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

Example 56 with RandomAccessInputStream

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

the class VectraReader method isThisType.

// -- IFormatReader API methods --
/* (non-Javadoc)
   * @see loci.formats.FormatReader#isThisType(java.lang.String, boolean)
   */
@Override
public boolean isThisType(String name, boolean open) {
    if (!open) {
        return checkSuffix(name, "qptiff");
    }
    try (RandomAccessInputStream 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;
        }
        tiffParser.fillInIFD(ifd);
        String software = ifd.getIFDTextValue(IFD.SOFTWARE);
        return software != null && software.startsWith(SOFTWARE_CHECK);
    } catch (IOException e) {
        LOGGER.debug("I/O exception during isThisType() evaluation.", e);
        return false;
    }
}

Example 57 with RandomAccessInputStream

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

the class VarianFDFReader 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);
    if (files.size() > 1) {
        in = new RandomAccessInputStream(files.get(no));
        in.order(isLittleEndian());
    }
    in.seek(pixelOffsets[no]);
    readPlane(in, x, getSizeY() - y - h, w, h, buf);
    int bpp = FormatTools.getBytesPerPixel(getPixelType());
    byte[] rowBuf = new byte[w * bpp];
    for (int row = 0; row < h / 2; row++) {
        int src = row * rowBuf.length;
        int dest = (h - row - 1) * rowBuf.length;
        System.arraycopy(buf, src, rowBuf, 0, rowBuf.length);
        System.arraycopy(buf, dest, buf, src, rowBuf.length);
        System.arraycopy(rowBuf, 0, buf, dest, rowBuf.length);
    }
    if (files.size() > 1) {
        in.close();
    }
    return buf;
}

Example 58 with RandomAccessInputStream

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

the class VarianFDFReader method parseFDF.

// -- Helper methods --
private void parseFDF(String file) throws FormatException, IOException {
    in = new RandomAccessInputStream(file);
    CoreMetadata m = core.get(0);
    boolean storedFloats = false;
    boolean multifile = false;
    String data = in.readString(Character.toString((char) 0x0c));
    String[] lines = data.split("\n");
    for (String line : lines) {
        line = line.trim();
        if (line.length() == 0)
            break;
        if (line.startsWith("#"))
            continue;
        int space = line.indexOf(' ');
        int eq = line.indexOf('=');
        String type = line.substring(0, space).trim();
        String var = line.substring(space, eq).trim();
        String value = line.substring(eq + 1, line.indexOf(';')).trim();
        if (var.equals("*storage")) {
            storedFloats = value.equals("\"float\"");
        }
        if (var.equals("bits")) {
            m.bitsPerPixel = Integer.parseInt(value);
            if (value.equals("8")) {
                m.pixelType = FormatTools.UINT8;
            } else if (value.equals("16")) {
                m.pixelType = FormatTools.UINT16;
            } else if (value.equals("32")) {
                if (storedFloats) {
                    m.pixelType = FormatTools.FLOAT;
                } else
                    m.pixelType = FormatTools.UINT32;
            } else
                throw new FormatException("Unsupported bits: " + value);
        } else if (var.equals("matrix[]")) {
            String[] values = parseArray(value);
            m.sizeX = (int) Double.parseDouble(values[0]);
            m.sizeY = (int) Double.parseDouble(values[1]);
            if (values.length > 2) {
                m.sizeZ = (int) Double.parseDouble(values[2]);
            }
        } else if (var.equals("slices")) {
            m.sizeZ = Integer.parseInt(value);
            multifile = true;
        } else if (var.equals("echoes")) {
            m.sizeT = Integer.parseInt(value);
            multifile = true;
        } else if (var.equals("span[]")) {
            String[] values = parseArray(value);
            if (values.length > 0) {
                pixelSizeX = computePhysicalSize(getSizeX(), values[0], units[0]);
            }
            if (values.length > 1) {
                pixelSizeY = computePhysicalSize(getSizeY(), values[1], units[1]);
            }
            if (values.length > 2) {
                pixelSizeZ = computePhysicalSize(getSizeZ(), values[2], units[2]);
            }
        } else if (var.equals("origin[]")) {
            String[] values = parseArray(value);
            if (values.length > 0) {
                final double size = computePhysicalSize(1, values[0], units[0]);
                originX = new Length(size, UNITS.REFERENCEFRAME);
                addGlobalMeta("X position for position #1", originX);
            }
            if (values.length > 1) {
                final double size = computePhysicalSize(1, values[1], units[1]);
                originY = new Length(size, UNITS.REFERENCEFRAME);
                addGlobalMeta("Y position for position #1", originY);
            }
            if (values.length > 2) {
                final double size = computePhysicalSize(1, values[2], units[2]);
                originZ = new Length(size, UNITS.REFERENCEFRAME);
                addGlobalMeta("Z position for position #1", originZ);
            }
        } else if (var.equals("*abscissa[]")) {
            units = parseArray(value);
        } else if (var.equals("bigendian")) {
            m.littleEndian = value.equals("0");
            in.order(isLittleEndian());
        }
        addGlobalMeta(var, value);
    }
    if (multifile && files.isEmpty()) {
        Location thisFile = new Location(file).getAbsoluteFile();
        Location parent = thisFile.getParentFile();
        String[] list = parent.list(true);
        Arrays.sort(list);
        for (String f : list) {
            if (checkSuffix(f, "fdf") && f.length() == thisFile.getName().length()) {
                files.add(new Location(parent, f).getAbsolutePath());
            }
        }
    }
}

