Generate OME-TIFF pyramids using Python

generate-pyramid-resolutions.py

#!/usr/env/bin python

# Generate pyramidal OME-TIFF.
# Adapted from:
# https://github.com/ome/bio-formats-examples/blob/88d3f109093fb3350242061b00624af001f495e8/src/main/java/GeneratePyramidResolutions.java#L39-L43

import sys

import scyjava

scyjava.config.endpoints.append('ome:formats-bsd:6.7.0')

Integer = scyjava.jimport('java.lang.Integer')
Arrays = scyjava.jimport('java.util.Arrays')

SimpleImageScaler = scyjava.jimport('loci.common.image.SimpleImageScaler')
ServiceFactory = scyjava.jimport('loci.common.services.ServiceFactory')
FormatTools = scyjava.jimport('loci.formats.FormatTools')
ImageReader = scyjava.jimport('loci.formats.ImageReader')
ImageWriter = scyjava.jimport('loci.formats.ImageWriter')
OMEXMLService = scyjava.jimport('loci.formats.services.OMEXMLService')

DimensionOrder = scyjava.jimport('ome.xml.model.enums.DimensionOrder')
PositiveInteger = scyjava.jimport('ome.xml.model.primitives.PositiveInteger')

args = sys.argv
args = [
    '/Users/curtis/data/FluorescentCells.jpg',
    '2',
    '4',
    '/Users/curtis/Desktop/FluorescentCells-pyramid.ome.tif'
]

if len(args) < 4:
    print("python generate-pyramid-resolutions.py input-file scale-factor resolution-count output-file")
    sys.exit(1)
in_file = args[0]
out_file = args[3]
scale = int(args[1])
resolutions = int(args[2])

reader = ImageReader()
factory = ServiceFactory()
service = factory.getInstance(OMEXMLService.class_)
meta =  service.createOMEXMLMetadata()
reader.setMetadataStore(meta)

reader.setId(in_file)

for i in range(1, resolutions):
    divScale = pow(scale, i)
    meta.setResolutionSizeX(PositiveInteger(Integer(reader.getSizeX() // divScale)), 0, i)
    meta.setResolutionSizeY(PositiveInteger(Integer(reader.getSizeY() // divScale)), 0, i)

scaler = SimpleImageScaler()
img = reader.openBytes(0)

# write image plane to disk
print("Writing image to '" + out_file + "'...")
writer = ImageWriter()
writer.setMetadataRetrieve(meta)
writer.setId(out_file)
writer.saveBytes(0, img)
pixelType = reader.getPixelType()
for i in range(1, resolutions):
    writer.setResolution(i)
    x = meta.getResolutionSizeX(0, i).getValue()
    y = meta.getResolutionSizeY(0, i).getValue()
    downsample = scaler.downsample(img, reader.getSizeX(), \
        reader.getSizeY(), pow(scale, i), \
        FormatTools.getBytesPerPixel(pixelType), reader.isLittleEndian(), \
        FormatTools.isFloatingPoint(pixelType), reader.getRGBChannelCount(), \
        reader.isInterleaved())
    writer.saveBytes(0, downsample)
writer.close()
reader.close()

print("Done.")