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

Example 36 with RandomAccessInputStream

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

the class ImagicReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (!checkSuffix(id, "hed")) {
        id = id.substring(0, id.lastIndexOf(".")) + ".hed";
    }
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    pixels = id.substring(0, id.lastIndexOf(".")) + ".img";
    pixelsFile = new RandomAccessInputStream(pixels);
    CoreMetadata m = core.get(0);
    m.littleEndian = true;
    in.order(isLittleEndian());
    pixelsFile.order(isLittleEndian());
    int nImages = (int) (in.length() / 1024);
    String imageName = null;
    double physicalXSize = 0d;
    double physicalYSize = 0d;
    double physicalZSize = 0d;
    for (int i = 0; i < nImages; i++) {
        in.seek(i * 1024);
        in.skipBytes(16);
        int month = in.readInt();
        int day = in.readInt();
        int year = in.readInt();
        int hour = in.readInt();
        int minute = in.readInt();
        int seconds = in.readInt();
        in.skipBytes(8);
        m.sizeY = in.readInt();
        m.sizeX = in.readInt();
        String type = in.readString(4);
        if (type.equals("REAL")) {
            m.pixelType = FormatTools.FLOAT;
        } else if (type.equals("INTG")) {
            m.pixelType = FormatTools.UINT16;
        } else if (type.equals("PACK")) {
            m.pixelType = FormatTools.UINT8;
        } else if (type.equals("COMP")) {
            throw new FormatException("Unsupported pixel type 'COMP'");
        } else if (type.equals("RECO")) {
            throw new FormatException("Unsupported pixel type 'RECO'");
        }
        int ixold = in.readInt();
        int iyold = in.readInt();
        float averageDensity = in.readFloat();
        float sigma = in.readFloat();
        in.skipBytes(8);
        float maxDensity = in.readFloat();
        float minDensity = in.readFloat();
        in.skipBytes(4);
        float defocus1 = in.readFloat();
        float defocus2 = in.readFloat();
        float defocusAngle = in.readFloat();
        float startAngle = in.readFloat();
        float endAngle = in.readFloat();
        imageName = in.readString(80);
        float ccc3d = in.readFloat();
        int ref3d = in.readInt();
        int micrographID = in.readInt();
        int zShift = in.readInt();
        float alpha = in.readFloat();
        float beta = in.readFloat();
        float gamma = in.readFloat();
        in.skipBytes(8);
        int nAliSum = in.readInt();
        int pointGroup = in.readInt();
        in.skipBytes(28);
        int version = in.readInt();
        int stamp = in.readInt();
        in.skipBytes(120);
        float angle = in.readFloat();
        float voltage = in.readFloat();
        float sphericalAberration = in.readFloat();
        float partialCoherence = in.readFloat();
        float ccc = in.readFloat();
        float errar = in.readFloat();
        float err3d = in.readFloat();
        int ref = in.readInt();
        float classNumber = in.readFloat();
        in.skipBytes(4);
        float representationQuality = in.readFloat();
        float eqZShift = in.readFloat();
        float xShift = in.readFloat();
        float yShift = in.readFloat();
        float numcls = in.readFloat();
        float overallQuality = in.readFloat();
