Release notes for 6.1

[sheryjoe]

Please add to this issue a paragraph (plus videos/snapshots for illustration) about each new/improved/bug-fix included in this release. Please add bullets to the below outline that are relevant to your contributions for the 6.1 release. I will consolidate and add to the documentation right away and put together the graphical abstract for release announcement before the SB3C workshop.

• What is new?
  • User's Support
  • ShapeWorks Back-end
  • All-in-one Studio Front-end
  • Deep Learning & Shape Modeling
• Improvements
  • User's Support
    • ShapeWorks Back-end
    • All-in-one Studio Front-end
    • Deep Learning & Shape Modeling
• Fixes
  • User's Support
  • ShapeWorks Back-end
  • All-in-one Studio Front-end
  • Deep Learning & Shape Modeling

NOTE: To add these comments to the documentation (markdown format), select "edit" on a message and cut-and-paste.

[iyerkrithika21]

-What is new?

-User's support

1. Ellipsoid joint generation added to ShapeWork's cohort generator python module. Cohorts of joints can be generated with options available for distance separating the joints, modes of variations(size/rotation). These cohorts can be used for troubleshooting multiple domain shape modeling workflow.

-ShapeWorks Back-end

1. Consolidation of PCA shape analysis tools: Updated shapeworks API to include PCA shape analysis tools (read particle files, calculate eigenvectors, eigenvalues, mode variance). A new use case ellipsoid_pca demonstrating the usage of PCA tools has been added.

-Improvements

-User's Support

1. Updated OptimizeUtils and AnalyzeUtils to handle multiple domain datasets.

2. Two new use cases - ellipsoid_multiple_domain and ellipsoid_multiple_domain_mesh added to demonstrate multiple domain use cases for segmentation images and meshes.

3. Depreciated GroomUtils and EvaluationUtils and restructured all use cases to make the grooming steps more transparent by using the python API.

[HeavenlyBerserker]

• What is new?
  • ShapeWorks Back-end: Constraints are now implemented by turning the problem into an unconstrained optimization using the augmented lagrangian inequality formulation. Now supports cutting planes and spheres.
• Improvements
  • ShapeWorks Back-end: Particle splitting and constraints will no longer require that no particle violates constraints. It will work even if a particle violates a constraint. Added multiple unit tests.

Results on new cutting_planes unit test with 3 cutting planes Results on new sphere_constraint unit test with 25 spheres Results on new sphere_cutting_plane_constraint unit test with 25 spheres and one cutting plane Results on ellipsoid_cut use case Results on femur_cut use case

For more information on augmented lagrangian inequality constraints, please see http://www.cs.cmu.edu/~pradeepr/convexopt/Lecture_Slides/Augmented-lagrangian.pdf.

[medakk]

• What is new?
  • ShapeWorks Back-end
    1. Geodesic distance based repulsion is now supported for mesh domains. This improves results on structures with thin and/or convoluted features at the cost of increased memory and runtime. Refer to the thin_cavity_bean use case for an example.
    2. N-dimensional contour domains are now supported in ShapeWorks. Refer to the supershapes_1mode_contour use case for an example.

[akenmorris]

What is new?

Grooming support for Meshes in Studio:

• Smoothing (two methods)
• Hole filling
• Center
• Iterative Closest Point (auto reference shape)

[cchriste]

• partitioned regions into both index (0-based) regions and physical regions
  • enabling exact specification of crop regions and clip plane for both images and meshes
• significant improvements to shapeworks Python module:
  • now installed with the rest of ShapeWorks
  • entire ShapeWorks library framework now accessible via Python bindings
  • no longer requires any special path modifications to import
  • uses generic Python types (e.g., numpy, arrays, lists) rather than opaque wrappers for parameters to/from ShapeWorks objects
  • now possible to instantiate shapeworks.Image from a numpy array
  • can now request raw image data as a numpy array
  • ability to safely “dot chain” operations (ex: img.translate([tx, ty, tz]).rotate(45, shapeworks::Z).scale([sx, sy, sz)) )
• more clear documentation both from Python, the command line, and online
• better error detection and handling
• more robust automated testing to ensure improvements do not break existing functionality

[jadie1]

Improvements - Deep Learning & Shape Modeling

• Defined a config file for DeepSSM parameters which is used in training and testing. This will be helpful for parameter tuning, model comparison, and adding additional functionality and parameters to DeepSSM.
• A fine-tuning option has been added to DeepSSM. This allows the model to learn the mapping between the PCA space to the correspondence point space , improving accuracy.
• DeepSSM evaluation has been adapted to use ShapeWorks mesh warp function and Python binding mesh distance function.
• The DeepSSM use case has been adapted to run on both GPU and CPU. It is considerably faster on GPU but no longer exits when running on CPU.

