class DangleGraphPopup(BasePopup): def __init__(self, parent): BasePopup.__init__(self, parent=parent, title=" Dangle Prediction Graph", transient=False, borderwidth=6) parent.protocol("WM_DELETE_WINDOW", self.close) self.geometry('700x700+50+50') def body(self, guiFrame): guiFrame.expandGrid(0,0) guiFrame.expandGrid(1,0) self.anglesGraph = ScrolledGraph(guiFrame, xLabel='Residue',yLabel='Angle', relief='flat', symbolSize=1, grid=(0,0), zoom=1.0,width=500,height=200, dataColors=['#D00000','#0000D0'], dataNames=['Phi','Psi']) self.anglesGraph.draw() self.islandsGraph = ScrolledGraph(guiFrame, xLabel='Residue',yLabel='No. Islands', relief='flat', graphType='histogram', zoom=1.0,width=500,height=200 ,grid=(1,0), dataColors=['#8080FF','#FFFF00','#E00000'], dataNames=['1','2-3','4+'],) self.islandsGraph.draw() def update(self, phiData, psiData, islandData): self.anglesGraph.update(dataSets=[phiData,psiData]) self.islandsGraph.update(dataSets=islandData)
def draw(self): self.drawContours() ScrolledGraph.draw(self) plotRegion = self.getPlotRegion() minX = self.minT1 maxX = self.maxT1 minY = self.minT2 maxY = self.maxT2 dataRegion = [minX, minY, maxX, maxY] deltaXplot = plotRegion[2] - plotRegion[0] deltaYplot = plotRegion[3] - plotRegion[1] deltaXdata = dataRegion[2] - dataRegion[0] deltaYdata = dataRegion[3] - dataRegion[1] ppvX = deltaXplot/float(deltaXdata) ppvY = deltaYplot/float(deltaYdata) createText = self.canvas.create_text for label, x, y in self.outlierLabels: x0 = (x - dataRegion[0])*ppvX y0 = (y - dataRegion[1])*ppvY x0 += plotRegion[0] y0 += plotRegion[1] item = createText(x0+8,y0, text=label, fill='#000000',anchor='w') self.contourItems.add(item)
class EditFitGraphPopup(BasePopup): """ **Analyse Function Curve Fitting to Peak Series Data** This popup is used to display the fit of a curve, of the displayed equation type, to data that has been extracted for a group of spectrum peaks from an NMR series. Precisely which kind of data is being fitted depends on the parent tool that this popup window was launched from. For example, for the `Follow Intensity Changes`_ tool the displayed graph is of a time or frequency value on the "X" axis (e.g. T1) verses peak intensity. For the `Follow Shift Changes`_ system the plot is for the parameters of the experiment titration on the "X" axis (e.g concentration) verses chemical shift distance. The upper graph shows the peak data that was used; the blue points, and the points of the fitted theoretical curve; red points. The lower table lists the data points for all of the peaks in the group, to which the data relates. There will be one peak for each row of the table, and hence point on the "X" axis. For each data point in the table the corresponding peak from which the data was extracted may be located with the "Follow in window" option, using the stated spectrum window and making marker lines as desired. Alternatively, the peak may be viewed in a table with [Show Peak] In general operation this system is used to check how well the selected function curve fits the peak data. The data that is displayed comes from the analysis tool that launched this popup. Any outliers may be removed using [Remove Point] (only with good reason) or the peaks themselves may be corrected if something has gone awry. Given that the display is launched from the selection of a specific group of peaks from a popup like `Follow Shift Changes`_ or `Follow Intensity Changes`_ and there are usually several peak groups that need to be analysed, the [Previous Set] and [Next Set] buttons can be used to quickly jump to the next peak group and see the next curve in the analysis results. .. _`Follow Intensity Changes`: CalcRatesPopup.html .. _`Follow Shift Changes`: FollowShiftChangesPopup.html """ def __init__(self, parent, dataFitting, getXYfunction, updateFunction, xLabel, yLabel, showObjectFunction=None, nextSetFunction=None, prevSetFunction=None, graphTitle='', **kw): self.guiParent = parent self.getXYfunction = getXYfunction self.updateFunction = updateFunction self.nextSetFunction = nextSetFunction self.prevSetFunction = prevSetFunction self.dataFitting = dataFitting self.object = None self.xLabel = xLabel self.yLabel = yLabel self.x = [] self.y = [] self.yFit = [] self.params = () self.chiSq = 0 self.method = dataFitting.fitFunction self.waiting = False self.noiseLevel = dataFitting.noiseLevel self.graphTitle = graphTitle self.windowPane = None self.mark = None BasePopup.