class MenueFrame(object):
def __init__(self):
self.mainDir = ""
self.frame = JFrame("Dots Quality Check", size=(250,300))
self.frame.setLocation(20,120)
self.Panel = JPanel(GridLayout(0,1))
self.frame.add(self.Panel)
self.openNextButton = JButton('Open Next Random',actionPerformed=openRandom)
self.Panel.add(self.openNextButton)
self.saveButton = JButton('Save',actionPerformed=save)
self.saveButton.setEnabled(False)
self.Panel.add(self.saveButton)
self.cropButton = JButton('Crop values from here', actionPerformed=cropVals)
self.Panel.add(self.cropButton)
self.DiscardButton = JButton('Discard cell', actionPerformed=discardCell)
self.DiscardButton.setEnabled(True)
self.Panel.add(self.DiscardButton)
self.quitButton = JButton('Quit script',actionPerformed=quit)
self.Panel.add(self.quitButton)
annoPanel = JPanel()
#add gridlayout
wtRButton = JRadioButton("wt", actionCommand="wt")
defectRButton = JRadioButton("Defect", actionCommand="defect")
annoPanel.add(wtRButton)
annoPanel.add(defectRButton)
self.aButtonGroup = ButtonGroup()
self.aButtonGroup.add(wtRButton)
self.aButtonGroup.add(defectRButton)
self.Panel.add(annoPanel)
self.ProgBar = JProgressBar()
self.ProgBar.setStringPainted(True)
self.ProgBar.setValue(0)
self.Panel.add(self.ProgBar)
self.pathLabel = JLabel("-- No main directory chosen --")
self.pathLabel.setHorizontalAlignment( SwingConstants.CENTER )
self.Panel.add(self.pathLabel)
WindowManager.addWindow(self.frame)
self.show()
def show(self):
self.frame.visible = True
def getFrame(self):
return self.frame
def setSaveActive(self):
self.saveButton.setEnabled(True)
self.show()
def setSaveInactive(self):
self.saveButton.setEnabled(False)
self.show()
def setMainDir(self, path):
self.mainDir = path
self.pathLabel.setText("MainDir: " + os.path.basename(os.path.split(self.mainDir)[0]))
def getMainDir(self):
return self.mainDir
def setProgBarMax(self, maximum):
self.ProgBar.setMaximum(maximum)
def setProgBarVal(self, value):
self.ProgBar.setValue(value)
def close():
WindowManager.removeWindow(self.frame)
self.frame.dispose()
class DetermineCookieFrame(JFrame):
""" This is the GUI for for the user to control the actions when
determining which cookie is the session cookie.
"""
def __init__(self, callbacks, selected_message):
super(DetermineCookieFrame, self).__init__()
self.callbacks = callbacks
self.selected_message = selected_message
self.windowClosing = self.close
def loadPanel(self):
panel = JPanel()
panel.setLayout(BoxLayout(panel, BoxLayout.Y_AXIS))
bottomButtonBarPanel = JPanel()
bottomButtonBarPanel.setLayout(
BoxLayout(bottomButtonBarPanel, BoxLayout.X_AXIS))
bottomButtonBarPanel.setAlignmentX(1.0)
self.runButton = JButton("Run", actionPerformed=self.start)
self.cancelButton = JButton("Close", actionPerformed=self.cancel)
bottomButtonBarPanel.add(Box.createHorizontalGlue())
bottomButtonBarPanel.add(self.runButton)
bottomButtonBarPanel.add(self.cancelButton)
# Dimension(width,height)
bottom = JPanel()
bottom.setLayout(BoxLayout(bottom, BoxLayout.X_AXIS))
bottom.setAlignmentX(1.0)
self.progressBar = JProgressBar()
self.progressBar.setIndeterminate(False)
self.progressBar.setMaximum(100)
self.progressBar.setValue(0)
bottom.add(self.progressBar)
self.statusTextArea = JTextArea()
self.statusTextArea.setEditable(False)
scrollPane = JScrollPane(self.statusTextArea)
scrollPanel = JPanel()
scrollPanel.setLayout(BoxLayout(scrollPanel, BoxLayout.X_AXIS))
scrollPanel.setAlignmentX(1.0)
scrollPanel.add(scrollPane)
panel.add(scrollPanel)
panel.add(bottomButtonBarPanel)
