def __add(self, event):
if ( not self.__init) :
IJ.showMessage("", "please start a new stack")
return
if ( not self.__initDIA) :
IJ.showMessage("", "please select an image for DIA")
return
if ( not self.__initFLUO) :
IJ.showMessage("", "please select an image for FLUO")
return
self.__widthl = self.__display2.getText()
roi = self.__impD.getRoi()
if roi == None :
IJ.showMessage("", "No selection")
return
if roi.getType() in [6,7] :
nslice = self.__impD.getCurrentSlice()
self.__impF.setSlice(nslice)
self.__impF.setRoi(roi)
elif roi.getType() in [2,4] :
nslice = self.__impD.getCurrentSlice()
self.__impF.setSlice(nslice)
m=Morph(self.__impF, roi)
m.setMidParams(10, 2)
roi=m.MidAxis
if roi == None :
self.__display.text = "roi fail"
if not self.__skip : IJ.showMessage("", "failed roi, please draw it as polyline")
return
#if roi.getType() != 6 : self.__impF.setRoi(roi)
else :
IJ.showMessage("", "This selection is not yet allowed")
return
self.__impF.setRoi(roi)
straightener = Straightener()
new_ip = straightener.straighten(self.__impF, roi, int(self.__widthl))
self.__iplist.append(new_ip)
self.__labels.append(self.__isF.getShortSliceLabel(nslice))
self.__display.text = self.__name + " cell " + str(len(self.__iplist)) +" width="+str(new_ip.getWidth())+ " height="+ str(new_ip.getHeight())
roi.setPosition(self.__impD.getCurrentSlice())
self.__rm = RoiManager.getInstance()
if (self.__rm==None): self.__rm = RoiManager()
self.__rm.add(self.__impD, roi, len(self.__iplist))
self.__cellsrois.append((roi, self.__impD.getCurrentSlice()))
#self.__rm.runCommand("Show All")
IJ.selectWindow(self.__impD.getTitle())
def __fmaxfinder(self) :
#stack = self.__impRes.getStack()
self.__impD.killRoi()
self.__impF.killRoi()
stack = self.__impF.getStack()
n_slices = stack.getSize()
#newstack=ImageStack(self.__impRes.getWidth(), self.__impRes.getHeight())
newstack=ImageStack(self.__impF.getWidth(), self.__impF.getHeight())
noise = self.__display3.text
for index in range(1,n_slices+1):
IJ.selectWindow(self.__impF.getTitle())
self.__impF.setSlice(index)
ip = self.__impF.getProcessor()
mf=MaximumFinder()
ipmax = mf.findMaxima(ip, int(noise), 0, 0, False, False)
newstack.addSlice("", ipmax)
newimage=ImagePlus("max points"+self.__name, newstack)
newimage.show()
newimage.updateAndDraw()
listip = []
maxh=self.__impRes.getHeight()
for roi in self.__cellsrois :
straightener = Straightener()
newimage.setSlice(roi[1])
newimage.setRoi(roi[0])
#listip.append(straightener.straighten(newimage, roi[0], int(self.__widthl)))
listip.append(straightener.straighten(newimage, roi[0], maxh))
listip.sort(key = lambda ip : ip.width)
ipw=[ ip.getWidth() for ip in listip ]
iph=[ ip.getHeight() for ip in listip ]
maxw=max(ipw)
maxh=max(iph)
if self.__enlarge : resizelist = [ ip.resize(maxw, maxh, True) for ip in listip ]
else :
resizelist = []
for ip in listip :
tempip = ByteProcessor(maxw, maxh)
xloc = int(math.floor((maxw/2.00) - (ip.width/2.00)))
yloc = int(math.floor((maxh/2.00) - (ip.height/2.00)))
tempip.copyBits(ip, xloc, yloc, Blitter.COPY)
resizelist.append(tempip)
ims = ImageStack(maxw, maxh)
#for ip in resizelist : ims.addSlice("", ip)
for i in range(len(resizelist)) :
ims.addSlice(self.__labels[i], resizelist[i])
