def makeUI(model): table = JTable(model) jsp = JScrollPane(table) regex_label = JLabel("Search: ") regex_field = JTextField(20) top = JPanel() top.add(regex_label) top.add(regex_field) top.setLayout(BoxLayout(top, BoxLayout.X_AXIS)) base_path_label = JLabel("Base path:") base_path_field = JTextField(50) bottom = JPanel() bottom.add(base_path_label) bottom.add(base_path_field) bottom.setLayout(BoxLayout(bottom, BoxLayout.X_AXIS)) all = JPanel() all.add(top) all.add(jsp) all.add(bottom) all.setLayout(BoxLayout(all, BoxLayout.Y_AXIS)) frame = JFrame("File paths") frame.getContentPane().add(all) frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE) frame.addWindowListener(Closing()) frame.pack() frame.setVisible(True) # Listeners regex_field.addKeyListener(EnterListener(table, model, frame)) table.addMouseListener(RowClickListener(base_path_field)) # return model, table, regex_field, frame
def makeUI(model): # Components: table = JTable(model) jsp = JScrollPane(table) regex_label = JLabel("Search: ") regex_field = JTextField(20) base_path_label = JLabel("Base path:") base_path_field = JTextField(50) if base_path is not None: base_path_field.setText(base_path) # Panel for all components all = JPanel() all.setBorder(EmptyBorder(20, 20, 20, 20)) layout, c = GridBagLayout(), GC() all.setLayout(layout) # First row: label and regex text field add(all, regex_label, gridx=0, gridy=0) # with default constraints add(all, regex_field, gridx=1, gridy=0, fill=GC.HORIZONTAL, weightx=1.0) # Second row: the table add(all, jsp, gridx=0, gridy=1, fill=GC.BOTH, gridwidth=2, weightx=1.0, weighty=1.0) # full weights so it stretches when resizing # Third row: the base path add(all, base_path_label, gridx=0, gridy=2) add(all, base_path_field, gridx=1, gridy=2, fill=GC.HORIZONTAL, weightx=1.0) # Window frame frame = JFrame("File paths") frame.getContentPane().add(all) #frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE) frame.addWindowListener(Closing()) frame.pack() frame.setVisible(True) # Listeners regex_field.addKeyListener(EnterListener(table)) table.addMouseListener(RowClickListener(base_path_field)) al = ArrowListener(table, regex_field) table.addKeyListener(al) regex_field.addKeyListener(al) # Instead of a KeyListener, use the input vs action map table.getInputMap().put(KeyStroke.getKeyStroke(KeyEvent.VK_ENTER, 0), "enter") table.getActionMap().put("enter", OpenImageFromTableCell()) # return model, table, regex_field, frame
class MandersPlugin(ImageListener, WindowAdapter): def __init__(self): self.imp = None self.preview = None self.createMainWindow() self.cells = None self.files = [] self.results = ResultsTable() ImagePlus.addImageListener(self) self.selectInputDir() self.selectOutputDir() self.pairs = [] self.methods = [] self.processNextFile() def selectInputDir(self): inputDialog = DirectoryChooser("Please select a directory contaning your images") inputDir = inputDialog.getDirectory() for imageFile in os.listdir(inputDir): self.files.append(inputDir + imageFile) def selectOutputDir(self): outputDialog = DirectoryChooser("Please select a directory to save your results") self.outputDir = outputDialog.getDirectory() def closeImage(self): if self.imp is not None: self.imp.close() self.imp = None if self.preview is not None: self.preview.close() self.preview = None def openImage(self, imageFile): try: images = BF.openImagePlus(imageFile) self.imp = images[0] except UnknownFormatException: return None if self.imp.getNChannels() < 2: IJ.error("Bad image format", "Image must contain at lease 2 channels!") return None if not self.pairs or \ not self.methods: self.getOptionsDialog(self.imp) title = self.imp.title self.imp.title = title[:title.rfind('.')] return self.imp def getOptionsDialog(self, imp): thr_methods = ["None", "Default", "Huang", "Intermodes", "IsoData", "Li", "MaxEntropy","Mean", "MinError(I)", "Minimum", "Moments", "Otsu", "Percentile", "RenyiEntropy", "Shanbhag" , "Triangle", "Yen"] gd = GenericDialog("Please select channels to collocalize") for i in range(1, imp.getNChannels() + 1): gd.addChoice("Threshold method for channel %i" % i, thr_methods, "None") gd.showDialog() if gd.wasCanceled(): self.exit() channels = [] for i in range(1, imp.getNChannels() + 1): method = gd.getNextChoice() self.methods.append(method) if method != "None": channels.append(i) for x in channels: for y in channels: if x < y: self.pairs.append((x, y)) def processNextFile(self): if self.files: imageFile = self.files.pop(0) return self.processFile(imageFile) else: return False def processFile(self, imageFile): imp = self.openImage(imageFile) if imp is not None: cell = Cell(imp.NSlices, 1) self.cells = DelegateListModel([]) self.cells.append(cell) self.showMainWindow(self.cells) if self.checkbox3D.isSelected(): self.displayImage(imp) else: self.displayImage(imp, False) self.preview = self.previewImage(imp) self.displayImage(self.preview) return True else: return self.processNextFile() def displayImage(self, imp, show = True): imp.setDisplayMode(IJ.COMPOSITE) enhancer = ContrastEnhancer() enhancer.setUseStackHistogram(True) splitter = ChannelSplitter() for c in range(1, imp.getNChannels() + 1): imp.c = c enhancer.stretchHistogram(imp, 0.35) if show: imp.show() def previewImage(self, imp): roi = imp.getRoi() splitter = ChannelSplitter() channels = [] for c in range(1, imp.getNChannels() + 1): channel = ImagePlus("Channel %i" % c, splitter.getChannel(imp, c)) projector = ZProjector(channel) projector.setMethod(ZProjector.MAX_METHOD) projector.doProjection() channels.append(projector.getProjection()) image = RGBStackMerge.mergeChannels(channels, False) image.title = imp.title + " MAX Intensity" image.luts = imp.luts imp.setRoi(roi) return image def getCroppedChannels(self, imp, cell): splitter = ChannelSplitter() imp.setRoi(None) if cell.mode3D: cropRoi = cell.getCropRoi() else: cropRoi = cell.roi if cropRoi is None: return None crop = cropRoi.getBounds() channels = [] for c in range(1, imp.getNChannels() + 1): slices = ImageStack(crop.width, crop.height) channel = splitter.getChannel(imp, c) for z in range(1, channel.getSize() + 1): zslice = channel.getProcessor(z) zslice.setRoi(cropRoi) nslice = zslice.crop() if cell.mode3D: oroi = cell.slices[z - 1].roi else: oroi = cell.roi if oroi is not None: roi = oroi.clone() bounds = roi.getBounds() roi.setLocation(bounds.x - crop.x, bounds.y - crop.y) nslice.setColor(Color.black) nslice.fillOutside(roi) slices.addSlice(nslice) channels.append(ImagePlus("Channel %i" % c, slices)) return channels def getThreshold(self, imp, method): thresholder = Auto_Threshold() duplicator = Duplicator() tmp = duplicator.run(imp) return thresholder.exec(tmp, method, False, False, True, False, False, True) def getContainer(self, impA, impB): imgA = ImagePlusAdapter.wrap(impA) imgB = ImagePlusAdapter.wrap(impB) return DataContainer(imgA, imgB, 1, 1, "imageA", "imageB") def getManders(self, imp, cell): ### Crop channels according to cell mask channels = self.getCroppedChannels(imp, cell) if channels is None: return None ### Calculate channel thresholds thrs = [] thrimps = [] for c, method in enumerate(self.methods): if method != "None": thr, thrimp = self.getThreshold(channels[c], method) else: thr, thrimp = None, None thrs.append(thr) thrimps.append(thrimp) ### Calculate manders colocalization manders = MandersColocalization() raws = [] thrds = [] for chA, chB in self.pairs: container = self.getContainer(channels[chA - 1], channels[chB - 1]) img1 = container.getSourceImage1() img2 = container.getSourceImage2() mask = container.getMask() cursor = TwinCursor(img1.randomAccess(), img2.randomAccess(), Views.iterable(mask).localizingCursor()) rtype = img1.randomAccess().get().createVariable() raw = manders.calculateMandersCorrelation(cursor, rtype) rthr1 = rtype.copy() rthr2 = rtype.copy() rthr1.set(thrs[chA - 1]) rthr2.set(thrs[chB - 1]) cursor.reset() thrd = manders.calculateMandersCorrelation(cursor, rthr1, rthr2, ThresholdMode.Above) raws.append(raw) thrds.append(thrd) return (channels, thrimps, thrs, raws, thrds) def saveMultichannelImage(self, title, channels, luts): tmp = RGBStackMerge.mergeChannels(channels, False) tmp.luts = luts saver = FileSaver(tmp) saver.saveAsTiffStack(self.outputDir + title + ".tif") tmp.close() def createMainWindow(self): self.frame = JFrame('Select cells and ROIs', defaultCloseOperation = JFrame.DISPOSE_ON_CLOSE ) self.frame.setLayout(GridBagLayout()) self.frame.addWindowListener(self) self.frame.add(JLabel("Cells"), GridBagConstraints(0, 0, 1, 1, 0, 0, GridBagConstraints.CENTER, GridBagConstraints.NONE, Insets(5, 2, 2, 0), 0, 0 )) self.cellList = JList(DelegateListModel([]), selectionMode = ListSelectionModel.SINGLE_SELECTION, cellRenderer = MyRenderer(), selectedIndex = 0, valueChanged = self.selectCell ) self.frame.add(JScrollPane(self.cellList), GridBagConstraints(0, 1, 1, 5, .5, 1, GridBagConstraints.CENTER, GridBagConstraints.BOTH, Insets(0, 2, 2, 0), 0, 0 )) self.frame.add(JButton('Add cell', actionPerformed = self.addCell), GridBagConstraints(1, 2, 1, 2, 0, .25, GridBagConstraints.CENTER, GridBagConstraints.NONE, Insets(0, 0, 0, 0), 0, 0 )) self.frame.add(JButton('Remove cell', actionPerformed = self.removeCell), GridBagConstraints(1, 4, 1, 2, 0, .25, GridBagConstraints.CENTER, GridBagConstraints.NONE, Insets(0, 5, 0, 5), 0, 0 )) self.frame.add(JLabel("Slices"), GridBagConstraints(0, 6, 1, 1, 0, 0, GridBagConstraints.CENTER, GridBagConstraints.NONE, Insets(5, 2, 2, 0), 0, 0 )) self.sliceList = JList(DelegateListModel([]), selectionMode = ListSelectionModel.SINGLE_SELECTION, cellRenderer = MyRenderer(), selectedIndex = 