Examples with RandomAccessInputStream loci.common.RandomAccessInputStream used on opensource projects

Example 96 with RandomAccessInputStream

use of loci.common.RandomAccessInputStream in project bioformats by openmicroscopy.

the class FormatReader method isThisType.

// -- IFormatReader API methods --
/**
 * Checks if a file matches the type of this format reader.
 * Checks filename suffixes against those known for this format.
 * If the suffix check is inconclusive and the open parameter is true,
 * the file is opened and tested with
 * {@link #isThisType(RandomAccessInputStream)}.
 *
 * @param open If true, and the file extension is insufficient to determine
 *   the file type, the (existing) file is opened for further analysis.
 */
@Override
public boolean isThisType(String name, boolean open) {
    // if file extension ID is insufficient and we can't open the file, give up
    if (!suffixSufficient && !open)
        return false;
    if (suffixNecessary || suffixSufficient) {
        // it's worth checking the file extension
        boolean suffixMatch = super.isThisType(name);
        // if suffix match is required but it doesn't match, failure
        if (suffixNecessary && !suffixMatch)
            return false;
        // if suffix matches and that's all we need, green light it
        if (suffixMatch && suffixSufficient)
            return true;
    }
    // not allowed to open any files
    if (!open)
        return false;
    try {
        RandomAccessInputStream stream = new RandomAccessInputStream(name);
        boolean isThisType = isThisType(stream);
        stream.close();
        return isThisType;
    } catch (IOException exc) {
        LOGGER.debug("", exc);
        return false;
    }
}

Example 97 with RandomAccessInputStream

use of loci.common.RandomAccessInputStream in project bioformats by openmicroscopy.

the class FormatReader method isThisType.

/* @see IFormatReader#isThisType(byte[]) */
@Override
public boolean isThisType(byte[] block) {
    try {
        RandomAccessInputStream stream = new RandomAccessInputStream(block);
        boolean isThisType = isThisType(stream);
        stream.close();
        return isThisType;
    } catch (IOException e) {
        LOGGER.debug("", e);
    }
    return false;
}

Example 98 with RandomAccessInputStream

use of loci.common.RandomAccessInputStream in project bioformats by openmicroscopy.

the class TestTools method mapFile.

/**
 * Map the given file into memory.
 *
 * @return true if the mapping was successful.
 */
public static boolean mapFile(String id) throws IOException {
    RandomAccessInputStream stream = new RandomAccessInputStream(id);
    Runtime rt = Runtime.getRuntime();
    long maxMem = rt.freeMemory();
    long length = stream.length();
    if (length < Integer.MAX_VALUE && length < maxMem) {
        stream.close();
        FileInputStream fis = new FileInputStream(id);
        FileChannel channel = fis.getChannel();
        ByteBuffer buf = channel.map(FileChannel.MapMode.READ_ONLY, 0, channel.size());
        ByteArrayHandle handle = new ByteArrayHandle(buf);
        Location.mapFile(id, handle);
        fis.close();
        return true;
    }
    stream.close();
    return false;
}

Example 99 with RandomAccessInputStream

use of loci.common.RandomAccessInputStream in project bioformats by openmicroscopy.

the class WritePrecompressedPlanes method main.

public static void main(String[] args) throws FormatException, IOException {
    // print usage if no args specified
    if (args.length == 0) {
        System.out.println("Usage: java WritePrecompressedPlanes " + "[input file 1] ... [input file n] [output file]");
        System.exit(0);
    }
    // first n - 1 args are the input files
    String[] inputFiles = new String[args.length - 1];
    System.arraycopy(args, 0, inputFiles, 0, inputFiles.length);
    // last arg is the output file
    String outputFile = args[args.length - 1];
    // open up one of the input files so that we can read the metadata
    // this assumes that the dimensions of the input files are the same
    ImageReader reader = new ImageReader();
    reader.setId(inputFiles[0]);
    int pixelType = reader.getPixelType();
    // write the pixel data to the output file
    RandomAccessOutputStream out = new RandomAccessOutputStream(outputFile);
    TiffSaver saver = new TiffSaver(out, outputFile);
    saver.setWritingSequentially(true);
    saver.setLittleEndian(reader.isLittleEndian());
    saver.setBigTiff(false);
    saver.writeHeader();
    for (int i = 0; i < inputFiles.length; i++) {
        RandomAccessInputStream in = new RandomAccessInputStream(inputFiles[i]);
        byte[] buf = new byte[(int) in.length()];
        in.readFully(buf);
        in.close();
        IFD ifd = new IFD();
        ifd.put(IFD.IMAGE_WIDTH, reader.getSizeX());
        ifd.put(IFD.IMAGE_LENGTH, reader.getSizeY());
        ifd.put(IFD.LITTLE_ENDIAN, reader.isLittleEndian());
        ifd.put(IFD.SAMPLE_FORMAT, FormatTools.isSigned(pixelType) ? 2 : FormatTools.isFloatingPoint(pixelType) ? 3 : 1);
        ifd.put(IFD.PLANAR_CONFIGURATION, 1);
        ifd.put(IFD.REUSE, out.length());
        out.seek(out.length());
        // this is very important
        // the data is already compressed in a single chunk, so setting the
        // number of rows per strip to something smaller than the full height
        // will require us to re-compress the data
        ifd.put(IFD.ROWS_PER_STRIP, reader.getSizeY());
        saver.writeImage(buf, ifd, i, pixelType, 0, 0, reader.getSizeX(), reader.getSizeY(), i == inputFiles.length - 1, reader.getRGBChannelCount(), true);
    }
    reader.close();
    out.close();
    // reset the TIFF file's compression flag
    // you cannot do this before the pixel data is written, otherwise
    // the pixels will be re-compressed
    saver = new TiffSaver(outputFile);
    for (int i = 0; i < inputFiles.length; i++) {
        RandomAccessInputStream in = new RandomAccessInputStream(outputFile);
        saver.overwriteLastIFDOffset(in);
        saver.overwriteIFDValue(in, i, IFD.COMPRESSION, TiffCompression.JPEG.getCode());
        in.close();
    }
    saver.getStream().close();
}

Example 100 with RandomAccessInputStream

use of loci.common.RandomAccessInputStream in project bioformats by openmicroscopy.

the class IOTester method testSequential.

/**
 * Searches for the divider tag using repeated readChar() calls.
 */
public long testSequential(String filename) throws IOException {
    LOGGER.info("Searching for divider tag sequentially...");
    long start = System.currentTimeMillis();
    RandomAccessInputStream in = new RandomAccessInputStream(filename);
    int matchIndex = 0;
    char matchChar = TAG.charAt(0);
    long inputLen = in.length();
    for (long i = 0; i < inputLen; i++) {
        char c = in.readChar();
        if (c == matchChar) {
            matchIndex++;
            if (matchIndex == TAG.length()) {
                break;
            } else {
                matchChar = TAG.charAt(matchIndex);
            }
        } else {
            matchIndex = 0;
            matchChar = TAG.charAt(0);
        }
    }
    long offset = in.getFilePointer();
    in.close();
    long end = System.currentTimeMillis();
    LOGGER.info("Search result: {} -- in {} ms", offset, end - start);
    return offset;
}