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

Example 91 with RandomAccessInputStream

use of loci.common.RandomAccessInputStream 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;
        }
    }
}

Example 92 with RandomAccessInputStream

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

the class BDReader method readMetaData.

private IniList readMetaData(String id) throws IOException {
    IniParser parser = new IniParser();
    RandomAccessInputStream idStream = new RandomAccessInputStream(id);
    IniList exp = parser.parseINI(new BufferedReader(new InputStreamReader(idStream, Constants.ENCODING)));
    IniList plate = null;
    IniList xyz = null;
    // Read Plate File
    for (String filename : metadataFiles) {
        if (checkSuffix(filename, "plt")) {
            RandomAccessInputStream stream = new RandomAccessInputStream(filename);
            plate = parser.parseINI(new BufferedReader(new InputStreamReader(stream, Constants.ENCODING)));
            stream.close();
        } else if (checkSuffix(filename, "xyz")) {
            RandomAccessInputStream stream = new RandomAccessInputStream(filename);
            xyz = parser.parseINI(new BufferedReader(new InputStreamReader(stream, Constants.ENCODING)));
            stream.close();
        } else if (filename.endsWith("RoiSummary.txt")) {
            roiFile = filename;
            if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
                RandomAccessInputStream s = new RandomAccessInputStream(filename);
                String line = s.readLine().trim();
                while (!line.endsWith(".adf\"")) {
                    line = s.readLine().trim();
                }
                plateName = line.substring(line.indexOf(':')).trim();
                plateName = plateName.replace('/', File.separatorChar);
                plateName = plateName.replace('\\', File.separatorChar);
                for (int i = 0; i < 3; i++) {
                    plateName = plateName.substring(0, plateName.lastIndexOf(File.separator));
                }
                plateName = plateName.substring(plateName.lastIndexOf(File.separator) + 1);
                s.close();
            }
        }
    }
    if (plate == null)
        throw new IOException("No Plate File");
    IniTable plateType = plate.getTable("PlateType");
    if (plateName == null) {
        plateName = plateType.get("Brand");
    }
    plateDescription = plateType.get("Brand") + " " + plateType.get("Description");
    int nWells = Integer.parseInt(plateType.get("Wells"));
    if (nWells == 96) {
        wellRows = 8;
        wellCols = 12;
    } else if (nWells == 384) {
        wellRows = 16;
        wellCols = 24;
    }
    for (String filename : rootList) {
        String name = new Location(filename).getName();
        if (name.startsWith("Well ")) {
            wellLabels.add(name.split("\\s|\\.")[1]);
        }
    }
    IniTable imageTable = exp.getTable("Image");
    boolean montage = imageTable.get("Montaged").equals("1");
    if (montage) {
        fieldRows = Integer.parseInt(imageTable.get("TilesY"));
        fieldCols = Integer.parseInt(imageTable.get("TilesX"));
    } else {
        fieldRows = 1;
        fieldCols = 1;
    }
    core.clear();
    int coresize = wellLabels.size() * fieldRows * fieldCols;
    CoreMetadata ms0 = new CoreMetadata();
    core.add(ms0);
    for (int i = 1; i < coresize; i++) {
        core.add(new CoreMetadata());
    }
    ms0.sizeC = Integer.parseInt(exp.getTable("General").get("Dyes"));
    ms0.bitsPerPixel = Integer.parseInt(exp.getTable("Camera").get("BitdepthUsed"));
    IniTable dyeTable = exp.getTable("Dyes");
    for (int i = 1; i <= getSizeC(); i++) {
        channelNames.add(dyeTable.get(Integer.toString(i)));
    }
    if (xyz != null) {
        IniTable zTable = xyz.getTable("Z1Axis");
        boolean zEnabled = "1".equals(zTable.get("Z1AxisEnabled")) && "1".equals(zTable.get("Z1AxisMode"));
        if (zEnabled) {
            ms0.sizeZ = (int) Double.parseDouble(zTable.get("Z1AxisValue")) + 1;
        } else {
            ms0.sizeZ = 1;
        }
    } else {
        ms0.sizeZ = 1;
    }
    // Count Images
    ms0.sizeT = 0;
    for (String channelName : channelNames) {
        int images = 0;
        for (String filename : wellList.get(1)) {
            if (filename.startsWith(channelName) && filename.endsWith(".tif")) {
                images++;
            }
        }
        if (images > getImageCount()) {
            ms0.sizeT = images / getSizeZ();
            ms0.imageCount = getSizeZ() * getSizeT() * channelNames.size();
        }
    }
    idStream.close();
    return exp;
}

Example 93 with RandomAccessInputStream

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

the class BDReader method getTimestamp.

private long getTimestamp(String file) throws FormatException, IOException {
    RandomAccessInputStream s = new RandomAccessInputStream(file, 16);
    TiffParser parser = new TiffParser(s);
    parser.setDoCaching(false);
    IFD firstIFD = parser.getFirstIFD();
    if (firstIFD != null) {
        TiffIFDEntry timestamp = (TiffIFDEntry) firstIFD.get(IFD.DATE_TIME);
        if (timestamp != null) {
            String stamp = parser.getIFDValue(timestamp).toString();
            s.close();
            stamp = DateTools.formatDate(stamp, BaseTiffReader.DATE_FORMATS, ".");
            Timestamp t = Timestamp.valueOf(stamp);
            // NPE if invalid input.
            return t.asInstant().getMillis();
        }
    }
    s.close();
    return new Location(file).lastModified();
}

Example 94 with RandomAccessInputStream

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

the class TiffPixelsTest method readSavedPlane.

// -- Helper method --
private byte[] readSavedPlane() throws FormatException, IOException {
    ByteArrayHandle savedData = new ByteArrayHandle();
    RandomAccessOutputStream out = new RandomAccessOutputStream(savedData);
    RandomAccessInputStream in = new RandomAccessInputStream(savedData);
    TiffSaver saver = new TiffSaver(out, savedData);
    // saver.setInputStream(in);
    saver.writeImage(data, ifd, 0, FormatTools.UINT16, false);
    out.close();
    TiffParser parser = new TiffParser(in);
    byte[] plane = new byte[data.length];
    parser.getSamples(ifd, plane);
    in.close();
    return plane;
}

Example 95 with RandomAccessInputStream

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

the class TiffComment method overwriteComment.

/**
 * Overwrites the comment.
 *
 * @param file The path to the file to handle.
 * @param comment The new comment to write.
 */
private static void overwriteComment(String file, String comment) {
    RandomAccessInputStream in = null;
    RandomAccessOutputStream out = null;
    try {
        in = new RandomAccessInputStream(file);
        out = new RandomAccessOutputStream(file);
        TiffSaver saver = new TiffSaver(out, file);
        saver.overwriteComment(in, comment);
    } catch (Exception e) {
        System.out.println(e.toString());
    } finally {
        try {
            if (in != null)
                in.close();
        } catch (Exception e) {
        }
        try {
            if (out != null)
                out.close();
        } catch (Exception e) {
        }
    }
}