def body(self, master): self.alarm_id = None self.root_widget = getRoot(self) row = 0 label = Label(master, text='Widget count:') label.grid(row=row, column=0, sticky=Tkinter.W) self.count_label = Label(master, text='', tipText='Number of Tkinter widget objects') self.count_label.grid(row=row, column=1, sticky=Tkinter.W) row = row + 1 ind = 1 label = Label(master, text='Auto count:') label.grid(row=row, column=0, sticky=Tkinter.W) self.on_off_buttons = RadioButtons(master, entries=self.on_off_entries, select_callback=self.applyAuto, selected_index=ind) self.on_off_buttons.grid(row=row, column=1, sticky=Tkinter.EW) row = row + 1 label = Label(master, text='Auto frequency:') label.grid(row=row, column=0, sticky=Tkinter.W) self.freq_entry = IntEntry(master, text=60, returnCallback=self.applyAuto) self.freq_entry.grid(row=row, column=1, sticky=Tkinter.EW) label = Label(master, text='seconds') label.grid(row=row, column=2, sticky=Tkinter.W) row = row + 1 texts = ['Do Immediate Count'] commands = [self.applyManual] buttons = createDismissHelpButtonList(master, texts=texts, commands=commands, help_msg=self.help_msg, help_url=self.help_url) buttons.grid(row=row, column=0, columnspan=3, sticky=Tkinter.EW) self.doCount()
def body(self, guiFrame): self.geometry('600x350') project = self.project analysisProject = self.analysisProject guiFrame.grid_columnconfigure(1, weight=1) row = 0 frame = Frame(guiFrame, grid=(0,0)) label = Label(frame, text=' Window:', grid=(0,0)) self.windowPulldown = PulldownList(frame, grid=(0,1), tipText='The window that will be printed out', callback=self.selectWindow) tipTexts = ['For the window pulldown, show all of the spectrum windows in the current project, irrespective of the active group', 'For the window pulldown, show only spectrum windows that are in the currently active window group'] self.whichWindows = RadioButtons(frame, grid=(0,2), entries=ACTIVE_OPTIONS, tipTexts=tipTexts, select_callback=self.updateWindows) texts = [ 'Save Print File' ] tipTexts = [ 'Save the printout to the specified file' ] commands = [ self.saveFile ] buttons = UtilityButtonList(guiFrame, helpUrl=self.help_url, grid=(row,2), commands=commands, texts=texts, tipTexts=tipTexts) self.buttons = buttons buttons.buttons[0].config(bg='#B0FFB0') row += 1 guiFrame.grid_rowconfigure(row, weight=1) options = ['Options', 'Spectra', 'Peak Lists', 'Region'] tipTexts = ['Optional settings for spectra', 'Optional settings for peak lists', 'Optional settings for the region'] tabbedFrame = TabbedFrame(guiFrame, options=options, tipTexts=tipTexts) tabbedFrame.grid(row=row, column=0, columnspan=3, sticky='nsew') self.tabbedFrame = tabbedFrame optionFrame, spectrumFrame, peakListFrame, regionFrame = tabbedFrame.frames optionFrame.expandGrid(0, 0) getOption = lambda key, defaultValue: PrintBasic.getPrintOption(analysisProject, key, defaultValue) setOption = lambda key, value: PrintBasic.setPrintOption(analysisProject, key, value) self.printFrame = PrintFrame(optionFrame, getOption=getOption, grid=(0,0), gridSpan=(1,1), setOption=setOption, haveTicks=True, doOutlineBox=False) spectrumFrame.expandGrid(0, 0) frame = Frame(spectrumFrame, grid=(0,0), gridSpan=(1,1)) frame.expandGrid(1,0) self.overrideSpectrum = CheckButton(frame, text='Use below settings when printing', tipText='Use below settings when printing instead of the window values', grid=(0,0), sticky='w') tipText = 'Change the settings of the selected spectra back to their window values' button = Button(frame, text='Reset Selected', tipText=tipText, command=self.resetSelected, grid=(0,1), sticky='e') self.posColorPulldown = PulldownList(self, callback=self.setPosColor) self.negColorPulldown = PulldownList(self, callback=self.setNegColor) headings = ['Spectrum', 'Pos. Contours\nDrawn', 'Neg. Contours\nDrawn', 'Positive\nColours', 'Negative\nColours'] tipTexts = ['Spectrum in window', 'Whether the positive contours should be drawn', 'Whether the negative contours should be drawn', 'Colour scheme for positive contours (can be a single colour)', 'Colour scheme for negative contours (can be a single colour)'] editWidgets = [ None, None, None, self.posColorPulldown, self.negColorPulldown] editGetCallbacks = [ None, self.togglePos, self.toggleNeg, self.getPosColor, self.getNegColor] editSetCallbacks = [ None, None, None, self.setPosColor, self.setNegColor] self.spectrumTable = ScrolledMatrix(frame, headingList=headings, tipTexts=tipTexts, multiSelect=True, editWidgets=editWidgets, editGetCallbacks=editGetCallbacks, editSetCallbacks=editSetCallbacks, grid=(1,0), gridSpan=(1,2)) peakListFrame.expandGrid(0, 0) frame = Frame(peakListFrame, grid=(0,0), gridSpan=(1,3)) frame.expandGrid(1,0) self.overridePeakList = CheckButton(frame, text='Use below settings when printing', tipText='Use below settings when printing instead of the window values', grid=(0,0)) tipText = 'Change the settings of the selected peak lists back to their window values' button = Button(frame, text='Reset Selected', tipText=tipText, command=self.resetSelected, grid=(0,1), sticky='e') colors = Color.standardColors self.peakColorPulldown = PulldownList(self, callback=self.setPeakColor, texts=[c.name for c in colors], objects=[c.hex for c in colors], colors=[c.hex for c in colors]) headings = [ 'Peak List', 'Symbols Drawn', 'Peak Font', 'Peak Colour'] self.fontMenu = FontList(self, mode='Print', extraTexts=[no_peak_text]) editWidgets = [ None, None, self.fontMenu, self.peakColorPulldown] editGetCallbacks = [ None, self.togglePeaks, self.getPeakFont, self.getPeakColor ] editSetCallbacks = [ None, None, self.setPeakFont, self.setPeakColor ] self.peakListTable = ScrolledMatrix(frame, headingList=headings, multiSelect=True, editWidgets=editWidgets, editGetCallbacks=editGetCallbacks, editSetCallbacks=editSetCallbacks, grid=(1,0), gridSpan=(1,2)) regionFrame.expandGrid(0, 0) frame = Frame(regionFrame, grid=(0,0), gridSpan=(1,3)) frame.expandGrid(3,0) tipText = 'Use the specified override region when printing rather than the window values' self.overrideButton = CheckButton(frame, text='Use override region when printing', tipText=tipText, callback=self.toggledOverride, grid=(0,0)) tipTexts = ('Use min and max to specify override region', 'Use center and width to specify override region') self.use_entry = USE_ENTRIES[0] self.useButtons = RadioButtons(frame, entries=USE_ENTRIES, tipTexts=tipTexts, select_callback=self.changedUseEntry, grid=(1,0)) texts = ('Set Region from Window', 'Set Center from Window', 'Set Width from Window') tipTexts = ('Set the override region to be the current window region', 'Set the center of the override region to be the center of the current window region', 'Set the width of the override region to be the width of the current window region') commands = (self.setRegionFromWindow, self.setCenterFromWindow, self.setWidthFromWindow) self.setRegionButton = ButtonList(frame, texts=texts, tipTexts=tipTexts, commands=commands, grid=(2,0)) self.minRegionWidget = FloatEntry(self, returnCallback=self.setMinRegion, width=10) self.maxRegionWidget = FloatEntry(self, returnCallback=self.setMaxRegion, width=10) headings = MIN_MAX_HEADINGS editWidgets = [ None, None, self.minRegionWidget, self.maxRegionWidget ] editGetCallbacks = [ None, None, self.getMinRegion, self.getMaxRegion ] editSetCallbacks = [ None, None, self.setMinRegion, self.setMaxRegion ] self.regionTable = RegionScrolledMatrix(frame, headingList=headings, editWidgets=editWidgets, editGetCallbacks=editGetCallbacks, editSetCallbacks=editSetCallbacks, grid=(3,0)) self.updateWindows() self.updateAfter() self.administerNotifiers(self.registerNotify)
def body(self): '''Describes the body of this tab. It consists out of a number of radio buttons, check buttons and number entries that allow the user to indicate which assignments should be transferred. ''' # self.frame.expandColumn(0) self.frame.expandGrid(8, 0) self.frame.expandGrid(8, 1) typeOfAssignmentFrame = LabelFrame( self.frame, text='type of assignment') typeOfAssignmentFrame.grid(row=0, column=0, sticky='nesw') # typeOfAssignmentFrame.expandGrid(0,5) peakSelectionFrame = LabelFrame( self.frame, text='which peaks to assign') peakSelectionFrame.grid(row=0, column=1, sticky='nesw', rowspan=2) spinSystemSelectionFrame = LabelFrame(self.frame, text='Which spin-systems to use') spinSystemSelectionFrame.grid(row=2, column=0, sticky='nesw') tipText = 'What to do when a residue has already a spin system assigned to it.' assignedResidueFrame = LabelFrame(self.frame, text='if residue already has spin-system', tipText=tipText) assignedResidueFrame.grid(row=2, column=1, sticky='nesw') spectrumSelectionFrame = LabelFrame(self.frame, text='spectra') spectrumSelectionFrame.grid(row=1, column=0, sticky='nesw') row = 0 Label(typeOfAssignmentFrame, text='Resonances to Peak Dimensions', grid=(row, 0)) self.peaksCheckButton = CheckButton(typeOfAssignmentFrame, selected=True, grid=(row, 1)) row += 1 Label(typeOfAssignmentFrame, text='SpinSystems to Residues', grid=(row, 0)) self.residuesCheckButton = CheckButton( typeOfAssignmentFrame, selected=True, grid=(row, 1)) row = 0 Label(peakSelectionFrame, text='Intra-Residual', grid=(row, 0)) self.intraCheckButton = CheckButton( peakSelectionFrame, selected=True, grid=(row, 1)) row += 1 Label(peakSelectionFrame, text='Sequential', grid=(row, 0)) self.sequentialCheckButton = CheckButton( peakSelectionFrame, selected=True, grid=(row, 1)) row += 1 Label(peakSelectionFrame, text='Do not assign diagonal peaks', grid=(row, 0)) self.noDiagonalCheckButton = CheckButton( peakSelectionFrame, selected=True, grid=(row, 1)) entries = ['Only assigned spin systems', 'All that have a score of at least: ', 'User Defined', 'Solution number:'] tipTexts = ['Only assign resonances of spin systems that already have a sequential assignment for the assignment of peak dimensions. Spin system to residue assignment is not relevant in this case.', 'Assign all spin systems that have a score of at least a given percentage. 50% or lower is not possible, because than spin systems might have to be assigned to more than 1 residue, which is impossible.', "As defined in the lower row of buttons in the 'results' tab.", 'One of the single solutions of the annealing.'] self.spinSystemTypeSelect = RadioButtons(spinSystemSelectionFrame, entries=entries, grid=(0, 0), select_callback=None, direction=VERTICAL, gridSpan=(4, 1), tipTexts=tipTexts) tipText = 'The minimal amount of colabelling the different nuclei should have in order to still give rise to a peak.' self.minScoreEntry = FloatEntry(spinSystemSelectionFrame, grid=(1, 1), width=7, text=str(self.minScore), returnCallback=self.changeMinScore, tipText=tipText) self.minScoreEntry.bind('<Leave>', self.changeMinScore, '+') self.solutionNumberEntry = IntEntry(spinSystemSelectionFrame, grid=(3, 1), width=7, text=1, returnCallback=self.solutionUpdate, tipText=tipText) self.solutionNumberEntry.bind('<Leave>', self.solutionUpdate, '+') #self.solutionPullDown = PulldownList(spinSystemSelectionFrame, None, grid=(3,1), sticky='w') entries = ['all spectra', 'only:'] tipTexts = ['Assign peaks in all the spectra that where selected before the annealing ran.', 'Only assign peaks in one particular spectrum. You can of course repeat this multiple times for different spectra.'] self.spectrumSelect = RadioButtons(spectrumSelectionFrame, entries=entries, grid=(0, 0), select_callback=None, direction=VERTICAL, gridSpan=(2, 1), tipTexts=tipTexts) self.spectraPullDown = PulldownList(spectrumSelectionFrame, self.changeSpectrum, grid=(1, 1), sticky='w') entries = ['skip this residue', 'de-assign old spin system from residue', 'assign, but never merge', 'warn to merge'] tipTexts = ["Don't assign the new spin system to the residue. The residue is not skipped when the old spin system does not contain any resonances", "De-assign old spin system from residue, unless the old spin system is a spin system without any resonances.", "Don't merge any spin systems, merging can be performed later if nescesary in the Resonance --> SpinSystems window.", "Ask to merge individually for each spin system, this might result in clicking on a lot of popups."] self.assignedResidueStrategySelect = RadioButtons(assignedResidueFrame, entries=entries, grid=(0, 0), select_callback=None, direction=VERTICAL, gridSpan=(2, 1), tipTexts=tipTexts) texts = ['Transfer Assignments'] commands = [self.transferAssignments] self.transferButton = ButtonList( self.frame, commands=commands, texts=texts) self.transferButton.grid(row=5, column=0, sticky='nsew', columnspan=2)
class TasksFrame(Frame): def __init__(self, guiParent, basePopup): self.guiParent = guiParent self.basePopup = basePopup # selection hash. This needs to be stored so that we can # refresh with the same criteria self.select = None # should the screen autorefresh self.autoRefresh = False # add this to shortcuts to ease navigation self.basePopup.frameShortcuts['Tasks'] = self #self.registerNotify=basePopup.registerNotify #self.unregisterNotify=basePopup.unregisterNotify #self.frames = [] # FIXME JMCI # This frame is specific for a single repository so we need a # method for identifying one from the whole set (or could have # subtabs) Frame.__init__(self, guiParent) # set up the grid self.grid_columnconfigure(0, weight=0, minsize=20) self.grid_columnconfigure(1, weight=1, minsize=30) self.grid_columnconfigure(2, weight=0, minsize=40) self.grid_rowconfigure(0, weight=0, minsize=20) self.grid_rowconfigure(1, weight=0, minsize=10) self.grid_rowconfigure(2, weight=0, minsize=0) self.grid_rowconfigure(3, weight=0, minsize=0) self.grid_rowconfigure(4, weight=0, minsize=0) self.grid_rowconfigure(5, weight=1, minsize=0) self.grid_rowconfigure(6, weight=0, minsize=10) self.grid_rowconfigure(7, weight=0, minsize=10) initial_cols = ['ID','Task','User','Status'] self.task_matrix = ScrolledMatrix(self, headingList=initial_cols, initialRows=15, doubleCallback=self.goto_task_tab) # Filters for narrowing down tasks. should probably code this # specifically inside this package #self.filter = FilterFrame(self, self.basePopup, text='Filter') self.filter = TaskFilterFrame(self, self.basePopup, text='Filter') # Frame for controlling the main client side daemon # seems to be a problem. add a simple button for now opts = ['Client','Server'] self.daemonFrame = TabbedFrame(self, options=opts, toggleOff=False, selected=0) self.daemonSwitchLabel = Label(self, text= 'Task Daemon') self.daemonSwitch = RadioButtons(self, ['on', 'off'], select_callback=self.set_daemon, selected_index = 1) sel = 1 if self.autoRefresh: sel = 0 self.autoRefreshSwitchLabel = Label(self, text= 'Auto Refresh') self.autoRefreshSwitch = RadioButtons(self, ['on', 'off'], select_callback=self.set_refresh, selected_index = sel) self.label_rep = Label(self, text='', font='Helvetica16') # set up a loop self.refresh() def drawFrame(self): # build up the body. # This is a very simple mock up. In reality we need to be # able to select a number of different input files that # depend on the task type # we need to have the current repository in context self.repository = self.basePopup.repList.currentRepository if self.repository == None: self.label_rep.grid_remove() self.task_matrix.grid_remove() self.filter.grid_remove() self.daemonSwitchLabel.grid_remove() self.daemonSwitch.grid_remove() else: strg = self.repository.user + '@' + self.repository.name + ' (' + self.repository.connect + ')' self.label_rep.set('TaskManager: Repository ' + strg) self.label_rep.grid(row=1, column=1, columnspan=2, sticky='w') self.task_matrix.grid(row=2, column=1, rowspan=4, sticky='nsew') loc = SharedBeanServiceLocator() port = loc.getSharedBean() request1 = getList(); request1._arg0 = 'org.pimslims.applet.server.TaskBean'; request1._arg1 = 'getListWithFields'; if self.select==None: request1._arg2 = '' else: wsstr_in = WSString(self.select) request1._arg2 = wsstr_in.str response1 = port.getList(request1) wsstr1 = WSString(response1._return) ss1 = wsstr1.getStruct() matrix = []; objs = []; for el in ss1: new_row = (el['serial'], 'TestTask1', 'jionides', el['status']) matrix.append(new_row) objs.append(el) self.task_matrix.update(objectList=objs, textMatrix=matrix) self.filter.grid(row=2, column=2, sticky='n') # FIXME JMCI # The tabbed frame seems to cause the GUI to hang over expansion. # use a simple radio button for now # self.daemonFrame.grid(row=3, column=2, padx=10, sticky='nsew') self.daemonSwitchLabel.grid(row=3, column=2, padx=10, sticky='n') self.daemonSwitch.grid(row=4, column=2, padx=10, sticky='n') self.autoRefreshSwitchLabel.grid(row=6, column=1, padx=10, sticky='w') self.autoRefreshSwitch.grid(row=6, column=1, padx=10, sticky='e') def selectTask(self): row = self.task_matrix.currentCell print 'in select task ', row def set_daemon(self, text): print 'setting daemon ', text if text == 'on': self.basePopup.taskDaemon.active = True else: self.basePopup.taskDaemon.active = False def set_refresh(self, text): print 'setting refresh ', text if text == 'on': self.autoRefresh = True else: self.autoRefresh = False def refresh(self): if self.autoRefresh: print 'refreshing frame ', time.time() self.drawFrame() self.after(5000, self.refresh) def goto_task_tab(self, obj, row, col): print obj self.basePopup.currentTask = obj['serial'].__str__() # This is really awkward because we actually have to go to the # correct tab. We have some horrible hacks here. Need a dictionary # that can take us straight to the correct frame based on a # keyword self.basePopup.tabbedFrame.select(2) #for ff in self.basePopup.tabbedFrame.frames[2].children.values(): # ff.tabbedFrame.select(0) if self.basePopup.frameShortcuts.has_key('Task'): taskFrame = self.basePopup.frameShortcuts['Task'] # really need to check on the type of task if taskFrame.frameShortcuts.has_key('Test1'): taskFrame.frameShortcuts['Test1'].drawFrame() # also need to select the current tabbed frame self.basePopup.tabbedFrame.select(2) def administerNotifiers(self, notifyFunc): for func in ('__init__','delete','setName'): notifyFunc(self.updateAllAfter, 'ccp.nmr.Nmr.Experiment', func) notifyFunc(self.updateAllAfter, 'ccp.nmr.Nmr.DataSource', func) def updateAllAfter(self, obj): self.after_idle(self.updateAll) def updateAll(self, project=None): return def quit(self): self.guiParent.parent.destroy() def destroy(self): #self.administerNotifiers(self.basePopup.unregisterNotify) Frame.destroy(self)
def body(self, mainFrame): mainFrame.grid_columnconfigure(1, weight=1, minsize=100) mainFrame.config(borderwidth=5, relief='solid') row = 0 label = Label(mainFrame, text="Frame (with sub-widgets):") label.grid(row=row, column=0, sticky=Tkinter.E) frame = Frame(mainFrame, relief='raised', border=2, background='#8080D0') # Frame expands East-West frame.grid(row=row, column=1, sticky=Tkinter.EW) # Last column expands => Widgets pusted to the West frame.grid_columnconfigure(3, weight=1) # Label is within the sub frame label = Label(frame, text='label ') label.grid(row=0, column=0, sticky=Tkinter.W) entry = Entry(frame, text='Entry', returnCallback=self.showWarning) entry.grid(row=0, column=1, sticky=Tkinter.W) self.check = CheckButton(frame, text='Checkbutton', selected=True, callback=self.updateObjects) self.check.grid(row=0, column=2, sticky=Tkinter.W) # stick a button to the East wall button = Button(frame, text='Button', command=self.pressButton) button.grid(row=0, column=3, sticky=Tkinter.E) row += 1 label = Label(mainFrame, text="Text:") label.grid(row=row, column=0, sticky=Tkinter.E) self.textWindow = Text(mainFrame, text='Initial Text\n', width=60, height=5) self.textWindow.grid(row=row, column=1, sticky=Tkinter.NSEW) row += 1 label = Label(mainFrame, text="CheckButtons:") label.grid(row=row, column=0, sticky=Tkinter.E) entries = ['Alpha','Beta','Gamma','Delta'] selected = entries[2:] self.checkButtons = CheckButtons(mainFrame, entries, selected=selected,select_callback=self.changedCheckButtons) self.checkButtons.grid(row=row, column=1, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="PartitionedSelector:") label.grid(row=row, column=0, sticky=Tkinter.E) labels = ['Bool','Int','Float','String'] objects = [type(0),type(1),type(1.0),type('a')] selected = [type('a')] self.partitionedSelector= PartitionedSelector(mainFrame, labels=labels, objects=objects, colors = ['red','yellow','green','#000080'], callback=self.toggleSelector,selected=selected) self.partitionedSelector.grid(row=row, column=1, sticky=Tkinter.EW) row += 1 label = Label(mainFrame, text="PulldownMenu") label.grid(row=row, column=0, sticky=Tkinter.E) entries = ['Frodo','Pipin','Merry','Sam','Bill','Gandalf','Strider','Gimli','Legolas'] self.pulldownMenu = PulldownMenu(mainFrame, callback=self.selectPulldown, entries=entries, selected_index=2, do_initial_callback=False) self.pulldownMenu.grid(row=row, column=1, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="RadioButtons in a\nScrolledFrame.frame:") label.grid(row=row, column=0, sticky=Tkinter.EW) frame = ScrolledFrame(mainFrame, yscroll = False, doExtraConfig = True, width=100) frame.grid(row=row, column=1, sticky=Tkinter.EW) frame.grid_columnconfigure(0, weight=1) self.radioButtons = RadioButtons(frame.frame, entries=entries, select_callback=self.checkRadioButtons, selected_index=1, relief='groove') self.radioButtons.grid(row=0, column=0, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="LabelFrame with\nToggleLabels inside:") label.grid(row=row, column=0, sticky=Tkinter.E) labelFrame = LabelFrame(mainFrame, text='Frame Title') labelFrame.grid(row=row, column=1, sticky=Tkinter.NSEW) labelFrame.grid_rowconfigure(0, weight=1) labelFrame.grid_columnconfigure(3, weight=1) self.toggleLabel1 = ToggleLabel(labelFrame, text='ScrolledMatrix', callback=self.toggleFrame1) self.toggleLabel1.grid(row=0, column=0, sticky=Tkinter.W) self.toggleLabel1.arrowOn() self.toggleLabel2 = ToggleLabel(labelFrame, text='ScrolledGraph', callback=self.toggleFrame2) self.toggleLabel2.grid(row=0, column=1, sticky=Tkinter.W) self.toggleLabel3 = ToggleLabel(labelFrame, text='ScrolledCanvas', callback=self.toggleFrame3) self.toggleLabel3.grid(row=0, column=2, sticky=Tkinter.W) row += 1 mainFrame.grid_rowconfigure(row, weight=1) label = Label(mainFrame, text="changing/shrinking frames:") label.grid(row=row, column=0, sticky=Tkinter.E) self.toggleRow = row self.toggleFrame = Frame(mainFrame) self.toggleFrame.grid(row=row, column=1, sticky=Tkinter.NSEW) self.toggleFrame.grid_rowconfigure(0, weight=1) self.toggleFrame.grid_columnconfigure(0, weight=1) # option 1 self.intEntry = IntEntry(self, returnCallback = self.setNumber, width=8) self.multiWidget = MultiWidget(self, Entry, options=None, values=None, callback=self.setKeywords, minRows=3, maxRows=5) editWidgets = [None, None, self.intEntry, self.multiWidget] editGetCallbacks = [None, None, self.getNumber, self.getKeywords] editSetCallbacks = [None, None, self.setNumber, self.setKeywords] headingList = ['Name','Color','Number','Keywords'] self.scrolledMatrix = ScrolledMatrix(self.toggleFrame, headingList=headingList, editSetCallbacks=editSetCallbacks, editGetCallbacks=editGetCallbacks, editWidgets=editWidgets, callback=self.selectObject, multiSelect=False) self.scrolledMatrix.grid(row=0, column=0, sticky=Tkinter.NSEW) # option 2 self.scrolledGraph = ScrolledGraph(self.toggleFrame, width=400, height=300, symbolSize=5, symbols=['square','circle'], dataColors=['#000080','#800000'], lineWidths=[0,1] ) self.scrolledGraph.setZoom(1.3) dataSet1 = [[0,0],[1,1],[2,4],[3,9],[4,16],[5,25]] dataSet2 = [[0,0],[1,3],[2,6],[3,9],[4,12],[5,15]] self.scrolledGraph.update(dataSets=[dataSet1,dataSet2], xLabel = 'X axis label', yLabel = 'Y axis label', title = 'Main Title') self.scrolledGraph.draw() # option 3 self.scrolledCanvas = ScrolledCanvas(self.toggleFrame,relief = 'groove', borderwidth = 2, resizeCallback=None) canvas = self.scrolledCanvas.canvas font = 'Helvetica 10' box = canvas.create_rectangle(10,10,150,200, outline='grey', fill='grey90') line = canvas.create_line(0,0,200,200,fill='#800000', width=2) text = canvas.create_text(120,50, text='Text', font=font, fill='black') circle = canvas.create_oval(30,30,50,50,outline='#008000',fill='#404040',width=3) row += 1 label = Label(mainFrame, text="FloatEntry:") label.grid(row=row, column=0, sticky=Tkinter.E) self.floatEntry = FloatEntry(mainFrame, text=3.14159265, returnCallback=self.floatEntryReturn) self.floatEntry.grid(row=row, column=1, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="Scale:") label.grid(row=row, column=0, sticky=Tkinter.E) self.scale = Scale(mainFrame, from_=10, to=90, value=50, orient=Tkinter.HORIZONTAL) self.scale.grid(row=row, column=1, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="Value Ramp:") label.grid(row=row, column=0, sticky=Tkinter.E) self.valueRamp = ValueRamp(mainFrame, self.valueRampCallback, speed = 1.5, delay = 50) self.valueRamp.grid(row=row, column=1, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="ButtonList:") label.grid(row=row, column=0, sticky=Tkinter.E) texts = ['Select File','Close','Quit'] commands = [self.selectFile, self.close, self.quit] bottomButtons = ButtonList(mainFrame, texts=texts, commands=commands, expands=True) bottomButtons.grid(row=row, column=1, sticky=Tkinter.EW) self.protocol('WM_DELETE_WINDOW', self.quit)
def body(self): '''Describes the body of this tab. It consists out of a number of radio buttons, check buttons and number entries that allow the user to indicate which assignments should be transferred. ''' # self.frame.expandColumn(0) self.frame.expandGrid(8, 0) self.frame.expandGrid(8, 1) typeOfAssignmentFrame = LabelFrame(self.frame, text='type of assignment') typeOfAssignmentFrame.grid(row=0, column=0, sticky='nesw') # typeOfAssignmentFrame.expandGrid(0,5) peakSelectionFrame = LabelFrame(self.frame, text='which peaks to assign') peakSelectionFrame.grid(row=0, column=1, sticky='nesw', rowspan=2) spinSystemSelectionFrame = LabelFrame(self.frame, text='Which spin-systems to use') spinSystemSelectionFrame.grid(row=2, column=0, sticky='nesw') tipText = 'What to do when a residue has already a spin system assigned to it.' assignedResidueFrame = LabelFrame( self.frame, text='if residue already has spin-system', tipText=tipText) assignedResidueFrame.grid(row=2, column=1, sticky='nesw') spectrumSelectionFrame = LabelFrame(self.frame, text='spectra') spectrumSelectionFrame.grid(row=1, column=0, sticky='nesw') row = 0 Label(typeOfAssignmentFrame, text='Resonances to Peak Dimensions', grid=(row, 0)) self.peaksCheckButton = CheckButton(typeOfAssignmentFrame, selected=True, grid=(row, 1)) row += 1 Label(typeOfAssignmentFrame, text='SpinSystems to Residues', grid=(row, 0)) self.residuesCheckButton = CheckButton(typeOfAssignmentFrame, selected=True, grid=(row, 1)) row = 0 Label(peakSelectionFrame, text='Intra-Residual', grid=(row, 0)) self.intraCheckButton = CheckButton(peakSelectionFrame, selected=True, grid=(row, 1)) row += 1 Label(peakSelectionFrame, text='Sequential', grid=(row, 0)) self.sequentialCheckButton = CheckButton(peakSelectionFrame, selected=True, grid=(row, 1)) row += 1 Label(peakSelectionFrame, text='Do not assign diagonal peaks', grid=(row, 0)) self.noDiagonalCheckButton = CheckButton(peakSelectionFrame, selected=True, grid=(row, 1)) entries = [ 'Only assigned spin systems', 'All that have a score of at least: ', 'User Defined', 'Solution number:' ] tipTexts = [ 'Only assign resonances of spin systems that already have a sequential assignment for the assignment of peak dimensions. Spin system to residue assignment is not relevant in this case.', 'Assign all spin systems that have a score of at least a given percentage. 50% or lower is not possible, because than spin systems might have to be assigned to more than 1 residue, which is impossible.', "As defined in the lower row of buttons in the 'results' tab.", 'One of the single solutions of the annealing.' ] self.spinSystemTypeSelect = RadioButtons(spinSystemSelectionFrame, entries=entries, grid=(0, 0), select_callback=None, direction=VERTICAL, gridSpan=(4, 1), tipTexts=tipTexts) tipText = 'The minimal amount of colabelling the different nuclei should have in order to still give rise to a peak.' self.minScoreEntry = FloatEntry(spinSystemSelectionFrame, grid=(1, 1), width=7, text=str(self.minScore), returnCallback=self.changeMinScore, tipText=tipText) self.minScoreEntry.bind('<Leave>', self.changeMinScore, '+') self.solutionNumberEntry = IntEntry(spinSystemSelectionFrame, grid=(3, 1), width=7, text=1, returnCallback=self.solutionUpdate, tipText=tipText) self.solutionNumberEntry.bind('<Leave>', self.solutionUpdate, '+') #self.solutionPullDown = PulldownList(spinSystemSelectionFrame, None, grid=(3,1), sticky='w') entries = ['all spectra', 'only:'] tipTexts = [ 'Assign peaks in all the spectra that where selected before the annealing ran.', 'Only assign peaks in one particular spectrum. You can of course repeat this multiple times for different spectra.' ] self.spectrumSelect = RadioButtons(spectrumSelectionFrame, entries=entries, grid=(0, 0), select_callback=None, direction=VERTICAL, gridSpan=(2, 1), tipTexts=tipTexts) self.spectraPullDown = PulldownList(spectrumSelectionFrame, self.changeSpectrum, grid=(1, 1), sticky='w') entries = [ 'skip this residue', 'de-assign old spin system from residue', 'assign, but never merge', 'warn to merge' ] tipTexts = [ "Don't assign the new spin system to the residue. The residue is not skipped when the old spin system does not contain any resonances", "De-assign old spin system from residue, unless the old spin system is a spin system without any resonances.", "Don't merge any spin systems, merging can be performed later if nescesary in the Resonance --> SpinSystems window.", "Ask to merge individually for each spin system, this might result in clicking on a lot of popups." ] self.assignedResidueStrategySelect = RadioButtons(assignedResidueFrame, entries=entries, grid=(0, 0), select_callback=None, direction=VERTICAL, gridSpan=(2, 1), tipTexts=tipTexts) texts = ['Transfer Assignments'] commands = [self.transferAssignments] self.transferButton = ButtonList(self.frame, commands=commands, texts=texts) self.transferButton.grid(row=5, column=0, sticky='nsew', columnspan=2)
def body(self, guiFrame): self.geometry('600x350') guiFrame.expandGrid(0, 0) tipTexts = ['', '', '', ''] options = [ 'Find Parameters', 'Spectrum Widths', 'Diagonal Exclusions', 'Region Peak Find' ] tabbedFrame = TabbedFrame(guiFrame, options=options, grid=(0, 0)) frameA, frameB, frameC, frameD = tabbedFrame.frames self.tabbedFrame = tabbedFrame # Find Params frameA.expandGrid(2, 0) row = 0 label = LabelFrame(frameA, text='Extrema to search for:', grid=(row, 0), gridSpan=(1, 2)) label.expandGrid(0, 1) entries = ['positive and negative', 'positive only', 'negative only'] tipTexts = [ 'Sets whether peak picking within spectra find intensity maxima, minima or both maxima and minima', ] self.extrema_buttons = RadioButtons(label, entries=entries, select_callback=self.apply, direction='horizontal', grid=(0, 0), tipTexts=tipTexts) row += 1 label = LabelFrame(frameA, text='Nearby points to check:', grid=(row, 0), gridSpan=(1, 2)) label.expandGrid(None, 1) entries = ['+-1 in at most one dim', '+-1 allowed in any dim'] tipTexts = [ 'Sets how permissive the peak picking in when searching for intensity extrema; by adding extra points to the selected search region', ] self.adjacent_buttons = RadioButtons(label, entries=entries, select_callback=self.apply, direction='horizontal', grid=(0, 0), tipTexts=tipTexts) row += 1 labelFrame = LabelFrame(frameA, text='Other parameters:', grid=(row, 0), gridSpan=(1, 2)) labelFrame.expandGrid(5, 2) frow = 0 label = Label(labelFrame, text='Scale relative to contour levels:', grid=(frow, 0), sticky='e') tipText = 'Threshold above which peaks are picked, relative to the lowest displayed contour; 1.0 means picking exactly what is visible' self.scale_entry = FloatEntry(labelFrame, grid=(frow, 1), tipText=tipText, returnCallback=self.apply, width=10) self.scale_entry.bind('<Leave>', self.apply, '+') frow += 1 label = Label(labelFrame, text='Exclusion buffer around peaks (in points):', grid=(frow, 0), sticky='e') tipText = 'The size of the no-pick region, in data points, around existing picked peaks; eliminates duplicate picking' self.buffer_entry = IntEntry(labelFrame, returnCallback=self.apply, grid=(frow, 1), width=10, tipText=tipText) self.buffer_entry.bind('<Leave>', self.apply, '+') frow += 1 label = Label(labelFrame, text='Extra thickness in orthogonal dims (in points):', grid=(frow, 0), sticky='e') tipText = 'Sets whether to consider any additional planes (Z dimension) when calculating peak volume integrals' self.thickness_entry = IntEntry(labelFrame, returnCallback=self.apply, width=10, grid=(frow, 1), tipText=tipText) self.thickness_entry.bind('<Leave>', self.apply, '+') frow += 1 label = Label(labelFrame, text='Minimum drop factor (0.0-1.0):', grid=(frow, 0), sticky='e') tipText = '' self.drop_entry = FloatEntry(labelFrame, returnCallback=self.apply, width=10, grid=(frow, 1), tipText=tipText) self.drop_entry.bind('<Leave>', self.apply, '+') frow += 1 label = Label(labelFrame, text='Volume method:', grid=(frow, 0), sticky='e') tipText = 'Selects which method to use to calculate peak volume integrals when peaks are picked; box sizes are specified in "Spectrum Widths"' self.method_menu = PulldownList(labelFrame, texts=PeakBasic.PEAK_VOLUME_METHODS, grid=(frow, 1), callback=self.apply, tipText=tipText) # Spectrum widths frameB.expandGrid(1, 1) label = Label(frameB, text='Spectrum: ') label.grid(row=0, column=0, sticky='e') tipText = 'The spectrum which determines the widths being shown' self.expt_spectrum = PulldownList(frameB, tipText=tipText, callback=self.setSpectrumProperties) self.expt_spectrum.grid(row=0, column=1, sticky='w') self.editLinewidthEntry = FloatEntry(self, text='', returnCallback=self.setLinewidth, width=10) self.editBoxwidthEntry = FloatEntry(self, text='', returnCallback=self.setBoxwidth, width=10) tipTexts = [ 'The number of the spectrum dimension to which the settings apply', 'The nuclear isotope measures in the spectrum dimension', 'The smallest value for the linewidth of a peak for it to be picked', 'The size of the spectrum region to perform the volume integral over' ] headingList = [ 'Dimension', 'Isotope', 'Minimum Linewidth (Hz)', 'Boxwidth' ] editSetCallbacks = [None, None, self.setLinewidth, self.setBoxwidth] editGetCallbacks = [None, None, self.getLinewidth, self.getBoxwidth] editWidgets = [ None, None, self.editLinewidthEntry, self.editBoxwidthEntry ] self.spectrumMatrix = ScrolledMatrix(frameB, initialRows=6, editSetCallbacks=editSetCallbacks, editGetCallbacks=editGetCallbacks, editWidgets=editWidgets, headingList=headingList, callback=self.selectCell, tipTexts=tipTexts) self.spectrumMatrix.grid(row=1, column=0, columnspan=2, sticky='nsew') # Diagonal Exclusions frameC.expandGrid(0, 0) tipTexts = [ 'The isotope as measures on the axis of a spectrum window', 'The distance from the homonuclear diagonal line within which no peak picking can occur' ] self.exclusionEntry = FloatEntry(self, text='', returnCallback=self.setExclusion, width=10) headingList = ['Isotope', 'Diagonal Exclusion (ppm)'] editSetCallbacks = [None, self.setExclusion] editGetCallbacks = [None, self.getExclusion] editWidgets = [None, self.exclusionEntry] self.isotopeMatrix = ScrolledMatrix(frameC, editSetCallbacks=editSetCallbacks, editGetCallbacks=editGetCallbacks, editWidgets=editWidgets, headingList=headingList, grid=(0, 0), tipTexts=tipTexts) # Region peak find self.regionFindPeakList = None self.regionCondition = None self.regionConditions = [] self.regionCol = 1 row = 0 label = Label(frameD, text='Peak List: ', grid=(0, 0)) tipText = 'Selects which peak list to perform region-wide peak picking for' self.regionPeakListPulldown = PulldownList( frameD, callback=self.changeRegionPeakList, grid=(0, 1), tipText=tipText) row += 1 frameD.expandGrid(row, 1) self.regionEntry = FloatEntry(self, text='', returnCallback=self.setRegion, width=10) self.conditionMenu = PulldownList(self, texts=('include', 'exclude'), callback=self.setCondition) tipTexts = [ 'Whether to include or exclude the states region from region-wide peak picking', ] headingList = ['Condition'] editSetCallbacks = [None] editGetCallbacks = [None] editWidgets = [self.conditionMenu] self.regionFindMatrix = ScrolledMatrix( frameD, headingList=headingList, callback=self.selectRegionCell, editWidgets=editWidgets, editGetCallbacks=editGetCallbacks, editSetCallbacks=editSetCallbacks, grid=(row, 0), gridSpan=(1, 2)) row += 1 tipTexts = [ 'Sets the currently selected region row to cover the whole spectrum', 'Add a new region row, which may them be set for exclusion or inclusion when peak picking large areas', 'Remove the selected region specification', 'Go to the panel for setting the parameters that control how peaks extrema are picked', 'Using the stated regions and parameters, perform region-wide peak picking' ] texts = [ 'Whole Region', 'Add Region', 'Delete Region', 'Adjust Params', 'Find Peaks!' ] commands = [ self.wholeRegion, self.addCondition, self.deleteCondition, self.adjustParams, self.regionFindPeaks ] buttons = ButtonList(frameD, texts=texts, commands=commands, grid=(row, 0), gridSpan=(1, 2), tipTexts=tipTexts) buttons.buttons[4].config(bg='#B0FFB0') utilButtons = UtilityButtonList(tabbedFrame.sideFrame, grid=(0, 0), helpUrl=self.help_url, sticky='e') self.dataDim = None self.setParamsEntries() self.updateSpectrum() self.setIsotopeProperties() self.updateRegionPeakLists() self.administerNotifiers(self.registerNotify)
