distMin = dist
return centPart, (x, y)
def isSpecialParticle(image, roim, iParticle, boundariesNuc, boundariesMito, pixelSize, z):
try:
image.setSlice(int(round(z)))
image2 = ImagePlus("slice",image.getProcessor())
roim.select(image2, iParticle)
image3 = Duplicator().run(image2);
image3.show()
sp = segment_Particles()
image3 = sp.preprocessImage(image3, "MAX", "C1", 0, 0)
image3 = sp.segmentParticles(image3, "Triangle", boundariesNuc[0], boundariesNuc[1], 0, 0)
if roim.getCount() > 0:
roim.select(image3, 0)
stats = image3.getStatistics(Measurements.AREA + Measurements.SHAPE_DESCRIPTORS)
IJ.log("Area (um2) " + str(stats.area*pixelSize*pixelSize) + "; Aspect Ratio " + str(stats.major/stats.minor))
if stats.area > boundariesMito[0] and stats.area < boundariesMito[1] and stats.major/stats.minor > boundariesMito[2]:
return 1
else:
return 0
except BaseException, err:
def run():
zk = ZeissKeys()
msg = Message()
timestart = time.clock()
channel = 1
#size in um2
minArea = 20
maxArea = 200
maxMetaArea = 70
minMetaAR = 1.8
method = "Triangle"
print "Enter run"
detectionNucleus = [minArea, maxArea]
detectionMetaphase = [minArea, maxMetaArea]
filepath = ""
try:
filepath = getArgument()
image = IJ.openImage(filepath) #arguments provided by runMacro
except NameError:
try:
filepath = newImagePath #argument provided by the macroRunner
except NameError: #no file name specified
errMsg = "Fiji error segmentNuclei.py: no filepath has been passed to the macro"
exitWithError(errMsg)
od = OpenDialog("Choose image file", None)
if od.getFileName() == None:
return
filepath = os.path.join(od.getDirectory(), od.getFileName())
# A roimanager is recquired
roim = RoiManager.getInstance()
if roim == None:
roim = RoiManager()
#test a last time
if roim == None:
print 'Fiji error segmentNuclei.py: no RoiManager!'
exitWithError('Fiji error segmentNuclei.py: no RoiManager!')
try:
IJ.run("Close all forced")
IJ.run("Clear Results")
IJ.log("\\Clear")
image = IJ.openImage(filepath)
IJ.log("File Path " + filepath)
try:
image.hide()
except:
image = IJ.getImage()
image.hide()
image.show()
if image is None:
exitWithError("Fiji failed to open image")
return 0
#convert um2 to pixels
pixelSize = image.getCalibration().pixelWidth
detectionNucleus = [area/pixelSize/pixelSize for area in detectionNucleus]
detectionMetaphase = [area/pixelSize/pixelSize for area in detectionMetaphase]
detectionMetaphase.append(minMetaAR)
title = image.getTitle()
imageC = None
#split colors if needed
if image.getNChannels() > 1:
chSp = ChannelSplitter()
imageC = chSp.split(image)
imageSeg = imageC[channel-1].duplicate()
else:
imageSeg = image.duplicate()
imageSeg.setTitle("SEG_"+title)
sp = segment_Particles()
imageSeg = sp.preprocessImage(imageSeg, "MAX", "C1", 2, 2)
imageSeg = sp.segmentParticles(imageSeg, method, detectionNucleus[0], detectionNucleus[1], 2, 2)
roim = RoiManager.getInstance()
if roim == None:
print 'Fiji error segmentNuclei.py: no RoiManager!'
exitWithError('Fiji error segmentNuclei.py: no RoiManager!')
#compute central object
if roim.getCount() > 0:
centPart, msg.position = centerParticle(imageSeg, roim)
msg.position = msg.position + (focusParticle(image, roim, centPart),)
writePositionToRegistry(msg.position)
else:
IJ.run("Read Write Windows Registry", "action=write location=[HKCU\\"+zk.regkey+"] key="+zk.subkey_codemic+" value=["+msg.CODE_NOTHING+"] windows=REG_SZ")
return 0
#create output image
if imageC is None:
impOut = createOutputImg(image, roim, centPart, 0)
else:
impOut = createOutputImg(imageC[channel-1], roim, centPart, 0)
impOut.show()
#save outut image
#saveOutputImg(impOut, filepath, 'Analyzed')
#check for roi properties to identofy metaphase
metaphase = isSpecialParticle(image, roim, centPart,detectionNucleus, detectionMetaphase,pixelSize, msg.position[2])
if os.path.basename(filepath).startswith('TR1_') or '_TR1_' in os.path.basename(filepath):
metaphase = 0
if metaphase:
IJ.run("Read Write Windows Registry", "action=write location=[HKCU\\"+zk.regkey+"] key="+zk.subkey_codemic+" value=["+msg.CODE_TRIGGER1+"] windows=REG_SZ")
else:
IJ.run("Read Write Windows Registry", "action=write location=[HKCU\\"+zk.regkey+"] key="+zk.subkey_codemic+" value=["+msg.CODE_FOCUS+"] windows=REG_SZ")
IJ.log("time focus " + str(time.clock() - timestart))
IJ.run("Collect Garbage")
#IJ.run("Close all forced")
#IJ.run("Clear Results")
except BaseException, err:
