Examples with MetadataStore loci.formats.meta.MetadataStore used on opensource projects

Example 81 with MetadataStore

use of loci.formats.meta.MetadataStore in project bioformats by openmicroscopy.

the class PCXReader 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("Reading file header");
    CoreMetadata m = core.get(0);
    m.littleEndian = true;
    in.order(isLittleEndian());
    in.seek(1);
    int version = in.read();
    in.skipBytes(1);
    int bitsPerPixel = in.read();
    int xMin = in.readShort();
    int yMin = in.readShort();
    int xMax = in.readShort();
    int yMax = in.readShort();
    m.sizeX = xMax - xMin;
    m.sizeY = yMax - yMin;
    in.skipBytes(version == 5 ? 53 : 51);
    nColorPlanes = in.read();
    bytesPerLine = in.readShort();
    int paletteType = in.readShort();
    offset = in.getFilePointer() + 58;
    if (version == 5 && nColorPlanes == 1) {
        in.seek(in.length() - 768);
        lut = new byte[3][256];
        for (int i = 0; i < lut[0].length; i++) {
            for (int j = 0; j < lut.length; j++) {
                lut[j][i] = in.readByte();
            }
        }
        m.indexed = true;
    }
    addGlobalMeta("Palette type", paletteType);
    m.sizeZ = 1;
    m.sizeT = 1;
    m.sizeC = nColorPlanes;
    m.rgb = nColorPlanes > 1;
    m.imageCount = 1;
    m.pixelType = FormatTools.UINT8;
    m.dimensionOrder = "XYCZT";
    m.interleaved = false;
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}

Example 82 with MetadataStore

use of loci.formats.meta.MetadataStore in project bioformats by openmicroscopy.

the class TextReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    // read file into memory
    LOGGER.info("Reading file");
    List<String> lines = readFile(id);
    // parse file header
    LOGGER.info("Parsing file header");
    final int headerRows = parseFileHeader(lines);
    LOGGER.info("Creating images");
    // allocate memory for image data
    // no Z or T for now
    final int sizeZ = 1, sizeT = 1;
    final int sizeC = channels.length;
    final int imageCount = sizeZ * sizeC * sizeT;
    final int planeSize = sizeX * sizeY;
    data = new float[imageCount][planeSize];
    // flag all values as missing by default
    for (int i = 0; i < imageCount; i++) Arrays.fill(data[i], Float.NaN);
    // read data into float array
    parseTableData(lines, headerRows);
    LOGGER.info("Populating metadata");
    // populate core metadata
    populateCoreMetadata(sizeX, sizeY, sizeZ, sizeC, sizeT);
    // populate OME metadata
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}

Example 83 with MetadataStore

use of loci.formats.meta.MetadataStore in project bioformats by openmicroscopy.

the class PGMReader 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);
    // Plain     Raw
    // B&W            P1      P4
    // Grayscale      P2      P5
    // RGB            P3      P6
    final String magic = in.readString(2);
    rawBits = magic.equals("P4") || magic.equals("P5") || magic.equals("P6");
    m.sizeC = (magic.equals("P3") || magic.equals("P6")) ? 3 : 1;
    final boolean isBlackAndWhite = magic.equals("P1") || magic.equals("P4");
    StreamTokenizer st = new StreamTokenizer(in);
    st.commentChar('#');
    int token;
    token = st.nextToken();
    m.sizeX = (int) st.nval;
    token = st.nextToken();
    m.sizeY = (int) st.nval;
    if (!isBlackAndWhite) {
        token = st.nextToken();
        final int max = (int) st.nval;
        if (max > 255)
            m.pixelType = FormatTools.UINT16;
        else
            m.pixelType = FormatTools.UINT8;
    }
    // After reading the 2 or 3 header entries, it is possible that there are
    // multiple comments before the actual pixel data.
    Byte c;
    do {
        c = in.readByte();
        if (c == 35) {
            // Found a # for comment
            do {
                c = in.readByte();
            } while (// comment only ends after CR or LF
            c != 13 && c != 10);
        }
    } while (c == 32 || c == 13 || c == 10 || c == 9 || c == 11 || c == 12);
    // space      CR         LF         TAB       VT         FF
    offset = in.getFilePointer() - 1;
    addGlobalMeta("Black and white", isBlackAndWhite);
    m.rgb = getSizeC() == 3;
    m.dimensionOrder = "XYCZT";
    m.littleEndian = true;
    m.interleaved = true;
    m.sizeZ = 1;
    m.sizeT = 1;
    m.indexed = false;
    m.falseColor = false;
    // This may not be true. Multiple images were added to the netpbm
    // formats in July 2000.
    m.imageCount = 1;
    // 1. the comments are being ignored;
    // 2. we may be missing some images (allowed in raw)
    m.metadataComplete = false;
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}

Example 84 with MetadataStore

use of loci.formats.meta.MetadataStore in project bioformats by openmicroscopy.

the class ImageInfo method readCoreMetadata.