def body(self, guiFrame): self.geometry('500x130') guiFrame.grid_columnconfigure(2, weight=1) guiFrame.grid_rowconfigure(3, weight=1) self.alarm_id = None row = 0 tipText = 'Browse for the directory into which project backups will be made' button = Button(guiFrame, text='Directory:', command=self.selectDir, grid=(row, 0), tipText=tipText, sticky='ew') repository = self.project.findFirstRepository(name='backup') if repository: text = repository.url.path else: # this is trouble, but should not happen text = '' tipText = 'Enter the name of the directory into which project backups will be made' self.dir_entry = Entry(guiFrame, text=text, tipText=tipText, width=40, returnCallback=self.applyAuto, grid=(row, 1), gridSpan=(1, 2), sticky='ew') row += 1 label = Label(guiFrame, text='Auto-backup:', grid=(row, 0)) if self.analysisProject.doAutoBackup: ind = 0 else: ind = 1 tipTexts = [ 'Toggle the timed automatic backup on', 'Toggle the timed automatic backup off' ] self.on_off_buttons = RadioButtons(guiFrame, entries=self.on_off_entries, tipTexts=tipTexts, select_callback=self.applyAuto, selected_index=ind, grid=(row, 1)) row += 1 tipText = 'The number of minutes to wait before automatic project backups' label = Label(guiFrame, text='Auto-backup frequency:', grid=(row, 0)) self.freq_entry = IntEntry(guiFrame, text=self.analysisProject.autoBackupFreq, returnCallback=self.applyAuto, tipText=tipText) self.freq_entry.grid(row=row, column=1) label = Label(guiFrame, text=' (minutes)', grid=(row, 2)) row = row + 1 # Blank for expansion row = row + 1 texts = ['Apply Auto Settings', 'Do Immediate Backup'] commands = [self.applyAuto, self.applyManual] tipTexts = [ 'Commit the specified settings and commence automated CCPN project backup', 'Backup the CCPN project now, into the specified backup directory' ] buttons = UtilityButtonList(guiFrame, texts=texts, commands=commands, doClone=False, helpMsg=self.help_msg, helpUrl=self.help_url, tipTexts=tipTexts, grid=(row, 0), gridSpan=(1, 3), sticky='nsew')
class CingGui(BasePopup): def __init__(self, parent, options, *args, **kw): # Fill in below variable once run generates some results self.haveResults = None # store the options self.options = options BasePopup.__init__(self, parent=parent, title='CING Setup', **kw) # self.setGeometry(850, 750, 50, 50) self.project = None # self.tk_strictMotif( True) self.updateGui() # end def __init__ def body(self, guiFrame): row = 0 col = 0 # frame = Frame( guiFrame ) # frame.grid(row=row, column=col, sticky='news') self.menuBar = Menu(guiFrame) self.menuBar.grid(row=row, column=col, sticky='ew') #---------------------------------------------------------------------------------- # Project frame #---------------------------------------------------------------------------------- # guiFrame.grid_columnconfigure(row, weight=1) # frame = LabelFrame(guiFrame, text='Project', font=medFont) row = +1 col = 0 frame = LabelFrame(guiFrame, text='Project', **labelFrameAttributes) print '>', frame.keys() frame.grid(row=row, column=col, sticky='nsew') frame.grid_columnconfigure(2, weight=1) # frame.grid_rowconfigure(0, weight=1) srow = 0 self.projectOptions = [ 'old', 'new from PDB', 'new from CCPN', 'new from CYANA' ] self.projOptionsSelect = RadioButtons(frame, selected_index=0, entries=self.projectOptions, direction='vertical', select_callback=self.updateGui) self.projOptionsSelect.grid(row=srow, column=0, rowspan=len(self.projectOptions), columnspan=2, sticky='w') if self.options.name: text = self.options.name else: text = '' # end if self.projEntry = Entry(frame, bd=1, text=text, returnCallback=self.updateGui) self.projEntry.grid(row=srow, column=2, columnspan=2, sticky='ew') # self.projEntry.bind('<Key>', self.updateGui) self.projEntry.bind('<Leave>', self.updateGui) projButton = Button(frame, bd=1, command=self.chooseOldProjectFile, text='browse') projButton.grid(row=srow, column=3, sticky='ew') srow += 1 self.pdbEntry = Entry(frame, bd=1, text='') self.pdbEntry.grid(row=srow, column=2, sticky='ew') self.pdbEntry.bind('<Leave>', self.updateGui) pdbButton = Button(frame, bd=1, command=self.choosePdbFile, text='browse') pdbButton.grid(row=srow, column=3, sticky='ew') srow += 1 self.ccpnEntry = Entry(frame, bd=1, text='') self.ccpnEntry.grid(row=srow, column=2, sticky='ew') self.ccpnEntry.bind('<Leave>', self.updateGui) ccpnButton = Button(frame, bd=1, command=self.chooseCcpnFile, text='browse') ccpnButton.grid(row=srow, column=3, sticky='ew') srow += 1 self.cyanaEntry = Entry(frame, bd=1, text='') self.cyanaEntry.grid(row=srow, column=2, sticky='ew') self.cyanaEntry.bind('<Leave>', self.updateGui) cyanaButton = Button(frame, bd=1, command=self.chooseCyanaFile, text='browse') cyanaButton.grid(row=srow, column=3, sticky='ew') #Empty row srow += 1 label = Label(frame, text='') label.grid(row=srow, column=0, sticky='nw') srow += 1 label = Label(frame, text='Project name:') label.grid(row=srow, column=0, sticky='nw') self.nameEntry = Entry(frame, bd=1, text='') self.nameEntry.grid(row=srow, column=2, sticky='w') #Empty row srow += 1 label = Label(frame, text='') label.grid(row=srow, column=0, sticky='nw') srow += 1 self.openProjectButton = Button(frame, command=self.openProject, text='Open Project', **actionButtonAttributes) self.openProjectButton.grid(row=srow, column=0, columnspan=4, sticky='ew') #---------------------------------------------------------------------------------- # status #---------------------------------------------------------------------------------- # guiFrame.grid_columnconfigure(1, weight=0) srow = 0 frame = LabelFrame(guiFrame, text='Status', **labelFrameAttributes) frame.grid(row=srow, column=1, sticky='wnes') self.projectStatus = Text(frame, height=11, width=70, borderwidth=0, relief='flat') self.projectStatus.grid(row=0, column=0, sticky='wen') #Empty row srow += 1 label = Label(frame, text='') label.grid(row=srow, column=0, sticky='nw') srow += 1 self.closeProjectButton = Button(frame, command=self.closeProject, text='Close Project', **actionButtonAttributes) self.closeProjectButton.grid(row=srow, column=0, columnspan=4, sticky='ew') #---------------------------------------------------------------------------------- # Validate frame #---------------------------------------------------------------------------------- row += 1 col = 0 frame = LabelFrame(guiFrame, text='Validate', **labelFrameAttributes) # frame = LabelFrame(guiFrame, text='Validate', font=medFont) frame.grid(row=row, column=col, sticky='nsew') # frame.grid_columnconfigure(2, weight=1) frame.grid_rowconfigure(0, weight=1) srow = 0 # label = Label(frame, text='validation') # label.grid(row=srow,column=0,sticky='nw') # # self.selectDoValidation = CheckButton(frame) # self.selectDoValidation.grid(row=srow, column=1,sticky='nw' ) # self.selectDoValidation.set(True) # # srow += 1 # label = Label(frame, text='') # label.grid(row=srow,column=0,sticky='nw') # # srow += 1 label = Label(frame, text='checks') label.grid(row=srow, column=0, sticky='nw') self.selectCheckAssign = CheckButton(frame) self.selectCheckAssign.grid(row=srow, column=1, sticky='nw') self.selectCheckAssign.set(True) label = Label(frame, text='assignments and shifts') label.grid(row=srow, column=2, sticky='nw') # srow += 1 # self.selectCheckQueen = CheckButton(frame) # self.selectCheckQueen.grid(row=srow, column=4,sticky='nw' ) # self.selectCheckQueen.set(False) # label = Label(frame, text='QUEEN') # label.grid(row=srow,column=5,sticky='nw') # # queenButton = Button(frame, bd=1,command=None, text='setup') # queenButton.grid(row=srow,column=6,sticky='ew') srow += 1 self.selectCheckResraint = CheckButton(frame) self.selectCheckResraint.grid(row=srow, column=1, sticky='nw') self.selectCheckResraint.set(True) label = Label(frame, text='restraints') label.grid(row=srow, column=2, sticky='nw') srow += 1 self.selectCheckStructure = CheckButton(frame) self.selectCheckStructure.grid(row=srow, column=1, sticky='nw') self.selectCheckStructure.set(True) label = Label(frame, text='structural') label.grid(row=srow, column=2, sticky='nw') srow += 1 self.selectMakeHtml = CheckButton(frame) self.selectMakeHtml.grid(row=srow, column=1, sticky='nw') self.selectMakeHtml.set(True) label = Label(frame, text='generate HTML') label.grid(row=srow, column=2, sticky='nw') srow += 1 self.selectCheckScript = CheckButton(frame) self.selectCheckScript.grid(row=srow, column=1, sticky='nw') self.selectCheckScript.set(False) label = Label(frame, text='user script') label.grid(row=srow, column=0, sticky='nw') self.validScriptEntry = Entry(frame, bd=1, text='') self.validScriptEntry.grid(row=srow, column=2, columnspan=3, sticky='ew') scriptButton = Button(frame, bd=1, command=self.chooseValidScript, text='browse') scriptButton.grid(row=srow, column=5, sticky='ew') srow += 1 label = Label(frame, text='ranges') label.grid(row=srow, column=0, sticky='nw') self.rangesEntry = Entry(frame, text='') self.rangesEntry.grid(row=srow, column=2, columnspan=3, sticky='ew') # self.validScriptEntry = Entry(frame, bd=1, text='') # self.validScriptEntry.grid(row=srow,column=3,sticky='ew') # # scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse') # scriptButton.grid(row=srow,column=4,sticky='ew') srow += 1 texts = ['Run Validation', 'View Results', 'Setup QUEEN'] commands = [self.runCing, None, None] buttonBar = ButtonList(frame, texts=texts, commands=commands, expands=True) buttonBar.grid(row=srow, column=0, columnspan=6, sticky='ew') for button in buttonBar.buttons: button.config(**actionButtonAttributes) # end for self.runButton = buttonBar.buttons[0] self.viewResultButton = buttonBar.buttons[1] self.queenButton = buttonBar.buttons[2] #---------------------------------------------------------------------------------- # Miscellaneous frame #---------------------------------------------------------------------------------- row += 0 col = 1 # frame = LabelFrame(guiFrame, text='Miscellaneous', font=medFont) frame = LabelFrame(guiFrame, text='Miscellaneous', **labelFrameAttributes) frame.grid(row=row, column=col, sticky='news') frame.grid_columnconfigure(2, weight=1) frame.grid_columnconfigure(4, weight=1, minsize=30) frame.grid_rowconfigure(0, weight=1) # Exports srow = 0 label = Label(frame, text='export to') label.grid(row=srow, column=0, sticky='nw') self.selectExportXeasy = CheckButton(frame) self.selectExportXeasy.grid(row=srow, column=1, sticky='nw') self.selectExportXeasy.set(True) label = Label(frame, text='Xeasy, Sparky, TALOS, ...') label.grid(row=srow, column=2, sticky='nw') srow += 1 self.selectExportCcpn = CheckButton(frame) self.selectExportCcpn.grid(row=srow, column=1, sticky='nw') self.selectExportCcpn.set(True) label = Label(frame, text='CCPN') label.grid(row=srow, column=2, sticky='nw') srow += 1 self.selectExportQueen = CheckButton(frame) self.selectExportQueen.grid(row=srow, column=1, sticky='nw') self.selectExportQueen.set(True) label = Label(frame, text='QUEEN') label.grid(row=srow, column=2, sticky='nw') srow += 1 self.selectExportRefine = CheckButton(frame) self.selectExportRefine.grid(row=srow, column=1, sticky='nw') self.selectExportRefine.set(True) label = Label(frame, text='refine') label.grid(row=srow, column=2, sticky='nw') srow += 1 label = Label(frame, text='') label.grid(row=srow, column=0, sticky='nw') # User script srow += 1 label = Label(frame, text='user script') label.grid(row=srow, column=0, sticky='nw') self.selectMiscScript = CheckButton(frame) self.selectMiscScript.grid(row=srow, column=1, sticky='nw') self.selectMiscScript.set(False) self.miscScriptEntry = Entry(frame, bd=1, text='') self.miscScriptEntry.grid(row=srow, column=3, sticky='ew') script2Button = Button(frame, bd=1, command=self.chooseMiscScript, text='browse') script2Button.grid(row=srow, column=4, sticky='ew') srow += 1 texts = ['Export', 'Run Script'] commands = [None, None] buttonBar = ButtonList(frame, texts=texts, commands=commands, expands=True) buttonBar.grid(row=srow, column=0, columnspan=5, sticky='ew') for button in buttonBar.buttons: button.config(**actionButtonAttributes) # end for self.exportButton = buttonBar.buttons[0] self.scriptButton = buttonBar.buttons[1] #---------------------------------------------------------------------------------- # Textarea #---------------------------------------------------------------------------------- row += 1 guiFrame.grid_rowconfigure(row, weight=1) self.outputTextBox = ScrolledText(guiFrame) self.outputTextBox.grid(row=row, column=0, columnspan=2, sticky='nsew') self.redirectConsole() #---------------------------------------------------------------------------------- # Buttons #---------------------------------------------------------------------------------- row += 1 col = 0 texts = ['Quit', 'Help'] commands = [self.close, None] self.buttonBar = ButtonList(guiFrame, texts=texts, commands=commands, expands=True) self.buttonBar.grid(row=row, column=col, columnspan=2, sticky='ew') # self.openProjectButton = self.buttonBar.buttons[0] # self.closeProjectButton = self.buttonBar.buttons[1] # self.runButton = self.buttonBar.buttons[0] # self.viewResultButton = self.buttonBar.buttons[1] for button in self.buttonBar.buttons: button.config(**actionButtonAttributes) # end for # end def body def getGuiOptions(self): projectName = self.projEntry.get() index = self.projOptionsSelect.getIndex() if index > 0: makeNewProject = True projectImport = None if index > 1: i = index - 2 format = ['PDB', 'CCPN', 'CYANA'][i] file = [self.pdbEntry, self.ccpnEntry, self.cyanaEntry][i].get() if not file: showWarning('Failure', 'No %s file selected' % format) return # end if projectImport = (format, file) # end if else: # Chould also check that any old project file exists makeNewProject = False projectImport = None # end if doValidation = self.selectDoValidation.get() checks = [] if doValidation: if self.selectCheckAssign.get(): checks.append('assignments') # end if if self.selectCheckResraint.get(): checks.append('restraints') # end if if self.selectCheckStructure.get(): checks.append('structural') # end if if self.selectMakeHtml.get(): checks.append('HTML') # end if if self.selectCheckScript.get(): script = self.validScriptEntry.get() if script: checks.append(('script', script)) # end if # end if if self.selectCheckQueen.get(): checks.append('queen') # end if # end if exports = [] if self.selectExportXeasy.get(): exports.append('Xeasy') # end if if self.selectExportCcpn.get(): exports.append('CCPN') # end if if self.selectExportQueen.get(): exports.append('QUEEN') # end if if self.selectExportRefine.get(): exports.append('refine') # end if miscScript = None if self.selectMiscScript.get(): script = self.miscScriptEntry.get() if script: miscScript = script # end if # end if return projectName, makeNewProject, projectImport, doValidation, checks, exports, miscScript # end def getGuiOptions def runCing(self): options = self.getGuiOptions() if options: projectName, makeNewProject, projectImport, doValidation, checks, exports, miscScript = options print 'Project name:', projectName print 'Make new project?', makeNewProject print 'Import source:', projectImport print 'Do vailidation?', doValidation print 'Validation checks:', ','.join(checks) print 'Export to:', ','.join(exports) print 'User script:', miscScript # end if # end def runCing # else there was already an error message def chooseOldProjectFile(self): fileTypes = [FileType('CING', ['project.xml']), FileType('All', ['*'])] popup = FileSelectPopup(self, file_types=fileTypes, title='Select CING project file', dismiss_text='Cancel', selected_file_must_exist=True) fileName = popup.getFile() # dirName = popup.getDirectory() if len(fileName) > 0: # Put text into entry,name widgets dummy, name = cing.Project.rootPath(fileName) self.projEntry.configure(state='normal') self.projEntry.set(fileName) self.nameEntry.configure(state='normal') self.nameEntry.set(name) self.nameEntry.configure(state='disabled') # choose the correct radiobutton self.projOptionsSelect.setIndex(0) self.updateGui() # end if #nd if popup.destroy() # end def chooseOldProjectFile def choosePdbFile(self): fileTypes = [FileType('PDB', ['*.pdb']), FileType('All', ['*'])] popup = FileSelectPopup(self, file_types=fileTypes, title='PDB file', dismiss_text='Cancel', selected_file_must_exist=True) fileName = popup.getFile() if len(fileName) > 0: # Put text into entry widget self.pdbEntry.configure(state='normal') self.pdbEntry.set(fileName) # Put text into name widget _dir, name, dummy = nTpath(fileName) self.nameEntry.configure(state='normal') self.nameEntry.set(name) # choose the correct radiobutton self.projOptionsSelect.setIndex(1) self.updateGui() #end if popup.destroy() # end def choosePdbFile def chooseCcpnFile(self): fileTypes = [FileType('XML', ['*.xml']), FileType('All', ['*'])] popup = FileSelectPopup(self, file_types=fileTypes, title='CCPN project XML file', dismiss_text='Cancel', selected_file_must_exist=True) fileName = popup.getFile() if len(fileName) > 0: self.pdbEntry.configure(state='normal') self.pdbEntry.set(fileName) self.projOptionsSelect.setIndex(1) _dir, name, dummy = nTpath(fileName) self.nameEntry.set(name) #end if self.ccpnEntry.set(fileName) self.projOptionsSelect.setIndex(2) popup.destroy() # end def chooseCcpnFile def chooseCyanaFile(self): # Prepend default Cyana file extension below fileTypes = [ FileType('All', ['*']), ] popup = FileSelectPopup(self, file_types=fileTypes, title='CYANA fproject file', dismiss_text='Cancel', selected_file_must_exist=True) fileName = popup.getFile() self.cyanaEntry.set(fileName) self.projOptionsSelect.setIndex(3) popup.destroy() # end def chooseCyanaFile def chooseValidScript(self): # Prepend default Cyana file extension below fileTypes = [ FileType('All', ['*']), ] popup = FileSelectPopup(self, file_types=fileTypes, title='Script file', dismiss_text='Cancel', selected_file_must_exist=True) fileName = popup.getFile() self.validScriptEntry.set(fileName) popup.destroy() # end def chooseValidScript def chooseMiscScript(self): # Prepend default Cyana file extension below fileTypes = [ FileType('All', ['*']), ] popup = FileSelectPopup(self, file_types=fileTypes, title='Script file', dismiss_text='Cancel', selected_file_must_exist=True) fileName = popup.getFile() self.miscScriptEntry.set(fileName) popup.destroy() # end def chooseMiscScript def openProject(self): projOption = self.projOptionsSelect.get() if projOption == self.projectOptions[0]: self.openOldProject() elif projOption == self.projectOptions[1]: self.initPdb() # end if if self.project: self.project.gui = self # end if self.updateGui() #end def def openOldProject(self): fName = self.projEntry.get() if not os.path.exists(fName): nTerror('Error: file "%s" does not exist\n', fName) #end if if self.project: self.closeProject() # end if self.project = cing.Project.open(name=fName, status='old', verbose=False) #end def def initPdb(self): fName = self.pdbEntry.get() if not os.path.exists(fName): nTerror('Error: file "%s" does not exist\n', fName) #end if self.project = cing.Project.open(self.nameEntry.get(), status='new') self.project.initPDB(pdbFile=fName, convention='PDB') #end def def closeProject(self): if self.project: self.project.close() # end if self.project = None self.updateGui() #end def def updateGui(self, event=None): projOption = self.projOptionsSelect.get() buttons = self.buttonBar.buttons # Disable entries for e in [ self.projEntry, self.pdbEntry, self.ccpnEntry, self.cyanaEntry, self.nameEntry ]: e.configure(state='disabled') #end for if projOption == self.projectOptions[0]: # Enable entries self.projEntry.configure(state='normal') if (len(self.projEntry.get()) > 0): self.openProjectButton.enable() self.runButton.enable() else: self.openProjectButton.disable() self.runButton.disable() #end if elif projOption == self.projectOptions[1]: # Enable entries self.pdbEntry.configure(state='normal') self.nameEntry.configure(state='normal') if (len(self.pdbEntry.get()) > 0 and len(self.nameEntry.get()) > 0): buttons[0].enable() buttons[1].enable() else: buttons[0].disable() buttons[1].disable() #end if #end if elif projOption == self.projectOptions[2]: # Enable entries self.ccpnEntry.configure(state='normal') self.nameEntry.configure(state='normal') if (len(self.ccpnEntry.get()) > 0 and len(self.nameEntry.get()) > 0): buttons[0].enable() buttons[1].enable() else: buttons[0].disable() buttons[1].disable() #end if #end if elif projOption == self.projectOptions[3]: # Enable entries self.cyanaEntry.configure(state='normal') self.nameEntry.configure(state='normal') if (len(self.cyanaEntry.get()) > 0 and len(self.nameEntry.get()) > 0): buttons[0].enable() buttons[1].enable() else: buttons[0].disable() buttons[1].disable() #end if #end if self.projectStatus.clear() if not self.project: self.projectStatus.setText('No open project') self.closeProjectButton.setText('Close Project') self.closeProjectButton.disable() else: self.projectStatus.setText(self.project.format()) self.closeProjectButton.enable() self.closeProjectButton.setText( sprintf('Close Project "%s"', self.project.name)) #end if #end def def redirectConsole(self): #pipe = TextPipe(self.inputTextBox.text_area) #sys.stdin = pipe pipe = TextPipe(self.outputTextBox.text_area) sys.stdout = pipe nTmessage.stream = pipe # end def redirectConsole # sys.stderr = pipe def resetConsole(self): #sys.stdin = stdin nTmessage.stream = stdout sys.stdout = stdout sys.stderr = stderr # end def resetConsole def open(self): self.redirectConsole() BasePopup.open(self) # end def open def close(self): geometry = self.getGeometry() self.resetConsole() BasePopup.close(self) print 'close:', geometry sys.exit(0) # remove later # end def close def destroy(self): geometry = self.getGeometry() self.resetConsole() BasePopup.destroy(self) print 'destroy:', geometry sys.exit(0) # remove later
def body(self, master): pseudoExpts = getSampledDimExperiments(self.parent.nmrProject) master.rowconfigure(0, weight=1) master.rowconfigure(1, weight=1) master.columnconfigure(0, weight=1) tipTexts = ['The experiment is pseudo-N dimensional, with a sampled axis', 'The experiment is the regular kind with only NMR frequency axes'] self.pseudoEntries = [x % len(self.params.npts) for x in PSEUDO_ENTRIES] self.pseudoButton = RadioButtons(master, entries=self.pseudoEntries, select_callback=self.changedPseudoMode, grid=(0,0), sticky='nw', tipTexts=tipTexts) frame = self.pseudoFrame = Frame(master) self.pseudoFrame.grid(row=1, column=0, sticky='nsew') row = 0 if pseudoExpts: tipText = 'Select from existing pseudo nD experiments to copy sampled axis values from' texts = [x.name for x in pseudoExpts] label = Label(frame, text='Existing pseudo expts: ') label.grid(row=row, column=0, sticky='e') self.pseudoList = PulldownList(frame, texts=texts, objects=pseudoExpts, tipText=tipText) self.pseudoList.grid(row=row, column=1, sticky='w') tipText = 'Transfer the sampled axis values from the existing experiment to the new one' Button(frame, text='Copy values down', command=self.copyValues, tipText=tipText, grid=(row,2)) row += 1 npts = self.params.npts[self.dim] tipText = 'Number of data points (planes) along sampled axis' label = Label(frame, text='Number of points: ') label.grid(row=row, column=0, sticky='e') self.nptsEntry = IntEntry(frame, text=npts, tipText=tipText, width=8, grid=(row,1)) tipText = 'Load the values for the sampled axis from a text file containing a list of numeric values' Button(frame, text='Load File', command=self.loadValues, tipText=tipText, grid=(row,2), sticky='ew') row += 1 tipText = 'The values (e.g. T1, T2) corresponding to each data point (plane) along sampled axis' label = Label(frame, text='Point values: ') label.grid(row=row, column=0, sticky='e') self.valueEntry = FloatEntry(frame, isArray=True, tipText=tipText) #minRows = self.params.npts[self.dim] #self.valueEntry = MultiWidget(frame, FloatEntry, callback=None, minRows=minRows, maxRows=None, # options=None, values=[], useImages=False) self.valueEntry.grid(row=row, column=1, columnspan=2, sticky='ew') row += 1 label = Label(frame, text='(requires comma-separated list, of length number of points)') label.grid(row=row, column=1, columnspan=2, sticky='w') row += 1 for n in range(row): frame.rowconfigure(n, weight=1) frame.columnconfigure(1, weight=1) buttons = UtilityButtonList(master, closeText='Ok', closeCmd=self.updateParams, helpUrl=self.help_url) buttons.grid(row=row, column=0, sticky='ew')
class BackupProjectPopup(BasePopup): """ **Create Automatic Project Backup** The purpose of this dialog is to allow the user to create backups of their project automatically. The XML files for the backup go into a separate directory from the project itself. If the project directory is called PROJECTDIR then the default for the backup directory is PROJECTDIR_backup, although that can be changed to something else in this dialog. Other than the backup directory, the user can specify the frequency of the backup, in minutes. The "Apply Auto Settings" does not have to be applied if the user has changed the on/off setting or if the user has changed the Auto-backup frequency and entered a carriage return. The "Do Immediate Backup" is in case the user wants to do a backup then and there. There is no backup for the backup. """ on_off_entries = ['on', 'off'] def __init__(self, parent, help_msg='', help_url='', *args, **kw): self.help_msg = help_msg self.help_url = help_url BasePopup.__init__(self, parent=parent, title='Project : Backup', **kw) def body(self, guiFrame): self.geometry('500x130') guiFrame.grid_columnconfigure(2, weight=1) guiFrame.grid_rowconfigure(3, weight=1) self.alarm_id = None row = 0 tipText = 'Browse for the directory into which project backups will be made' button = Button(guiFrame, text='Directory:', command=self.selectDir, grid=(row, 0), tipText=tipText, sticky='ew') repository = self.project.findFirstRepository(name='backup') if repository: text = repository.url.path else: # this is trouble, but should not happen text = '' tipText = 'Enter the name of the directory into which project backups will be made' self.dir_entry = Entry(guiFrame, text=text, tipText=tipText, width=40, returnCallback=self.applyAuto, grid=(row, 1), gridSpan=(1, 2), sticky='ew') row += 1 label = Label(guiFrame, text='Auto-backup:', grid=(row, 0)) if self.analysisProject.doAutoBackup: ind = 0 else: ind = 1 tipTexts = [ 'Toggle the timed automatic backup on', 'Toggle the timed automatic backup off' ] self.on_off_buttons = RadioButtons(guiFrame, entries=self.on_off_entries, tipTexts=tipTexts, select_callback=self.applyAuto, selected_index=ind, grid=(row, 1)) row += 1 tipText = 'The number of minutes to wait before automatic project backups' label = Label(guiFrame, text='Auto-backup frequency:', grid=(row, 0)) self.freq_entry = IntEntry(guiFrame, text=self.analysisProject.autoBackupFreq, returnCallback=self.applyAuto, tipText=tipText) self.freq_entry.grid(row=row, column=1) label = Label(guiFrame, text=' (minutes)', grid=(row, 2)) row = row + 1 # Blank for expansion row = row + 1 texts = ['Apply Auto Settings', 'Do Immediate Backup'] commands = [self.applyAuto, self.applyManual] tipTexts = [ 'Commit the specified settings and commence automated CCPN project backup', 'Backup the CCPN project now, into the specified backup directory' ] buttons = UtilityButtonList(guiFrame, texts=texts, commands=commands, doClone=False, helpMsg=self.help_msg, helpUrl=self.help_url, tipTexts=tipTexts, grid=(row, 0), gridSpan=(1, 3), sticky='nsew') def selectDir(self): popup = FileSelectPopup(self, show_file=False) dir = popup.getDirectory() popup.destroy() if (dir): self.dir_entry.set(dir) self.setDir() def setDir(self): directory = self.dir_entry.get() if not directory: showWarning('No directory', 'No directory specified, not setting backup directory', parent=self) return if not os.path.abspath(directory): directory = joinPath(os.getcwd(), directory) if os.path.exists(directory): if not os.path.isdir(directory): showWarning('Path not directory', 'Path "%s" exists but is not a directory' % directory, parent=self) return else: if showYesNo( 'Directory does not exist', 'Directory "%s" does not exist, should it be created?' % directory, parent=self): os.mkdir(directory) else: showWarning( 'Directory not created', 'Directory "%s" not created so not setting backup directory' % directory, parent=self) return repository = self.project.findFirstRepository(name='backup') if not repository: showWarning( 'No backup repository', 'No backup repository found (something wrong somewhere)', parent=self) return url = repository.url if url.path != directory: repository.url = Url(path=normalisePath(directory)) def setFreq(self): freq = self.freq_entry.get() if (freq is None): freq = 0 self.analysisProject.autoBackupFreq = freq def setInfo(self): self.setFreq() self.setDir() on_off = (self.on_off_buttons.get() == 'on') self.analysisProject.doAutoBackup = on_off def applyAuto(self, *event): self.setInfo() on_off = self.on_off_buttons.get() if on_off == 'on': self.parent.setBackupOn() else: self.parent.setBackupOff() def applyManual(self): self.setDir() self.parent.doBackup()