self.__impMax = ImagePlus(self.__name+"-max", ims)
self.__impMax.show()
stack = self.__impMax.getStack() # get the stack within the ImagePlus
n_slices = stack.getSize()
for index in range(1, n_slices+1):
self.__impMax.killRoi()
self.__impMax.setSlice(index)
roi = self.__listrois[index-1]
if self.__sens[index-1]<0 :
self.__impMax.setRoi(roi)
ip1 = self.__impMax.getProcessor()
ip1.flipHorizontal()
self.__impMax.killRoi()
self.__impMax.updateAndDraw()
ip = self.__impMax.getProcessor()
for i in range(ip.getWidth()*ip.getHeight()) :
if ip.getf(i) > 0 : ip.setf(i, 255)
#else : ip.setf(i, 0)
IJ.run(self.__impMax, "8-bit", "")
IJ.run(self.__impMax, "Options...", "iterations=2 count=1 black edm=Overwrite do=Close stack")
IJ.run(self.__impMax, "Ultimate Points", "stack")
self.__impMax.updateAndDraw()
def __addroi(self, event) :
if ( not self.__init) :
IJ.showMessage("", "please start a new stack")
return
if ( not self.__initDIA) :
IJ.showMessage("", "please select an image for DIA")
return
if ( not self.__initFLUO) :
IJ.showMessage("", "please select an image for FLUO")
return
twres = TextWindow("measures-"+self.__name, "label\tname\tsol\tarea\tcirc\tAR\tFeret\taxis\traf\tdMajor\tdFeret\tdArea", "", 300, 450)
tab="\t"
self.__widthl = self.__display2.getText()
IJ.selectWindow(self.__impF.getTitle())
self.__rm = RoiManager.getInstance()
if (self.__rm==None): self.__rm = RoiManager()
if self.__impF.getImageStackSize() > 1 :
roisarray =[(roi, self.__rm.getSliceNumber(roi.getName())) for roi in self.__rm.getRoisAsArray()]
else :
roisarray =[(roi, 1) for roi in self.__rm.getRoisAsArray()]
self.__rm.runCommand("reset")
#self.__rm.runCommand("Delete")
IJ.selectWindow(self.__impF.getTitle())
self.__maxraf=float(self.__display19.text)
self.__minraf=float(self.__display20.text)
count=1
for roielement in roisarray :
roi = roielement[0]
pos = roielement[1]
lab = self.__impF.getImageStack().getShortSliceLabel(pos)
if lab==None : lab=str(pos)
if self.__conEllipses :
IJ.selectWindow(self.__impF.getTitle())
self.__impF.setSlice(pos)
self.__impF.setRoi(roi)
self.__rm.runCommand("Add")
IJ.run(self.__impF, "Fit Ellipse", "")
ellipse=self.__impF.getRoi()
params = ellipse.getParams()
ferets = ellipse.getFeretValues()
imp2 = Duplicator().run(self.__impF,pos,pos)
IJ.run(imp2, "Rotate... ", "angle="+str(ferets[1])+" grid=0 interpolation=Bilinear enlarge slice")
temproi=Roi((imp2.getWidth()-ferets[0])/2.0,(imp2.getHeight()-ferets[2])/2.0,ferets[0],ferets[2])
imp2.setRoi(temproi)
imp3 = Duplicator().run(imp2,1,1)
ip3=imp3.getProcessor()
if int(self.__display5.text) < ip3.getWidth() < int(self.__display6.text) :
self.__iplist.append(ip3)
self.__display.text = self.__name + " cell " + str(len(self.__iplist))
fer=Line(params[0],params[1],params[2],params[3])
self.__cellsrois.append((fer, pos))
self.__labels.append(self.__isF.getShortSliceLabel(pos))
m=Morph(self.__impF, roi)
twres.append(lab+tab+str(roi.getName())+tab+str(m.Solidity)+tab+str(m.Area)+tab+str(m.Circ)+tab+str(m.AR)+tab+str(m.MaxFeret)+tab+str(fer.getLength())+tab+str(1)+tab+str(0)+tab+str(0)+tab+str(0))
self.__dictCells[count]=(str(roi.getName()), lab, roi)
count=count+1
continue
if roi.getType() in [6,7] :
