Examples with Compression org.janelia.saalfeldlab.n5.Compression used on opensource projects

Example 1 with Compression

use of org.janelia.saalfeldlab.n5.Compression in project bigwarp by saalfeldlab.

the class BigWarp method exportAsImagePlus.

public void exportAsImagePlus(boolean virtual, String path) {
    if (ij == null)
        return;
    final GenericDialogPlus gd = new GenericDialogPlus("Apply Big Warp transform");
    gd.addMessage("Field of view and resolution:");
    gd.addChoice("Resolution", new String[] { ApplyBigwarpPlugin.TARGET, ApplyBigwarpPlugin.MOVING, ApplyBigwarpPlugin.SPECIFIED }, ApplyBigwarpPlugin.TARGET);
    gd.addChoice("Field of view", new String[] { ApplyBigwarpPlugin.TARGET, ApplyBigwarpPlugin.MOVING_WARPED, ApplyBigwarpPlugin.UNION_TARGET_MOVING, ApplyBigwarpPlugin.LANDMARK_POINTS, ApplyBigwarpPlugin.LANDMARK_POINT_CUBE_PIXEL, ApplyBigwarpPlugin.LANDMARK_POINT_CUBE_PHYSICAL, ApplyBigwarpPlugin.SPECIFIED_PIXEL, ApplyBigwarpPlugin.SPECIFIED_PHYSICAL }, ApplyBigwarpPlugin.TARGET);
    gd.addStringField("point filter", "");
    gd.addMessage("Resolution");
    gd.addNumericField("x", 1.0, 4);
    gd.addNumericField("y", 1.0, 4);
    gd.addNumericField("z", 1.0, 4);
    gd.addMessage("Offset");
    gd.addNumericField("x", 0.0, 4);
    gd.addNumericField("y", 0.0, 4);
    gd.addNumericField("z", 0.0, 4);
    gd.addMessage("Field of view");
    gd.addNumericField("x", -1, 0);
    gd.addNumericField("y", -1, 0);
    gd.addNumericField("z", -1, 0);
    gd.addMessage("Other Output options");
    gd.addChoice("Interpolation", new String[] { "Nearest Neighbor", "Linear" }, "Linear");
    gd.addMessage("Virtual: fast to display,\n" + "low memory requirements,\nbut slow to navigate");
    gd.addCheckbox("virtual?", false);
    int defaultCores = (int) Math.ceil(Runtime.getRuntime().availableProcessors() / 4);
    gd.addNumericField("threads", defaultCores, 0);
    gd.addMessage("Writing options (leave empty to opena new image window)");
    gd.addDirectoryOrFileField("File or n5 root", "");
    gd.addStringField("n5 dataset", "");
    gd.addStringField("n5 block size", "32");
    gd.addChoice("n5 compression", new String[] { N5Exporter.GZIP_COMPRESSION, N5Exporter.RAW_COMPRESSION, N5Exporter.LZ4_COMPRESSION, N5Exporter.XZ_COMPRESSION, N5Exporter.BLOSC_COMPRESSION }, N5Exporter.GZIP_COMPRESSION);
    gd.showDialog();
    if (gd.wasCanceled())
        return;
    final String resolutionOption = gd.getNextChoice();
    final String fieldOfViewOption = gd.getNextChoice();