        float equivalentAngle = in.readFloat();
        float eqXShift = in.readFloat();
        float eqYShift = in.readFloat();
        float cmToVar = in.readFloat();
        float informat = in.readFloat();
        int nEigenvalues = in.readInt();
        int nActiveImages = in.readInt();
        physicalXSize = in.readFloat();
        physicalYSize = in.readFloat();
        physicalZSize = in.readFloat();
        addGlobalMeta("IXOLD", ixold);
        addGlobalMeta("IYOLD", iyold);
        addGlobalMeta("Average density (AVDENS)", averageDensity);
        addGlobalMeta("SIGMA", sigma);
        addGlobalMeta("Maximum density (DENSMAX)", maxDensity);
        addGlobalMeta("Minimum density (DENSMIN)", minDensity);
        addGlobalMeta("DEFOCUS1", defocus1);
        addGlobalMeta("DEFOCUS2", defocus2);
        addGlobalMeta("Defocus angle (DEFANGLE)", defocusAngle);
        addGlobalMeta("SINOSTRT", startAngle);
        addGlobalMeta("SINOEND", endAngle);
        addGlobalMeta("Image name", imageName);
        addGlobalMeta("CCC3D", ccc3d);
        addGlobalMeta("REF3D", ref3d);
        addGlobalMeta("MIDENT", micrographID);
        addGlobalMeta("EZSHIFT", zShift);
        addGlobalMeta("EALPHA", alpha);
        addGlobalMeta("EBETA", beta);
        addGlobalMeta("EGAMMA", gamma);
        addGlobalMeta("NALISUM", nAliSum);
        addGlobalMeta("PGROUP", pointGroup);
        addGlobalMeta("IMAGIC Version (IMAVERS)", version);
        addGlobalMeta("REALTYPE", stamp);
        addGlobalMeta("ANGLE", angle);
        addGlobalMeta("VOLTAGE (in kV)", voltage);
        addGlobalMeta("SPABERR (in mm)", sphericalAberration);
        addGlobalMeta("PCOHER", partialCoherence);
        addGlobalMeta("CCC", ccc);
        addGlobalMeta("ERRAR", errar);
        addGlobalMeta("ERR3D", err3d);
        addGlobalMeta("REF", ref);
        addGlobalMeta("CLASSNO", classNumber);
        addGlobalMeta("REPQUAL", representationQuality);
        addGlobalMeta("ZSHIFT", eqZShift);
        addGlobalMeta("XSHIFT", xShift);
        addGlobalMeta("YSHIFT", yShift);
        addGlobalMeta("NUMCLS", numcls);
        addGlobalMeta("OVQUAL", overallQuality);
        addGlobalMeta("EANGLE", equivalentAngle);
        addGlobalMeta("EXSHIFT", eqXShift);
        addGlobalMeta("EYSHIFT", eqYShift);
        addGlobalMeta("CMTOTVAR", cmToVar);
        addGlobalMeta("INFORMAT", informat);
        addGlobalMeta("NUMEIGEN", nEigenvalues);
        addGlobalMeta("NIACTIVE", nActiveImages);
        addGlobalMeta("RESOLX", physicalXSize);
        addGlobalMeta("RESOLY", physicalYSize);
        addGlobalMeta("RESOLZ", physicalZSize);
    }
    m.sizeZ = nImages;
    m.sizeC = 1;
    m.sizeT = 1;
    m.imageCount = nImages;
    m.dimensionOrder = "XYZCT";
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    store.setImageName(imageName.trim(), 0);
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        Length sizeX = FormatTools.getPhysicalSizeX(physicalXSize * 0.0001);
        Length sizeY = FormatTools.getPhysicalSizeY(physicalYSize * 0.0001);
        Length sizeZ = FormatTools.getPhysicalSizeZ(physicalZSize * 0.0001);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, 0);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, 0);
        }
        if (sizeZ != null) {
            store.setPixelsPhysicalSizeZ(sizeZ, 0);
        }
    }
}

