Documentation ToDo List
To add/edit for docs
index.md#shapeworks-in-action: Add the box bump examples and reference our benchmark study.
index.md#shapeworks-in-action: Add video for illustration
index.md#with-shapeworks-you-can: show case ShapeWorks in different studies (e.g., ortho and cardilogy) and cite relevant papers
index.mdand repo readme: Showcase our SSM benchmark study
users/papers.md: Add links to the papers and update the list of papers with recent ones
about/release-notes.md: Fix links in release notes
about/team.md: May be some pics
dev/autodoc.md: Which dir to use for autodoc for commands?
- Spell and grammar check all markdown files
use-cases/ellipsoid.md: Add a figure showing some samples of the dataset that highlight the mode of variation
- Be consistent: multi-scale vs multiscale in the md files
- Be consistent: we vs you (e.g., in use cases)
- Add illustrating images to the groom steps in groom and specific use cases
- Update md files for groom/optimize and use cases to reflect the new workflow (icp, bounding box, crop) that does not apply explicitly resample images/segmentations beyond the isoresample step and use transforamtions as input to the optimization
- For groom and use cases, update the reference selection documentation to reflect any recent updates in this process (e.g., meshes, pairwise distance matrix ... etc)
workflow/XX.md: Review and edit the workflow md files. Add/update the decription of single vs multiscale.
use-cases/ellipsoid.md: Add video/snapshots for the optimized model and groomed data
use-cases/XX.md: Update optimization parameters based on Examples/Python
use-cases/XX.md: Update use cases to reflect multi-scale being integrated into the optimizer
- Add documentation for femur_mesh and lumps use cases
use-cases/left-atrium.md:Check the left atrium use case for saving txt files to carry over images to reflect recent changes (consolidation)
- Consolidate docs/pdfs
- Consolidate docs/backlog
- Add to use cases how to run with prepped data
- Add mean and PCA visuals for ellipsoid and fixed domain ellipsoid use cases
- Review and edit ellipsoid use cases
- Review and edit femur use case
- Review and edit right ventricle use case
- Once meshes work, update the femur use case to indicate that this is optional and add femur_mesh use case
- Instructions on how to add videos to the documentation (thumbnails that link to youtube)
- Instructions to add a new use case
- Revise the right ventricle use case after release it. Might need more results to illustrate group differences.
- Instructions for Doxygen and building doxygen.
dev/commands.md:How to add shapeworks commands?
dev/gh-actions.md: getting started with github actions
dev/python-apis.md: How to Add Python APIs?
dev/tests.md: How to Add and Run Unit Tests?
- Remove all hard-coded links outside docs (relative paths) except for (1) web links (e.g. segmentation softwares, markdown edits ... etc) and (2) shapeworks releases, and shapeworks data portal.
To investigate for docs
- How can we use repo_url in markdown files to link to repo files? -- not needed any more, we won't include any links outside docs except for weblinks, shapeworks releases and data portal.
- How to use google_analytics?
For ShapeWorks repo
- Change the autodoc dir for commands in github action and release, see 'dev/autodoc.md'
DocumentationUtilsPackageto generate md for mkdocs (ShapeworksCommand.md)
mkdocs buildfor autodoc (deploy) to github actions and release
- When a use case launches Studio, does it load groomed data? It does, based on the launch function that takes in distance transforms, local, and world point files.
- Review and edit comments in the
- A fixed domain use case that include grooming the new samples
- Revisit the fixed domain use case, why do we need the path for the mean shape? why not use the mean of the fixed domains?
- Release and update the right ventricle use case
- Add link to documentation http://sciinstitute.github.io/ShapeWorks/ to shapeworks.sci.utah.edu
- Prepped vs groomed? Be consistent in documentation, tags for RunUseCase, and output folders from running use cases