__init__(self, parent=parent, title='Fit Graph', **kw) parent.protocol("WM_DELETE_WINDOW", self.close) def body(self, guiFrame): guiFrame.grid_columnconfigure(0, weight=1) row = 0 self.scrolledGraph = ScrolledGraph(guiFrame, width=400, height=300, symbolSize=5, symbols=['square', 'circle'], dataColors=['#000080', '#800000'], lineWidths=[0, 1], grid=(row, 0)) #self.scrolledGraph.setZoom(0.7) row += 1 frame = Frame(guiFrame, grid=(row, 0), sticky='ew') label = Label(frame, text='Fitting Function:', grid=(0, 0)) tipText = 'Selects which form of function to fit to the experimental data' self.methodPulldown = PulldownList(frame, self.changeMethod, grid=(0, 1), tipText=tipText) row += 1 frame = Frame(guiFrame, grid=(row, 0), sticky='ew') tipText = 'The effective equation of the final fitted graph, incorporating all parameters' self.equationLabel = Label(frame, text='Equation:', grid=(0, 0), tipText=tipText) tipText = 'The error in the fit of the selected parameterised function to the experimental data' self.errorLabel = Label(frame, text='Fit Error:', grid=(0, 1), tipText=tipText) row += 1 frame = Frame(guiFrame, grid=(row, 0), sticky='ew') label = Label(frame, text='Include x origin?:', grid=(0, 0)) tipText = 'Whether to include the x=0 point in the drawing' self.xOriginSelect = CheckButton(frame, callback=self.draw, grid=(0, 1), selected=False, tipText=tipText) label = Label(frame, text='Include y origin?:', grid=(0, 2)) tipText = 'Whether to include the y=0 point in the drawing' self.yOriginSelect = CheckButton(frame, callback=self.draw, grid=(0, 3), selected=False, tipText=tipText) label = Label(frame, text='Include y error?:', grid=(0, 4)) tipText = 'Whether to include the y error bars in the drawing (if these exist)' self.yErrorSelect = CheckButton(frame, callback=self.draw, grid=(0, 5), selected=False, tipText=tipText) row += 1 frame = Frame(guiFrame, grid=(row, 0), sticky='ew') label = Label(frame, text='Navigation Window:', grid=(0, 0)) tipText = 'Selects which spectrum window will be used for navigating to peak positions' self.windowPanePulldown = PulldownList(frame, self.changeWindow, grid=(0, 1), tipText=tipText) label = Label(frame, text='Follow in window?:', grid=(0, 2)) tipText = 'Whether to navigate to the position of the reference peak (for the group), in the selected window' self.followSelect = CheckButton(frame, callback=self.windowPaneNavigate, grid=(0, 3), selected=False, tipText=tipText) label = Label(frame, text='Mark Ref Peak?:', grid=(0, 4)) tipText = 'Whether to put a multi-dimensional cross-mark through the reference peak position, so it can be identified in spectra' self.markSelect = CheckButton(frame, callback=None, tipText=tipText, grid=(0, 5), selected=False) row += 1 guiFrame.grid_rowconfigure(row, weight=1) tipTexts = [ 'The number of the data point, in order of increasing X-axis value', 'For each point, the value of the parameter which is varied in the NMR series, e.g. T1, temperature, concentration etc.', 'For each point, the experimental value being fitted, e.g. peak intensity of chemical shift distance', 'The value of the best-fit function at the X-axis location', 'The difference between the experimental (Y-axis) value and the fitted value', 'The error in the experimental (Y-axis) value' ] headingList = ['Point', 'x', 'y', 'Fitted y', u'\u0394', 'y error'] self.scrolledMatrix = ScrolledMatrix(guiFrame, headingList=headingList, callback=self.selectObject, tipTexts=tipTexts, grid=(row, 