panel.add(bottom)
self.add(panel)
self.setTitle("Determine Session Cookie(s)")
self.setSize(450, 300)
self.setLocationRelativeTo(None)
self.setVisible(True)
original_request_bytes = self.selected_message.getRequest()
http_service = self.selected_message.getHttpService()
helpers = self.callbacks.getHelpers()
request_info = helpers.analyzeRequest(http_service,
original_request_bytes)
parameters = request_info.getParameters()
cookie_parameters = [
parameter for parameter in parameters
if parameter.getType() == IParameter.PARAM_COOKIE
]
num_requests_needed = len(cookie_parameters) + 2
self.statusTextArea.append(
"This may require up to " + str(num_requests_needed) +
" requests to be made. Hit 'Run' to begin.\n")
def start(self, event):
global cancelThread
cancelThread = False
self.runButton.setEnabled(False)
self.cancelButton.setText("Cancel")
thread = ThreadDetermineCookie(self.callbacks, self.selected_message,
self.statusTextArea, self.progressBar)
thread.start()
def cancel(self, event):
self.setVisible(False)
self.dispose()
def close(self, event):
global cancelThread
cancelThread = True
class BottomPanel(JPanel):
def __init__(self):
self.holdPanel = JPanel()
self.topPanel = JPanel()
self.bottomPanel = JPanel()
self.holdPanel.setBackground(Color.decode('#dddee6'))
self.topPanel.setBackground(Color.decode('#dddee6'))
self.bottomPanel.setBackground(Color.decode('#dddee6'))
self.topPanel.setPreferredSize(Dimension(300, 30))
self.regBar = JProgressBar()
self.gatePassBar = JProgressBar()
self.regLabel = JLabel('Register : ')
self.gatepassLabel = JLabel(' Gate Pass : '******'')
self.gatePercentlabel = JLabel('')
self.refreshButton = JButton('Refresh',
actionPerformed=self.updateProgress)
self.regBar.setMinimum(0)
self.regBar.setMaximum(100)
self.regBar.setStringPainted(True)
self.gatePassBar.setMinimum(0)
self.gatePassBar.setMaximum(100)
self.gatePassBar.setStringPainted(True)
self.setLayout(BorderLayout())
self.updateProgress(None)
def updateProgress(self, e):
progress = client.get_progress()
regTotal = progress[0]
regRecog = progress[1]
gateTotal = progress[2]
gateRecog = progress[3]
regPercent = int((regRecog * 100) / regTotal)
gatePercent = int((gateRecog * 100) / gateTotal)
self.regBar.setValue(regPercent)
self.gatePassBar.setValue(gatePercent)
self.regBar.setString(str(regPercent) + '%')
self.gatePassBar.setString(str(gatePercent) + '%')
self.regPercentlabel.setText(str(regRecog) + '/' + str(regTotal))
self.gatePercentlabel.setText(
str(gateRecog) + '/' + str(gateTotal) + ' ')
if regPercent <= 30:
regColor = Color.RED
elif regPercent > 30 and regPercent < 50:
regColor = Color.ORANGE
elif regPercent >= 50 and regPercent <= 100:
regColor = Color.GREEN
if gatePercent <= 30:
gateColor = Color.RED
elif gatePercent > 30 and gatePercent < 50:
gateColor = Color.ORANGE
elif gatePercent >= 50 and gatePercent <= 100:
gateColor = Color.GREEN
self.regBar.setForeground(regColor)
self.gatePassBar.setForeground(gateColor)
self.holdPanel.add(self.regLabel)
self.holdPanel.add(self.regBar)
self.holdPanel.add(self.regPercentlabel)
self.holdPanel.add(self.gatepassLabel)
self.holdPanel.add(self.gatePassBar)
self.holdPanel.add(self.gatePercentlabel)
self.holdPanel.add(self.refreshButton)
self.add(self.holdPanel, BorderLayout.CENTER)
self.add(self.topPanel, BorderLayout.PAGE_START)
self.add(self.bottomPanel, BorderLayout.PAGE_END)
self.validate()
class DetermineCookieFrame(JFrame):
""" This is the GUI for for the user to control the actions when
determining which cookie is the session cookie.
