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

Example 6 with MetadataRetrieve

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

the class ImageConverter method convertTilePlane.

/**
 * Convert the specified plane as a set of tiles, using the specified writer.
 * @param writer the {@link loci.formats.IFormatWriter} to use for writing the plane
 * @param index the index of the plane to convert in the input file
 * @param outputIndex the index of the plane to convert in the output file
 * @param currentFile the file name or pattern being written to
 * @return the time at which conversion started, in milliseconds
 * @throws FormatException
 * @throws IOException
 */
private long convertTilePlane(IFormatWriter writer, int index, int outputIndex, String currentFile) throws FormatException, IOException {
    int w = reader.getOptimalTileWidth();
    int h = reader.getOptimalTileHeight();
    if (saveTileWidth > 0 && saveTileWidth <= width) {
        w = saveTileWidth;
    }
    if (saveTileHeight > 0 && saveTileHeight <= height) {
        h = saveTileHeight;
    }
    if (firstTile) {
        LOGGER.info("Tile size = {} x {}", w, h);
        firstTile = false;
    }
    int nXTiles = width / w;
    int nYTiles = height / h;
    if (nXTiles * w != width) {
        nXTiles++;
    }
    if (nYTiles * h != height) {
        nYTiles++;
    }
    IFD ifd = new IFD();
    ifd.put(IFD.TILE_WIDTH, w);
    ifd.put(IFD.TILE_LENGTH, h);
    Long m = null;
    for (int y = 0; y < nYTiles; y++) {
        for (int x = 0; x < nXTiles; x++) {
            int tileX = xCoordinate + x * w;
            int tileY = yCoordinate + y * h;
            int tileWidth = x < nXTiles - 1 ? w : width - (w * x);
            int tileHeight = y < nYTiles - 1 ? h : height - (h * y);
            byte[] buf = reader.openBytes(index, tileX, tileY, tileWidth, tileHeight);
            String tileName = FormatTools.getTileFilename(x, y, y * nXTiles + x, currentFile);
            if (!currentFile.equals(tileName)) {
                int nTileRows = getTileRows(currentFile);
                int nTileCols = getTileColumns(currentFile);
                int sizeX = nTileCols == 1 ? width : tileWidth;
                int sizeY = nTileRows == 1 ? height : tileHeight;
                MetadataRetrieve retrieve = writer.getMetadataRetrieve();
                if (retrieve instanceof MetadataStore) {
                    ((MetadataStore) retrieve).setPixelsSizeX(new PositiveInteger(sizeX), reader.getSeries());
                    ((MetadataStore) retrieve).setPixelsSizeY(new PositiveInteger(sizeY), reader.getSeries());
                }
                writer.close();
                writer.setMetadataRetrieve(retrieve);
                writer.setId(tileName);
                if (compression != null)
                    writer.setCompression(compression);
                outputIndex = 0;
                if (nextOutputIndex.containsKey(tileName)) {
                    outputIndex = nextOutputIndex.get(tileName);
                }
                nextOutputIndex.put(tileName, outputIndex + 1);
                if (nTileRows > 1) {
                    tileY = 0;
                }
                if (nTileCols > 1) {
                    tileX = 0;
                }
            }
            autoscalePlane(buf, index);
            applyLUT(writer);
            if (m == null) {
                m = System.currentTimeMillis();
            }
            if (writer instanceof TiffWriter) {
                ((TiffWriter) writer).saveBytes(outputIndex, buf, ifd, tileX, tileY, tileWidth, tileHeight);
            } else if (writer instanceof ImageWriter) {
                IFormatWriter baseWriter = ((ImageWriter) writer).getWriter(out);
                if (baseWriter instanceof TiffWriter) {
                    ((TiffWriter) baseWriter).saveBytes(outputIndex, buf, ifd, tileX, tileY, tileWidth, tileHeight);
                }
            }
        }
    }
    return m;
}

Example 7 with MetadataRetrieve

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

the class ImageInfo method printOMEXML.

