def tabbuttonPressed(event) :
tab="\t"
headings=[]
measures=[]
#img=IJ.getImage()
#for i in range(self.__img.getImageStackSize()+1) :
for i in range(self.__maxLife+1) :
headings.append("Slice "+str(i))
headings[0]=WindowManager.getUniqueName(self.__img.getShortTitle())
#for m in self.__measurescompl :
for m in self.__dictMeasures[dico[self.__listcellname[0]]].keys() :
headstring=""
for head in headings:
headstring+=head+tab
tw=TextWindow(self.__listfiles[0]+"-"+m,headstring,"",800,600)
tp=tw.getTextPanel()
#for cellname in dico.keys() :
for cellname in self.__listcellname :
line=[]
line=[str(meas)+tab for meas in self.__dictMeasures[dico[cellname]][m]]
line.insert(0, cellname+tab)
linestr=""
for s in line: linestr+=s
tp.appendLine(linestr)
tp.updateDisplay()
if self.__measuresparambool_global[0] :
tw=TextWindow("Latency","cell\tLatency", "",800,600)
tp=tw.getTextPanel()
for i in range(len(self.__listcellname)) :
#if latencies[i][0] : line=self.__listcellname[i]+"\t"+str(latencies[i][1])
#else : line=self.__listcellname[i]+"\t"+"NaN"
line=self.__listcellname[i]+"\t"+str(latencies[i][1])
tp.appendLine(line)
tp.updateDisplay()
def __buildstack(self, listfiles):
"""
Creates stacks according to the list of paths given by the user.
"""
if not isinstance(listfiles[0],list) and os.path.isfile(listfiles[0]) :
if len(self.__positionsList)==0 : tempname = WindowManager.getUniqueName("image")
else : tempname = self.__positionsList[0]
tempd = tempfile.mkdtemp()
fichier = open(tempd+"/"+tempname+".tif","w")
rawtimes=[]
rawtimes.append(0)
zerotimes=0
for i in range(len(listfiles)-1) :
difftimes=int((os.stat(listfiles[i+1]).st_mtime-os.stat(listfiles[i]).st_mtime))
if difftimes==0 : zerotimes+=1
rawtimes.append(rawtimes[-1]+difftimes)
fichier.writelines(listfiles[i]+"\n")
fichier.writelines(listfiles[-1]+"\n")
fichier.close()
IJ.run("Stack From List...","open="+tempd+"/"+tempname+".tif")
n=WindowManager.getImageCount()
tempid=WindowManager.getNthImageID(n)
tempimg=WindowManager.getImage(tempid)
if self.__batch : tempimg.hide()
else : tempimg.show()
self.__dictImages[tempname]=tempimg
tempimg.hide()
nameimages=tempname
if zerotimes/len(rawtimes) > 0.5 : rawtimes=range(len(listfiles))
self.__dictTimeStack["image1"]=rawtimes
#elif isinstance(listfiles[0][0],str) :
elif os.path.isfile(listfiles[0][0]) :
nameimages=[]
rawtimes=[]
rawtimes.append(0)
for i in range(len(listfiles)) :
if len(self.__positionsList)==0 : tempname = WindowManager.getUniqueName("image"+str(i+1))
else : tempname = self.__positionsList[i]
tempd = tempfile.mkdtemp()
fichier = open(tempd+"/"+tempname+".tif","w")
zerotimes=0
for j in range(len(listfiles[i])-1) :
difftimes=int((os.stat(listfiles[i][j+1]).st_mtime-os.stat(listfiles[i][j]).st_mtime))
if difftimes==0 : zerotimes+=1
rawtimes.append(rawtimes[-1]+difftimes)
fichier.writelines(listfiles[i][j]+"\n")
fichier.writelines(listfiles[i][-1]+"\n")
fichier.close()
IJ.run("Stack From List...","open="+tempd+"/"+tempname+".tif")
n=WindowManager.getImageCount()
tempid=WindowManager.getNthImageID(n)
tempimg=WindowManager.getImage(tempid)
#self.__dictImages["image"+str(i+1)]=tempimg
#nameimages.append("image"+str(i+1))
self.__dictImages[tempname]=tempimg
nameimages.append(tempname)
if zerotimes/len(rawtimes) > 0.5 : rawtimes=range(len(listfiles[i]))
#self.__dictTimeStack["image"+str(i+1)]=rawtimes
self.__dictTimeStack[tempname]=rawtimes
rawtimes=[]
rawtimes.append(0)
tempimg.hide()
else :
nameimages=[]
print "ERROR IN BUILDSTACK"
return nameimages
def graphbuttonPressed(event) :
colors=[]
#img=IJ.getImage()
#nbslices=self.__img.getImageStackSize()
nbslices=self.__maxLife
acell=dico.values()[0]
if self.__useTime :
x = acell.getListTimes()
namex="Time sec"
else :
x = range(1,nbslices+1)
namex = "Frame"
maxx=max(x)
minx=min(x)
#x=[i for i in range(1,nbslices+1)]
font=Font("new", Font.BOLD, 14)
tempname = WindowManager.getUniqueName(self.__img.getShortTitle())
for i in range(len(self.__measures)) :
#print "i", i, self.__measures[i]
yarray=[]
flag=True
miny=10000000000
maxy=-1000000000
#we find the min and max values in order to set the scale.