0)) row += 1 tipTexts = [ 'Remove the selected data point, optionally removing the underlying peak', 'Show a table of spectrum peaks that correspond to the selected data point' ] texts = ['Remove Point', 'Show Peak'] commands = [self.removePoint, self.showObject] if self.prevSetFunction: texts.append('Previous Set') tipTexts.append( 'Move to the previous set of fitted values; the next group of peaks, often corresponding to a different residue or resonance' ) commands.append(self.prevSet) if self.nextSetFunction: tipTexts.append( 'Move to the next set of fitted values; the next group of peaks, often corresponding to a different residue or resonance' ) texts.append('Next Set') commands.append(self.nextSet) bottomButtons = UtilityButtonList(guiFrame, texts=texts, commands=commands, helpUrl=self.help_url, tipTexts=tipTexts, grid=(row, 0), doClone=False) self.removeButton = bottomButtons.buttons[0] for func in ('__init__', 'delete', 'setName'): self.registerNotify(self.updateWindows, 'ccpnmr.Analysis.SpectrumWindow', func) self.update() def destroy(self): for func in ('__init__', 'delete', 'setName'): self.unregisterNotify(self.updateWindows, 'ccpnmr.Analysis.SpectrumWindow', func) BasePopup.destroy(self) def nextSet(self): if self.nextSetFunction: self.nextSetFunction() self.windowPaneNavigate() def prevSet(self): if self.prevSetFunction: self.prevSetFunction() self.windowPaneNavigate() def windowPaneNavigate(self, event=None): if self.followSelect.get() and self.dataFitting: peaks = self.dataFitting.objects if self.windowPane and peaks: peak = peaks[int(len(peaks) / 2)] windowFrame = self.windowPane.getWindowFrame() windowFrame.gotoPeak(peak) if self.markSelect.get(): if self.mark and not self.mark.isDeleted: self.mark.delete() self.mark = createPeakMark(self.dataFitting.refObject) def getWindows(self): peaks = self.scrolledMatrix.objectList windowPanes = [] if peaks: peak = peaks[0] project = peak.root spectrum = peak.peakList.dataSource tryWindows = getActiveWindows(project) for window in tryWindows: for windowPane in window.sortedSpectrumWindowPanes(): if isSpectrumInWindowPane(windowPane, spectrum): windowPanes.append(windowPane) return windowPanes def changeWindow(self, windowPane): if windowPane is not self.windowPane: self.windowPane = windowPane self.windowPaneNavigate() def updateWindows(self, window=None): windowPanes = self.getWindows() index = -1 names = [getWindowPaneName(wp) for wp in windowPanes] windowPane = self.windowPane if windowPanes: if windowPane not in windowPanes: windowPane = windowPanes[0] index = windowPanes.index(windowPane) if windowPane is not self.windowPane: self.windowPane = windowPane self.windowPaneNavigate() self.windowPanePulldown.setup(names, windowPanes, index) def showObject(self): if self.object and (self.object.className == 'Peak'): peaks = [self.object] self.guiParent.guiParent.viewPeaks(peaks) def close(self): BasePopup.close(self) def changeMethod(self, index): if self.dataFitting: self.method = index self.dataFitting.fitFunction = self.method self.updateAfter() def updateMethods(self, *opt): n = len(METHOD_NAMES) if self.method >= n: self.method = 1 self.methodPulldown.setup(METHOD_NAMES, range(n), self.method) def selectObject(self, object, row, col): if object: self.object = object self.updateButtons() def removePoint(self): if self.object and (len(self.dataFitting.objects) > 2): self.dataFitting.objects.remove(self.object) if showYesNo('Query', 'Delete the corresponding %s?' % (self.object.className), parent=self): self.object.delete() self.updateAfter() def draw(self, *junk): title = '%s Function fit %s' % (self.graphTitle, METHOD_NAMES[self.method]) dataSet1 = [] dataSet2 = [] useErr = self.yErrorSelect.isSelected() if not useErr: useErr = None for i in range(len(self.scrolledMatrix.textMatrix)): row = self.scrolledMatrix.textMatrix[i] x = row[1] y = row[2] y2 = row[3] err = useErr and row[5] dataSet1.append([x, y, err]) dataSet2.append([x, y2]) dataSet1.sort() dataSet2.sort() if