Export all channels as single channel tifs for a given ROI in QP v0.5

exportROIv05_allChannels.groovy

import qupath.lib.images.servers.ImageServers.*
import qupath.lib.io.PathIO
import qupath.fx.dialogs.*
import javax.imageio.ImageIO


// Get the current image
def imageData = getCurrentImageData()
def server = imageData.getServer()
// change this to 2 or more to get lower resolution
def downSample =1 
// Get the number of channels
def nChannels = server.nChannels()
print nChannels.toString()+" channels"
// Prompt the user for the output directory
outputDir = FileChoosers.promptForDirectory()

if (outputDir == null) {
    print "No output directory selected. Exiting..."
    return
}
def roi = getSelectedROI()
def requestROI = RegionRequest.createInstance(server.getPath(), downSample, roi)
// Read the region


def img = server.readBufferedImage(requestROI)
def raster = img.getRaster()
// Loop over each channel
for (int c = 1; c <= nChannels; c++) {
    // Create a new single-channel image server
    // Extract a single channel (e.g., the n-th channel)
    def channelData = raster.getSamples(0, 0, img.getWidth(), img.getHeight(), c-1, (int[])null)

    def channelImg = new BufferedImage(img.getWidth(), img.getHeight(), BufferedImage.TYPE_BYTE_GRAY)
    channelImg.getRaster().setSamples(0, 0, img.getWidth(), img.getHeight(), 0, channelData)        
    def cID  = (c-1).toString()
    print(cID)
    
    // Define the output file path
    if (nChannels <100){
         cID = String.format("%02d", c-1)
        }else {
          cID = String.format("%03d", c-1)
        }
    def outputPath = outputDir.toString()+ "/c" + cID +"_"+server.getChannel(c-1).getName() + ".tif"

    // Write the image to a .tif file
    ImageIO.write(channelImg, "TIFF", new File(outputPath))
}