0, valueChanged = self.selectSlice ) self.frame.add(JScrollPane(self.sliceList), GridBagConstraints(0, 7, 1, 5, .5, 1, GridBagConstraints.CENTER, GridBagConstraints.BOTH, Insets(0, 2, 2, 0), 0, 0 )) self.frame.add(JButton('Update ROI', actionPerformed = self.updateSlice), GridBagConstraints(1, 8, 1, 2, 0, .25, GridBagConstraints.CENTER, GridBagConstraints.NONE, Insets(0, 0, 0, 0), 0, 0 )) self.frame.add(JButton('Done', actionPerformed = self.doneSelecting), GridBagConstraints(1, 10, 1, 2, 0, .25, GridBagConstraints.CENTER, GridBagConstraints.NONE, Insets(0, 0, 0, 0), 0, 0 )) self.checkbox3D = JCheckBox('3D selection mode', True, actionPerformed=self.toggle3D) self.frame.add(self.checkbox3D, GridBagConstraints(0, 13, 2, 1, 0, 1, GridBagConstraints.WEST, GridBagConstraints.NONE, Insets(0, 0, 0, 0), 0, 0 )) def showMainWindow(self, cells = None): if cells is not None: self.cellList.model = cells if cells: self.cellList.selectedIndex = 0 self.frame.pack() self.frame.visible = True def hideMainWindow(self): self.frame.visible = False def closeMainWindow(self): self.frame.dispose() def toggle3D(self, event): mode3D = self.checkbox3D.isSelected() if mode3D: self.sliceList.enabled = True if self.imp is not None: self.imp.show() if self.preview is not None: self.preview.hide() else: self.sliceList.enabled = False if self.preview is None: self.preview = self.previewImage(self.imp) self.displayImage(self.preview) else: self.preview.show() if self.imp is not None: self.imp.hide() selectedCell = self.cellList.selectedIndex if selectedCell >= 0: cell = self.cells[selectedCell] self.sliceList.model = cell.slices self.sliceList.selectedIndex = 0 def addCell(self, event): size = len(self.cells) if (size > 0): last = self.cells[size - 1] n = last.n + 1 else: n = 1 self.cells.append(Cell(self.imp.NSlices, n)) self.cellList.selectedIndex = size def removeCell(self, event): selected = self.cellList.selectedIndex if selected >= 0: self.cells.remove(self.cells[selected]) if (selected >= 1): self.cellList.selectedIndex = selected - 1 else: self.cellList.selectedIndex = 0 def selectCell(self, event): selected = self.cellList.selectedIndex if selected >= 0: cell = self.cells[selected] self.sliceList.model = cell.slices self.sliceList.selectedIndex = 0 else: self.sliceList.model = DelegateListModel([]) if self.preview is not None: self.preview.setRoi(cell.roi) def selectSlice(self, event): selectedCell = self.cellList.selectedIndex selectedSlice = self.sliceList.selectedIndex if selectedCell >= 0 and selectedSlice >= 0: cell = self.cells[selectedCell] image = self.imp mode3D = self.checkbox3D.isSelected() if image is not None and cell is not None and mode3D: roi = cell.slices[selectedSlice].roi if (image.z - 1 != selectedSlice): image.z = selectedSlice + 1 image.setRoi(roi, True) if self.preview is not None and not mode3D: self.preview.setRoi(cell.roi, True) def updateSlice(self, event): if self.checkbox3D.isSelected(): self.updateSlice3D(self.imp) else: self.updateSlice2D(self.preview) def updateSlice3D(self, imp): selectedCell = self.cellList.selectedIndex selectedSlice = self.sliceList.selectedIndex if selectedCell >= 0 and selectedSlice >= 0 and imp is not None: cell = self.cells[selectedCell] impRoi = imp.getRoi() if cell is not None and impRoi is not None: index = selectedSlice + 1 roi = ShapeRoi(impRoi, position = index) cell.mode3D = True cell.name = "Cell %i (3D)" % cell.n cell.slices[selectedSlice].roi = roi if (index + 1 <= len(cell.slices)): imp.z = index + 1 self.cellList.repaint(self.cellList.getCellBounds(selectedCell, selectedCell)) self.sliceList.repaint(self.sliceList.getCellBounds(selectedSlice, selectedSlice)) def updateSlice2D(self, imp): selectedCell = self.cellList.selectedIndex if selectedCell >= 0 and imp is not None: cell = self.cells[selectedCell] impRoi = imp.getRoi() if cell is not None and impRoi is not None: roi = ShapeRoi(impRoi, position = 1) cell.mode3D = False cell.name = "Cell %i (2D)" % cell.n cell.roi = roi self.cellList.repaint(self.cellList.getCellBounds(selectedCell, selectedCell)) def imageOpened(self, imp): pass def imageClosed(self, imp): pass def imageUpdated(self, imp): if self.checkbox3D.isSelected(): if imp is not None: selectedCell = self.cellList.selectedIndex selectedSlice = imp.z - 1 if imp == self.imp and selectedSlice != self.sliceList.selectedIndex: self.sliceList.selectedIndex = selectedSlice def doneSelecting(self, event): oluts = self.imp.luts luts = [] channels = [] for c, method in enumerate(self.methods): if method != "None": luts.append(oluts[c]) channels.append(c) for cell in self.cells: manders = self.getManders(self.imp, cell) if manders is not None: chimps, thrimps, thrs, raws, thrds = manders index = self.cells.index(cell) + 1 title = "Cell_%i-" % index + self.imp.title self.saveMultichannelImage(title, chimps, oluts) title = "Cell_%i_thrd-" % index + self.imp.title self.saveMultichannelImage(title, thrimps, luts) self.results.incrementCounter() row = self.results.getCounter() - 1 for i, thr in enumerate(thrs): if thr is not None: self.results.setValue("Threshold %i" % (i + 1), row, int(thr)) for i, pair in enumerate(self.pairs): self.results.setValue("%i-%i M1 raw" % pair, row, float(raws[i].m1)) self.results.setValue("%i-%i M2 raw" % pair, row, float(raws[i].m2)) self.results.setValue("%i-%i M1 thrd" % pair, row, float(thrds[i].m1)) self.results.setValue("%i-%i M2 thrd" % pair, row, float(thrds[i].m2)) self.closeImage() if not self.processNextFile(): print "All done - happy analysis!" self.results.show("Manders collocalization results") self.exit() def windowClosing(self, e): print "Closing plugin - BYE!!!" self.exit() def exit(self): ImagePlus.removeImageListener(self) self.closeImage() self.closeMainWindow()
class TicTacToeGame(WindowAdapter): # Tic Tac Toe game with Mario and Dizzy animated icons/music. # Computer plays with Mario and player plays with Dizzy. # game title game_title = "Tic Tac Toe: You vs Mario" # welcome status message. welcome_status = "Welcome! Please make your first move." # in-game status message. in_game_status = "Mario chases You! Hurry up!" # board 3x3 with the default color - white board = [[' ', ' ', ' '], [' ', ' ', ' '], [' ', ' ', ' ']] # total number of cells size = len(board) * len(board) # size of cell tile_size = 128 # status bar height status_bar_height = 50 # status bar top margin status_bar_margin_top = -15 # status bar left margin status_bar_margin_left = 10 # number of cells in a row/column cells = 3 # winner winner = None # Mario image mario = '/MARIO_128x128.gif' # Dizzy image dizzy = None # Blank blank = '/BLANK.gif' # supported musice sounds sounds = ['/DIZZY.wav', '/MARIO.wav'] # currently played sound sound = None # last chosen sound last_sound = 0 # won sound won_sound = '/WON.wav' # lose sound lose_sound = '/LOSE.wav' # tie sound tie_sound = '/TIE.wav' # action sound action_sound = '/ACTION.wav' def __init__(self, resources_directory): # Game constructor. # # Parameters: # resources_directory Directory to look for images and audio files. is_windows = platform.platform().lower().find('win') > 0 self.main_window_padding_right = 20 if is_windows else 0 self.main_window_padding_bottom = 40 if is_windows else 0 self.resources_directory = resources_directory self.button1 = JButton("", actionPerformed=self.clicked1) self.button2 = JButton("", actionPerformed=self.clicked2) self.button3 = JButton("", actionPerformed=self.clicked3) self.button4 = JButton("", actionPerformed=self.clicked4) self.button5 = JButton("", actionPerformed=self.clicked5) self.button6 = JButton("", actionPerformed=self.clicked6) self.button7 = JButton("", actionPerformed=self.clicked7) self.button8 = JButton("", actionPerformed=self.clicked8) self.button9 = JButton("", actionPerformed=self.clicked9) image_size = self.tile_size self.button1.setBounds(0 * image_size, 0 * image_size, image_size, image_size) self.button2.setBounds(1 * image_size, 0 * image_size, image_size, image_size) self.button3.setBounds(2 * image_size, 0 * image_size, image_size, image_size) self.button4.setBounds(0 * image_size, 1 * image_size, image_size, image_size) self.button5.setBounds(1 * image_size, 1 * image_size, image_size, image_size) self.button6.setBounds(2 * image_size, 1 * image_size, image_size, image_size) self.button7.setBounds(0 * image_size, 2 * image_size, image_size, image_size) self.button8.setBounds(1 * image_size, 2 * image_size, image_size, image_size) self.button9.setBounds(2 * image_size, 2 * image_size, image_size, image_size) self.buttons = [ self.button1, self.button2, self.button3, self.button4, self.button5, self.button6, self.button7, self.button8, self.button9 ] self.buttons_mapped = [[self.button1, self.button2, self.button3], [self.button4, self.button5, self.button6], [self.button7, self.button8, self.button9]] width = self.tile_size * self.cells height = width self.frame = JFrame(self.game_title, size=(width, height + self.status_bar_height)) self.frame.setLocation(200, 100) self.frame.setLayout(None) for button in self.buttons: self.frame.add(button) self.status_label = JLabel("") self.status_label.setBounds(self.status_bar_margin_left, height + self.status_bar_margin_top, width, self.status_bar_height) self.frame.add(self.status_label) self.frame.setVisible(True) self.frame.addWindowListener(self) random.shuffle(self.sounds) self.restart() # Restarts the game. def restart(self): self.dizzy = None self.dizzy = self.choosePlayer() self.winner = None self.board = [[' ', ' ', ' '], [' ', ' ', ' '], [' ', ' ', ' ']] for button in self.buttons: button.setIcon(ImageIcon(self.resources_directory + self.blank)) self.stop_playing_background() self.sound = self.play_sound_safe(self.sounds[self.last_sound]) self.last_sound = self.last_sound + 1 if self.last_sound >= len(self.sounds): self.last_sound = 0 self.status_label.setText(self.welcome_status) # Stops playing any background music, if any playing now. def stop_playing_background(self): if self.sound != None: self.sound.stopPlaying() self.sound = None def set_dizzy(self, button): # Draws Dizzy in a given button, sets game status to "Playing" and # plays action sound. # # Parameters: # button to set Dizzy icon to. button.setIcon(ImageIcon(self.resources_directory + self.dizzy)) self.status_label.setText(self.in_game_status) self.play_sound_safe(self.action_sound) def set_mario(self, button): # Draws Mario in a given button. # # Parameters: # button to set Mario icon to. button.setIcon(ImageIcon(self.resources_directory + self.mario)) def clicked1(self, event): # Event listener method for the button of the game at 0x0. # # Parameters: # event Click event. if self.board[0][0] != ' ': return self.board[0][0] = 'X' self.set_dizzy(self.button1) self.computer_move() def clicked2(self, event): # Event listener method for the button of the game at 0x1. # # Parameters: # event Click event. if self.board[0][1] != ' ': return self.board[0][1] = 'X' self.set_dizzy(self.button2) self.computer_move() def clicked3(self, event): # Event listener method for the button of the game at 0x2. # # Parameters: # event Click event. if self.board[0][2] != ' ': return self.board[0][2] = 'X' self.set_dizzy(self.button3) self.computer_move() def clicked4(self, event): # Event listener method for the button of the game at 1x0. # # Parameters: # event Click event. if self.board[1][0] != ' ': return self.board[1][0] = 'X' self.set_dizzy(self.button4) self.computer_move() def clicked5(self, event): # Event listener method for the button of the game at 1x1. # # Parameters: # event Click event. if self.board[1][1] != ' ': return self.board[1][1] = 'X' self.set_dizzy(self.button5) self.computer_move() def clicked6(self, event): # Event listener method for the button of the game at 1x2. # # Parameters: # event Click event. if self.board[1][2] != ' ': return self.board[1][2] = 'X' self.set_dizzy(self.button6) self.computer_move() def clicked7(self, event): # Event listener method for the button of the game at 2x0. # # Parameters: # event Click event. if self.board[2][0] != ' ': return self.board[2][0] = 'X' self.set_dizzy(self.button7) self.computer_move() def clicked8(self, event): # Event listener method for the button of the game at 2x1. # Parameters: # event Click event. if self.board[2][1] != ' ': return self.board[2][1] = 'X' self.set_dizzy(self.button8) self.computer_move() def clicked9(self, event): # Event listener method for the button of the game at 2x2. # # Parameters: # event Click event. if self.board[2][2] != ' ': return self.board[2][2] = 'X' self.set_dizzy(self.button9) self.computer_move() # Makes the next move on the board on behalf of the computer. def computer_move(self): # first move optimization - always start in the middle if possible if self.board[1][1] == ' ': self.board[1][1] = '0' self.set_mario(self.buttons_mapped[1][1]) self.test_state() return while self.has_empty_cell(): y = random.randint(0, self.cells - 1) x = random.randint(0, self.cells - 1) if self.board[y][x] == ' ': self.board[y][x] = '0' self.set_mario(self.buttons_mapped[y][x]) break self.test_state() def test_state(self): # Tests the board for a winning state. # If there is a winner then stops currently playing # background sound, creates winning label, plays result # sound and notifies/asks the user about continuation. if self.is_any_line_filled('X'): self.winner = self.dizzy # dizzy elif self.is_any_line_filled('0'): self.winner = self.mario # mario elif not self.has_empty_cell(): self.winner = self.blank # tie if self.winner: label = 'Tie.' self.stop_playing_background() if self.winner == self.mario: label = 'You lose!' self.play_sound_safe(self.lose_sound) elif self.winner == self.dizzy: label = 'You won!' self.play_sound_safe(self.won_sound) else: self.play_sound_safe(self.tie_sound) self.notify_and_ask_about_continuation(label) def notify_and_ask_about_continuation(self, label): # Shows modal window with the result of the game and asks the use whether they want to # continue the game. # If user answers "Y" or "y" restarts the game. # If user answers "N" or "n" closes the game window and frees the resources. # Parameters: # label Game result label. answer = None self.status_label.setText(label) while True: answer = str( requestString(label + "\r\n" + "Do you want to play again? (Y/N)")) if answer.lower() == "y": self.restart() break elif answer.lower() == "n": self.windowClosing(None) break def is_any_line_filled(self, character): # Checks the winning condition for the given character 'X' or '0'. # # Returns: # Whether the given character 'X' or '0' has a winning line filled. is_row = self.is_row_filled(character) is_col = self.is_col_filled(character) is_d1 = self.is_diag_filled1(character) is_d2 = self.is_diag_filled2(character) return is_row or is_col or is_d1 or is_d2 def has_empty_cell(self): #Checks if the game board contains an empty cell for the next move. # #Returns: # Whether there is an empty cell on the board. for row in range(len(self.board)): for col in range(len(self.board)): if self.board[row][col] == ' ': return True return False def is_row_filled(self, color): # Check row win condition. # # Parameters: # color (string) - color to check if the whole row of the same color # Returns: # True (boolean) - if the whole row of the same color # False (boolean) - if the row is not of the same color for row in range(len(self.board)): count = 0 for col in range(len(self.board)): if self.board[row][col] == color: count = count + 1 if count == self.cells: return True return False def is_col_filled(self, color): #Check column win condition. # # Parameters: # color (string) - color to check if the whole column of the same color # Returns: # True (boolean) - if the whole column of the same color # False (boolean) - if the column is not of the same color for col in range(len(self.board)): count = 0 for row in range(len(self.board)): if self.board[row][col] == color: count = count + 1 if count == self.cells: return True return False def is_diag_filled1(self, color): # Checks first diagonal win condition. # # Parameters: # color (string) - color to check if the whole diagonal of the same color # Returns: # True (boolean) - if the whole diagonal of the same color # False (boolean) - if the diagonal is not of the same color count = 0 for idx in range(len(self.board)): if self.board[idx][idx] == color: count = count + 1 return count == self.cells def is_diag_filled2(self, color): # Checks second diagonal win condition. # # Parameters: # color (string) - color to check if the whole diagonal of the same color # Returns: # True (boolean) - if the whole diagonal of the same color # False (boolean) - if the diagonal is not of the same color count = 0 for idx in range(len(self.board)): if self.board[idx][self.cells - 1 - idx] == color: count = count + 1 return count == self.cells def play_sound_safe(self, sound): # Method tries to play given sound catching possible exceptions. # For example, if the sound wasn't found in resource directory # # Parameters: # sound string with a file of a sound with leading slash '/'. # Returns: # Created Sound object fromo makeSound. snd = None try: snd = makeSound(self.resources_directory + sound) play(snd) except: showError("Error while playing sound " + str(sound) + ".") return snd def windowClosing(self, event): # Method is invoked when a user closes game window or finishes playing. # It is the implementation of WindowAdapter interface. # # Parameters: final event from Swing/AWT self.stop_playing_background() self.buttons = [] self.buttons_mapped = [] self.button1 = None self.button2 = None self.button3 = None self.button4 = None self.button5 = None self.button6 = None self.button7 = None self.button8 = None self.button9 = None self.status_label = None self.frame.getContentPane().removeAll() self.frame.dispose() self.frame = None def choosePlayer(self): while true: select = requestString( "You are against Mario. Choose Your Character: penguin chrome fox fish bird charizard sonic " ) selection = select.lower() if selection == "penguin": return rpenguin break if selection == "chrome": return rchrome break if selection == "fox": return rfox break if selection == "fish": return rfish break if selection == "bird": return rbird break if selection == "charizard": return rcharizard break if selection == "sonic": return rsonic break