class BrukerPseudoPopup(BasePopup): def __init__(self, parent, params, dim, *args, **kw): self.dim = dim self.params = params BasePopup.__init__(self, parent=parent, title='Bruker Pseudo Data', modal=True, **kw) def body(self, master): pseudoExpts = getSampledDimExperiments(self.parent.nmrProject) master.rowconfigure(0, weight=1) master.rowconfigure(1, weight=1) master.columnconfigure(0, weight=1) tipTexts = ['The experiment is pseudo-N dimensional, with a sampled axis', 'The experiment is the regular kind with only NMR frequency axes'] self.pseudoEntries = [x % len(self.params.npts) for x in PSEUDO_ENTRIES] self.pseudoButton = RadioButtons(master, entries=self.pseudoEntries, select_callback=self.changedPseudoMode, grid=(0,0), sticky='nw', tipTexts=tipTexts) frame = self.pseudoFrame = Frame(master) self.pseudoFrame.grid(row=1, column=0, sticky='nsew') row = 0 if pseudoExpts: tipText = 'Select from existing pseudo nD experiments to copy sampled axis values from' texts = [x.name for x in pseudoExpts] label = Label(frame, text='Existing pseudo expts: ') label.grid(row=row, column=0, sticky='e') self.pseudoList = PulldownList(frame, texts=texts, objects=pseudoExpts, tipText=tipText) self.pseudoList.grid(row=row, column=1, sticky='w') tipText = 'Transfer the sampled axis values from the existing experiment to the new one' Button(frame, text='Copy values down', command=self.copyValues, tipText=tipText, grid=(row,2)) row += 1 npts = self.params.npts[self.dim] tipText = 'Number of data points (planes) along sampled axis' label = Label(frame, text='Number of points: ') label.grid(row=row, column=0, sticky='e') self.nptsEntry = IntEntry(frame, text=npts, tipText=tipText, width=8, grid=(row,1)) tipText = 'Load the values for the sampled axis from a text file containing a list of numeric values' Button(frame, text='Load File', command=self.loadValues, tipText=tipText, grid=(row,2), sticky='ew') row += 1 tipText = 'The values (e.g. T1, T2) corresponding to each data point (plane) along sampled axis' label = Label(frame, text='Point values: ') label.grid(row=row, column=0, sticky='e') self.valueEntry = FloatEntry(frame, isArray=True, tipText=tipText) #minRows = self.params.npts[self.dim] #self.valueEntry = MultiWidget(frame, FloatEntry, callback=None, minRows=minRows, maxRows=None, # options=None, values=[], useImages=False) self.valueEntry.grid(row=row, column=1, columnspan=2, sticky='ew') row += 1 label = Label(frame, text='(requires comma-separated list, of length number of points)') label.grid(row=row, column=1, columnspan=2, sticky='w') row += 1 for n in range(row): frame.rowconfigure(n, weight=1) frame.columnconfigure(1, weight=1) buttons = UtilityButtonList(master, closeText='Ok', closeCmd=self.updateParams, helpUrl=self.help_url) buttons.grid(row=row, column=0, sticky='ew') def loadValues(self): directory = self.parent.fileSelect.getDirectory() fileSelectPopup = FileSelectPopup(self, title='Select Sampled Data File', dismiss_text='Cancel', selected_file_must_exist=True, multiSelect=False, directory=directory) fileName = fileSelectPopup.file_select.getFile() fileObj = open(fileName, 'rU') data = '' line = fileObj.readline() while line: data += line line = fileObj.readline() data = re.sub(',\s+', ',', data) data = re.sub('\s+', ',', data) data = re.sub(',,', ',', data) data = re.sub('[^0-9,.\-+eE]', '', data) self.valueEntry.set(data) def copyValues(self): expt = self.pseudoList.getObject() if expt: dataDim = getExperimentSampledDim(expt) values = dataDim.pointValues self.nptsEntry.set(len(values)) self.valueEntry.set(values) def updateParams(self): params = self.params if self.pseudoButton.get() == self.pseudoEntries[0]: npts = self.nptsEntry.get() params.npts[self.dim] = npts values = self.valueEntry.get() try: params.setSampledDim(self.dim, values) except ApiError, e: showError('Set Sampled Dim', e.error_msg, parent=self) return else:
class EditContourLevelsPopup(BasePopup): """ **Change Levels in Spectrum Contour Displays** This popup window is used to specify which contour levels (lines of constant intensity) are drawn for spectra within the spectrum windows of Analysis. A spectrum can have both positive and negative levels, and the user can set these on an individual basis or as a regular incremental (usually geometric) series. It should be noted that spectrum contour colours, which may be different for positive and negative levels, is set elsewhere, in the main Spectra_ table. In normal operation the user first selects the spectrum to change the contours for in the upper left pulldown menu. Although contour levels are specified for individual spectra, if there are several spectra that share the same levels (for example if they form a series of some kind) then the user may spread the contour level information from one to many via the [Propagate Contours] function within the "Display Options" of the main Spectra_ table. The user may also affect the contour levels of multiple spectra by changing the "Global scale" settings. This global scale will affect *all spectra* in the project; the scale value multiplies all of the contour levels for all spectra, although in practice it is rarely changed. Using a global scale gives the advantage of being able to specify smaller numbers for the levels. The individual contour levels for a spectrum are listed in the "positive levels" and "Negative levels" fields. They are multiplied by the global scale factor when they are used for spectrum display. The user may type in values for the levels directly into these field, or they can be filled using the "Auto contour levels" mechanism. If manual levels are specified the user should press [Apply manual Levels] when done to commit the changes and see the results. The [Apply Auto Levels] function differs in that it always applies a regular series of levels, according to the settings, and these will overwrite any manual specifications when committed; the actual levels applied are always displayed in the levels field. The setting of "Auto" levels using a series involves choosing a base level, which represents the first contour (closest to zero). This base level is usually set according to the level of noise in the spectrum. Typically it is a value just above most of the noise, so the noise is not seen, but it may be set lower in some instances to show weak signals. The base level applies to both positive and negative contour series, although for the negative side it is naturally used with negative sign. The user sets how many levels there should be in total; the subsequent levels start from the base level and move away from zero. Normally this involves a geometric series, with a constant multiplication factor applied to a value to generate the next in the series. This factor is set in the "Level multiplier", although some of the commonly used values are quickly set via the adjacent buttons. Under a few special circumstances it is helpful to have a constant difference between levels, in which case "Add levels" may be used instead of "Multiply levels". **Caveats & Tips** Often it is useful to initially setup contours using an "Auto" series, but then manually remove some of the levels. For example having all the positive levels but only the first negative level may be helpful to show where peaks are truncated. Note this system sets the levels that would be used to make any contour files (an optional way of working, especially for 4D spectra etc.). However, once contour files are made then this system will not affect the levels within the files. .. _Spectra: EditSpectrumPopup.html """ def __init__(self, parent, *args, **kw): BasePopup.__init__(self, parent=parent, title='Spectrum Contour Levels', **kw) def body(self, guiFrame): self.doUpdateForm = True self.spectrum = None guiFrame.grid_columnconfigure(1, weight=1) row = 0 specFrame = LabelFrame(guiFrame, text='Spectrum', grid=(row, 0)) tipText = 'The spectrum for which you are setting the contour levels' self.expt_spectrum = PulldownList(specFrame, grid=(0, 0), tipText=tipText, callback=self.setSpectrumDetails) tipText = 'Open the edit spectrum table to view and change other properties associated with the selected spectrum' button = Button(specFrame, text='Spectrum Properties', command=self.editProperties, borderwidth=1, grid=(1, 0), sticky='ew', tipText=tipText) globalFrame = LabelFrame(guiFrame, text='Global scale') globalFrame.grid(row=row, column=1, sticky='nsew') globalFrame.grid_columnconfigure(0, weight=1) tipText = 'The value by which all contour levels in all spectra are multiplied; to give the actual contour level in terms of the stored spectrum data' self.global_entry = FloatEntry( globalFrame, width=10, tipText=tipText, text=self.analysisProject.globalContourScale, returnCallback=self.applyAuto, grid=(0, 0), gridSpan=(1, 2), sticky='ew') tipText = 'Divide the global scaling factor by two; moving all contour for all spectra levels closer to zero' button = Button(globalFrame, borderwidth=1, text='/2', sticky='ew', tipText=tipText, command=lambda: self.changeGlobalScale(0.5), grid=(0, 2)) tipText = 'Multiple the global scaling factor by two; moving all contour for all spectra levels away from zero' button = Button(globalFrame, borderwidth=1, text='*2', sticky='ew', tipText=tipText, command=lambda: self.changeGlobalScale(2.0), grid=(0, 3)) tipText = 'Set the global contour scale for all spectra to the default of 100,000' button = Button(globalFrame, borderwidth=1, text='10^5', tipText=tipText, command=self.defaultGlobalScale, grid=(1, 0)) tipText = 'Click to decrease "-" or increase "+" the global contour scale by small amounts' frame = ValueRamp(globalFrame, callback=self.changeGlobalScale, tipText=tipText) frame.grid(row=1, column=1, columnspan=3, sticky='e') row += 1 self.autoFrame = LabelFrame(guiFrame, text='Auto contour levels') self.autoFrame.grid(row=row, column=0, columnspan=5, sticky='nsew') self.autoFrame.grid_columnconfigure(1, weight=1) frow = 0 label = Label(self.autoFrame, text='Base level:', grid=(frow, 0), sticky='e') tipText = 'The first contour level (closest to zero) for an automated series of levels: the start of a geometric or arithmetic series defining levels' self.base_entry = FloatEntry(self.autoFrame, returnCallback=self.applyAuto, width=10, grid=(frow, 1), sticky='ew', tipText=tipText) command = lambda: self.changeBaseLevel(0.5) tipText = 'Lower the base contour level so that it is half of the previous value; moving the series of contour levels closer to zero' button = Button(self.autoFrame, borderwidth=1, text='/2', tipText=tipText, command=command, grid=(frow, 2), sticky='ew') command = lambda: self.changeBaseLevel(2.0) tipText = 'Raise the base contour level so that it is double the previous value; moving the series of contour levels further from zero' button = Button(self.autoFrame, borderwidth=1, text='*2', tipText=tipText, command=command, grid=(frow, 3), sticky='ew') tipText = 'Click to decrease "-" or increase "+" the base contour level by small amounts' frame = ValueRamp(self.autoFrame, callback=self.changeBaseLevel, tipText=tipText) frame.grid(row=frow, column=4, columnspan=3, sticky='ew') frow += 1 label = Label(self.autoFrame, text='Number of levels:', grid=(frow, 0), sticky='e') #self.numberEntry = IntEntry(guiFrame, text=numberLevels, # returnCallback=self.applyAuto) tipText = 'The number of contour levels to make in the automated series' self.numberEntry = IntEntry(self.autoFrame, returnCallback=self.applyAuto, width=10, grid=(frow, 1), sticky='ew', tipText=tipText) command = lambda w=-1: self.changeNumberLevels(w) tipText = 'Decrease the number of contour levels in the series by one' button = Button(self.autoFrame, borderwidth=1, text='-1', tipText=tipText, command=command, grid=(frow, 2), sticky='ew') command = lambda w=1: self.changeNumberLevels(w) tipText = 'Increase the number of contour levels in the series by one' button = Button(self.autoFrame, borderwidth=1, text='+1', tipText=tipText, command=command, grid=(frow, 3), sticky='ew') n = 4 for w in (5, 10, 15, 20): tipText = 'Set the number of contour levels in the series to %d' % w command = lambda w=w: self.setNumberLevels(w) button = Button(self.autoFrame, borderwidth=1, text='%d' % w, command=command, grid=(frow, n), sticky='ew', tipText=tipText) n += 1 frow += 1 self.change_label = Label(self.autoFrame, text='%s:' % multiplier_text, grid=(frow, 0), sticky='e') tipText = 'The multiplication factor (or increment if adding levels) to repetitively apply to the base level to generate the series of levels' self.change_entry = FloatEntry(self.autoFrame, returnCallback=self.applyAuto, width=10, grid=(frow, 1), sticky='ew', tipText=tipText) self.change_level_buttons = [] n = 2 for w in multiplier_changes: tipText = 'Set the automated series multiplication factor or increment to %f' % w command = lambda w=w: self.setChange(w) button = Button(self.autoFrame, borderwidth=1, text=str(w), command=command, grid=(frow, n), sticky='ew', tipText=tipText) self.change_level_buttons.append(button) n += 1 frow += 1 frame = Frame(self.autoFrame, grid=(frow, 0), gridSpan=(1, 7), sticky='ew') tipTexts = [ 'Toggles whether positive contour levels from the automated series will be used. Overrides any manual settings', 'Toggles whether negative contour levels from the automated series will be used. Overrides any manual settings' ] entries = ('Positive', 'Negative') selected = (True, False) self.which_buttons = CheckButtons(frame, entries, selected=selected, select_callback=self.applyAuto, grid=(0, 0), sticky='w', tipTexts=tipTexts) tipTexts = [ 'Set the contour level generation to use a geometric series, starting from the base level and using the specified factor', 'Set the contour level generation to use an arithmetic series, starting from the base level and using the specified increment' ] entries = ('Multiply levels', 'Add levels') self.change_mode_buttons = RadioButtons( frame, entries, grid=(0, 1), sticky='ew', select_callback=self.modeChanged, tipTexts=tipTexts) row += 1 manualFrame = LabelFrame(guiFrame, text='Positive levels', grid=(row, 0), gridSpan=(1, 2)) manualFrame.expandGrid(None, 0) tipText = 'The positive contour levels that will be used for the spectrum; filled in by the automation or set/modified manually' self.posLevelsEntry = FloatEntry(manualFrame, isArray=True, width=60, returnCallback=self.applyManual, tipText=tipText, grid=(0, 0), sticky='ew') row += 1 manualFrame = LabelFrame(guiFrame, text='Negative levels', grid=(row, 0), gridSpan=(1, 2)) manualFrame.expandGrid(None, 0) tipText = 'The negative contour levels that will be used for the spectrum; filled in by the automation or set/modified manually' self.negLevelsEntry = FloatEntry(manualFrame, isArray=True, width=60, returnCallback=self.applyManual, tipText=tipText, grid=(0, 0), sticky='ew') row += 1 tipTexts = [ 'Set the spectrum contour levels, updating the display, to the automated series, ignoring any manual edits.', 'Set the spectrum contour levels, updating the display, to the values displayed in the level entry fields' ] texts = ['Apply Auto Levels', 'Apply Manual Edits'] commands = [self.applyAuto, self.applyManual] self.buttons = UtilityButtonList(guiFrame, texts=texts, commands=commands, helpUrl=self.help_url, grid=(row, 0), gridSpan=(1, 2), tipTexts=tipTexts) guiFrame.grid_rowconfigure(row, weight=1) self.curateNotifiers(self.registerNotify) self.update() def update(self, spectrum=None): if not spectrum: spectrum = self.spectrum spectra = self.parent.getSpectra() if spectra: if spectrum not in spectra: spectrum = spectra[0] index = spectra.index(spectrum) names = ['%s:%s' % (x.experiment.name, x.name) for x in spectra] else: index = 0 names = [] self.expt_spectrum.setup(names, spectra, index) self.setSpectrumDetails(spectrum) def updateNotifier(self, *extra): self.update() def open(self): self.updateForm() BasePopup.open(self) def modeChanged(self, *entry): spectrum = self.spectrum if not spectrum or spectrum.isDeleted: return analysisSpectrum = spectrum.analysisSpectrum changeMode = self.change_mode_buttons.getIndex( ) and 'add' or 'multiply' if changeMode == 'add': text = adder_text changes = adder_changes else: text = multiplier_text changes = multiplier_changes self.change_label.set('%s:' % text) n = 0 for button in self.change_level_buttons: w = changes[n] command = lambda w=w: self.setChange(w) button.config(command=command) button.setText(str(w)) n = n + 1 levelChanger = changes[2] self.doUpdateForm = False analysisSpectrum.autoLevelChanger = levelChanger analysisSpectrum.autoLevelMode = changeMode self.doUpdateForm = True self.setContourLevels() def defaultGlobalScale(self): self.global_entry.set(100000) self.applyAuto() def close(self): self.applyManual() BasePopup.close(self) def destroy(self): self.curateNotifiers(self.unregisterNotify) BasePopup.destroy(self) def curateNotifiers(self, notifyFunc): notifyFunc(self.updateContourLevels, 'ccpnmr.Analysis.AnalysisSpectrum', 'setPosLevels') notifyFunc(self.updateContourLevels, 'ccpnmr.Analysis.AnalysisSpectrum', 'setNegLevels') notifyFunc(self.updateForm, 'ccpnmr.Analysis.AnalysisSpectrum', 'setAutoLevelChanger') notifyFunc(self.updateForm, 'ccpnmr.Analysis.AnalysisSpectrum', 'setAutoLevelMode') notifyFunc(self.updateForm, 'ccpnmr.Analysis.AnalysisSpectrum', 'setAutoNumLevels') notifyFunc(self.updateForm, 'ccpnmr.Analysis.AnalysisSpectrum', 'setAutoBaseLevel') notifyFunc(self.updateForm, 'ccpnmr.Analysis.AnalysisProject', 'setGlobalContourScale') for clazz in ('Experiment', 'DataSource'): for func in ('__init__', 'delete', 'setName'): notifyFunc(self.updateNotifier, 'ccp.nmr.Nmr.%s' % clazz, func) def editProperties(self): self.parent.editSpectrum(self.spectrum) def updateForm(self, *extra): #print 'updateForm' if (not self.doUpdateForm): return self.global_entry.set(self.analysisProject.globalContourScale) spectrum = self.spectrum if spectrum and not spectrum.isDeleted: analysisSpectrum = spectrum.analysisSpectrum self.base_entry.set(analysisSpectrum.autoBaseLevel) self.numberEntry.set(analysisSpectrum.autoNumLevels) self.change_entry.set(analysisSpectrum.autoLevelChanger) if analysisSpectrum.autoLevelMode == 'add': i = 1 else: i = 0 self.change_mode_buttons.setIndex(i) def updateContourLevels(self, analysisSpectrum): spectrum = self.spectrum if spectrum and not spectrum.isDeleted: analysisSpectrum = spectrum.analysisSpectrum posLevels = list(analysisSpectrum.posLevels) negLevels = list(analysisSpectrum.negLevels) self.posLevelsEntry.set(posLevels) self.negLevelsEntry.set(negLevels) self.doUpdateForm = False updateSpectrumLevelParams(analysisSpectrum, posLevels, negLevels) self.doUpdateForm = True self.base_entry.set(analysisSpectrum.autoBaseLevel) self.numberEntry.set(analysisSpectrum.autoNumLevels) self.change_entry.set(analysisSpectrum.autoLevelChanger) self.setWhichLevels(spectrum) if analysisSpectrum.autoLevelMode == 'add': i = 1 else: i = 0 self.change_mode_buttons.setIndex(i) def setWhichLevels(self, spectrum): analysisSpectrum = spectrum.analysisSpectrum posLevels = analysisSpectrum.posLevels negLevels = analysisSpectrum.negLevels if posLevels: isSelected = True else: isSelected = False self.which_buttons.setIndexSelection(0, isSelected) if negLevels: isSelected = True else: isSelected = False self.which_buttons.setIndexSelection(1, isSelected) def setSpectrum(self, spectrum): if spectrum is not self.spectrum: self.update(spectrum) #if (spectrum and not spectrum.isDeleted): # self.setWhichLevels(spectrum) speed_scale = 6.0 speed_delay = 50 # msec def changeGlobalScale(self, multiplier): self.analysisProject.globalContourScale = multiplier * self.analysisProject.globalContourScale def changeBaseLevel(self, multiplier): spectrum = self.spectrum if (not spectrum or spectrum.isDeleted is True): return analysisSpectrum = spectrum.analysisSpectrum baseLevel = multiplier * analysisSpectrum.autoBaseLevel self.base_entry.set(baseLevel) self.doUpdateForm = False analysisSpectrum.autoBaseLevel = abs(baseLevel) self.doUpdateForm = True self.setContourLevels() def changeNumberLevels(self, change): spectrum = self.spectrum if not spectrum or spectrum.isDeleted is True: return analysisSpectrum = spectrum.analysisSpectrum numberLevels = analysisSpectrum.autoNumLevels + change self.numberEntry.set(numberLevels) self.doUpdateForm = False analysisSpectrum.autoNumLevels = numberLevels self.doUpdateForm = True self.setContourLevels() def setChange(self, levelChanger): spectrum = self.spectrum if not spectrum or spectrum.isDeleted: return self.doUpdateForm = False analysisSpectrum = spectrum.analysisSpectrum analysisSpectrum.autoLevelChanger = levelChanger self.doUpdateForm = True self.setContourLevels() def setNumberLevels(self, numberLevels): spectrum = self.spectrum if (not spectrum or spectrum.isDeleted is True): return self.doUpdateForm = False analysisSpectrum = spectrum.analysisSpectrum analysisSpectrum.autoNumLevels = numberLevels self.doUpdateForm = True self.setContourLevels() def setSpectrumDetails(self, spectrum): if spectrum is self.spectrum: return self.spectrum = spectrum if spectrum and not spectrum.isDeleted: analysisSpectrum = spectrum.analysisSpectrum posLevels = list(analysisSpectrum.posLevels) negLevels = list(analysisSpectrum.negLevels) self.posLevelsEntry.set(posLevels) self.negLevelsEntry.set(negLevels) self.doUpdateForm = False updateSpectrumLevelParams(analysisSpectrum, posLevels, negLevels) self.doUpdateForm = True self.base_entry.set(analysisSpectrum.autoBaseLevel) self.numberEntry.set(analysisSpectrum.autoNumLevels) self.change_entry.set(analysisSpectrum.autoLevelChanger) self.autoFrame.setText('Auto contour levels - %s:%s' % (spectrum.experiment.name, spectrum.name)) self.setWhichLevels(spectrum) else: self.posLevelsEntry.set('') self.negLevelsEntry.set('') self.autoFrame.setText('Auto contour levels') def setContourLevels(self): spectrum = self.spectrum if not spectrum or spectrum.isDeleted is True: return try: analysisSpectrum = spectrum.analysisSpectrum baseLevel = analysisSpectrum.autoBaseLevel numberLevels = analysisSpectrum.autoNumLevels levelChanger = analysisSpectrum.autoLevelChanger changeMode = analysisSpectrum.autoLevelMode posLevels = [] if self.which_buttons.isIndexSelected(0): posLevels.extend( calcContourLevels(baseLevel, numberLevels, levelChanger, changeMode)) negLevels = [] if self.which_buttons.isIndexSelected(1): if changeMode == 'add': levelChanger = -levelChanger negLevels.extend( calcContourLevels(-baseLevel, numberLevels, levelChanger, changeMode)) self.posLevelsEntry.set(posLevels) self.negLevelsEntry.set(negLevels) analysisSpectrum.posLevels = posLevels analysisSpectrum.negLevels = negLevels except Implementation.ApiError, e: showError('Contour levels error', e.error_msg, parent=self)
def body(self, guiFrame): self.doUpdateForm = True self.spectrum = None guiFrame.grid_columnconfigure(1, weight=1) row = 0 specFrame = LabelFrame(guiFrame, text='Spectrum', grid=(row, 0)) tipText = 'The spectrum for which you are setting the contour levels' self.expt_spectrum = PulldownList(specFrame, grid=(0, 0), tipText=tipText, callback=self.setSpectrumDetails) tipText = 'Open the edit spectrum table to view and change other properties associated with the selected spectrum' button = Button(specFrame, text='Spectrum Properties', command=self.editProperties, borderwidth=1, grid=(1, 0), sticky='ew', tipText=tipText) globalFrame = LabelFrame(guiFrame, text='Global scale') globalFrame.grid(row=row, column=1, sticky='nsew') globalFrame.grid_columnconfigure(0, weight=1) tipText = 'The value by which all contour levels in all spectra are multiplied; to give the actual contour level in terms of the stored spectrum data' self.global_entry = FloatEntry( globalFrame, width=10, tipText=tipText, text=self.analysisProject.globalContourScale, returnCallback=self.applyAuto, grid=(0, 0), gridSpan=(1, 2), sticky='ew') tipText = 'Divide the global scaling factor by two; moving all contour for all spectra levels closer to zero' button = Button(globalFrame, borderwidth=1, text='/2', sticky='ew', tipText=tipText, command=lambda: self.changeGlobalScale(0.5), grid=(0, 2)) tipText = 'Multiple the global scaling factor by two; moving all contour for all spectra levels away from zero' button = Button(globalFrame, borderwidth=1, text='*2', sticky='ew', tipText=tipText, command=lambda: self.changeGlobalScale(2.0), grid=(0, 3)) tipText = 'Set the global contour scale for all spectra to the default of 100,000' button = Button(globalFrame, borderwidth=1, text='10^5', tipText=tipText, command=self.defaultGlobalScale, grid=(1, 0)) tipText = 'Click to decrease "-" or increase "+" the global contour scale by small amounts' frame = ValueRamp(globalFrame, callback=self.changeGlobalScale, tipText=tipText) frame.grid(row=1, column=1, columnspan=3, sticky='e') row += 1 self.autoFrame = LabelFrame(guiFrame, text='Auto contour levels') self.autoFrame.grid(row=row, column=0, columnspan=5, sticky='nsew') self.autoFrame.grid_columnconfigure(1, weight=1) frow = 0 label = Label(self.autoFrame, text='Base level:', grid=(frow, 0), sticky='e') tipText = 'The first contour level (closest to zero) for an automated series of levels: the start of a geometric or arithmetic series defining levels' self.base_entry = FloatEntry(self.autoFrame, returnCallback=self.applyAuto, width=10, grid=(frow, 1), sticky='ew', tipText=tipText) command = lambda: self.changeBaseLevel(0.5) tipText = 'Lower the base contour level so that it is half of the previous value; moving the series of contour levels closer to zero' button = Button(self.autoFrame, borderwidth=1, text='/2', tipText=tipText, command=command, grid=(frow, 2), sticky='ew') command = lambda: self.changeBaseLevel(2.0) tipText = 'Raise the base contour level so that it is double the previous value; moving the series of contour levels further from zero' button = Button(self.autoFrame, borderwidth=1, text='*2', tipText=tipText, command=command, grid=(frow, 3), sticky='ew') tipText = 'Click to decrease "-" or increase "+" the base contour level by small amounts' frame = ValueRamp(self.autoFrame, callback=self.changeBaseLevel, tipText=tipText) frame.grid(row=frow, column=4, columnspan=3, sticky='ew') frow += 1 label = Label(self.autoFrame, text='Number of levels:', grid=(frow, 0), sticky='e') #self.numberEntry = IntEntry(guiFrame, text=numberLevels, # returnCallback=self.applyAuto) tipText = 'The number of contour levels to make in the automated series' self.numberEntry = IntEntry(self.autoFrame, returnCallback=self.applyAuto, width=10, grid=(frow, 1), sticky='ew', tipText=tipText) command = lambda w=-1: self.changeNumberLevels(w) tipText = 'Decrease the number of contour levels in the series by one' button = Button(self.autoFrame, borderwidth=1, text='-1', tipText=tipText, command=command, grid=(frow, 2), sticky='ew') command = lambda w=1: self.changeNumberLevels(w) tipText = 'Increase the number of contour levels in the series by one' button = Button(self.autoFrame, borderwidth=1, text='+1', tipText=tipText, command=command, grid=(frow, 3), sticky='ew') n = 4 for w in (5, 10, 15, 20): tipText = 'Set the number of contour levels in the series to %d' % w command = lambda w=w: self.setNumberLevels(w) button = Button(self.autoFrame, borderwidth=1, text='%d' % w, command=command, grid=(frow, n), sticky='ew', tipText=tipText) n += 1 frow += 1 self.change_label = Label(self.autoFrame, text='%s:' % multiplier_text, grid=(frow, 0), sticky='e') tipText = 'The multiplication factor (or increment if adding levels) to repetitively apply to the base level to generate the series of levels' self.change_entry = FloatEntry(self.autoFrame, returnCallback=self.applyAuto, width=10, grid=(frow, 1), sticky='ew', tipText=tipText) self.change_level_buttons = [] n = 2 for w in multiplier_changes: tipText = 'Set the automated series multiplication factor or increment to %f' % w command = lambda w=w: self.setChange(w) button = Button(self.autoFrame, borderwidth=1, text=str(w), command=command, grid=(frow, n), sticky='ew', tipText=tipText) self.change_level_buttons.append(button) n += 1 frow += 1 frame = Frame(self.autoFrame, grid=(frow, 0), gridSpan=(1, 7), sticky='ew') tipTexts = [ 'Toggles whether positive contour levels from the automated series will be used. Overrides any manual settings', 'Toggles whether negative contour levels from the automated series will be used. Overrides any manual settings' ] entries = ('Positive', 'Negative') selected = (True, False) self.which_buttons = CheckButtons(frame, entries, selected=selected, select_callback=self.applyAuto, grid=(0, 0), sticky='w', tipTexts=tipTexts) tipTexts = [ 'Set the contour level generation to use a geometric series, starting from the base level and using the specified factor', 'Set the contour level generation to use an arithmetic series, starting from the base level and using the specified increment' ] entries = ('Multiply levels', 'Add levels') self.change_mode_buttons = RadioButtons( frame, entries, grid=(0, 1), sticky='ew', select_callback=self.modeChanged, tipTexts=tipTexts) row += 1 manualFrame = LabelFrame(guiFrame, text='Positive levels', grid=(row, 0), gridSpan=(1, 2)) manualFrame.expandGrid(None, 0) tipText = 'The positive contour levels that will be used for the spectrum; filled in by the automation or set/modified manually' self.posLevelsEntry = FloatEntry(manualFrame, isArray=True, width=60, returnCallback=self.applyManual, tipText=tipText, grid=(0, 0), sticky='ew') row += 1 manualFrame = LabelFrame(guiFrame, text='Negative levels', grid=(row, 0), gridSpan=(1, 2)) manualFrame.expandGrid(None, 0) tipText = 'The negative contour levels that will be used for the spectrum; filled in by the automation or set/modified manually' self.negLevelsEntry = FloatEntry(manualFrame, isArray=True, width=60, returnCallback=self.applyManual, tipText=tipText, grid=(0, 0), sticky='ew') row += 1 tipTexts = [ 'Set the spectrum contour levels, updating the display, to the automated series, ignoring any manual edits.', 'Set the spectrum contour levels, updating the display, to the values displayed in the level entry fields' ] texts = ['Apply Auto Levels', 'Apply Manual Edits'] commands = [self.applyAuto, self.applyManual] self.buttons = UtilityButtonList(guiFrame, texts=texts, commands=commands, helpUrl=self.help_url, grid=(row, 0), gridSpan=(1, 2), tipTexts=tipTexts) guiFrame.grid_rowconfigure(row, weight=1) self.curateNotifiers(self.registerNotify) self.update()
