nYTiles = nYTiles + 1
for y in range(nYTiles):
for x in range(nXTiles):
# Calculate the correct size and offset for each tile
tileX = x * tileSizeX
tileY = y * tileSizeY
effTileSizeX = tileSizeX * currentScale
if ((tileX * currentScale) + effTileSizeX) >= width:
effTileSizeX = width - (tileX * currentScale)
effTileSizeY = tileSizeY * currentScale
if ((tileY * currentScale) + effTileSizeY) >= height:
effTileSizeY = height - (tileY * currentScale)
# Read the tile, create the downsampled version and then write to output
tile = reader.openBytes(image, tileX * currentScale, tileY * currentScale, effTileSizeX, effTileSizeY)
downsample = scaler.downsample(tile, effTileSizeX, effTileSizeY, currentScale, FormatTools.getBytesPerPixel(type), reader.isLittleEndian(),
FormatTools.isFloatingPoint(type), reader.getRGBChannelCount(), reader.isInterleaved())
writer.saveBytes(image, downsample, tileX, tileY, effTileSizeX / currentScale, effTileSizeY / currentScale)
writer.close();
reader.close();
IJ.log("Done")
options = ImporterOptions()
options.setColorMode(ImporterOptions.COLOR_MODE_COMPOSITE)
options.setId(outFile)
options.setSeriesOn(2, True);
imps = BF.openImagePlus(options)
for imp in imps:
imp.show()
for i in range(resolutions):
divScale = Math.pow(scale, i + 1)
omeMeta.setResolutionSizeX(PositiveInteger(int(reader.getSizeX() / divScale)), 0, i + 1)
omeMeta.setResolutionSizeY(PositiveInteger(int(reader.getSizeY() / divScale)), 0, i + 1)
# setup writer
writer = OMETiffWriter()
writer.setMetadataRetrieve(omeMeta)
writer.setId(outFile)
type = reader.getPixelType()
# read and write main image
img = reader.openBytes(0)
writer.saveBytes(0, img)
# create ImageScaler for downsampling
scaler = SimpleImageScaler()
# generate downsampled resolutions and write to output
for i in range(resolutions):
writer.setResolution(i + 1)
x = omeMeta.getResolutionSizeX(0, i + 1).getValue()
y = omeMeta.getResolutionSizeY(0, i + 1).getValue()
downsample = scaler.downsample(img, reader.getSizeX(), reader.getSizeY(), Math.pow(scale, i + 1),
FormatTools.getBytesPerPixel(type), reader.isLittleEndian(),
FormatTools.isFloatingPoint(type), reader.getRGBChannelCount(),
reader.isInterleaved())
writer.saveBytes(0, downsample)
writer.close()
reader.close()
