Examples with ImagePlusImgLoader bdv.ij.export.imgloader.ImagePlusImgLoader used on opensource projects

Example 1 with ImagePlusImgLoader

use of bdv.ij.export.imgloader.ImagePlusImgLoader in project imagej-utils by embl-cba.

the class BdvImagePlusExport method saveAsBdv.

public static void saveAsBdv(ImagePlus imp, File xmlOutputPath) {
    if (!xmlOutputPath.getAbsolutePath().endsWith(".xml"))
        xmlOutputPath = new File(xmlOutputPath.getAbsolutePath() + ".xml");
    // check the image type
    switch(imp.getType()) {
        case ImagePlus.GRAY8:
        case ImagePlus.GRAY16:
        case ImagePlus.GRAY32:
            break;
        default:
            IJ.showMessage("Only 8, 16, 32-bit images are supported currently!");
            return;
    }
    // check the image dimensionality
    if (imp.getNDimensions() < 3) {
        IJ.showMessage("Image must be at least 3-dimensional!");
        return;
    }
    // get calibration and image size
    final double pw = imp.getCalibration().pixelWidth;
    final double ph = imp.getCalibration().pixelHeight;
    final double pd = imp.getCalibration().pixelDepth;
    String punit = imp.getCalibration().getUnit();
    if (punit == null || punit.isEmpty())
        punit = "px";
    final FinalVoxelDimensions voxelSize = new FinalVoxelDimensions(punit, pw, ph, pd);
    final int w = imp.getWidth();
    final int h = imp.getHeight();
    final int d = imp.getNSlices();
    final FinalDimensions size = new FinalDimensions(new int[] { w, h, d });
    // propose reasonable mipmap settings
    final ExportMipmapInfo autoMipmapSettings = ProposeMipmaps.proposeMipmaps(new BasicViewSetup(0, "", size, voxelSize));
    // get output paths, resolutions, subdivisions, min-max option
    final Parameters params = getParametersAutomated(imp.getBitDepth(), autoMipmapSettings, xmlOutputPath.getAbsolutePath());
    final String autoSubsampling = ProposeMipmaps.getArrayString(autoMipmapSettings.getExportResolutions());
    final String autoChunkSizes = ProposeMipmaps.getArrayString(autoMipmapSettings.getSubdivisions());
    final ProgressWriter progressWriter = new ProgressWriterIJ();
    progressWriter.out().println("Subsampling: " + autoSubsampling);
    progressWriter.out().println("Chunking: " + autoChunkSizes);
    progressWriter.out().println("starting export...");
    // create ImgLoader wrapping the image
    final ImagePlusImgLoader<?> imgLoader;
    switch(imp.getType()) {
        case ImagePlus.GRAY8:
            imgLoader = ImagePlusImgLoader.createGray8(imp, params.minMaxOption, params.rangeMin, params.rangeMax);
            break;
        case ImagePlus.GRAY16:
            imgLoader = ImagePlusImgLoader.createGray16(imp, params.minMaxOption, params.rangeMin, params.rangeMax);
            break;
        case ImagePlus.GRAY32:
        default:
            imgLoader = ImagePlusImgLoader.createGray32(imp, params.minMaxOption, params.rangeMin, params.rangeMax);
            break;
    }
    final int numTimepoints = imp.getNFrames();
    final int numSetups = imp.getNChannels();
    // create SourceTransform from the images calibration
    final AffineTransform3D sourceTransform = new AffineTransform3D();
    sourceTransform.set(pw, 0, 0, 0, 0, ph, 0, 0, 0, 0, pd, 0);
    // write hdf5
    final HashMap<Integer, BasicViewSetup> setups = new HashMap<>(numSetups);
    for (int s = 0; s < numSetups; ++s) {
        final BasicViewSetup setup = new BasicViewSetup(s, String.format("channel %d", s + 1), size, voxelSize);
        setup.setAttribute(new Channel(s + 1));
        setups.put(s, setup);
    }
    final ArrayList<TimePoint> timepoints = new ArrayList<>(numTimepoints);
    for (int t = 0; t < numTimepoints; ++t) timepoints.add(new TimePoint(t));
    final SequenceDescriptionMinimal seq = new SequenceDescriptionMinimal(new TimePoints(timepoints), setups, imgLoader, null);
    Map<Integer, ExportMipmapInfo> perSetupExportMipmapInfo;
    perSetupExportMipmapInfo = new HashMap<>();
    final ExportMipmapInfo mipmapInfo = new ExportMipmapInfo(params.resolutions, params.subdivisions);
    for (final BasicViewSetup setup : seq.getViewSetupsOrdered()) perSetupExportMipmapInfo.put(setup.getId(), mipmapInfo);
    // LoopBackHeuristic:
    // - If saving more than 8x on pixel reads use the loopback image over
    // original image
    // - For virtual stacks also consider the cache size that would be
    // required for all original planes contributing to a "plane of
    // blocks" at the current level. If this is more than 1/4 of
    // available memory, use the loopback image.
    final boolean isVirtual = imp.getStack().isVirtual();
    final long planeSizeInBytes = imp.getWidth() * imp.getHeight() * imp.getBytesPerPixel();
    final long ijMaxMemory = IJ.maxMemory();
    final int numCellCreatorThreads = Math.max(1, PluginHelper.numThreads() - 1);
    final ExportScalePyramid.LoopbackHeuristic loopbackHeuristic = (originalImg, factorsToOriginalImg, previousLevel, factorsToPreviousLevel, chunkSize) -> {
        if (previousLevel < 0)
            return false;
        if (Intervals.numElements(factorsToOriginalImg) / Intervals.numElements(factorsToPreviousLevel) >= 8)
            return true;
        if (isVirtual) {
            final long requiredCacheSize = planeSizeInBytes * factorsToOriginalImg[2] * chunkSize[2];
            if (requiredCacheSize > ijMaxMemory / 4)
                return true;
        }
        return false;
    };
    final ExportScalePyramid.AfterEachPlane afterEachPlane = new ExportScalePyramid.AfterEachPlane() {

