Amira io

[iarganda]

These changes correct different bugs when saving/loading images as AmiraMesh:

• The jzlib compression was creating corrupted files. It has been substituted by calls to the compression methods in java.util.zip methods.
• The voxel calibration was not read accordingly to the way it was saved.
• Avizo (new version of Amira) files are now readable as well.

[dscho]

Cool! But hey, how about removing the jzlib dependency now?

[dscho]

Looks pretty good already! A couple of changes here and there and we're good to merge! Thanks!

[iarganda]

@dscho Thanks for your useful remarks! How should we proceed now? Do you want to pick some of the changes and remove the other ones? What should I use?

[dscho]

How should we proceed now?

I would really appreciate it if you could spend a little bit of time to address the concerns I raised...

[iarganda]

Yes, yes, of course. I was just wondering if I should continue adding new commits in this branch since you didn't like some of them.

Working on it!

[dscho]

I was just wondering if I should continue adding new commits in this branch

Please avoid adding on top of flawed commits, and rewrite the branch instead. I provided some hints in that regard for another OSS project.

[iarganda]

I see, that's what I was wondering. Thanks for the link! There are not too many changes so I could actually write the whole branch from scratch instead of rebasing.

[iarganda]

@dscho OK, i think i addressed all your comments, but please, make sure i did.

I left the reading/writing of each slice as it was before (with one I/O file access per slice). I you don't mind, I would like to write a couple of public methods to do it in a single access at the cost of more memory so I still have that possibility.

[dscho]

This looks already pretty good! I wrote up in a pretty detailed way how I would suggest to address the remaining issues.

I[f] you don't mind, I would like to write a couple of public methods to do it in a single access at the cost of more memory so I still have that possibility.

Oh, I would welcome that!

[iarganda]

That was really useful! Thanks again, Dscho, and sorry for all the corrections you still had to point out.

[dscho]

sorry for all the corrections you still had to point out.

No worries. I wonder whether you could add some documentation that would have helped you better than I did, i.e. before opening the Pull Request? I believe that the future contributors would benefit a lot from it.

[dscho]

I will release a new version and upload it later today, thank you very much for your contribution!

[iarganda]

Oops, I think I added some changes after you closed the pull request. I'll upload them in a few minutes. Sorry about that.

I'll definitely work in that documentation.

[iarganda]

Please, do not make that release yet. I might have found another problem. Working on it!