Export annotation rendered ROI script with channel names and scale bar for QuPath v0.5.0

exportROIv05.groovy

import qupath.lib.gui.images.servers.RenderedImageServer
import qupath.lib.gui.viewer.overlays.HierarchyOverlay
import qupath.lib.gui.viewer.Scalebar
import qupath.lib.gui.QuPathGUI
import qupath.lib.gui.viewer.OverlayOptions
import qupath.lib.regions.*
import ij.*
import java.awt.Color
import java.awt.image.BufferedImage
import qupath.lib.roi.RectangleROI

import qupath.fx.dialogs.*
import java.awt.Font




//CUSTOM: change this to 1.0 for original resolution -- may be slow depending on the ROI size
double downsample=1

def imageData = getCurrentImageData()

def viewer = getCurrentViewer()

def server = new RenderedImageServer.Builder(imageData)
    .display(viewer.getImageDisplay())
    .downsamples(downsample)
    .layers(new HierarchyOverlay(viewer.getImageRegionStore(), viewer.getOverlayOptions(), imageData))
    .build()

def roi = getSelectedROI()
// change this to value to a larger number if the yellow box from the original ROI still shows up
def removeBox = 10
// HACK! make a new ROI within the first one to remove the yellow border from showing up
// will lost about 10 pixels but should be fine
roi2 = new RectangleROI(roi.x+removeBox , roi.y+removeBox , roi.getBoundsWidth()-removeBox*2, roi.getBoundsHeight()-removeBox*2) 
def requestROI = RegionRequest.createInstance(server.getPath(), downsample, roi2)
def img = server.readRegion(requestROI)

//find the channels and keep them in the starting order (C1-CX)
def imageDisplay  = viewer.getImageDisplay()
def availableChannels = imageDisplay.availableChannels()
def channels = imageDisplay.selectedChannels()
def sortedChannels = channels.sorted((c1, c2) -> {
    // Compare in a better way here...
    int i1 = availableChannels.indexOf(c1)
    int i2 = availableChannels.indexOf(c2)
    return Integer.compare(i1, i2)
})


def img2 = new ImagePlus("Image", img)//.show()
def imY = img2.getHeight()
def imX = img2.getWidth()
int fScale = (imX+imY)/2//Math.max(imY,imX)

// CUSTOM: Change this to a higher value to get smaller font. 
// Essentially sets the font size to 1/ScaleFactor of the image size
// TODO: may be there are better ways to do this?
def ScaleFactor  = 45
def fSize = (fScale/ScaleFactor).round() as int
Font font = new Font("Calibri", Font.PLAIN,fSize);
print(font)
ij.process.ImageProcessor ip = img2.getProcessor();
// Change this if the text is too close to origin
ij.Prefs.setTransparentIndex(50)
def offsetDefault = 5
def offsetX = offsetDefault
def offset =  offsetDefault
def bxheight = []
for (x in sortedChannels){
def y = x
if (x==sortedChannels[sortedChannels.size()-1]){
y = x.toString().split('\\(')[0].toString()
}else{
y = x.toString().split('\\(')[0].toString() +' '
}
ip.setFont(font);
//ip.setAntialiasedText(true)
bxheight.add(ip.getStringBounds(y).getHeight().toInteger())
offsetX+=  ip.getStringWidth(y)
}
Color bx = new Color(0,0,0)
//ip.setColor( bx)
//ip.fillRect(0, imY-bxheight.max()-10*offsetDefault, offsetX-2*offsetDefault, bxheight.max()-offsetDefault)


// To remove the black text box, comment lines 87-93
// Or remove ", Color.black" in line 92
def y = ''
for (x in sortedChannels){
ip.setFont(font);
ip.setColor(x.getColor());
y = x.toString().split('\\(')[0].toString() +' '
ip.drawString(y, offset, imY-offsetDefault*4, Color.black);
offset+=  ip.getStringWidth(y)
}
println(sortedChannels)
offset=5
for (x in sortedChannels){
ip.setFont(font);
println()
bx = new Color(ColorTools.red(x.getColor()),ColorTools.green(x.getColor()),ColorTools.blue(x.getColor()))
ip.setColor(bx);
//ip.setColor(Color.WHITE);
println(x)

y = x.toString().split('\\(')[0].toString() +' '
ip.drawString(y, offset, imY-offsetDefault*4, );
offset+=  ip.getStringWidth(y)
}


// SCALEBAR
def scLen = 0.1
def roundUp = { int x, int roundTo ->
    def remainder = x%roundTo
    if (remainder>0){
     x+= (roundTo - remainder)
     }
     return x
}

def cal = server.getPixelCalibration()
Color bx2 = new Color(255,255,255,1)
int scaleRect = scLen*imX
// account for downsampling. the numbers are accurate if downsample=1.0
// for ds=2, the imX is half the size so need to multiply with downsample
int scaleValum = downsample*scLen*imX*cal.getPixelWidthMicrons()
println scaleValum
def scaleVal = 0
if (scaleValum<=50) {
   println "Less than 50" 
 scaleVal = roundUp(scaleValum,10).toString()+ ' µm'
}else if (scaleValum>50 & scaleValum<=100) {
     println "Less than 100"  
    scaleVal = roundUp(scaleValum,20).toString()+ ' µm' 
} else {
        println "Greater than than 100"   
     scaleVal = roundUp(scaleValum,50).toString()+ ' µm'  

}

if (roundUp(scaleValum,50)>1000){
scaleVal = (roundUp(scaleValum,50)/1000).round().toString()+ ' mm'
}
ip.setColor(bx2)
//CUSTOM: To remove Scale bar comment ines 122-124
ip.fillRect(imX-scaleRect-2*offsetDefault, imY-offsetDefault*8, scaleRect, offsetDefault*2)
ip.setColor(Color.WHITE)
ip.drawString(scaleVal, imX-scaleRect-2*offsetDefault,  imY-offsetDefault*10);
println(scaleVal)
//img2.show()
// By default, saves as a png
//CUSTOM: To change from png to something else, edit .png in line 128


fileName = FileChoosers.promptToSaveFile("Export to file", null,FileChoosers.createExtensionFilter("PNG image", ".png"))
println(fileName.toString())
IJ.save(img2,fileName.toString())