gputools - OpenCL accelerated volume processing in Python

This package aims to provide GPU accelerated implementations of common volume processing algorithms to the python ecosystem, such as

• convolutions
• denoising
• synthetic noise
• ffts (simple wrapper around [reikna])
• affine transforms

For that, pputools mostly uses the excellent pyopencl bindings.

Requirements

• python 2.7 / 3.5+
• a working OpenCL environment (check with clinfo).

Installation

pip3 install gputools

check if basic stuff is working:

python3 -m gputools

Usage

Docs are still to be done ;)

Most of the methods work on both numpy arrays or GPU memory objects (gputools.OCLArrays/OCLImage). The latter saving the memory transfer (which e.g. for simple convolutions accounts for the main run time)

Convolutions

• 2D-3D convolutions
• separable convolutions
• fft based convolution
• spatially varying convolutions

import gputools

d = np.zeros((128,128))
d[64,64] = 1.
h = np.ones((17,17))
res = gputools.convolve(d,h)

d = np.zeros((128,128,128))
d[64,64,64] = 1.
hx,hy,hz = np.ones(7),np.ones(9),np.ones(11)
res = gputools.convolve_sep3(d,hx,hy,hz)

Denoising

bilateral filter, non local means

...
d = np.zeros((128,128,128))
d[50:78,50:78,50:78:2] = 4.
d = d+np.random.normal(0,1,d.shape)
res_nlm = gputools.denoise.nlm3(d,2.,2,3)
res_bilat = gputools.denoise.bilateral3(d,3,4.)

Perlin noise

fast 2d and 3d perlin noise calculations

gputools.perlin3(size = (256,256,256), scale = (10.,10.,10.))

Transforms

scaling, translate, rotate, affine...

gputools.transforms.scale(d,.2)
gputools.transforms.rotate(d,(64,64,64),(1,0,0),pi/4)
gputools.transforms.translate(d,10,20,30)
...

fft

wraps around reikna

gputools.fft(d)
gputools.fft(d, inverse = True)

Configuration

Some configuration data (e.g. the default OpenCL platform and devic) can be changed in the config file "~/.gputools" (create it if necessary)

#~/.gputools

id_platform = 0
id_device = 1

See

gputools.config.defaults

for available keys and their defaults.

Troubleshooting

pyopencl: _cffi.so ImportError

If you see a

ImportError: _cffi.so: undefined symbol: clSVMFree

after importing gputools, this is most likely a problem of pyopencl being installed with an incorrent OpenCL version. Check the OpenCL version for your GPU with clinfo (e.g. 1.2):

clinfo | grep Version

and install pyopencl manually while enforcing your opencl version:

# uninstall pyopencl
pip uninstall pyopencl cffi
  
# get pyopencl source
git clone https://github.com/pyopencl/pyopencl.git
cd pyopencl
python configure.py
	
# add in siteconf.py the line
# CL_PRETEND_VERSION = "1.2"
echo 'CL_PRETEND_VERSION = "1.2"' >> siteconf.py

pip install .

where e.g. "1.2" is your version of OpenCL.