Examples with ByteOrder java.nio.ByteOrder used on opensource projects

Example 26 with ByteOrder

use of java.nio.ByteOrder in project javacv by bytedeco.

the class DC1394FrameGrabber method grab.

public Frame grab() throws Exception {
    enqueue();
    if (linux) {
        fds.events(POLLIN);
        if (poll(fds, 1, timeout) == 0) {
            throw new Exception("poll() Error: Timeout occured. (Has start() been called?)");
        }
    }
    int i = 0;
    int err = dc1394_capture_dequeue(camera, DC1394_CAPTURE_POLICY_WAIT, raw_image[i]);
    if (err != DC1394_SUCCESS) {
        throw new Exception("dc1394_capture_dequeue(WAIT) Error " + err + ": Could not capture a frame. (Has start() been called?)");
    }
    // try to poll for more images, to get the most recent one...
    int numDequeued = 0;
    while (!raw_image[i].isNull()) {
        enqueue();
        enqueue_image = raw_image[i];
        i = (i + 1) % 2;
        numDequeued++;
        err = dc1394_capture_dequeue(camera, DC1394_CAPTURE_POLICY_POLL, raw_image[i]);
        if (err != DC1394_SUCCESS) {
            throw new Exception("dc1394_capture_dequeue(POLL) Error " + err + ": Could not capture a frame.");
        }
    }
    frame = raw_image[(i + 1) % 2];
    int w = frame.size(0);
    int h = frame.size(1);
    int depth = frame.data_depth();
    int iplDepth = 0;
    switch(depth) {
        case 8:
            iplDepth = IPL_DEPTH_8U;
            break;
        case 16:
            iplDepth = IPL_DEPTH_16U;
            break;
        default:
            assert false;
    }
    int stride = frame.stride();
    int size = frame.image_bytes();
    int numChannels = stride / w * 8 / depth;
    ByteOrder frameEndian = frame.little_endian() != 0 ? ByteOrder.LITTLE_ENDIAN : ByteOrder.BIG_ENDIAN;
    boolean alreadySwapped = false;
    int color_coding = frame.color_coding();
    boolean colorbayer = color_coding == DC1394_COLOR_CODING_RAW8 || color_coding == DC1394_COLOR_CODING_RAW16;
    boolean colorrgb = color_coding == DC1394_COLOR_CODING_RGB8 || color_coding == DC1394_COLOR_CODING_RGB16;
    boolean coloryuv = color_coding == DC1394_COLOR_CODING_YUV411 || color_coding == DC1394_COLOR_CODING_YUV422 || color_coding == DC1394_COLOR_CODING_YUV444;
    BytePointer imageData = frame.image();
    if ((depth <= 8 || frameEndian.equals(ByteOrder.nativeOrder())) && !coloryuv && (imageMode == ImageMode.RAW || (imageMode == ImageMode.COLOR && numChannels == 3) || (imageMode == ImageMode.GRAY && numChannels == 1 && !colorbayer))) {
        if (return_image == null) {
            return_image = IplImage.createHeader(w, h, iplDepth, numChannels);
        }
        return_image.widthStep(stride);
        return_image.imageSize(size);
        return_image.imageData(imageData);
    } else {
        // in the padding, there's sometimes timeframe information and stuff
        // that libdc1394 will copy for us, so we need to allocate it
        int padding_bytes = frame.padding_bytes();
        int padding1 = (int) Math.ceil((double) padding_bytes / (w * depth / 8));
        int padding3 = (int) Math.ceil((double) padding_bytes / (w * 3 * depth / 8));
        if (return_image == null) {
            int c = imageMode == ImageMode.COLOR ? 3 : 1;
            int padding = imageMode == ImageMode.COLOR ? padding3 : padding1;
            return_image = IplImage.create(w, h + padding, iplDepth, c);
            return_image.height(return_image.height() - padding);
        }
        if (temp_image == null) {
            if (imageMode == ImageMode.COLOR && (numChannels > 1 || depth > 8) && !coloryuv && !colorbayer) {
                temp_image = IplImage.create(w, h + padding1, iplDepth, numChannels);
                temp_image.height(temp_image.height() - padding1);
            } else if (imageMode == ImageMode.GRAY && (coloryuv || colorbayer || (colorrgb && depth > 8))) {
                temp_image = IplImage.create(w, h + padding3, iplDepth, 3);
                temp_image.height(temp_image.height() - padding3);
            } else if (imageMode == ImageMode.GRAY && colorrgb) {
                temp_image = IplImage.createHeader(w, h, iplDepth, 3);
            } else if (imageMode == ImageMode.COLOR && numChannels == 1 && !coloryuv && !colorbayer) {
                temp_image = IplImage.createHeader(w, h, iplDepth, 1);
            } else {
                temp_image = return_image;
            }
        }
        conv_image.size(0, temp_image.width());