Example 37 with RandomAccessInputStream

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

the class InveonReader 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 {
    FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
    long planeSize = (long) FormatTools.getPlaneSize(this);
    int index = getCoreIndex();
    RandomAccessInputStream dat = new RandomAccessInputStream(datFile);
    try {
        dat.order(isLittleEndian());
        dat.seek(dataPointers.get(index) + no * planeSize);
        readPlane(dat, x, y, w, h, buf);
    } finally {
        dat.close();
    }
    return buf;
}

Example 38 with RandomAccessInputStream

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

the class IvisionReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    LOGGER.info("Populating metadata");
    String version = in.readString(4);
    addGlobalMeta("Version", version);
    int fileFormat = in.read();
    int dataType = in.read();
    CoreMetadata m = core.get(0);
    m.sizeC = 1;
    switch(dataType) {
        case 0:
            m.pixelType = FormatTools.UINT8;
            break;
        case 1:
            m.pixelType = FormatTools.INT16;
            break;
        case 2:
            m.pixelType = FormatTools.INT32;
            break;
        case 3:
            m.pixelType = FormatTools.FLOAT;
            break;
        case 4:
            m.pixelType = FormatTools.UINT8;
            m.sizeC = 3;
            color16 = true;
            break;
        case 5:
            m.pixelType = FormatTools.UINT8;
            m.sizeC = 3;
            hasPaddingByte = true;
            break;
        case 6:
            m.pixelType = FormatTools.UINT16;
            break;
        case 7:
            m.pixelType = FormatTools.FLOAT;
            squareRoot = true;
            break;
        case 8:
            m.pixelType = FormatTools.UINT16;
            m.sizeC = 3;
            break;
    }
    m.sizeX = in.readInt();
    m.sizeY = in.readInt();
    in.skipBytes(6);
    m.sizeZ = in.readShort();
    in.skipBytes(50);
    m.sizeT = 1;
    if (getSizeX() > 1 && getSizeY() > 1) {
        lut = new byte[2048];
        in.read(lut);
    }
    imageOffset = in.getFilePointer();
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        in.skipBytes(getSizeZ() * getSizeC() * getSizeT() * getSizeX() * getSizeY() * FormatTools.getBytesPerPixel(getPixelType()));
        // look for block of XML data
        LOGGER.info("Looking for XML metadata");
        in.findString(false, "<?xml");
        if (in.getFilePointer() < in.length()) {
            in.seek(in.getFilePointer() - 5);
            String xml = in.readString((int) (in.length() - in.getFilePointer()));
            xml = xml.substring(xml.indexOf('<'), xml.lastIndexOf("plist>") + 6);
            IvisionHandler handler = new IvisionHandler();
            try {
                XMLTools.parseXML(xml, handler);
            } catch (IOException e) {
                LOGGER.debug("", e);
            }
        } else
            LOGGER.debug("XML metadata not found");
    }
    LOGGER.info("Populating core metadata");
    m.rgb = getSizeC() > 1;
    m.dimensionOrder = "XYCZT";
    m.littleEndian = false;
    m.interleaved = true;
    m.indexed = false;
    m.imageCount = getSizeZ() * getSizeT();
    LOGGER.info("Populating MetadataStore");
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    if (creationDate != null) {
        String date = DateTools.formatDate(creationDate, DATE_FORMAT);
        if (date != null) {
            store.setImageAcquisitionDate(new Timestamp(date), 0);
        }
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        String instrumentID = MetadataTools.createLSID("Instrument", 0);
        store.setInstrumentID(instrumentID, 0);
        store.setImageInstrumentRef(instrumentID, 0);
        if (deltaT != null) {
            Double increment = 0d;
            try {
                increment = new Double(deltaT);
            } catch (NumberFormatException e) {
                LOGGER.debug("Failed to parse time increment", e);
            }
            if (increment != null) {
                store.setPixelsTimeIncrement(new Time(increment, UNITS.SECOND), 0);
            }
        }
        String objectiveID = MetadataTools.createLSID("Objective", 0, 0);
        store.setObjectiveID(objectiveID, 0, 0);
        store.setObjectiveSettingsID(objectiveID, 0);
        store.setObjectiveCorrection(getCorrection("Other"), 0, 0);
        store.setObjectiveImmersion(getImmersion("Other"), 0, 0);
        if (lensNA != null)
            store.setObjectiveLensNA(lensNA, 0, 0);
        if (magnification != null) {
            store.setObjectiveNominalMagnification(magnification, 0, 0);
        }
        if (refractiveIndex != null) {
            store.setObjectiveSettingsRefractiveIndex(refractiveIndex, 0);
        }
        String detectorID = MetadataTools.createLSID("Detector", 0, 0);
        store.setDetectorID(detectorID, 0, 0);
        store.setDetectorSettingsID(detectorID, 0, 0);
        store.setDetectorType(getDetectorType("Other"), 0, 0);
        store.setDetectorSettingsBinning(getBinning(binX + "x" + binY), 0, 0);
        if (gain != null) {
            try {
                store.setDetectorSettingsGain(new Double(gain), 0, 0);
            } catch (NumberFormatException e) {
                LOGGER.debug("Failed to parse detector gain", e);
            }
        }
    }
}

