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

Example 61 with RandomAccessInputStream

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

the class VolocityClippingReader 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);
    CoreMetadata m = core.get(0);
    m.littleEndian = in.read() == 'I';
    in.order(isLittleEndian());
    in.skipBytes(4);
    String magicString = in.readString(4);
    if (!magicString.equals(CLIPPING_MAGIC_STRING)) {
        throw new FormatException("Found invalid magic string: " + magicString);
    }
    int check = in.readInt();
    while (check != 0x208 && check != AISF) {
        in.seek(in.getFilePointer() - 3);
        check = in.readInt();
    }
    if (check == AISF) {
        m.littleEndian = false;
        in.order(isLittleEndian());
        in.skipBytes(28);
    }
    m.sizeX = in.readInt();
    m.sizeY = in.readInt();
    m.sizeZ = in.readInt();
    m.sizeC = 1;
    m.sizeT = 1;
    m.imageCount = getSizeZ() * getSizeT();
    m.dimensionOrder = "XYCZT";
    m.pixelType = FormatTools.UINT8;
    pixelOffset = in.getFilePointer() + 65;
    if (getSizeX() * getSizeY() * 100 >= in.length()) {
        while (in.getFilePointer() < in.length()) {
            try {
                byte[] b = new LZOCodec().decompress(in, null);
                if (b.length > 0 && (b.length % (getSizeX() * getSizeY())) == 0) {
                    int bytes = b.length / (getSizeX() * getSizeY());
                    m.pixelType = FormatTools.pixelTypeFromBytes(bytes, false, false);
                    break;
                }
            } catch (EOFException e) {
            }
            pixelOffset++;
            in.seek(pixelOffset);
        }
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}