dataSet1 and dataSet2: drawOriginX = self.xOriginSelect.isSelected() drawOriginY = self.yOriginSelect.isSelected() self.scrolledGraph.update(dataSets=[dataSet1, dataSet2], xLabel=self.xLabel, yLabel=self.yLabel, title=title, drawOriginX=drawOriginX, drawOriginY=drawOriginY) self.scrolledGraph.draw() def updateAfter(self, *object): if self.waiting: return else: self.waiting = True self.after_idle(self.update) def update(self, dataFitting=None, xLabel=None, yLabel=None, graphTitle=None, force=False): if (not force) and dataFitting and (self.dataFitting is dataFitting): if (self.method, self.xLabel, self.yLabel, self.noiseLevel) == \ (self.dataFitting.fitFunction, xLabel, yLabel, self.dataFitting.noiseLevel): self.waiting = False return if dataFitting: self.dataFitting = dataFitting self.xLabel = xLabel or self.xLabel self.yLabel = yLabel or self.yLabel self.graphTitle = graphTitle or self.graphTitle if not self.dataFitting: self.waiting = False return else: dataFitting = self.dataFitting dataFitting = self.getXYfunction(dataFitting) if dataFitting.fitFunction is not None: self.method = dataFitting.fitFunction self.noiseLevel = dataFitting.noiseLevel or self.noiseLevel self.updateMethods() isFitted = dataFitting.fit() textMatrix = [] objectList = [] if isFitted and self.method: methodInfo = getFitMethodInfo()[self.method - 1] textFormat, indices = methodInfo[2] textParams = [dataFitting.parameters[i] or 0 for i in indices] equationText = textFormat % tuple(textParams) errorText = '%4f' % dataFitting.fitError x = dataFitting.dataX y = dataFitting.dataY yFit = dataFitting.fittedY N = len(x) err = hasattr(dataFitting, 'dataErr') and dataFitting.dataErr if not err: err = None # wb104: 10 Mar 2014: not sure why the below was here, it isn't needed #if self.method == 10: # x = [sqrt(v) for v in x] data = [(x[i], y[i], yFit[i], y[i] - yFit[i], dataFitting.objects[i], err and err[i]) for i in range(N)] data.sort() for i in range(N): xi, yi, yFiti, deltai, object, erri = data[i] textMatrix.append([i + 1, xi, yi, yFiti, deltai, erri]) objectList.append(object) else: equationText = 'Equation: <No Fit>' errorText = '<None>' x = dataFitting.dataX y = dataFitting.dataY for i, x in enumerate(x): textMatrix.append([i + 1, x, y[i], None, None, None]) objectList.append(dataFitting.objects[i]) self.equationLabel.set('Equation: %s' % equationText) self.errorLabel.set('Fit Error: %s' % errorText) self.scrolledMatrix.update(textMatrix=textMatrix, objectList=objectList) self.updateWindows() self.updateButtons() self.draw() if self.updateFunction: self.updateFunction(dataFitting) self.waiting = False def updateButtons(self): if self.object: self.removeButton.enable() else: self.removeButton.disable()
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)
class AnnealingSettingsTab(object): '''This class describes the tab in the GUI where the user can change setting that govern the monte carlo / annleaing procedure. This also includes which information from the ccpn analysis project is used and which information is ignored. This includes: * present sequential assignments * tentative assignments * amino acid type information * whether to include untyped spin systems * assignments to peak dimensions ALso the chain can be selected here. Furthermore the user can set the temperature regime of the annealing, the amount of times the procedure is repeated to obtain statistics. The fraction of peaks that is left out in each run to diversify the results, the treshhold score for amino acid typing and the treshhold collabelling for a peak to be expected. ''' 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 self.project = parent.project self.nmrProject = parent.nmrProject self.minIsoFrac = 0.1 self.leavePeaksOutFraction = 0.0 self.minTypeScore = 1.0 self.chain = None self.amountOfRepeats = 10 self.amountOfSteps = 10000 self.acceptanceConstantList = [0.0, 0.01, 0.015, 0.022, 0.033, 0.050, 0.075, 0.113, 0.170, 