Handling of X and Y axes of an image by IJM.show()
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- Java
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Description
Following discussion in [here](http://forum.imagej.net/t/ijm-show-in-imagej-matlab-does-not-support-multi-dimentional-or-multi-channel-images/10156/3), I'd like to raise an issue about` IJM.show()`.
`IJM.show('I')` or `net.imagej.matlab.ImageJMATLABCommands.show('I')` is a great way to transfer array data from MATLAB workspace to ImageJ, thanks to `ImageJ-MATLAB`.
However, I’ve noticed that X and Y of axes of images are flipped over between MATLAB and ImageJ, which is not smart at all.
MATLAB's `permute` can manipulate data to avoid this problem. But, because it apparently needs to [copy data internally](https://stackoverflow.com/questions/36065182/why-does-matlabs-permute-not-need-extra-memory), it requires double memory, which is not ideal. An imglib2 /ImageJ2 -style permute (which re-indexes but does not copy) might be a better solution.
This issue is also related, but more specifically about multidimensional images.
https://github.com/imagej/imagej-matlab/issues/17
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start at the IJM.show('I') and net.imagej.matlab.ImageJMATLABCommands.show('I') entry points, then compare MATLAB and ImageJ X/Y axis conventions. Review the related multidimensional-image issue #17 and verify that transferred images retain the expected orientation without requiring MATLAB permute.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- java, matlab
- Domain
- api
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 38/100