    final String fieldOfViewPointFilter = gd.getNextString();
    final double[] resolutionSpec = new double[3];
    resolutionSpec[0] = gd.getNextNumber();
    resolutionSpec[1] = gd.getNextNumber();
    resolutionSpec[2] = gd.getNextNumber();
    final double[] offsetSpec = new double[3];
    offsetSpec[0] = gd.getNextNumber();
    offsetSpec[1] = gd.getNextNumber();
    offsetSpec[2] = gd.getNextNumber();
    final double[] fovSpec = new double[3];
    fovSpec[0] = gd.getNextNumber();
    fovSpec[1] = gd.getNextNumber();
    fovSpec[2] = gd.getNextNumber();
    final String interpType = gd.getNextChoice();
    final boolean isVirtual = gd.getNextBoolean();
    final int nThreads = (int) gd.getNextNumber();
    final String fileOrN5Root = gd.getNextString();
    final String n5Dataset = gd.getNextString();
    final String blockSizeString = gd.getNextString();
    final String compressionString = gd.getNextChoice();
    final int[] blockSize = ApplyBigwarpPlugin.parseBlockSize(blockSizeString, this.ndims);
    final Compression compression = ApplyBigwarpPlugin.getCompression(compressionString);
    final WriteDestinationOptions writeOpts = new ApplyBigwarpPlugin.WriteDestinationOptions(fileOrN5Root, n5Dataset, blockSize, compression);
    final Interpolation interp;
    if (interpType.equals("Nearest Neighbor"))
        interp = Interpolation.NEARESTNEIGHBOR;
    else
        interp = Interpolation.NLINEAR;
    double[] res = ApplyBigwarpPlugin.getResolution(this.data, resolutionOption, resolutionSpec);
    List<Interval> outputIntervalList = ApplyBigwarpPlugin.getPixelInterval(this.data, this.landmarkModel, this.currentTransform, fieldOfViewOption, fieldOfViewPointFilter, fovSpec, offsetSpec, res);
    final List<String> matchedPtNames = new ArrayList<>();
    if (outputIntervalList.size() > 1)
        ApplyBigwarpPlugin.fillMatchedPointNames(matchedPtNames, getLandmarkPanel().getTableModel(), fieldOfViewPointFilter);
    // landmark centers (because multiple images can be exported this way )
    if (matchedPtNames.size() > 0) {
        BigwarpLandmarkSelectionPanel<T> selection = new BigwarpLandmarkSelectionPanel<>(data, sources, fieldOfViewOption, outputIntervalList, matchedPtNames, interp, offsetSpec, res, isVirtual, nThreads, progressWriter);
    } else {
        if (writeOpts.n5Dataset != null && !writeOpts.n5Dataset.isEmpty()) {
            final String unit = ApplyBigwarpPlugin.getUnit(data, resolutionOption);
            // export async
            new Thread() {