# Pack all the fields into a JPanel all = JPanel() layout = GridLayout(4, 1) all.setLayout(layout) all.add( JLabel(" ") ) all.add( button ) all.add( JLabel("Min") ) all.add( minField ) all.add( JLabel("Max") ) all.add(maxField ) all.add( JLabel("Score :") ) all.add(scoreField) frame = JFrame("CCM scoring") frame.getContentPane().add(JScrollPane(all)) frame.pack() frame.addWindowListener( Closing() ) scoreField.requestFocusInWindow() # Get the grid files chooser = JFileChooser() chooser.setDialogTitle("Choose plate grids") chooser.setMultiSelectionEnabled(True) chooser.setCurrentDirectory( File(os.path.expanduser("~"))) chooser.showOpenDialog(JPanel()) # This is a hack to get a file path from the # sun.awt.shell.DefaultShellFolder object returned by the chooser fp = [str(i) for i in chooser.getSelectedFiles()] if len(fp) != 0: gd = GenericDialog("Name your output file")
class Pipeline(): def __init__(self): #If a swing interface is asked for this will be the JFrame. self.frame = None #Keeps track of the number of queries processed. self.jobCount = 0 #Keeps track of the query currently being processed. self.currentJob = "" #Keeps track of the massage to be displayed. self.message = 0 #Messages to be displayed at each stage in the processing of a single query. self.messages = ["Searching for genes via genemark", "Extending genes found via genemark", "Searching for intergenic genes", "Removing overlapping genes", "Searching for promoters", "Using transterm to find terminators", "Removing transcription signals which conflict with genes", "Using tRNAscan to find transfer RNAs", "Writing Artemis file", "Writing summary .xml, .html, and .xls files"] self.exception = None def initializeDisplay(self, queries, swing): """ queries: A list of the fasts files to be processed. swing: If true then updates about progress will be displayed in a swing window, otherwise they will be written to stdout. Initializes the interface for telling the user about progress in the pipeline. Queries is used to count the number of queries the pipeline will process and to size the swing display(if it is used) so that text isn't cutoff at the edge of the window. The swing display is setup if swing is true. """ self.numJobs = len(queries) if swing: self.frame = JFrame("Neofelis") self.frame.addWindowListener(PipelineWindowAdapter(self)) contentPane = JPanel(GridBagLayout()) self.frame.setContentPane(contentPane) self.globalLabel = JLabel(max(queries, key = len)) self.globalProgress = JProgressBar(0, self.numJobs) self.currentLabel = JLabel(max(self.messages, key = len)) self.currentProgress = JProgressBar(0, len(self.messages)) self.doneButton = JButton(DoneAction(self.frame)) self.doneButton.setEnabled(False) constraints = GridBagConstraints() constraints.gridx, constraints.gridy = 0, 0 constraints.gridwidth, constraints.gridheight = 1, 1 constraints.weightx = 1 constraints.fill = GridBagConstraints.HORIZONTAL contentPane.add(self.globalLabel, constraints) constraints.gridy = 1 contentPane.add(self.globalProgress, constraints) constraints.gridy = 2 contentPane.add(self.currentLabel, constraints) constraints.gridy = 3 contentPane.add(self.currentProgress, constraints) constraints.gridy = 4 constraints.weightx = 0 constraints.fill = GridBagConstraints.NONE constraints.anchor = GridBagConstraints.LINE_END contentPane.add(self.doneButton, constraints) self.frame.pack() self.frame.setResizable(False) self.globalLabel.setText(" ") self.currentLabel.setText(" ") self.frame.setLocationRelativeTo(None) self.frame.setVisible(True) def updateProgress(self, job): """ query: Name of the query currently being processed. This function use used for updating the progress shown in the interface. If job is not equal to currentJob then global progress is incremented and shown and the currentProgress is reset and shown. If job is equal to currentJob then the globalProgress does not change and currentProgress is increased. """ if self.exception: raise self.exception if self.frame: if job != self.currentJob: self.currentProgress.setValue(self.currentProgress.getMaximum()) self.globalLabel.setText(job) self.globalProgress.setValue(self.jobCount) print "Processing %s, %.2f%% done" % (job, 100.0*self.jobCount/self.numJobs) self.jobCount += 1 self.currentJob = job self.message = -1 self.message += 1 print " %s, %.2f%% done" % (self.messages[self.message], 100.0*self.message/len(self.messages)) self.currentProgress.setValue(self.message) self.currentLabel.setText(self.messages[self.message]) else: if job != self.currentJob: print "Processing %s, %.2f%% done" % (job, 100.0*self.jobCount/self.numJobs) self.jobCount += 1 self.currentJob = job self.message = -1 self.message += 1 print " %s, %.2f%% done" % (self.messages[self.message], 100.0*self.message/len(self.messages)) def finished(self): """ This function is to be called at the end of the pipeline. Informs the user that the pipeline is finished and if a swing interface is being used the Done button is enabled. """ print "Processing 100.00% done" if self.frame: self.globalLabel.setText("Finished") self.globalProgress.setValue(self.globalProgress.getMaximum()) self.currentLabel.setText(" ") self.currentProgress.setValue(self.currentProgress.getMaximum()) self.doneButton.setEnabled(True) while self.frame.isVisible(): pass def run(self, blastLocation, genemarkLocation, transtermLocation, tRNAscanLocation, database, eValue, matrix, minLength, scaffoldingDistance, promoterScoreCutoff, queries, swing = False, email = ""): """ blastLocation: Directory blast was installed in. genemarkLocation: Directory genemark was installed in. transtermLocation: Directory transterm was installed in. tRNAscanLocation: Directory tRNAscan was installed in. database: Name of the blast database to use. eValue: The e value used whenever a blast search is done. matrix: The matrix to use when running genemark. If None then genemark is run heuristically. minLength: Minimum length of any genes included in the resulting annotation. scaffoldingDistance: The maximum length allowed between genes when contiguous regions of genes are being identified promoterScoreCutoff: Minimum score allowed for any promoters included in the resulting annotation queries: A list of faster files to process. swing: If true a swing window will be used to updated the user about the pipeline's progress. email: If this is a non-empty string an email will be sent to the address in the string when the pipeline is done. This will be attempted with the sendmail command on the local computer. The main pipeline function. For every query genemark is used to predict genes, these genes are then extended to any preferable starts. Then the pipeline searches for any intergenic genes(genes between those found by genemark) and these are combined with the extended genemark genes. Then the genes are pruned to remove any undesirable genes found in the intergenic stage. BPROM and Transterm are used to find promoters and terminators, which are then pruned to remove any signals which are inside or too far away from any genes. Next, tRNAscan is used to find any transfer RNAs in the genome. Finally, all the remaining genes, promoters, and terminators are written to an artemis file in the directory of the query with the same name but with a .art extension, and .xml, .html, and .xls files will be generating describing the blast results of the final genes. """ self.initializeDisplay(queries, swing) try: for query in queries: name = os.path.splitext(query)[0] queryDirectory, name = os.path.split(name) genome = utils.loadGenome(query) swapFileName = "query" + str(id(self)) + ".fas" queryFile = open(swapFileName, "w") queryFile.write(">" + name + "\n") for i in range(0, len(genome), 50): queryFile.write(genome[i:min(i+50, len(genome))] + "\n") queryFile.close() self.updateProgress(query) initialGenes = genemark.findGenes(swapFileName, name, blastLocation, database, eValue, genemarkLocation, matrix, self) self.updateProgress(query) extendedGenes = extend.extendGenes(swapFileName, initialGenes, name, blastLocation, database, eValue, self) self.updateProgress(query) intergenicGenes = intergenic.findIntergenics(swapFileName, extendedGenes, name, minLength, blastLocation, database, eValue, self) genes = {} for k, v in extendedGenes.items() + intergenicGenes.items(): genes[k] = v self.updateProgress(query) scaffolded = scaffolds.refineScaffolds(genes, scaffoldingDistance) self.updateProgress(query) initialPromoters = promoters.findPromoters(swapFileName, name, promoterScoreCutoff, self.frame) self.updateProgress(query) initialTerminators = terminators.findTerminators(swapFileName, name, genes.values(), transtermLocation) self.updateProgress(query) filteredSignals = signals.filterSignals(scaffolded.values(), initialPromoters + initialTerminators) filteredPromoters = filter(lambda x: isinstance(x, promoters.Promoter), filteredSignals) filteredTerminators = filter(lambda x: isinstance(x, terminators.Terminator), filteredSignals) self.updateProgress(query) transferRNAs = rna.findtRNAs(tRNAscanLocation, swapFileName) os.remove(swapFileName) self.updateProgress(query) artemis.writeArtemisFile(os.path.splitext(query)[0] + ".art", genome, scaffolded.values(), filteredPromoters, filteredTerminators, transferRNAs) self.updateProgress(query) report.report(name, scaffolded, os.path.splitext(query)[0]) if email: if not os.path.isfile("EMAIL_MESSAGE"): message = open("EMAIL_MESSAGE", "w") message.write("Subject: Annotation Complete\nYour genome has been annotated.\n") message.close() sent = False while not sent: message = open("EMAIL_MESSAGE", "r") sendmailProcess = subprocess.Popen(["/usr/sbin/sendmail", "-F", "Neofelis", "-f", "*****@*****.**", email], stdin = message, stdout = subprocess.PIPE) result = "" nextRead = sendmailProcess.stdout.read() while nextRead: result += nextRead nextRead = sendmailProcess.stdout.read() sent = not result.strip() message.close() self.finished() except PipelineException: return
