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.md and 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'
  • Update DocumentationUtilsPackage to generate md for mkdocs (ShapeworksCommand.md)
  • Add mkdocs build for 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 .py
  • 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

Misc

  • 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