"""
def __init__(self, callbacks, selected_message):
super(DetermineCookieFrame, self).__init__()
self.callbacks = callbacks
self.selected_message = selected_message
self.windowClosing = self.close
def loadPanel(self):
panel = JPanel()
panel.setLayout(BoxLayout(panel, BoxLayout.Y_AXIS))
bottomButtonBarPanel = JPanel()
bottomButtonBarPanel.setLayout(BoxLayout(bottomButtonBarPanel, BoxLayout.X_AXIS))
bottomButtonBarPanel.setAlignmentX(1.0)
self.runButton = JButton("Run", actionPerformed=self.start)
self.cancelButton = JButton("Close", actionPerformed=self.cancel)
bottomButtonBarPanel.add(Box.createHorizontalGlue());
bottomButtonBarPanel.add(self.runButton)
bottomButtonBarPanel.add(self.cancelButton)
# Dimension(width,height)
bottom = JPanel()
bottom.setLayout(BoxLayout(bottom, BoxLayout.X_AXIS))
bottom.setAlignmentX(1.0)
self.progressBar = JProgressBar()
self.progressBar.setIndeterminate(False)
self.progressBar.setMaximum(100)
self.progressBar.setValue(0)
bottom.add(self.progressBar)
self.statusTextArea = JTextArea()
self.statusTextArea.setEditable(False)
scrollPane = JScrollPane(self.statusTextArea)
scrollPanel = JPanel()
scrollPanel.setLayout(BoxLayout(scrollPanel, BoxLayout.X_AXIS))
scrollPanel.setAlignmentX(1.0)
scrollPanel.add(scrollPane)
panel.add(scrollPanel)
panel.add(bottomButtonBarPanel)
panel.add(bottom)
self.add(panel)
self.setTitle("Determine Session Cookie(s)")
self.setSize(450, 300)
self.setLocationRelativeTo(None)
self.setVisible(True)
original_request_bytes = self.selected_message.getRequest()
http_service = self.selected_message.getHttpService()
helpers = self.callbacks.getHelpers()
request_info = helpers.analyzeRequest(http_service, original_request_bytes)
parameters = request_info.getParameters();
cookie_parameters = [parameter for parameter in parameters if parameter.getType() == IParameter.PARAM_COOKIE]
num_requests_needed = len(cookie_parameters) + 2
self.statusTextArea.append("This may require up to " + str(num_requests_needed) + " requests to be made. Hit 'Run' to begin.\n")
def start(self, event):
global cancelThread
cancelThread = False
self.runButton.setEnabled(False)
self.cancelButton.setText("Cancel")
thread = ThreadDetermineCookie(self.callbacks, self.selected_message, self.statusTextArea, self.progressBar)
thread.start()
def cancel(self, event):
self.setVisible(False);
self.dispose();
def close(self, event):
global cancelThread
cancelThread = True
def __init__(self, imgData):
n = imgData.size()
win = JFrame("Point Marker Panel")
win.setPreferredSize(Dimension(350, 590))
win.setSize(win.getPreferredSize())
pan = JPanel()
pan.setLayout(BoxLayout(pan, BoxLayout.Y_AXIS))
win.getContentPane().add(pan)
progressPanel = JPanel()
progressPanel.setLayout(BoxLayout(progressPanel, BoxLayout.Y_AXIS))
positionBar = JProgressBar()
positionBar.setMinimum(0)
positionBar.setMaximum(n)
positionBar.setStringPainted(True)
progressPanel.add(Box.createGlue())
progressPanel.add(positionBar)
progressBar = JProgressBar()
progressBar.setMinimum(0)
progressBar.setMaximum(n)
progressBar.setStringPainted(True)
progressPanel.add(progressBar)
progressPanel.setBorder(BorderFactory.createEmptyBorder(0, 10, 0, 10))
pan.add(progressPanel)
pan.add(Box.createRigidArea(Dimension(5, 5)))
savePanel = JPanel()