class CingGui(BasePopup): def __init__(self, parent, options, *args, **kw): # Fill in below variable once run generates some results self.haveResults = None # store the options self.options = options BasePopup.__init__(self, parent=parent, title='CING Setup', **kw) # self.setGeometry(850, 750, 50, 50) self.project = None # self.tk_strictMotif( True) self.updateGui() # end def __init__ def body(self, guiFrame): row = 0 col =0 # frame = Frame( guiFrame ) # frame.grid(row=row, column=col, sticky='news') self.menuBar = Menu( guiFrame) self.menuBar.grid( row=row, column=col, sticky='ew') #---------------------------------------------------------------------------------- # Project frame #---------------------------------------------------------------------------------- # guiFrame.grid_columnconfigure(row, weight=1) # frame = LabelFrame(guiFrame, text='Project', font=medFont) row = +1 col =0 frame = LabelFrame(guiFrame, text='Project', **labelFrameAttributes ) print '>', frame.keys() frame.grid(row=row, column=col, sticky='nsew' ) frame.grid_columnconfigure(2, weight=1) # frame.grid_rowconfigure(0, weight=1) srow = 0 self.projectOptions = ['old','new from PDB','new from CCPN','new from CYANA'] self.projOptionsSelect = RadioButtons(frame, selected_index=0, entries=self.projectOptions, direction='vertical', select_callback=self.updateGui ) self.projOptionsSelect.grid(row=srow,column=0,rowspan=len(self.projectOptions),columnspan=2, sticky='w') if self.options.name: text = self.options.name else: text='' # end if self.projEntry = Entry(frame, bd=1, text=text, returnCallback=self.updateGui) self.projEntry.grid(row=srow,column=2,columnspan=2,sticky='ew') # self.projEntry.bind('<Key>', self.updateGui) self.projEntry.bind('<Leave>', self.updateGui) projButton = Button(frame, bd=1,command=self.chooseOldProjectFile, text='browse') projButton.grid(row=srow,column=3,sticky='ew') srow += 1 self.pdbEntry = Entry(frame, bd=1, text='') self.pdbEntry.grid(row=srow,column=2,sticky='ew') self.pdbEntry.bind('<Leave>', self.updateGui) pdbButton = Button(frame, bd=1,command=self.choosePdbFile, text='browse') pdbButton.grid(row=srow,column=3,sticky='ew') srow += 1 self.ccpnEntry = Entry(frame, bd=1, text='') self.ccpnEntry.grid(row=srow,column=2,sticky='ew') self.ccpnEntry.bind('<Leave>', self.updateGui) ccpnButton = Button(frame, bd=1,command=self.chooseCcpnFile, text='browse') ccpnButton.grid(row=srow,column=3,sticky='ew') srow += 1 self.cyanaEntry = Entry(frame, bd=1, text='') self.cyanaEntry.grid(row=srow,column=2,sticky='ew') self.cyanaEntry.bind('<Leave>', self.updateGui) cyanaButton = Button(frame, bd=1,command=self.chooseCyanaFile, text='browse') cyanaButton.grid(row=srow,column=3,sticky='ew') #Empty row srow += 1 label = Label(frame, text='') label.grid(row=srow,column=0,sticky='nw') srow += 1 label = Label(frame, text='Project name:') label.grid(row=srow,column=0,sticky='nw') self.nameEntry = Entry(frame, bd=1, text='') self.nameEntry.grid(row=srow,column=2,sticky='w') #Empty row srow += 1 label = Label(frame, text='') label.grid(row=srow,column=0,sticky='nw') srow += 1 self.openProjectButton = Button(frame, command=self.openProject, text='Open Project', **actionButtonAttributes ) self.openProjectButton.grid(row=srow,column=0, columnspan=4, sticky='ew') #---------------------------------------------------------------------------------- # status #---------------------------------------------------------------------------------- # guiFrame.grid_columnconfigure(1, weight=0) srow = 0 frame = LabelFrame(guiFrame, text='Status', **labelFrameAttributes) frame.grid( row=srow, column=1, sticky='wnes') self.projectStatus = Text(frame, height=11, width=70, borderwidth=0, relief='flat') self.projectStatus.grid(row=0, column=0, sticky='wen') #Empty row srow += 1 label = Label(frame, text='') label.grid(row=srow,column=0,sticky='nw') srow += 1 self.closeProjectButton = Button(frame, command=self.closeProject, text='Close Project', **actionButtonAttributes) self.closeProjectButton.grid(row=srow,column=0, columnspan=4, sticky='ew') #---------------------------------------------------------------------------------- # Validate frame #---------------------------------------------------------------------------------- row +=1 col=0 frame = LabelFrame(guiFrame, text='Validate', **labelFrameAttributes) # frame = LabelFrame(guiFrame, text='Validate', font=medFont) frame.grid(row=row, column=col, sticky='nsew') # frame.grid_columnconfigure(2, weight=1) frame.grid_rowconfigure(0, weight=1) srow = 0 # label = Label(frame, text='validation') # label.grid(row=srow,column=0,sticky='nw') # # self.selectDoValidation = CheckButton(frame) # self.selectDoValidation.grid(row=srow, column=1,sticky='nw' ) # self.selectDoValidation.set(True) # # srow += 1 # label = Label(frame, text='') # label.grid(row=srow,column=0,sticky='nw') # # srow += 1 label = Label(frame, text='checks') label.grid(row=srow,column=0,sticky='nw') self.selectCheckAssign = CheckButton(frame) self.selectCheckAssign.grid(row=srow, column=1,sticky='nw' ) self.selectCheckAssign.set(True) label = Label(frame, text='assignments and shifts') label.grid(row=srow,column=2,sticky='nw') # srow += 1 # self.selectCheckQueen = CheckButton(frame) # self.selectCheckQueen.grid(row=srow, column=4,sticky='nw' ) # self.selectCheckQueen.set(False) # label = Label(frame, text='QUEEN') # label.grid(row=srow,column=5,sticky='nw') # # queenButton = Button(frame, bd=1,command=None, text='setup') # queenButton.grid(row=srow,column=6,sticky='ew') srow += 1 self.selectCheckResraint = CheckButton(frame) self.selectCheckResraint.grid(row=srow, column=1,sticky='nw' ) self.selectCheckResraint.set(True) label = Label(frame, text='restraints') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectCheckStructure = CheckButton(frame) self.selectCheckStructure.grid(row=srow, column=1,sticky='nw' ) self.selectCheckStructure.set(True) label = Label(frame, text='structural') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectMakeHtml = CheckButton(frame) self.selectMakeHtml.grid(row=srow, column=1,sticky='nw' ) self.selectMakeHtml.set(True) label = Label(frame, text='generate HTML') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectCheckScript = CheckButton(frame) self.selectCheckScript.grid(row=srow, column=1,sticky='nw' ) self.selectCheckScript.set(False) label = Label(frame, text='user script') label.grid(row=srow,column=0,sticky='nw') self.validScriptEntry = Entry(frame, bd=1, text='') self.validScriptEntry.grid(row=srow,column=2,columnspan=3, sticky='ew') scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse') scriptButton.grid(row=srow,column=5,sticky='ew') srow += 1 label = Label(frame, text='ranges') label.grid(row=srow,column=0,sticky='nw') self.rangesEntry = Entry( frame, text='' ) self.rangesEntry.grid( row=srow, column=2, columnspan=3, sticky='ew') # self.validScriptEntry = Entry(frame, bd=1, text='') # self.validScriptEntry.grid(row=srow,column=3,sticky='ew') # # scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse') # scriptButton.grid(row=srow,column=4,sticky='ew') srow += 1 texts = ['Run Validation','View Results','Setup QUEEN'] commands = [self.runCing, None, None] buttonBar = ButtonList(frame, texts=texts, commands=commands,expands=True) buttonBar.grid(row=srow, column=0, columnspan=6, sticky='ew') for button in buttonBar.buttons: button.config(**actionButtonAttributes) # end for self.runButton = buttonBar.buttons[0] self.viewResultButton = buttonBar.buttons[1] self.queenButton = buttonBar.buttons[2] #---------------------------------------------------------------------------------- # Miscellaneous frame #---------------------------------------------------------------------------------- row +=0 col=1 # frame = LabelFrame(guiFrame, text='Miscellaneous', font=medFont) frame = LabelFrame(guiFrame, text='Miscellaneous', **labelFrameAttributes) frame.grid(row=row, column=col, sticky='news') frame.grid_columnconfigure(2, weight=1) frame.grid_columnconfigure(4, weight=1,minsize=30) frame.grid_rowconfigure(0, weight=1) # Exports srow = 0 label = Label(frame, text='export to') label.grid(row=srow,column=0,sticky='nw') self.selectExportXeasy = CheckButton(frame) self.selectExportXeasy.grid(row=srow, column=1,sticky='nw' ) self.selectExportXeasy.set(True) label = Label(frame, text='Xeasy, Sparky, TALOS, ...') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectExportCcpn = CheckButton(frame) self.selectExportCcpn.grid(row=srow, column=1,sticky='nw' ) self.selectExportCcpn.set(True) label = Label(frame, text='CCPN') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectExportQueen = CheckButton(frame) self.selectExportQueen.grid(row=srow, column=1,sticky='nw' ) self.selectExportQueen.set(True) label = Label(frame, text='QUEEN') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectExportRefine = CheckButton(frame) self.selectExportRefine.grid(row=srow, column=1,sticky='nw' ) self.selectExportRefine.set(True) label = Label(frame, text='refine') label.grid(row=srow,column=2,sticky='nw') srow += 1 label = Label(frame, text='') label.grid(row=srow,column=0,sticky='nw') # User script srow += 1 label = Label(frame, text='user script') label.grid(row=srow,column=0,sticky='nw') self.selectMiscScript = CheckButton(frame) self.selectMiscScript.grid(row=srow, column=1,sticky='nw' ) self.selectMiscScript.set(False) self.miscScriptEntry = Entry(frame, bd=1, text='') self.miscScriptEntry.grid(row=srow,column=3,sticky='ew') script2Button = Button(frame, bd=1,command=self.chooseMiscScript, text='browse') script2Button.grid(row=srow,column=4,sticky='ew') srow += 1 texts = ['Export','Run Script'] commands = [None, None] buttonBar = ButtonList(frame, texts=texts, commands=commands,expands=True) buttonBar.grid(row=srow, column=0, columnspan=5, sticky='ew') for button in buttonBar.buttons: button.config(**actionButtonAttributes) # end for self.exportButton = buttonBar.buttons[0] self.scriptButton = buttonBar.buttons[1] #---------------------------------------------------------------------------------- # Textarea #---------------------------------------------------------------------------------- row +=1 guiFrame.grid_rowconfigure(row, weight=1) self.outputTextBox = ScrolledText(guiFrame) self.outputTextBox.grid(row=row, column=0, columnspan=2, sticky='nsew') self.redirectConsole() #---------------------------------------------------------------------------------- # Buttons #---------------------------------------------------------------------------------- row +=1 col=0 texts = ['Quit', 'Help'] commands = [self.close, None] self.buttonBar = ButtonList(guiFrame, texts=texts, commands=commands,expands=True) self.buttonBar.grid(row=row, column=col, columnspan=2, sticky='ew') # self.openProjectButton = self.buttonBar.buttons[0] # self.closeProjectButton = self.buttonBar.buttons[1] # self.runButton = self.buttonBar.buttons[0] # self.viewResultButton = self.buttonBar.buttons[1] for button in self.buttonBar.buttons: button.config(**actionButtonAttributes) # end for # end def body def getGuiOptions(self): projectName = self.projEntry.get() index = self.projOptionsSelect.getIndex() if index > 0: makeNewProject = True projectImport = None if index > 1: i = index-2 format = ['PDB','CCPN','CYANA'][i] file = [self.pdbEntry, self.ccpnEntry, self.cyanaEntry][i].get() if not file: showWarning('Failure','No %s file selected' % format) return # end if projectImport = (format, file) # end if else: # Chould also check that any old project file exists makeNewProject = False projectImport = None # end if doValidation = self.selectDoValidation.get() checks = [] if doValidation: if self.selectCheckAssign.get(): checks.append('assignments') # end if if self.selectCheckResraint.get(): checks.append('restraints') # end if if self.selectCheckStructure.get(): checks.append('structural') # end if if self.selectMakeHtml.get(): checks.append('HTML') # end if if self.selectCheckScript.get(): script = self.validScriptEntry.get() if script: checks.append( ('script',script) ) # end if # end if if self.selectCheckQueen.get(): checks.append('queen') # end if # end if exports = [] if self.selectExportXeasy.get(): exports.append('Xeasy') # end if if self.selectExportCcpn.get(): exports.append('CCPN') # end if if self.selectExportQueen.get(): exports.append('QUEEN') # end if if self.selectExportRefine.get(): exports.append('refine') # end if miscScript = None if self.selectMiscScript.get(): script = self.miscScriptEntry.get() if script: miscScript = script # end if # end if return projectName, makeNewProject, projectImport, doValidation, checks, exports, miscScript # end def getGuiOptions def runCing(self): options = self.getGuiOptions() if options: projectName, makeNewProject, projectImport, doValidation, checks, exports, miscScript = options print 'Project name:', projectName print 'Make new project?', makeNewProject print 'Import source:', projectImport print 'Do vailidation?', doValidation print 'Validation checks:', ','.join(checks) print 'Export to:', ','.join(exports) print 'User script:', miscScript # end if # end def runCing # else there was already an error message def chooseOldProjectFile(self): fileTypes = [ FileType('CING', ['project.xml']), FileType('All', ['*']) ] popup = FileSelectPopup(self, file_types = fileTypes, title = 'Select CING project file', dismiss_text = 'Cancel', selected_file_must_exist = True) fileName = popup.getFile() # dirName = popup.getDirectory() if len(fileName) > 0: # Put text into entry,name widgets dummy,name = cing.Project.rootPath(fileName) self.projEntry.configure(state='normal') self.projEntry.set(fileName) self.nameEntry.configure(state='normal') self.nameEntry.set(name) self.nameEntry.configure(state='disabled') # choose the correct radiobutton self.projOptionsSelect.setIndex(0) self.updateGui() # end if #nd if popup.destroy() # end def chooseOldProjectFile def choosePdbFile(self): fileTypes = [ FileType('PDB', ['*.pdb']), FileType('All', ['*'])] popup = FileSelectPopup(self, file_types = fileTypes, title = 'PDB file', dismiss_text = 'Cancel', selected_file_must_exist = True) fileName = popup.getFile() if len(fileName)>0: # Put text into entry widget self.pdbEntry.configure(state='normal') self.pdbEntry.set(fileName) # Put text into name widget _dir,name,dummy = nTpath( fileName ) self.nameEntry.configure(state='normal') self.nameEntry.set(name) # choose the correct radiobutton self.projOptionsSelect.setIndex(1) self.updateGui() #end if popup.destroy() # end def choosePdbFile def chooseCcpnFile(self): fileTypes = [ FileType('XML', ['*.xml']), FileType('All', ['*'])] popup = FileSelectPopup(self, file_types = fileTypes, title = 'CCPN project XML file', dismiss_text = 'Cancel', selected_file_must_exist = True) fileName = popup.getFile() if len(fileName)>0: self.pdbEntry.configure(state='normal') self.pdbEntry.set(fileName) self.projOptionsSelect.setIndex(1) _dir,name,dummy = nTpath( fileName ) self.nameEntry.set(name) #end if self.ccpnEntry.set(fileName) self.projOptionsSelect.setIndex(2) popup.destroy() # end def chooseCcpnFile def chooseCyanaFile(self): # Prepend default Cyana file extension below fileTypes = [ FileType('All', ['*']), ] popup = FileSelectPopup(self, file_types = fileTypes, title = 'CYANA fproject file', dismiss_text = 'Cancel', selected_file_must_exist = True) fileName = popup.getFile() self.cyanaEntry.set(fileName) self.projOptionsSelect.setIndex(3) popup.destroy() # end def chooseCyanaFile def chooseValidScript(self): # Prepend default Cyana file extension below fileTypes = [ FileType('All', ['*']), ] popup = FileSelectPopup(self, file_types = fileTypes, title = 'Script file', dismiss_text = 'Cancel', selected_file_must_exist = True) fileName = popup.getFile() self.validScriptEntry.set(fileName) popup.destroy() # end def chooseValidScript def chooseMiscScript(self): # Prepend default Cyana file extension below fileTypes = [ FileType('All', ['*']), ] popup = FileSelectPopup(self, file_types = fileTypes, title = 'Script file', dismiss_text = 'Cancel', selected_file_must_exist = True) fileName = popup.getFile() self.miscScriptEntry.set(fileName) popup.destroy() # end def chooseMiscScript def openProject(self ): projOption = self.projOptionsSelect.get() if projOption == self.projectOptions[0]: self.openOldProject() elif projOption == self.projectOptions[1]: self.initPdb() # end if if self.project: self.project.gui = self # end if self.updateGui() #end def def openOldProject(self ): fName = self.projEntry.get() if not os.path.exists( fName ): nTerror('Error: file "%s" does not exist\n', fName) #end if if self.project: self.closeProject() # end if self.project = cing.Project.open( name=fName, status='old', verbose=False ) #end def def initPdb(self ): fName = self.pdbEntry.get() if not os.path.exists( fName ): nTerror('Error: file "%s" does not exist\n', fName) #end if self.project = cing.Project.open( self.nameEntry.get(), status='new' ) self.project.initPDB( pdbFile=fName, convention = 'PDB' ) #end def def closeProject(self): if self.project: self.project.close() # end if self.project = None self.updateGui() #end def def updateGui(self, event=None): projOption = self.projOptionsSelect.get() buttons = self.buttonBar.buttons # Disable entries for e in [self.projEntry, self.pdbEntry, self.ccpnEntry, self.cyanaEntry, self.nameEntry]: e.configure(state='disabled') #end for if projOption == self.projectOptions[0]: # Enable entries self.projEntry.configure(state='normal') if (len(self.projEntry.get()) > 0): self.openProjectButton.enable() self.runButton.enable() else: self.openProjectButton.disable() self.runButton.disable() #end if elif projOption == self.projectOptions[1]: # Enable entries self.pdbEntry.configure(state='normal') self.nameEntry.configure(state='normal') if (len(self.pdbEntry.get()) > 0 and len(self.nameEntry.get()) > 0): buttons[0].enable() buttons[1].enable() else: buttons[0].disable() buttons[1].disable() #end if #end if elif projOption == self.projectOptions[2]: # Enable entries self.ccpnEntry.configure(state='normal') self.nameEntry.configure(state='normal') if (len(self.ccpnEntry.get()) > 0 and len(self.nameEntry.get()) > 0): buttons[0].enable() buttons[1].enable() else: buttons[0].disable() buttons[1].disable() #end if #end if elif projOption == self.projectOptions[3]: # Enable entries self.cyanaEntry.configure(state='normal') self.nameEntry.configure(state='normal') if (len(self.cyanaEntry.get()) > 0 and len(self.nameEntry.get()) > 0): buttons[0].enable() buttons[1].enable() else: buttons[0].disable() buttons[1].disable() #end if #end if self.projectStatus.clear() if not self.project: self.projectStatus.setText('No open project') self.closeProjectButton.setText('Close Project') self.closeProjectButton.disable() else: self.projectStatus.setText(self.project.format()) self.closeProjectButton.enable() self.closeProjectButton.setText(sprintf('Close Project "%s"', self.project.name)) #end if #end def def redirectConsole(self): #pipe = TextPipe(self.inputTextBox.text_area) #sys.stdin = pipe pipe = TextPipe(self.outputTextBox.text_area) sys.stdout = pipe nTmessage.stream = pipe # end def redirectConsole # sys.stderr = pipe def resetConsole(self): #sys.stdin = stdin nTmessage.stream = stdout sys.stdout = stdout sys.stderr = stderr # end def resetConsole def open(self): self.redirectConsole() BasePopup.open(self) # end def open def close(self): geometry = self.getGeometry() self.resetConsole() BasePopup.close(self) print 'close:',geometry sys.exit(0) # remove later # end def close def destroy(self): geometry = self.getGeometry() self.resetConsole() BasePopup.destroy(self) print 'destroy:',geometry sys.exit(0) # remove later
def body(self, guiFrame): row = 0 col = 0 # frame = Frame( guiFrame ) # frame.grid(row=row, column=col, sticky='news') self.menuBar = Menu(guiFrame) self.menuBar.grid(row=row, column=col, sticky='ew') #---------------------------------------------------------------------------------- # Project frame #---------------------------------------------------------------------------------- # guiFrame.grid_columnconfigure(row, weight=1) # frame = LabelFrame(guiFrame, text='Project', font=medFont) row = +1 col = 0 frame = LabelFrame(guiFrame, text='Project', **labelFrameAttributes) print '>', frame.keys() frame.grid(row=row, column=col, sticky='nsew') frame.grid_columnconfigure(2, weight=1) # frame.grid_rowconfigure(0, weight=1) srow = 0 self.projectOptions = [ 'old', 'new from PDB', 'new from CCPN', 'new from CYANA' ] self.projOptionsSelect = RadioButtons(frame, selected_index=0, entries=self.projectOptions, direction='vertical', select_callback=self.updateGui) self.projOptionsSelect.grid(row=srow, column=0, rowspan=len(self.projectOptions), columnspan=2, sticky='w') if self.options.name: text = self.options.name else: text = '' # end if self.projEntry = Entry(frame, bd=1, text=text, returnCallback=self.updateGui) self.projEntry.grid(row=srow, column=2, columnspan=2, sticky='ew') # self.projEntry.bind('<Key>', self.updateGui) self.projEntry.bind('<Leave>', self.updateGui) projButton = Button(frame, bd=1, command=self.chooseOldProjectFile, text='browse') projButton.grid(row=srow, column=3, sticky='ew') srow += 1 self.pdbEntry = Entry(frame, bd=1, text='') self.pdbEntry.grid(row=srow, column=2, sticky='ew') self.pdbEntry.bind('<Leave>', self.updateGui) pdbButton = Button(frame, bd=1, command=self.choosePdbFile, text='browse') pdbButton.grid(row=srow, column=3, sticky='ew') srow += 1 self.ccpnEntry = Entry(frame, bd=1, text='') self.ccpnEntry.grid(row=srow, column=2, sticky='ew') self.ccpnEntry.bind('<Leave>', self.updateGui) ccpnButton = Button(frame, bd=1, command=self.chooseCcpnFile, text='browse') ccpnButton.grid(row=srow, column=3, sticky='ew') srow += 1 self.cyanaEntry = Entry(frame, bd=1, text='') self.cyanaEntry.grid(row=srow, column=2, sticky='ew') self.cyanaEntry.bind('<Leave>', self.updateGui) cyanaButton = Button(frame, bd=1, command=self.chooseCyanaFile, text='browse') cyanaButton.grid(row=srow, column=3, sticky='ew') #Empty row srow += 1 label = Label(frame, text='') label.grid(row=srow, column=0, sticky='nw') srow += 1 label = Label(frame, text='Project name:') label.grid(row=srow, column=0, sticky='nw') self.nameEntry = Entry(frame, bd=1, text='') self.nameEntry.grid(row=srow, column=2, sticky='w') #Empty row srow += 1 label = Label(frame, text='') label.grid(row=srow, column=0, sticky='nw') srow += 1 self.openProjectButton = Button(frame, command=self.openProject, text='Open Project', **actionButtonAttributes) self.openProjectButton.grid(row=srow, column=0, columnspan=4, sticky='ew') #---------------------------------------------------------------------------------- # status #---------------------------------------------------------------------------------- # guiFrame.grid_columnconfigure(1, weight=0) srow = 0 frame = LabelFrame(guiFrame, text='Status', **labelFrameAttributes) frame.grid(row=srow, column=1, sticky='wnes') self.projectStatus = Text(frame, height=11, width=70, borderwidth=0, relief='flat') self.projectStatus.grid(row=0, column=0, sticky='wen') #Empty row srow += 1 label = Label(frame, text='') label.grid(row=srow, column=0, sticky='nw') srow += 1 self.closeProjectButton = Button(frame, command=self.closeProject, text='Close Project', **actionButtonAttributes) self.closeProjectButton.grid(row=srow, column=0, columnspan=4, sticky='ew') #---------------------------------------------------------------------------------- # Validate frame #---------------------------------------------------------------------------------- row += 1 col = 0 frame = LabelFrame(guiFrame, text='Validate', **labelFrameAttributes) # frame = LabelFrame(guiFrame, text='Validate', font=medFont) frame.grid(row=row, column=col, sticky='nsew') # frame.grid_columnconfigure(2, weight=1) frame.grid_rowconfigure(0, weight=1) srow = 0 # label = Label(frame, text='validation') # label.grid(row=srow,column=0,sticky='nw') # # self.selectDoValidation = CheckButton(frame) # self.selectDoValidation.grid(row=srow, column=1,sticky='nw' ) # self.selectDoValidation.set(True) # # srow += 1 # label = Label(frame, text='') # label.grid(row=srow,column=0,sticky='nw') # # srow += 1 label = Label(frame, text='checks') label.grid(row=srow, column=0, sticky='nw') self.selectCheckAssign = CheckButton(frame) self.selectCheckAssign.grid(row=srow, column=1, sticky='nw') self.selectCheckAssign.set(True) label = Label(frame, text='assignments and shifts') label.grid(row=srow, column=2, sticky='nw') # srow += 1 # self.selectCheckQueen = CheckButton(frame) # self.selectCheckQueen.grid(row=srow, column=4,sticky='nw' ) # self.selectCheckQueen.set(False) # label = Label(frame, text='QUEEN') # label.grid(row=srow,column=5,sticky='nw') # # queenButton = Button(frame, bd=1,command=None, text='setup') # queenButton.grid(row=srow,column=6,sticky='ew') srow += 1 self.selectCheckResraint = CheckButton(frame) self.selectCheckResraint.grid(row=srow, column=1, sticky='nw') self.selectCheckResraint.set(True) label = Label(frame, text='restraints') label.grid(row=srow, column=2, sticky='nw') srow += 1 self.selectCheckStructure = CheckButton(frame) self.selectCheckStructure.grid(row=srow, column=1, sticky='nw') self.selectCheckStructure.set(True) label = Label(frame, text='structural') label.grid(row=srow, column=2, sticky='nw') srow += 1 self.selectMakeHtml = CheckButton(frame) self.selectMakeHtml.grid(row=srow, column=1, sticky='nw') self.selectMakeHtml.set(True) label = Label(frame, text='generate HTML') label.grid(row=srow, column=2, sticky='nw') srow += 1 self.selectCheckScript = CheckButton(frame) self.selectCheckScript.grid(row=srow, column=1, sticky='nw') self.selectCheckScript.set(False) label = Label(frame, text='user script') label.grid(row=srow, column=0, sticky='nw') self.validScriptEntry = Entry(frame, bd=1, text='') self.validScriptEntry.grid(row=srow, column=2, columnspan=3, sticky='ew') scriptButton = Button(frame, bd=1, command=self.chooseValidScript, text='browse') scriptButton.grid(row=srow, column=5, sticky='ew') srow += 1 label = Label(frame, text='ranges') label.grid(row=srow, column=0, sticky='nw') self.rangesEntry = Entry(frame, text='') self.rangesEntry.grid(row=srow, column=2, columnspan=3, sticky='ew') # self.validScriptEntry = Entry(frame, bd=1, text='') # self.validScriptEntry.grid(row=srow,column=3,sticky='ew') # # scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse') # scriptButton.grid(row=srow,column=4,sticky='ew') srow += 1 texts = ['Run Validation', 'View Results', 'Setup QUEEN'] commands = [self.runCing, None, None] buttonBar = ButtonList(frame, texts=texts, commands=commands, expands=True) buttonBar.grid(row=srow, column=0, columnspan=6, sticky='ew') for button in buttonBar.buttons: button.config(**actionButtonAttributes) # end for self.runButton = buttonBar.buttons[0] self.viewResultButton = buttonBar.buttons[1] self.queenButton = buttonBar.buttons[2] #---------------------------------------------------------------------------------- # Miscellaneous frame #---------------------------------------------------------------------------------- row += 0 col = 1 # frame = LabelFrame(guiFrame, text='Miscellaneous', font=medFont) frame = LabelFrame(guiFrame, text='Miscellaneous', **labelFrameAttributes) frame.grid(row=row, column=col, sticky='news') frame.grid_columnconfigure(2, weight=1) frame.grid_columnconfigure(4, weight=1, minsize=30) frame.grid_rowconfigure(0, weight=1) # Exports srow = 0 label = Label(frame, text='export to') label.grid(row=srow, column=0, sticky='nw') self.selectExportXeasy = CheckButton(frame) self.selectExportXeasy.grid(row=srow, column=1, sticky='nw') self.selectExportXeasy.set(True) label = Label(frame, text='Xeasy, Sparky, TALOS, ...') label.grid(row=srow, column=2, sticky='nw') srow += 1 self.selectExportCcpn = CheckButton(frame) self.selectExportCcpn.grid(row=srow, column=1, sticky='nw') self.selectExportCcpn.set(True) label = Label(frame, text='CCPN') label.grid(row=srow, column=2, sticky='nw') srow += 1 self.selectExportQueen = CheckButton(frame) self.selectExportQueen.grid(row=srow, column=1, sticky='nw') self.selectExportQueen.set(True) label = Label(frame, text='QUEEN') label.grid(row=srow, column=2, sticky='nw') srow += 1 self.selectExportRefine = CheckButton(frame) self.selectExportRefine.grid(row=srow, column=1, sticky='nw') self.selectExportRefine.set(True) label = Label(frame, text='refine') label.grid(row=srow, column=2, sticky='nw') srow += 1 label = Label(frame, text='') label.grid(row=srow, column=0, sticky='nw') # User script srow += 1 label = Label(frame, text='user script') label.grid(row=srow, column=0, sticky='nw') self.selectMiscScript = CheckButton(frame) self.selectMiscScript.grid(row=srow, column=1, sticky='nw') self.selectMiscScript.set(False) self.miscScriptEntry = Entry(frame, bd=1, text='') self.miscScriptEntry.grid(row=srow, column=3, sticky='ew') script2Button = Button(frame, bd=1, command=self.chooseMiscScript, text='browse') script2Button.grid(row=srow, column=4, sticky='ew') srow += 1 texts = ['Export', 'Run Script'] commands = [None, None] buttonBar = ButtonList(frame, texts=texts, commands=commands, expands=True) buttonBar.grid(row=srow, column=0, columnspan=5, sticky='ew') for button in buttonBar.buttons: button.config(**actionButtonAttributes) # end for self.exportButton = buttonBar.buttons[0] self.scriptButton = buttonBar.buttons[1] #---------------------------------------------------------------------------------- # Textarea #---------------------------------------------------------------------------------- row += 1 guiFrame.grid_rowconfigure(row, weight=1) self.outputTextBox = ScrolledText(guiFrame) self.outputTextBox.grid(row=row, column=0, columnspan=2, sticky='nsew') self.redirectConsole() #---------------------------------------------------------------------------------- # Buttons #---------------------------------------------------------------------------------- row += 1 col = 0 texts = ['Quit', 'Help'] commands = [self.close, None] self.buttonBar = ButtonList(guiFrame, texts=texts, commands=commands, expands=True) self.buttonBar.grid(row=row, column=col, columnspan=2, sticky='ew') # self.openProjectButton = self.buttonBar.buttons[0] # self.closeProjectButton = self.buttonBar.buttons[1] # self.runButton = self.buttonBar.buttons[0] # self.viewResultButton = self.buttonBar.buttons[1] for button in self.buttonBar.buttons: button.config(**actionButtonAttributes)
def body(self, guiFrame): row = 0 col =0 # frame = Frame( guiFrame ) # frame.grid(row=row, column=col, sticky='news') self.menuBar = Menu( guiFrame) self.menuBar.grid( row=row, column=col, sticky='ew') #---------------------------------------------------------------------------------- # Project frame #---------------------------------------------------------------------------------- # guiFrame.grid_columnconfigure(row, weight=1) # frame = LabelFrame(guiFrame, text='Project', font=medFont) row = +1 col =0 frame = LabelFrame(guiFrame, text='Project', **labelFrameAttributes ) print '>', frame.keys() frame.grid(row=row, column=col, sticky='nsew' ) frame.grid_columnconfigure(2, weight=1) # frame.grid_rowconfigure(0, weight=1) srow = 0 self.projectOptions = ['old','new from PDB','new from CCPN','new from CYANA'] self.projOptionsSelect = RadioButtons(frame, selected_index=0, entries=self.projectOptions, direction='vertical', select_callback=self.updateGui ) self.projOptionsSelect.grid(row=srow,column=0,rowspan=len(self.projectOptions),columnspan=2, sticky='w') if self.options.name: text = self.options.name else: text='' # end if self.projEntry = Entry(frame, bd=1, text=text, returnCallback=self.updateGui) self.projEntry.grid(row=srow,column=2,columnspan=2,sticky='ew') # self.projEntry.bind('<Key>', self.updateGui) self.projEntry.bind('<Leave>', self.updateGui) projButton = Button(frame, bd=1,command=self.chooseOldProjectFile, text='browse') projButton.grid(row=srow,column=3,sticky='ew') srow += 1 self.pdbEntry = Entry(frame, bd=1, text='') self.pdbEntry.grid(row=srow,column=2,sticky='ew') self.pdbEntry.bind('<Leave>', self.updateGui) pdbButton = Button(frame, bd=1,command=self.choosePdbFile, text='browse') pdbButton.grid(row=srow,column=3,sticky='ew') srow += 1 self.ccpnEntry = Entry(frame, bd=1, text='') self.ccpnEntry.grid(row=srow,column=2,sticky='ew') self.ccpnEntry.bind('<Leave>', self.updateGui) ccpnButton = Button(frame, bd=1,command=self.chooseCcpnFile, text='browse') ccpnButton.grid(row=srow,column=3,sticky='ew') srow += 1 self.cyanaEntry = Entry(frame, bd=1, text='') self.cyanaEntry.grid(row=srow,column=2,sticky='ew') self.cyanaEntry.bind('<Leave>', self.updateGui) cyanaButton = Button(frame, bd=1,command=self.chooseCyanaFile, text='browse') cyanaButton.grid(row=srow,column=3,sticky='ew') #Empty row srow += 1 label = Label(frame, text='') label.grid(row=srow,column=0,sticky='nw') srow += 1 label = Label(frame, text='Project name:') label.grid(row=srow,column=0,sticky='nw') self.nameEntry = Entry(frame, bd=1, text='') self.nameEntry.grid(row=srow,column=2,sticky='w') #Empty row srow += 1 label = Label(frame, text='') label.grid(row=srow,column=0,sticky='nw') srow += 1 self.openProjectButton = Button(frame, command=self.openProject, text='Open Project', **actionButtonAttributes ) self.openProjectButton.grid(row=srow,column=0, columnspan=4, sticky='ew') #---------------------------------------------------------------------------------- # status #---------------------------------------------------------------------------------- # guiFrame.grid_columnconfigure(1, weight=0) srow = 0 frame = LabelFrame(guiFrame, text='Status', **labelFrameAttributes) frame.grid( row=srow, column=1, sticky='wnes') self.projectStatus = Text(frame, height=11, width=70, borderwidth=0, relief='flat') self.projectStatus.grid(row=0, column=0, sticky='wen') #Empty row srow += 1 label = Label(frame, text='') label.grid(row=srow,column=0,sticky='nw') srow += 1 self.closeProjectButton = Button(frame, command=self.closeProject, text='Close Project', **actionButtonAttributes) self.closeProjectButton.grid(row=srow,column=0, columnspan=4, sticky='ew') #---------------------------------------------------------------------------------- # Validate frame #---------------------------------------------------------------------------------- row +=1 col=0 frame = LabelFrame(guiFrame, text='Validate', **labelFrameAttributes) # frame = LabelFrame(guiFrame, text='Validate', font=medFont) frame.grid(row=row, column=col, sticky='nsew') # frame.grid_columnconfigure(2, weight=1) frame.grid_rowconfigure(0, weight=1) srow = 0 # label = Label(frame, text='validation') # label.grid(row=srow,column=0,sticky='nw') # # self.selectDoValidation = CheckButton(frame) # self.selectDoValidation.grid(row=srow, column=1,sticky='nw' ) # self.selectDoValidation.set(True) # # srow += 1 # label = Label(frame, text='') # label.grid(row=srow,column=0,sticky='nw') # # srow += 1 label = Label(frame, text='checks') label.grid(row=srow,column=0,sticky='nw') self.selectCheckAssign = CheckButton(frame) self.selectCheckAssign.grid(row=srow, column=1,sticky='nw' ) self.selectCheckAssign.set(True) label = Label(frame, text='assignments and shifts') label.grid(row=srow,column=2,sticky='nw') # srow += 1 # self.selectCheckQueen = CheckButton(frame) # self.selectCheckQueen.grid(row=srow, column=4,sticky='nw' ) # self.selectCheckQueen.set(False) # label = Label(frame, text='QUEEN') # label.grid(row=srow,column=5,sticky='nw') # # queenButton = Button(frame, bd=1,command=None, text='setup') # queenButton.grid(row=srow,column=6,sticky='ew') srow += 1 self.selectCheckResraint = CheckButton(frame) self.selectCheckResraint.grid(row=srow, column=1,sticky='nw' ) self.selectCheckResraint.set(True) label = Label(frame, text='restraints') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectCheckStructure = CheckButton(frame) self.selectCheckStructure.grid(row=srow, column=1,sticky='nw' ) self.selectCheckStructure.set(True) label = Label(frame, text='structural') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectMakeHtml = CheckButton(frame) self.selectMakeHtml.grid(row=srow, column=1,sticky='nw' ) self.selectMakeHtml.set(True) label = Label(frame, text='generate HTML') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectCheckScript = CheckButton(frame) self.selectCheckScript.grid(row=srow, column=1,sticky='nw' ) self.selectCheckScript.set(False) label = Label(frame, text='user script') label.grid(row=srow,column=0,sticky='nw') self.validScriptEntry = Entry(frame, bd=1, text='') self.validScriptEntry.grid(row=srow,column=2,columnspan=3, sticky='ew') scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse') scriptButton.grid(row=srow,column=5,sticky='ew') srow += 1 label = Label(frame, text='ranges') label.grid(row=srow,column=0,sticky='nw') self.rangesEntry = Entry( frame, text='' ) self.rangesEntry.grid( row=srow, column=2, columnspan=3, sticky='ew') # self.validScriptEntry = Entry(frame, bd=1, text='') # self.validScriptEntry.grid(row=srow,column=3,sticky='ew') # # scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse') # scriptButton.grid(row=srow,column=4,sticky='ew') srow += 1 texts = ['Run Validation','View Results','Setup QUEEN'] commands = [self.runCing, None, None] buttonBar = ButtonList(frame, texts=texts, commands=commands,expands=True) buttonBar.grid(row=srow, column=0, columnspan=6, sticky='ew') for button in buttonBar.buttons: button.config(**actionButtonAttributes) # end for self.runButton = buttonBar.buttons[0] self.viewResultButton = buttonBar.buttons[1] self.queenButton = buttonBar.buttons[2] #---------------------------------------------------------------------------------- # Miscellaneous frame #---------------------------------------------------------------------------------- row +=0 col=1 # frame = LabelFrame(guiFrame, text='Miscellaneous', font=medFont) frame = LabelFrame(guiFrame, text='Miscellaneous', **labelFrameAttributes) frame.grid(row=row, column=col, sticky='news') frame.grid_columnconfigure(2, weight=1) frame.grid_columnconfigure(4, weight=1,minsize=30) frame.grid_rowconfigure(0, weight=1) # Exports srow = 0 label = Label(frame, text='export to') label.grid(row=srow,column=0,sticky='nw') self.selectExportXeasy = CheckButton(frame) self.selectExportXeasy.grid(row=srow, column=1,sticky='nw' ) self.selectExportXeasy.set(True) label = Label(frame, text='Xeasy, Sparky, TALOS, ...') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectExportCcpn = CheckButton(frame) self.selectExportCcpn.grid(row=srow, column=1,sticky='nw' ) self.selectExportCcpn.set(True) label = Label(frame, text='CCPN') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectExportQueen = CheckButton(frame) self.selectExportQueen.grid(row=srow, column=1,sticky='nw' ) self.selectExportQueen.set(True) label = Label(frame, text='QUEEN') label.grid(row=srow,column=2,sticky='nw') srow += 1 self.selectExportRefine = CheckButton(frame) self.selectExportRefine.grid(row=srow, column=1,sticky='nw' ) self.selectExportRefine.set(True) label = Label(frame, text='refine') label.grid(row=srow,column=2,sticky='nw') srow += 1 label = Label(frame, text='') label.grid(row=srow,column=0,sticky='nw') # User script srow += 1 label = Label(frame, text='user script') label.grid(row=srow,column=0,sticky='nw') self.selectMiscScript = CheckButton(frame) self.selectMiscScript.grid(row=srow, column=1,sticky='nw' ) self.selectMiscScript.set(False) self.miscScriptEntry = Entry(frame, bd=1, text='') self.miscScriptEntry.grid(row=srow,column=3,sticky='ew') script2Button = Button(frame, bd=1,command=self.chooseMiscScript, text='browse') script2Button.grid(row=srow,column=4,sticky='ew') srow += 1 texts = ['Export','Run Script'] commands = [None, None] buttonBar = ButtonList(frame, texts=texts, commands=commands,expands=True) buttonBar.grid(row=srow, column=0, columnspan=5, sticky='ew') for button in buttonBar.buttons: button.config(**actionButtonAttributes) # end for self.exportButton = buttonBar.buttons[0] self.scriptButton = buttonBar.buttons[1] #---------------------------------------------------------------------------------- # Textarea #---------------------------------------------------------------------------------- row +=1 guiFrame.grid_rowconfigure(row, weight=1) self.outputTextBox = ScrolledText(guiFrame) self.outputTextBox.grid(row=row, column=0, columnspan=2, sticky='nsew') self.redirectConsole() #---------------------------------------------------------------------------------- # Buttons #---------------------------------------------------------------------------------- row +=1 col=0 texts = ['Quit', 'Help'] commands = [self.close, None] self.buttonBar = ButtonList(guiFrame, texts=texts, commands=commands,expands=True) self.buttonBar.grid(row=row, column=col, columnspan=2, sticky='ew') # self.openProjectButton = self.buttonBar.buttons[0] # self.closeProjectButton = self.buttonBar.buttons[1] # self.runButton = self.buttonBar.buttons[0] # self.viewResultButton = self.buttonBar.buttons[1] for button in self.buttonBar.buttons: button.config(**actionButtonAttributes)
