Examples with TiffRational loci.formats.tiff.TiffRational used on opensource projects

Example 11 with TiffRational

use of loci.formats.tiff.TiffRational in project bioformats by openmicroscopy.

the class GelReader method initMetadata.

// -- Internal BaseTiffReader API methods --
/* @see BaseTiffReader#initMetadata() */
@Override
protected void initMetadata() throws FormatException, IOException {
    ifds = tiffParser.getIFDs();
    if (ifds.size() > 1) {
        IFDList tmpIFDs = ifds;
        ifds = new IFDList();
        for (int i = 0; i < tmpIFDs.size() / 2; i++) {
            IFD ifd = new IFD();
            ifds.add(ifd);
            ifd.putAll(tmpIFDs.get(i * 2 + 1));
            ifd.putAll(tmpIFDs.get(i * 2));
            tiffParser.fillInIFD(ifd);
        }
    }
    IFD firstIFD = ifds.get(0);
    tiffParser.fillInIFD(firstIFD);
    super.initStandardMetadata();
    fmt = firstIFD.getIFDLongValue(MD_FILETAG, LINEAR);
    if (fmt == SQUARE_ROOT)
        core.get(0).pixelType = FormatTools.FLOAT;
    TiffRational scale = (TiffRational) firstIFD.getIFDValue(MD_SCALE_PIXEL);
    if (scale == null)
        scale = new TiffRational(1, 1);
    core.get(0).imageCount = ifds.size();
    core.get(0).sizeT = getImageCount();
    // ignore MD_COLOR_TABLE
    String info = firstIFD.getIFDStringValue(MD_SAMPLE_INFO);
    String prepDate = firstIFD.getIFDStringValue(MD_PREP_DATE);
    String prepTime = firstIFD.getIFDStringValue(MD_PREP_TIME);
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        String units = firstIFD.getIFDStringValue(MD_FILE_UNITS);
        String lab = firstIFD.getIFDStringValue(MD_LAB_NAME);
        addGlobalMeta("Scale factor", scale);
        addGlobalMeta("Lab name", lab);
        addGlobalMeta("Sample info", info);
        addGlobalMeta("Date prepared", prepDate);
        addGlobalMeta("Time prepared", prepTime);
        addGlobalMeta("File units", units);
        addGlobalMeta("Data format", fmt == SQUARE_ROOT ? "square root" : "linear");
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    String parsedDate = DateTools.formatDate(prepDate, FORMATS);
    String parsedTime = DateTools.formatDate(prepTime, FORMATS);
    if (parsedDate != null) {
        store.setImageAcquisitionDate(new Timestamp(parsedDate), 0);
    } else if (parsedTime != null) {
        store.setImageAcquisitionDate(new Timestamp(parsedTime), 0);
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        Double pixelSize = new Double(scale.doubleValue());
        Length sizeX = FormatTools.getPhysicalSizeX(pixelSize);
        Length sizeY = FormatTools.getPhysicalSizeY(pixelSize);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, 0);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, 0);
        }
    }
}

Example 12 with TiffRational

use of loci.formats.tiff.TiffRational in project bioformats by openmicroscopy.

the class GelReader method openBytes.

/**
 * @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
 */
@Override
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException {
    IFD ifd = ifds.get(no);
    if (fmt == SQUARE_ROOT) {
        if (tiffParser == null) {
            initTiffParser();
        }
        float scale = ((TiffRational) ifd.getIFDValue(MD_SCALE_PIXEL)).floatValue();
        byte[] tmp = new byte[buf.length];
        // DO NOT call super.openBytes here. MinimalTiffReader will interpret
        // the pixels as half-floats, when really they are unsigned shorts.
        tiffParser.getSamples(ifds.get(no), tmp, x, y, w, h);
        int originalBytes = ifd.getBitsPerSample()[0] / 8;
        for (int i = 0; i < tmp.length / 4; i++) {
            long value = DataTools.bytesToShort(tmp, i * originalBytes, originalBytes, isLittleEndian());
            long square = value * value;
            float pixel = square * scale;
            DataTools.unpackBytes(Float.floatToIntBits(pixel), buf, i * 4, 4, isLittleEndian());
        }
    } else
        super.openBytes(no, buf, x, y, w, h);
    return buf;
}