[riddhishb]

What Is New?

• Extending the warp-mesh command to work with multiple meshes at the same time.

[sheryjoe]

@iyerkrithika21

Consolidation of PCA shape analysis tools: Updated shapeworks API to include PCA shape analysis tools (read particle files, calculate eigenvectors, eigenvalues, mode variance). A new use case ellipsoid_pca demonstrating the usage of PCA tools has been added.

• Do you mean by API here the shapeworks command or python API or both?
• what is the difference between calculating eigenvalues and mode variance?

[sheryjoe]

What Is New?

• Extending the warp-mesh command to work with multiple meshes at the same time.

@riddhishb please share a snapshot to show case this feature to be used for the graphical abstract.

[sheryjoe]

@akenmorris

N-dimensional contour domains are now supported in ShapeWorks. Refer to the supershapes_1mode_contour use case for an example.

Want to make sure about adding the above to the release notes. I think the PR has been merged, but the full support with Studio is pushed to 6.2. right?

[sheryjoe]

@akenmorris

I think we should include multi-domain support to what is new in studio.

[sheryjoe]

@akenmorris @jadie1 @riddhishb @archanasri @cchriste @HeavenlyBerserker

Any significant bug fixes we can highlight in the release notes?

[akenmorris]

I think we should include multi-domain support to what is new in studio.

Of course. Somehow I was thinking that was in 6.0, but I guess it wasn't.

[akenmorris]

Want to make sure about adding the above to the release notes. I think the PR has been merged, but the full support with Studio is pushed to 6.2. right?

That's right.

[sheryjoe]

@akenmorris

I think we should include multi-domain support to what is new in studio.

Of course. Somehow I was thinking that was in 6.0, but I guess it wasn't.

@akenmorris can we add multiple domains to studio documentation?

[akenmorris]

can we add multiple domains to studio documentation?

Yep

[sheryjoe]

can we add multiple domains to studio documentation?

Yep

@akenmorris please at a high level description in "New in Studio" page with a link to the multiple domain page (more detailed documentation) in the "ShapeWorks Studio" group. You can also add videos and snapshots that you have previously generated.

[sheryjoe]

@akenmorris @jadie1 @iyerkrithika21 @cchriste @archanasri @riddhishb @HeavenlyBerserker

Please let me know if you have any comments/suggestions to make it better.

[HeavenlyBerserker]

That looks sick! I like it

On Wed, Jun 16, 2021, 8:38 PM Shireen Elhabian @.***> wrote:

@akenmorris https://github.com/akenmorris @jadie1 https://github.com/jadie1 @iyerkrithika21 https://github.com/iyerkrithika21 @cchriste https://github.com/cchriste @archanasri https://github.com/archanasri @riddhishb https://github.com/riddhishb @HeavenlyBerserker https://github.com/HeavenlyBerserker

Please let me know if you have any comments/suggestions to make it better. [image: image] https://user-images.githubusercontent.com/3253036/122322390-a15ba280-cee2-11eb-8370-9b637bee1d95.png

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/SCIInstitute/ShapeWorks/issues/1285#issuecomment-862870976, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACVO6GH2RXYOTHKHSBOT7STTTFN2LANCNFSM46T4FC4Q .

[cchriste]

Improved installation

• users no longer required to modify PATHs or pass parameters to find executables or import python module
  • works even if non-standard installation directories are used
  • works on all platforms
• new shapeworks environments can now be created using install_shapeworks [name]
  • this supports multiple installations for anyone
  • can change installation just by activating a different conda environment

[cchriste]

Improved developer support to facilitate more independent and robust testing

• devenv scripts for all platforms now ensure deliberate testing of specific binaries and a developer's code are always matched with no presumption or accidental inclusion of the wrong python libraries or binaries.
• unit tests suites that once required a setup environment test that all the other tests depended upon no longer have such a dependency, enabling --gtest_filter="*testname*" to be used when working on a specific feature.
  • suites that had this requirement include Python, shapeworks, and UseCaseTests.

[cchriste]

RunUseCase improvements

• no longer requires --use_case before use case.
  • this makes it simpler to use since omitting a use case name immediately prints help, which itself shows the list of use cases as a required argument rather than listing them with the other optional args
• no longer accepts paths to shapeworks executables or python modules
  • all of these are in the user's conda environment, or set using devenv for testing by developers

[sheryjoe]

Done and added to the docs.