savePanel.setLayout(BoxLayout(savePanel, BoxLayout.Y_AXIS))
saveMessageLabel = JLabel("<html><u>Save Often</u></html>")
savePanel.add(saveMessageLabel)
savePanel.setAlignmentX(Component.CENTER_ALIGNMENT)
savePanel.setBorder(BorderFactory.createEmptyBorder(0, 10, 0, 10))
pan.add(savePanel)
# pan.add(saveMessageLabel)
pan.add(Box.createRigidArea(Dimension(5, 5)))
calPanel = JPanel()
calPanel.setLayout(BoxLayout(calPanel, BoxLayout.Y_AXIS))
calPanelIn = JPanel()
calPanelIn.setLayout(BoxLayout(calPanelIn, BoxLayout.X_AXIS))
pixelSizeText = JTextField(12)
pixelSizeText.setHorizontalAlignment(JTextField.RIGHT)
# pixelSizeText.setMaximumSize(pixelSizeText.getPreferredSize())
unitText = JTextField(10)
# unitText.setMaximumSize(unitText.getPreferredSize())
pixelSizeText.setText("Enter Pixel Size Here")
calPanelIn.add(pixelSizeText)
unitText.setText("Unit")
calPanelIn.add(unitText)
calPanelIn.setAlignmentX(Component.CENTER_ALIGNMENT)
calPanelIn.setBorder(
BorderFactory.createTitledBorder("Custom Calibration"))
calPanel.add(calPanelIn)
calPanelIn.setAlignmentX(Component.CENTER_ALIGNMENT)
calPanel.setBorder(BorderFactory.createEmptyBorder(0, 10, 0, 10))
pan.add(calPanel)
pan.add(Box.createRigidArea(Dimension(5, 5)))
helpPanel = JPanel()
helpPanel.setLayout(BoxLayout(helpPanel, BoxLayout.Y_AXIS))
helpLable = JLabel("<html><ul>\
<li>Focus on Image Window</li>\
<li>Select multi-point Tool</li>\
<li>Click to Draw Points</li>\
<li>Drag to Move Points</li>\
<li>\"Alt\" + Click to Erase Points</li>\
<li>Optional: Customize Calibration Above\
and Refresh Images\
(won't be written to files)</li>\
</html>")
helpLable.setBorder(BorderFactory.createTitledBorder("Usage"))
keyTagOpen = "<span style=\"background-color: #FFFFFF\"><b><kbd>"
keyTagClose = "</kbd></b></span>"
keyLable = JLabel("<html><ul>\
<li>Next Image --- " + keyTagOpen + "<" + \
keyTagClose + "</li>\
<li>Previous Image --- " + keyTagOpen + ">" + \
keyTagClose + "</li>\
<li>Save --- " + keyTagOpen + "`" + keyTagClose + \
" (upper-left to TAB key)</li>\
<li>Next Unmarked Image --- " + keyTagOpen + \
"TAB" + keyTagClose + "</li></ul>\
</html>" )
keyLable.setBorder(
BorderFactory.createTitledBorder("Keyboard Shortcuts"))
helpPanel.add(helpLable)
helpPanel.add(keyLable)
helpPanel.setAlignmentX(Component.CENTER_ALIGNMENT)
helpPanel.setBorder(BorderFactory.createEmptyBorder(0, 10, 0, 10))
pan.add(helpPanel)
# pan.add(Box.createRigidArea(Dimension(0, 10)))
infoPanel = JPanel()
infoPanel.setLayout(BoxLayout(infoPanel, BoxLayout.Y_AXIS))
infoLabel = JLabel()
infoLabel.setBorder(BorderFactory.createTitledBorder("Project Info"))
infoPanel.add(infoLabel)
infoPanel.setAlignmentX(Component.CENTER_ALIGNMENT)
infoPanel.setBorder(BorderFactory.createEmptyBorder(0, 10, 0, 10))
pan.add(infoPanel)
win.setVisible(True)
self.imgData = imgData
self.win = win
# self.progressPanel = progressPanel
self.positionBar = positionBar
self.progressBar = progressBar
self.saveMessageLabel = saveMessageLabel
self.infoLabel = infoLabel
self.pixelSizeText = pixelSizeText
self.unitText = unitText
self.update()
def __init__(self, imgData):
n = imgData.size()
win = JFrame("Point Marker Panel")
win.setPreferredSize(Dimension(350, 590))
win.setSize(win.getPreferredSize())
pan = JPanel()
