLong == "Dirichlet Process Mixture Model - CPU Version":
            self.log.log['modelToRun'] = "dpmm-cpu"
        elif modelSelectedLong == "Dirichlet Process Mixture Model - GPU Version":
            self.log.log['modelToRun'] = "dpmm-gpu"
        elif modelSelectedLong == "Spectral Clustering - Ng Algorithm":
            self.log.log['modelToRun'] = "sc-ng"
        else:
            print "ERROR: run selected model returned a bad model name:%s"%modelSelectedLong

        self.controller.run_selected_model()
        self.status.set("Model run finished")

    ##############################################################################
    #
    # functions that control the state transitions
    #
    ##############################################################################

    def handle_state_transition(self):
        state = self.stateBar.get_current_state()

        #if self.stateList.__contains__(self.log.log['currentState']):
        if self.stateList.index(state) > self.log.log['highestState']:
            self.display_warning('User must follow the flow of the pipeline \n i.e. please do not skip steps')
            self.render_state()
        else:

            ## reset stage specific variables
            self.resultsMode = 'model select'
            self.selectedResultsChannel1 = None
            self.selectedResultsChannel2 = None
            self.selectedComponents = None

            self.set_state(state)


    def processing_to_qa(self):
        #self.set_selected_channel_states()
        #if np.array(selectedChannels).sum() < 2:
        #    self.display_error("you must select at least 2 channels")
        #else:
        self.set_state('Progressbar',progressbarMsg="Creating all specified images...")
        self.status.set("addressing subsampling...")
        self.set_subsample()
        self.controller.handle_subsampling()
        self.set_selected_channel_states()
        self.status.set("Rendering images...")
        self.controller.process_images()
        self.status.set("Assess the quality and return to previous steps if necessary")
        self.set_state('Quality Assurance')
            
    def qa_to_model(self):
        self.set_state('Model')

    def model_to_results_navigation(self):
        self.run_selected_model()
        self.set_state('Progressbar',progressbarMsg="Rendering images'...")
        self.controller.process_results_images(self.log.log['modelToRun'])
        self.set_state('Results Navigation')

    def enable_cluster_selection(self):
        self.canvas.unbind("<ButtonPress-1>")
        self.canvas.unbind("<ButtonRelease-1>")
        self.canvas.bind("<ButtonPress-1>", self.model.press)
        self.canvas.bind("<ButtonRelease-1>", self.model.release)


    ##############################################################################
    #
    # basic message functions
    #
    ##############################################################################

    def display_info(self,message):
        tkMessageBox.showinfo(self.controller.appName, message)
        self.status.set("info: %s"%message)

    def display_warning(self,message):
        tkMessageBox.showwarning(self.controller.appName, message)
        self.status.set("warning: %s"%message)

    def display_error(self,message):
        tkMessageBox.showerror(self.controller.appName, message)
        self.status.set("error: %s"%message)

    def callback(self):
        tkMessageBox.showinfo(self.controller.appName, "this function does not exist yet")
        self.status.set("this function does not exist yet")


    ##############################################################################
    #
    # system specific functions
    #
    ##############################################################################

    def set_default_screen_resolution(self):
        self.set_state('configuration')

    def change_default_screen_resolution(self):
        newRes = self.resolutionSelector.get_selected_resolution()
        width,height = newRes.split('x')
        self.w = float(width)
        self.h = float(height)
        self.master.geometry("%dx%d+0+0"%(self.w,self.h))

        ### create the top area
        self.topArea.destroy()
        self.filemenu.destroy()
        self.leftAreaFrame.destroy()
        self.rightAreaFrame.destroy()
        self.centerAreaFrame.destroy()

        self.topArea = tk.Frame(self.master)
        self.topArea.pack(fill=tk.X,side=tk.TOP)
        self.topArea.config(bg=self.bgcolor)

        ### create frame pieces 
        self.render_menus()
        self.render_rt_side()
        self.render_main_canvas()
        self.render_left_side()

        self.status.destroy()
        self.status = StatusBar(self.master,self.controller)
        self.status.set('resolution has been set to %s'%newRes)