Add orthoview AFID plot #45
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@ataha24 - Added you to review this one since you may have some thoughts about additional features / changes regarding the plotting. |
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I am merging this in to push development forward. |
- Add nilearn for orthogonal plotting, with matplotlib installation - Separately install plotly (nilearn's plotly version requires another library that does not appear to support py3.10+) - By adding this through extras instead of group dependencies, this should enable the ability to install using `pip install afids-utils[plotting]`
This commit adds the functionality to create a view object with AFIDs overlaid on an nifti image. To do so, a nifti image with just the fiducials are created with an intensity value equal to the labels. This serves as a "segmentation" or "label" map. A custom 32-discrete colormap object is created to visualize these different fiducials. Additionally, to allow for either voxel coordinates or positional coordinates to be passed, a conversion to voxel coordinates is performed when the plotting function is called. Note, plotting is not limited to complete `AfidSet`s. Individual and incomplete `AfidSet`s can also be plotted. Finally stubs have been created for `matplotlib` and `nilearn` to correct for pyright errors. `# pyright: ignore` was added where appropriate to bypass issues false errors.
Also fix type to afids_utils/afids.py
Issue with matplotlib installation that prevented the plotting page to be loaded. This was due to a `poetry` installation command. Also added intersphinx mappings for plotting functionality and made some text changes to docstrings.
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Proposed changes
This PR adds some plotting functionality to visualize the AFIDs provided by returning a view object with N number of AFIDs (up to 32) overlaid on a nifti image. The one caveat is that AFIDs are assumed to be in the same space as the provided image.
This plotting functionality is also setup as an extra dependency - that is by default, installing
afids-utilswill not provide plotting capabilities. To do so, one would have to specify it (e.g. usingpip-pip install afids-utils[plotting]). This choice was made to avoid installation of extra libraries if the end-user does not intend to use it.Types of changes
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