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04-QualityControl_v8j.py
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04-QualityControl_v8j.py
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from javax.swing import JButton, JFrame, JPanel, JLabel, JTextArea, JScrollPane, JProgressBar, SwingConstants, WindowConstants, JRadioButton, ButtonGroup
from java.awt import Component, GridLayout
import re, random, os, sys, glob
from java.awt.event import KeyEvent, KeyAdapter, MouseEvent, MouseAdapter
from ij.plugin import Zoom
from ij import WindowManager, IJ, ImagePlus
from ij.text import TextWindow, TextPanel
from ij.io import DirectoryChooser
# go through frames with arrowleft ()
# 0: anaphase Onset
# q: delete measurement
G_SAVESUBDIR = "qc-meas"
G_OPENSUBDIR = "meas"
def bigRound(x, base):
return int(base * round(float(x)/base))
def quit(event):
try:
meas.closeWindows()
finally:
WindowManager.removeWindow(mF.frame)
mF.frame.dispose()
def openE(event):
meas.closeWindows()
meas.measure()
def openRandom(event): # when click here: get random cell and meas.measure(tsv, tif, savePath)
if mF.getMainDir() == "":
mainDir = DirectoryChooser("Random QC - Please choose main directory containing ctrl and test folders").getDirectory()
mF.setMainDir(mainDir)
print "Setting new main dir to", mainDir
try:
meas.closeWindows()
finally:
inFiles = glob.glob(os.path.join(mF.getMainDir(),"*", G_OPENSUBDIR ,"val_*.tsv")) # glob.glob returns list of paths
print inFiles
uncheckedCells = [cell(tsvPath) for tsvPath in inFiles if cell(tsvPath).processed == False]
if len(uncheckedCells) > 0:
randomCell = random.choice(uncheckedCells)
mF.setProgBarMax(len(inFiles)-1)
mF.setProgBarVal(len(inFiles)-len(uncheckedCells))
meas.measure(randomCell)
else:
print "All cells measured!"
def changeFrame(tp):
imp = IJ.getImage() # wrong. how can I propagate the imp of meas?
if tp.getSelectionEnd() >= 0:
frame, dist, AOCol = tp.getLine(tp.getSelectionEnd()).split("\t")
imp.setSlice(int(frame))
class ListenToKey(KeyAdapter):
def keyPressed(this, event):
eventSrc = event.getSource()
tp = eventSrc.getParent() #panel is the parent, canvas being component.
if event.getKeyCode() == 37 and tp.getSelectionEnd() > 0: # KeyCode 37 : arrowLeft
tp.setSelection(tp.getSelectionEnd()-1, tp.getSelectionEnd()-1)
if event.getKeyCode() == 39 and tp.getSelectionEnd() < tp.getLineCount(): # KeyCode 39 : arrowRight
tp.setSelection(tp.getSelectionEnd()+1, tp.getSelectionEnd()+1)
changeFrame(tp)
if event.getKeyCode() == 48: # Anaphase Onset Def. KeyCode 48 : 0
setAnaphase(tp, event)
meas.tw.toFront()
if event.getKeyCode() == 81: # KeyCode 81: q
delVal(tp, event)
# Prevent further propagation of the key event:
keyEvent.consume()
class ListenToMouse(MouseAdapter):
def mouseClicked(this, event):
tp = event.getSource().getParent()
changeFrame(tp)
class cell:
def __init__(self, tsvPath):
self.tsvPath = tsvPath
self.openDir, self.filename = os.path.split(self.tsvPath)
tsvRE = re.compile( os.path.join('(?P<mainDir>.*)', '(?P<strain>.*)', G_OPENSUBDIR ,'val_p(?P<position>\d+)_c(?P<cell>\d+).tsv') )
pathMO = re.match(tsvRE, tsvPath)
self.mainDir = pathMO.group('mainDir')
self.strain = pathMO.group('strain')
self.position = int(pathMO.group('position'))
self.cellNo = int(pathMO.group('cell'))
self.tifPath = os.path.join(self.openDir, "zi_p%i_c%i.tif" %(self.position, self.cellNo))
self.savePath = os.path.join(self.mainDir, self.strain, G_SAVESUBDIR, "qc_val_p%i_c%i.tsv") %(self.position, self.cellNo)
self.isProcessed()
def isProcessed(self):
if os.path.exists(self.savePath):
self.processed = True
else:
self.processed = False
def hasTif(self):
if os.path.exists(self.tifPath):
self.processed = True
else:
self.processed = False
def setAnOn(self, anOn):
self.anOn = anOn
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 Measurer:
"class contains the table (TextWindow and TextPanel) and imp for"
def __init__(self):
self.anOnFrame = 0
def measure(self, cell):
self.cell = cell
self.imp = self.openImp(cell.tifPath)
self.tw = self.openTW(cell.tsvPath)
self.tp = self.tw.getTextPanel()
self.tp.addKeyListener(ListenToKey())
self.tp.addMouseListener(ListenToMouse())
self.tp.setSelection(0,0) # int startLine, int endLine
frame, distance, AO = self.tp.getLine(self.tp.getSelectionEnd()).split("\t")
self.imp.setSlice(int(frame))
mF.setSaveInactive()