public void printOMEXML() throws MissingLibraryException, ServiceException {
    LOGGER.info("");
    MetadataStore ms = reader.getMetadataStore();
    if (baseReader instanceof ImageReader) {
        baseReader = ((ImageReader) baseReader).getReader();
    }
    OMEXMLService service;
    try {
        ServiceFactory factory = new ServiceFactory();
        service = factory.getInstance(OMEXMLService.class);
    } catch (DependencyException de) {
        throw new MissingLibraryException(OMEXMLServiceImpl.NO_OME_XML_MSG, de);
    }
    String version = service.getOMEXMLVersion(ms);
    if (version == null)
        LOGGER.info("Generating OME-XML");
    else {
        LOGGER.info("Generating OME-XML (schema version {})", version);
    }
    if (ms instanceof MetadataRetrieve) {
        if (omexmlOnly) {
            DebugTools.setRootLevel("INFO");
        }
        String xml = service.getOMEXML((MetadataRetrieve) ms);
        LOGGER.info("{}", XMLTools.indentXML(xml, xmlSpaces, true));
        if (omexmlOnly) {
            DebugTools.setRootLevel("OFF");
        }
    } else {
        LOGGER.info("The metadata could not be converted to OME-XML.");
        if (omexmlVersion == null) {
            LOGGER.info("The OME-XML Java library is probably not available.");
        } else {
            LOGGER.info("{} is probably not a legal schema version.", omexmlVersion);
        }
    }
}

Example 8 with MetadataRetrieve

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

the class FormatTools method convert.

/**
 * Convenience method for writing all of the images and metadata obtained
 * from the specified IFormatReader into the specified IFormatWriter.
 *
 * It is required that setId(String) be called on the IFormatReader
 * object before it is passed to convert(...).  setMetadataStore(...)
 * should also have been called with an appropriate instance of IMetadata.
 *
 * The setId(String) method must not be called on the IFormatWriter
 * object; this is taken care of internally.  Additionally, the
 * setMetadataRetrieve(...) method in IFormatWriter should not be called.
 *
 * @param input the pre-initialized IFormatReader used for reading data.
 * @param output the uninitialized IFormatWriter used for writing data.
 * @param outputFile the full path name of the output file to be created.
 * @throws FormatException if there is a general problem reading from or
 * writing to one of the files.
 * @throws IOException if there is an I/O-related error.
 */
public static void convert(IFormatReader input, IFormatWriter output, String outputFile) throws FormatException, IOException {
    MetadataStore store = input.getMetadataStore();
    MetadataRetrieve meta = null;
    try {
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        meta = service.asRetrieve(store);
    } catch (DependencyException de) {
        throw new MissingLibraryException(OMEXMLServiceImpl.NO_OME_XML_MSG, de);
    }
    output.setMetadataRetrieve(meta);
    output.setId(outputFile);
    for (int series = 0; series < input.getSeriesCount(); series++) {
        input.setSeries(series);
        output.setSeries(series);
        byte[] buf = new byte[getPlaneSize(input)];
        for (int image = 0; image < input.getImageCount(); image++) {
            input.openBytes(image, buf);
            output.saveBytes(image, buf);
        }
    }
    input.close();
    output.close();
}

Example 9 with MetadataRetrieve

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

the class LociFunctions method getPixelsPhysicalSizeX.

public void getPixelsPhysicalSizeX(Double[] sizeX) {
    int imageIndex = r.getSeries();
    MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore();
    Length x = retrieve.getPixelsPhysicalSizeX(imageIndex);
    if (x != null) {
        sizeX[0] = x.value(UNITS.MICROMETER).doubleValue();
    }
    if (sizeX[0] == null)
        sizeX[0] = new Double(Double.NaN);
}

Example 10 with MetadataRetrieve

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

the class LociFunctions method getPixelsTimeIncrement.

public void getPixelsTimeIncrement(Double[] sizeT) {
    int imageIndex = r.getSeries();
    MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore();
    sizeT[0] = retrieve.getPixelsTimeIncrement(imageIndex).value(UNITS.SECOND).doubleValue();
    if (sizeT[0] == null)
        sizeT[0] = new Double(Double.NaN);
}