stk

Toolkit for 3D volume processing

Build

mkdir build && cd build
cmake ..
make

CMake options:

• STK_BUILD_EXAMPLES: build example programs
• STK_BUILD_TESTS: build tests
• STK_USE_CUDA: build with CUDA support
• STK_WARNINGS_ARE_ERRORS: compilation will fail on warnings
• STK_BUILD_WITH_DEBUG_INFO: include debug symbols in the binaries
• STK_ENABLE_FAST_MATH: enable unsafe (non IEEE 754-compliant) optimisations
• STK_LOGGING_PREFIX_FILE: add the file name as prefix to each log message

When building with STK_USE_CUDA, in case the version of gcc selected by CMake was not compatible with the one required by CUDA, it is possible to specify a different executable with -DCMAKE_CUDA_FLAGS="-ccbin gcc-XX", where gcc-XX is a version of gcc compatible with your CUDA version.

Python API

A minimalistic Python API is also provided.

Install

python setup.py install

Example usage

import stk
import numpy as np

# Create volume directly from numpy
vol = stk.Volume(np.zeros((5,5,5)).astype(np.float32), spacing=(2,2,2))
# or read volume from file
vol = stk.read_volume('test.nrrd')

# Modify data (numpy array points to the volume data)
data = np.array(vol, copy=False)
data[0:10] = 0.0

# Access meta data
vol.origin = (2, 2, 2)
vol.spacing = (3, 3, 3)

# Write volume
stk.write_volume('test-out.nrrd', vol)