Examples with AmiraParameters loci.formats.tools.AmiraParameters used on opensource projects

Example 1 with AmiraParameters

use of loci.formats.tools.AmiraParameters in project bioformats by openmicroscopy.

the class AmiraReader method initFile.

/* (non-Javadoc)
   * @see loci.formats.FormatReader#initFile(java.lang.String)
   */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    AmiraParameters parameters = new AmiraParameters(in);
    offsetOfFirstStream = in.getFilePointer();
    LOGGER.info("Populating metadata hashtable");
    addGlobalMeta("Image width", parameters.width);
    addGlobalMeta("Image height", parameters.height);
    addGlobalMeta("Number of planes", parameters.depth);
    addGlobalMeta("Bits per pixel", 8);
    LOGGER.info("Populating core metadata");
    int channelIndex = 1;
    while (parameters.getStreams().get("@" + channelIndex) != null) {
        channelIndex++;
    }
    CoreMetadata m = core.get(0);
    m.sizeX = parameters.width;
    m.sizeY = parameters.height;
    m.sizeZ = parameters.depth;
    m.sizeT = 1;
    m.sizeC = channelIndex - 1;
    m.imageCount = getSizeZ() * getSizeC();
    m.littleEndian = parameters.littleEndian;
    m.dimensionOrder = "XYZCT";
    String streamType = parameters.streamTypes[0].toLowerCase();
    if (streamType.equals("byte")) {
        m.pixelType = FormatTools.UINT8;
    } else if (streamType.equals("short")) {
        m.pixelType = FormatTools.INT16;
        addGlobalMeta("Bits per pixel", 16);
    } else if (streamType.equals("ushort")) {
        m.pixelType = FormatTools.UINT16;
        addGlobalMeta("Bits per pixel", 16);
    } else if (streamType.equals("int")) {
        m.pixelType = FormatTools.INT32;
        addGlobalMeta("Bits per pixel", 32);
    } else if (streamType.equals("float")) {
        m.pixelType = FormatTools.FLOAT;
        addGlobalMeta("Bits per pixel", 32);
    } else {
        LOGGER.warn("Assuming data type is byte");
        m.pixelType = FormatTools.UINT8;
    }
    LOGGER.info("Populating metadata store");
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    // The bounding box is the range of the centre of the voxels
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        double pixelWidth = (double) (parameters.x1 - parameters.x0) / (parameters.width - 1);
        double pixelHeight = (double) (parameters.y1 - parameters.y0) / (parameters.height - 1);
        // TODO - what is correct setting if single slice?
        double pixelDepth = (double) (parameters.z1 - parameters.z0) / (parameters.depth - 1);
        // Amira does not have a standard form for encoding units, so we just
        // have to assume microns for microscopy data
        addGlobalMeta("Pixels per meter (X)", 1e6 / pixelWidth);
        addGlobalMeta("Pixels per meter (Y)", 1e6 / pixelHeight);
        addGlobalMeta("Pixels per meter (Z)", 1e6 / pixelDepth);
        Length sizeX = FormatTools.getPhysicalSizeX(pixelWidth);
        Length sizeY = FormatTools.getPhysicalSizeY(pixelHeight);
        Length sizeZ = FormatTools.getPhysicalSizeZ(pixelDepth);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, 0);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, 0);
        }
        if (sizeZ != null) {
            store.setPixelsPhysicalSizeZ(sizeZ, 0);
        }
    }
    ascii = parameters.ascii;
    ArrayList streamData = (ArrayList) parameters.getStreams().get("@1");
    if (streamData.size() > 2) {
        compression = (String) streamData.get(2);
    }
    initPlaneReader();
    hasPlaneReader = planeReader != null;
    addGlobalMeta("Compression", compression);
    Map params = (Map) parameters.getMap().get("Parameters");
    if (params != null) {
        Map materials = (Map) params.get("Materials");
        if (materials != null) {
            lut = getLookupTable(materials);
            m.indexed = true;
        }
    }
}