Example 39 with RandomAccessInputStream

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

the class KhorosReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    in.skipBytes(4);
    in.order(true);
    int dependency = in.readInt();
    addGlobalMeta("Comment", in.readString(512));
    in.order(dependency == 4 || dependency == 8);
    CoreMetadata m = core.get(0);
    m.sizeX = in.readInt();
    m.sizeY = in.readInt();
    in.skipBytes(28);
    m.imageCount = in.readInt();
    if (getImageCount() == 0)
        m.imageCount = 1;
    m.sizeC = in.readInt();
    int type = in.readInt();
    switch(type) {
        case 0:
            m.pixelType = FormatTools.INT8;
            break;
        case 1:
            m.pixelType = FormatTools.UINT8;
            break;
        case 2:
            m.pixelType = FormatTools.UINT16;
            break;
        case 4:
            m.pixelType = FormatTools.INT32;
            break;
        case 5:
            m.pixelType = FormatTools.FLOAT;
            break;
        case 9:
            m.pixelType = FormatTools.DOUBLE;
            break;
        default:
            throw new FormatException("Unsupported pixel type : " + type);
    }
    // read lookup table
    in.skipBytes(12);
    int c = in.readInt();
    if (c > 1) {
        m.sizeC = c;
        int n = in.readInt();
        lut = new byte[c][n];
        in.skipBytes(436);
        for (int i = 0; i < lut.length; i++) {
            for (int j = 0; j < lut[0].length; j++) {
                lut[i][j] = in.readByte();
            }
        }
    } else
        in.skipBytes(440);
    offset = in.getFilePointer();
    m.sizeZ = getImageCount();
    m.sizeT = 1;
    m.rgb = getSizeC() > 1;
    m.interleaved = false;
    m.littleEndian = dependency == 4 || dependency == 8;
    m.dimensionOrder = "XYCZT";
    m.indexed = lut != null;
    m.falseColor = false;
    m.metadataComplete = true;
    if (isIndexed()) {
        m.sizeC = 1;
        m.rgb = false;
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}

Example 40 with RandomAccessInputStream

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

the class SBIGReader 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 {
    FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
    in.seek(HEADER_SIZE);
    int width = getSizeX() * 2;
    if (compressed) {
        byte[] b = new byte[FormatTools.getPlaneSize(this)];
        for (int row = 0; row < getSizeY(); row++) {
            int rowLen = in.readShort();
            if (rowLen == width) {
                in.read(b, row * width, rowLen);
            } else {
                int bufferPointer = row * width;
                in.read(b, bufferPointer, 2);
                while (bufferPointer - row * width < width - 2) {
                    short prevPixel = DataTools.bytesToShort(b, bufferPointer, isLittleEndian());
                    bufferPointer += 2;
                    byte check = in.readByte();
                    if (check == -128) {
                        in.read(b, bufferPointer, 2);
                    } else {
                        prevPixel += check;
                        DataTools.unpackBytes(prevPixel, b, bufferPointer, 2, isLittleEndian());
                    }
                }
            }
        }
        RandomAccessInputStream stream = new RandomAccessInputStream(b);
        readPlane(stream, x, y, w, h, buf);
        stream.close();
    } else
        readPlane(in, x, y, w, h, buf);
    return buf;
}