        conv_image.size(1, temp_image.height());
        if (depth > 8) {
            conv_image.color_coding(imageMode == ImageMode.RAW ? DC1394_COLOR_CODING_RAW16 : temp_image.nChannels() == 1 ? DC1394_COLOR_CODING_MONO16 : DC1394_COLOR_CODING_RGB16);
            conv_image.data_depth(16);
        } else {
            conv_image.color_coding(imageMode == ImageMode.RAW ? DC1394_COLOR_CODING_RAW8 : temp_image.nChannels() == 1 ? DC1394_COLOR_CODING_MONO8 : DC1394_COLOR_CODING_RGB8);
            conv_image.data_depth(8);
        }
        conv_image.stride(temp_image.widthStep());
        int temp_size = temp_image.imageSize();
        conv_image.allocated_image_bytes(temp_size).total_bytes(temp_size).image_bytes(temp_size);
        conv_image.image(temp_image.imageData());
        if (colorbayer) {
            // from raw Bayer... invert R and B to get BGR images
            // (like OpenCV wants them) instead of RGB
            int c = frame.color_filter();
            if (c == DC1394_COLOR_FILTER_RGGB) {
                frame.color_filter(DC1394_COLOR_FILTER_BGGR);
            } else if (c == DC1394_COLOR_FILTER_GBRG) {
                frame.color_filter(DC1394_COLOR_FILTER_GRBG);
            } else if (c == DC1394_COLOR_FILTER_GRBG) {
                frame.color_filter(DC1394_COLOR_FILTER_GBRG);
            } else if (c == DC1394_COLOR_FILTER_BGGR) {
                frame.color_filter(DC1394_COLOR_FILTER_RGGB);
            } else {
                assert false;
            }
            // other better methods than "simple" give garbage at 16 bits..
            err = dc1394_debayer_frames(frame, conv_image, DC1394_BAYER_METHOD_SIMPLE);
            frame.color_filter(c);
            if (err != DC1394_SUCCESS) {
                throw new Exception("dc1394_debayer_frames() Error " + err + ": Could not debayer frame.");
            }
        } else if (depth > 8 && frame.data_depth() == conv_image.data_depth() && frame.color_coding() == conv_image.color_coding() && frame.stride() == conv_image.stride()) {
            // we just need a copy to swap bytes..
            ShortBuffer in = frame.getByteBuffer().order(frameEndian).asShortBuffer();
            ShortBuffer out = temp_image.getByteBuffer().order(ByteOrder.nativeOrder()).asShortBuffer();
            out.put(in);
            alreadySwapped = true;
        } else if ((imageMode == ImageMode.GRAY && colorrgb) || (imageMode == ImageMode.COLOR && numChannels == 1 && !coloryuv && !colorbayer)) {
            temp_image.widthStep(stride);
            temp_image.imageSize(size);
            temp_image.imageData(imageData);
        } else if (!colorrgb && (colorbayer || coloryuv || numChannels > 1)) {
            // from YUV, etc.
            err = dc1394_convert_frames(frame, conv_image);
            if (err != DC1394_SUCCESS) {
                throw new Exception("dc1394_convert_frames() Error " + err + ": Could not convert frame.");
            }
        }
        if (!alreadySwapped && depth > 8 && !frameEndian.equals(ByteOrder.nativeOrder())) {
            // ack, the camera's endianness doesn't correspond to our machine ...
            // swap bytes of 16-bit images
            ByteBuffer bb = temp_image.getByteBuffer();
            ShortBuffer in = bb.order(frameEndian).asShortBuffer();
            ShortBuffer out = bb.order(ByteOrder.nativeOrder()).asShortBuffer();
            out.put(in);
        }
        // should we copy the padding as well?
        if (imageMode == ImageMode.COLOR && numChannels == 1 && !coloryuv && !colorbayer) {
            cvCvtColor(temp_image, return_image, CV_GRAY2BGR);
        } else if (imageMode == ImageMode.GRAY && (colorbayer || colorrgb || coloryuv)) {
            cvCvtColor(temp_image, return_image, CV_BGR2GRAY);
        }
    }
    switch(frame.color_filter()) {
        case DC1394_COLOR_FILTER_RGGB:
            sensorPattern = SENSOR_PATTERN_RGGB;
            break;
        case DC1394_COLOR_FILTER_GBRG:
            sensorPattern = SENSOR_PATTERN_GBRG;
            break;
        case DC1394_COLOR_FILTER_GRBG:
            sensorPattern = SENSOR_PATTERN_GRBG;
            break;
        case DC1394_COLOR_FILTER_BGGR:
            sensorPattern = SENSOR_PATTERN_BGGR;
            break;
        default:
            sensorPattern = -1L;
    }
    enqueue_image = frame;
    timestamp = frame.timestamp();
    frameNumber += numDequeued;
    // System.out.println("frame age = " + (local_time[0] - timestamp));
    return converter.convert(return_image);
}

