#181 Package brain2mesh
Closed: Fixed 3 months ago by fangq. Opened a year ago by mhough.

URL: http://mcx.space/wiki/index.cgi?Brain2Mesh

The Brain2Mesh toolbox is extensively dependent on the Iso2Mesh toolbox (http://iso2mesh.sf.net) with additional dependency on MATLAB Image-Processing toolbox (imfill, ordfilt2) and 3rd party open-source toolboxes: intriangulation.m (by Adam Aitkenhead and Johannes Korsawe) and max_filter.m.

Last time I saw Qianqian Fang at biophotonics he said he fully supports a complete end-to-end octave compatible pipeline so I need to see what the options octave options are for imfill and ordfilt2.


The details of this toolbox can be found in the following paper: Anh Phong Tran and Qianqian Fang, "Fast and high-quality tetrahedral mesh generation from neuroanatomical scans,". In: arXiv pre-print (August 2017). arXiv:1708.08954v1 [physics.med-ph] URL: https://arxiv.org/abs/1708.08954

Metadata Update from @mhough:
- Issue marked as blocking: #146

5 months ago

Metadata Update from @mhough:
- Issue marked as blocking: #146

5 months ago

in terms of dependency, I suggest to change #146 from "blocking" to "depending on", as brain2mesh depends on iso2mesh.

in terms of dependency, I suggest to change #146 from "blocking" to "depending on", as brain2mesh depends on iso2mesh.

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Metadata Update from @ankursinha:
- Issue unmarked as blocking: #146
- Issue marked as depending on: #146

3 months ago

@ankursinha, thank you, will do.

I was just reading your github rpm-specs repo (https://github.com/sanjayankur31/rpm-specs), is that the preferred way to submit/review/revise specs files? happy to follow your suggestions.

Metadata Update from @fangq:
- Issue unmarked as depending on: #146
- Issue marked as blocking: #146

3 months ago

Metadata Update from @fangq:
- Issue unmarked as blocking: #146
- Issue marked as depending on: #146

3 months ago

@ankursinha, thank you, will do.
I was just reading your github rpm-specs repo (https://github.com/sanjayankur31/rpm-specs), is that the preferred way to submit/review/revise specs files? happy to follow your suggestions.

Ah, no---that's just a repository for the specs I work on. Since all these tools are simply packages in Fedora, we follow the standard packaging workflow: https://fedoraproject.org/wiki/New_package_process_for_existing_contributors

The packaging guidelines are all here now:
https://docs.fedoraproject.org/en-US/packaging-guidelines/

The octave guidelines, with an example spec template are here: https://docs.fedoraproject.org/en-US/packaging-guidelines/Octave/

to make things simpler, I will merge brain2mesh into iso2mesh.

please review the iso2mesh package I just submitted a moment ago, once it is approved, I will either add brain2mesh as Source4, and combine during packaging, or I can merge directly in the upstream.

Metadata Update from @fangq:
- Issue unmarked as depending on: #146
- Issue assigned to fangq

3 months ago

Metadata Update from @fangq:
- Issue untagged with: S: Needs packaging
- Issue tagged with: S: Needs review

3 months ago

now I know how to set package dependencies in octave, so, it makes more sense now to submit this as a separate package for better modularity

my spec file can be found here, appreciated if someone want to review it, pretty straightforward, only two .m units.

https://bugzilla.redhat.com/show_bug.cgi?id=1761011

Metadata Update from @fangq:
- Issue close_status updated to: Fixed
- Issue status updated to: Closed (was: Open)

3 months ago

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