Usage¶

Running a reconstruction server¶

Before running the reconstruction server, start up a visualization server like RECAST3D. To run the server:

./slicerecon_server [options]

The server is now waiting until (projection) data is pushed to it. For example, we can push prerecorded FleX-ray data:

python slicerecon_push_flexray.py [path]

Developing a plugin¶

Developing a post-processing plugin is as easy as implementing a single Python function that takes a 2D numpy array (the reconstructed slice), and returns a 2D numpy array (the postprocessed slice). An example plugin looks like this.

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()

This plugin listens to incoming SliceData packets on port 5652, and connects to a visualization software (or another plugin) listening on port 5555. These are the default values. If you use the standard slicerecon_server program, connecting the Python plugin is as easy as passing –pyplugin as a flag.

Testing your plugin¶

Start RECAST3D:
```
module load recast3d
recast3d
```

Start slicerecon_server, e.g.:

slicerecon_server --slice-size 512 --pyplugin

Run your plugin, e.g.:
```
python plugin.py
```

Stream projection data to the slicerecon_server, e.g.:

python slicerecon_push_flexdata.py [path_to_data] --sample 2