Example 62 with RandomAccessInputStream

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

the class SPCReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    allFiles = new ArrayList<String>();
    // get the working directory
    Location tmpFile = new Location(id).getAbsoluteFile();
    Location workingDir = tmpFile.getParentFile();
    if (workingDir == null)
        workingDir = new Location(".");
    String workingDirPath = workingDir.getPath();
    if (!workingDirPath.equals(""))
        workingDirPath += File.separator;
    String[] ls = workingDir.list(true);
    if (!new Location(id).exists()) {
        ls = Location.getIdMap().keySet().toArray(new String[0]);
        workingDirPath = "";
    }
    String name = tmpFile.getName();
    // generate the name of the two matching files
    String setName = null;
    String spcName = null;
    int pos = name.lastIndexOf(".");
    if (pos != -1) {
        setName = tmpFile.getName().substring(0, pos) + ".set";
        spcName = tmpFile.getName().substring(0, pos) + ".spc";
        for (String l : ls) {
            if (l.equalsIgnoreCase(setName))
                setName = l;
            if (l.equalsIgnoreCase(spcName))
                spcName = l;
        }
    }
    if (setName == null) {
        throw new FormatException("Failed to find a matching .set file!");
    }
    if (spcName == null) {
        throw new FormatException("Failed to find a matching .spc file!");
    }
    frameClockList = new ArrayList<>();
    endOfFrameList = new ArrayList<>();
    allFiles.add(workingDirPath + setName);
    allFiles.add(workingDirPath + spcName);
    in = new RandomAccessInputStream(workingDirPath + setName);
    LOGGER.info("Reading info from .set file");
    in.order(true);
    in.skip(8);
    Integer setuppos = in.readInt();
    Short setupcount = in.readShort();
    String module = "";
    try {
        // Arbitrary length established by trial and error
        String header = in.readString(600);
        int index = header.indexOf("module SPC-");
        module = header.substring(index + 7, index + 14);
    } catch (IOException exc) {
        LOGGER.debug("Failed to read header from .set file!", exc);
    }
    if (!module.equalsIgnoreCase("SPC-134") && !module.equalsIgnoreCase("SPC-144") && !module.equalsIgnoreCase("SPC-154") && !module.equalsIgnoreCase("SPC-830")) {
        throw new FormatException("Failed to find a matching .set file!");
    }
    // goto start of setup information
    in.seek(setuppos);
    String setup = in.readString(setupcount);
    in.close();
    // get the tac range from the setup information
    double tacRange = parseSetup(TAC_RANGE, setup);
    // get the tac range from the setup information
    double tacGain = parseSetup(TAC_GAIN, setup);
    double timeBase;
    if (tacGain != 0.0 && tacRange != 0.0) {
        timeBase = 4095 * tacRange / (tacGain * 4096);
        // convert from s to ps
        timeBase *= 1.000e12;
    } else {
        throw new FormatException("Failed to parse setup file!");
    }
    LOGGER.debug("timeBase = " + Double.toString(timeBase));
    // Now read .spc file
    spcId = workingDirPath + spcName;
    in = new RandomAccessInputStream(spcId);
    in.order(true);
    LOGGER.info("Reading info from .spc file");
    /* The first 3 bytes in the file contain information about the 
     * macro time clock in 0.1 ns units ("500" for 50ns clock)
    */
    in.skip(3);
    /*
     * The 4th byte contains information about the number of 
     * routing channels in bits 3 to 6.
     * Bits 0-2 reserved bit 7 = 1 ("Data invalid")
    */
    byte routing = in.readByte();
    if ((routing & 0x10) != 0) {
        throw new FormatException("Invalid data!");
    }
    nChannels = (routing & 0x78) >> 3;
    currentPixel = 0;
    currentLine = -1;
    currentFrame = -1;
    rawBuf = new byte[bufLength];
    endOfFrameFlag = false;
    nBuffers = 0;
    bufLength = 1024;
    rawBuf = new byte[bufLength];
    int noOfBytes;
    nBuffers = 0;
    byte adcL;
    byte adcLM;
    while ((noOfBytes = in.read(rawBuf)) != -1) {
        for (int bb = 3; bb < noOfBytes; bb += 4) {
            // even nybble adc
            // get upper byte containing ADC data
            adcL = rawBuf[bb];
            // mask out upper 4 bits
            adcLM = (byte) (adcL & 0xF0);
            // at this point only the various clocks are of interest
            switch(adcLM) {
                case (byte) 0x90:
                    invalidAndMarkInit(bb);
                    break;
                case // Invalid, Mark and MTOV all set.
                (byte) 0xd0:
                    // Unsure about this-- Not well documented!
                    invalidAndMarkInit(bb);
                    break;
                default:
                    break;
            }
        // end switch
        }
        // end for
        nBuffers++;
    }
    nTimebins = (0xFFF >> adcResShift) + 1;
    nFrames = currentFrame - 1;
    addGlobalMeta("time bins", nTimebins);
    addGlobalMeta("nChannels", nChannels);
    addGlobalMeta("time base", timeBase);
    LOGGER.info("Populating metadata");
    CoreMetadata m = core.get(0);
    // Duplicates the behaviour of U.Lorenzo's Matlab code.
    if (nLines < 530) {
        // return an image
        lineMode = false;
        m.sizeY = nLines;
    } else {
        LOGGER.info("Single line mode");
        // return a single line
        lineMode = true;
        m.sizeY = 1;
    }
    Integer frameLength;
    Integer maxFrameLength = 0;
    for (int T = 0; T < nFrames; T++) {
        frameLength = (int) (endOfFrameList.get(T + 1) - frameClockList.get(T));
        if (frameLength > maxFrameLength)
            maxFrameLength = frameLength;
    }
    rawBuf = new byte[maxFrameLength];
    m.sizeX = nPixels;
    m.sizeZ = 1;
    m.sizeT = nTimebins * nFrames;
    m.sizeC = nChannels;
    m.dimensionOrder = "XYZTC";
    m.pixelType = FormatTools.UINT16;
    m.rgb = false;
    m.littleEndian = true;
    m.imageCount = m.sizeZ * m.sizeC * m.sizeT;
    m.indexed = false;
    m.falseColor = false;
    m.metadataComplete = true;
    m.moduloT.type = FormatTools.LIFETIME;
    m.moduloT.parentType = FormatTools.SPECTRA;
    m.moduloT.typeDescription = "TCSPC";
    m.moduloT.start = 0;
    m.moduloT.step = timeBase / nTimebins;
    m.moduloT.end = m.moduloT.step * (nTimebins - 1);
    m.moduloT.unit = "ps";
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}

Example 63 with RandomAccessInputStream

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

the class SVSReader method isThisType.