Example 27 with ByteOrder

use of java.nio.ByteOrder in project javacv by bytedeco.

the class FlyCapture2FrameGrabber method grab.

public Frame grab() throws FrameGrabber.Exception {
    Error error = camera.RetrieveBuffer(raw_image);
    if (error.notEquals(PGRERROR_OK)) {
        throw new FrameGrabber.Exception("flycaptureGrabImage2() Error " + error + " (Has start() been called?)");
    }
    int w = raw_image.GetCols();
    int h = raw_image.GetRows();
    int format = raw_image.GetPixelFormat();
    int depth = getDepth(format);
    int stride = raw_image.GetStride();
    int size = h * stride;
    int numChannels = getNumChannels(format);
    error = camera.ReadRegister(IMAGE_DATA_FORMAT, regOut);
    if (error.notEquals(PGRERROR_OK)) {
        throw new FrameGrabber.Exception("flycaptureGetCameraRegister() Error " + error);
    }
    ByteOrder frameEndian = (regOut[0] & 0x1) != 0 ? ByteOrder.BIG_ENDIAN : ByteOrder.LITTLE_ENDIAN;
    boolean alreadySwapped = false;
    boolean colorbayer = raw_image.GetBayerTileFormat() != NONE;
    boolean colorrgb = format == PIXEL_FORMAT_RGB8 || format == PIXEL_FORMAT_RGB16 || format == PIXEL_FORMAT_BGR || format == PIXEL_FORMAT_BGRU;
    boolean coloryuv = format == PIXEL_FORMAT_411YUV8 || format == PIXEL_FORMAT_422YUV8 || format == PIXEL_FORMAT_444YUV8;
    BytePointer imageData = raw_image.GetData().capacity(raw_image.GetDataSize());
    if ((depth == IPL_DEPTH_8U || frameEndian.equals(ByteOrder.nativeOrder())) && (imageMode == FrameGrabber.ImageMode.RAW || (imageMode == FrameGrabber.ImageMode.COLOR && numChannels == 3) || (imageMode == FrameGrabber.ImageMode.GRAY && numChannels == 1 && !colorbayer))) {
        if (return_image == null) {
            return_image = IplImage.createHeader(w, h, depth, numChannels);
        }
        return_image.widthStep(stride);
        return_image.imageSize(size);
        return_image.imageData(imageData);
    } else {
        if (return_image == null) {
            return_image = IplImage.create(w, h, depth, imageMode == FrameGrabber.ImageMode.COLOR ? 3 : 1);
        }
        if (temp_image == null) {
            if (imageMode == FrameGrabber.ImageMode.COLOR && (numChannels > 1 || depth > 8) && !coloryuv && !colorbayer) {
                temp_image = IplImage.create(w, h, depth, numChannels);
            } else if (imageMode == FrameGrabber.ImageMode.GRAY && colorbayer) {
                temp_image = IplImage.create(w, h, depth, 3);
            } else if (imageMode == FrameGrabber.ImageMode.GRAY && colorrgb) {
                temp_image = IplImage.createHeader(w, h, depth, 3);
            } else if (imageMode == FrameGrabber.ImageMode.COLOR && numChannels == 1 && !coloryuv && !colorbayer) {
                temp_image = IplImage.createHeader(w, h, depth, 1);
            } else {
                temp_image = return_image;
            }
        }
        setStride(conv_image, temp_image.widthStep());
        conv_image.SetData(temp_image.imageData(), temp_image.width() * temp_image.height() * temp_image.depth());
        if (depth == IPL_DEPTH_8U) {