for cellname in self.__listcellname :
colors.append(dico[cellname].getColor())
yarray.append(self.__dictMeasures[dico[cellname]][self.__measures[i]])
#for meas in self.__dictMeasures[dico[cellname]][self.__measures[i]] :
for meas in yarray[-1] :
if (meas<miny) and (Double.isNaN(meas)==False) :
miny=meas
if max(yarray[-1])>maxy : maxy=max(yarray[-1])
miny-=0.1*miny
maxy+=0.1*maxy
count=0.05
for j in range(len(yarray)) :
if j==0 :
if len(self.__measures)>1 :
plot=Plot("Plots-"+str(self.__measures[i]),namex,str(self.__measures[i]),x,yarray[j])
else :
plot=Plot("Plot-"+tempname,namex,str(self.__measures[i]),x,yarray[j])
plot.setLimits(minx,maxx,miny,maxy)
plot.setColor(colors[j])
plot.changeFont(font)
plot.addLabel(0.05, count, self.__listcellname[j])
else :
plot.setColor(colors[j])
plot.setLineWidth(3)
plot.addPoints(x,yarray[j],Plot.LINE)
plot.addLabel(0.05, count, self.__listcellname[j])
count+=0.05
plot.setColor(colors[0])
plot.show()
if len(self.__measures)>1 :
IJ.run("Images to Stack", "name="+tempname+"-plots title=Plots- use")
def __buildstacks(self) :
listfiles = self.__listfiles[2]
positionsList = self.__imagesnames
if not isinstance(listfiles[0],list) and os.path.isfile(listfiles[0]) :
if len(positionsList)==0 : tempname = WindowManager.getUniqueName("image")
else : tempname = positionsList[0]
tempd = tempfile.mkdtemp()
fichier = open(tempd+os.path.sep+tempname+".tif","w")
rawtimes=[]
rawtimes.append(0)
zerotimes=0
for i in range(len(listfiles)-1) :
difftimes=int((os.stat(listfiles[i+1]).st_mtime-os.stat(listfiles[i]).st_mtime))
if difftimes==0 : zerotimes+=1
rawtimes.append(rawtimes[-1]+difftimes)
fichier.writelines(listfiles[i]+"\n")
fichier.writelines(listfiles[-1]+"\n")
fichier.close()
IJ.run("Stack From List...","open="+tempd+os.path.sep+tempname+".tif")
n=WindowManager.getImageCount()
tempid=WindowManager.getNthImageID(n)
tempimg=WindowManager.getImage(tempid)
tempimg.show()
#self.__dictImages[tempname]=tempimg
#tempimg.hide()
nameimages=tempname+"tif"
#if zerotimes/len(rawtimes) > 0.5 : rawtimes=range(len(listfiles))
#self.__dictTimeStack[tempname]=rawtimes
#elif isinstance(listfiles[0][0],str) :
elif os.path.isfile(listfiles[0][0]) :
nameimages=[]
rawtimes=[]
rawtimes.append(0)
for i in range(len(listfiles)) :
if len(positionsList)==0 : tempname = WindowManager.getUniqueName("image"+str(i+1))
else : tempname = positionsList[i]
tempd = tempfile.mkdtemp()
fichier = open(tempd+os.path.sep+tempname+".tif","w")
zerotimes=0
for j in range(len(listfiles[i])-1) :
difftimes=int((os.stat(listfiles[i][j+1]).st_mtime-os.stat(listfiles[i][j]).st_mtime))
if difftimes==0 : zerotimes+=1
rawtimes.append(rawtimes[-1]+difftimes)
fichier.writelines(listfiles[i][j]+"\n")
fichier.writelines(listfiles[i][-1]+"\n")
fichier.close()
IJ.run("Stack From List...","open="+tempd+os.path.sep+tempname+".tif")
n=WindowManager.getImageCount()
tempid=WindowManager.getNthImageID(n)
tempimg=WindowManager.getImage(tempid)
tempimg.show()
#self.__dictImages[tempname]=tempimg
nameimages.append(tempname)
#if zerotimes/len(rawtimes) > 0.5 : rawtimes=range(len(listfiles[i]))
#self.__dictTimeStack[tempname]=rawtimes
rawtimes=[]
rawtimes.append(0)
else :
nameimages=[]
print "ERROR IN BUILDSTACK"
return nameimages