def makeRegistrationUI(original_images, original_calibration, coarse_affines, params, images, minC, maxC, cropped, cropped_imp): """ Register cropped images either all to all or all to the first one, and print out a config file with the coarse affines, the ROI for cropping, and the refined affines post-crop. original_images: the original, raw images, with original dimensions. original_calibration: the calibration of the images as they are on disk. coarse_affines: list of AffineTransform3D, one per image, that specify the translation between images as manually set using the makeTranslationUI. params: dictionary with parameters for registering the given cropped images. This includes a calibration that is likely [1.0, 1.0, 1.0] as the cropped images are expected to have been scaled to isotropy. images: the list of near-original images but scaled (by calibration) to isotropy. (These are really views of the original images, using nearest neighbor interpolation to scale them to isotropy.) minC, maxC: the minimum and maximum coordinates of a ROI with which the cropped images were made. cropped: the list of images that have been scaled to isotropy, translated and cropped by the ROI. (These are really interval views of the images, the latter using nearest neighbor interpolation.) cropped_imp: the ImagePlus holding the virtual stack of cropped image views. The computed registration will merge the scaling to isotropy + first transform (a translation) + roi cropping translation + the params["modelclass"] registration transform, to read directly from the original images using a nearest interpolation, for best performance (piling two nearest interpolations over one another would result in very slow access to pixel data). """ panel = JPanel() panel.setBorder(BorderFactory.createEmptyBorder(10,10,10,10)) gb = GridBagLayout() panel.setLayout(gb) gc = GBC() calibration = params["calibration"] params["cal X"] = calibration[0] params["cal Y"] = calibration[1] params["cal Z"] = calibration[2] # Add a label and a text field for every parameter, with titles for every block strings = [["Calibration", "cal X", "cal Y", "cal Z"], ["Difference of Gaussian", "minPeakValue", "sigmaSmaller", "sigmaLarger"], ["Feature extraction", "radius", "min_angle", "max_per_peak", "angle_epsilon", "len_epsilon_sq", "pointmatches_nearby", "pointmatches_search_radius"], ["RANSAC parameters for the model", "maxEpsilon", "minInlierRatio", "minNumInliers", "n_iterations", "maxTrust"], ["All to all registration", "maxAllowedError", "maxPlateauwidth", "maxIterations", "damp"]] # Insert all as fields, with values populated from the params dictionary # and updating dynamically the params dictionary params = dict(params) # copy, will be updated insertFloatFields(panel, gb, gc, params, strings) # Identity transforms prior to registration affines = [affine3D([1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0]) for img in cropped] def run(): exe = newFixedThreadPool(min(len(cropped), numCPUs())) try: # Dummy for in-RAM reading of isotropic images img_filenames = [str(i) for i in xrange(len(cropped))] loader = InRAMLoader(dict(zip(img_filenames, cropped))) getCalibration = params.get("getCalibration", None) if not getCalibration: getCalibration = lambda img: [1.0] * cropped[0].numDimensions() csv_dir = params["csv_dir"] modelclass = params["modelclass"] # Matrices describing the registration on the basis of the cropped images matrices = computeOptimizedTransforms(img_filenames, loader, getCalibration, csv_dir, exe, modelclass, params) # Store outside, so they can be e.g. printed, and used beyond here for matrix, affine in zip(matrices, affines): affine.set(*matrix) # Combine the transforms: scaling (by calibration) # + the coarse registration (i.e. manual translations) # + the translation introduced by the ROI cropping # + the affine matrices computed above over the cropped images. coarse_matrices = [] for coarse_affine in coarse_affines: matrix = zeros(12, 'd') coarse_affine.toArray(matrix) coarse_matrices.append(matrix) # NOTE: both coarse_matrices and matrices are from the camera X to camera 0. No need to invert them. # NOTE: uses identity calibration because the coarse_matrices already include the calibration scaling to isotropy transforms = mergeTransforms([1.0, 1.0, 1.0], coarse_matrices, [minC, maxC], matrices, invert2=False) print "calibration:", [1.0, 1.0, 1.0] print "cmTransforms:\n %s\n %s\n %s\n %s" % tuple(str(m) for m in coarse_matrices) print "ROI", [minC, maxC] print "fineTransformsPostROICrop:\n %s\n %s\n %s\n %s" % tuple(str(m) for m in matrices) print "invert2:", False # Show registered images registered = [transformedView(img, transform, interval=cropped[0]) for img, transform in izip(original_images, transforms)] registered_imp = showAsStack(registered, title="Registered with %s" % params["modelclass"].getSimpleName()) registered_imp.setDisplayRange(cropped_imp.getDisplayRangeMin(), cropped_imp.getDisplayRangeMax()) """ # TEST: same as above, but without merging the transforms. WORKS, same result # Copy into ArrayImg, otherwise they are rather slow to browse def copy(img1, affine): # Copy in two steps. Otherwise the nearest neighbor interpolation on top of another # nearest neighbor interpolation takes a huge amount of time dimensions = Intervals.dimensionsAsLongArray(img1) aimg1 = ArrayImgs.unsignedShorts(dimensions) ImgUtil.copy(ImgView.wrap(img1, aimg1.factory()), aimg1) img2 = transformedView(aimg1, affine) aimg2 = ArrayImgs.unsignedShorts(dimensions) ImgUtil.copy(ImgView.wrap(img2, aimg2.factory()), aimg2) return aimg2 futures = [exe.submit(Task(copy, img, affine)) for img, affine in izip(cropped, affines)] aimgs = [f.get() for f in futures] showAsStack(aimgs, title="DEBUG Registered with %s" % params["modelclass"].getSimpleName()) """ except: print sys.exc_info() finally: exe.shutdown() SwingUtilities.invokeLater(lambda: run_button.setEnabled(True)) def launchRun(event): # Runs on the event dispatch thread run_button.setEnabled(False) # will be re-enabled at the end of run() # Fork: Thread(run).start() def printAffines(event): for i, affine in enumerate(affines): matrix = zeros(12, 'd') affine.toArray(matrix) msg = "# Refined post-crop affine matrix " + str(i) + ": \n" + \ "affine" + str(i) + ".set(*[%f, %f, %f, %f,\n %f, %f, %f, %f,\n %f, %f, %f, %f])" % tuple(matrix.tolist()) # Print everywhere print msg IJ.log(msg) System.out.println(msg) def prepareDeconvolutionScriptUI(event): """ # DEBUG generateDeconvolutionScriptUI: generate params as a loadable serialized file with open("/tmp/parameters.pickle", 'w') as f: import pickle def asArrays(affines): arrays = [] for affine in affines: matrix = zeros(12, 'd') affine.toArray(matrix) arrays.append(matrix) return arrays pickle.dump([params["srcDir"], params["tgtDir"], calibration, asArrays(coarse_affines), [minC, maxC], asArrays(affines)], f) """ generateDeconvolutionScriptUI(params["srcDir"], params["tgtDir"], calibration, coarse_affines, [minC, maxC], affines) # Buttons panel_buttons = JPanel() gc.gridx = 0 gc.gridy += 1 gc.gridwidth = 2 gb.setConstraints(panel_buttons, gc) panel.add(panel_buttons) run_button = JButton("Run") run_button.addActionListener(launchRun) gb.setConstraints(run_button, gc) panel_buttons.add(run_button) print_button = JButton("Print affines") print_button.addActionListener(printAffines) panel_buttons.add(print_button) prepare_button = JButton("Prepare deconvolution script") prepare_button.addActionListener(prepareDeconvolutionScriptUI) panel_buttons.add(prepare_button) frame = JFrame("Registration") frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE) frame.addWindowListener(CloseControl()) frame.getContentPane().add(panel) frame.pack() frame.setLocationRelativeTo(None) # center in the screen frame.setVisible(True)
def makeCropUI(imp, images, tgtDir, panel=None, cropContinuationFn=None): """ imp: the ImagePlus to work on. images: the list of ImgLib2 images, one per frame, not original but already isotropic. (These are views that use a nearest neighbor interpolation using the calibration to scale to isotropy.) tgtDir: the target directory where e.g. CSV files will be stored, for ROI, features, pointmatches. panel: optional, a JPanel controlled by a GridBagLayout. cropContinuationFn: optional, a function to execute after cropping, which is given as arguments the original images, minC, maxC (both define a ROI), and the cropped images. """ independent = None == panel if not panel: panel = JPanel() panel.setBorder(BorderFactory.createEmptyBorder(10,10,10,10)) gb = GridBagLayout() gc = GBC() else: gb = panel.getLayout() # Constraints of the last component gc = gb.getConstraints(panel.getComponent(panel.getComponentCount() - 1)) # Horizontal line to separate prior UI components from crop UI gc.gridx = 0 gc.gridy += 1 gc.gridwidth = 4 gc.anchor = GBC.WEST gc.fill = GBC.HORIZONTAL sep = JSeparator() sep.setMinimumSize(Dimension(200, 10)) gb.setConstraints(sep, gc) panel.add(sep) # ROI UI header title = JLabel("ROI controls:") gc.gridy +=1 gc.anchor = GBC.WEST gc.gridwidth = 4 gb.setConstraints(title, gc) panel.add(title) # Column labels for the min and max coordinates gc.gridy += 1 gc.gridwidth = 1 for i, title in enumerate(["", "X", "Y", "Z"]): gc.gridx = i gc.anchor = GBC.CENTER label = JLabel(title) gb.setConstraints(label, gc) panel.add(label) textfields = [] rms = [] # Load stored ROI if any roi_path = path = os.path.join(tgtDir, "crop-roi.csv") if os.path.exists(roi_path): with open(roi_path, 'r') as csvfile: reader = csv.reader(csvfile, delimiter=',', quotechar="\"") reader.next() # header minC = map(int, reader.next()[1:]) maxC = map(int, reader.next()[1:]) # Place the ROI over the ImagePlus imp.setRoi(Roi(minC[0], minC[1], maxC[0] + 1 - minC[0], maxC[1] + 1 - minC[1])) else: # Use whole image dimensions minC = [0, 0, 0] maxC = [v -1 for v in Intervals.dimensionsAsLongArray(images[0])] # Text fields for the min and max coordinates for rowLabel, coords in izip(["min coords: ", "max coords: "], [minC, maxC]): gc.gridx = 0 gc.gridy += 1 label = JLabel(rowLabel) gb.setConstraints(label, gc) panel.add(label) for i in xrange(3): gc.gridx += 