            setPixelFormat(conv_image, imageMode == FrameGrabber.ImageMode.RAW ? PIXEL_FORMAT_RAW8 : temp_image.nChannels() == 1 ? PIXEL_FORMAT_MONO8 : PIXEL_FORMAT_BGR);
        } else {
            setPixelFormat(conv_image, imageMode == FrameGrabber.ImageMode.RAW ? PIXEL_FORMAT_RAW16 : temp_image.nChannels() == 1 ? PIXEL_FORMAT_MONO16 : PIXEL_FORMAT_RGB16);
        }
        if (depth != IPL_DEPTH_8U && conv_image.GetPixelFormat() == format && conv_image.GetStride() == stride) {
            // we just need a copy to swap bytes..
            ShortBuffer in = imageData.asByteBuffer().order(frameEndian).asShortBuffer();
            ShortBuffer out = temp_image.getByteBuffer().order(ByteOrder.nativeOrder()).asShortBuffer();
            out.put(in);
            alreadySwapped = true;
        } else if ((imageMode == FrameGrabber.ImageMode.GRAY && colorrgb) || (imageMode == FrameGrabber.ImageMode.COLOR && numChannels == 1 && !coloryuv && !colorbayer)) {
            temp_image.widthStep(stride);
            temp_image.imageSize(size);
            temp_image.imageData(imageData);
        } else if (!colorrgb && (colorbayer || coloryuv || numChannels > 1)) {
            error = raw_image.Convert(conv_image);
            // error = flycaptureConvertImage(context, raw_image, conv_image);
            if (error.notEquals(PGRERROR_OK)) {
                PrintError(error);
                throw new FrameGrabber.Exception("raw_image.Convert Error " + error);
            }
        }
        if (!alreadySwapped && depth != IPL_DEPTH_8U && !frameEndian.equals(ByteOrder.nativeOrder())) {
            // ack, the camera's endianness doesn't correspond to our machine ...
            // swap bytes of 16-bit images
            ByteBuffer bb = temp_image.getByteBuffer();
            ShortBuffer in = bb.order(frameEndian).asShortBuffer();
            ShortBuffer out = bb.order(ByteOrder.nativeOrder()).asShortBuffer();
            out.put(in);
        }
        if (imageMode == FrameGrabber.ImageMode.COLOR && numChannels == 1 && !coloryuv && !colorbayer) {
            cvCvtColor(temp_image, return_image, CV_GRAY2BGR);
        } else if (imageMode == FrameGrabber.ImageMode.GRAY && (colorbayer || colorrgb)) {
            cvCvtColor(temp_image, return_image, CV_BGR2GRAY);
        }
    }
    int bayerFormat = cameraInfo.bayerTileFormat();
    switch(bayerFormat) {
        case BGGR:
            sensorPattern = SENSOR_PATTERN_BGGR;
            break;
        case GBRG:
            sensorPattern = SENSOR_PATTERN_GBRG;
            break;
        case GRBG:
            sensorPattern = SENSOR_PATTERN_GRBG;
            break;
        case RGGB:
            sensorPattern = SENSOR_PATTERN_RGGB;
            break;
        default:
            sensorPattern = -1L;
    }
    TimeStamp timeStamp = raw_image.GetTimeStamp();
    timestamp = timeStamp.seconds() * 1000000L + timeStamp.microSeconds();
    return converter.convert(return_image);
}

Example 28 with ByteOrder

use of java.nio.ByteOrder in project ffx by mjschnie.

the class CCP4MapFilter method getCrystal.