0.256, 0.384, 0.576, 0.864, 1.297, 1.946, 2.919, 4.378, 6.568, 9.852, 14.77, 22.16, 33.25] self.energyDataSets = [[]] self.residues = [] self.body() def body(self): '''describes the body of this tab. It bascically consists of some field to fill out for the user at the top and a ScrolledGraph that shows the progess of the annealing procedure a the bottom. ''' frame = self.frame # frame.expandGrid(13,0) frame.expandGrid(15, 1) row = 0 text = 'Calculate Assignment Suggestions' command = self.runCalculations self.startButton = Button(frame, command=command, text=text) self.startButton.grid(row=row, column=0, sticky='nsew', columnspan=2) row += 1 Label(frame, text='Amount of runs: ', grid=(row, 0)) tipText = 'The amount of times the whole optimization procedure is performed, each result is safed' self.repeatEntry = IntEntry(frame, grid=(row, 1), width=7, text=10, returnCallback=self.updateRepeatEntry, tipText=tipText, sticky='nsew') self.repeatEntry.bind('<Leave>', self.updateRepeatEntry, '+') row += 1 Label(frame, text='Temperature regime: ', grid=(row, 0)) tipText = 'This list of numbers govern the temperature steps during the annealing, every number represents 1/(kb*t), where kb is the Boltzmann constant and t the temperature of one step.' self.tempEntry = Entry(frame, text=map(str, self.acceptanceConstantList), width=64, grid=(row, 1), isArray=True, returnCallback=self.updateAcceptanceConstantList, tipText=tipText, sticky='nsew') row += 1 Label(frame, text='Amount of attempts per temperature:', grid=(row, 0)) tipText = 'The amount of attempts to switch the position of two spinsystems in the sequence are performed for each temperature point' self.NAStepEntry = IntEntry(frame, grid=(row, 1), width=7, text=10000, returnCallback=self.updateStepEntry, tipText=tipText, sticky='nsew') self.NAStepEntry.bind('<Leave>', self.updateStepEntry, '+') row += 1 Label(frame, text='Fraction of peaks to leave out:', grid=(row, 0)) tipText = 'In each run a fraction of the peaks can be left out of the optimization, thereby increasing the variability in the outcome and reducing false negatives. In each run this will be different randomly chosen sub-set of all peaks. 0.1 (10%) can be a good value.' self.leaveOutPeaksEntry = FloatEntry(frame, grid=(row, 1), width=7, text=0.0, returnCallback=self.updateLeavePeaksOutEntry, tipText=tipText, sticky='nsew') self.leaveOutPeaksEntry.bind( '<Leave>', self.updateLeavePeaksOutEntry, '+') row += 1 Label(frame, text='Minmal amino acid typing score:', grid=(row, 0)) tipText = 'If automatic amino acid typing is selected, a cut-off value has to set. Every amino acid type that scores higher than the cut-off is taken as a possible type. This is the same score as can be found under resonance --> spin systems --> predict type. Value should be between 0 and 100' self.minTypeScoreEntry = FloatEntry(frame, grid=(row, 1), width=7, text=1.0, returnCallback=self.updateMinTypeScoreEntry, tipText=tipText, sticky='nsew') self.minTypeScoreEntry.bind( '<Leave>', self.updateMinTypeScoreEntry, '+') row += 1 Label(frame, text='Minimal colabelling fraction:', grid=(row, 0)) tipText = 'The minimal amount of colabelling the different nuclei should have in order to still give rise to a peak.' self.minLabelEntry = FloatEntry(frame, grid=(row, 1), width=7, text=0.1, returnCallback=self.updateMinLabelEntry, tipText=tipText, sticky='nsew') self.minLabelEntry.bind('<Leave>', self.updateMinLabelEntry, '+') row += 1 Label(frame, text='Use sequential assignments:', grid=(row, 0)) tipText = 'When this option is select the present sequential assignments will be kept in place' self.useAssignmentsCheck = CheckButton( frame, selected=True, tipText=tipText, grid=(row, 1)) row += 1 Label(frame, text='Use tentative assignments:', grid=(row, 0)) tipText = 'If a spin system has tentative assignments this can be used to narrow down the amount of possible sequential assignments.' self.useTentativeCheck = CheckButton( frame, selected=True, tipText=tipText, grid=(row, 1)) row += 1 Label(frame, text='Use amino acid types:', grid=(row, 0)) tipText = 'Use amino acid types of the spin systems. If this option is not checked the spin systems are re-typed, only resonance names and frequencies are used' self.useTypeCheck = CheckButton( frame, selected=True, tipText=tipText, grid=(row, 1)) row += 1 Label(frame, text='Include untyped spin systems:', grid=(row, 0)) tipText = 'Also include spin system that have no type information. Amino acid typing will be done on the fly.' self.useAlsoUntypedSpinSystemsCheck = CheckButton( frame, selected=True, tipText=tipText, grid=(row, 1)) row += 1 Label(frame, text='Use dimensional assignments:', grid=(row, 0)) tipText = 'If one or more dimensions of a peak is already assigned, assume that this assignment is the only option. If not the check the program will consider all possibilities for the assignment of the dimension.' self.useDimensionalAssignmentsCheck = CheckButton( frame, selected=True, tipText=tipText, grid=(row, 1)) row += 1 Label(frame, text='Chain:', grid=(row, 0)) self.molPulldown = PulldownList( frame, callback=self.changeMolecule, grid=(row, 1)) self.updateChains() row += 1 Label(frame, text='Residue ranges: ', grid=(row, 0)) tipText = 'Which residues should be included. Example: "10-35, 62-100, 130".' self.residueRangeEntry = Entry(frame, text=None, width=64, grid=(row, 1), isArray=True, returnCallback=self.updateResidueRanges, tipText=tipText, sticky='nsew') self.updateResidueRanges(fromChain=True) row += 1 self.energyPlot = ScrolledGraph(frame, symbolSize=2, width=600, height=200, title='Annealing', xLabel='temperature step', yLabel='energy') self.energyPlot.grid(row=row, column=0, columnspan=2, sticky='nsew') def runCalculations(self): '''Run all calculations. Also triggers the disabling of some buttons and fields. ''' self.startButton.disable() self.disableIllegalButtonsAfterPrecalculations() self.guiParent.connector.runAllCalculations() self.startButton.configure(text='More runs') self.startButton.enable() def disableIllegalButtonsAfterPrecalculations(self): '''Disable buttons and field the user can not alter any longer after the model is set up and the 'pre-calculations' have finished. This is done because this part of the calculation should only be run once. All settings that would be changed after this point will not have any influence. ''' illegalButtons = [self.minTypeScoreEntry, self.minLabelEntry, self.useAlsoUntypedSpinSystemsCheck, self.useAssignmentsCheck, self.useTypeCheck, self.useDimensionalAssignmentsCheck, self.useTentativeCheck] for illegalButton in illegalButtons: illegalButton.configure(state='disabled') self.molPulldown.disable() def getChainName(self, chain): '''Get the name for a chain. args: chain: ccpn analysis chain object returns: chain name ''' return '%s:%s (%s)' % (chain.molSystem.code, chain.code, chain.molecule.molType) def getChains(self): '''Get all chains present in the project. returns: list of ccpn analysis chain objects ''' chains = [] if self.project: for molSystem in self.project.sortedMolSystems(): for chain in molSystem.sortedChains(): if chain.residues: chains.append(chain) return chains def updateChains(self, *opt): '''Updates the list of chains if a new one is added to or deleted from the project. Updates the pull down list where a chain can be selected. ''' index = 0 texts = [] chains = self.getChains() chain = self.chain if chains: if chain not in chains: chain = chains[0] texts = [self.getChainName(c) for c in chains] index = chains.index(chain) else: chain = None self.molPulldown.setup(texts, chains, index) if chain is not self.chain: self.chain = chain def changeMolecule(self, chain): '''Select a molecular chain.''' if chain is not self.chain: self.chain = chain self.updateResidueRanges(fromChain=True) def updateStepEntry(self, event=None): '''Update the value and entry that sets the amount of steps per temperature point. ''' value = self.NAStepEntry.get() if value == self.amountOfSteps: return if value < 1: self.NAStepEntry.set(1) self.amountOfSteps = 1 else: self.amountOfSteps = value self.NAStepEntry.set(value) def updateRepeatEntry(self, event=None): '''Update the value and entry of that sets the amount of times the whole annealing procedure is repeated in order to obtain statistics. ''' value = self.repeatEntry.get() if value == self.amountOfRepeats: return if value < 1: self.repeatEntry.set(1) self.amountOfRepeats = 1 else: self.amountOfRepeats = value self.repeatEntry.set(value) def updateMinTypeScoreEntry(self, event=None): '''Updates the value and the entry for the treshhold value for amino acid typing. ''' value = self.minTypeScoreEntry.get() if value == self.minTypeScore: return if value < 0: self.minTypeScoreEntry.set(0.0) self.minTypeScore = 0.0 elif value > 100: self.minTypeScoreEntry.set(100.0) self.minTypeScore = 100.0 else: self.minTypeScoreEntry.set(value) self.minTypeScore = value def updateMinLabelEntry(self, event=None): '''Updates the minimum colabelling fraction for which a peak is expected to be present in the spectra. ''' value = self.minLabelEntry.get() if value == self.minIsoFrac: return if value < 0: self.minIsoFrac = 0.0 self.minLabelEntry.set(0.0) elif value > 1: self.minIsoFrac = 1.0 self.minLabelEntry.set(1.0) else: self.minIsoFrac = value self.minLabelEntry.set(value) def updateLeavePeaksOutEntry(self, event=None): '''Updates the value and entry of the fraction of peaks that should be left out in each run in order to diversify the results. ''' value = self.leaveOutPeaksEntry.get() if value == self.leavePeaksOutFraction: return if value < 0: self.leavePeaksOutFraction = 0.0 self.leaveOutPeaksEntry.set(0.0) elif value > 1: self.leavePeaksOutFraction = 1.0 self.leaveOutPeaksEntry.set(1.0) else: self.leavePeaksOutFraction = value self.leaveOutPeaksEntry.set(value) def updateAcceptanceConstantList(self, event=None): '''Updates the list with constants that are used during the monte carlo procedure to decide whether a changed is accepted or not. ''' acList = self.tempEntry.get() newList = [] for constant in acList: try: number = float(constant) newList.append(number) except ValueError: string = constant + \ ' in temperature constants is not a number.' showWarning('Not A Number', string, parent=self.guiParent) return False self.acceptanceConstantList = newList return True def updateResidueRanges(self, event=None, fromChain=False): self.residues = set() subRanges = self.residueRangeEntry.get() if not subRanges or fromChain: self.residues = set(self.chain.residues) residues = self.chain.sortedResidues() text = '{}-{}'.format(residues[0].seqCode, residues[-1].seqCode) self.residueRangeEntry.set(text=text) return for subRange in subRanges: indeces = subRange.split('-') start = int(indeces[0]) stop = int(indeces[-1]) + 1 for seqCode in range(start, stop): residue = self.chain.findFirstResidue(seqCode=seqCode) if not residue: showWarning('Residue out of range.', 'There is no residue at position {}'.format(seqCode), parent=self.guiParent) self.residues = set() return self.residues.add(residue) def addEnergyPoint(self, energy, time): '''Adds a point to the graph that shows the progress of the annealling procedure. args: energy: the y-value time: the x-value ''' point = (time, energy * -1) # This means one run has finished if len(self.energyDataSets[-1]) / (len(self.acceptanceConstantList) + 1): self.energyDataSets.append([point]) else: self.energyDataSets[-1].append(point) colors = colorSeries Ncolors = len(colors) NdataSets = len(self.energyDataSets) colorList = (NdataSets / Ncolors) * colors + \ colors[:NdataSets % Ncolors] self.energyPlot.update(dataSets=self.energyDataSets, dataColors=colorList) # Forcing the graph to draw, eventhough calculations # are still running. Only do this with high numbers of # steps, otherwise drawing takes longer than annealling. if self.amountOfSteps >= 100000: self.energyPlot.draw()