[SciPy-Dev] Contribution: Estimating the overlap of a ray with volume-cells (voxels) for e.g. tomography

[Ralf Gommers]

Hi Sebastian,


On Tue, Oct 8, 2019 at 1:33 PM Sebastian A. Mueller <
sebastian-achim.mueller at mpi-hd.mpg.de> wrote:

> Dear scipy,
>
> I wrote a package to estimate the distances a ray overlaps with
> volume-cells in three dimensions. This is needed to estimate
> system-matrices in tomography. The interface is only one function. It
> takes the ray's support and direction vectors, and the bin-edges for the
> space partitioning. It returns the overlaps of the ray and the voxels.
> The space-partitioning must be rectangular, but it does not need to be
> equally spaced. In combination with scipy.sparse, it can efficiently
> create system-matrices for iterative, tomographic reconstructions. The
> algorithm uses oct-tree-traversal for efficiency.
>
> On pypi:
> https://pypi.org/project/ray-voxel-overlap/0.0.2/
>
> On github:
> https://github.com/cherenkov-plenoscope/ray_voxel_overlap
>
> I would like to contribute this to scipy. It addresses multiple fields
> in science such as medicine, biology, microscopy, physics, astronomy,
> geo-earth, image-processing.
> At its core, it is pure linear algebra. My package contains a pure
> python-implementation for development and testing, and a (much faster)
> C-implementation wrapped in cython.
>
> Do you think such a tool belongs into scipy? If not, where else should
> it go?
>

It could fit in the scope of SciPy. We don't have much other functionality
like it though. My first thought was that it perhaps fits better in
scikit-image, which already has a 2-D radon transform:
https://scikit-image.org/docs/dev/auto_examples/transform/plot_radon_transform.html.
Does that make sense?


> This is my first attempt to contribute to scipy.
>

Welcome!

Cheers,
Ralf
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