Examples with Region loci.common.Region used on opensource projects

Example 16 with Region

use of loci.common.Region in project bioformats by openmicroscopy.

the class JPEGTurboServiceImpl method getTile.

@Override
public byte[] getTile(byte[] buf, int xCoordinate, int yCoordinate, int width, int height) throws IOException {
    Region image = new Region(xCoordinate, yCoordinate, width, height);
    int bufX = 0;
    int bufY = 0;
    int outputRowLen = width * 3;
    Region intersection = null;
    Region tileBoundary = new Region(0, 0, 0, 0);
    byte[] tile = null;
    for (int row = 0; row < yTiles; row++) {
        tileBoundary.height = row < yTiles - 1 ? tileDim : imageHeight - (tileDim * row);
        tileBoundary.y = row * tileDim;
        for (int col = 0; col < xTiles; col++) {
            tileBoundary.x = col * tileDim;
            tileBoundary.width = col < xTiles - 1 ? tileDim : imageWidth - (tileDim * col);
            if (tileBoundary.intersects(image)) {
                intersection = image.intersection(tileBoundary);
                tile = getTile(col, row);
                int rowLen = 3 * (int) Math.min(tileBoundary.width, intersection.width);
                int outputOffset = bufY * outputRowLen + bufX;
                int intersectionX = 0;
                if (tileBoundary.x < image.x) {
                    intersectionX = image.x - tileBoundary.x;
                }
                for (int trow = 0; trow < intersection.height; trow++) {
                    int realRow = trow + intersection.y - tileBoundary.y;
                    int inputOffset = 3 * (realRow * tileDim + intersectionX);
                    System.arraycopy(tile, inputOffset, buf, outputOffset, rowLen);
                    outputOffset += outputRowLen;
                }
                bufX += rowLen;
            }
        }
        if (intersection != null) {
            bufX = 0;
            bufY += intersection.height;
        }
        if (bufY >= height) {
            break;
        }
    }
    return buf;
}

Example 17 with Region

use of loci.common.Region in project bioformats by openmicroscopy.

the class TiffWriter method saveBytes.

/**
 * Saves the given image to the specified series in the current file.
 * The IFD hashtable allows specification of TIFF parameters such as bit
 * depth, compression and units.
 */
public void saveBytes(int no, byte[] buf, IFD ifd, int x, int y, int w, int h) throws IOException, FormatException {
    if (checkParams)
        checkParams(no, buf, x, y, w, h);
    if (ifd == null)
        ifd = new IFD();
    MetadataRetrieve retrieve = getMetadataRetrieve();
    int type = FormatTools.pixelTypeFromString(retrieve.getPixelsType(series).toString());
    int index = no;
    int imageWidth = retrieve.getPixelsSizeX(series).getValue().intValue();
    int imageHeight = retrieve.getPixelsSizeY(series).getValue().intValue();
    int currentTileSizeX = getTileSizeX();
    int currentTileSizeY = getTileSizeY();
    if (currentTileSizeX != imageWidth || currentTileSizeY != imageHeight) {
        ifd.put(new Integer(IFD.TILE_WIDTH), new Long(currentTileSizeX));
        ifd.put(new Integer(IFD.TILE_LENGTH), new Long(currentTileSizeY));
    }
    if (currentTileSizeX < w || currentTileSizeY < h) {
        int numTilesX = (w + (x % currentTileSizeX) + currentTileSizeX - 1) / currentTileSizeX;
        int numTilesY = (h + (y % currentTileSizeY) + currentTileSizeY - 1) / currentTileSizeY;
        for (int yTileIndex = 0; yTileIndex < numTilesY; yTileIndex++) {
            for (int xTileIndex = 0; xTileIndex < numTilesX; xTileIndex++) {
                Region tileParams = new Region();
                tileParams.width = xTileIndex < numTilesX - 1 ? currentTileSizeX - (x % currentTileSizeX) : w - (currentTileSizeX * xTileIndex);
                tileParams.height = yTileIndex < numTilesY - 1 ? currentTileSizeY - (y % currentTileSizeY) : h - (currentTileSizeY * yTileIndex);
                tileParams.x = x + (xTileIndex * currentTileSizeX) - (xTileIndex > 0 ? (x % currentTileSizeX) : 0);
                tileParams.y = y + (yTileIndex * currentTileSizeY) - (yTileIndex > 0 ? (y % currentTileSizeY) : 0);
                byte[] tileBuf = getTile(buf, tileParams, new Region(x, y, w, h));
                // This operation is synchronized
                synchronized (this) {
                    // This operation is synchronized against the TIFF saver.
                    synchronized (tiffSaver) {
                        index = prepareToWriteImage(no, tileBuf, ifd, tileParams.x, tileParams.y, tileParams.width, tileParams.height);
                        if (index == -1) {
                            return;
                        }
                    }
                }
                tiffSaver.writeImage(tileBuf, ifd, index, type, tileParams.x, tileParams.y, tileParams.width, tileParams.height, no == getPlaneCount() - 1 && getSeries() == retrieve.getImageCount() - 1);
            }
        }
    } else {
        // This operation is synchronized
        synchronized (this) {
            // This operation is synchronized against the TIFF saver.
            synchronized (tiffSaver) {
                index = prepareToWriteImage(no, buf, ifd, x, y, w, h);
                if (index == -1) {
                    return;
                }
            }
        }
        tiffSaver.writeImage(buf, ifd, index, type, x, y, w, h, no == getPlaneCount() - 1 && getSeries() == retrieve.getImageCount() - 1);
    }
}