                public void run() {
                    progressWriter.setProgress(0.01);
                    ApplyBigwarpPlugin.runN5Export(data, sources, fieldOfViewOption, outputIntervalList.get(0), interp, offsetSpec, res, unit, progressWriter, writeOpts, Executors.newFixedThreadPool(nThreads));
                    progressWriter.setProgress(1.00);
                }
            }.start();
        } else {
            // export
            final boolean show = (writeOpts.pathOrN5Root == null || writeOpts.pathOrN5Root.isEmpty());
            ApplyBigwarpPlugin.runExport(data, sources, fieldOfViewOption, outputIntervalList, matchedPtNames, interp, offsetSpec, res, isVirtual, nThreads, progressWriter, show, false, writeOpts);
        }
    }
}

Example 2 with Compression

use of org.janelia.saalfeldlab.n5.Compression in project bigwarp by saalfeldlab.

the class ApplyBigwarpPlugin method run.

@Override
public void run(String arg) {
    if (IJ.versionLessThan("1.40"))
        return;
    // Find any open images
    final int[] ids = WindowManager.getIDList();
    final int N = ids == null ? 0 : ids.length;
    final String[] titles = new String[N + 1];
    for (int i = 0; i < N; ++i) {
        titles[i] = (WindowManager.getImage(ids[i])).getTitle();
    }
    titles[N] = "<None>";
    final GenericDialogPlus gd = new GenericDialogPlus("Apply Big Warp transform");
    gd.addMessage("File Selection:");
    gd.addFileField("landmarks_image_file", "");
    ImagePlus currimg = WindowManager.getCurrentImage();
    String current = titles[N];
    if (currimg != null) {
        current = currimg.getTitle();
    }
    gd.addChoice("moving_image", titles, current);
    if (titles.length > 1)
        gd.addChoice("target_image", titles, current.equals(titles[0]) ? titles[1] : titles[0]);
    else
        gd.addChoice("target_image", titles, titles[0]);
    gd.addMessage("\nN5/Zarr/HDF5/BDV-XML");
    gd.addDirectoryOrFileField("Moving", "");
    gd.addStringField("Moving_dataset", "");
    gd.addDirectoryOrFileField("Target", "");
    gd.addStringField("Target_dataset", "");
    gd.addChoice("Transform type", new String[] { TransformTypeSelectDialog.TPS, TransformTypeSelectDialog.AFFINE, TransformTypeSelectDialog.SIMILARITY, TransformTypeSelectDialog.ROTATION, TransformTypeSelectDialog.TRANSLATION }, TransformTypeSelectDialog.TPS);
    gd.addMessage("Field of view and resolution:");
    gd.addChoice("Resolution", new String[] { TARGET, MOVING, SPECIFIED }, TARGET);
    gd.addChoice("Field of view", new String[] { TARGET, MOVING_WARPED, LANDMARK_POINTS, SPECIFIED_PIXEL, SPECIFIED_PHYSICAL }, TARGET);
    gd.addStringField("point filter", "");
    gd.addMessage("Resolution");
    gd.addNumericField("x", 1.0, 4);
    gd.addNumericField("y", 1.0, 4);
    gd.addNumericField("z", 1.0, 4);
    gd.addMessage("Offset");
    gd.addNumericField("x", 0.0, 4);
    gd.addNumericField("y", 0.0, 4);
    gd.addNumericField("z", 0.0, 4);
    gd.addMessage("Field of view");
    gd.addNumericField("x", -1, 0);
    gd.addNumericField("y", -1, 0);
    gd.addNumericField("z", -1, 0);
    gd.addMessage("Output options");
    gd.addChoice("Interpolation", new String[] { "Nearest Neighbor", "Linear" }, "Linear");
    gd.addCheckbox("virtual?", false);
    gd.addNumericField("threads", 4, 0);
    gd.addMessage("Writing options (leave empty to opena new image window)");
    gd.addDirectoryOrFileField("File or n5 root", "");
    gd.addStringField("n5 dataset", "");
    gd.addStringField("n5 block size", "32");
    gd.addChoice("n5 compression", new String[] { N5Exporter.GZIP_COMPRESSION, N5Exporter.RAW_COMPRESSION, N5Exporter.LZ4_COMPRESSION, N5Exporter.XZ_COMPRESSION, N5Exporter.BLOSC_COMPRESSION }, N5Exporter.GZIP_COMPRESSION);
    gd.showDialog();
    if (gd.wasCanceled())
        return;
