Python and 16 Bit Tiff

Question

How can I convert and save a 16 bit single-channel TIF in Python?

I can load a 16 and 32 bit image without an issue, and see that the 32 bit image is mode F and the 16 bit image is mode I;16S:

import Image
i32 = Image.open('32.tif')
i16 = Image.open('16.tif')
i32
# <TiffImagePlugin.TiffImageFile image mode=F size=2000x1600 at 0x1098E5518>
i16
# <TiffImagePlugin.TiffImageFile image mode=I;16S size=2000x1600 at 0x1098B6DD0>

But I am having trouble working with the 16 bit image. If I want to save either as PNG, I cannot do so directly:

i32.save('foo.png')
# IOError: cannot write mode F as PNG
i16.save('foo.png')
# ValueError: unrecognized mode

If I convert the 32 bit image, I can save it:

i32.convert('L').save('foo.png')

But the same command will not work with the 16 bit image:

i16.convert('L').save('foo.png')
# ValueError: unrecognized mode

Answer 1

Stumbled on this thread trying to save 16 bit TIFF images with PIL / numpy.

Versions: python 2.7.1 - numpy 1.6.1 - PIL 1.1.7

Here's a quick test I wrote. uint16 numpy array -> converted to string -> converted to a PIL image of type 'I;16' -> saved as a 16 bit TIFF.

Opening the image in ImageJ shows the right horizontal gradient pattern and the image type is 'Bits per pixel: 16 (unsigned)'

import Image
import numpy

data = numpy.zeros((1024,1024),numpy.uint16)

h,w = data.shape

for i in range(h):
    data[i,:] = numpy.arange(w)

im = Image.fromstring('I;16',(w,h),data.tostring())
im.save('test_16bit.tif')

edit: As of 1.1.7, PIL does not support writing compressed files, but pylibtiff does (lzw compression). The test code thus becomes (tested with pylibtiff 0.3):

import Image
import numpy
from libtiff import TIFFimage

data = numpy.zeros((1024,1024),numpy.uint16)

h,w = data.shape

for i in range(w):
    data[:,i] = numpy.arange(h)

tiff = TIFFimage(data, description='')
tiff.write_file('test_16bit.tif', compression='lzw')
#flush the file to disk:
del tiff

Please note: test code changed to generate a vertical gradient otherwise, no compression achieved (refer to warning: pylibtiff currently supports reading and writing images that are stored using TIFF strips).