+ * Create an OME-Zarr file writer as described by version 0.4 of the specifications of the + * Next-generation file formats (NGFF). + *
+ *+ * Use a {@link Builder} to create an instance of this class. + *
+ *+ * This class is thread-safe but already uses concurrency internally to write tiles. + *
+ *+ * This writer has to be {@link #close() closed} once no longer used. + *
+ */ +public class OMEZarrWriter implements AutoCloseable { + + private static final Logger logger = LoggerFactory.getLogger(OMEZarrWriter.class); + private final ImageServer+ * Write the entire image in a background thread. + *
+ *+ * The image will be written from an internal pool of thread, so this function may + * return before the image is actually written. + *
+ */ + public void writeImage() { + for (TileRequest tileRequest: server.getTileRequestManager().getAllTileRequests()) { + writeTile(tileRequest); + } + } + + /** + *+ * Write the provided tile in a background thread. + *
+ *+ * The tile will be written from an internal pool of thread, so this function may + * return before the tile is actually written. + *
+ *+ * Note that the image server used internally by this writer may not be the one given in + * {@link Builder#Builder(ImageServer, String)}. Therefore, the {@link ImageServer#getTileRequestManager() TileRequestManager} + * of the internal image server may be different from the one of the provided image server, + * so functions like {@link TileRequestManager#getAllTileRequests()} may not return the expected tiles. + * Use the {@link ImageServer#getTileRequestManager() TileRequestManager} of {@link #getReaderServer()} + * to get accurate tiles. + *
+ * + * @param tileRequest the tile to write + */ + public void writeTile(TileRequest tileRequest) { + executorService.execute(() -> { + try { + levelArrays.get(tileRequest.getLevel()).write( + getData(server.readRegion(tileRequest.getRegionRequest())), + getDimensionsOfTile(tileRequest), + getOffsetsOfTile(tileRequest) + ); + } catch (Exception e) { + logger.error("Error when writing tile", e); + } + }); + } + + /** + * + *+ * Get the image server used internally by this writer to read the tiles. It can be + * different from the one given in {@link Builder#Builder(ImageServer, String)}. + *
+ *+ * This function can be useful to get information like the tiles used by this server + * (for example when using the {@link #writeTile(TileRequest)} function). + *
+ * + * @return the image server used internally by this writer to read the tiles + */ + public ImageServer+ * Enable the creation of a pyramidal image with the provided downsamples. The levels corresponding + * to the provided downsamples will be automatically generated. + *
+ *+ * If this function is not called (or if it is called with no parameters), the downsamples of + * the provided image server will be used instead. + *
+ * + * @param downsamples the downsamples of the pyramid to generate + * @return this builder + */ + public Builder setDownsamples(double... downsamples) { + this.downsamples = downsamples; + return this; + } + + /** + *+ * In Zarr files, data is stored in chunks. This parameter defines the maximum number + * of chunks on the x,y, and z dimensions. By default, this value is set to 50. + *
+ *+ * Use a negative value to not define any maximum number of chunks. + *
+ * + * @param maxNumberOfChunks the maximum number of chunks on the x,y, and z dimensions + * @return this builder + */ + public Builder setMaxNumberOfChunksOnEachSpatialDimension(int maxNumberOfChunks) { + this.maxNumberOfChunks = maxNumberOfChunks; + return this; + } + + /** + *+ * In Zarr files, data is stored in chunks. This parameter defines the size + * of chunks on the x dimension. By default, this value is set to 512. + *
+ *+ * Use a negative value to use the tile width of the provided image server. + *
+ *+ * The provided tile width may not be used if this implies creating more chunks + * than the value given in {@link #setMaxNumberOfChunksOnEachSpatialDimension(int)}. + *
+ * + * @param tileWidth the width each chunk should have + * @return this builder + */ + public Builder setTileWidth(int tileWidth) { + this.tileWidth = tileWidth; + return this; + } + + /** + *+ * In Zarr files, data is stored in chunks. This parameter defines the size + * of chunks on the y dimension. By default, this value is set to 512. + *
+ *+ * Use a negative value to use the tile height of the provided image server. + *
+ *+ * The provided tile height may not be used if this implies creating more chunks + * than the value given in {@link #setMaxNumberOfChunksOnEachSpatialDimension(int)}. + *
+ * + * @param tileHeight the height each chunk should have + * @return this builder + */ + public Builder setTileHeight(int tileHeight) { + this.tileHeight = tileHeight; + return this; + } + + /** + * Create a new instance of {@link OMEZarrWriter}. This will also + * create an empty image on the provided path. + * + * @return the new {@link OMEZarrWriter} + * @throws IOException when the empty image cannot be created. This can happen + * if the provided path is incorrect or if the user doesn't have enough permissions + */ + public OMEZarrWriter build() throws IOException { + return new OMEZarrWriter(this); + } + } + + private static int getChunkSize(int tileSize, int maxNumberOfChunks, int imageSize) { + return maxNumberOfChunks > 0 ? + Math.max(tileSize, imageSize / maxNumberOfChunks) : + tileSize; + } + + private static Map