dmpelt / SliceRecon

A library for on-demand tomographic reconstructions of arbitrary slices.

SliceRecon

A library for on-demand tomographic reconstructions of arbitrary slices.

This project contains efficient reconstruction code for reconstructing arbitrarily oriented slices through a 3D volume. It defines servers that are able to communicate to data sources (using TomoPackets) and visualization software (such as RECAST3D).

Installation

Dependencies

• ASTRA + CUDA (required). We use the ASTRA toolbox for reconstructing the slices.
• Eigen (submodule).
• TomoPackets (submodule)
• Tomos (submodule)
• ZeroMQ / cppzmq (optional)

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

C++

Building the reference server, and example data adapters:

module load [...] # optional: load in preinstalled dependencies
git submodule update --init --remote --recursive
mkdir build
cd build
cmake ..
make -j8

Python

The supplied Python bindings are intended for plugin development. Install using:

cd python
pip install -e .

Examples

Developing a plugin using Python:

import numpy as np
import slicerecon


def callback(shape, xs, idx):
xs = np.array(xs).reshape(shape)

    print("callback called", shape)
    xs[xs <= 3.0] = 0.0
    xs[xs > 3.0] = 10.0

    return [shape, xs.ravel().tolist()]


p = slicerecon.plugin("tcp://*:5652", "tcp://localhost:5555")
p.set_slice_callback(callback)

p.listen()

Host a projection and visualization server:

// ...
// 1. setup reconstructor
auto recon = std::make_unique<slicerecon::reconstructor>(params);

// 2. listen to projection stream
// projection callback, push to projection stream
// all raw data
auto proj = slicerecon::projection_server(host, port, *recon,
                                          use_reqrep ? ZMQ_REP : ZMQ_PULL);
proj.serve();

// 3. connect with (recast3d) visualization server
auto viz = slicerecon::visualization_server(
    "slicerecon test", "tcp://"s + recast_host + ":5555"s,
    "tcp://"s + recast_host + ":5556"s);
viz.set_slice_callback(
    [&](auto x, auto idx) { return recon->reconstruct_slice(x); });

recon->add_listener(&viz);
viz.serve();
// ...

Authors and contributors

SliceRecon 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 SliceRecon 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.