# here: putFocus on tw
# arrange Windows properly!
def openImp(self, path):
imp = ImagePlus(path) # open associated tif file
imp.show()
imp.getWindow().setLocationAndSize(280, 120, imp.getWidth()*4, imp.getHeight()*4) # int x, int y, int width, int height
return imp
def openTW(self, openPath_tsv):
txtfile = open(openPath_tsv)
heads = txtfile.readlines(1)[0].split("\t")
tw = TextWindow("Results", heads[0]+"\t"+heads[2]+"\t Anaphase", "", 50, 500)
#tw.setLocation(20+, 5)
for line in txtfile.readlines(): # load file lines in textPanel.
frame, timeA, dist, volChI, volChII = line.split("\t")
tw.append(frame + "\t" + dist + "\t" )
return tw
def getCell(self):
return self.cell
def getImp(self):
return self.imp
def getTw(self):
return self.tw
def setAnOn(self, anOn):
self.anOnFrame = anOn
def getAnOn(self):
return self.anOnFrame
def closeWindows(self):
self.imp.close()
self.tw.close()
def setAnaphase(tp, event):
mF.setSaveActive()
anOnFrame, anOnDistance, AOCol = tp.getLine(tp.getSelectionEnd()).split("\t")
print "Setting anaphase onset to frame " + anOnFrame
meas.setAnOn(anOnFrame)
for i in range(tp.getLineCount()): # very unelegantly solved, I admit. but it works.
blFr, blDist, blAOCol = tp.getLine(i).split("\t")
tp.setLine(i, blFr + "\t" + blDist + "\t")
frame, distance, AOCol = tp.getLine(tp.getSelectionEnd()).split("\t") # get old line
tp.setLine(tp.getSelectionEnd(), frame + "\t" + distance + "\tX")
# setFocus back to tw,tp
def delVal(tp, event):
frame, distance, AOCol = tp.getLine(tp.getSelectionEnd()).split("\t")
tp.setLine(tp.getSelectionEnd(), frame + "\tNA" + "\t" + AOCol)
def cropVals(event): #"this function deletes all values with frame > current cursor"
print meas.tp.getLineCount()
for line in range(meas.tp.getSelectionEnd(), meas.tp.getLineCount(), 1):
frame, distance, AOCol = meas.tp.getLine(line).split("\t")
#print line
meas.tp.setLine(line, frame + "\tNA" + "\t" + AOCol)
def save(event):
ana = meas.getAnOn()
tp_save = TextPanel("SavePanel")
tp_save.appendLine("Position\tCell\tFrame\tTime\tDistance\tAnOn")
timeInterval = meas.getImp().getCalibration().frameInterval
for i in range(meas.tp.getLineCount()):
oFrame, oDist, oAOCol = meas.tp.getLine(i).split("\t")
oFrame = int(oFrame)-int(ana)
oTime = "%.f" % (round(timeInterval) * int(oFrame)) #
print "test"
phenotype = meas.aButtonGroup.getSelected().getActionCommand()
print phenotype
if oAOCol == "X":
tp_save.appendLine(str(meas.cell.position) + "\t" + str(meas.cell.cellNo) + "\t0\t0\t" + oDist + "\t" + meas.getAnOn())
else:
tp_save.appendLine(str(meas.cell.position) + "\t" + str(meas.cell.cellNo) + "\t" + str(oFrame) + "\t" + oTime + "\t" + oDist + "\t" + meas.getAnOn())
if not os.path.exists(os.path.split(meas.cell.savePath)[0]): # check if save folder present!
os.makedirs(os.path.split(meas.cell.savePath)[0]) # create save folder, if not present
tp_save.saveAs(meas.cell.savePath)
print "Successfully saved ", meas.cell.savePath
def discardCell(event):
tp_save = TextPanel("SavePanel")
tp_save.appendLine("Position\tCell\tFrame\tTime\tDistance\tAnOn")
if not os.path.exists(os.path.split(meas.cell.savePath)[0]): # check if save folder present!
print "in if"
os.makedirs(os.path.split(meas.cell.savePath)[0])
print "behind if"
tp_save.saveAs(meas.cell.savePath)
print "Discarded cell - dummy saved as ", meas.getSavePath()
# - - - M A I N - - -
random.seed()
mF = MenueFrame()
meas = Measurer()