self.__impF.setSlice(pos)
self.__impF.setRoi(roi)
self.__rm.runCommand("Add")
elif roi.getType() in [2,4] :
self.__impF.setSlice(pos)
self.__impF.setRoi(roi)
m=Morph(self.__impF, roi)
m.setMidParams(10, 2)
midroi=m.MidAxis
if midroi == None : continue
raf = m.MaxFeret/midroi.getLength()
if (self.__maxraf < raf) or (raf < self.__minraf) : continue
maxsol = float(self.__display7.text)
minsol = float(self.__display8.text)
maxarea = float(self.__display9.text)
minarea = float(self.__display10.text)
maxcirc = float(self.__display11.text)
mincirc = float(self.__display12.text)
maxar = float(self.__display13.text)
minar = float(self.__display14.text)
maxfer = float(self.__display15.text)
minfer = float(self.__display16.text)
maxmean = float(self.__display17.text)
minmean = float(self.__display18.text)
maxmferet = float(self.__display21.text)
minmferet = float(self.__display22.text)
testsol = (minsol<= m.Solidity <= maxsol)
testarea = (minarea<= m.Area <= maxarea)
testcirc = (mincirc<= m.Circ <= maxcirc)
testar = (minar<= m.AR <= maxar)
testfer = (minfer<= m.MaxFeret <= maxfer)
testmean = (minmean <= m.Mean <= maxmean)
testmferet = (minmferet <= m.MinFeret <= maxmferet)
#print minmferet , m.MinFeret , maxmferet
test = (testsol+testarea+testcirc+testar+testfer+testmean+testmferet)/7
if test :
fmaj, ffmx, fa =[],[],[]
for r in m.getMidSegments(10, 40, 0)[0] :
if r == None : continue
m2=Morph(self.__impF, r)
fmaj.append(m2.Major)
ffmx.append(m2.MaxFeret)
fa.append(m2.Area)
diffmajor, diffferet, diffarea = 0,0,0
if len(fa) > 4 :
medfmaj = self.listmean(fmaj[1:-1])
medffmx = self.listmean(ffmx[1:-1])
medfa = self.listmean(fa[1:-1])
diffmajor = (max(fmaj[1:-1])-medfmaj)/medfmaj
diffferet = (max(ffmx[1:-1])-medffmx)/medffmx
diffarea = (max(fa[1:-1])-medfa)/medfa
twres.append(lab+tab+str(roi.getName())+tab+str(m.Solidity)+tab+str(m.Area)+tab+str(m.Circ)+tab+str(m.AR)+tab+str(m.MaxFeret)+tab+str(midroi.getLength())+tab+str(m.MaxFeret/midroi.getLength())+tab+str(diffmajor)+tab+str(diffferet)+tab+str(diffarea))
#print lab+tab+str(roi.getName())+tab+str(m.Solidity)+tab+str(m.Area)+tab+str(m.Circ)+tab+str(m.AR)+tab+str(m.MaxFeret)+tab+str(midroi.getLength())+tab+str(m.MaxFeret/midroi.getLength())+tab+str(diffmajor)+tab+str(diffferet)+tab+str(diffarea)
self.__impF.setRoi(roi)
self.__rm.runCommand("Add")
self.__impF.killRoi()
self.__impF.setRoi(midroi)
#self.__dictCells[str(roi.getName())]=(str(roi.getName()), lab, roi)
self.__dictCells[count]=(str(roi.getName()), lab, roi)
count=count+1
else :
#print "test falls"
continue
else :
print "out loop"
continue
straightener = Straightener()
new_ip = straightener.straighten(self.__impF, midroi, int(self.__widthl))
if int(self.__display5.text) < new_ip.getWidth() < int(self.__display6.text) :
self.__iplist.append(new_ip.convertToShort(False))
self.__display.text = self.__name + " cell " + str(len(self.__iplist))
#print "add", roi.getName(), roi.getType()
self.__cellsrois.append((midroi, pos))
self.__labels.append(self.__isF.getShortSliceLabel(pos))
#roisarray=self.__rm.getRoisAsArray()
#self.__rm.runCommand("reset")
#self.__rm.runCommand("Delete")
self.__impD.killRoi()
self.__impF.killRoi()
IJ.selectWindow(self.__impD.getTitle())