pan.setLayout(BoxLayout(pan, BoxLayout.Y_AXIS))
win.getContentPane().add(pan)
progressPanel = JPanel()
progressPanel.setLayout(BoxLayout(progressPanel, BoxLayout.Y_AXIS))
positionBar = JProgressBar()
positionBar.setMinimum(0)
positionBar.setMaximum(n)
positionBar.setStringPainted(True)
progressPanel.add(Box.createGlue())
progressPanel.add(positionBar)
progressBar = JProgressBar()
progressBar.setMinimum(0)
progressBar.setMaximum(n)
progressBar.setStringPainted(True)
progressPanel.add(progressBar)
progressPanel.setBorder(BorderFactory.createEmptyBorder(0,10,0,10))
pan.add(progressPanel)
pan.add(Box.createRigidArea(Dimension(5,5)))
savePanel = JPanel()
savePanel.setLayout(BoxLayout(savePanel, BoxLayout.Y_AXIS))
saveMessageLabel = JLabel("<html><u>Save Often</u></html>")
savePanel.add(saveMessageLabel)
savePanel.setAlignmentX(Component.CENTER_ALIGNMENT)
savePanel.setBorder(BorderFactory.createEmptyBorder(0,10,0,10))
pan.add(savePanel)
# pan.add(saveMessageLabel)
pan.add(Box.createRigidArea(Dimension(5,5)))
calPanel = JPanel()
calPanel.setLayout(BoxLayout(calPanel, BoxLayout.Y_AXIS))
calPanelIn = JPanel()
calPanelIn.setLayout(BoxLayout(calPanelIn, BoxLayout.X_AXIS))
pixelSizeText = JTextField(12)
pixelSizeText.setHorizontalAlignment(JTextField.RIGHT)
# pixelSizeText.setMaximumSize(pixelSizeText.getPreferredSize())
unitText = JTextField(10)
# unitText.setMaximumSize(unitText.getPreferredSize())
pixelSizeText.setText("Enter Pixel Size Here")
calPanelIn.add(pixelSizeText)
unitText.setText("Unit")
calPanelIn.add(unitText)
calPanelIn.setAlignmentX(Component.CENTER_ALIGNMENT)
calPanelIn.setBorder(BorderFactory.createTitledBorder("Custom Calibration"))
calPanel.add(calPanelIn)
calPanelIn.setAlignmentX(Component.CENTER_ALIGNMENT)
calPanel.setBorder(BorderFactory.createEmptyBorder(0,10,0,10))
pan.add(calPanel)
pan.add(Box.createRigidArea(Dimension(5,5)))
helpPanel = JPanel()
helpPanel.setLayout(BoxLayout(helpPanel, BoxLayout.Y_AXIS))
helpLable = JLabel("<html><ul>\
<li>Focus on Image Window</li>\
<li>Select multi-point Tool</li>\
<li>Click to Draw Points</li>\
<li>Drag to Move Points</li>\
<li>\"Alt\" + Click to Erase Points</li>\
<li>Optional: Customize Calibration Above\
and Refresh Images\
(won't be written to files)</li>\
</html>")
helpLable.setBorder(BorderFactory.createTitledBorder("Usage"))
keyTagOpen = "<span style=\"background-color: #FFFFFF\"><b><kbd>"
keyTagClose = "</kbd></b></span>"
keyLable = JLabel("<html><ul>\
<li>Next Image --- " + keyTagOpen + "<" + \
keyTagClose + "</li>\
<li>Previous Image --- " + keyTagOpen + ">" + \
keyTagClose + "</li>\
<li>Save --- " + keyTagOpen + "`" + keyTagClose + \
" (upper-left to TAB key)</li>\
<li>Next Unmarked Image --- " + keyTagOpen + \
"TAB" + keyTagClose + "</li></ul>\
</html>")
keyLable.setBorder(BorderFactory.createTitledBorder("Keyboard Shortcuts"))
helpPanel.add(helpLable)
helpPanel.add(keyLable)
helpPanel.setAlignmentX(Component.CENTER_ALIGNMENT)
helpPanel.setBorder(BorderFactory.createEmptyBorder(0,10,0,10))
pan.add(helpPanel)
# pan.add(Box.createRigidArea(Dimension(0, 10)))
infoPanel = JPanel()
infoPanel.setLayout(BoxLayout(infoPanel, BoxLayout.Y_AXIS))
infoLabel = JLabel()
infoLabel.setBorder(BorderFactory.createTitledBorder("Project Info"))