1 tf = JTextField(str(coords[i]), 10) gb.setConstraints(tf, gc) panel.add(tf) textfields.append(tf) listener = RoiMaker(imp, textfields, len(textfields) -1) rms.append(listener) tf.addKeyListener(listener) tf.addMouseWheelListener(listener) # Listen to changes in the ROI of imp rfl = RoiFieldListener(imp, textfields) Roi.addRoiListener(rfl) # ... and enable cleanup ImagePlus.addImageListener(FieldDisabler(rfl, rms)) # Functions for cropping images cropped = None cropped_imp = None def storeRoi(minC, maxC): if os.path.exists(roi_path): # Load ROI with open(path, 'r') as csvfile: reader = csv.reader(csvfile, delimiter=',', quotechar="\"") reader.next() # header same = True for a, b in izip(minC + maxC, map(int, reader.next()[1:] + reader.next()[1:])): if a != b: same = False # Invalidate any CSV files for features and pointmatches: different cropping for filename in os.listdir(tgtDir): if filename.endswith("features.csv") or filename.endswith("pointmatches.csv"): os.remove(os.path.join(tgtDir, filename)) break if same: return # Store the ROI as crop-roi.csv with open(roi_path, 'w') as csvfile: w = csv.writer(csvfile, delimiter=',', quotechar="\"", quoting=csv.QUOTE_NONNUMERIC) w.writerow(["coords", "x", "y", "z"]) w.writerow(["min"] + map(int, minC)) w.writerow(["max"] + map(int, maxC)) def crop(event): global cropped, cropped_imp coords = [int(float(tf.getText())) for tf in textfields] minC = [max(0, c) for c in coords[0:3]] maxC = [min(d -1, c) for d, c in izip(Intervals.dimensionsAsLongArray(images[0]), coords[3:6])] storeRoi(minC, maxC) print "ROI min and max coordinates" print minC print maxC cropped = [Views.zeroMin(Views.interval(img, minC, maxC)) for img in images] cropped_imp = showAsStack(cropped, title="cropped") cropped_imp.setDisplayRange(imp.getDisplayRangeMin(), imp.getDisplayRangeMax()) if cropContinuationFn: cropContinuationFn(images, minC, maxC, cropped, cropped_imp) # Buttons to create a ROI and to crop to ROI, # which when activated enables the fine registration buttons crop_button = JButton("Crop to ROI") crop_button.addActionListener(crop) gc.gridx = 0 gc.gridy += 1 gc.gridwidth = 4 gc.anchor = GBC.WEST buttons_panel = JPanel() buttons_panel.add(crop_button) gb.setConstraints(buttons_panel, gc) panel.add(buttons_panel) if independent: frame = JFrame("Crop by ROI") frame.getContentPane().add(panel) frame.pack() frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE) frame.addWindowListener(CloseControl(destroyables=rms + [rfl])) frame.setVisible(True) else: # Re-pack the JFrame parent = panel.getParent() while not isinstance(parent, JFrame) and parent is not None: parent = parent.getParent() if parent: frame = parent frame.pack() found = False for wl in frame.getWindowListeners(): if isinstance(wl, CloseControl): wl.addDestroyables(rms + [rfl]) found = True break if not found: frame.addWindowListener(CloseControl(destroyables=rms + [rfl])) frame.setVisible(True) return panel
def makeTranslationUI(affines, imp, show=True, print_button_text="Print transforms"): """ A GUI to control the translation components of a list of AffineTransform3D instances. When updated, the ImagePlus is refreshed. affines: a list (will be read multiple times) of one affine transform per image. imp: the ImagePlus that hosts the virtual stack with the transformed images. show: defaults to True, whether to make the GUI visible. print_button_text: whatever you want the print button to read like, defaults to "Print transforms". Returns the JFrame, the main JPanel and the lower JButton panel. """ panel = JPanel() panel.setBorder(BorderFactory.createEmptyBorder(10,10,10,10)) gb = GridBagLayout() panel.setLayout(gb) gc = GBC() gc.anchor = GBC.WEST gc.fill = GBC.NONE # Column labels gc.gridy = 0 for i, title in enumerate(["Camera", "translation X", "translation Y", "translation Z"]): gc.gridx = i gc.anchor = GBC.CENTER label = JLabel(title) gb.setConstraints(label, gc) panel.add(label) gc.anchor = GBC.WEST listeners = [] # One row per affine to control: skip the first for i, affine in enumerate(affines[1:]): gc.gridx = 0 gc.gridy += 1 label = JLabel("CM0%i: " % (i + 1)) gb.setConstraints(label, gc) panel.add(label) # One JTextField per dimension for dimension, translation in enumerate(affine.getTranslation()): tf = JTextField(str(translation), 10) listener = MatrixTextFieldListener(affine, dimension, tf, imp) listeners.append(listener) imp.addImageListener(listener) # to disable the JTextField when closed tf.addKeyListener(listener) tf.addMouseWheelListener(listener) gc.gridx += 1 gb.setConstraints(tf, gc) panel.add(tf) # Documentation for the user help_lines = ["Type a number and push enter,", "or use the scroll wheel."] gc.gridx = 0 gc.gridwidth = 4 for line in help_lines: gc.gridy += 1 help = JLabel(line) gb.setConstraints(help, gc) panel.add(help) # Buttons printButton = JButton(print_button_text) def printTransforms(event): for i, aff in enumerate(affines): # print all, including the first matrix = zeros(12, 'd') aff.toArray(matrix) msg = "# Coarse affine matrix " + str(i) + ": \n" + \ "affine" + str(i) + ".set(*[%f, %f, %f, %f,\n %f, %f, %f, %f,\n %f, %f, %f, %f])" % tuple(matrix.tolist()) # Print everywhere print msg IJ.log(msg) System.out.println(msg) printButton.addActionListener(printTransforms) gc.gridx = 0 gc.gridy += 1 gc.gridwidth = 4 button_panel = JPanel() button_panel.add(printButton) gb.setConstraints(button_panel, gc) panel.add(button_panel) frame = JFrame("Translation control") frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE) frame.addWindowListener(CloseControl(destroyables=listeners)) frame.getContentPane().add(panel) frame.pack() frame.setLocationRelativeTo(None) # center in the screen frame.setVisible(show) return frame, panel, button_panel
class PropertyEditor(WindowAdapter): """ Edits Tabular Properties of a given WindowAdapter """ instances = {} last_location = None locations = {} last_size = None sizes = {} NEW_WINDOW_OFFSET = 32 offset = NEW_WINDOW_OFFSET @staticmethod def get_instance(text="Property Editor", columns=None, data=None, empty=None, add_actions=True, actions=None): """ Singleton Method based on the text property. It tries to generate only one property configuration page per text. :param text: getinstance key :param columns: proparty columns it should be an array alike :param data: it contains the current property rows :param empty: empty row property when adding a new one :param add_actions: include or not new actions :param actions: default set of actions to be appended to Add and Delete Rows :return: a new instance of PropertyEditor or a reused one. """ if not actions: actions = [] if not columns: columns = [] if data == None: data = [] if not empty: empty = [] try: PropertyEditor.instances[text] except KeyError: PropertyEditor.instances[text] = \ PropertyEditor().__private_init__(text, columns, data, empty, add_actions, actions) try: PropertyEditor.instances[text].this.setLocation( PropertyEditor.locations[text]) except KeyError: if PropertyEditor.last_location: PropertyEditor.instances[text].this.setLocation( PropertyEditor.last_location.x + PropertyEditor.offset, PropertyEditor.last_location.y + PropertyEditor.offset) PropertyEditor.offset = PropertyEditor.NEW_WINDOW_OFFSET try: PropertyEditor.instances[text].this.setSize( PropertyEditor.sizes[text]) except KeyError: if PropertyEditor.last_size: PropertyEditor.instances[text].this.setSize( PropertyEditor.last_size) PropertyEditor.last_location = PropertyEditor.instances[ text].this.getLocation() PropertyEditor.last_size = PropertyEditor.instances[ text].this.getSize() ## Hack ON: Bring on Front PropertyEditor.instances[text].this.setAlwaysOnTop(True) PropertyEditor.instances[text].this.setAlwaysOnTop(False) ## Hack OFF return PropertyEditor.instances[text] def __private_init__(self, text="Property Editor", columns=None, data=None, empty=None, add_actions=True, actions=None): if not actions: actions = [] if not columns: columns = [] if data == None: data = [] if not empty: empty = [] self._text = text self.this = JFrame(text) self._table = JTable() self._dtm = DefaultTableModel(0, 0) self._dtm.setColumnIdentifiers(columns) self._table.setModel(self._dtm) self._data = data for d in data: self._dtm.addRow(d) self._pane = JScrollPane(self._table) self.this.add(self._pane) self._empty = empty self.this.addWindowListener(self) self._dtm.addTableModelListener(lambda _: self._update_model()) self.this.setLocation(PropertyEditor.NEW_WINDOW_OFFSET, PropertyEditor.NEW_WINDOW_OFFSET) if add_actions: self._popup = JPopupMenu() self._pane.setComponentPopupMenu(self._popup) inherits_popup_menu(self._pane) self._actions = actions self._actions.append( ExecutorAction('Remove Selected Rows', action=lambda e: self._remove_row())) self._actions.append( ExecutorAction('Add New Row', action=lambda e: self._add_row())) for action in self._actions: self._popup.add(action.menuitem) self.this.setForeground(Color.black) self.this.setBackground(Color.lightGray) self.this.pack() self.this.setVisible(True) self.this.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE) return self def _add_row(self): """ Add a new row the selection :return: None """ self._dtm.addRow(self._empty) def _remove_row(self): """ Remove all the selected rows from the selection :return: """ rows = self._table.getSelectedRows() for i in range(0, len(rows)): self._dtm.removeRow(rows[i] - i) def windowClosing(self, evt): """ Overrides WindowAdapter method :param evt: unused :return: None """ PropertyEditor.locations[self._text] = self.this.getLocation() PropertyEditor.sizes[self._text] = self.this.getSize() PropertyEditor.last_location = self.this.getLocation() PropertyEditor.last_size = self.this.getSize() PropertyEditor.offset = 0 self.this.setVisible(False) self.this.dispose() del PropertyEditor.instances[self._text] def _update_model(self): """ Update the data content with the updated rows :return: None """ del self._data[:] nRow = self._dtm.getRowCount() nCol = self._dtm.getColumnCount() for i in range(0, nRow): self._data.append([None] * nCol) for j in range(0, nCol): d = str(self._dtm.getValueAt(i, j)).lower() if d == 'none' or d == '': self._data[i][j] = None elif d == 'true' or d == 't': self._data[i][j] = True elif d == 'false' or d == 'f': self._data[i][j] = False else: try: self._data[i][j] = int(self._dtm.getValueAt(i, j)) except ValueError: self._data[i][j] = self._dtm.getValueAt(i, j)