public void readCoreMetadata() throws FormatException, IOException {
    // skip core metadata printout
    if (!doCore)
        return;
    // read basic metadata
    LOGGER.info("");
    LOGGER.info("Reading core metadata");
    LOGGER.info("{} = {}", stitch ? "File pattern" : "filename", stitch ? id : reader.getCurrentFile());
    if (map != null)
        LOGGER.info("Mapped filename = {}", map);
    if (usedFiles) {
        String[] used = reader.getUsedFiles();
        boolean usedValid = used != null && used.length > 0;
        if (usedValid) {
            for (int u = 0; u < used.length; u++) {
                if (used[u] == null) {
                    usedValid = false;
                    break;
                }
            }
        }
        if (!usedValid) {
            LOGGER.warn("************ invalid used files list ************");
        }
        if (used == null) {
            LOGGER.info("Used files = null");
        } else if (used.length == 0) {
            LOGGER.info("Used files = []");
        } else if (used.length > 1) {
            LOGGER.info("Used files:");
            for (int u = 0; u < used.length; u++) LOGGER.info("\t{}", used[u]);
        } else if (!id.equals(used[0])) {
            LOGGER.info("Used files = [{}]", used[0]);
        }
    }
    int seriesCount = reader.getSeriesCount();
    LOGGER.info("Series count = {}", seriesCount);
    MetadataStore ms = reader.getMetadataStore();
    MetadataRetrieve mr = ms instanceof MetadataRetrieve ? (MetadataRetrieve) ms : null;
    for (int j = 0; j < seriesCount; j++) {
        reader.setSeries(j);
        // read basic metadata for series #i
        int imageCount = reader.getImageCount();
        int resolutions = reader.getResolutionCount();
        boolean rgb = reader.isRGB();
        int sizeX = reader.getSizeX();
        int sizeY = reader.getSizeY();
        int sizeZ = reader.getSizeZ();
        int sizeC = reader.getSizeC();
        int sizeT = reader.getSizeT();
        int pixelType = reader.getPixelType();
        int validBits = reader.getBitsPerPixel();
        int effSizeC = reader.getEffectiveSizeC();
        int rgbChanCount = reader.getRGBChannelCount();
        boolean indexed = reader.isIndexed();
        boolean falseColor = reader.isFalseColor();
        byte[][] table8 = reader.get8BitLookupTable();
        short[][] table16 = reader.get16BitLookupTable();
        Modulo moduloZ = reader.getModuloZ();
        Modulo moduloC = reader.getModuloC();
        Modulo moduloT = reader.getModuloT();
        int thumbSizeX = reader.getThumbSizeX();
        int thumbSizeY = reader.getThumbSizeY();
        int tileSizeX = reader.getOptimalTileWidth();
        int tileSizeY = reader.getOptimalTileHeight();
        boolean little = reader.isLittleEndian();
        String dimOrder = reader.getDimensionOrder();
        boolean orderCertain = reader.isOrderCertain();
        boolean thumbnail = reader.isThumbnailSeries();
        boolean interleaved = reader.isInterleaved();
        boolean metadataComplete = reader.isMetadataComplete();
        // output basic metadata for series #i
        String seriesName = mr == null ? null : mr.getImageName(j);
        LOGGER.info("Series #{}{}{}:", new Object[] { j, seriesName == null ? " " : " -- ", seriesName == null ? "" : seriesName });
        if (flat == false && resolutions > 1) {
            LOGGER.info("\tResolutions = {}", resolutions);
            for (int i = 0; i < resolutions; i++) {
                reader.setResolution(i);
                LOGGER.info("\t\tsizeX[{}] = {}", i, reader.getSizeX());
            }
            reader.setResolution(0);
        }
        LOGGER.info("\tImage count = {}", imageCount);
        LOGGER.info("\tRGB = {} ({}) {}", new Object[] { rgb, rgbChanCount, merge ? "(merged)" : separate ? "(separated)" : "" });
        if (rgb != (rgbChanCount != 1)) {
            LOGGER.warn("\t************ RGB mismatch ************");
        }
        LOGGER.info("\tInterleaved = {}", interleaved);
        StringBuilder sb = new StringBuilder();
        sb.append("\tIndexed = ");
        sb.append(indexed);
        sb.append(" (");
        sb.append(!falseColor);
        sb.append(" color");
        if (table8 != null) {
            sb.append(", 8-bit LUT: ");
            sb.append(table8.length);
            sb.append(" x ");
            sb.append(table8[0] == null ? "null" : "" + table8[0].length);
        }
        if (table16 != null) {
            sb.append(", 16-bit LUT: ");
            sb.append(table16.length);
            sb.append(" x ");
            sb.append(table16[0] == null ? "null" : "" + table16[0].length);
        }
        sb.append(")");
        LOGGER.info(sb.toString());
        if (table8 != null && table16 != null) {
            LOGGER.warn("\t************ multiple LUTs ************");
        }
        LOGGER.info("\tWidth = {}", sizeX);
        LOGGER.info("\tHeight = {}", sizeY);
        printDimension("SizeZ", sizeZ, sizeZ, moduloZ);
        printDimension("SizeT", sizeT, sizeT, moduloT);
        printDimension("SizeC", sizeC, effSizeC, moduloC);
        if (imageCount != sizeZ * effSizeC * sizeT) {
            LOGGER.info("\t************ ZCT mismatch ************");
        }
        LOGGER.info("\tTile size = {} x {}", tileSizeX, tileSizeY);
        LOGGER.info("\tThumbnail size = {} x {}", thumbSizeX, thumbSizeY);
        LOGGER.info("\tEndianness = {}", little ? "intel (little)" : "motorola (big)");
        LOGGER.info("\tDimension order = {} ({})", dimOrder, orderCertain ? "certain" : "uncertain");
        LOGGER.info("\tPixel type = {}", FormatTools.getPixelTypeString(pixelType));
        LOGGER.info("\tValid bits per pixel = {}", validBits);
        LOGGER.info("\tMetadata complete = {}", metadataComplete);
        LOGGER.info("\tThumbnail series = {}", thumbnail);
        if (doMeta) {
            LOGGER.info("\t-----");
            int[] indices;
            if (imageCount > 6) {
                int q = imageCount / 2;
                indices = new int[] { 0, q - 2, q - 1, q, q + 1, q + 2, imageCount - 1 };
            } else if (imageCount > 2) {
                indices = new int[] { 0, imageCount / 2, imageCount - 1 };
            } else if (imageCount > 1)
                indices = new int[] { 0, 1 };
            else
                indices = new int[] { 0 };
            int[][] zct = new int[indices.length][];
            int[] indices2 = new int[indices.length];
            sb.setLength(0);
            for (int i = 0; i < indices.length; i++) {
                zct[i] = reader.getZCTCoords(indices[i]);
                indices2[i] = reader.getIndex(zct[i][0], zct[i][1], zct[i][2]);
                sb.append("\tPlane #");
                sb.append(indices[i]);
                sb.append(" <=> Z ");
                sb.append(zct[i][0]);
                sb.append(", C ");
                sb.append(zct[i][1]);
                sb.append(", T ");
                sb.append(zct[i][2]);
                if (indices[i] != indices2[i]) {
                    sb.append(" [mismatch: ");
                    sb.append(indices2[i]);
                    sb.append("]");
                    sb.append(NEWLINE);
                } else
                    sb.append(NEWLINE);
            }
            LOGGER.info(sb.toString());
        }
    }
}