class NmrPipePseudoPopup(BasePopup): pseudoEntries = ('Is Pseudo Expt', 'Is Not Pseudo Expt') def __init__(self, parent, params, dim, fileName='', *args, **kw): self.dim = dim self.params = params self.fileName = fileName m = template_re.match(fileName) if m: n = len(m.groups(2)) ss = '%%0%dd' % n template = re.sub(template_re, r'\1%s\3' % ss, fileName) else: template = fileName self.template = template BasePopup.__init__(self, parent=parent, title='NMRPipe Pseudo Data', modal=True, **kw) def body(self, master): fileName = self.fileName directory = os.path.dirname(fileName) if not directory: directory = os.getcwd() fileName = os.path.basename(fileName) m = template_re.match(fileName) if m: n = len(m.groups(2)) ss = '%%0%dd' % n template = re.sub(template_re, r'\1%s\3' % ss, fileName) else: template = fileName master.rowconfigure(0, weight=1) master.rowconfigure(1, weight=1) master.columnconfigure(1, weight=1) tipTexts = [ 'The experiment is pseudo-N dimensional, with a sampled axis', 'The experiment is the regular kind with only NMR frequency axes' ] self.pseudoButton = RadioButtons( master, entries=self.pseudoEntries, select_callback=self.changedPseudoMode, grid=(0, 0), sticky='nw', tipTexts=tipTexts) frame = self.pseudoFrame = Frame(master) self.pseudoFrame.grid(row=1, column=0, sticky='nsew') row = 0 npts = self.params.npts[self.dim] tipText = 'Number of data points (planes) along sampled axis' label = Label(frame, text='Number of points: ') label.grid(row=row, column=0, sticky='e') self.nptsEntry = IntEntry(frame, text=npts, tipText=tipText, width=8, grid=(row, 1)) tipText = 'Load the values for the sampled axis from a text file containing a list of numeric values' Button(frame, text='Load values from text file', command=self.loadValues, tipText=tipText, grid=(row, 2), sticky='ew') row = row + 1 tipText = 'The values (e.g. T1, T2) corresponding to each data point (plane) along sampled axis' label = Label(frame, text='Point values: ') label.grid(row=row, column=0, sticky='e') self.valueEntry = FloatEntry(frame, isArray=True, tipText=tipText) self.valueEntry.grid(row=row, column=1, columnspan=2, sticky='ew') row = row + 1 tipText = 'Fetch the Point values from the files given by the NMRPipe template' button = Button( frame, text='Fetch values from file(s) specified by template below', command=self.fetchValues, tipText=tipText) button.grid(row=row, column=1, columnspan=2, sticky='w') row = row + 1 tipText = 'The directory where the data files reside' button = Button(frame, text='Data directory: ', command=self.chooseDirectory) button.grid(row=row, column=0, sticky='e') self.directoryEntry = Entry(frame, text=directory, width=40, tipText=tipText) self.directoryEntry.grid(row=row, column=1, columnspan=2, sticky='ew') row = row + 1 tipText = 'The NMRPipe template for the data files, if you want to use these to fetch the point values from' button = Button(frame, text='NMRPipe template: ', command=self.chooseFile) button.grid(row=row, column=0, sticky='e') self.templateEntry = Entry(frame, text=template, tipText=tipText) self.templateEntry.grid(row=row, column=1, columnspan=2, sticky='ew') for n in range(row): frame.rowconfigure(n, weight=1) frame.columnconfigure(1, weight=1) buttons = UtilityButtonList(master, closeText='Ok', doClone=False, closeCmd=self.updateParams, helpUrl=self.help_url) buttons.grid(row=2, column=0, sticky='ew') def loadValues(self): directory = self.parent.fileSelect.getDirectory() fileSelectPopup = FileSelectPopup(self, title='Select Sampled Data File', dismiss_text='Cancel', selected_file_must_exist=True, multiSelect=False, directory=directory) fileName = fileSelectPopup.file_select.getFile() if not fileName: return fileObj = open(fileName, 'rU') data = '' line = fileObj.readline() while line: data += line line = fileObj.readline() fileObj.close() data = re.sub(',\s+', ',', data) data = re.sub('\s+', ',', data) data = re.sub(',,', ',', data) data = re.sub('[^0-9,.\-+eE]', '', data) self.valueEntry.set(data) def chooseDirectory(self): directory = os.path.dirname(self.fileName) if not directory: directory = os.getcwd() popup = FileSelectPopup(self, directory=directory, show_file=False) directory = popup.getDirectory() popup.destroy() if directory: self.directoryEntry.set(directory) def chooseFile(self): directory = self.directoryEntry.get() if not directory: directory = os.getcwd() popup = FileSelectPopup(self, directory=directory) file = popup.getFile() popup.destroy() if file: template = os.path.basename(file) self.templateEntry.set(template) def updateParams(self): params = self.params if self.pseudoButton.get() == self.pseudoEntries[0]: npts = self.nptsEntry.get() params.npts[self.dim] = npts values = self.valueEntry.get() try: params.setSampledDim(self.dim, values) except ApiError, e: showError('Set Sampled Dim', e.error_msg, parent=self) return params.fixNullDims(ignoreDim=self.dim) else:
class AssignMentTransferTab(object): '''the tab in the GUI where assignments can be transferred in bulk to the ccpn analysis project. A difference is made between two types of assignments: 1) spin systems to residues, which also implies resonanceSets to atomSets. 2) resonances to peak dimensions. The user is able to configure which assignments should be transferred to the project. Attributes: guiParent: gui object this tab is part of. frame: the frame in which this element lives. dataModel(src.cython.malandro.DataModel): dataModel object describing the assignment proposed by the algorithm. selectedSolution (int): The index of the solution/run that is used asa the template to make the assignments. resonanceToDimension (bool): True if resonances should be assigned to peak dimensions. False if not. spinSystemToResidue (bool): True if spin system to residue assignment should be carried out. minScore (float): The minimal score of a spin system assignment to a residue to be allowed to transfer this assignment to the project intra (bool): True if intra-residual peaks should be assigned. sequential (bool): True if sequential peaks should be assigned. noDiagonal (bool): If True, purely diagonal peaks are ignored during the transfer of assignments. allSpectra (bool): If True, all spectra will be assigned. If False, one specified spectrum will be assigned. spectrum (src.cython.malandro.Spectrum): The spectrum that should be assigned. ''' def __init__(self, parent, frame): '''Init. args: parent: the guiElement that this tab is part of. frame: the frame this part of the GUI lives in. ''' self.guiParent = parent self.frame = frame # Buttons and fields, # will be set in body(): self.peaksCheckButton = None self.residuesCheckButton = None self.intraCheckButton = None self.sequentialCheckButton = None self.noDiagonalCheckButton = None self.spinSystemTypeSelect = None self.minScoreEntry = None self.solutionNumberEntry = None self.spectrumSelect = None self.spectraPullDown = None self.assignedResidueStrategySelect = None self.transferButton = None # Settings that determine how assignments # are transferred to the analysis project: self.minScore = 80.0 self.dataModel = None self.spectrum = None self.selectedSolution = 1 self.body() self.resonanceToDimension = True self.spinSystemToResidue = True self.intra = True self.sequential = True self.noDiagonal = True self.allSpectra = True self.spinSystemType = 0 self.strategy = 0 def body(self): '''Describes the body of this tab. It consists out of a number of radio buttons, check buttons and number entries that allow the user to indicate which assignments should be transferred. ''' # self.frame.expandColumn(0) self.frame.expandGrid(8, 0) self.frame.expandGrid(8, 1) typeOfAssignmentFrame = LabelFrame(self.frame, text='type of assignment') typeOfAssignmentFrame.grid(row=0, column=0, sticky='nesw') # typeOfAssignmentFrame.expandGrid(0,5) peakSelectionFrame = LabelFrame(self.frame, text='which peaks to assign') peakSelectionFrame.grid(row=0, column=1, sticky='nesw', rowspan=2) spinSystemSelectionFrame = LabelFrame(self.frame, text='Which spin-systems to use') spinSystemSelectionFrame.grid(row=2, column=0, sticky='nesw') tipText = 'What to do when a residue has already a spin system assigned to it.' assignedResidueFrame = LabelFrame( self.frame, text='if residue already has spin-system', tipText=tipText) assignedResidueFrame.grid(row=2, column=1, sticky='nesw') spectrumSelectionFrame = LabelFrame(self.frame, text='spectra') spectrumSelectionFrame.grid(row=1, column=0, sticky='nesw') row = 0 Label(typeOfAssignmentFrame, text='Resonances to Peak Dimensions', grid=(row, 0)) self.peaksCheckButton = CheckButton(typeOfAssignmentFrame, selected=True, grid=(row, 1)) row += 1 Label(typeOfAssignmentFrame, text='SpinSystems to Residues', grid=(row, 0)) self.residuesCheckButton = CheckButton(typeOfAssignmentFrame, selected=True, grid=(row, 1)) row = 0 Label(peakSelectionFrame, text='Intra-Residual', grid=(row, 0)) self.intraCheckButton = CheckButton(peakSelectionFrame, selected=True, grid=(row, 1)) row += 1 Label(peakSelectionFrame, text='Sequential', grid=(row, 0)) self.sequentialCheckButton = CheckButton(peakSelectionFrame, selected=True, grid=(row, 1)) row += 1 Label(peakSelectionFrame, text='Do not assign diagonal peaks', grid=(row, 0)) self.noDiagonalCheckButton = CheckButton(peakSelectionFrame, selected=True, grid=(row, 1)) entries = [ 'Only assigned spin systems', 'All that have a score of at least: ', 'User Defined', 'Solution number:' ] tipTexts = [ 'Only assign resonances of spin systems that already have a sequential assignment for the assignment of peak dimensions. Spin system to residue assignment is not relevant in this case.', 'Assign all spin systems that have a score of at least a given percentage. 50% or lower is not possible, because than spin systems might have to be assigned to more than 1 residue, which is impossible.', "As defined in the lower row of buttons in the 'results' tab.", 'One of the single solutions of the annealing.' ] self.spinSystemTypeSelect = RadioButtons(spinSystemSelectionFrame, entries=entries, grid=(0, 0), select_callback=None, direction=VERTICAL, gridSpan=(4, 1), tipTexts=tipTexts) tipText = 'The minimal amount of colabelling the different nuclei should have in order to still give rise to a peak.' self.minScoreEntry = FloatEntry(spinSystemSelectionFrame, grid=(1, 1), width=7, text=str(self.minScore), returnCallback=self.changeMinScore, tipText=tipText) self.minScoreEntry.bind('<Leave>', self.changeMinScore, '+') self.solutionNumberEntry = IntEntry(spinSystemSelectionFrame, grid=(3, 1), width=7, text=1, returnCallback=self.solutionUpdate, tipText=tipText) self.solutionNumberEntry.bind('<Leave>', self.solutionUpdate, '+') #self.solutionPullDown = PulldownList(spinSystemSelectionFrame, None, grid=(3,1), sticky='w') entries = ['all spectra', 'only:'] tipTexts = [ 'Assign peaks in all the spectra that where selected before the annealing ran.', 'Only assign peaks in one particular spectrum. You can of course repeat this multiple times for different spectra.' ] self.spectrumSelect = RadioButtons(spectrumSelectionFrame, entries=entries, grid=(0, 0), select_callback=None, direction=VERTICAL, gridSpan=(2, 1), tipTexts=tipTexts) self.spectraPullDown = PulldownList(spectrumSelectionFrame, self.changeSpectrum, grid=(1, 1), sticky='w') entries = [ 'skip this residue', 'de-assign old spin system from residue', 'assign, but never merge', 'warn to merge' ] tipTexts = [ "Don't assign the new spin system to the residue. The residue is not skipped when the old spin system does not contain any resonances", "De-assign old spin system from residue, unless the old spin system is a spin system without any resonances.", "Don't merge any spin systems, merging can be performed later if nescesary in the Resonance --> SpinSystems window.", "Ask to merge individually for each spin system, this might result in clicking on a lot of popups." ] self.assignedResidueStrategySelect = RadioButtons(assignedResidueFrame, entries=entries, grid=(0, 0), select_callback=None, direction=VERTICAL, gridSpan=(2, 1), tipTexts=tipTexts) texts = ['Transfer Assignments'] commands = [self.transferAssignments] self.transferButton = ButtonList(self.frame, commands=commands, texts=texts) self.transferButton.grid(row=5, column=0, sticky='nsew', columnspan=2) def update(self): '''Update the nescesary elements in the tab. Is called when the algorithm has produced possible assignments. The only thing that has to be updated in practice in this tab is the pulldown with spectra. ''' self.dataModel = self.guiParent.connector.results self.updateSpectra() def setDataModel(self, dataModel): '''Here the dataModel, which is the dataModel containing the suggested assignments body the algorithm, can be set. ''' self.dataModel = dataModel self.update() def updateSpectra(self, *opt): '''Updates the spectra shown in the spectra pulldown. These are only the spectra that were used by the algorithm. All other spectra in the project are not relevant since for those no simulated peaks have been matched to real peaks. ''' if not self.dataModel: return spectrum = self.spectrum spectra = self.dataModel.getSpectra() if spectra: names = [spectrum.name for spectrum in spectra] index = 0 if self.spectrum not in spectra: self.spectrum = spectra[0] else: index = spectra.index(self.spectrum) self.spectraPullDown.setup(names, spectra, index) def changeSpectrum(self, spectrum): '''Select a spectum to be assigned.''' self.spectrum = spectrum def solutionUpdate(self, event=None, value=None): '''Select a solution. A solution is a one to one mapping of spin systems to residues produced by one run of the algorithm. args: event: event object, this is one of the values the number entry calls his callback function with. value: the index of the solution/run. ''' if not self.dataModel: return Nsolutions = len(self.dataModel.chain.residues[0].solutions) if value is None: value = self.solutionNumberEntry.get() if value == self.selectedSolution: return else: self.selectedSolution = value if value < 1: self.solutionNumberEntry.set(1) self.selectedSolution = 1 elif value > Nsolutions: self.selectedSolution = Nsolutions self.solutionNumberEntry.set(self.selectedSolution) else: self.solutionNumberEntry.set(self.selectedSolution) def fetchOptions(self): '''Fetches user set options from the gui in one go and stores them in their corresponding instance variables. ''' self.resonanceToDimension = self.peaksCheckButton.get() self.spinSystemToResidue = self.residuesCheckButton.get() self.intra = self.intraCheckButton.get() self.sequential = self.sequentialCheckButton.get() self.noDiagonal = self.noDiagonalCheckButton.get() self.spinSystemType = self.spinSystemTypeSelect.getIndex() self.strategy = ['skip', 'remove', 'noMerge', None][self.assignedResidueStrategySelect.getIndex()] self.allSpectra = [True, False][self.spectrumSelect.getIndex()] def changeMinScore(self, event=None): '''Set the minimal score for which a spin system to residue assignment gets transferred to the ccpn analysis project. ''' newMinScore = self.minScoreEntry.get() if self.minScore != newMinScore: if newMinScore <= 50.0: self.minScore = 51.0 self.minScoreEntry.set(51.0) elif newMinScore > 100.0: self.minScore = 100.0 self.minScoreEntry.set(100.0) else: self.minScore = newMinScore def transferAssignments(self): '''Transfer assignments to project depending on the settings from the GUI. ''' self.fetchOptions() if not self.dataModel or (not self.resonanceToDimension and not self.spinSystemToResidue): return strategy = self.strategy lookupSpinSystem = [ self.getAssignedSpinSystem, self.getBestScoringSpinSystem, self.getUserDefinedSpinSystem, self.getSelectedSolutionSpinSystem ][self.spinSystemType] residues = self.dataModel.chain.residues spinSystemSequence = [lookupSpinSystem(res) for res in residues] ccpnSpinSystems = [] ccpnResidues = [] # if self.spinSystemType == 0 it means that it for sure already # assigned like this if self.spinSystemToResidue and not self.spinSystemType == 0: for spinSys, res in zip(spinSystemSequence, residues): if spinSys and res: ccpnSpinSystems.append(spinSys.getCcpnResonanceGroup()) ccpnResidues.append(res.getCcpnResidue()) assignSpinSystemstoResidues(ccpnSpinSystems, ccpnResidues, strategy=strategy, guiParent=self.guiParent) if self.resonanceToDimension: allSpectra = self.allSpectra if self.intra: for residue, spinSystem in zip(residues, spinSystemSequence): if not spinSystem: continue intraLink = residue.getIntraLink(spinSystem) for pl in intraLink.getPeakLinks(): peak = pl.getPeak() if not allSpectra and peak.getSpectrum( ) is not self.spectrum: continue if not peak: continue resonances = pl.getResonances() if self.noDiagonal and len( set(resonances)) < len(resonances): continue for resonance, dimension in zip( resonances, peak.getDimensions()): ccpnResonance = resonance.getCcpnResonance() ccpnDimension = dimension.getCcpnDimension() assignResToDim(ccpnDimension, ccpnResonance) if self.sequential: for residue, spinSystemA, spinSystemB in zip( residues, spinSystemSequence, spinSystemSequence[1:]): if not spinSystemA or not spinSystemB: continue link = residue.getLink(spinSystemA, spinSystemB) for pl in link.getPeakLinks(): peak = pl.getPeak() if not allSpectra and peak.getSpectrum( ) is not self.spectrum: continue if not peak: continue resonances = pl.getResonances() if self.noDiagonal and len( set(resonances)) < len(resonances): continue for resonance, dimension in zip( resonances, peak.getDimensions()): ccpnResonance = resonance.getCcpnResonance() ccpnDimension = dimension.getCcpnDimension() assignResToDim(ccpnDimension, ccpnResonance) self.guiParent.resultsTab.update() def getAssignedSpinSystem(self, residue): '''Get the spinSystem that is assigned in the project to a residue. args: residue (src.cython.malandro.Residue) return: spinSystem (src.cython.malandro.SpinSystem) ''' ccpCode = residue.ccpCode seqCode = residue.getSeqCode() spinSystems = self.dataModel.getSpinSystems()[ccpCode] ccpnResidue = residue.getCcpnResidue() if ccpnResidue: assignedResonanceGroups = ccpnResidue.getResonanceGroups() if len(assignedResonanceGroups) > 1: print 'There is more than one spin system assigned to residue %s, did not know which one to use to assign peaks. Therefor this residue is skipped.' % ( seqCode) return assignedResonanceGroup = ccpnResidue.findFirstResonanceGroup() if assignedResonanceGroup: for spinSystem in spinSystems: if spinSystem.getSerial() == assignedResonanceGroup.serial: # Just checking to make sure, analysis project could # have changed if not self.skipResidue(residue, spinSystem): return spinSystem def getBestScoringSpinSystem(self, residue): '''Get the spinSystem that scores the highest, i.e. is assigned in most of the runs to the given residue. args: residue (src.cython.malandro.Residue) return: spinSystem (src.cython.malandro.SpinSystem) ''' solutions = residue.solutions weigth = 1.0 / len(solutions) score, bestSpinSystem = max([ (solutions.count(solution) * weigth * 100.0, solution) for solution in solutions ]) if score >= self.minScore and not bestSpinSystem.getIsJoker( ) and not self.skipResidue(residue, bestSpinSystem): return bestSpinSystem return None def getUserDefinedSpinSystem(self, residue): '''Get the spinSystem that is defined by the user (probably in the resultsTab) as the correct assignment of the given residue. args: residue (src.cython.malandro.Residue) return: spinSystem (src.cython.malandro.SpinSystem) ''' userDefinedSpinSystem = residue.userDefinedSolution if userDefinedSpinSystem and not userDefinedSpinSystem.getIsJoker( ) and not self.skipResidue(residue, userDefinedSpinSystem): return userDefinedSpinSystem return None def getSelectedSolutionSpinSystem(self, residue): '''I a solution corresponding to one specific run of the algorithm is defined, return which spinSystem in that run got assigned to the given residue. args: residue (src.cython.malandro.Residue) return: spinSystem (src.cython.malandro.SpinSystem) ''' solutions = residue.solutions spinSystem = solutions[self.selectedSolution - 1] if not spinSystem.getIsJoker() and not self.skipResidue( residue, spinSystem): return spinSystem return None def skipResidue(self, residue, spinSystem): '''One strategy is to skip all residues that already have a spin system assignment. If that is the case determine whether to skip the given residue. args: residue (src.cython.malandro.Residue) spinSystem (src.cython.malandro.SpinSystem) return: boolean, True if residue should be skipped. ''' if self.strategy == 0: assignedGroups = residue.getCcpnResidue().getResonanceGroups() assignedSerials = set( [spinSys.serial for spinSys in assignedGroups]) if assignedSerials and spinSystem.getSerial( ) not in assignedSerials: return True return False
def body(self, master): fileName = self.fileName directory = os.path.dirname(fileName) if not directory: directory = os.getcwd() fileName = os.path.basename(fileName) m = template_re.match(fileName) if m: n = len(m.groups(2)) ss = '%%0%dd' % n template = re.sub(template_re, r'\1%s\3' % ss, fileName) else: template = fileName master.rowconfigure(0, weight=1) master.rowconfigure(1, weight=1) master.columnconfigure(1, weight=1) tipTexts = [ 'The experiment is pseudo-N dimensional, with a sampled axis', 'The experiment is the regular kind with only NMR frequency axes' ] self.pseudoButton = RadioButtons( master, entries=self.pseudoEntries, select_callback=self.changedPseudoMode, grid=(0, 0), sticky='nw', tipTexts=tipTexts) frame = self.pseudoFrame = Frame(master) self.pseudoFrame.grid(row=1, column=0, sticky='nsew') row = 0 npts = self.params.npts[self.dim] tipText = 'Number of data points (planes) along sampled axis' label = Label(frame, text='Number of points: ') label.grid(row=row, column=0, sticky='e') self.nptsEntry = IntEntry(frame, text=npts, tipText=tipText, width=8, grid=(row, 1)) tipText = 'Load the values for the sampled axis from a text file containing a list of numeric values' Button(frame, text='Load values from text file', command=self.loadValues, tipText=tipText, grid=(row, 2), sticky='ew') row = row + 1 tipText = 'The values (e.g. T1, T2) corresponding to each data point (plane) along sampled axis' label = Label(frame, text='Point values: ') label.grid(row=row, column=0, sticky='e') self.valueEntry = FloatEntry(frame, isArray=True, tipText=tipText) self.valueEntry.grid(row=row, column=1, columnspan=2, sticky='ew') row = row + 1 tipText = 'Fetch the Point values from the files given by the NMRPipe template' button = Button( frame, text='Fetch values from file(s) specified by template below', command=self.fetchValues, tipText=tipText) button.grid(row=row, column=1, columnspan=2, sticky='w') row = row + 1 tipText = 'The directory where the data files reside' button = Button(frame, text='Data directory: ', command=self.chooseDirectory) button.grid(row=row, column=0, sticky='e') self.directoryEntry = Entry(frame, text=directory, width=40, tipText=tipText) self.directoryEntry.grid(row=row, column=1, columnspan=2, sticky='ew') row = row + 1 tipText = 'The NMRPipe template for the data files, if you want to use these to fetch the point values from' button = Button(frame, text='NMRPipe template: ', command=self.chooseFile) button.grid(row=row, column=0, sticky='e') self.templateEntry = Entry(frame, text=template, tipText=tipText) self.templateEntry.grid(row=row, column=1, columnspan=2, sticky='ew') for n in range(row): frame.rowconfigure(n, weight=1) frame.columnconfigure(1, weight=1) buttons = UtilityButtonList(master, closeText='Ok', doClone=False, closeCmd=self.updateParams, helpUrl=self.help_url) buttons.grid(row=2, column=0, sticky='ew')
class EditPeakFindParamsPopup(BasePopup): """ ** Peak Settings and Non-Interactive Peak Finding ** The purpose of this dialog is to allow the user to select settings for finding and integrating peaks, and also to be able to find peaks in an arbitrary region that is specified in a table rather than via a spectrum window. ** Find Parameters tab ** This can be used to specify how peak finding works. First of all, you can search for just positive peaks, just negative peaks or both, and the default is that it is just positive peaks. However, this is further filtered by what the contour levels are. If there are no positive contour levels for a given spectrum then positive peaks are not found even if this dialog says they can be, and similarly if there are no negative contour levels for a given spectrum then negative peaks are not found even if this dialog says they can be. The peak finding algorithm looks for local extrema (maximum for positive peaks and minima for negative peaks). But on a grid there are various ways to define what you mean by an extremum. Suppose you are trying to determine if point p is a maximum (similar considerations apply for minimum). You would want the intensity at all nearby points to be less than or equal to the intensity at p. You can just check points that are just +- one point from p in each dimension, or you can also check "diagonal" points. For example, if you are looking at point p = (x, y) in 2D, then the former would mean checking the four points (x-1, y), (x+1, y) (x, y-1) and (x, y+1), whereas for the latter you would also have to check (x-1, y-1), (x-1, y+1), (x+1, y-1) and (x+1, y+1). In N dimensions the "diagonal" method involves checking 3^N-1 points whereas the "non-diagonal" method involves checking only 2N points. In general the "non-diagonal" method is probably the one to use, and it is the default. Peaks are only found above (for positive peaks) or below (for negative peaks) some threshold. By default this is determined by the contour level for the spectrum. For positive peaks the threshold is the minimum positive contour level, and for negative peaks the threshold is the maximum negative contour level. However these levels can be scaled up (or down) using the "Scale relative to contour levels" option (default value 1). For example, if you have drawn the contour levels low to show a bit of noise, but do not want the noise picked as peaks, then you could select a scale of 2 (or whatever) to increase the threshold. The "Exclusion buffer around peaks" is so that in crowded regions you do not get too many peaks near one location. By default the exclusion buffer is 1 point in each dimension, but this can be increased to make the algorithm find fewer peaks. By default the peak finding only looks at the orthogonal region that is displayed in the given window where peak finding is taking place. Sometimes it looks like a peak should be found because in x, y you can see an extremum, but unless it is also an extremum in the orthogonal dimensions it is not picked. You can widen out the points being examined in the orthogonal dimensions by using the "Extra thickness in orthogonal dims" option, which is specified in points. The "Minimum drop factor" is by what factor the intensity needs to drop from its extreme value for there to be considered to be a peak. This could help remove sinc wiggle peaks, for example. The default is that the drop factor is 0, which in effect means that there is no condition. The "Volume method" is what is used to estimate the volume of peaks that are found. The default is "box sum", which just looks at a fixed size box around the peak centre and sums the intensities in that. The size of the box is set in the table in the Spectrum Widths tab. The "truncated box sum" is the same as "box sum" except that the summing stops in a given direction when (if) the intensities start increasing. The "parabolic" fit fits a quadratic equation in each dimension to the intensity at the peak centre and ad +- 1 points and then uses the equivalent Gaussian fit to estimate the volume. ** Spectrum Widths ** This can be used to specify minimum linewidths (in Hz) for there to be considered a peak to exist in the peak finding algorithm. It is also where the Boxwidth for each dimension in each spectrum is specified. ** Diagonal Exclusions ** This can be used to exclude peaks from being found in regions near the diagonal (so in homonuclear experiments). The exclusion region is specified in ppm and is independent of spectrum. ** Region Peak Find ** This can be used to find peaks non-interactively (so not having to control shift drag inside a spectrum window). The region being analysed is specified in the table. There are two types of conditions that can be specified, "include" for regions that should be included and "exclude" for regions that should be excluded. The regions are specified in ppm. The "Whole Region" button will set the selected row in the table to be the entire fundamental region of the spectrum. The "Add Region" button adds an extra row to the table, and the "Delete Region" button removes the selected row. The "Adjust Params" button goes to the Find Parameters tab. The "Find Peaks!" button does the peak finding. """ def __init__(self, parent, *args, **kw): self.spectrum = None BasePopup.