This project aims to re-produce and re-implement the methods published in the paper "X-ray Focal Spot Reconstruction by Circular Penumbra Analysis" by Dr. Giovanni Di Domenico et al.

To begin, either clone the project and install

    pip install .

Or install directly with pip

    pip install git+https://github.com/brikwerk/pypenumbra

PyPenumbra comes with an API and a CLI

The API extends two main functions: "reconstruct_from_image" and "reconstruct_from_cr_data".

The image reconstruction function requires a path to an image and outputs the focal spot image and the sinogram in float64 format.

    import pypenumbra
    from skimage import io, img_as_ubyte
    from skimage.exposure import equalize_adapthist
    import os

    focal_spot, sinogram = pypenumbra.reconstruct_from_image("image.tif")
    io.imsave("focal_spot.png", img_as_ubyte(equalize_adapthist(focal_spot)))
    io.imsave("sinogram.png", img_as_ubyte(equalize_adapthist(sinogram)))

The binary reconstruction function requires the path to the data, the width of the data, the height of the data, and the data type. The focal spot image and the sinogram image are output in float 64 format. This function would be used to reconstruct from raw CR or DR data.

    import pypenumbra
    from skimage import io, img_as_ubyte
    from skimage.exposure import equalize_adapthist
    import os

    focal_spot, sinogram = pypenumbra.reconstruct_from_cr_data("image.std", 2370, 1770, dtype="uint16")
    io.imsave("focal_spot.png", img_as_ubyte(equalize_adapthist(focal_spot)))
    io.imsave("sinogram.png", img_as_ubyte(equalize_adapthist(sinogram)))

Once PyPenumbra has been installed with pip, reconstruction from images and binary images is made available on the command line.

    pypenumbra image_reconstruct image.png
    pypenumbra binary_reconstruct image.std 2140 1760 dtype="uint16"

Details about these commands and command flags/options can be found through the use of the --help flag.

The original paper by Dr. Giovanni Di Domenico:

    Di Domenico, Giovanni, et al. "X‐ray focal spot reconstruction by circular penumbra analysis—Application to digital radiography systems." Medical physics 43.1 (2016): 294-302.

The original ImageJ plugin that this code is based off of:

http://www.fe.infn.it/~didomeni/focalspot/focalspot.html