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

Example 31 with MetadataRetrieve

use of loci.formats.meta.MetadataRetrieve 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 32 with MetadataRetrieve

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

the class FormatTools method getFilename.

/**
 * @throws FormatException Never actually thrown.
 * @throws IOException Never actually thrown.
 */
public static String getFilename(int series, int image, IFormatReader r, String pattern, boolean padded) throws FormatException, IOException {
    MetadataStore store = r.getMetadataStore();
    MetadataRetrieve retrieve = store instanceof MetadataRetrieve ? (MetadataRetrieve) store : new DummyMetadata();
    return getFilename(series, image, retrieve, pattern, padded);
}

Example 33 with MetadataRetrieve

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

the class FormatWriter method setId.

// -- IFormatHandler API methods --
/**
 * Initializes a writer from the input file name.
 *
 * Initializes a {@link RandomAccessOutputStream} for the output
 * file and initializes the metadata for all the series using
 * {@link #setSeries(int)}.
 *
 *  @param id a {@link String} specifying the path to the file
 */
@Override
public void setId(String id) throws FormatException, IOException {
    if (id.equals(currentId))
        return;
    currentId = id;
    if (out != null) {
        out.close();
    }
    out = createOutputStream();
    MetadataRetrieve r = getMetadataRetrieve();
    initialized = new boolean[r.getImageCount()][];
    for (int i = 0; i < r.getImageCount(); i++) {
        initialized[i] = new boolean[getPlaneCount(i)];
    }
}

Example 34 with MetadataRetrieve

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

the class FormatWriter method checkParams.

// -- Helper methods --
/**
 * Ensure that the arguments that are being passed to saveBytes(...) are
 * valid.
 * @throws FormatException if any of the arguments is invalid.
 */
protected void checkParams(int no, byte[] buf, int x, int y, int w, int h) throws FormatException {
    MetadataRetrieve r = getMetadataRetrieve();
    MetadataTools.verifyMinimumPopulated(r, series);
    if (buf == null)
        throw new FormatException("Buffer cannot be null.");
    int z = r.getPixelsSizeZ(series).getValue().intValue();
    int t = r.getPixelsSizeT(series).getValue().intValue();
    int c = r.getChannelCount(series);
    int planes = z * c * t;
    if (no < 0)
        throw new FormatException(String.format("Plane index:%d must be >= 0", no));
    if (no >= planes) {
        throw new FormatException(String.format("Plane index:%d must be < %d", no, planes));
    }
    int sizeX = r.getPixelsSizeX(series).getValue().intValue();
    int sizeY = r.getPixelsSizeY(series).getValue().intValue();
    if (x < 0)
        throw new FormatException(String.format("X:%d must be >= 0", x));
    if (y < 0)
        throw new FormatException(String.format("Y:%d must be >= 0", y));
    if (x >= sizeX) {
        throw new FormatException(String.format("X:%d must be < %d", x, sizeX));
    }
    if (y >= sizeY) {
        throw new FormatException(String.format("Y:%d must be < %d", y, sizeY));
    }
    if (w <= 0)
        throw new FormatException(String.format("Width:%d must be > 0", w));
    if (h <= 0)
        throw new FormatException(String.format("Height:%d must be > 0", h));
    if (x + w > sizeX)
        throw new FormatException(String.format("(w:%d + x:%d) must be <= %d", w, x, sizeX));
    if (y + h > sizeY)
        throw new FormatException(String.format("(h:%d + y:%d) must be <= %d", h, y, sizeY));
    int pixelType = FormatTools.pixelTypeFromString(r.getPixelsType(series).toString());
    int bpp = FormatTools.getBytesPerPixel(pixelType);
    PositiveInteger samples = r.getChannelSamplesPerPixel(series, 0);
    if (samples == null)
        samples = new PositiveInteger(1);
    int minSize = bpp * w * h * samples.getValue();
    if (buf.length < minSize) {
        throw new FormatException("Buffer is too small; expected " + minSize + " bytes, got " + buf.length + " bytes.");
    }
    if (!DataTools.containsValue(getPixelTypes(compression), pixelType)) {
        throw new FormatException("Unsupported image type '" + FormatTools.getPixelTypeString(pixelType) + "'.");
    }
}

Example 35 with MetadataRetrieve

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

the class FormatWriter method isFullPlane.

/**
 * Returns true if the given rectangle coordinates correspond to a full
 * image in the given series.
 */
protected boolean isFullPlane(int x, int y, int w, int h) {
    MetadataRetrieve r = getMetadataRetrieve();
    int sizeX = r.getPixelsSizeX(series).getValue().intValue();
    int sizeY = r.getPixelsSizeY(series).getValue().intValue();
    return x == 0 && y == 0 && w == sizeX && h == sizeY;
}