infoPanel.add(infoLabel)
infoPanel.setAlignmentX(Component.CENTER_ALIGNMENT)
infoPanel.setBorder(BorderFactory.createEmptyBorder(0,10,0,10))
pan.add(infoPanel)
win.setVisible(True)
self.imgData = imgData
self.win = win
# self.progressPanel = progressPanel
self.positionBar = positionBar
self.progressBar = progressBar
self.saveMessageLabel = saveMessageLabel
self.infoLabel = infoLabel
self.pixelSizeText = pixelSizeText
self.unitText = unitText
self.update()
class MenueFrame(JFrame, ActionListener, WindowFocusListener): # should extend JFrame
def __init__(self):
self.mainDir = ""
self.setTitle("Dots Quality Check")
self.setSize(250, 300)
self.setLocation(20,120)
self.addWindowFocusListener(self)
self.Panel = JPanel(GridLayout(0,1))
self.add(self.Panel)
self.openNextButton = JButton("Open Next Random", actionPerformed=self.openRandom)
self.Panel.add(self.openNextButton)
self.saveButton = JButton("Save", actionPerformed=self.save, enabled=False)
self.Panel.add(self.saveButton)
self.cropButton = JButton("Crop values from here", actionPerformed=self.cropVals)
self.Panel.add(self.cropButton)
self.DiscardButton = JButton("Discard cell", actionPerformed=self.discardCell)
self.Panel.add(self.DiscardButton)
self.quitButton = JButton("Quit script",actionPerformed=self.quit)
self.Panel.add(self.quitButton)
annoPanel = JPanel()
#add gridlayout
self.wtRButton = JRadioButton("wt", actionCommand="wt")
self.wtRButton.addActionListener(self)
self.defectRButton = JRadioButton("Defect", actionCommand="defect")
self.defectRButton.addActionListener(self)
annoPanel.add(self.wtRButton)
annoPanel.add(self.defectRButton)
self.aButtonGroup = ButtonGroup()
self.aButtonGroup.add(self.wtRButton)
self.aButtonGroup.add(self.defectRButton)
self.Panel.add(annoPanel)
self.ProgBar = JProgressBar()
self.ProgBar.setStringPainted(True)
self.ProgBar.setValue(0)
self.Panel.add(self.ProgBar)
self.pathLabel = JLabel("-- No main directory chosen --")
self.pathLabel.setHorizontalAlignment( SwingConstants.CENTER )
self.Panel.add(self.pathLabel)
WindowManager.addWindow(self)
self.show()
# - - - - B U T T O N M E T H O D S - - - -
# - - - - - - - - - - - - - - - - - - - - - - -
def openRandom(self, event): # when click here: get random cell and meas.measure(csv, tif, savePath)
if self.mainDir == "":
self.mainDir = DirectoryChooser("Random QC - Please choose main directory containing ctrl and test folders").getDirectory()
self.pathLabel.setText("MainDir: " + os.path.basename(os.path.split(self.mainDir)[0]))
try:
# should be complete disposal!
self.cT.closeWindows()
finally:
inFiles = glob.glob(os.path.join(self.mainDir, "*", G_OPENSUBDIR, "val_*.csv")) # glob.glob returns list of paths
uncheckedCells = [cell(csvPath) for csvPath in inFiles if cell(csvPath).processed == False]
if len(uncheckedCells) > 0:
self.cell = random.choice(uncheckedCells)
#update progressbar
self.ProgBar.setMaximum(len(inFiles)-1)
self.ProgBar.setValue(len(inFiles)-len(uncheckedCells))
# open imp and resultstable
self.cT = correctionTable(self.cell, self) #self, openPath_csv, mF
self.RBActionListener.setCell(self.cell)
# delete previous Radiobutton annotation
self.wtRButton.setSelected(False)
self.defectRButton.setSelected(True)
else:
print "All cells measured!"