/**
 * {@inheritDoc}
 */
@Override
public Crystal getCrystal(String fileName, CompositeConfiguration properties) {
    int imapData;
    int spaceGroup = -1;
    double cellA = -1.0;
    double cellB = -1.0;
    double cellC = -1.0;
    double cellAlpha = -1.0;
    double cellBeta = -1.0;
    double cellGamma = -1.0;
    ByteOrder byteOrder = ByteOrder.nativeOrder();
    FileInputStream fileInputStream;
    DataInputStream dataInputStream;
    // first determine byte order of file versus system
    try {
        fileInputStream = new FileInputStream(fileName);
        dataInputStream = new DataInputStream(fileInputStream);
        dataInputStream.skipBytes(212);
        byte[] bytes = new byte[4];
        dataInputStream.read(bytes, 0, 4);
        ByteBuffer byteBuffer = ByteBuffer.wrap(bytes);
        imapData = byteBuffer.order(ByteOrder.BIG_ENDIAN).getInt();
        String stampString = Integer.toHexString(imapData);
        switch(stampString.charAt(0)) {
            case '1':
            case '3':
                if (byteOrder.equals(ByteOrder.LITTLE_ENDIAN)) {
                    byteOrder = ByteOrder.BIG_ENDIAN;
                }
                break;
            case '4':
                if (byteOrder.equals(ByteOrder.BIG_ENDIAN)) {
                    byteOrder = ByteOrder.LITTLE_ENDIAN;
                }
                break;
        }
        fileInputStream.close();
    } catch (Exception e) {
        String message = " Fatal exception reading CCP4 map.\n";
        logger.log(Level.SEVERE, message, e);
    }
    try {
        fileInputStream = new FileInputStream(fileName);
        dataInputStream = new DataInputStream(fileInputStream);
        dataInputStream.skipBytes(40);
        byte[] bytes = new byte[80];
        dataInputStream.read(bytes, 0, 80);
        ByteBuffer byteBuffer = ByteBuffer.wrap(bytes);
        cellA = byteBuffer.order(byteOrder).getFloat();
        cellB = byteBuffer.order(byteOrder).getFloat();
        cellC = byteBuffer.order(byteOrder).getFloat();
        cellAlpha = byteBuffer.order(byteOrder).getFloat();
        cellBeta = byteBuffer.order(byteOrder).getFloat();
        cellGamma = byteBuffer.order(byteOrder).getFloat();
        for (int i = 0; i < 3; i++) {
            byteBuffer.order(byteOrder).getInt();
        }
        for (int i = 0; i < 3; i++) {
            byteBuffer.order(byteOrder).getFloat();
        }
        spaceGroup = byteBuffer.order(byteOrder).getInt();
        fileInputStream.close();
    } catch (Exception e) {
        String message = " Fatal exception reading CCP4 map.\n";
        logger.log(Level.SEVERE, message, e);
    }
    return new Crystal(cellA, cellB, cellC, cellAlpha, cellBeta, cellGamma, SpaceGroup.spaceGroupNames[spaceGroup - 1]);
}

Example 29 with ByteOrder

use of java.nio.ByteOrder in project ffx by mjschnie.

the class MTZFilter method readFcs.