Example 85 with MetadataStore

use of loci.formats.meta.MetadataStore in project bioformats by openmicroscopy.

the class FormatReader method setId.

/**
 * Initializes a reader from the input file name.
 *
 * Calls {@link #initFile(String id)} to initializes the input file, reads
 * all of the metadata and sets the reader up for reading planes.
 * The performance of this method depends on the format and can be up to
 * several minutes for large file sets.
 *
 *  @param id a {@link String} specifying the path to the file
 */
@Override
public void setId(String id) throws FormatException, IOException {
    LOGGER.debug("{} initializing {}", this.getClass().getSimpleName(), id);
    if (currentId == null || !new Location(id).getAbsolutePath().equals(new Location(currentId).getAbsolutePath())) {
        initFile(id);
        MetadataStore store = getMetadataStore();
        if (saveOriginalMetadata) {
            if (store instanceof OMEXMLMetadata) {
                setupService();
                Hashtable<String, Object> allMetadata = new Hashtable<String, Object>();
                allMetadata.putAll(metadata);
                for (int series = 0; series < getSeriesCount(); series++) {
                    String name = "Series " + series;
                    try {
                        String realName = ((IMetadata) store).getImageName(series);
                        if (realName != null && realName.trim().length() != 0) {
                            name = realName;
                        }
                    } catch (Exception e) {
                    }
                    setSeries(series);
                    MetadataTools.merge(getSeriesMetadata(), allMetadata, name + " ");
                }
                setSeries(0);
                service.populateOriginalMetadata((OMEXMLMetadata) store, allMetadata);
            }
        }
        if (store instanceof OMEXMLMetadata) {
            ((OMEXMLMetadata) store).resolveReferences();
            setupService();
            if (getMetadataOptions().isValidate()) {
                try {
                    String omexml = service.getOMEXML((MetadataRetrieve) store);
                    service.validateOMEXML(omexml);
                } catch (ServiceException | NullPointerException e) {
                    LOGGER.warn("OMEXMLService unable to create OME-XML metadata object.", e);
                }
            }
            for (int series = 0; series < getSeriesCount(); series++) {
                setSeries(series);
                if (getModuloZ().length() > 1 || getModuloC().length() > 1 || getModuloT().length() > 1) {
                    service.addModuloAlong((OMEXMLMetadata) store, core.get(series), series);
                }
            }
            setSeries(0);
        }
    }
}