        @Override
        public void afterEachPlane(final boolean usedLoopBack) {
            if (!usedLoopBack && isVirtual) {
                final long free = Runtime.getRuntime().freeMemory();
                final long total = Runtime.getRuntime().totalMemory();
                final long max = Runtime.getRuntime().maxMemory();
                final long actuallyFree = max - total + free;
                if (actuallyFree < max / 2)
                    imgLoader.clearCache();
            }
        }
    };
    final ArrayList<Partition> partitions;
    if (params.split) {
        final String xmlFilename = params.seqFile.getAbsolutePath();
        final String basename = xmlFilename.endsWith(".xml") ? xmlFilename.substring(0, xmlFilename.length() - 4) : xmlFilename;
        partitions = Partition.split(timepoints, seq.getViewSetupsOrdered(), params.timepointsPerPartition, params.setupsPerPartition, basename);
        for (int i = 0; i < partitions.size(); ++i) {
            final Partition partition = partitions.get(i);
            final ProgressWriter p = new SubTaskProgressWriter(progressWriter, 0, 0.95 * i / partitions.size());
            WriteSequenceToHdf5.writeHdf5PartitionFile(seq, perSetupExportMipmapInfo, params.deflate, partition, loopbackHeuristic, afterEachPlane, numCellCreatorThreads, p);
        }
        WriteSequenceToHdf5.writeHdf5PartitionLinkFile(seq, perSetupExportMipmapInfo, partitions, params.hdf5File);
    } else {
        partitions = null;
        WriteSequenceToHdf5.writeHdf5File(seq, perSetupExportMipmapInfo, params.deflate, params.hdf5File, loopbackHeuristic, afterEachPlane, numCellCreatorThreads, new SubTaskProgressWriter(progressWriter, 0, 0.95));
    }
    // write xml sequence description
    final Hdf5ImageLoader hdf5Loader = new Hdf5ImageLoader(params.hdf5File, partitions, null, false);
    final SequenceDescriptionMinimal seqh5 = new SequenceDescriptionMinimal(seq, hdf5Loader);
    final ArrayList<ViewRegistration> registrations = new ArrayList<>();
    for (int t = 0; t < numTimepoints; ++t) for (int s = 0; s < numSetups; ++s) registrations.add(new ViewRegistration(t, s, sourceTransform));
    final File basePath = params.seqFile.getParentFile();
    final SpimDataMinimal spimData = new SpimDataMinimal(basePath, seqh5, new ViewRegistrations(registrations));
    try {
        new XmlIoSpimDataMinimal().save(spimData, params.seqFile.getAbsolutePath());
        progressWriter.setProgress(1.0);
    } catch (final Exception e) {
        throw new RuntimeException(e);
    }
    progressWriter.out().println("done");
}