Examples with CoreMetadata loci.formats.CoreMetadata used on opensource projects

Example 66 with CoreMetadata

use of loci.formats.CoreMetadata in project bioformats by openmicroscopy.

the class VGSAMReader 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);
    in.seek(348);
    m.sizeX = in.readInt();
    m.sizeY = in.readInt();
    in.skipBytes(4);
    int bpp = in.readInt();
    addGlobalMeta("Bytes per pixel", bpp);
    m.pixelType = FormatTools.pixelTypeFromBytes(bpp, false, bpp == 4);
    m.littleEndian = false;
    m.sizeZ = 1;
    m.sizeC = 1;
    m.sizeT = 1;
    m.imageCount = 1;
    m.rgb = false;
    m.interleaved = false;
    m.dimensionOrder = "XYZCT";
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}

Example 67 with CoreMetadata

use of loci.formats.CoreMetadata in project bioformats by openmicroscopy.

the class VectraReader method initStandardMetadata.

// -- Internal BaseTiffReader API methods --
/* @see loci.formats.BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
    super.initStandardMetadata();
    ifds = tiffParser.getIFDs();
    thumbnailIFDs = null;
    for (IFD ifd : ifds) {
        tiffParser.fillInIFD(ifd);
    }
    // count number of channels
    CoreMetadata m = core.get(0);
    m.sizeC = 1;
    if (ifds.get(0).getSamplesPerPixel() == 1) {
        long width = ifds.get(0).getImageWidth();
        long height = ifds.get(0).getImageLength();
        int ifd = 1;
        while (ifds.get(ifd).getImageWidth() == width && ifds.get(ifd).getImageLength() == height) {
            m.sizeC++;
            ifd++;
        }
    }
    for (int start = m.sizeC + 1; start < ifds.size(); start += m.sizeC) {
        IFD ifd = ifds.get(start);
        if (ifd.getIFDIntValue(IFD.NEW_SUBFILE_TYPE) == 1) {
            pyramidDepth++;
        } else
            break;
    }
    int coreSize = ifds.size() - (pyramidDepth * (m.sizeC - 1));
    // repopulate core metadata
    core.clear();
    for (int s = 0; s < coreSize; s++) {
        CoreMetadata ms = new CoreMetadata(m);
        if (s == 0) {
            ms.resolutionCount = pyramidDepth;
        }
        core.add(ms);
    }
    for (int s = 0; s < core.size(); s++) {
        CoreMetadata ms = core.get(s);
        int index = getIFDIndex(s, 0);
        IFD ifd = ifds.get(index);
        PhotoInterp p = ifd.getPhotometricInterpretation();
        int samples = ifd.getSamplesPerPixel();
        ms.rgb = samples > 1 || p == PhotoInterp.RGB;
        ms.sizeX = (int) ifd.getImageWidth();
        ms.sizeY = (int) ifd.getImageLength();
        ms.sizeZ = 1;
        ms.sizeT = 1;
        if (ms.rgb) {
            ms.sizeC = samples;
        }
        ms.littleEndian = ifd.isLittleEndian();
        ms.indexed = p == PhotoInterp.RGB_PALETTE && (get8BitLookupTable() != null || get16BitLookupTable() != null);
        ms.imageCount = ms.sizeC / samples;
        ms.pixelType = ifd.getPixelType();
        ms.metadataComplete = true;
        ms.interleaved = false;
        ms.falseColor = false;
        ms.dimensionOrder = "XYCZT";
        ms.thumbnail = s != 0;
    }
}

Example 68 with CoreMetadata

use of loci.formats.CoreMetadata 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 69 with CoreMetadata

use of loci.formats.CoreMetadata 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 70 with CoreMetadata

use of loci.formats.CoreMetadata 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);
}