Examples with DimensionOrder ome.xml.model.enums.DimensionOrder used on opensource projects

Example 1 with DimensionOrder

use of ome.xml.model.enums.DimensionOrder in project bioformats by openmicroscopy.

the class ImportProcess method initializeDimOrder.

/**
 * Performed following ImportStep.DIM_ORDER notification.
 */
private void initializeDimOrder() {
    final int seriesCount = getSeriesCount();
    final String stackOrder = getStackOrder();
    for (int s = 0; s < seriesCount; s++) {
        reader.setSeries(s);
        // set input order
        String dimOrder = options.getInputOrder(s);
        if (dimOrder != null)
            dimensionSwapper.swapDimensions(dimOrder);
        // set output order
        getDimensionSwapper().setOutputOrder(stackOrder);
        try {
            DimensionOrder order = DimensionOrder.fromString(stackOrder);
            getOMEMetadata().setPixelsDimensionOrder(order, s);
        } catch (EnumerationException e) {
        }
    }
}

Example 2 with DimensionOrder

use of ome.xml.model.enums.DimensionOrder in project bioformats by openmicroscopy.

the class CellH5Writer method saveBytes.

/**
 * Saves the given image to the specified (possibly already open) file.
 */
@Override
public void saveBytes(int no, byte[] buf) throws IOException, FormatException {
    LOGGER.info("CellH5Writer: Save image to HDF5 path: " + outputPath);
    MetadataRetrieve r = getMetadataRetrieve();
    int sizeX = r.getPixelsSizeX(series).getValue();
    int sizeY = r.getPixelsSizeY(series).getValue();
    int sizeC = r.getPixelsSizeC(series).getValue();
    int sizeT = r.getPixelsSizeT(series).getValue();
    int sizeZ = r.getPixelsSizeZ(series).getValue();
    DimensionOrder dimo = r.getPixelsDimensionOrder(0);
    int c, z, t;
    if (dimo.equals(DimensionOrder.XYCZT)) {
        c = no % sizeC;
        z = ((no - c) / sizeC) % sizeZ;
        t = (((no - c) / sizeC)) / sizeZ;
    } else if (dimo.equals(DimensionOrder.XYCTZ)) {
        c = no % sizeC;
        t = ((no - c) / sizeC) % sizeT;
        z = (((no - c) / sizeC)) / sizeT;
    } else if (dimo.equals(DimensionOrder.XYZTC)) {
        z = no % sizeZ;
        t = ((no - z) / sizeZ) % sizeT;
        c = (((no - z) / sizeZ)) / sizeT;
    } else {
        throw new FormatException("CellH5Writer: Dimension order not understood: " + dimo.getValue());
    }
    LOGGER.info("CellH5Writer.saveBytes(): Current c, t, z == {} {} {}", c, t, z);
    LOGGER.info("CellH5Writer.saveBytes(): bpp {} byte buffer len {}", bpp, buf.length);
    if (bpp == 1) {
        MDByteArray image = new MDByteArray(new int[] { 1, 1, 1, sizeY, sizeX });
        for (int x_i = 0; x_i < sizeX; x_i++) {
            for (int y_i = 0; y_i < sizeY; y_i++) {
                byte value = (byte) buf[y_i * sizeX + x_i];
                image.set(value, 0, 0, 0, y_i, x_i);
            }
        }
        jhdf.writeArraySlice(outputPath, image, new long[] { c, t, z, 0, 0 });
    } else if (bpp == 2) {
        ByteBuffer bb = ByteBuffer.wrap(buf);
        ShortBuffer sb = bb.asShortBuffer();
        MDShortArray image = new MDShortArray(new int[] { 1, 1, 1, sizeY, sizeX });
        for (int x_i = 0; x_i < sizeX; x_i++) {
            for (int y_i = 0; y_i < sizeY; y_i++) {
                short value = sb.get(y_i * sizeX + x_i);
                image.set(value, 0, 0, 0, y_i, x_i);
            }
        }
        jhdf.writeArraySlice(outputPath, image, new long[] { c, t, z, 0, 0 });
    } else if (bpp == 4) {
        ByteBuffer bb = ByteBuffer.wrap(buf);
        IntBuffer ib = bb.asIntBuffer();
        MDIntArray image = new MDIntArray(new int[] { 1, 1, 1, sizeY, sizeX });
        for (int x_i = 0; x_i < sizeX; x_i++) {
            for (int y_i = 0; y_i < sizeY; y_i++) {
                int value = (int) ib.get(y_i * sizeX + x_i);
                image.set(value, 0, 0, 0, y_i, x_i);
            }
        }
        jhdf.writeArraySlice(outputPath, image, new long[] { c, t, z, 0, 0 });
    } else {
        throw new FormatException("CellH5Writer: Pixel type not supported");
    }
}