/* (non-Javadoc)
   * @see loci.formats.FormatReader#isThisType(java.lang.String, boolean)
   */
@Override
public boolean isThisType(String name, boolean open) {
    boolean isThisType = super.isThisType(name, open);
    if (!isThisType && open) {
        RandomAccessInputStream stream = null;
        try {
            stream = new RandomAccessInputStream(name);
            TiffParser tiffParser = new TiffParser(stream);
            tiffParser.setDoCaching(false);
            if (!tiffParser.isValidHeader()) {
                return false;
            }
            IFD ifd = tiffParser.getFirstIFD();
            if (ifd == null) {
                return false;
            }
            Object description = ifd.get(IFD.IMAGE_DESCRIPTION);
            if (description != null) {
                String imageDescription = null;
                if (description instanceof TiffIFDEntry) {
                    Object value = tiffParser.getIFDValue((TiffIFDEntry) description);
                    if (value != null) {
                        imageDescription = value.toString();
                    }
                } else if (description instanceof String) {
                    imageDescription = (String) description;
                }
                if (imageDescription != null && imageDescription.startsWith(APERIO_IMAGE_DESCRIPTION_PREFIX)) {
                    return true;
                }
            }
            return false;
        } catch (IOException e) {
            LOGGER.debug("I/O exception during isThisType() evaluation.", e);
            return false;
        } finally {
            try {
                if (stream != null) {
                    stream.close();
                }
            } catch (IOException e) {
                LOGGER.debug("I/O exception during stream closure.", e);
            }
        }
    }
    return isThisType;
}

Example 64 with RandomAccessInputStream

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

the class SlidebookTiffReader method getFirstChannel.

private String getFirstChannel(String path) throws FormatException, IOException {
    RandomAccessInputStream s = new RandomAccessInputStream(path);
    TiffParser parser = new TiffParser(s);
    IFD ifd = parser.getFirstIFD();
    Object channel = ifd.getIFDValue(CHANNEL_TAG);
    s.close();
    parser.getStream().close();
    return channel == null ? null : channel.toString();
}

Example 65 with RandomAccessInputStream

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

the class TargaReader 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(offset);
    int planeSize = FormatTools.getPlaneSize(this);
    TargaRLECodec codec = new TargaRLECodec();
    CodecOptions options = new CodecOptions();
    options.maxBytes = planeSize;
    options.bitsPerSample = bits;
    RandomAccessInputStream s = in;
    if (compressed) {
        byte[] b = codec.decompress(in, options);
        s = new RandomAccessInputStream(b);
        s.order(isLittleEndian());
    }
    int bpp = bits;
    while (bpp % 8 != 0) bpp++;
    bpp /= 8;
    int rowSkip = orientation < 2 ? (getSizeY() - h - y) : y;
    int colSkip = (orientation % 2) == 1 ? (getSizeX() - w - x) : x;
    s.skipBytes(rowSkip * getSizeX() * bpp);
    for (int row = 0; row < h; row++) {
        if (s.getFilePointer() >= s.length())
            break;
        s.skipBytes(colSkip * bpp);
        for (int col = 0; col < w; col++) {
            if (s.getFilePointer() >= s.length())
                break;
            int rowIndex = orientation < 2 ? h - row - 1 : row;
            int colIndex = (orientation % 2) == 1 ? w - col - 1 : col;
            int index = getSizeC() * (rowIndex * w + colIndex);
            if (bpp == 2) {
                int v = s.readShort();
                buf[index] = (byte) ((v & 0x7c00) >> 10);
                buf[index + 1] = (byte) ((v & 0x3e0) >> 5);
                buf[index + 2] = (byte) (v & 0x1f);
            } else if (bpp == 4) {
                buf[index + 2] = s.readByte();
                buf[index + 1] = s.readByte();
                buf[index] = s.readByte();
                s.skipBytes(1);
            } else {
                for (int c = getSizeC() - 1; c >= 0; c--) {
                    buf[index + c] = s.readByte();
                }
            }
        }
        s.skipBytes(bpp * (getSizeX() - w - colSkip));
    }
    return buf;
}