__init__(self, parent=parent, title='Peak : Peak Finding', **kw) def body(self, guiFrame): self.geometry('600x350') guiFrame.expandGrid(0, 0) tipTexts = ['', '', '', ''] options = [ 'Find Parameters', 'Spectrum Widths', 'Diagonal Exclusions', 'Region Peak Find' ] tabbedFrame = TabbedFrame(guiFrame, options=options, grid=(0, 0)) frameA, frameB, frameC, frameD = tabbedFrame.frames self.tabbedFrame = tabbedFrame # Find Params frameA.expandGrid(2, 0) row = 0 label = LabelFrame(frameA, text='Extrema to search for:', grid=(row, 0), gridSpan=(1, 2)) label.expandGrid(0, 1) entries = ['positive and negative', 'positive only', 'negative only'] tipTexts = [ 'Sets whether peak picking within spectra find intensity maxima, minima or both maxima and minima', ] self.extrema_buttons = RadioButtons(label, entries=entries, select_callback=self.apply, direction='horizontal', grid=(0, 0), tipTexts=tipTexts) row += 1 label = LabelFrame(frameA, text='Nearby points to check:', grid=(row, 0), gridSpan=(1, 2)) label.expandGrid(None, 1) entries = ['+-1 in at most one dim', '+-1 allowed in any dim'] tipTexts = [ 'Sets how permissive the peak picking in when searching for intensity extrema; by adding extra points to the selected search region', ] self.adjacent_buttons = RadioButtons(label, entries=entries, select_callback=self.apply, direction='horizontal', grid=(0, 0), tipTexts=tipTexts) row += 1 labelFrame = LabelFrame(frameA, text='Other parameters:', grid=(row, 0), gridSpan=(1, 2)) labelFrame.expandGrid(5, 2) frow = 0 label = Label(labelFrame, text='Scale relative to contour levels:', grid=(frow, 0), sticky='e') tipText = 'Threshold above which peaks are picked, relative to the lowest displayed contour; 1.0 means picking exactly what is visible' self.scale_entry = FloatEntry(labelFrame, grid=(frow, 1), tipText=tipText, returnCallback=self.apply, width=10) self.scale_entry.bind('<Leave>', self.apply, '+') frow += 1 label = Label(labelFrame, text='Exclusion buffer around peaks (in points):', grid=(frow, 0), sticky='e') tipText = 'The size of the no-pick region, in data points, around existing picked peaks; eliminates duplicate picking' self.buffer_entry = IntEntry(labelFrame, returnCallback=self.apply, grid=(frow, 1), width=10, tipText=tipText) self.buffer_entry.bind('<Leave>', self.apply, '+') frow += 1 label = Label(labelFrame, text='Extra thickness in orthogonal dims (in points):', grid=(frow, 0), sticky='e') tipText = 'Sets whether to consider any additional planes (Z dimension) when calculating peak volume integrals' self.thickness_entry = IntEntry(labelFrame, returnCallback=self.apply, width=10, grid=(frow, 1), tipText=tipText) self.thickness_entry.bind('<Leave>', self.apply, '+') frow += 1 label = Label(labelFrame, text='Minimum drop factor (0.0-1.0):', grid=(frow, 0), sticky='e') tipText = '' self.drop_entry = FloatEntry(labelFrame, returnCallback=self.apply, width=10, grid=(frow, 1), tipText=tipText) self.drop_entry.bind('<Leave>', self.apply, '+') frow += 1 label = Label(labelFrame, text='Volume method:', grid=(frow, 0), sticky='e') tipText = 'Selects which method to use to calculate peak volume integrals when peaks are picked; box sizes are specified in "Spectrum Widths"' self.method_menu = PulldownList(labelFrame, texts=PeakBasic.PEAK_VOLUME_METHODS, grid=(frow, 1), callback=self.apply, tipText=tipText) # Spectrum widths frameB.expandGrid(1, 1) label = Label(frameB, text='Spectrum: ') label.grid(row=0, column=0, sticky='e') tipText = 'The spectrum which determines the widths being shown' self.expt_spectrum = PulldownList(frameB, tipText=tipText, callback=self.setSpectrumProperties) self.expt_spectrum.grid(row=0, column=1, sticky='w') self.editLinewidthEntry = FloatEntry(self, text='', returnCallback=self.setLinewidth, width=10) self.editBoxwidthEntry = FloatEntry(self, text='', returnCallback=self.setBoxwidth, width=10) tipTexts = [ 'The number of the spectrum dimension to which the settings apply', 'The nuclear isotope measures in the spectrum dimension', 'The smallest value for the linewidth of a peak for it to be picked', 'The size of the spectrum region to perform the volume integral over' ] headingList = [ 'Dimension', 'Isotope', 'Minimum Linewidth (Hz)', 'Boxwidth' ] editSetCallbacks = [None, None, self.setLinewidth, self.setBoxwidth] editGetCallbacks = [None, None, self.getLinewidth, self.getBoxwidth] editWidgets = [ None, None, self.editLinewidthEntry, self.editBoxwidthEntry ] self.spectrumMatrix = ScrolledMatrix(frameB, initialRows=6, editSetCallbacks=editSetCallbacks, editGetCallbacks=editGetCallbacks, editWidgets=editWidgets, headingList=headingList, callback=self.selectCell, tipTexts=tipTexts) self.spectrumMatrix.grid(row=1, column=0, columnspan=2, sticky='nsew') # Diagonal Exclusions frameC.expandGrid(0, 0) tipTexts = [ 'The isotope as measures on the axis of a spectrum window', 'The distance from the homonuclear diagonal line within which no peak picking can occur' ] self.exclusionEntry = FloatEntry(self, text='', returnCallback=self.setExclusion, width=10) headingList = ['Isotope', 'Diagonal Exclusion (ppm)'] editSetCallbacks = [None, self.setExclusion] editGetCallbacks = [None, self.getExclusion] editWidgets = [None, self.exclusionEntry] self.isotopeMatrix = ScrolledMatrix(frameC, editSetCallbacks=editSetCallbacks, editGetCallbacks=editGetCallbacks, editWidgets=editWidgets, headingList=headingList, grid=(0, 0), tipTexts=tipTexts) # Region peak find self.regionFindPeakList = None self.regionCondition = None self.regionConditions = [] self.regionCol = 1 row = 0 label = Label(frameD, text='Peak List: ', grid=(0, 0)) tipText = 'Selects which peak list to perform region-wide peak picking for' self.regionPeakListPulldown = PulldownList( frameD, callback=self.changeRegionPeakList, grid=(0, 1), tipText=tipText) row += 1 frameD.expandGrid(row, 1) self.regionEntry = FloatEntry(self, text='', returnCallback=self.setRegion, width=10) self.conditionMenu = PulldownList(self, texts=('include', 'exclude'), callback=self.setCondition) tipTexts = [ 'Whether to include or exclude the states region from region-wide peak picking', ] headingList = ['Condition'] editSetCallbacks = [None] editGetCallbacks = [None] editWidgets = [self.conditionMenu] self.regionFindMatrix = ScrolledMatrix( frameD, headingList=headingList, callback=self.selectRegionCell, editWidgets=editWidgets, editGetCallbacks=editGetCallbacks, editSetCallbacks=editSetCallbacks, grid=(row, 0), gridSpan=(1, 2)) row += 1 tipTexts = [ 'Sets the currently selected region row to cover the whole spectrum', 'Add a new region row, which may them be set for exclusion or inclusion when peak picking large areas', 'Remove the selected region specification', 'Go to the panel for setting the parameters that control how peaks extrema are picked', 'Using the stated regions and parameters, perform region-wide peak picking' ] texts = [ 'Whole Region', 'Add Region', 'Delete Region', 'Adjust Params', 'Find Peaks!' ] commands = [ self.wholeRegion, self.addCondition, self.deleteCondition, self.adjustParams, self.regionFindPeaks ] buttons = ButtonList(frameD, texts=texts, commands=commands, grid=(row, 0), gridSpan=(1, 2), tipTexts=tipTexts) buttons.buttons[4].config(bg='#B0FFB0') utilButtons = UtilityButtonList(tabbedFrame.sideFrame, grid=(0, 0), helpUrl=self.help_url, sticky='e') self.dataDim = None self.setParamsEntries() self.updateSpectrum() self.setIsotopeProperties() self.updateRegionPeakLists() self.administerNotifiers(self.registerNotify) def administerNotifiers(self, notifyFunc): # Many more needed here, esp on the AnalysisProject prams for func in ('__init__', 'delete', 'setName'): notifyFunc(self.updateRegionPeakLists, 'ccp.nmr.Nmr.DataSource', func) notifyFunc(self.updateRegionPeakLists, 'ccp.nmr.Nmr.Experiment', func) for func in ('__init__', 'delete'): notifyFunc(self.updateRegionPeakLists, 'ccp.nmr.Nmr.PeakList', func) for clazz in ('Experiment', 'DataSource'): for func in ('__init__', 'delete', 'setName'): notifyFunc(self.updateSpectrumTable, 'ccp.nmr.Nmr.%s' % clazz, func) for func in ('setPeakFindBoxWidth', 'setPeakFindMinLineWidth'): notifyFunc(self.updateSpectrumTable, 'ccpnmr.Analysis.AnalysisDataDim', func) def destroy(self): self.administerNotifiers(self.unregisterNotify) BasePopup.destroy(self) def updateSpectrum(self, spectrum=None): if not spectrum: spectrum = self.spectrum spectra = self.parent.getSpectra() if spectra: if spectrum not in spectra: spectrum = spectra[0] index = spectra.index(spectrum) names = ['%s:%s' % (x.experiment.name, x.name) for x in spectra] else: index = 0 names = [] self.expt_spectrum.setup(names, spectra, index) self.setSpectrumProperties(spectrum) def updateNotifier(self, *extra): self.updateSpectrum() def setLinewidth(self, *event): value = self.editLinewidthEntry.get() if value is not None: PeakFindParams.setPeakFindMinLinewidth(self.dataDim, value) self.setSpectrumProperties(self.dataDim.dataSource) def getLinewidth(self, dataDim): if dataDim: self.editLinewidthEntry.set( PeakFindParams.getPeakFindMinLinewidth(self.dataDim)) def setBoxwidth(self, *event): value = self.editBoxwidthEntry.get() if value is not None: PeakFindParams.setPeakFindBoxwidth(self.dataDim, value) self.setSpectrumProperties(self.dataDim.dataSource) def getBoxwidth(self, dataDim): if dataDim: self.editBoxwidthEntry.set( PeakFindParams.getPeakFindBoxwidth(self.dataDim)) def selectCell(self, object, row, col): self.dataDim = object def setExclusion(self, *extra): isotope = self.isotopeMatrix.currentObject if not isotope: return value = self.exclusionEntry.get() if value is not None: setIsotopeExclusion(isotope, value) self.setIsotopeProperties() def getExclusion(self, isotope): value = getIsotopeExclusion(isotope) self.exclusionEntry.set(value) def setParamsEntries(self): project = self.project params = PeakFindParams.getPeakFindParams(project) self.scale_entry.set(params['scale']) self.buffer_entry.set(params['buffer']) self.thickness_entry.set(params['thickness']) self.drop_entry.set(params['drop']) volumeMethod = params['volumeMethod'] if volumeMethod == 'parabolic fit': volumeMethod = PeakBasic.PEAK_VOLUME_METHODS[0] self.method_menu.set(params['volumeMethod']) if (params['nonadjacent']): n = 1 else: n = 0 self.adjacent_buttons.setIndex(n) have_high = params['haveHigh'] have_low = params['haveLow'] if (have_high and have_low): n = 0 elif (have_high): n = 1 else: n = 2 self.extrema_buttons.setIndex(n) def apply(self, *extra): params = {} params['scale'] = self.scale_entry.get() params['buffer'] = self.buffer_entry.get() params['thickness'] = self.thickness_entry.get() params['drop'] = self.drop_entry.get() params['volumeMethod'] = self.method_menu.getText() n = self.adjacent_buttons.getIndex() if (n == 0): nonadjacent = False else: nonadjacent = True params['nonadjacent'] = nonadjacent n = self.extrema_buttons.getIndex() if (n == 0): have_high = True have_low = True elif (n == 1): have_high = True have_low = False elif (n == 2): have_high = False have_low = True params['haveHigh'] = have_high params['haveLow'] = have_low project = self.project try: PeakFindParams.setPeakFindParams(project, params) except Implementation.ApiError, e: showError('Parameter error', e.error_msg, parent=self)
class RepositoryFrame(Frame): def __init__(self, guiParent, basePopup): # Base popup required to handle notification of data model changes # e.g. new peak lists, so that the GUI can update to the latest # state self.basePopup = basePopup self.guiParent = guiParent # should the screen autorefresh self.autoRefresh = False # add this to shortcuts to ease navigation self.basePopup.frameShortcuts['Repository'] = self # get a port proxy instance # this should probably belong to the repository directly # or else should belong in a dictionary in the main gui # layer when it can be picked up easily # FIXME JMCI # need to work out how to get a number of these! loc = SharedBeanServiceLocator() self.port = loc.getSharedBean() self.registerNotify = basePopup.registerNotify self.unregisterNotify = basePopup.unregisterNotify Frame.__init__(self, guiParent) # set up the grid self.grid_columnconfigure(0, weight=0, minsize=20) self.grid_columnconfigure(1, weight=1, minsize=10) self.grid_columnconfigure(2, weight=0, minsize=20) self.grid_rowconfigure(0, weight=0, minsize=5) self.grid_rowconfigure(1, weight=0, minsize=0) self.grid_rowconfigure(2, weight=0, minsize=10) self.grid_rowconfigure(3, weight=0, minsize=10) self.grid_rowconfigure(4, weight=0, minsize=10) self.grid_rowconfigure(5, weight=1, minsize=10) self.grid_rowconfigure(6, weight=0, minsize=10) self.grid_rowconfigure(7, weight=0, minsize=10) # widgets for view when no data self.noDataWidgets = [] self.noRepLabel = Label(self, text='No repository currently selected.') self.noDataWidgets.append(self.noRepLabel) # widgets for view when current repository set self.dataWidgets = [] self.repTitle = Label(self, text='Repository:', font='Helvetica16') self.dataWidgets.append(self.repTitle) #self.repLabel = Label(self,text='All Projects in Repository') #self.dataWidgets.append(self.repLabel) self.repTree = Tree(self, doubleCallback=self.goto_project_tab) self.dataWidgets.append(self.repTree) sel = 1 if self.autoRefresh: sel = 0 self.autoRefreshSwitchLabel = Label(self, text='Auto Refresh') self.autoRefreshSwitch = RadioButtons(self, ['on', 'off'], select_callback=self.set_refresh, selected_index=sel) # need to decide whether this is static or not r_button_texts = [ 'Add to Basket', ' Import ', ' Export ', ' Refresh ', 'Properties' ] r_button_cmds = [ self.tmpCall, self.import_project, self.export_project, self.drawFrame, self.goto_project_tab ] self.rep_button_list = ButtonList(self, r_button_texts, r_button_cmds) self.dataWidgets.append(self.rep_button_list) self.filterFrame = FilterFrame(self, self.basePopup, text='Filter') self.dataWidgets.append(self.filterFrame) baskets = ('basket1', 'basket2', 'basket3') self.basketSelect = PulldownList(self, self.tmpCall, baskets) self.dataWidgets.append(self.basketSelect) basketElements = ('1ay3', '1ay7') self.basketList = ScrolledListbox(self, basketElements, 25, 18) self.dataWidgets.append(self.basketList) b_button_texts = ['Remove from Basket', 'New Basket'] b_button_cmds = [self.tmpCall, self.tmpCall] self.b_button_list = ButtonList(self, b_button_texts, b_button_cmds) self.dataWidgets.append(self.b_button_list) # draw if not automatically refreshing if sel == 1: self.drawFrame() # set up a loop self.refresh() def drawFrame(self): if self.basePopup.repList.currentRepository == None: for widget in self.dataWidgets: widget.grid_remove() self.noRepLabel.grid(row=1, column=1, sticky='n') else: self.repository = self.basePopup.repList.currentRepository for widget in self.noDataWidgets: widget.grid_remove() # Column headers # want to have a general admin panel; current repository, button to change, info # about login and so on self.repTitle.set('Repository: ' + self.repository.user + '@' + self.repository.name + ' ( ' + self.repository.connect + ' )') self.repTitle.grid(row=1, column=1, sticky='w') # self.repLabel.grid(row=2, column=1, sticky='w') # Repository block #grid and update self.repTree.grid(row=3, column=1, rowspan=3, sticky='nsew') self.updateRepTree() self.autoRefreshSwitchLabel.grid(row=6, column=1, padx=10, sticky='w') self.autoRefreshSwitch.grid(row=6, column=1, padx=10, sticky='e') # the buttons for functionality in repository area self.rep_button_list.grid(row=7, column=1, padx=3, sticky='ew') # filter frame self.filterFrame.grid(row=3, column=2, stick='nsew') # list of baskest. Will callback to change current basket self.basketSelect.grid(row=4, column=2, padx=10, stick='w') # lists projects per basket self.basketList.grid(row=5, rowspan=2, column=2, padx=10, stick='nsew') self.b_button_list.grid(row=7, column=2, padx=5, stick='ew') def openLink(self, node): tree = node.tree par = node.object # this should be associated with the repository object request = getList() # FIXME JMCI # 1. Potentially need to traverse up the node tree # 2. Currently there is bug in expansion/contraction # 3. Search needs to work off proxy method (not off # generated stubs # pass the parent name for now. may need other criteria later h1 = {'name': par.__str__()} h2 = {'project': h1} wsstr_in = WSString(h2) request._arg0 = 'org.pimslims.applet.server.ProjectVersionBean' request._arg1 = 'getListWithFields' request._arg2 = wsstr_in.str # get the response response = self.port.getList(request) # currently we just get a list of numbers. May want to send # all the fields for every object too to cut down on db calls wsstr_out = WSString(response._return) ss = wsstr_out.getStruct() for hm in ss: print 'handling ', hm, ', ', hm['status'].__str__() #if hm['status'].__str__() == 'AVAILABLE': icon = 'text-x-generic' #else: # icon='emblem-readonly' pv = par.__str__() + '::' + hm['versionTag'].__str__() obj = pv text = hm['versionTag'].__str__() callback = None tree.add(node, obj, text, icon, callback) def set_refresh(self, text): print 'setting refresh ', text if text == 'on': self.autoRefresh = True else: self.autoRefresh = False def refresh(self): if self.autoRefresh: print 'refreshing frame ', time.time() self.drawFrame() self.after(5000, self.refresh) # FIME JMCI # it would probably be a good idea to have a method that allowed # a user to unlock a given project version. Would need to check # permissions very carefully, though def unlock_project_version(self): pass def goto_project_tab(self, node=None): if node is None: # get the selected node selected_nodes = self.repTree.getSelectedNodes() # restrict the choice to one node = selected_nodes[0] # we really need to traverse the tree a lot more carefully pv = node.object.__str__() print 'GOTO PROJECT ', pv, ', ', node, ', ', node.object pat = re.compile('::') matcher = pat.search(pv, 0) name = pv[0:matcher.start()] versionTag = pv[matcher.end():] print 'GOTO PROJECT ', name, ', ', versionTag #versionTag = node.object.__str__() #name = node.parent.object.__str__() #print node.__dict__ #print node.parent.__dict__ self.basePopup.repList.currentRepository.currentProjectName = name self.basePopup.repList.currentRepository.currentVersionTag = versionTag # this is going to have to be keyed on a natural key that then # gets set into the criteria of a ws query # hack for now. build in later. Essentially, we have to handle two # cases; that of a specific projectVersion request and that of a # request on a project alone. Probably the best behaviour would be # for the project-only request to default to the latest trunk # version of the project and the most elegent way of triggering # this would probably be to have this as a property of the project # returned in the main hash from Project.getFields(). self.basePopup.tabbedFrame.select(1) if self.basePopup.frameShortcuts.has_key('Project'): self.basePopup.frameShortcuts['Project'].drawFrame() def import_project(self): # FIXME JMCI # need to preserve the current status. Take default from the # Wms layer rootDir = self.basePopup.repList.current_import_dir fileSelectPopup = FileSelectPopup(self, None, rootDir) new_project_dir = fileSelectPopup.getDirectory() self.basePopup.repList.current_import_dir = new_project_dir print 'in import project with directory', new_project_dir idx = new_project_dir.rfind('/') new_project_name = new_project_dir[idx + 1:] print 'in import project with project', new_project_name # FIXME # need to set the project version number somewhere. For now set to none # and this gets picked up and set to a default 1.1 later self.repository.import_project(new_project_name, None, new_project_dir) self.drawFrame() def export_project(self): # get the selected node selected_nodes = self.repTree.getSelectedNodes() # restrict the choice to one node = selected_nodes[0] # we really need to traverse the tree a lot more carefully name = node.parent.object.__str__() versionTag = node.object.__str__()[len(name) + 2:] # need to preserve the current status. Take a default from the # Wms layer rootDir = self.basePopup.repList.current_export_dir # This should be obtained from a query box. Hard code for now fileSelectPopup = FileSelectPopup(self, None, rootDir) exp_project_dir = fileSelectPopup.getDirectory() self.basePopup.repList.current_export_dir = exp_project_dir self.repository.export_project(name, versionTag, exp_project_dir) def disconnectRepository(self): # do we need to formally break a connection and destroy the session? # yes we probably should. # need an "are you sure" dialog box # need to protect self.repository.repList.repositories.remove(self.repository) self.grid_remove() for ff in self.guiParent.guiParent.parent.frames[0].children.values(): ff.drawFrame() def tmpCall(self): return # This will need a separate call to the WS with an additional # criterion (picking up the checkout version) def updateRepTree(self): texts = [] icons = [] parents = [] callbacks = [] objects = [] # OK, this would be a good point to access the list # this should be associated with the repository object loc = SharedBeanServiceLocator() port = loc.getSharedBean() request = getList() # these are actually static request._arg0 = 'org.pimslims.applet.server.ProjectBean' request._arg1 = 'getList' request._arg2 = '' # get the response response = port.getList(request) # this is a hack at present. It needs to be written properly wsstr = WSString(response._return) ss = wsstr.getStruct() for strg in ss: texts.append(strg) icons.append('folder') parents.append(None) objects.append(strg) callbacks.append(self.openLink) print 'UPDATE ', ss print 'UPDATE ', len(ss) if len(ss) > 0: print 'UPDATE: updating ' self.repTree.update(parents, objects, texts, icons, callbacks) def administerNotifiers(self, notifyFunc): for func in ('__init__', 'delete', 'setName'): notifyFunc(self.updateAllAfter, 'ccp.nmr.Nmr.Experiment', func) notifyFunc(self.updateAllAfter, 'ccp.nmr.Nmr.DataSource', func) def updateAllAfter(self, obj): self.after_idle(self.updateAll) def updateAll(self, project=None): return def quit(self): self.guiParent.parent.destroy() def destroy(self): self.administerNotifiers(self.basePopup.unregisterNotify) Frame.destroy(self)
def __init__(self, guiParent, basePopup): self.guiParent = guiParent self.basePopup = basePopup # selection hash. This needs to be stored so that we can # refresh with the same criteria self.select = None # should the screen autorefresh self.autoRefresh = False # add this to shortcuts to ease navigation self.basePopup.frameShortcuts['Tasks'] = self #self.registerNotify=basePopup.registerNotify #self.unregisterNotify=basePopup.unregisterNotify #self.frames = [] # FIXME JMCI # This frame is specific for a single repository so we need a # method for identifying one from the whole set (or could have # subtabs) Frame.__init__(self, guiParent) # set up the grid self.grid_columnconfigure(0, weight=0, minsize=20) self.grid_columnconfigure(1, weight=1, minsize=30) self.grid_columnconfigure(2, weight=0, minsize=40) self.grid_rowconfigure(0, weight=0, minsize=20) self.grid_rowconfigure(1, weight=0, minsize=10) self.grid_rowconfigure(2, weight=0, minsize=0) self.grid_rowconfigure(3, weight=0, minsize=0) self.grid_rowconfigure(4, weight=0, minsize=0) self.grid_rowconfigure(5, weight=1, minsize=0) self.grid_rowconfigure(6, weight=0, minsize=10) self.grid_rowconfigure(7, weight=0, minsize=10) initial_cols = ['ID','Task','User','Status'] self.task_matrix = ScrolledMatrix(self, headingList=initial_cols, initialRows=15, doubleCallback=self.goto_task_tab) # Filters for narrowing down tasks. should probably code this # specifically inside this package #self.filter = FilterFrame(self, self.basePopup, text='Filter') self.filter = TaskFilterFrame(self, self.basePopup, text='Filter') # Frame for controlling the main client side daemon # seems to be a problem. add a simple button for now opts = ['Client','Server'] self.daemonFrame = TabbedFrame(self, options=opts, toggleOff=False, selected=0) self.daemonSwitchLabel = Label(self, text= 'Task Daemon') self.daemonSwitch = RadioButtons(self, ['on', 'off'], select_callback=self.set_daemon, selected_index = 1) sel = 1 if self.autoRefresh: sel = 0 self.autoRefreshSwitchLabel = Label(self, text= 'Auto Refresh') self.autoRefreshSwitch = RadioButtons(self, ['on', 'off'], select_callback=self.set_refresh, selected_index = sel) self.label_rep = Label(self, text='', font='Helvetica16') # set up a loop self.refresh()
def __init__(self, guiParent, basePopup): # Base popup required to handle notification of data model changes # e.g. new peak lists, so that the GUI can update to the latest # state self.basePopup = basePopup self.guiParent = guiParent # should the screen autorefresh self.autoRefresh = False # add this to shortcuts to ease navigation self.basePopup.frameShortcuts['Repository'] = self # get a port proxy instance # this should probably belong to the repository directly # or else should belong in a dictionary in the main gui # layer when it can be picked up easily # FIXME JMCI # need to work out how to get a number of these! loc = SharedBeanServiceLocator() self.port = loc.getSharedBean() self.registerNotify = basePopup.registerNotify self.unregisterNotify = basePopup.unregisterNotify Frame.__init__(self, guiParent) # set up the grid self.grid_columnconfigure(0, weight=0, minsize=20) self.grid_columnconfigure(1, weight=1, minsize=10) self.grid_columnconfigure(2, weight=0, minsize=20) self.grid_rowconfigure(0, weight=0, minsize=5) self.grid_rowconfigure(1, weight=0, minsize=0) self.grid_rowconfigure(2, weight=0, minsize=10) self.grid_rowconfigure(3, weight=0, minsize=10) self.grid_rowconfigure(4, weight=0, minsize=10) self.grid_rowconfigure(5, weight=1, minsize=10) self.grid_rowconfigure(6, weight=0, minsize=10) self.grid_rowconfigure(7, weight=0, minsize=10) # widgets for view when no data self.noDataWidgets = [] self.noRepLabel = Label(self, text='No repository currently selected.') self.noDataWidgets.append(self.noRepLabel) # widgets for view when current repository set self.dataWidgets = [] self.repTitle = Label(self, text='Repository:', font='Helvetica16') self.dataWidgets.append(self.repTitle) #self.repLabel = Label(self,text='All Projects in Repository') #self.dataWidgets.append(self.repLabel) self.repTree = Tree(self, doubleCallback=self.goto_project_tab) self.dataWidgets.append(self.repTree) sel = 1 if self.autoRefresh: sel = 0 self.autoRefreshSwitchLabel = Label(self, text='Auto Refresh') self.autoRefreshSwitch = RadioButtons(self, ['on', 'off'], select_callback=self.set_refresh, selected_index=sel) # need to decide whether this is static or not r_button_texts = [ 'Add to Basket', ' Import ', ' Export ', ' Refresh ', 'Properties' ] r_button_cmds = [ self.tmpCall, self.import_project, self.export_project, self.drawFrame, self.goto_project_tab ] self.rep_button_list = ButtonList(self, r_button_texts, r_button_cmds) self.dataWidgets.append(self.rep_button_list) self.filterFrame = FilterFrame(self, self.basePopup, text='Filter') self.dataWidgets.append(self.filterFrame) baskets = ('basket1', 'basket2', 'basket3') self.basketSelect = PulldownList(self, self.tmpCall, baskets) self.dataWidgets.append(self.basketSelect) basketElements = ('1ay3', '1ay7') self.basketList = ScrolledListbox(self, basketElements, 25, 18) self.dataWidgets.append(self.basketList) b_button_texts = ['Remove from Basket', 'New Basket'] b_button_cmds = [self.tmpCall, self.tmpCall] self.b_button_list = ButtonList(self, b_button_texts, b_button_cmds) self.dataWidgets.append(self.b_button_list) # draw if not automatically refreshing if sel == 1: self.drawFrame() # set up a loop self.refresh()
class PopupTemplate(BasePopup): def __init__(self, parent, project=None, *args, **kw): self.project = project self.parent = parent self.objects = self.getObjects() self.object = None BasePopup.__init__(self, parent=parent, title='Popup Template', **kw) self.updateObjects() def body(self, mainFrame): mainFrame.grid_columnconfigure(1, weight=1, minsize=100) mainFrame.config(borderwidth=5, relief='solid') row = 0 label = Label(mainFrame, text="Frame (with sub-widgets):") label.grid(row=row, column=0, sticky=Tkinter.E) frame = Frame(mainFrame, relief='raised', border=2, background='#8080D0') # Frame expands East-West frame.grid(row=row, column=1, sticky=Tkinter.EW) # Last column expands => Widgets pusted to the West frame.grid_columnconfigure(3, weight=1) # Label is within the sub frame label = Label(frame, text='label ') label.grid(row=0, column=0, sticky=Tkinter.W) entry = Entry(frame, text='Entry', returnCallback=self.showWarning) entry.grid(row=0, column=1, sticky=Tkinter.W) self.check = CheckButton(frame, text='Checkbutton', selected=True, callback=self.updateObjects) self.check.grid(row=0, column=2, sticky=Tkinter.W) # stick a button to the East wall button = Button(frame, text='Button', command=self.pressButton) button.grid(row=0, column=3, sticky=Tkinter.E) row += 1 label = Label(mainFrame, text="Text:") label.grid(row=row, column=0, sticky=Tkinter.E) self.textWindow = Text(mainFrame, text='Initial Text\n', width=60, height=5) self.textWindow.grid(row=row, column=1, sticky=Tkinter.NSEW) row += 1 label = Label(mainFrame, text="CheckButtons:") label.grid(row=row, column=0, sticky=Tkinter.E) entries = ['Alpha','Beta','Gamma','Delta'] selected = entries[2:] self.checkButtons = CheckButtons(mainFrame, entries, selected=selected,select_callback=self.changedCheckButtons) self.checkButtons.grid(row=row, column=1, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="PartitionedSelector:") label.grid(row=row, column=0, sticky=Tkinter.E) labels = ['Bool','Int','Float','String'] objects = [type(0),type(1),type(1.0),type('a')] selected = [type('a')] self.partitionedSelector= PartitionedSelector(mainFrame, labels=labels, objects=objects, colors = ['red','yellow','green','#000080'], callback=self.toggleSelector,selected=selected) self.partitionedSelector.grid(row=row, column=1, sticky=Tkinter.EW) row += 1 label = Label(mainFrame, text="PulldownMenu") label.grid(row=row, column=0, sticky=Tkinter.E) entries = ['Frodo','Pipin','Merry','Sam','Bill','Gandalf','Strider','Gimli','Legolas'] self.pulldownMenu = PulldownMenu(mainFrame, callback=self.selectPulldown, entries=entries, selected_index=2, do_initial_callback=False) self.pulldownMenu.grid(row=row, column=1, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="RadioButtons in a\nScrolledFrame.frame:") label.grid(row=row, column=0, sticky=Tkinter.EW) frame = ScrolledFrame(mainFrame, yscroll = False, doExtraConfig = True, width=100) frame.grid(row=row, column=1, sticky=Tkinter.EW) frame.grid_columnconfigure(0, weight=1) self.radioButtons = RadioButtons(frame.frame, entries=entries, select_callback=self.checkRadioButtons, selected_index=1, relief='groove') self.radioButtons.grid(row=0, column=0, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="LabelFrame with\nToggleLabels inside:") label.grid(row=row, column=0, sticky=Tkinter.E) labelFrame = LabelFrame(mainFrame, text='Frame Title') labelFrame.grid(row=row, column=1, sticky=Tkinter.NSEW) labelFrame.grid_rowconfigure(0, weight=1) labelFrame.grid_columnconfigure(3, weight=1) self.toggleLabel1 = ToggleLabel(labelFrame, text='ScrolledMatrix', callback=self.toggleFrame1) self.toggleLabel1.grid(row=0, column=0, sticky=Tkinter.W) self.toggleLabel1.arrowOn() self.toggleLabel2 = ToggleLabel(labelFrame, text='ScrolledGraph', callback=self.toggleFrame2) self.toggleLabel2.grid(row=0, column=1, sticky=Tkinter.W) self.toggleLabel3 = ToggleLabel(labelFrame, text='ScrolledCanvas', callback=self.toggleFrame3) self.toggleLabel3.grid(row=0, column=2, sticky=Tkinter.W) row += 1 mainFrame.grid_rowconfigure(row, weight=1) label = Label(mainFrame, text="changing/shrinking frames:") label.grid(row=row, column=0, sticky=Tkinter.E) self.toggleRow = row self.toggleFrame = Frame(mainFrame) self.toggleFrame.grid(row=row, column=1, sticky=Tkinter.NSEW) self.toggleFrame.grid_rowconfigure(0, weight=1) self.toggleFrame.grid_columnconfigure(0, weight=1) # option 1 self.intEntry = IntEntry(self, returnCallback = self.setNumber, width=8) self.multiWidget = MultiWidget(self, Entry, options=None, values=None, callback=self.setKeywords, minRows=3, maxRows=5) editWidgets = [None, None, self.intEntry, self.multiWidget] editGetCallbacks = [None, None, self.getNumber, self.getKeywords] editSetCallbacks = [None, None, self.setNumber, self.setKeywords] headingList = ['Name','Color','Number','Keywords'] self.scrolledMatrix = ScrolledMatrix(self.toggleFrame, headingList=headingList, editSetCallbacks=editSetCallbacks, editGetCallbacks=editGetCallbacks, editWidgets=editWidgets, callback=self.selectObject, multiSelect=False) self.scrolledMatrix.grid(row=0, column=0, sticky=Tkinter.NSEW) # option 2 self.scrolledGraph = ScrolledGraph(self.toggleFrame, width=400, height=300, symbolSize=5, symbols=['square','circle'], dataColors=['#000080','#800000'], lineWidths=[0,1] ) self.scrolledGraph.setZoom(1.3) dataSet1 = [[0,0],[1,1],[2,4],[3,9],[4,16],[5,25]] dataSet2 = [[0,0],[1,3],[2,6],[3,9],[4,12],[5,15]] self.scrolledGraph.update(dataSets=[dataSet1,dataSet2], xLabel = 'X axis label', yLabel = 'Y axis label', title = 'Main Title') self.scrolledGraph.draw() # option 3 self.scrolledCanvas = ScrolledCanvas(self.toggleFrame,relief = 'groove', borderwidth = 2, resizeCallback=None) canvas = self.scrolledCanvas.canvas font = 'Helvetica 10' box = canvas.create_rectangle(10,10,150,200, outline='grey', fill='grey90') line = canvas.create_line(0,0,200,200,fill='#800000', width=2) text = canvas.create_text(120,50, text='Text', font=font, fill='black') circle = canvas.create_oval(30,30,50,50,outline='#008000',fill='#404040',width=3) row += 1 label = Label(mainFrame, text="FloatEntry:") label.grid(row=row, column=0, sticky=Tkinter.E) self.floatEntry = FloatEntry(mainFrame, text=3.14159265, returnCallback=self.floatEntryReturn) self.floatEntry.grid(row=row, column=1, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="Scale:") label.grid(row=row, column=0, sticky=Tkinter.E) self.scale = Scale(mainFrame, from_=10, to=90, value=50, orient=Tkinter.HORIZONTAL) self.scale.grid(row=row, column=1, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="Value Ramp:") label.grid(row=row, column=0, sticky=Tkinter.E) self.valueRamp = ValueRamp(mainFrame, self.valueRampCallback, speed = 1.5, delay = 50) self.valueRamp.grid(row=row, column=1, sticky=Tkinter.W) row += 1 label = Label(mainFrame, text="ButtonList:") label.grid(row=row, column=0, sticky=Tkinter.E) texts = ['Select File','Close','Quit'] commands = [self.selectFile, self.close, self.quit] bottomButtons = ButtonList(mainFrame, texts=texts, commands=commands, expands=True) bottomButtons.grid(row=row, column=1, sticky=Tkinter.EW) self.protocol('WM_DELETE_WINDOW', self.quit) def floatEntryReturn(self, event): value = self.floatEntry.get() self.textWindow.setText('%s\n' % value) def selectObject(self, object, row, col): self.object = object def getKeywords(self, object): if object : values = object.keywords self.multiWidget.set(values) def setKeywords(self, event): values = self.multiWidget.get() self.object.keywords = values self.updateObjects() def getNumber(self, object): if object : self.intEntry.set(object.quantity) def setNumber(self, event): value = self.intEntry.get() self.object.quantity = value self.updateObjects() def toggleFrame1(self, isHidden): if isHidden: self.scrolledMatrix.grid_forget() self.toggleFrame.grid_forget() else: self.scrolledGraph.grid_forget() self.scrolledCanvas.grid_forget() self.scrolledMatrix.grid(row=0, column=0, sticky=Tkinter.NSEW) self.toggleFrame.grid(row=self.toggleRow, column=1,sticky=Tkinter.NSEW) self.toggleLabel2.arrowOff() self.toggleLabel3.arrowOff() def toggleFrame2(self, isHidden): if isHidden: self.scrolledGraph.grid_forget() self.toggleFrame.grid_forget() else: self.scrolledMatrix.grid_forget() self.scrolledCanvas.grid_forget() self.scrolledGraph.grid(row=0, column=0, sticky=Tkinter.NSEW) self.toggleFrame.grid(row=self.toggleRow, column=1,sticky=Tkinter.NSEW) self.toggleLabel1.arrowOff() self.toggleLabel3.arrowOff() def toggleFrame3(self, isHidden): if isHidden: self.scrolledCanvas.grid_forget() self.toggleFrame.grid_forget() else: self.scrolledMatrix.grid_forget() self.scrolledGraph.grid_forget() self.scrolledCanvas.grid(row=0, column=0, sticky=Tkinter.NSEW) self.toggleFrame.grid(row=self.toggleRow, column=1,sticky=Tkinter.NSEW) self.toggleLabel1.arrowOff() self.toggleLabel2.arrowOff() def valueRampCallback(self, value): self.textWindow.setText('%s\n' % value) def checkRadioButtons(self, value): self.textWindow.setText('%s\n' % value) def selectPulldown(self, index, name): self.textWindow.setText('%d, %s\n' % (index, name)) def toggleSelector(self, value): self.textWindow.setText('%s\n' % value) def changedCheckButtons(self, values): self.textWindow.setText(','.join(values) + '\n') def getObjects(self): objects = [] objects.append( Fruit('Lemon', '#FFFF00',1,keywords=['Bitter','Tangy'] ) ) objects.append( Fruit('Orange', '#FF8000',4 ) ) objects.append( Fruit('Banana', '#FFF000',5 ) ) objects.append( Fruit('Pinapple','#FFD000',9 ) ) objects.append( Fruit('Kiwi', '#008000',12) ) objects.append( Fruit('Lime', '#00FF00',2 ) ) objects.append( Fruit('Apple', '#800000',5,keywords=['Crunchy'] ) ) objects.append( Fruit('Pear', '#408000',6 ) ) objects.append( Fruit('Peach', '#FFE0C0',2,keywords=['Sweet','Furry'] ) ) objects.append( Fruit('Plumb', '#800080',7 ) ) return objects def updateObjects(self, event=None): textMatrix = [] objectList = [] colorMatrix = [] for object in self.objects: datum = [] datum.append( object.name ) datum.append( None ) datum.append( object.quantity ) datum.append( ','.join(object.keywords) ) colors = [None, object.color, None, None] textMatrix.append(datum) objectList.append(object) colorMatrix.append(colors) if self.check.get(): self.scrolledMatrix.update(textMatrix=textMatrix, objectList=objectList) else: self.scrolledMatrix.update(textMatrix=textMatrix, objectList=objectList, colorMatrix=colorMatrix) def selectFile(self): fileSelectPopup = FileSelectPopup(self, title = 'Choose file', dismiss_text = 'Cancel', selected_file_must_exist = True) fileName = fileSelectPopup.getFile() self.textWindow.setText('File Selected: %s\n' % fileName) def showWarning(self, eventObject): self.textWindow.setText('Text Entry Return Pressed\n') showWarning('Warning Title','Warning Message') return def pressButton(self): self.textWindow.setText('Button Pressed\n') if showYesNo('Title','Prompt: Clear text window?'): self.textWindow.clear() return def quit(self): BasePopup.destroy(self)