    final String landmarksPath = gd.getNextString();
    ImagePlus movingIp = null;
    ImagePlus targetIp = null;
    final int mvgImgIdx = gd.getNextChoiceIndex();
    final int tgtImgIdx = gd.getNextChoiceIndex();
    movingIp = mvgImgIdx < N ? WindowManager.getImage(ids[mvgImgIdx]) : null;
    targetIp = tgtImgIdx < N ? WindowManager.getImage(ids[tgtImgIdx]) : null;
    final String mvgRoot = gd.getNextString();
    final String mvgDataset = gd.getNextString();
    final String tgtRoot = gd.getNextString();
    final String tgtDataset = gd.getNextString();
    final String transformTypeOption = gd.getNextChoice();
    final String resOption = gd.getNextChoice();
    final String fovOption = gd.getNextChoice();
    final String fovPointFilter = gd.getNextString();
    final double[] resolutions = new double[3];
    resolutions[0] = gd.getNextNumber();
    resolutions[1] = gd.getNextNumber();
    resolutions[2] = gd.getNextNumber();
    final double[] offset = new double[3];
    offset[0] = gd.getNextNumber();
    offset[1] = gd.getNextNumber();
    offset[2] = gd.getNextNumber();
    final double[] fov = new double[3];
    fov[0] = gd.getNextNumber();
    fov[1] = gd.getNextNumber();
    fov[2] = gd.getNextNumber();
    final String interpType = gd.getNextChoice();
    boolean isVirtual = gd.getNextBoolean();
    int nThreads = (int) gd.getNextNumber();
    final String fileOrN5Root = gd.getNextString();
    final String n5Dataset = gd.getNextString();
    final String blockSizeString = gd.getNextString();
    final String compressionString = gd.getNextChoice();
    // load the image data
    BigWarpData<?> bigwarpdata = BigWarpInit.initData();
    int id = 0;
    if (movingIp != null) {
        id += BigWarpInit.add(bigwarpdata, movingIp, id, 0, true);
    } else if (mvgDataset != null && !mvgDataset.isEmpty()) {
        BigWarpInit.addToData(bigwarpdata, true, id, mvgRoot, mvgDataset);
        id++;
    } else if (mvgRoot != null && !mvgRoot.isEmpty()) {
        try {
            ImagePlus movingFromFile = IJ.openImage(mvgRoot);
            id += BigWarpInit.add(bigwarpdata, movingFromFile, id, 0, true);
        } catch (Exception e) {
            IJ.showMessage("could not read from file: " + mvgRoot);
            return;
        }
    }
    if (targetIp != null) {
        id += BigWarpInit.add(bigwarpdata, targetIp, id, 0, false);
    } else if (tgtDataset != null && !tgtDataset.isEmpty()) {
        BigWarpInit.addToData(bigwarpdata, false, id, tgtRoot, tgtDataset);
        id++;
    } else if (tgtRoot != null && !tgtRoot.isEmpty()) {
        try {
            final ImagePlus targetFromFile = IJ.openImage(tgtRoot);
            id += BigWarpInit.add(bigwarpdata, targetFromFile, id, 0, false);
        } catch (Exception e) {
        // we're allowed not to have a target image
        }
    }
    bigwarpdata.wrapUp();
    final int nd = BigWarp.detectNumDims(bigwarpdata.sources);
    final int[] blockSize = ApplyBigwarpPlugin.parseBlockSize(blockSizeString, nd);
    final Compression compression = ApplyBigwarpPlugin.getCompression(compressionString);
    final WriteDestinationOptions writeOpts = new ApplyBigwarpPlugin.WriteDestinationOptions(fileOrN5Root, n5Dataset, blockSize, compression);
    LandmarkTableModel ltm = new LandmarkTableModel(nd);
    try {
        ltm.load(new File(landmarksPath));
    } catch (IOException e) {
        e.printStackTrace();
        return;
    }
    final Interpolation interp;
    if (interpType.equals("Nearest Neighbor"))
        interp = Interpolation.NEARESTNEIGHBOR;
    else
        interp = Interpolation.NLINEAR;
    List<ImagePlus> warpedIpList = apply(bigwarpdata, ltm, transformTypeOption, fovOption, fovPointFilter, resOption, resolutions, fov, offset, interp, isVirtual, nThreads, false, writeOpts);
}

