Examples with OMEPyramidSeries qupath.lib.images.writers.ome.OMEPyramidWriter.OMEPyramidSeries used on opensource projects

Example 1 with OMEPyramidSeries

use of qupath.lib.images.writers.ome.OMEPyramidWriter.OMEPyramidSeries in project qupath by qupath.

the class OMEPyramidWriterCommand method run.

@Override
public void run() {
    if (currentTask != null && !currentTask.isDone()) {
        if (!Dialogs.showConfirmDialog("OME Pyramid writer", "Do you want to stop the current export?"))
            // TODO: Delete exporting file?
            return;
        else {
            currentTask.cancel(true);
        }
    }
    QuPathViewer viewer = qupath.getViewer();
    int zPos = viewer.getZPosition();
    int tPos = viewer.getTPosition();
    ImageData<BufferedImage> imageData = viewer.getImageData();
    if (imageData == null) {
        Dialogs.showNoImageError("OME Pyramid writer");
        return;
    }
    ImageServer<BufferedImage> server = imageData.getServer();
    // Region
    PathObject selected = imageData.getHierarchy().getSelectionModel().getSelectedObject();
    ImageRegion region = null;
    int width, height;
    if (selected == null || !selected.hasROI() || !selected.getROI().isArea()) {
        width = server.getWidth();
        height = server.getHeight();
    } else {
        region = ImageRegion.createInstance(selected.getROI());
        width = region.getWidth();
        height = region.getHeight();
    }
    // Set compression - with a sanity check for validity, defaulting to another comparable method if necessary
    CompressionType compression = getDefaultPyramidCompression();
    List<String> compatibleCompression = Arrays.stream(CompressionType.values()).filter(c -> c.supportsImage(server)).map(c -> c.toFriendlyString()).collect(Collectors.toList());
    if (!compatibleCompression.contains(compression.toFriendlyString()))
        compression = CompressionType.DEFAULT;
    var params = new ParameterList().addChoiceParameter("compression", "Compression type", compression.toFriendlyString(), compatibleCompression).addIntParameter("scaledDownsample", "Pyramidal downsample", scaledDownsample.get(), "", 1, 8, "Amount to downsample each consecutive pyramidal level; use 1 to indicate the image should not be pyramidal").addIntParameter("tileSize", "Tile size", getDefaultTileSize(), "px", "Tile size for export (should be between 128 and 8192)").addBooleanParameter("parallelize", "Parallelize export", parallelizeTiling.get(), "Export image tiles in parallel - " + "this should be faster, best keep it on unless you encounter export problems").addBooleanParameter("allZ", "All z-slices", allZ.get(), "Include all z-slices in the stack").addBooleanParameter("allT", "All timepoints", allT.get(), "Include all timepoints in the time-series");
    boolean singleTile = server.getTileRequestManager().getTileRequests(RegionRequest.createInstance(server)).size() == 1;
    params.setHiddenParameters(server.nZSlices() == 1, "allZ");
    params.setHiddenParameters(server.nTimepoints() == 1, "allT");
    params.setHiddenParameters(singleTile, "tileSize", "parallelize");
    if (!Dialogs.showParameterDialog("Export OME-TIFF", params))
        return;
    compression = CompressionType.fromFriendlyString((String) params.getChoiceParameterValue("compression"));
    defaultPyramidCompression.set(compression);
    int downsampleScale = params.getIntParameterValue("scaledDownsample");
    scaledDownsample.set(downsampleScale);
    int tileSize = params.getIntParameterValue("tileSize");
    boolean parallelize = params.getBooleanParameterValue("parallelize");
    if (!singleTile) {
        tileSize = GeneralTools.clipValue(tileSize, 128, 8192);
        defaultTileSize.set(tileSize);
        parallelizeTiling.set(parallelize);
    }
    boolean doAllZ = false;
    boolean doAllT = false;
    if (server.nZSlices() > 1) {
        doAllZ = params.getBooleanParameterValue("allZ");
        allZ.set(doAllZ);
    }
    if (server.nTimepoints() > 1) {
        doAllT = params.getBooleanParameterValue("allT");
        allT.set(doAllT);
    }
    OMEPyramidWriter.Builder builder = new OMEPyramidWriter.Builder(server);
    if (region != null) {
        builder = builder.region(region);
    } else {
        if (server.nZSlices() > 1 && !doAllZ)
            builder.zSlice(zPos);
        if (server.nTimepoints() > 1 && !doAllT)
            builder.timePoint(tPos);
    }
    builder.compression(compression);
    if (downsampleScale <= 1 || Math.max(width, height) / server.getDownsampleForResolution(0) < minSizeForTiling.get())
        builder.downsamples(server.getDownsampleForResolution(0));
    else
        builder.scaledDownsampling(server.getDownsampleForResolution(0), downsampleScale);
    // Set tile size; if we just have one tile, use the image width & height
    if (singleTile)
        builder = builder.tileSize(width, height);
    else
        builder = builder.tileSize(tileSize).parallelize(parallelize);
    if (server.nZSlices() > 1 && doAllZ)
        builder.allZSlices();
    if (server.nTimepoints() > 1 && doAllT)
        builder.allTimePoints();
    // Prompt for file
    File fileOutput = Dialogs.promptToSaveFile("Write pyramid", null, null, "OME TIFF pyramid", ".ome.tif");
    if (fileOutput == null)
        return;
    String name = fileOutput.getName();
    // We can have trouble with only the '.tif' part of the name being included
    if (name.endsWith(".tif") && !name.endsWith(".ome.tif"))
        fileOutput = new File(fileOutput.getParentFile(), name.substring(0, name.length() - 4) + ".ome.tif");
    OMEPyramidSeries writer = builder.build();
    if (pool == null) {
        pool = Executors.newSingleThreadExecutor(ThreadTools.createThreadFactory("ome-pyramid-export", false));
    }
    currentTask = pool.submit(new WriterTask(OMEPyramidWriter.createWriter(writer), fileOutput.getAbsolutePath()));
}