def body(self, guiFrame): self.geometry('450x500') guiFrame.grid_rowconfigure(0, weight=1) guiFrame.grid_columnconfigure(0, weight=1) options = ['Peak Separator', 'Advanced Settings'] tabbedFrame = TabbedFrame(guiFrame, options=options) tabbedFrame.grid(row=0, column=0, sticky='nsew') buttons = UtilityButtonList(tabbedFrame.sideFrame, helpUrl=self.help_url) buttons.grid(row=0, column=0, sticky='e') self.tabbedFrame = tabbedFrame frameA, frameB = tabbedFrame.frames # # FrameA : Main Settings # frameA.grid_columnconfigure(1, weight=1) row = 0 # Label row row += 1 div = LabelDivider(frameA, text='Peak Separator Parameters') div.grid(row=row, column=0, columnspan=2, sticky='ew') row += 1 label = Label(frameA, text='Min. number of peaks:') label.grid(row=row, column=0, sticky='w') self.minPeaksEntry = IntEntry(frameA, returnCallback=self.applyChange, width=10, \ tipText='Minimum number of peaks to find (must be > 0)') self.minPeaksEntry.grid(row=row, column=1, sticky='n') self.minPeaksEntry.bind('<Leave>', self.applyChange, '+') row += 1 label = Label(frameA, text='Max. number of peaks:') label.grid(row=row, column=0, sticky='w') self.maxPeaksEntry = IntEntry(frameA, returnCallback=self.applyChange, width=10, \ tipText='Maximum number of peaks to find (0 is unlimited - not recommended)') self.maxPeaksEntry.grid(row=row, column=1, sticky='n') self.maxPeaksEntry.bind('<Leave>', self.applyChange, '+') row += 1 label = Label(frameA, text='Only pick positive peaks:') label.grid(row=row, column=0, sticky='w') entries = ['False', 'True'] self.posPeaksButtons = RadioButtons( frameA, entries=entries, select_callback=self.applyChange, direction='horizontal', tipTexts=[ 'Search for both positive and negative intensity peaks', 'Limit search to only positive peaks' ]) self.posPeaksButtons.grid(row=row, column=1, sticky='n') row += 1 label = Label(frameA, text='Peak Model:') label.grid(row=row, column=0, sticky='w') ### G/L Mixture works, but volume calculation involves Gamma function # entries = ['Gaussian', 'Lorentzian', 'G/L Mixture'] entries = ['Gaussian', 'Lorentzian'] self.shapeButtons = RadioButtons( frameA, entries=entries, select_callback=self.applyChange, direction='horizontal', tipTexts=[ 'Choose a Gaussian model peak shape to fit to peaks', 'Choose a Lorentzian model peak shape to fit to peaks' ]) self.shapeButtons.grid(row=row, column=1, sticky='n') row += 1 div = LabelDivider(frameA, text='Region', tipText='Region that search will limit itself to') div.grid(row=row, column=0, columnspan=2, sticky='ew') row += 1 label = Label(frameA, text='Peak List:') label.grid(row=row, column=0, sticky='nw') self.peakListPulldown = PulldownList( frameA, callback=self.setManuallyPickPeakList, tipText='Select which peak list new peaks are to be added to') self.peakListPulldown.grid(row=row, column=1, sticky='nw') # tricky scrolled matrix row += 1 self.regionTable = None frameA.grid_rowconfigure(row, weight=1) headings = ('dim.', 'start (ppm)', 'end (ppm)', 'actual size') self.editDimEntry = IntEntry(self, returnCallback=self.applyChange, width=5, tipText='Dimension number') self.editStartEntry = FloatEntry(self, returnCallback=self.applyChange, width=5, tipText='Search area lower bound') self.editEndEntry = FloatEntry(self, returnCallback=self.applyChange, width=5, tipText='Search area upper bound') editWidgets = [ self.editDimEntry, self.editStartEntry, self.editEndEntry, None ] editGetCallbacks = [None, None, None, None] editSetCallbacks = [None, None, None, None] self.regionTable = ScrolledMatrix(frameA, headingList=headings, multiSelect=False, editWidgets=editWidgets, editGetCallbacks=editGetCallbacks, editSetCallbacks=editSetCallbacks, initialRows=5) self.regionTable.grid(row=row, column=0, columnspan=2, sticky='nsew') # Run Button row += 1 texts = ['Add Region'] commands = [self.updateFromRegion] self.addResetButtons = ButtonList( frameA, texts=texts, commands=commands, tipTexts=['Add selected specrtral region']) self.addResetButtons.grid(row=row, column=0, columnspan=2, sticky='ew') row += 1 texts = ['Separate Peaks'] commands = [self.runPeakSeparator] self.runButton = ButtonList(frameA, texts=texts, commands=commands, expands=True, tipTexts=['Run peak search now']) self.runButton.grid(row=row, column=0, columnspan=2, sticky='nsew') # # FrameB : Further Settings # frameB.grid_columnconfigure(0, weight=1) row = 0 div = LabelDivider(frameB, text='Rate:') div.grid(row=row, column=0, columnspan=2, sticky='ew') row += 1 label = Label(frameB, text='Rate of MCMC step size change') label.grid(row=row, column=0, columnspan=1, sticky='w') self.rateEntry = FloatEntry(frameB, returnCallback=self.applyChange, width=10, \ tipText='Rate effects speed of run, smaller values take longer but may produce better results') self.rateEntry.grid(row=row, column=1, sticky='n') self.rateEntry.bind('<Leave>', self.applyChange, '+') self.rateEntry.set(self.params.rate) # tricky scrolled matrix for line width row += 2 div = LabelDivider(frameB, text='Line Width (Hz):') div.grid(row=row, column=0, columnspan=2, sticky='ew') row += 1 label = Label(frameB, text="Descr.") label.grid(row=row, rowspan=2, column=0, sticky='w') row += 1 self.lineWidthTable = None frameB.grid_rowconfigure(row, weight=1) lineWidthHeadings = ('dim.', 'min. σ (Hz)', 'max. σ (Hz)') self.editMinSigmaEntry = FloatEntry(self, returnCallback=self.applyChange, width=5, tipText='Minimum line width (Hz)') self.editMaxSigmaEntry = FloatEntry(self, returnCallback=self.applyChange, width=5, tipText='Maximum line width (Hz)') # self.editDimEntry is also from regionTable initialWidthRows = 4 editLineWidthWidgets = [ None, self.editMinSigmaEntry, self.editMaxSigmaEntry ] editLineWidthGetCallbacks = [None, self.getSigmaMin, self.getSigmaMax] editLineWidthSetCallbacks = [None, self.setSigmaMin, self.setSigmaMax] self.lineWidthTable = ScrolledMatrix( frameB, headingList=lineWidthHeadings, multiSelect=False, editWidgets=editLineWidthWidgets, editGetCallbacks=editLineWidthGetCallbacks, editSetCallbacks=editLineWidthSetCallbacks, initialRows=initialWidthRows) self.lineWidthTable.grid(row=row, column=0, columnspan=2, sticky='nsew') # option to 'repick' exisiting peak list row += initialWidthRows div = LabelDivider(frameB, text='(optional - repick entire peak list)') div.grid(row=row, column=0, columnspan=2, sticky='ew') row += 1 self.repickListPulldown = PulldownList( frameB, callback=self.setRePickPeakList, tipText= 'Select which peak list to repick (new peaks will be put into a new peak list)' ) self.repickListPulldown.grid(row=row, column=0, sticky='nw') texts = ['Repick Peak List'] commands = [self.runRepickPeaks] self.runButton = ButtonList( frameB, texts=texts, commands=commands, expands=True, tipTexts=['Repick selected peak list into a new peak list.']) self.runButton.grid(row=row, column=1, columnspan=1, sticky='nsew') row += 1 div = LabelDivider(frameB) row += 1 texts = ['Separate Peaks'] commands = [self.runPeakSeparator] self.runButton = ButtonList(frameB, texts=texts, commands=commands, expands=True, tipTexts=['Run peak search now']) self.runButton.grid(row=row, column=0, columnspan=2, sticky='nsew') self.setWidgetEntries() self.administerNotifiers(self.registerNotify)
class PrintWindowPopup(BasePopup): """ **Print Window to Output File** The purpose of this dialog is to allow the saving of the drawing of one of the spectrum windows to a file, in one of the following formats: PostScript (PS), Encapsulated PostScript (EPS) or Portable Document Format (PDF). The one window that is being printed out is specified at the top. There are four tabs. The first one, Options, is the most important. In particular, it is used to specify the File name. At its simplest to print out a window you just need to specify the File name, and then click "Save Print File". But it is likely you will at the very least want to change some of the settings in the Options tab. You can specify a Title and a label for the X axis and/or Y axis. This tab is also used to specify the Paper size (default A4), the Orientation of the paper (default Portrait), whether the printout is Color or Black and white (the Style, default Color), and what the Format is (PS, EPS or PDF, default PS). The ticks for the rulers can be chosen to be Inside or Outside the main frame and can be in any combination of the Top, Bottom, Left or Right side of the main frame. The Tick Font includes the option of not printing the tick labels at all. The Tick spacing between the major and minor ticks can be set automatically (so the program determines it) or manually. For the latter the user has to specify the Major and Minor spacings in terms of the unit of the display (normally ppm), and also the number of decimal places for the Tick labels. How the main frame fits into the paper is determined by the Scaling option. The Percentage option just means that the main frame is scaled by that amount relative to the biggest size it could be and still fit on the paper. The remaining options are if you want to specify the cms or inches per unit (normally ppm), or the inverse of these. In this case it could be the case that the main frame actually exceeds the size of the paper. You can also include the Time and Date and/or the File Name in the printout, and you can specify the font used for this. The same font is used for the Title and X and Y axis labels, except that the Title font is 6 pts bigger. Finally, you can also set the linewidth, in points (the default is 0.1). The other three tabs provide fine tuning of what is output. In many cases they can be ignored. The Spectra tab lets you choose settings for which of the window's spectra are drawn, in terms of both the positive and negative contours. This is independent of what is actually drawn on the screen. But you need to check the "Use below settings when printing" checkbutton if you want the values specified here to be used rather than the screen settings. The values in the table are initially set to be the screen values but afterwards can only be changed manually. Clicking on the "Reset Selected" button changes the values in the table to the current screen ones. The Peak Lists tab is similar, except it applies to the peak lists in the window rather than the spectra. Again, if you want the values in the table to be used then you need to check the "Use below settings when printing" checkbutton. The Region tab is for specifying the region for the x, y and orthogonal axes, if you do not want to use the regions as seen in the window on the screen. Again, you have to check "Use override region when printing" checkbutton to actually have the values in the table be used in the printout. By default, the override region is set to the current window region if it is not set already, otherwise it is left to the previous value unless you click the "Set Region from Window" or the "Set Width from Window" or the "Set Center from Window" buttons. And the override region can be specified either using the min and max values of the region, or the center and width. """ def __init__(self, parent, *args, **kw): self.waiting = False title='Window : Print Window' BasePopup.__init__(self, parent=parent, title=title, **kw) def body(self, guiFrame): self.geometry('600x350') project = self.project analysisProject = self.analysisProject guiFrame.grid_columnconfigure(1, weight=1) row = 0 frame = Frame(guiFrame, grid=(0,0)) label = Label(frame, text=' Window:', grid=(0,0)) self.windowPulldown = PulldownList(frame, grid=(0,1), tipText='The window that will be printed out', callback=self.selectWindow) tipTexts = ['For the window pulldown, show all of the spectrum windows in the current project, irrespective of the active group', 'For the window pulldown, show only spectrum windows that are in the currently active window group'] self.whichWindows = RadioButtons(frame, grid=(0,2), entries=ACTIVE_OPTIONS, tipTexts=tipTexts, select_callback=self.updateWindows) texts = [ 'Save Print File' ] tipTexts = [ 'Save the printout to the specified file' ] commands = [ self.saveFile ] buttons = UtilityButtonList(guiFrame, helpUrl=self.help_url, grid=(row,2), commands=commands, texts=texts, tipTexts=tipTexts) self.buttons = buttons buttons.buttons[0].config(bg='#B0FFB0') row += 1 guiFrame.grid_rowconfigure(row, weight=1) options = ['Options', 'Spectra', 'Peak Lists', 'Region'] tipTexts = ['Optional settings for spectra', 'Optional settings for peak lists', 'Optional settings for the region'] tabbedFrame = TabbedFrame(guiFrame, options=options, tipTexts=tipTexts) tabbedFrame.grid(row=row, column=0, columnspan=3, sticky='nsew') self.tabbedFrame = tabbedFrame optionFrame, spectrumFrame, peakListFrame, regionFrame = tabbedFrame.frames optionFrame.expandGrid(0, 0) getOption = lambda key, defaultValue: PrintBasic.getPrintOption(analysisProject, key, defaultValue) setOption = lambda key, value: PrintBasic.setPrintOption(analysisProject, key, value) self.printFrame = PrintFrame(optionFrame, getOption=getOption, grid=(0,0), gridSpan=(1,1), setOption=setOption, haveTicks=True, doOutlineBox=False) spectrumFrame.expandGrid(0, 0) frame = Frame(spectrumFrame, grid=(0,0), gridSpan=(1,1)) frame.expandGrid(1,0) self.overrideSpectrum = CheckButton(frame, text='Use below settings when printing', tipText='Use below settings when printing instead of the window values', grid=(0,0), sticky='w') tipText = 'Change the settings of the selected spectra back to their window values' button = Button(frame, text='Reset Selected', tipText=tipText, command=self.resetSelected, grid=(0,1), sticky='e') self.posColorPulldown = PulldownList(self, callback=self.setPosColor) self.negColorPulldown = PulldownList(self, callback=self.setNegColor) headings = ['Spectrum', 'Pos. Contours\nDrawn', 'Neg. Contours\nDrawn', 'Positive\nColours', 'Negative\nColours'] tipTexts = ['Spectrum in window', 'Whether the positive contours should be drawn', 'Whether the negative contours should be drawn', 'Colour scheme for positive contours (can be a single colour)', 'Colour scheme for negative contours (can be a single colour)'] editWidgets = [ None, None, None, self.posColorPulldown, self.negColorPulldown] editGetCallbacks = [ None, self.togglePos, self.toggleNeg, self.getPosColor, self.getNegColor] editSetCallbacks = [ None, None, None, self.setPosColor, self.setNegColor] self.spectrumTable = ScrolledMatrix(frame, headingList=headings, tipTexts=tipTexts, multiSelect=True, editWidgets=editWidgets, editGetCallbacks=editGetCallbacks, editSetCallbacks=editSetCallbacks, grid=(1,0), gridSpan=(1,2)) peakListFrame.expandGrid(0, 0) frame = Frame(peakListFrame, grid=(0,0), gridSpan=(1,3)) frame.expandGrid(1,0) self.overridePeakList = CheckButton(frame, text='Use below settings when printing', tipText='Use below settings when printing instead of the window values', grid=(0,0)) tipText = 'Change the settings of the selected peak lists back to their window values' button = Button(frame, text='Reset Selected', tipText=tipText, command=self.resetSelected, grid=(0,1), sticky='e') colors = Color.standardColors self.peakColorPulldown = PulldownList(self, callback=self.setPeakColor, texts=[c.name for c in colors], objects=[c.hex for c in colors], colors=[c.hex for c in colors]) headings = [ 'Peak List', 'Symbols Drawn', 'Peak Font', 'Peak Colour'] self.fontMenu = FontList(self, mode='Print', extraTexts=[no_peak_text]) editWidgets = [ None, None, self.fontMenu, self.peakColorPulldown] editGetCallbacks = [ None, self.togglePeaks, self.getPeakFont, self.getPeakColor ] editSetCallbacks = [ None, None, self.setPeakFont, self.setPeakColor ] self.peakListTable = ScrolledMatrix(frame, headingList=headings, multiSelect=True, editWidgets=editWidgets, editGetCallbacks=editGetCallbacks, editSetCallbacks=editSetCallbacks, grid=(1,0), gridSpan=(1,2)) regionFrame.expandGrid(0, 0) frame = Frame(regionFrame, grid=(0,0), gridSpan=(1,3)) frame.expandGrid(3,0) tipText = 'Use the specified override region when printing rather than the window values' self.overrideButton = CheckButton(frame, text='Use override region when printing', tipText=tipText, callback=self.toggledOverride, grid=(0,0)) tipTexts = ('Use min and max to specify override region', 'Use center and width to specify override region') self.use_entry = USE_ENTRIES[0] self.useButtons = RadioButtons(frame, entries=USE_ENTRIES, tipTexts=tipTexts, select_callback=self.changedUseEntry, grid=(1,0)) texts = ('Set Region from Window', 'Set Center from Window', 'Set Width from Window') tipTexts = ('Set the override region to be the current window region', 'Set the center of the override region to be the center of the current window region', 'Set the width of the override region to be the width of the current window region') commands = (self.setRegionFromWindow, self.setCenterFromWindow, self.setWidthFromWindow) self.setRegionButton = ButtonList(frame, texts=texts, tipTexts=tipTexts, commands=commands, grid=(2,0)) self.minRegionWidget = FloatEntry(self, returnCallback=self.setMinRegion, width=10) self.maxRegionWidget = FloatEntry(self, returnCallback=self.setMaxRegion, width=10) headings = MIN_MAX_HEADINGS editWidgets = [ None, None, self.minRegionWidget, self.maxRegionWidget ] editGetCallbacks = [ None, None, self.getMinRegion, self.getMaxRegion ] editSetCallbacks = [ None, None, self.setMinRegion, self.setMaxRegion ] self.regionTable = RegionScrolledMatrix(frame, headingList=headings, editWidgets=editWidgets, editGetCallbacks=editGetCallbacks, editSetCallbacks=editSetCallbacks, grid=(3,0)) self.updateWindows() self.updateAfter() self.administerNotifiers(self.registerNotify) def administerNotifiers(self, notifyFunc): for func in ('__init__', 'delete', 'setOverrideRegion'): notifyFunc(self.updateAfter, 'ccpnmr.Analysis.AxisRegion', func) notifyFunc(self.updateAfter, 'ccpnmr.Analysis.SpectrumWindow', 'setUseOverrideRegion') for func in ('__init__', 'delete', 'setName'): notifyFunc(self.updateWindows, 'ccpnmr.Analysis.SpectrumWindow', func) notifyFunc(self.updateWindows, 'ccpnmr.Analysis.SpectrumWindowPane', func) for func in ('addSpectrumWindow', 'removeSpectrumWindow'): notifyFunc(self.updateWindows, 'ccpnmr.Analysis.SpectrumWindowGroup', func) def destroy(self): self.administerNotifiers(self.unregisterNotify) BasePopup.destroy(self) def changedUseEntry(self, entry): self.use_entry = entry self.updateRegionTable() def resetSpectrum(self): spectrumWindowViews = self.spectrumTable.currentObjects analysisSpectra = set() for spectrumWindowView in spectrumWindowViews: PrintBasic.setPrintOption(spectrumWindowView, 'PositiveOn', spectrumWindowView.isPosVisible) PrintBasic.setPrintOption(spectrumWindowView, 'NegativeOn', spectrumWindowView.isNegVisible) analysisSpectra.add(spectrumWindowView.analysisSpectrum) for analysisSpectrum in analysisSpectra: PrintBasic.setPrintOption(analysisSpectrum, 'PositiveColors', analysisSpectrum.posColors) PrintBasic.setPrintOption(analysisSpectrum, 'NegativeColors', analysisSpectrum.negColors) self.updateAfter() def resetPeakList(self): windowPeakLists = self.peakListTable.currentObjects analysisPeakLists = set() for windowPeakList in windowPeakLists: PrintBasic.setPrintOption(windowPeakList, 'PeaksOn', windowPeakList.isSymbolDrawn) PrintBasic.setPrintOption(windowPeakList, 'PeakFont', windowPeakList.spectrumWindowView.analysisSpectrum.font) analysisPeakLists.add(windowPeakList.analysisPeakList) for analysisPeakList in analysisPeakLists: PrintBasic.setPrintOption(analysisPeakList, 'PeakColor', analysisPeakList.symbolColor) self.updateAfter() def resetSelected(self): n = self.tabbedFrame.selected if n == 0: self.resetSpectrum() elif n == 1: self.resetPeakList() def togglePos(self, spectrumWindowView): PrintBasic.setPrintOption(spectrumWindowView, 'PositiveOn', not PrintBasic.getPrintOption(spectrumWindowView, 'PositiveOn', defaultValue=spectrumWindowView.isPosVisible)) self.updateAfter() def toggleNeg(self, spectrumWindowView): PrintBasic.setPrintOption(spectrumWindowView, 'NegativeOn', not PrintBasic.getPrintOption(spectrumWindowView, 'NegativeOn', defaultValue=spectrumWindowView.isNegVisible)) self.updateAfter() def getPosColor(self, spectrumWindowView): schemes = getHueSortedColorSchemes(self.analysisProfile) names = [s.name for s in schemes] colors = [list(s.colors) for s in schemes] index = 0 analysisSpec = spectrumWindowView.analysisSpectrum posColors = list(PrintBasic.getPrintOption(analysisSpec, 'PositiveColors', defaultValue=analysisSpec.posColors)) if posColors in colors: index = colors.index(posColors) self.posColorPulldown.setup(names, schemes, index, colors) def setPosColor(self, *extra): spectrumWindowView = self.spectrumTable.currentObject if spectrumWindowView: analysisSpec = spectrumWindowView.analysisSpectrum PrintBasic.setPrintOption(analysisSpec, 'PositiveColors', self.posColorPulldown.getObject().colors) self.updateSpectrumTable() def getNegColor(self, spectrumWindowView): schemes = getHueSortedColorSchemes(self.analysisProfile) names = [s.name for s in schemes] colors = [list(s.colors) for s in schemes] index = 0 analysisSpec = spectrumWindowView.analysisSpectrum negColors = list(PrintBasic.getPrintOption(analysisSpec, 'NegativeColors', defaultValue=analysisSpec.negColors)) if negColors in colors: index = colors.index(negColors) self.negColorPulldown.setup(names, schemes, index, colors) def setNegColor(self, *extra): spectrumWindowView = self.spectrumTable.currentObject if spectrumWindowView: analysisSpec = spectrumWindowView.analysisSpectrum PrintBasic.setPrintOption(analysisSpec, 'NegativeColors', self.negColorPulldown.getObject().colors) self.updateSpectrumTable() def getPeakColor(self, windowPeakList): color = windowPeakList.analysisPeakList.symbolColor self.peakColorPulldown.set(color) def setPeakColor(self, *extra): windowPeakList = self.peakListTable.currentObject if windowPeakList: color = self.peakColorPulldown.getObject() scheme = self.analysisProfile.findFirstColorScheme(colors=(color,)) if scheme: color = scheme.name analysisPeakList = windowPeakList.analysisPeakList PrintBasic.setPrintOption(analysisPeakList, 'PeakColor', color) self.updatePeakListTable() def togglePeaks(self, windowPeakList): PrintBasic.setPrintOption(windowPeakList, 'PeaksOn', not PrintBasic.getPrintOption(windowPeakList, 'PeaksOn', defaultValue=windowPeakList.isSymbolDrawn)) self.updateAfter() def getPeakFont(self, windowPeakList): if windowPeakList.isAnnotationDrawn: default = windowPeakList.analysisPeakList.analysisSpectrum.font else: default = no_peak_text font = PrintBasic.getPrintOption(windowPeakList, 'PeakFont', defaultValue=default) self.fontMenu.set(font) def setPeakFont(self, windowPeakList): PrintBasic.setPrintOption(windowPeakList, 'PeakFont', self.fontMenu.getText()) self.updateAfter() def updateWindows(self, obj=None): useAll = (self.whichWindows.get() == ACTIVE_OPTIONS[0]) index = 0 windowPane = self.windowPulldown.getObject() windowPanes = [] names = [] if not windowPane: application = self.project.application name = application.getValue(self.analysisProject, keyword='printWindowWindow') if useAll: window = self.analysisProject.findFirstSpectrumWindow(name=name) if window: windowPane = window.findFirstSpectrumWindowPane() else: for window in self.analysisProject.sortedSpectrumWindows(): if isActiveWindow(window): windowPane = window.findFirstSpectrumWindowPane() break else: window = None for window in self.analysisProject.sortedSpectrumWindows(): if useAll or isActiveWindow(window): for windowPane0 in window.sortedSpectrumWindowPanes(): windowPanes.append(windowPane0) names.append(getWindowPaneName(windowPane0)) if windowPanes: if windowPane not in windowPanes: windowPane = windowPanes[0] index = windowPanes.index(windowPane) else: windowPane = None self.selectWindow(windowPane) self.windowPulldown.setup(names, windowPanes, index) def saveFile(self): windowPane = self.windowPulldown.getObject() if not windowPane: return axisPanels = windowPane.sortedAxisPanels() aspectRatio = self.getPrintAspectRatio() pixelWidth = self.totalSize(axisPanels[0]) pixelHeight = aspectRatio*self.totalSize(axisPanels[1]) unitWidth = self.totalOverrideRegion(axisPanels[0]) unitHeight = self.totalOverrideRegion(axisPanels[1]) printFrame = self.printFrame isOverrideSpectrumSelected = self.overrideSpectrum.isSelected() if isOverrideSpectrumSelected: spectrumWindowViews = self.spectrumTable.objectList # alternatively, spectrumWindowViews = windowPane.spectrumWindowViews analysisSpectra = set() for spectrumWindowView in spectrumWindowViews: spectrumWindowView.printPositive = PrintBasic.getPrintOption(spectrumWindowView, 'PositiveOn', spectrumWindowView.isPosVisible) spectrumWindowView.printNegative = PrintBasic.getPrintOption(spectrumWindowView, 'NegativeOn', spectrumWindowView.isNegVisible) analysisSpectra.add(spectrumWindowView.analysisSpectrum) for analysisSpectrum in analysisSpectra: analysisSpectrum.printPositiveColors = PrintBasic.getPrintOption(analysisSpectrum, 'PositiveColors', analysisSpectrum.posColors) analysisSpectrum.printNegativeColors = PrintBasic.getPrintOption(analysisSpectrum, 'NegativeColors', analysisSpectrum.negColors) isOverridePeakListSelected = self.overridePeakList.isSelected() if isOverridePeakListSelected: windowPeakLists = self.peakListTable.objectList analysisPeakLists = set() for windowPeakList in windowPeakLists: windowPeakList.printPeaks = PrintBasic.getPrintOption(windowPeakList, 'PeaksOn', windowPeakList.isSymbolDrawn) if windowPeakList.isAnnotationDrawn: default = windowPeakList.analysisPeakList.analysisSpectrum.font else: default = no_peak_text windowPeakList.printFont = PrintBasic.getPrintOption(windowPeakList, 'PeakFont', default) analysisPeakLists.add(windowPeakList.analysisPeakList) for analysisPeakList in analysisPeakLists: analysisPeakList.printColor = PrintBasic.getPrintOption(analysisPeakList, 'PeakColor', analysisPeakList.symbolColor) xrr = axisPanels[0].findFirstAxisRegion().region dxx = abs(xrr[0]-xrr[1]) yrr = axisPanels[1].findFirstAxisRegion().region dyy = abs(yrr[0]-yrr[1]) try: outputHandler = printFrame.getOutputHandler(pixelWidth, pixelHeight, unitWidth, unitHeight, fonts=printNames) if not outputHandler: return analysisProject = self.analysisProject major_minor_dict = {} spacing_choice = PrintBasic.getPrintOption(analysisProject, 'SpacingChoice', spacing_choices[0]) if spacing_choice != spacing_choices[0]: for attr in ('XMajor', 'XMinor', 'XDecimal', 'YMajor', 'YMinor', 'YDecimal',): val = PrintBasic.getPrintOption(analysisProject, attr, None) if val is not None: major_minor_dict[attr] = val tick_length_choice = PrintBasic.getPrintOption(analysisProject, 'TickLengthChoice', tick_length_choices[0]) if tick_length_choice != tick_length_choices[0]: for attr in ('TickMajor', 'TickMinor'): val = PrintBasic.getPrintOption(analysisProject, attr, None) if val is not None: major_minor_dict[attr] = val windowDraw = WindowDraw(self.parent, windowPane) PrintBasic.printWindow(windowDraw, outputHandler, printFrame.tick_location, printFrame.tick_placement, aspectRatio, printFrame.tick_font, major_minor_dict) msg = 'Saved to file "%s"' % printFrame.file_name showInfo('Success', msg, parent=self) except IOError, e: showError('IO Error', str(e), parent=self) if isOverrideSpectrumSelected: analysisSpectra = set() for spectrumWindowView in spectrumWindowViews: del spectrumWindowView.printPositive del spectrumWindowView.printNegative analysisSpectra.add(spectrumWindowView.analysisSpectrum) for analysisSpectrum in analysisSpectra: del analysisSpectrum.printPositiveColors del analysisSpectrum.printNegativeColors if isOverridePeakListSelected: analysisPeakLists = set() for windowPeakList in windowPeakLists: del windowPeakList.printPeaks del windowPeakList.printFont analysisPeakLists.add(windowPeakList.analysisPeakList) for analysisPeakList in analysisPeakLists: del analysisPeakList.printColor