Example 59 with RandomAccessInputStream

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

the class VarianFDFReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    CoreMetadata m = core.get(0);
    m.sizeZ = 1;
    m.sizeC = 1;
    m.sizeT = 1;
    parseFDF(id);
    m.imageCount = getSizeZ() * getSizeC() * getSizeT();
    m.dimensionOrder = "XYTZC";
    if (files.size() > getImageCount()) {
        int rem = files.size() / getImageCount();
        m.sizeT *= rem;
        m.imageCount = getSizeZ() * getSizeC() * getSizeT();
    }
    pixelOffsets = new long[getImageCount()];
    int planeSize = FormatTools.getPlaneSize(this);
    for (int i = 0; i < pixelOffsets.length; i++) {
        if (files.size() > 1) {
            in.close();
            in = new RandomAccessInputStream(files.get(i));
            pixelOffsets[i] = in.length() - planeSize;
        } else {
            pixelOffsets[i] = in.length() - (planeSize * (getImageCount() - i));
        }
    }
    boolean minMetadata = getMetadataOptions().getMetadataLevel() == MetadataLevel.MINIMUM;
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, !minMetadata);
    if (!minMetadata) {
        Length sizeX = FormatTools.getPhysicalSizeX(pixelSizeX);
        Length sizeY = FormatTools.getPhysicalSizeY(pixelSizeY);
        Length sizeZ = FormatTools.getPhysicalSizeZ(pixelSizeZ);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, 0);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, 0);
        }
        if (sizeZ != null) {
            store.setPixelsPhysicalSizeZ(sizeZ, 0);
        }
        for (int i = 0; i < getImageCount(); i++) {
            store.setPlanePositionX(originX, 0, i);
            store.setPlanePositionY(originY, 0, i);
            store.setPlanePositionZ(originZ, 0, i);
        }
    }
}

Example 60 with RandomAccessInputStream

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

the class VolocityClippingReader 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(pixelOffset);
    if (FormatTools.getPlaneSize(this) * 2 + in.getFilePointer() < in.length()) {
        readPlane(in, x, y, w, h, buf);
        return buf;
    }
    byte[] b = new LZOCodec().decompress(in, null);
    RandomAccessInputStream s = new RandomAccessInputStream(b);
    s.seek(0);
    readPlane(s, x, y, w, h, buf);
    s.close();
    return buf;
}