Example 3 with DimensionOrder

use of ome.xml.model.enums.DimensionOrder in project bioformats by openmicroscopy.

the class FormatTools method getFilename.

public static String getFilename(int series, int image, MetadataRetrieve retrieve, String pattern, boolean padded) throws FormatException, IOException {
    String sPlaces = "%d";
    if (padded) {
        sPlaces = "%0" + String.valueOf(retrieve.getImageCount()).length() + "d";
    }
    String filename = pattern.replaceAll(SERIES_NUM, String.format(sPlaces, series));
    String imageName = retrieve.getImageName(series);
    if (imageName == null)
        imageName = "Series" + series;
    imageName = imageName.replaceAll("/", "_");
    imageName = imageName.replaceAll("\\\\", "_");
    filename = filename.replaceAll(SERIES_NAME, imageName);
    DimensionOrder order = retrieve.getPixelsDimensionOrder(series);
    int sizeC = retrieve.getChannelCount(series);
    int sizeT = retrieve.getPixelsSizeT(series).getValue();
    int sizeZ = retrieve.getPixelsSizeZ(series).getValue();
    int[] coordinates = FormatTools.getZCTCoords(order.getValue(), sizeZ, sizeC, sizeT, sizeZ * sizeC * sizeT, image);
    String zPlaces = "%d";
    String tPlaces = "%d";
    String cPlaces = "%d";
    if (padded) {
        zPlaces = "%0" + String.valueOf(sizeZ).length() + "d";
        tPlaces = "%0" + String.valueOf(sizeT).length() + "d";
        cPlaces = "%0" + String.valueOf(sizeC).length() + "d";
    }
    filename = filename.replaceAll(Z_NUM, String.format(zPlaces, coordinates[0]));
    filename = filename.replaceAll(T_NUM, String.format(tPlaces, coordinates[2]));
    filename = filename.replaceAll(CHANNEL_NUM, String.format(cPlaces, coordinates[1]));
    String channelName = retrieve.getChannelName(series, coordinates[1]);
    if (channelName == null)
        channelName = String.valueOf(coordinates[1]);
    channelName = channelName.replaceAll("/", "_");
    channelName = channelName.replaceAll("\\\\", "_");
    filename = filename.replaceAll(CHANNEL_NAME, channelName);
    Timestamp timestamp = retrieve.getImageAcquisitionDate(series);
    long stamp = 0;
    String date = null;
    if (timestamp != null) {
        date = timestamp.getValue();
        if (retrieve.getPlaneCount(series) > image) {
            Time deltaT = retrieve.getPlaneDeltaT(series, image);
            if (deltaT != null) {
                stamp = (long) (deltaT.value(UNITS.SECOND).doubleValue() * 1000);
            }
        }
        stamp += DateTools.getTime(date, DateTools.ISO8601_FORMAT);
    } else {
        stamp = System.currentTimeMillis();
    }
    date = DateTools.convertDate(stamp, (int) DateTools.UNIX_EPOCH);
    filename = filename.replaceAll(TIMESTAMP, date);
    return filename;
}