/**
 * Read the structure factors.
 *
 * @param mtzFile
 * @param reflectionList
 * @param fcData
 * @param properties
 * @return
 */
public boolean readFcs(File mtzFile, ReflectionList reflectionList, DiffractionRefinementData fcData, CompositeConfiguration properties) {
    int nRead, nIgnore, nRes, nFriedel, nCut;
    ByteOrder byteOrder = ByteOrder.nativeOrder();
    FileInputStream fileInputStream;
    DataInputStream dataInputStream;
    StringBuilder sb = new StringBuilder();
    try {
        fileInputStream = new FileInputStream(mtzFile);
        dataInputStream = new DataInputStream(fileInputStream);
        byte[] headerOffset = new byte[4];
        byte[] bytes = new byte[80];
        int offset = 0;
        // Eat "MTZ" title.
        dataInputStream.read(bytes, offset, 4);
        String mtzString = null;
        // Header offset.
        dataInputStream.read(headerOffset, offset, 4);
        // Machine stamp.
        dataInputStream.read(bytes, offset, 4);
        ByteBuffer byteBuffer = ByteBuffer.wrap(bytes);
        int stamp = byteBuffer.order(ByteOrder.BIG_ENDIAN).getInt();
        String stampString = Integer.toHexString(stamp);
        switch(stampString.charAt(0)) {
            case '1':
            case '3':
                if (byteOrder.equals(ByteOrder.LITTLE_ENDIAN)) {
                    byteOrder = ByteOrder.BIG_ENDIAN;
                }
                break;
            case '4':
                if (byteOrder.equals(ByteOrder.BIG_ENDIAN)) {
                    byteOrder = ByteOrder.LITTLE_ENDIAN;
                }
                break;
        }
        byteBuffer = ByteBuffer.wrap(headerOffset);
        int headerOffsetI = byteBuffer.order(byteOrder).getInt();
        // Skip to header and parse.
        dataInputStream.skipBytes((headerOffsetI - 4) * 4);
        for (Boolean parsing = true; parsing; dataInputStream.read(bytes, offset, 80)) {
            mtzString = new String(bytes);
            parsing = parseHeader(mtzString);
        }
        // Column identifiers.
        fc = phiC = fs = phiS = -1;
        boolean print = true;
        parseFcColumns(print);
        if (h < 0 || k < 0 || l < 0) {
            String message = " Fatal error in MTZ file - no H K L indexes?\n";
            logger.log(Level.SEVERE, message);
            return false;
        }
        // Reopen to start at beginning.
        fileInputStream = new FileInputStream(mtzFile);
        dataInputStream = new DataInputStream(fileInputStream);
        // Skip initial header.
        dataInputStream.skipBytes(80);
        float[] data = new float[nColumns];
        HKL mate = new HKL();
        // Read in data.
        ComplexNumber complexNumber = new ComplexNumber();
        nRead = nIgnore = nRes = nFriedel = nCut = 0;
        for (int i = 0; i < nReflections; i++) {
            for (int j = 0; j < nColumns; j++) {
                dataInputStream.read(bytes, offset, 4);
                byteBuffer = ByteBuffer.wrap(bytes);
                data[j] = byteBuffer.order(byteOrder).getFloat();
            }
            int ih = (int) data[h];
            int ik = (int) data[k];
            int il = (int) data[l];
            boolean friedel = reflectionList.findSymHKL(ih, ik, il, mate, false);
            HKL hkl = reflectionList.getHKL(mate);
            if (hkl != null) {
                if (fc > 0 && phiC > 0) {
                    complexNumber.re(data[fc] * cos(toRadians(data[phiC])));
                    complexNumber.im(data[fc] * sin(toRadians(data[phiC])));
                    fcData.setFc(hkl.index(), complexNumber);
                }
                if (fs > 0 && phiS > 0) {
                    complexNumber.re(data[fs] * cos(toRadians(data[phiS])));
                    complexNumber.im(data[fs] * sin(toRadians(data[phiS])));
                    fcData.setFs(hkl.index(), complexNumber);
                }
                nRead++;
            } else {
                HKL tmp = new HKL(ih, ik, il);
                if (!reflectionList.resolution.inInverseResSqRange(Crystal.invressq(reflectionList.crystal, tmp))) {
                    nRes++;
                } else {
                    nIgnore++;
                }
            }
        }
        if (logger.isLoggable(Level.INFO)) {
            sb.append(format(" MTZ file type (machine stamp): %s\n", stampString));
            sb.append(format(" Fc HKL read in:                             %d\n", nRead));
            sb.append(format(" Fc HKL read as friedel mates:               %d\n", nFriedel));
            sb.append(format(" Fc HKL NOT read in (too high resolution):   %d\n", nRes));
            sb.append(format(" Fc HKL NOT read in (not in internal list?): %d\n", nIgnore));
            sb.append(format(" Fc HKL NOT read in (F/sigF cutoff):         %d\n", nCut));
            sb.append(format(" HKL in internal list:                       %d\n", reflectionList.hkllist.size()));
            logger.info(sb.toString());
        }
    } catch (EOFException e) {
        String message = " MTZ end of file reached.";
        logger.log(Level.WARNING, message, e);
        return false;
    } catch (IOException e) {
        String message = " MTZ IO Exception.";
        logger.log(Level.WARNING, message, e);
        return false;
    }
    return true;
}

Example 30 with ByteOrder

use of java.nio.ByteOrder in project ffx by mjschnie.

the class MTZFilter method getReflectionList.