def specifyRoiUI(roi=Roi(0, 0, 0, 0)): # A panel in which to place UI elements panel = JPanel() panel.setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10)) gb = GridBagLayout() panel.setLayout(gb) gc = GBC() bounds = roi.getBounds() if roi else Rectangle() textfields = [] roimakers = [] # Basic properties of most UI elements, will edit when needed gc.gridx = 0 # can be any natural number gc.gridy = 0 # idem. gc.gridwidth = 1 # when e.g. 2, the UI element will occupy two horizontally adjacent grid cells gc.gridheight = 1 # same but vertically gc.fill = GBC.NONE # can also be BOTH, VERTICAL and HORIZONTAL for title in ["x", "y", "width", "height"]: # label gc.gridx = 0 gc.anchor = GBC.EAST label = JLabel(title + ": ") gb.setConstraints(label, gc) # copies the given constraints 'gc', # so we can modify and reuse gc later. panel.add(label) # text field, below the title gc.gridx = 1 gc.anchor = GBC.WEST text = str(getattr(bounds, title)) # same as e.g. bounds.x, bounds.width, ... textfield = JTextField(text, 10) # 10 is the size of the field, in digits gb.setConstraints(textfield, gc) panel.add(textfield) textfields.append( textfield) # collect all 4 created textfields for the listeners # setup ROI and text field listeners listener = RoiMaker(textfields, len(textfields) - 1) # second argument is the index of textfield # in the list of textfields. roimakers.append(listener) textfield.addKeyListener(listener) textfield.addMouseWheelListener(listener) # Position next ROI property in a new row by increasing the Y coordinate of the layout grid gc.gridy += 1 # User documentation (uses HTML to define line breaks) doc = JLabel( "<html><body><br />Click on a field to activate it, then:<br />" + "Type in integer numbers<br />" + "or use arrow keys to increase by 1<br />" + "or use the scroll wheel on a field.</body></html>") gc.gridx = 0 # start at the first column gc.gridwidth = 2 # Spans both columns gb.setConstraints(doc, gc) panel.add(doc) # Listen to changes in the ROI of imp roilistener = TextFieldUpdater(textfields) Roi.addRoiListener(roilistener) # Show window frame = JFrame("Specify rectangular ROI") frame.getContentPane().add(panel) frame.pack() frame.setLocationRelativeTo(None) # center in the screen frame.setDefaultCloseOperation( JFrame.DO_NOTHING_ON_CLOSE) # prevent closing the window frame.addWindowListener( CloseControl(roilistener)) # handles closing the window frame.setVisible(True)
class Pipeline(): def __init__(self): #If a swing interface is asked for this will be the JFrame. self.frame = None #Keeps track of the number of queries processed. self.jobCount = 0 #Keeps track of the query currently being processed. self.currentJob = "" #Keeps track of the massage to be displayed. self.message = 0 #Messages to be displayed at each stage in the processing of a single query. self.messages = [ "Searching for genes via genemark", "Extending genes found via genemark", "Searching for intergenic genes", "Removing overlapping genes", "Searching for promoters", "Using transterm to find terminators", "Removing transcription signals which conflict with genes", "Writing Artemis file", "Writing summary file" ] self.exception = None def initializeDisplay(self, queries, swing): """ queries: A list of the fasts files to be processed. swing: If true then updates about progress will be displayed in a swing window, otherwise they will be written to stdout. Initializes the interface for telling the user about progress in the pipeline. Queries is used to count the number of queries the pipeline will process and to size the swing display(if it is used) so that text isn't cutoff at the edge of the window. The swing display is setup if swing is true. """ self.numJobs = len(queries) if swing: self.frame = JFrame("Neofelis") self.frame.addWindowListener(PipelineWindowAdapter(self)) contentPane = JPanel(GridBagLayout()) self.frame.setContentPane(contentPane) self.globalLabel = JLabel(max(queries, key=len)) self.globalProgress = JProgressBar(0, self.numJobs) self.currentLabel = JLabel(max(self.messages, key=len)) self.currentProgress = JProgressBar(0, len(self.messages)) self.doneButton = JButton(DoneAction(self.frame)) self.doneButton.setEnabled(False) constraints = GridBagConstraints() constraints.gridx, constraints.gridy = 0, 0 constraints.gridwidth, constraints.gridheight = 1, 1 constraints.weightx = 1 constraints.fill = GridBagConstraints.HORIZONTAL contentPane.add(self.globalLabel, constraints) constraints.gridy = 1 contentPane.add(self.globalProgress, constraints) constraints.gridy = 2 contentPane.add(self.currentLabel, constraints) constraints.gridy = 3 contentPane.add(self.currentProgress, constraints) constraints.gridy = 4 constraints.weightx = 0 constraints.fill = GridBagConstraints.NONE constraints.anchor = GridBagConstraints.LINE_END contentPane.add(self.doneButton, constraints) self.frame.pack() self.frame.setResizable(False) self.globalLabel.setText(" ") self.currentLabel.setText(" ") self.frame.setLocationRelativeTo(None) self.frame.setVisible(True) def updateProgress(self, job): """ query: Name of the query currently being processed. This function use used for updating the progress shown in the interface. If job is not equal to currentJob then global progress is incremented and shown and the currentProgress is reset and shown. If job is equal to currentJob then the globalProgress does not change and currentProgress is incremented. """ if self.exception: raise self.exception if self.frame: if job != self.currentJob: self.currentProgress.setValue( self.currentProgress.getMaximum()) self.globalLabel.setText(job) self.globalProgress.setValue(self.jobCount) print "Processing %s, %.2f%% done" % ( job, 100.0 * self.jobCount / self.numJobs) self.jobCount += 1 self.currentJob = job self.message = -1 self.message += 1 print " %s, %.2f%% done" % (self.messages[self.message], 100.0 * self.message / len(self.messages)) self.currentProgress.setValue(self.message) self.currentLabel.setText(self.messages[self.message]) else: if job != self.currentJob: print "Processing %s, %.2f%% done" % ( job, 100.0 * self.jobCount / self.numJobs) self.jobCount += 1 self.currentJob = job self.message = -1 self.message += 1 print " %s, %.2f%% done" % (self.messages[self.message], 100.0 * self.message / len(self.messages)) def finished(self): """ This function is to be called at the end of the pipeline. Informs the user that the pipeline is finished and if a swing interface is being used the Done button is enabled. """ print "Processing 100.00% done" if self.frame: self.globalLabel.setText("Finished") self.globalProgress.setValue(self.globalProgress.getMaximum()) self.currentLabel.setText(" ") self.currentProgress.setValue(self.currentProgress.getMaximum()) self.doneButton.setEnabled(True) while self.frame.isVisible(): pass def run(self, blastLocation, genemarkLocation, transtermLocation, database, eValue, matrix, minLength, scaffoldingDistance, ldfCutoff, queries, swing=False, email=""): """ blastLocation: Directory blast was installed in. genemarkLocation: Directory genemark was installed in. transtermLocation: Directory transterm was installed in. database: Name of the blast database to use. eValue: The e value used whenever a blast search is done. matrix: The matrix to use when running genemark. If None then genemark is run heuristically. minLength: Minimum length of any genes included in the resulting annotation. scaffoldingDistance: The maximum length allowed between genes when contiguous regions of genes are being identified ldfCutoff: Minimum LDF allowed for any promoters included in the resulting annotation queries: A list of faster files to process. swing: If true a swing window will be used to updated the user about the pipeline's progress. email: If this is a non-empty string an email will be sent to the address in the string when the pipeline is done. The local machine will be used as an SMTP server and this will not work if it isn't. The main pipeline function. For every query genemark is used to predict genes, these genes are then extended to any preferable starts. Then the pipeline searches for any intergenic genes(genes between those found by genemark) and these are combined with the extended genemark genes. Then the genes are pruned to remove any undesirable genes found in the intergenic stage. BPROM and Transterm are used to find promoters and terminators, which are then pruned to remove any signals which are inside or too far away from any genes. Finally, all the remaining genes, promoters, and terminators ar written to an artemis file in the directory of the query with the same name but with a .art extension, and .dat and .xls files will be generating describing the blast results of the final genes. """ self.initializeDisplay(queries, swing) try: for query in queries: name = os.path.splitext(query)[0] queryDirectory, name = os.path.split(name) genome = utils.loadGenome(query) swapFileName = "query" + str(id(self)) + ".fas" queryFile = open(swapFileName, "w") queryFile.write(">" + name + "\n") for i in range(0, len(genome), 50): queryFile.write(genome[i:min(i + 50, len(genome))] + "\n") queryFile.close() self.updateProgress(query) initialGenes = genemark.findGenes(swapFileName, name, blastLocation, database, eValue, genemarkLocation, matrix, self) #artemis.writeArtemisFile(os.path.splitext(query)[0] + ".genemark.art", genome, initialGenes.values()) self.updateProgress(query) extendedGenes = extend.extendGenes(swapFileName, initialGenes, name, blastLocation, database, eValue, self) #artemis.writeArtemisFile(os.path.splitext(query)[0] + ".extended.art", genome, extendedGenes.values()) self.updateProgress(query) intergenicGenes = intergenic.findIntergenics( swapFileName, extendedGenes, name, minLength, blastLocation, database, eValue, self) #artemis.writeArtemisFile(os.path.splitext(query)[0] + ".intergenic.art", genome, intergenicGenes.values()) genes = {} for k, v in extendedGenes.items() + intergenicGenes.items(): genes[k] = v self.updateProgress(query) scaffolded = scaffolds.refineScaffolds(genes, scaffoldingDistance) self.updateProgress(query) initialPromoters = promoters.findPromoters(swapFileName, name) self.updateProgress(query) initialTerminators = terminators.findTerminators( swapFileName, name, genes.values(), transtermLocation) self.updateProgress(query) filteredSignals = signals.filterSignals( scaffolded.values(), initialPromoters + initialTerminators) filteredPromoters = filter( lambda x: isinstance(x, promoters.Promoter), filteredSignals) filteredTerminators = filter( lambda x: isinstance(x, terminators.Terminator), filteredSignals) self.updateProgress(query) artemis.writeArtemisFile( os.path.splitext(query)[0] + ".art", genome, scaffolded.values(), filteredPromoters, filteredTerminators) self.updateProgress(query) report.report(name, scaffolded, os.path.splitext(query)[0]) if email: message = MIMEText("Your genome has been annotated.") message["Subject"] = "Annotation complete" message["From"] = "Neofelis" message["To"] = email smtp = smtplib.SMTP("tmpl.arizona.edu", 587) smtp.ehlo() smtp.starttls() smtp.ehlo smtp.sendmail("Neofelis", [email], message.as_string()) smtp.close() self.finished() except PipelineException: return
class Window (object): def __init__(self, windowManager, commandConsoleFactory, subject, windowTitle): self._windowManager = windowManager self.onCloseRequestListener = None # EDIT MENU transferActionListener = _TransferActionListener() editMenu = JMenu( 'Edit' ) if Platform.getPlatform() is Platform.MAC: command_key_mask = ActionEvent.META_MASK else: command_key_mask = ActionEvent.CTRL_MASK; self.__editUndoItem = JMenuItem( 'Undo' ) undoAction = _action( 'undo', self.__onUndo ) self.__editUndoItem.setActionCommand( undoAction.getValue( Action.NAME ) ) self.__editUndoItem.addActionListener( undoAction ) self.__editUndoItem.setAccelerator( KeyStroke.getKeyStroke( KeyEvent.VK_Z, command_key_mask ) ) self.__editUndoItem.setMnemonic( KeyEvent.VK_U ) editMenu.add( self.__editUndoItem ) self.__editRedoItem = JMenuItem( 'Redo' ) redoAction = _action( 'redo', self.__onRedo ) self.__editRedoItem.setActionCommand( redoAction.getValue( Action.NAME ) ) self.__editRedoItem.addActionListener( redoAction ) self.__editRedoItem.setAccelerator( KeyStroke.getKeyStroke( KeyEvent.VK_Y, command_key_mask ) ) self.__editRedoItem.setMnemonic( KeyEvent.VK_R ) editMenu.add( self.__editRedoItem ) editMenu.addSeparator() editCutItem = JMenuItem( 'Cut' ) editCutItem.setActionCommand( TransferHandler.getCutAction().getValue( Action.NAME ) ) editCutItem.addActionListener( transferActionListener ) editCutItem.setAccelerator( KeyStroke.getKeyStroke( KeyEvent.VK_X, command_key_mask ) ) editCutItem.setMnemonic( KeyEvent.VK_T ) editMenu.add( editCutItem ) editCopyItem = JMenuItem( 'Copy' ) editCopyItem.setActionCommand( TransferHandler.getCopyAction().getValue( Action.NAME ) ) editCopyItem.addActionListener( transferActionListener ) editCopyItem.setAccelerator( KeyStroke.getKeyStroke( KeyEvent.VK_C, command_key_mask ) ) editCopyItem.setMnemonic( KeyEvent.VK_C ) editMenu.add( editCopyItem ) editPasteItem = JMenuItem( 'Paste' ) editPasteItem.setActionCommand( TransferHandler.getPasteAction().getValue( Action.NAME ) ) editPasteItem.addActionListener( transferActionListener ) editPasteItem.setAccelerator( KeyStroke.getKeyStroke( KeyEvent.VK_V, command_key_mask ) ) editPasteItem.setMnemonic( KeyEvent.VK_P ) editMenu.add( editPasteItem ) editMenu.addSeparator() self.__showUndoHistoryItem = JMenuItem( 'Show undo history' ) self.__showUndoHistoryItem.addActionListener( _action( 'Show undo history', self.__onShowUndoHistory ) ) editMenu.add( self.__showUndoHistoryItem ) # HELP MENU helpMenu = JMenu( 'Help' ) helpToggleTooltipHighlightsItem = JMenuItem( 'Toggle tooltip highlights' ) toggleTooltipHighlightsAction = _action( 'Toggle tooltip highlights', self.__onToggleTooltipHighlights ) helpToggleTooltipHighlightsItem.setActionCommand( toggleTooltipHighlightsAction.getValue( Action.NAME ) ) helpToggleTooltipHighlightsItem.addActionListener( toggleTooltipHighlightsAction ) helpToggleTooltipHighlightsItem.setAccelerator( KeyStroke.getKeyStroke( KeyEvent.VK_F2, 0 ) ) helpMenu.add( helpToggleTooltipHighlightsItem ) helpMenu.add( _action( 'Show all tip boxes', self.__onShowAllTipBoxes ) ) # MENU BAR menuBar = JMenuBar() menuBar.add( editMenu ) menuBar.add( helpMenu ) # BROWSER # Initialise here, as the browser listener may invoke methods upon the browser's creation class _BrowserListener (TabbedBrowser.TabbedBrowserListener): def createNewBrowserWindow(_self, subject): self._onOpenNewWindow( subject ) def onTabbledBrowserChangePage(_self, browser): pass def inspectFragment(fragment, sourceElement, triggeringEvent): return self._windowManager.world.inspectFragment( fragment, sourceElement, triggeringEvent ) def onChangeHistoryChanged(history): self.__refreshChangeHistoryControls( history ) self._browser = TabbedBrowser( self._windowManager.world.rootSubject, subject, inspectFragment, _BrowserListener(), commandConsoleFactory ) self._browser.getComponent().setPreferredSize( Dimension( 800, 600 ) ) changeHistory = self._browser.getChangeHistory() self._browser.getChangeHistory().addChangeHistoryListener(onChangeHistoryChanged) # MAIN PANEL windowPanel = JPanel() windowPanel.setLayout( BoxLayout( windowPanel, BoxLayout.Y_AXIS ) ) windowPanel.add( self._browser.getComponent() ) # WINDOW class _WindowLister (WindowListener): def windowActivated(listenerSelf, event): pass def windowClosed(listenerSelf, event): pass def windowClosing(listenerSelf, event): if self.onCloseRequestListener is not None: self.onCloseRequestListener( self ) def windowDeactivated(listenerSelf, event): pass def windowDeiconified(listenerSelf, event): pass def windowIconified(listenerSelf, event): pass def windowOpened(listenerSelf, event): pass self.__frame = JFrame( windowTitle ) self.__frame.setJMenuBar( menuBar ) self.__frame.add( windowPanel ) self.__frame.addWindowListener( _WindowLister() ) self.__frame.setDefaultCloseOperation( JFrame.DO_NOTHING_ON_CLOSE ) self.__frame.pack() # Cause command history controls to refresh self.__refreshChangeHistoryControls( None ) @property def frame(self): return self.__frame @property def tabbedBrowser(self): return self._browser @property def currentBrowser(self): return self._browser.getCurrentBrowser() def show(self): self.__frame.setVisible( True ) def close(self): self.__frame.dispose() def __refreshChangeHistoryControls(self, changeHistory): if changeHistory is not None: self.__editUndoItem.setEnabled( changeHistory.canUndo() ) self.__editRedoItem.setEnabled( changeHistory.canRedo() ) self.__showUndoHistoryItem.setEnabled( True ) else: self.__editUndoItem.setEnabled( False ) self.__editRedoItem.setEnabled( False ) self.__showUndoHistoryItem.setEnabled( False ) def _onOpenNewWindow(self, subject): self._windowManager._createNewWindow( subject ) def __onUndo(self): changeHistory = self._browser.getChangeHistory() if changeHistory.canUndo(): changeHistory.concreteChangeHistory().undo() def __onRedo(self): changeHistory = self._browser.getChangeHistory() if changeHistory.canRedo(): changeHistory.concreteChangeHistory().redo() def __onShowUndoHistory(self): changeHistory = self._browser.getChangeHistory().concreteChangeHistory() if changeHistory is not None: subject = DefaultPerspective.instance.objectSubject( changeHistory ) self._browser.openSubjectInNewWindow( subject ) def __onToggleTooltipHighlights(self): AttachTooltip.toggleHighlights() def __onShowAllTipBoxes(self): TipBox.resetTipHiddenStates()
IJ.log("Discarded note for image at:") IJ.log(path.getText()) IJ.log(textarea.getText()) IJ.log("===") # Function to run upon closing the window class Cleanup(WindowAdapter): def windowClosing(self, event): askToSaveUnsavedChanges(getSelectedRowIndex()) exe.shutdown() ImagePlus.removeImageListener(open_imp_listener) event.getSource().dispose() # same as frame.dispose() frame.addWindowListener(Cleanup()) def addOrUpdateEntry(imp): """ This function runs in response to an image being opened, and finds out whether a new entry should be added to the table (and CSV file) or whether an existing entry ought to be added, or whether there's nothing to do because it's a new image not opened from a file. imp: an ImagePlus """ # Was the image opened from a file? fi = imp.getOriginalFileInfo() if not fi: # Image was created new, not from a file: ignore