| 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() | |