/**
 * {@inheritDoc}
 */
@Override
public ReflectionList getReflectionList(File mtzFile, CompositeConfiguration properties) {
    ByteOrder byteOrder = ByteOrder.nativeOrder();
    FileInputStream fileInputStream;
    DataInputStream dataInputStream;
    try {
        fileInputStream = new FileInputStream(mtzFile);
        dataInputStream = new DataInputStream(fileInputStream);
        byte[] headerOffset = new byte[4];
        byte[] bytes = new byte[80];
        int offset = 0;
        // Eat "MTZ" title.
        dataInputStream.read(bytes, offset, 4);
        String mtzstr = new String(bytes);
        // Header offset.
        dataInputStream.read(headerOffset, offset, 4);
        // Machine stamp.
        dataInputStream.read(bytes, offset, 4);
        ByteBuffer byteBuffer = ByteBuffer.wrap(bytes);
        int stamp = byteBuffer.order(ByteOrder.BIG_ENDIAN).getInt();
        String stampstr = Integer.toHexString(stamp);
        switch(stampstr.charAt(0)) {
            case '1':
            case '3':
                if (byteOrder.equals(ByteOrder.LITTLE_ENDIAN)) {
                    byteOrder = ByteOrder.BIG_ENDIAN;
                }
                break;
            case '4':
                if (byteOrder.equals(ByteOrder.BIG_ENDIAN)) {
                    byteOrder = ByteOrder.LITTLE_ENDIAN;
                }
                break;
        }
        byteBuffer = ByteBuffer.wrap(headerOffset);
        int headerOffsetI = byteBuffer.order(byteOrder).getInt();
        // skip to header and parse
        dataInputStream.skipBytes((headerOffsetI - 4) * 4);
        for (Boolean parsing = true; parsing; dataInputStream.read(bytes, offset, 80)) {
            mtzstr = new String(bytes);
            parsing = parseHeader(mtzstr);
        }
    } catch (EOFException e) {
        String message = " MTZ end of file reached.";
        logger.log(Level.WARNING, message, e);
        return null;
    } catch (IOException e) {
        String message = " MTZ IO exception.";
        logger.log(Level.WARNING, message, e);
        return null;
    }
    // column identifiers
    foString = sigFoString = rFreeString = null;
    if (properties != null) {
        foString = properties.getString("fostring", null);
        sigFoString = properties.getString("sigfostring", null);
        rFreeString = properties.getString("rfreestring", null);
    }
    h = k = l = fo = sigFo = rFree = -1;
    fPlus = sigFPlus = fMinus = sigFMinus = rFreePlus = rFreeMinus = -1;
    fc = phiC = -1;
    boolean print = false;
    parseColumns(print);
    parseFcColumns(print);
    if (fo < 0 && fPlus < 0 && sigFo < 0 && sigFPlus < 0 && fc < 0 && phiC < 0) {
        logger.info(" The MTZ header contains insufficient information to generate the reflection list.");
        logger.info(" For non-default column labels set fostring/sigfostring in the properties file.");
        return null;
    }
    Column column;
    if (fo > 0) {
        column = (Column) columns.get(fo);
    } else if (fPlus > 0) {
        column = (Column) columns.get(fPlus);
    } else {
        column = (Column) columns.get(fc);
    }
    Dataset dataSet = (Dataset) dataSets.get(column.id - dsetOffset);
    if (logger.isLoggable(Level.INFO)) {
        StringBuilder sb = new StringBuilder();
        sb.append(format("\n Reading %s\n\n", mtzFile.getName()));
        sb.append(format(" Setting up reflection list based on MTZ file.\n"));
        sb.append(format("  Space group number: %d (name: %s)\n", spaceGroupNum, SpaceGroup.spaceGroupNames[spaceGroupNum - 1]));
        sb.append(format("  Resolution:         %8.3f\n", 0.999999 * resHigh));
        sb.append(format("  Cell:               %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f\n", dataSet.cell[0], dataSet.cell[1], dataSet.cell[2], dataSet.cell[3], dataSet.cell[4], dataSet.cell[5]));
        logger.info(sb.toString());
    }
    Crystal crystal = new Crystal(dataSet.cell[0], dataSet.cell[1], dataSet.cell[2], dataSet.cell[3], dataSet.cell[4], dataSet.cell[5], SpaceGroup.spaceGroupNames[spaceGroupNum - 1]);
    double sampling = 0.6;
    if (properties != null) {
        sampling = properties.getDouble("sampling", 0.6);
    }
    Resolution resolution = new Resolution(0.999999 * resHigh, sampling);
    return new ReflectionList(crystal, resolution, properties);
}