TomoPackets

A library for real-time tomography pipelines based on ZeroMQ.

This library defines a protocol for sending messages between the different components (scanners, reconstruction nodes, visualization workstations) for real-time tomographic reconstruction.

Installation

Dependencies

• Boost (required). We use Boost.Hana for struct introspection. CMake tries to find Boost with find_package.
• pybind11 (submodule). Supplied as a git submodule. Run git submodule --init --remote --recursive before following the language specific instructions below.
• ZeroMQ (optional).
• cppzmq (optional).

If optional dependencies are not found using CMake find_package, they will be cloned as a git submodule and built from source.

C++

The easiest way to interface with tomopackets is using CMake. We define a INTERFACE target tomop that can be used as follows. We assume the TomoPackets repository is in ext/tomop. For example, by managing it as a Git submodule:

git submodule add https://www.github.com/cicwi/tomopackets ext/tomop
git submodule update --init

Next, add the repository as a subdirectory and link your targets against tomop.

add_subdirectory("ext/tomop")
target_link_libraries(your_program tomop)

Python

To install the library locally, simply run:

pip install -e .

Examples

The following example sets up a reconstruction server for on-demand slice reconstruction:

import tomop
import numpy as np


def callback(orientation, slice_id):
    print("callback called")
    print(orientation)
    return [4, 4], np.array([0, 255, 0, 255, 255, 0, 255, 0, 255,
                             0, 0, 255, 255, 0, 0,
                             255], dtype='float32')

serv = tomop.server("hi")

vdp = tomop.volume_data_packet(
    serv.scene_id(),
    np.array([2, 2, 2], dtype='int32').tolist(),
    np.array([0, 255, 128, 255, 255, 128, 255, 0], dtype='float32'))

serv.send(vdp)

serv.set_callback(callback)
serv.serve()

Authors and contributors

TomoPackets is developed at Centrum Wiskunde & Informatica (CWI) in Amsterdam by:

• Jan-Willem Buurlage (@jwbuurlage)

Also thanks to:

• Willem Jan Palenstijn (@wjp)

Contributing

We welcome contributions. Please submit pull requests against the develop branch.

If you have any issues, questions, or remarks, then please open an issue on GitHub.

Please Cite Us

If you have used TomoPackets for a scientific publication, we would appreciate citations to the following paper:

Real-time quasi-3D tomographic reconstruction. JW Buurlage, H Kohr, WJ Palenstijn, KJ Batenburg. Measurement Science and Technology (2018)

License

This project is licensed under the GPL. See LICENSE.md for details.