Examples with FormatException loci.formats.FormatException used on opensource projects

Example 56 with FormatException

use of loci.formats.FormatException 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 57 with FormatException

use of loci.formats.FormatException in project bioformats by openmicroscopy.

the class PrintROIs method main.

public static void main(String[] args) throws Exception {
    ImageReader reader = new ImageReader();
    IMetadata omexml;
    try {
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        omexml = service.createOMEXMLMetadata();
    } catch (DependencyException exc) {
        throw new FormatException("Could not create OME-XML store.", exc);
    } catch (ServiceException exc) {
        throw new FormatException("Could not create OME-XML store.", exc);
    }
    reader.setMetadataStore(omexml);
    reader.setId(args[0]);
    printAllROIs(omexml);
    System.out.println();
    for (int series = 0; series < reader.getSeriesCount(); series++) {
        printSeriesROIs(omexml, series);
    }
    reader.close();
}

Example 58 with FormatException

use of loci.formats.FormatException in project bioformats by openmicroscopy.

the class WlzServiceImpl method saveBytes.

@Override
public void saveBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException {
    if (state == WLZ_SERVICE_WRITE) {
        WlzIVertex3 og = new WlzIVertex3(x + bBox.xMin, y + bBox.yMin, no + bBox.zMin);
        WlzIVertex2 sz = new WlzIVertex2(w, h);
        try {
            wlzObj = WlzObject.WlzBuildObj3B(wlzObj, og, sz, objGType, buf.length, buf);
        } catch (WlzException e) {
            throw new FormatException("Failed save bytes to Woolz object", e);
        }
    }
}

Example 59 with FormatException

use of loci.formats.FormatException in project bioformats by openmicroscopy.

the class WlzServiceImpl method open.

@Override
public void open(String file, String rw) throws FormatException, IOException {
    try {
        String[] v = new String[1];
        WlzObject.WlzGetVersion(v);
        wlzVersion = new String(v[0]);
    } catch (UnsatisfiedLinkError e) {
        throw new FormatException(NO_WLZ_MSG, e);
    }
    if (rw.equals("r")) {
        openRead(file);
    } else if (rw.equals("w")) {
        openWrite(file);
    } else {
        throw new IOException("Failed to open file " + file);
    }
}

Example 60 with FormatException

use of loci.formats.FormatException in project bioformats by openmicroscopy.

the class CellWorxReader method getReader.

private IFormatReader getReader(String file, boolean omexml) throws FormatException, IOException {
    IFormatReader pnl = new DeltavisionReader();
    if (checkSuffix(file, "tif")) {
        pnl = new MetamorphReader();
    }
    if (omexml) {
        IMetadata metadata;
        try {
            metadata = service.createOMEXMLMetadata();
        } catch (ServiceException exc) {
            throw new FormatException("Could not create OME-XML store.", exc);
        }
        pnl.setMetadataStore(metadata);
    }
    pnl.setId(file);
    return pnl;
}