Examples with SDTReader loci.formats.in.SDTReader used on opensource projects

Example 1 with SDTReader

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

the class ExtractSDTData method main.

public static void main(String[] args) throws Exception {
    if (args.length < 1) {
        System.out.println("Usage: java ExtractSDTData file.sdt");
        System.exit(1);
    }
    String id = args[0];
    String tid = id.substring(0, id.indexOf('.'));
    SDTReader r = new SDTReader();
    r.setId(id);
    int bins = r.getTimeBinCount();
    int chan = r.getChannelCount();
    int w = r.getSizeX();
    int h = r.getSizeY();
    System.out.println("Data is " + w + " x " + h + ", bins=" + bins + ", channels=" + chan);
    byte[][] data = new byte[chan][h * w * bins * 2];
    for (int c = 0; c < chan; c++) {
        System.out.println("Reading channel #" + c + "...");
        r.openBytes(c, data[c]);
        int i = 0;
        for (int y = 0; y < h; y++) {
            for (int x = 0; x < w; x++) {
                String oid = tid + "-c" + c + "-row" + y + "-col" + x;
                System.out.println(oid);
                PrintWriter out = new PrintWriter(new FileWriter(oid));
                for (int b = 0; b < bins; b++) {
                    i += 2;
                    int v0 = data[c][i];
                    int v1 = data[c][i + 1];
                    int v = (v0 << 8) & v1;
                    out.println(b + " " + v);
                }
                out.close();
            }
        }
    }
}

Example 2 with SDTReader

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

the class LociPrefs method makeImageReader.

// -- Utility methods --
/**
 * Creates an image reader according to the current configuration settings,
 * including which format readers are currently enabled, as well as
 * format-specific configuration settings.
 */
public static ImageReader makeImageReader() {
    ClassList<IFormatReader> defaultClasses = ImageReader.getDefaultReaderClasses();
    Class<? extends IFormatReader>[] c = defaultClasses.getClasses();
    // include only enabled classes
    ClassList<IFormatReader> enabledClasses = new ClassList<IFormatReader>(IFormatReader.class);
    for (int i = 0; i < c.length; i++) {
        boolean on = LociPrefs.isReaderEnabled(c[i]);
        if (on)
            enabledClasses.addClass(c[i]);
    }
    ImageReader reader = new ImageReader(enabledClasses);
    MetadataOptions options = reader.getMetadataOptions();
    if (options instanceof DynamicMetadataOptions) {
        ((DynamicMetadataOptions) options).setBoolean(ZeissCZIReader.ALLOW_AUTOSTITCHING_KEY, allowCZIAutostitch());
        ((DynamicMetadataOptions) options).setBoolean(ZeissCZIReader.INCLUDE_ATTACHMENTS_KEY, includeCZIAttachments());
        ((DynamicMetadataOptions) options).setBoolean(NativeND2Reader.USE_CHUNKMAP_KEY, useND2Chunkmap());
        ((DynamicMetadataOptions) options).setBoolean(LIFReader.OLD_PHYSICAL_SIZE_KEY, isLeicaLIFPhysicalSizeBackwardsCompatible());
        ((DynamicMetadataOptions) options).setBoolean(CellSensReader.FAIL_ON_MISSING_KEY, isCellsensFailOnMissing());
        reader.setMetadataOptions(options);
    }
    // toggle reader-specific options
    boolean nd2Nikon = LociPrefs.isND2Nikon();
    boolean pictQTJava = LociPrefs.isPictQTJava();
    boolean qtQTJava = LociPrefs.isQTQTJava();
    boolean sdtIntensity = LociPrefs.isSDTIntensity();
    boolean tiffImageIO = LociPrefs.isTiffImageIO();
    IFormatReader[] r = reader.getReaders();
    for (int i = 0; i < r.length; i++) {
        if (r[i] instanceof ND2Reader) {
            ND2Reader nd2 = (ND2Reader) r[i];
            nd2.setLegacy(nd2Nikon);
        } else if (r[i] instanceof PictReader) {
            PictReader pict = (PictReader) r[i];
            pict.setLegacy(pictQTJava);
        } else if (r[i] instanceof QTReader) {
            QTReader qt = (QTReader) r[i];
            qt.setLegacy(qtQTJava);
        } else if (r[i] instanceof SDTReader) {
            SDTReader sdt = (SDTReader) r[i];
            sdt.setIntensity(sdtIntensity);
        } else if (r[i] instanceof TiffDelegateReader) {
            TiffDelegateReader tiff = (TiffDelegateReader) r[i];
            tiff.setLegacy(tiffImageIO);
        }
    }
    return reader;
}