Hi all,
I would like to have a script which is exporting an annotated region as image tiles. I first tried with Pete’s example on Tiling a whole slide image and Exporting labelled images, however I would like pixels outside the annotations to be removed (i.e. set to white or so).
So what I tried based on the mentioned scripts was to convert the image to an ImagePlus, create a mask image of identical size and use the ImageJ calculator to remove the disturbing pixels:
/**
* Export annotation partitioned to png-tiles setting pixels outside the annotation to white
* 07/17/2019
*/
import ij.IJ
import ij.ImagePlus
import ij.plugin.ImageCalculator
import qupath.imagej.helpers.IJTools
import qupath.lib.gui.scripting.QPEx
import qupath.lib.images.servers.ImageServer
import qupath.lib.regions.RegionRequest
import qupath.lib.roi.PathROIToolsAwt
import qupath.lib.scripting.QP
import java.awt.Color
import java.awt.image.BufferedImage
Date date=new Date()
println(date)
//set tile size
int tileHeight=1200
int tileWidth=1200
//some parameters to discard tiles
//discard tiles smaller than 100px in any dimension
int minImageDimension=100
//discard empty tiles (avg.int.=255)
boolean doNotSaveEmptyTiles=true
//Indicate low content (avg.int>245 or stdDev<10) in filename of tiles
boolean indicateAlmostEmptyTiles=true
//downsample exported tiles
double downsample=1
//set format of exported tiles
String format="png"
String ext
if (format.startsWith("."))
ext=format.substring(1).toLowerCase()
else
ext=format.toLowerCase()
ImageServer<BufferedImage> serverOriginal= QP.getCurrentImageData().getServer()
String path = serverOriginal.getPath()
String serverName = serverOriginal.getShortServerName()
//only the first annotation is considered
annotation =QP.getAnnotationObjects().get(0)
roi=annotation.getROI()
//get pixel data from annotation and convert to IJ ImagePlus
RegionRequest request1 =RegionRequest.createInstance(path,downsample,roi)
imp1= IJTools.convertToImagePlus(serverOriginal,request1).getImage()
//get image dimensions
width = imp1.getWidth()
height= imp1.getHeight()
//create an empty RGB image of identical dimensions
def imgMask = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB)
//draw shape of annotation into the empty image
def g2d = imgMask.createGraphics()
g2d.translate(-request1.getX(), -request1.getY())
def shape = PathROIToolsAwt.getShape(roi)
Color white = new Color(1,1,1)
g2d.setColor(white)
g2d.fill(shape)
maskImp =new ImagePlus("maskImage",imgMask)
//multiply maskImage to remove pixels outside annotation area
ImageCalculator ic = new ImageCalculator()
ImagePlus maskedImp = ic.run("Multiply create", imp1, maskImp)
//multiply by 255 and invert mask image
IJ.run(maskImp, "Multiply...", "value=255")
IJ.run(maskImp, "Invert", "")
//perform OR operation of inverted mask and masked image to set pixels outside of the annotation to white
ImagePlus fullyMaskedImp=ic.run("OR create", maskedImp, maskImp)
//extract and save tiles from the masked annotation image
counter=0
for(double y=0;y<fullyMaskedImp.getHeight();y+=tileHeight){
int yi=(int)(y+0.5)
int y2i=(int)Math.min((int)(y+tileHeight+0.5),fullyMaskedImp.getHeight())
int hi =y2i-yi
if(hi/downsample<minImageDimension){
//println("skipping row")
continue
}
for(double x=0;x<fullyMaskedImp.getWidth();x+=tileWidth){
int xi=(int)(x+0.5)
int x2i=(int)Math.min((int)(x+tileWidth+0.5),fullyMaskedImp.getWidth())
int wi=x2i-xi
if(wi/downsample<minImageDimension){
if (y > 0)
//println("skipping column")
continue
}
fullyMaskedImp.setRoi(xi,yi,wi,hi)
tileImp = fullyMaskedImp.crop()
stat=tileImp.getStatistics(6)
println(stat.stdDev)
println(stat.mean)
resultfoldername=QP.getCurrentImageData().getServer().getDisplayedImageName().toUpperCase().replaceAll("\\s","")
resultfolder=QPEx.buildFilePath(QPEx.PROJECT_BASE_DIR, resultfoldername)
String tileName=String.format("%s(d=%.2f,x=%d,y=%d,w=%d,h=%d).%s",serverName,downsample,xi,yi,wi,hi,ext)
if (doNotSaveEmptyTiles) {
if (stat.mean > 254.9) {
//println("Skipping empty tile " + tileName)
continue
}
}
if (indicateAlmostEmptyTiles) {
if (stat.mean > 245 || stat.stdDev < 10) {
tileName = "00-lowContent_" + tileName
}
}
saved = saveTile(resultfolder, tileName, tileImp)
}
}
println("Done.")
boolean saveTile(resultfolder,tileName,tileImp){
try {
dirOut=new File(resultfolder)
if (!dirOut.exists()) {
dirOut.mkdirs()
println("Created folder "+dirOut)
}
File tileFile= new File(dirOut,tileName)
IJ.save(tileImp,tileFile.getAbsolutePath())
//println("Written tile "+tileName+ " to "+ tileFile.getAbsolutePath())
} catch(Exception e){
e.printStackTrace()
println("To many errors, aborting...")
e.printStackTrace()
return false
}
return true
}
I understand that this is no good idea as it loads the potentially huge annotation image and a mask image of the same size into the memory. Now I am considering to apply the mask on the image tiles - though I do not know yet how to get “mask tiles”…
So my question is does maybe anyone here have an idea how to solve this more elegantly?
Cheers, Peter