class PeakSeparatorGui(BasePopup): """ **Separate Merged Peaks Using Peak Models** The Peak Separator code uses a Markov Chain Monte Carlo search which, using idealised peak shapes, attempts to deconvolve overlapped peak regions into their separate constituent peaks. This routine is also suitable for accurately fitting model shapes to single peaks in order to calculate precise intensities. **Options Peak Separator Parameters** *Min. Number of peaks* is by default set to one, it is not possible to set this to a value less than one. *Max. Number of peaks* is by default set to one, increasing this value allows the search routine to fit more models. The best fit may be found with fewer than the maximum number models. Higher numbers slow the routine, and setting this value to 0 allows the routine to (effectively) fit unlimited peaks. *Only pick positive peaks*. If you are not interested in negative peaks, removing the possibility of fitting negative peaks can reduce search time. *Peak Model* fits the spectra with either a Gaussian peak model or a Lorentzian peak model. **Options Region** *Peak List* choose which peak list newly picked peaks should be added to. Peaks picked using this method will have their details appended with 'PeakSepartor' so you know where they came from. *Region Table* shows which area of the current spectrum is about to be searched. *Add Region*. Once an area of spectra has been highlighted clicking this button will pass it's details on to the Peak Separator. *Reset All* will reset all search parameters. *Separate Peaks* will run the Peak Separator code with your current settings. This may take a few minutes to run, depending on the size of the spectral region being searched, the number of peaks being fitted and the speed of your machine. Please wait while this completes. After a successful Peak Separation run, the found peaks will be added to the selected peak list. These peaks intensties (volume) have been found using the peak model selected. **Advanced Settings Tab** *Rate* affects the speed of the Markov Chain Monte Carlo routine. A smaller value results in longer execution, but possibly higher quality results. The default setting is deemed sensible for the majority of runs. *Line Width* offers a finer degree of control over maximum and minimum peak widths for each dimension. The default values are *very* stupid and could do with re-checking for each experiment. *Re-Pick Entire Peak List* if you would like to use the Peak Separator to repick *every* peak in your peak list, try this option - but note that this may take a very long time! """ def __init__(self, parent, programName='Peak Separator', **kw): self.parent = parent self.programName = programName self.versionInfo = 'Version 0.2' self.help_url = 'http://www.ccpn.ac.uk/' self.window = None self.waiting = False self.rootWindow = None # just used for display - PeakSeparator will not see this self._minSigmaHz = None self._maxSigmaHz = None self.customSigma = False self.rePickPeakList = False self._sampleStartPpm = None self._sampleEndPpm = None try: self.project = parent.project except: pass self.params = PeakSeparatorParams() BasePopup.__init__(self, parent=parent, title=programName, location='+100+100', **kw) if not self.analysisProject: print '&&& init: No analysis project found ...' try: if parent.argumentServer: self.argServer = parent.argumentServer else: print '&&& init: No argument server found...' except: print '&&& init: Test' ########################################################################### def body(self, guiFrame): self.geometry('450x500') guiFrame.grid_rowconfigure(0, weight=1) guiFrame.grid_columnconfigure(0, weight=1) options = ['Peak Separator', 'Advanced Settings'] tabbedFrame = TabbedFrame(guiFrame, options=options) tabbedFrame.grid(row=0, column=0, sticky='nsew') buttons = UtilityButtonList(tabbedFrame.sideFrame, helpUrl=self.help_url) buttons.grid(row=0, column=0, sticky='e') self.tabbedFrame = tabbedFrame frameA, frameB = tabbedFrame.frames # # FrameA : Main Settings # frameA.grid_columnconfigure(1, weight=1) row = 0 # Label row row += 1 div = LabelDivider(frameA, text='Peak Separator Parameters') div.grid(row=row, column=0, columnspan=2, sticky='ew') row += 1 label = Label(frameA, text='Min. number of peaks:') label.grid(row=row, column=0, sticky='w') self.minPeaksEntry = IntEntry(frameA, returnCallback=self.applyChange, width=10, \ tipText='Minimum number of peaks to find (must be > 0)') self.minPeaksEntry.grid(row=row, column=1, sticky='n') self.minPeaksEntry.bind('<Leave>', self.applyChange, '+') row += 1 label = Label(frameA, text='Max. number of peaks:') label.grid(row=row, column=0, sticky='w') self.maxPeaksEntry = IntEntry(frameA, returnCallback=self.applyChange, width=10, \ tipText='Maximum number of peaks to find (0 is unlimited - not recommended)') self.maxPeaksEntry.grid(row=row, column=1, sticky='n') self.maxPeaksEntry.bind('<Leave>', self.applyChange, '+') row += 1 label = Label(frameA, text='Only pick positive peaks:') label.grid(row=row, column=0, sticky='w') entries = ['False', 'True'] self.posPeaksButtons = RadioButtons( frameA, entries=entries, select_callback=self.applyChange, direction='horizontal', tipTexts=[ 'Search for both positive and negative intensity peaks', 'Limit search to only positive peaks' ]) self.posPeaksButtons.grid(row=row, column=1, sticky='n') row += 1 label = Label(frameA, text='Peak Model:') label.grid(row=row, column=0, sticky='w') ### G/L Mixture works, but volume calculation involves Gamma function # entries = ['Gaussian', 'Lorentzian', 'G/L Mixture'] entries = ['Gaussian', 'Lorentzian'] self.shapeButtons = RadioButtons( frameA, entries=entries, select_callback=self.applyChange, direction='horizontal', tipTexts=[ 'Choose a Gaussian model peak shape to fit to peaks', 'Choose a Lorentzian model peak shape to fit to peaks' ]) self.shapeButtons.grid(row=row, column=1, sticky='n') row += 1 div = LabelDivider(frameA, text='Region', tipText='Region that search will limit itself to') div.grid(row=row, column=0, columnspan=2, sticky='ew') row += 1 label = Label(frameA, text='Peak List:') label.grid(row=row, column=0, sticky='nw') self.peakListPulldown = PulldownList( frameA, callback=self.setManuallyPickPeakList, tipText='Select which peak list new peaks are to be added to') self.peakListPulldown.grid(row=row, column=1, sticky='nw') # tricky scrolled matrix row += 1 self.regionTable = None frameA.grid_rowconfigure(row, weight=1) headings = ('dim.', 'start (ppm)', 'end (ppm)', 'actual size') self.editDimEntry = IntEntry(self, returnCallback=self.applyChange, width=5, tipText='Dimension number') self.editStartEntry = FloatEntry(self, returnCallback=self.applyChange, width=5, tipText='Search area lower bound') self.editEndEntry = FloatEntry(self, returnCallback=self.applyChange, width=5, tipText='Search area upper bound') editWidgets = [ self.editDimEntry, self.editStartEntry, self.editEndEntry, None ] editGetCallbacks = [None, None, None, None] editSetCallbacks = [None, None, None, None] self.regionTable = ScrolledMatrix(frameA, headingList=headings, multiSelect=False, editWidgets=editWidgets, editGetCallbacks=editGetCallbacks, editSetCallbacks=editSetCallbacks, initialRows=5) self.regionTable.grid(row=row, column=0, columnspan=2, sticky='nsew') # Run Button row += 1 texts = ['Add Region'] commands = [self.updateFromRegion] self.addResetButtons = ButtonList( frameA, texts=texts, commands=commands, tipTexts=['Add selected specrtral region']) self.addResetButtons.grid(row=row, column=0, columnspan=2, sticky='ew') row += 1 texts = ['Separate Peaks'] commands = [self.runPeakSeparator] self.runButton = ButtonList(frameA, texts=texts, commands=commands, expands=True, tipTexts=['Run peak search now']) self.runButton.grid(row=row, column=0, columnspan=2, sticky='nsew') # # FrameB : Further Settings # frameB.grid_columnconfigure(0, weight=1) row = 0 div = LabelDivider(frameB, text='Rate:') div.grid(row=row, column=0, columnspan=2, sticky='ew') row += 1 label = Label(frameB, text='Rate of MCMC step size change') label.grid(row=row, column=0, columnspan=1, sticky='w') self.rateEntry = FloatEntry(frameB, returnCallback=self.applyChange, width=10, \ tipText='Rate effects speed of run, smaller values take longer but may produce better results') self.rateEntry.grid(row=row, column=1, sticky='n') self.rateEntry.bind('<Leave>', self.applyChange, '+') self.rateEntry.set(self.params.rate) # tricky scrolled matrix for line width row += 2 div = LabelDivider(frameB, text='Line Width (Hz):') div.grid(row=row, column=0, columnspan=2, sticky='ew') row += 1 label = Label(frameB, text="Descr.") label.grid(row=row, rowspan=2, column=0, sticky='w') row += 1 self.lineWidthTable = None frameB.grid_rowconfigure(row, weight=1) lineWidthHeadings = ('dim.', 'min. σ (Hz)', 'max. σ (Hz)') self.editMinSigmaEntry = FloatEntry(self, returnCallback=self.applyChange, width=5, tipText='Minimum line width (Hz)') self.editMaxSigmaEntry = FloatEntry(self, returnCallback=self.applyChange, width=5, tipText='Maximum line width (Hz)') # self.editDimEntry is also from regionTable initialWidthRows = 4 editLineWidthWidgets = [ None, self.editMinSigmaEntry, self.editMaxSigmaEntry ] editLineWidthGetCallbacks = [None, self.getSigmaMin, self.getSigmaMax] editLineWidthSetCallbacks = [None, self.setSigmaMin, self.setSigmaMax] self.lineWidthTable = ScrolledMatrix( frameB, headingList=lineWidthHeadings, multiSelect=False, editWidgets=editLineWidthWidgets, editGetCallbacks=editLineWidthGetCallbacks, editSetCallbacks=editLineWidthSetCallbacks, initialRows=initialWidthRows) self.lineWidthTable.grid(row=row, column=0, columnspan=2, sticky='nsew') # option to 'repick' exisiting peak list row += initialWidthRows div = LabelDivider(frameB, text='(optional - repick entire peak list)') div.grid(row=row, column=0, columnspan=2, sticky='ew') row += 1 self.repickListPulldown = PulldownList( frameB, callback=self.setRePickPeakList, tipText= 'Select which peak list to repick (new peaks will be put into a new peak list)' ) self.repickListPulldown.grid(row=row, column=0, sticky='nw') texts = ['Repick Peak List'] commands = [self.runRepickPeaks] self.runButton = ButtonList( frameB, texts=texts, commands=commands, expands=True, tipTexts=['Repick selected peak list into a new peak list.']) self.runButton.grid(row=row, column=1, columnspan=1, sticky='nsew') row += 1 div = LabelDivider(frameB) row += 1 texts = ['Separate Peaks'] commands = [self.runPeakSeparator] self.runButton = ButtonList(frameB, texts=texts, commands=commands, expands=True, tipTexts=['Run peak search now']) self.runButton.grid(row=row, column=0, columnspan=2, sticky='nsew') self.setWidgetEntries() self.administerNotifiers(self.registerNotify) def administerNotifiers(self, notifyFunc): for func in ('__init__', 'delete'): notifyFunc(self.updateAfter, 'ccp.nmr.Nmr.PeakList', func) notifyFunc(self.updateAfter, 'ccp.nmr.Nmr.Experiment', 'setName') notifyFunc(self.updateAfter, 'ccp.nmr.Nmr.DataSource', 'setName') def destroy(self): self.administerNotifiers(self.unregisterNotify) BasePopup.destroy(self) ########################################################################### # update parameters from PS Region def updateFromRegion(self): if not self.params.peakList: print '&&& update from region: Need a peak list' return if (self.argServer.parent.currentRegion) == None: showError('No Region', 'Please select a peak region to be separated') return self.rePickPeakList = False getRegionParams(self.params, argServer=self.argServer) if not self.customSigma: self.initSigmaParams() self.setWidgetEntries() ########################################################################### # update parameters from PS PeakList def updateFromPeakList(self): if not self.params.peakList: print '&&& update from peakList: Need a peak list' return getPeakListParams(self.params) if not self.customSigma: self.initSigmaParams() self.setWidgetEntries() ########################################################################### # Run the C library! def runPeakSeparator(self): """ run the peak separator """ # hack for Macs - focus isn't always lost on mouse move # so bind event not always called. Shouldn't affect other OS. self.applyChange() if not self.params.peakList: print '&&& Peak list not yet set' else: # SeparatePeakRoutine(self.params, self.params.peakList, routine='pymc' ) SeparatePeakRoutine(self.params, self.params.peakList, routine='bayesys') def runRepickPeaks(self): """ Run the Peak Separator on entire chosen peak list """ # hack for Macs - focus isn't always lost on mouse move # so bind event not always called. Shouldn't affect other OS. self.applyChange() if not self.params.peakList: print '&&& Peak list not yet set' else: SeparatePeaksInPeakList(self.params) ########################################################################### def setWidgetEntries(self): ### Page One widgets self.minPeaksEntry.set(self.params.minAtoms) self.maxPeaksEntry.set(self.params.maxAtoms) if self.params.positivePeaks == 1: self.posPeaksButtons.set('True') # only pick pos peaks else: self.posPeaksButtons.set('False') # do something fancy if different shapes for each dim! n = self.params.peakShape - 3 # shape is only 3, 4, (5) self.shapeButtons.setIndex(n) if self.project is not None: self.updatePeakListList() self.updateSpectrumWindow() if self.params.sampleStart and self.params.peakList: if not self.rePickPeakList: objectList = [] textMatrix = [] if len(self.params.samplePpmStart) != self.params.Ndim: return for i in range(self.params.Ndim): dim_entry = [] dim_entry.append('%2d' % (i + 1)) dim_entry.append('%7.3f' % self.params.samplePpmStart[i]) dim_entry.append('%7.3f' % self.params.samplePpmEnd[i]) dim_entry.append('%3d' % self.params.sampleSize[i]) textMatrix.append(dim_entry) self.regionTable.update(textMatrix=textMatrix, objectList=objectList) ### Page Two widgets self.rateEntry.set(self.params.rate) if self.params.peakList and self.params.Ndim: textMatrix = [] objectList = [] for i in range(self.params.Ndim): if self.params.isFreqDim[i]: dim_entry = [] objectList.append(i) dim_entry.append('%2d' % (i + 1)) dim_entry.append('%7.3f' % self._minSigmaHz[i]) dim_entry.append('%7.3f' % self._maxSigmaHz[i]) textMatrix.append(dim_entry) self.lineWidthTable.update(textMatrix=textMatrix, objectList=objectList) def applyChange(self, *event): """ Upon change, add settings to params """ # Page One apply changes self.params.minAtoms = self.minPeaksEntry.get() self.params.maxAtoms = self.maxPeaksEntry.get() if self.posPeaksButtons.get() == 'True': # asked only pick pos peaks self.params.positivePeaks = 1 else: self.params.positivePeaks = 0 # do something fancy if different shapes for each dim! n = self.shapeButtons.getIndex() # shape is only 3, 4, (5) self.params.peakShape = n + 3 # Page Two apply changes self.params.rate = float(self.rateEntry.get()) self.updateSigmaParams() ########################################################################### # Peak list functions provide PeakSeparator some inherited params def getPeakListList(self): """ given a spectrum, get list of peak lists """ project = self.project peakLists = [] for experiment in self.nmrProject.experiments: for spectrum in experiment.dataSources: for peakList in spectrum.peakLists: peakLists.append([ '%s:%s:%d' % (experiment.name, spectrum.name, peakList.serial), peakList ]) peakLists.sort() return peakLists def updatePeakListList(self): """ set the peaklist list in the pulldown menu """ peakListData = self.getPeakListList() index = -1 names = [] peakList = self.params.peakList if peakListData: names = [x[0] for x in peakListData] peakLists = [x[1] for x in peakListData] if peakList not in peakLists: peakList = peakLists[0] index = peakLists.index(peakList) else: peakList = None peakLists = [] if peakList is not self.params.peakList: self.params.peakList = peakList self.peakListPulldown.setup(names, peakLists, index) self.repickListPulldown.setup(names, peakLists, index) def setRePickPeakList(self, peakList): """ Set the peak list to be repicked (and hit a Flag) """ self.rePickPeakList = True self.setPeakList(peakList) def setManuallyPickPeakList(self, peakList): """ Set the peak list to add new peaks to (and hit a Flag) """ self.rePickPeakList = False self.setPeakList(peakList) def setPeakList(self, peakList): """ Sets the Peak List """ if peakList is not self.params.peakList: self.params.peakList = peakList # # interrogate the peak list and get all the usefull parameters out self.updateFromPeakList() self.updateSpectrumWindow() self.setWidgetEntries() ########################################################################### # TBD I suspect this is for matching region with peak list, but may be obsolete now def getSpectrumWindowList(self): """ get list of windows which spectrum could be in """ windows = {} if self.params.peakList: views = getSpectrumViews(self.params.peakList.dataSource) for view in views: windows[view.spectrumWindowPane.spectrumWindow] = None return [[w.name, w] for w in windows.keys()] def updateSpectrumWindow(self): """ update the spectrum window """ windowData = self.getSpectrumWindowList() index = -1 names = [] window = self.rootWindow if windowData: names = [x[0] for x in windowData] windows = [x[1] for x in windowData] if window not in windows: window = windows[0] index = windows.index(window) else: window = None windows = [] if window is not self.rootWindow: self.rootWindow = window ########################################################################### # get and set sigma stuff def setSigmaMin(self, dim): value = self.editMinSigmaEntry.get() self._minSigmaHz[dim] = value # dont go and re-write users settings self.customSigma = True # make sure changes are in params object self.updateSigmaParams(dim) self.setWidgetEntries() def getSigmaMin(self, dim): if dim is not None: self.editMinSigmaEntry.set(self._minSigmaHz[dim]) def setSigmaMax(self, dim): value = self.editMaxSigmaEntry.get() self._maxSigmaHz[dim] = value # dont go and re-write users settings self.customSigma = True # make sure changes are in params object self.updateSigmaParams(dim) self.setWidgetEntries() def getSigmaMax(self, dim): if dim is not None: self.editMaxSigmaEntry.set(self._maxSigmaHz[dim]) def updateSigmaParams(self, dim=None): """ updateSigmaParams Just updates the parameters (params obj) for sigma values. If dim is None, do this for each dim """ dataDimRefs = self.params.dataDimRefs if not dataDimRefs: return if not self.params.minSigma or len( self.params.minSigma) != self.params.Ndim: self.params.minSigma = [0.] * self.params.Ndim if not self.params.maxSigma or len( self.params.maxSigma) != self.params.Ndim: self.params.maxSigma = [0.] * self.params.Ndim def updateSigmaParam(dim, dataDimRefs): """ Convert and update sigma for dim """ if self.params.isFreqDim[dim]: # note factor of two! self.params.minSigma[dim] = self.rHz2pnt( self._minSigmaHz[dim], dataDimRefs[dim]) / 2. self.params.maxSigma[dim] = self.rHz2pnt( self._maxSigmaHz[dim], dataDimRefs[dim]) / 2. else: self.params.minSigma[dim] = 1.0 self.params.maxSigma[dim] = 1.0 if dim: updateSigmaParam(dim, dataDimRefs) else: for dim in range(self.params.Ndim): updateSigmaParam(dim, dataDimRefs) # utility functions for sigma values def pnt2rHz(self, point, dataDimRef): """ Point to relative Hz frequency relative to frequency at Zeroeth point Necessary when (for example) looking for width of peak in Hz """ assert point, dataDimRef sigmaBase = pnt2hz(0, dataDimRef) sigmaHz = pnt2hz(point, dataDimRef) return abs(sigmaHz - sigmaBase) def rHz2pnt(self, freq, dataDimRef): """ Relative Hz to point frequency relative to frequency at Zeroeth point Necessary when (for example) looking for width of peak in Hz """ assert freq, dataDimRef sigmaBase = hz2pnt(0, dataDimRef) sigmaPoint = hz2pnt(freq, dataDimRef) return abs(sigmaPoint - sigmaBase) def initSigmaParams(self): """ Set some initial default values for sigma """ self._minSigmaHz = [] self._maxSigmaHz = [] if self.params.Ndim: for dim in range(self.params.Ndim): self._minSigmaHz.append(6.) self._maxSigmaHz.append(28.) ########################################################################### def updateAll(self): self.updateSpectrumWindow() self.updatePeakListList() self.waiting = False def updateAfter(self, obj=None): if self.waiting: return else: self.waiting = True self.after_idle(self.updateAll)
class AssignMentTransferTab(object): '''the tab in the GUI where assignments can be transferred in bulk to the ccpn analysis project. A difference is made between two types of assignments: 1) spin systems to residues, which also implies resonanceSets to atomSets. 2) resonances to peak dimensions. The user is able to configure which assignments should be transferred to the project. Attributes: guiParent: gui object this tab is part of. frame: the frame in which this element lives. dataModel(src.cython.malandro.DataModel): dataModel object describing the assignment proposed by the algorithm. selectedSolution (int): The index of the solution/run that is used asa the template to make the assignments. resonanceToDimension (bool): True if resonances should be assigned to peak dimensions. False if not. spinSystemToResidue (bool): True if spin system to residue assignment should be carried out. minScore (float): The minimal score of a spin system assignment to a residue to be allowed to transfer this assignment to the project intra (bool): True if intra-residual peaks should be assigned. sequential (bool): True if sequential peaks should be assigned. noDiagonal (bool): If True, purely diagonal peaks are ignored during the transfer of assignments. allSpectra (bool): If True, all spectra will be assigned. If False, one specified spectrum will be assigned. spectrum (src.cython.malandro.Spectrum): The spectrum that should be assigned. ''' def __init__(self, parent, frame): '''Init. args: parent: the guiElement that this tab is part of. frame: the frame this part of the GUI lives in. ''' self.guiParent = parent self.frame = frame # Buttons and fields, # will be set in body(): self.peaksCheckButton = None self.residuesCheckButton = None self.intraCheckButton = None self.sequentialCheckButton = None self.noDiagonalCheckButton = None self.spinSystemTypeSelect = None self.minScoreEntry = None self.solutionNumberEntry = None self.spectrumSelect = None self.spectraPullDown = None self.assignedResidueStrategySelect = None self.transferButton = None # Settings that determine how assignments # are transferred to the analysis project: self.minScore = 80.0 self.dataModel = None self.spectrum = None self.selectedSolution = 1 self.body() self.resonanceToDimension = True self.spinSystemToResidue = True self.intra = True self.sequential = True self.noDiagonal = True self.allSpectra = True self.spinSystemType = 0 self.strategy = 0 def body(self): '''Describes the body of this tab. It consists out of a number of radio buttons, check buttons and number entries that allow the user to indicate which assignments should be transferred. ''' # self.frame.expandColumn(0) self.frame.expandGrid(8, 0) self.frame.expandGrid(8, 1) typeOfAssignmentFrame = LabelFrame( self.frame, text='type of assignment') typeOfAssignmentFrame.grid(row=0, column=0, sticky='nesw') # typeOfAssignmentFrame.expandGrid(0,5) peakSelectionFrame = LabelFrame( self.frame, text='which peaks to assign') peakSelectionFrame.grid(row=0, column=1, sticky='nesw', rowspan=2) spinSystemSelectionFrame = LabelFrame(self.frame, text='Which spin-systems to use') spinSystemSelectionFrame.grid(row=2, column=0, sticky='nesw') tipText = 'What to do when a residue has already a spin system assigned to it.' assignedResidueFrame = LabelFrame(self.frame, text='if residue already has spin-system', tipText=tipText) assignedResidueFrame.grid(row=2, column=1, sticky='nesw') spectrumSelectionFrame = LabelFrame(self.frame, text='spectra') spectrumSelectionFrame.grid(row=1, column=0, sticky='nesw') row = 0 Label(typeOfAssignmentFrame, text='Resonances to Peak Dimensions', grid=(row, 0)) self.peaksCheckButton = CheckButton(typeOfAssignmentFrame, selected=True, grid=(row, 1)) row += 1 Label(typeOfAssignmentFrame, text='SpinSystems to Residues', grid=(row, 0)) self.residuesCheckButton = CheckButton( typeOfAssignmentFrame, selected=True, grid=(row, 1)) row = 0 Label(peakSelectionFrame, text='Intra-Residual', grid=(row, 0)) self.intraCheckButton = CheckButton( peakSelectionFrame, selected=True, grid=(row, 1)) row += 1 Label(peakSelectionFrame, text='Sequential', grid=(row, 0)) self.sequentialCheckButton = CheckButton( peakSelectionFrame, selected=True, grid=(row, 1)) row += 1 Label(peakSelectionFrame, text='Do not assign diagonal peaks', grid=(row, 0)) self.noDiagonalCheckButton = CheckButton( peakSelectionFrame, selected=True, grid=(row, 1)) entries = ['Only assigned spin systems', 'All that have a score of at least: ', 'User Defined', 'Solution number:'] tipTexts = ['Only assign resonances of spin systems that already have a sequential assignment for the assignment of peak dimensions. Spin system to residue assignment is not relevant in this case.', 'Assign all spin systems that have a score of at least a given percentage. 50% or lower is not possible, because than spin systems might have to be assigned to more than 1 residue, which is impossible.', "As defined in the lower row of buttons in the 'results' tab.", 'One of the single solutions of the annealing.'] self.spinSystemTypeSelect = RadioButtons(spinSystemSelectionFrame, entries=entries, grid=(0, 0), select_callback=None, direction=VERTICAL, gridSpan=(4, 1), tipTexts=tipTexts) tipText = 'The minimal amount of colabelling the different nuclei should have in order to still give rise to a peak.' self.minScoreEntry = FloatEntry(spinSystemSelectionFrame, grid=(1, 1), width=7, text=str(self.minScore), returnCallback=self.changeMinScore, tipText=tipText) self.minScoreEntry.bind('<Leave>', self.changeMinScore, '+') self.solutionNumberEntry = IntEntry(spinSystemSelectionFrame, grid=(3, 1), width=7, text=1, returnCallback=self.solutionUpdate, tipText=tipText) self.solutionNumberEntry.bind('<Leave>', self.solutionUpdate, '+') #self.solutionPullDown = PulldownList(spinSystemSelectionFrame, None, grid=(3,1), sticky='w') entries = ['all spectra', 'only:'] tipTexts = ['Assign peaks in all the spectra that where selected before the annealing ran.', 'Only assign peaks in one particular spectrum. You can of course repeat this multiple times for different spectra.'] self.spectrumSelect = RadioButtons(spectrumSelectionFrame, entries=entries, grid=(0, 0), select_callback=None, direction=VERTICAL, gridSpan=(2, 1), tipTexts=tipTexts) self.spectraPullDown = PulldownList(spectrumSelectionFrame, self.changeSpectrum, grid=(1, 1), sticky='w') entries = ['skip this residue', 'de-assign old spin system from residue', 'assign, but never merge', 'warn to merge'] tipTexts = ["Don't assign the new spin system to the residue. The residue is not skipped when the old spin system does not contain any resonances", "De-assign old spin system from residue, unless the old spin system is a spin system without any resonances.", "Don't merge any spin systems, merging can be performed later if nescesary in the Resonance --> SpinSystems window.", "Ask to merge individually for each spin system, this might result in clicking on a lot of popups."] self.assignedResidueStrategySelect = RadioButtons(assignedResidueFrame, entries=entries, grid=(0, 0), select_callback=None, direction=VERTICAL, gridSpan=(2, 1), tipTexts=tipTexts) texts = ['Transfer Assignments'] commands = [self.transferAssignments] self.transferButton = ButtonList( self.frame, commands=commands, texts=texts) self.transferButton.grid(row=5, column=0, sticky='nsew', columnspan=2) def update(self): '''Update the nescesary elements in the tab. Is called when the algorithm has produced possible assignments. The only thing that has to be updated in practice in this tab is the pulldown with spectra. ''' self.dataModel = self.guiParent.connector.results self.updateSpectra() def setDataModel(self, dataModel): '''Here the dataModel, which is the dataModel containing the suggested assignments body the algorithm, can be set. ''' self.dataModel = dataModel self.update() def updateSpectra(self, *opt): '''Updates the spectra shown in the spectra pulldown. These are only the spectra that were used by the algorithm. All other spectra in the project are not relevant since for those no simulated peaks have been matched to real peaks. ''' if not self.dataModel: return spectrum = self.spectrum spectra = self.dataModel.getSpectra() if spectra: names = [spectrum.name for spectrum in spectra] index = 0 if self.spectrum not in spectra: self.spectrum = spectra[0] else: index = spectra.index(self.spectrum) self.spectraPullDown.setup(names, spectra, index) def changeSpectrum(self, spectrum): '''Select a spectum to be assigned.''' self.spectrum = spectrum def solutionUpdate(self, event=None, value=None): '''Select a solution. A solution is a one to one mapping of spin systems to residues produced by one run of the algorithm. args: event: event object, this is one of the values the number entry calls his callback function with. value: the index of the solution/run. ''' if not self.dataModel: return Nsolutions = len(self.dataModel.chain.residues[0].solutions) if value is None: value = self.solutionNumberEntry.get() if value == self.selectedSolution: return else: self.selectedSolution = value if value < 1: self.solutionNumberEntry.set(1) self.selectedSolution = 1 elif value > Nsolutions: self.selectedSolution = Nsolutions self.solutionNumberEntry.set(self.selectedSolution) else: self.solutionNumberEntry.set(self.selectedSolution) def fetchOptions(self): '''Fetches user set options from the gui in one go and stores them in their corresponding instance variables. ''' self.resonanceToDimension = self.peaksCheckButton.get() self.spinSystemToResidue = self.residuesCheckButton.get() self.intra = self.intraCheckButton.get() self.sequential = self.sequentialCheckButton.get() self.noDiagonal = self.noDiagonalCheckButton.get() self.spinSystemType = self.spinSystemTypeSelect.getIndex() self.strategy = ['skip', 'remove', 'noMerge', None][ self.assignedResidueStrategySelect.getIndex()] self.allSpectra = [True, False][self.spectrumSelect.getIndex()] def changeMinScore(self, event=None): '''Set the minimal score for which a spin system to residue assignment gets transferred to the ccpn analysis project. ''' newMinScore = self.minScoreEntry.get() if self.minScore != newMinScore: if newMinScore <= 50.0: self.minScore = 51.0 self.minScoreEntry.set(51.0) elif newMinScore > 100.0: self.minScore = 100.0 self.minScoreEntry.set(100.0) else: self.minScore = newMinScore def transferAssignments(self): '''Transfer assignments to project depending on the settings from the GUI. ''' self.fetchOptions() if not self.dataModel or (not self.resonanceToDimension and not self.spinSystemToResidue): return strategy = self.strategy lookupSpinSystem = [self.getAssignedSpinSystem, self.getBestScoringSpinSystem, self.getUserDefinedSpinSystem, self.getSelectedSolutionSpinSystem][self.spinSystemType] residues = self.dataModel.chain.residues spinSystemSequence = [lookupSpinSystem(res) for res in residues] ccpnSpinSystems = [] ccpnResidues = [] # if self.spinSystemType == 0 it means that it for sure already # assigned like this if self.spinSystemToResidue and not self.spinSystemType == 0: for spinSys, res in zip(spinSystemSequence, residues): if spinSys and res: ccpnSpinSystems.append(spinSys.getCcpnResonanceGroup()) ccpnResidues.append(res.getCcpnResidue()) assignSpinSystemstoResidues(ccpnSpinSystems, ccpnResidues, strategy=strategy, guiParent=self.guiParent) if self.resonanceToDimension: allSpectra = self.allSpectra if self.intra: for residue, spinSystem in zip(residues, spinSystemSequence): if not spinSystem: continue intraLink = residue.getIntraLink(spinSystem) for pl in intraLink.getPeakLinks(): peak = pl.getPeak() if not allSpectra and peak.getSpectrum() is not self.spectrum: continue if not peak: continue resonances = pl.getResonances() if self.noDiagonal and len(set(resonances)) < len(resonances): continue for resonance, dimension in zip(resonances, peak.getDimensions()): ccpnResonance = resonance.getCcpnResonance() ccpnDimension = dimension.getCcpnDimension() assignResToDim(ccpnDimension, ccpnResonance) if self.sequential: for residue, spinSystemA, spinSystemB in zip(residues, spinSystemSequence, spinSystemSequence[1:]): if not spinSystemA or not spinSystemB: continue link = residue.getLink(spinSystemA, spinSystemB) for pl in link.getPeakLinks(): peak = pl.getPeak() if not allSpectra and peak.getSpectrum() is not self.spectrum: continue if not peak: continue resonances = pl.getResonances() if self.noDiagonal and len(set(resonances)) < len(resonances): continue for resonance, dimension in zip(resonances, peak.getDimensions()): ccpnResonance = resonance.getCcpnResonance() ccpnDimension = dimension.getCcpnDimension() assignResToDim(ccpnDimension, ccpnResonance) self.guiParent.resultsTab.update() def getAssignedSpinSystem(self, residue): '''Get the spinSystem that is assigned in the project to a residue. args: residue (src.cython.malandro.Residue) return: spinSystem (src.cython.malandro.SpinSystem) ''' ccpCode = residue.ccpCode seqCode = residue.getSeqCode() spinSystems = self.dataModel.getSpinSystems()[ccpCode] ccpnResidue = residue.getCcpnResidue() if ccpnResidue: assignedResonanceGroups = ccpnResidue.getResonanceGroups() if len(assignedResonanceGroups) > 1: print 'There is more than one spin system assigned to residue %s, did not know which one to use to assign peaks. Therefor this residue is skipped.' % (seqCode) return assignedResonanceGroup = ccpnResidue.findFirstResonanceGroup() if assignedResonanceGroup: for spinSystem in spinSystems: if spinSystem.getSerial() == assignedResonanceGroup.serial: # Just checking to make sure, analysis project could # have changed if not self.skipResidue(residue, spinSystem): return spinSystem def getBestScoringSpinSystem(self, residue): '''Get the spinSystem that scores the highest, i.e. is assigned in most of the runs to the given residue. args: residue (src.cython.malandro.Residue) return: spinSystem (src.cython.malandro.SpinSystem) ''' solutions = residue.solutions weigth = 1.0 / len(solutions) score, bestSpinSystem = max([(solutions.count(solution) * weigth * 100.0, solution) for solution in solutions]) if score >= self.minScore and not bestSpinSystem.getIsJoker() and not self.skipResidue(residue, bestSpinSystem): return bestSpinSystem return None def getUserDefinedSpinSystem(self, residue): '''Get the spinSystem that is defined by the user (probably in the resultsTab) as the correct assignment of the given residue. args: residue (src.cython.malandro.Residue) return: spinSystem (src.cython.malandro.SpinSystem) ''' userDefinedSpinSystem = residue.userDefinedSolution if userDefinedSpinSystem and not userDefinedSpinSystem.getIsJoker() and not self.skipResidue(residue, userDefinedSpinSystem): return userDefinedSpinSystem return None def getSelectedSolutionSpinSystem(self, residue): '''I a solution corresponding to one specific run of the algorithm is defined, return which spinSystem in that run got assigned to the given residue. args: residue (src.cython.malandro.Residue) return: spinSystem (src.cython.malandro.SpinSystem) ''' solutions = residue.solutions spinSystem = solutions[self.selectedSolution - 1] if not spinSystem.getIsJoker() and not self.skipResidue(residue, spinSystem): return spinSystem return None def skipResidue(self, residue, spinSystem): '''One strategy is to skip all residues that already have a spin system assignment. If that is the case determine whether to skip the given residue. args: residue (src.cython.malandro.Residue) spinSystem (src.cython.malandro.SpinSystem) return: boolean, True if residue should be skipped. ''' if self.strategy == 0: assignedGroups = residue.getCcpnResidue().getResonanceGroups() assignedSerials = set([spinSys.serial for spinSys in assignedGroups]) if assignedSerials and spinSystem.getSerial() not in assignedSerials: return True return False
class WidgetCountPopup(BasePopup): on_off_entries = ['on', 'off'] def __init__(self, parent, help_msg='', help_url='', *args, **kw): self.help_msg = help_msg self.help_url = help_url BasePopup.__init__(self, parent=parent, title='Widget Count', *args, **kw) def body(self, master): self.alarm_id = None self.root_widget = getRoot(self) row = 0 label = Label(master, text='Widget count:') label.grid(row=row, column=0, sticky=Tkinter.W) self.count_label = Label(master, text='', tipText='Number of Tkinter widget objects') self.count_label.grid(row=row, column=1, sticky=Tkinter.W) row = row + 1 ind = 1 label = Label(master, text='Auto count:') label.grid(row=row, column=0, sticky=Tkinter.W) self.on_off_buttons = RadioButtons(master, entries=self.on_off_entries, select_callback=self.applyAuto, selected_index=ind) self.on_off_buttons.grid(row=row, column=1, sticky=Tkinter.EW) row = row + 1 label = Label(master, text='Auto frequency:') label.grid(row=row, column=0, sticky=Tkinter.W) self.freq_entry = IntEntry(master, text=60, returnCallback=self.applyAuto) self.freq_entry.grid(row=row, column=1, sticky=Tkinter.EW) label = Label(master, text='seconds') label.grid(row=row, column=2, sticky=Tkinter.W) row = row + 1 texts = ['Do Immediate Count'] commands = [self.applyManual] buttons = createDismissHelpButtonList(master, texts=texts, commands=commands, help_msg=self.help_msg, help_url=self.help_url) buttons.grid(row=row, column=0, columnspan=3, sticky=Tkinter.EW) self.doCount() def applyAuto(self, *event): on_off = self.on_off_buttons.get() if on_off == 'on': self.setCountOn() else: self.setCountOff() def applyManual(self): self.doCount() def setCountOn(self): self.setCountOff() freq = self.freq_entry.get() if freq is not None and freq > 0: freq *= 1000 # convert from sec to msec self.alarm_id = self.after(freq, self.doCountAuto) def setCountOff(self): if self.alarm_id: self.after_cancel(self.alarm_id) self.alarm_id = None def doCountAuto(self): if self.on_off_buttons.get() == 'on': self.doCount() freq = self.freq_entry.get() if freq is not None and freq > 0: freq *= 1000 # convert from sec to msec self.alarm_id = self.after(freq, self.doCountAuto) def doCount(self): count = getWidgetCount(self.root_widget) self.count_label.set('%d' % count)