# Convert the main image for y in range(nYTiles): for x in range(nXTiles): writer.setResolution(0); # The x and y coordinates for the current tile tileX = x * tileSizeX; tileY = y * tileSizeY; effTileSizeX = tileSizeX if (tileX + tileSizeX) >= width: effTileSizeX = width - tileX effTileSizeY = tileSizeY if (tileY + tileSizeY) >= height: effTileSizeY = height - tileY # Read tiles from the input file and write them to the output OME-Tiff buf = reader.openBytes(image, tileX, tileY, effTileSizeX, effTileSizeY) writer.saveBytes(image, buf, tileX, tileY, effTileSizeX, effTileSizeY) # Create the downsampled resolutions and write to output for i in range(resolutions): currentScale = int(Math.pow(scale, i + 1)) writer.setResolution(i + 1) resolutionWidth = width / currentScale resolutionHeight = height / currentScale nXTiles = int(math.floor(resolutionWidth / tileSizeX)) nYTiles = int(math.floor(resolutionHeight / tileSizeY)) if nXTiles * tileSizeX != resolutionWidth: nXTiles = nXTiles + 1 if nYTiles * tileSizeY != resolutionHeight: nYTiles = nYTiles + 1 for y in range(nYTiles):
## Outputs each stitched z plane as a separate file
iReader = ImageReader()
iReader.setId(parentLSMFilePath)
for z in range(max_coords[2]+basic_info[4]):
## for z in range(50,51):
IJ.showStatus("z: "+str(z+1)+" of "+str(max_coords[2]+basic_info[4]))
chIps = []
resImages = []
for ch in range(basic_info[0]):
chIps.append(ByteProcessor(max_coords[0]+scale_info[2],max_coords[1]+scale_info[2]))
for ch in range(basic_info[0]):
resImages.append(ImagePlus("ch"+str(ch+1),chIps[ch]))
for se in range(basic_info[1]):
IJ.showProgress(se,basic_info[1])
if z >= coords_upscaled[se][2] and z <= coords_upscaled[se][2]+basic_info[4]-1:
iReader.setSeries(se)
for ch in range(basic_info[0]):
byteArray = iReader.openBytes((z-coords_upscaled[se][2])*basic_info[0]+ch)
testIp = ByteProcessor(scale_info[2],scale_info[2],byteArray)
testImage = ImagePlus("tester",testIp)
Image_stamper.stampStack(testImage,resImages[ch],coords_upscaled[se][0],coords_upscaled[se][1],0)
activeIp = chIps[ch]
testImage.close()
for ch in range(len(resImages)):
IJ.saveAsTiff(resImages[ch],parentLSMFilePath+"_tiles/v_img/img_z_"+str(z+1)+"_c_"+str(ch+1)+".tif")
#outPlaneImage = RGBStackMerge.mergeChannels(resImages,False)
#IJ.saveAsTiff(outPlaneImage,parentLSMFilePath+"_tiles/v_img/img_z_"+str(z+1)+".tif")
#outPlaneImage.close()
reader.setId(file)
# setup resolutions
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)
for series in range(reader.getSeriesCount()):
reader.setSeries(series)
writer.setSeries(series)
# convert each image in the current series
for image in range(reader.getImageCount()):
width = reader.getSizeX()
height = reader.getSizeY()
# Determined the number of tiles to read and write
nXTiles = int(math.floor(width / tileSizeX))
nYTiles = int(math.floor(height / tileSizeY))
if nXTiles * tileSizeX != width:
nXTiles = nXTiles + 1
if nYTiles * tileSizeY != height:
nYTiles = nYTiles + 1
for y in range(nYTiles):
for x in range(nXTiles):
# The x and y coordinates for the current tile
tileX = x * tileSizeX
tileY = y * tileSizeY
# Read tiles from the input file and write them to the output OME-Tiff
buf = reader.openBytes(image, tileX, tileY, tileSizeX,
tileSizeY)
writer.saveBytes(image, buf, tileX, tileY, tileSizeX,
tileSizeY)
# close reader and writer
writer.close()
reader.close()
IJ.log("Done")
