[Tomviz] Adding a file reader to Tomviz

Marcus D. Hanwell marcus.hanwell at kitware.com
Tue Jan 30 10:06:32 EST 2018

On Mon, Jan 29, 2018 at 6:56 PM, Nathan Hughes <nathan1hughes at gmail.com>

> Hello,
> At the end of last year, our paper was published (
> https://plantmethods.biomedcentral.com/articles/10.1186/s13007-017-0229-8)
> and I used Tomviz for a lot of visual analysis.

Great to hear about Tomviz being used in new areas! Thanks for the link,
and for citing Tomviz.

> I'm currently in the process of moving a lot of my segmentation methods
> from MATLAB into Python and I would like to use Tomviz further. However we
> use a Scanco MicroCT scanner which produces a proprietary ISQ file format.
> I have written a file reader for it, both in Python and MATLAB, I could
> also rewrite it in C/C++ if needed and would like to add it to Tomviz as it
> would be extremely useful for my Institute to use for a lot of our
> projects, I also know others in my field who would appreciate this addition
> too.
> Would someone be able to advise on how I could go about making this
> addition to the Tomviz software? Obviously, I can navigate the code, I just
> want to do this correctly and in a way in which I can feed this back to
> other users on Github.

I don't have a definite timeline, but we are hoping to add the ability to
use Python code to read and write data. This may be a good use case, as I
have discussed file formats with a number of people it is clear that Tomviz
would benefit from a simple method of adding new formats using Python
scripts - there are one or two others on my RADAR with existing
Python-based readers too.

> Mostly I am unsure of which specific files are needed to be altered in
> order to accept another file type and how to point to the function to
> handle it.
> As you can see here: https://gist.github.com/
> SirSharpest/fd0a039547eb4ca5f00b02de1216917f it's a
> straightforward process (this is just a quick example).
> Hope I can get some advise on this.

As Cory pointed out the quickest method is to convert to C++, I hope to
make this much easier in the next few months at least for cases where you
have a simple 3D volumetric dataset.

Hope that helps, and thanks for getting in touch!


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