def save(self, event):
savepath = self.cell.getQcCsvPath()
anaphase = self.cell.getAnOn()
timeInterval = self.cT.getImp().getCalibration().frameInterval
annotation = self.getAnnotation()
position = str(self.cell.position)
cellIndex = str(self.cell.cellNo)
if not os.path.exists(os.path.split(savepath)[0]): # check if save folder present.
os.makedirs(os.path.split(savepath)[0]) # create save folder, if not present
f = open(savepath, "w")
# Position Cell Phenotype Frame Time AnOn Distance ch0x ch0y ch0z ch0vol ch1x ch1y ch1z ch1vol
f.write("Position,Cell,Phenotype,Frame,Time,Anaphase,Distance,ch0x,ch0y,ch0z,ch0vol,ch1x,ch1y,ch1z,ch1vol\n")
for i in range(self.cT.getLineCount()):
frame, distance, a = self.cT.getLine(i).split("\t")
corrFrame = str(int(frame)-int(anaphase))
time = "%.f" % (round(timeInterval) * int(corrFrame))
if distance == "NA":
ch0x, ch0y, ch0z, ch0vol, ch1x, ch1y, ch1z, ch1vol = ("NA," * 7 + "NA\n").split(",")
else:
ch0x, ch0y, ch0z, ch0vol, ch1x, ch1y, ch1z, ch1vol = self.cT.getXYZtable()[i]
f.write(position+","+cellIndex+","+annotation+","+corrFrame+","+time+","+anaphase+","+distance+","+ch0x+","+ch0y+","+ch0z+","+ch0vol+","+ch1x+","+ch1y+","+ch1z+","+ch1vol)
f.close()
print "Successfully saved!"
def cropVals(self, event): #"this function deletes all values with frame > current cursor"
for line in range(self.cT.getSelectionEnd(), self.cT.getLineCount(), 1):
frame, distance, AOCol = self.cT.getLine(line).split("\t")
self.cT.setLine(line, frame + "\tNA" + "\t" + AOCol)
def discardCell(self, event):
if not os.path.exists(os.path.split(self.cell.getQcCsvPath() )[0]): # check if save folder present.
os.makedirs(os.path.split(self.cell.getQcCsvPath() )[0]) # create save folder, if not present.
f = open(self.cell.getQcCsvPath() ,"w")
# Write dummy header. Position Cell Phenotype Frame Time AnOn Distance ch0x ch0y ch0z ch0vol ch1x ch1y ch1z ch1vol
f.write("Position,Cell,Phenotype,Frame,Time,AnOn,Distance,ch0x,ch0y,ch0z,ch0vol,ch1x,ch1y,ch1z,ch1vol\n")
f.close()
print "Discarded cell - saved dummy"
def quit(self, event):
try:
self.cT.closeWindows()
finally:
WindowManager.removeWindow(self)
self.dispose()
# Methods implementing ActionListener interfaces:
def actionPerformed(self, e):
# this function is called when RadioButtons are changed
self.cell.annotate( e.getSource().getActionCommand() )
self.setSaveActive()
def windowGainedFocus(self, e):
pass
def windowLostFocus(self, e):
pass
# - - - - - - - - - - - - -
# - get and set methods - -
# - - - - - - - - - - - - -
def getAnnotation(self):
return self.aButtonGroup.getSelection().getActionCommand()
def getMainDir(self):
return self.mainDir
def setSaveActive(self):
if (self.cell.getAnnotation() != None and self.cell.getAnOn() != None):
self.saveButton.setEnabled(True)
self.show()
def setSaveInactive(self):
self.saveButton.setEnabled(False)
self.show()
def setMainDir(self, path):
self.mainDir = path
self.pathLabel.setText("MainDir: " + os.path.basename(os.path.split(self.mainDir)[0]))
