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