Example 3 with Compression

use of org.janelia.saalfeldlab.n5.Compression in project bigwarp by saalfeldlab.

the class ApplyBigwarpPlugin method runN5Export.

public static <S, T extends NativeType<T> & NumericType<T>> void runN5Export(final BigWarpData<S> data, final List<SourceAndConverter<S>> sources, final String fieldOfViewOption, final Interval outputInterval, final Interpolation interp, final double[] offset, final double[] resolution, final String unit, final ProgressWriter progressWriter, final WriteDestinationOptions writeOpts, final ExecutorService exec) {
    final int nd = BigWarp.detectNumDims(data.sources);
    // setup n5 parameters
    final String dataset = writeOpts.n5Dataset;
    final int[] blockSize = writeOpts.blockSize;
    final Compression compression = writeOpts.compression;
    if (dataset == null || dataset.isEmpty()) {
        return;
    }
    N5Writer n5;
    try {
        n5 = new N5Factory().openWriter(writeOpts.pathOrN5Root);
    } catch (IOException e1) {
        e1.printStackTrace();
        return;
    }
    // build metadata
    final String[] axes = nd == 2 ? new String[] { "y", "x" } : new String[] { "z", "y", "x" };
    final String[] units = nd == 2 ? new String[] { unit, unit } : new String[] { unit, unit, unit };
    final N5CosemMetadata metadata = new N5CosemMetadata("", new N5CosemMetadata.CosemTransform(axes, resolution, offset, units), null);
    N5CosemMetadataParser parser = new N5CosemMetadataParser();
    // setup physical to pixel transform
    final AffineTransform3D resolutionTransform = new AffineTransform3D();
    resolutionTransform.set(resolution[0], 0, 0);
    resolutionTransform.set(resolution[1], 1, 1);
    if (resolution.length > 2)
        resolutionTransform.set(resolution[2], 2, 2);
    final AffineTransform3D offsetTransform = new AffineTransform3D();
    offsetTransform.set(offset[0], 0, 3);
    offsetTransform.set(offset[1], 1, 3);
    if (resolution.length > 2)
        offsetTransform.set(offset[2], 2, 3);
    final AffineTransform3D pixelRenderToPhysical = new AffineTransform3D();
    pixelRenderToPhysical.concatenate(resolutionTransform);
    pixelRenderToPhysical.concatenate(offsetTransform);
    // render and write
    final int N = data.movingSourceIndices.length;
    for (int i = 0; i < N; i++) {
        final int movingSourceIndex = data.movingSourceIndices[i];
        @SuppressWarnings("unchecked") final RealRandomAccessible<T> raiRaw = (RealRandomAccessible<T>) sources.get(movingSourceIndex).getSpimSource().getInterpolatedSource(0, 0, interp);
        // to pixel space
        final AffineRandomAccessible<T, AffineGet> rai = RealViews.affine(raiRaw, pixelRenderToPhysical.inverse());
        final IntervalView<T> img = Views.interval(Views.raster(rai), Intervals.zeroMin(outputInterval));
        final String srcName = data.sources.get(data.movingSourceIndices[i]).getSpimSource().getName();
        String destDataset = dataset;
        if (N > 1)
            destDataset = dataset + String.format("/%s", srcName.replace(" ", "_"));
        RandomAccessibleInterval<T> imgToWrite;
        if (nd == 2)
            imgToWrite = Views.hyperSlice(img, 2, 0);
        else
            imgToWrite = img;
        try {
            N5Utils.save(imgToWrite, n5, destDataset, blockSize, compression, exec);
            if (parser != null && metadata != null)
                parser.writeMetadata(metadata, n5, destDataset);
        } catch (Exception e) {
            e.printStackTrace();
        }
        progressWriter.setProgress((i + 1) / ((double) N));
    }
    progressWriter.setProgress(1.0);
}

Example 4 with Compression

use of org.janelia.saalfeldlab.n5.Compression in project bigwarp by saalfeldlab.

the class BigWarpToDeformationFieldPlugIn method writeN5.

public static void writeN5(final String n5BasePath, final String n5Dataset, final LandmarkTableModel ltm, final long[] dims, final double[] spacing, final int[] spatialBlockSize, final Compression compression, final int nThreads) throws IOException {
    final ThinPlateR2LogRSplineKernelTransform tpsRaw = ltm.getTransform();
    final AffineGet affine = toAffine(tpsRaw);
    /*
		 * "remove the affine" from the total transform
		 * by concatenating the inverse of the affine to be removed
		 */
    final ThinplateSplineTransform tpsTotal = new ThinplateSplineTransform(tpsRaw);
    final RealTransformSequence seq = new RealTransformSequence();
    seq.add(tpsTotal);
    seq.add(affine.inverse());
    AffineGet pixelToPhysical = null;
    if (spacing.length == 2)
        pixelToPhysical = new Scale2D(spacing);
    else if (spacing.length == 3)
        pixelToPhysical = new Scale3D(spacing);
    FloatImagePlus<FloatType> dfieldRaw = convertToDeformationField(dims, seq, pixelToPhysical, nThreads);
    // this works for both 2d and 3d, it turn out
    RandomAccessibleInterval<FloatType> dfield = Views.permute(Views.permute(dfieldRaw, 0, 2), 1, 2);
    int[] blockSize = new int[spatialBlockSize.length + 1];
    blockSize[0] = spatialBlockSize.length;
    for (int i = 0; i < spatialBlockSize.length; i++) {
        blockSize[i + 1] = spatialBlockSize[i];
    }
    final N5Writer n5 = new N5Factory().openWriter(n5BasePath);
    N5DisplacementField.save(n5, n5Dataset, affine, dfield, spacing, blockSize, compression);
    N5DisplacementField.saveAffine(affine, n5, n5Dataset);
}