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import qupath.lib.images.servers.LabeledImageServer
def imageData = getCurrentImageData()
// Define output path (relative to project)
def name = GeneralTools.getNameWithoutExtension(imageData.getServer().getMetadata().getName())
// Define output resolution
double augmentation = 5
String set = "val"
def pathOutput = "SET PATH HERE"+String.valueOf(augmentation)+"/"+set
mkdirs(pathOutput)
// Convert to downsample
// double downsample = requestedPixelSize / imageData.getServer().getPixelCalibration().getAveragedPixelSize()
// Define output downsample
// - 20x --> 1.0
// - 10x --> 2.0
// - 5x --> 4.0
// - 2.5x --> 8.0
double downsample = 20/augmentation
// Create an ImageServer where the pixels are derived from annotations
def labelServer = new LabeledImageServer.Builder(imageData)
.backgroundLabel(0, ColorTools.BLACK) // Specify background label
.downsample(downsample) // Choose server resolution; this should match the resolution at which tiles are exported
.addLabel('Other', 1, ColorTools.makeRGB(85, 85, 85)) // Classes labels (the order matters!)
.addLabel('Tumor', 2, ColorTools.makeRGB(170, 170, 170))
.addLabel('In situ', 3, ColorTools.makeRGB(255, 255, 255))
.multichannelOutput(false) // If true, each label is a different channel (required for multiclass probability)
.build()
// Create an exporter that requests corresponding tiles from the original & labeled image servers
new TileExporter(imageData)
.downsample(downsample) // Define export resolution
.imageExtension('.png') // Define file extension for original pixels (often .tif, .jpg, '.png' or '.ome.tif')
.imageSubDir('Images') // Subdirectory to save the original images
// .labeledImageExtension('.png')
.labeledImageSubDir('Masks') // Subdirectory to save the masks
.tileSize(512) // Define size of each tile, in pixels
.labeledServer(labelServer) // Define the labeled image server to use (i.e. the one we just built)
// .annotatedTilesOnly(true) // If true, only export tiles if there is a (labeled) annotation present
.annotatedCentroidTilesOnly(true) // If true, only export tiles if the centroid pixels has an annotation
.overlap(0) // Define overlap, in pixel units at the EXPORT resolution
.writeTiles(pathOutput) // Write tiles to the specified directory
print 'Done!'
// Bounds de la WSI (offset que s'ha d'aplicar per aconseguir les coordenades correctes amb OpenSlide)
double dx = -getCurrentServer().boundsX
double dy = -getCurrentServer().boundsY
print dx
print dy
print imageData.getServer().getPixelCalibration().getAveragedPixelSize()
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