/**
* Read a plane and update the pixels checksum
*
* @param size Sizes of the Pixels set.
* @param z The Z-section offset to write to.
* @param c The channel offset to write to.
* @param t The timepoint offset to write to.
* @param bytesPerPixel Number of bytes per pixel.
* @param fileName Name of the file.
* @param md Current Pixels set message digest.
* @throws FormatException If there is an error reading Pixel data via Bio-Formats.
* @throws IOException If there is an I/O error reading Pixel data via Bio-Formats.
*/
private void parseDataByPlane(
ImportSize size, int z, int c, int t, int bytesPerPixel, String fileName, MessageDigest md)
throws FormatException, IOException {
int tileHeight = reader.getOptimalTileHeight();
int tileWidth = reader.getOptimalTileWidth();
int planeNumber, x, y, w, h;
for (int tileOffsetY = 0;
tileOffsetY < (size.sizeY + tileHeight - 1) / tileHeight;
tileOffsetY++) {
for (int tileOffsetX = 0;
tileOffsetX < (size.sizeX + tileWidth - 1) / tileWidth;
tileOffsetX++) {
x = tileOffsetX * tileWidth;
y = tileOffsetY * tileHeight;
w = tileWidth;
h = tileHeight;
if ((x + tileWidth) > size.sizeX) {
w = size.sizeX - x;
}
if ((y + tileHeight) > size.sizeY) {
h = size.sizeY - y;
}
int bytesToRead = w * h * bytesPerPixel;
if (arrayBuf.length != bytesToRead) {
arrayBuf = new byte[bytesToRead];
}
planeNumber = reader.getIndex(z, c, t);
if (log.isDebugEnabled()) {
log.debug(
String.format(
"Plane:%d X:%d Y:%d TileWidth:%d TileHeight:%d " + "arrayBuf.length:%d",
planeNumber, x, y, w, h, arrayBuf.length));
}
arrayBuf = reader.openBytes(planeNumber, arrayBuf, x, y, w, h);
try {
md.update(arrayBuf);
} catch (Exception e) {
// This better not happen. :)
throw new RuntimeException(e);
}
}
}
}
