From 9762183e510e31f23a76ab00e6c76a26831df26e Mon Sep 17 00:00:00 2001 From: Alan Morris Date: Fri, 17 Mar 2023 11:57:58 -0600 Subject: [PATCH 1/9] List updates --- docs/about/release-notes.md | 60 +++++++++++++++++++++++++++++++++++++ 1 file changed, 60 insertions(+) diff --git a/docs/about/release-notes.md b/docs/about/release-notes.md index 226c040cd5..15e209c5c8 100644 --- a/docs/about/release-notes.md +++ b/docs/about/release-notes.md @@ -1,6 +1,66 @@ # Release Notes + + • Studio + ○ Fix #1976, domain type switching bug #1981 + ○ Multi-level analysis? + ○ Studio: feature to overlay/compare mean shape + § https://github.com/SCIInstitute/ShapeWorks/pull/1950 + ○ Per domain particle display and alternate color support (#1935) + ○ Fixes: + § #1946 + § #1947 + § #1944 + § #1755 + § #1923 (#1928) + § #1387 + § #1915 + § #1914 + § #1848 + § #1830 + § #1860 + § #1862 + § #1853 + § #1849 - logging library + § #1845 + § #1837 - JSON (swproj) + § #1764 - color map support (Is this in 6.3.0?) + ○ Studio file associations (#1921) + ○ Ability to scale arrows (#1897) + ○ #1893 (save_init_splits, checkpointin) + ○ Shapeworks as a 3rd party library (#1889) + + + + + + + • Offline analysis? + • FFC changes (donut working) + • Data Portal migration + + + +## ShapeWorks 6.4.0 - 2023-03-?? +### What is new? + * **ShapeWorks Back-end** + * **ShapeWorks Front-end** + * ShapeWorks Studio can now automatically check for updates and prompt the user to download them + * Improved progress bar in ShapeWorks Studio that shows time remaining + * **User's Support** +### Fixes + * Fix Studio python problem causing crash on group differences (#1781) + * Fix Studio slow/hanging on certain free form constraints (#1817, #1801) + * Fix crashes on certain projects (#1800, #1815) + * Fix Stud + +## ShapeWorks 6.3.2 - 2022-10-04 +### Fixes + + * Fix install_shapeworks.sh on Linux (#1883) + + ## ShapeWorks 6.3.1 - 2022-07-22 ### Fixes From c05f5095267bf4b0ae40f02b6a5766c3dd6ee685 Mon Sep 17 00:00:00 2001 From: Alan Morris Date: Sat, 18 Mar 2023 10:31:20 -0600 Subject: [PATCH 2/9] Adding to 6.4 release notes --- docs/about/release-notes.md | 73 ++++++++++++++--------------------- docs/studio/studio-analyze.md | 2 + 2 files changed, 30 insertions(+), 45 deletions(-) diff --git a/docs/about/release-notes.md b/docs/about/release-notes.md index 15e209c5c8..03dacce092 100644 --- a/docs/about/release-notes.md +++ b/docs/about/release-notes.md @@ -1,59 +1,42 @@ # Release Notes - - - • Studio - ○ Fix #1976, domain type switching bug #1981 - ○ Multi-level analysis? - ○ Studio: feature to overlay/compare mean shape - § https://github.com/SCIInstitute/ShapeWorks/pull/1950 - ○ Per domain particle display and alternate color support (#1935) - ○ Fixes: - § #1946 - § #1947 - § #1944 - § #1755 - § #1923 (#1928) - § #1387 - § #1915 - § #1914 - § #1848 - § #1830 - § #1860 - § #1862 - § #1853 - § #1849 - logging library - § #1845 - § #1837 - JSON (swproj) - § #1764 - color map support (Is this in 6.3.0?) - ○ Studio file associations (#1921) - ○ Ability to scale arrows (#1897) - ○ #1893 (save_init_splits, checkpointin) - ○ Shapeworks as a 3rd party library (#1889) - - - - - - - • Offline analysis? - • FFC changes (donut working) - • Data Portal migration - - - ## ShapeWorks 6.4.0 - 2023-03-?? ### What is new? * **ShapeWorks Back-end** + * New shapeworks 'analyze' command for offline analysis of shape models + * Improved free form constraints that now support doubly connected areas (e.g. donut-like) + * Data Portal migrated to new ShapeWorks Cloud and swcc (ShapeWorks Cloud Client) tool + * ShapeWorks can now be used as a 3rd party library ([details here](http://sciinstitute.github.io/ShapeWorks/6.4/dev/shapeworks-library.html)) + * Added support for 'save_init_splits' and 'checkpointing_interval' parameters in the project spreadsheet formats + * Added new JSON based file format for storing ShapeWorks projects (swproj) + * Added a unified logging library for ShapeWorks (spdlog) + * Uniform numerical computation of specificity across platforms * **ShapeWorks Front-end** - * ShapeWorks Studio can now automatically check for updates and prompt the user to download them - * Improved progress bar in ShapeWorks Studio that shows time remaining + * ShapeWorks Studio can now automatically check for updates and prompt the user to download them + * Improved progress bar in ShapeWorks Studio that shows time remaining + * Added ability to scale difference arrows in ShapeWorks Studio + * Added file association support for swproj file extension on Windows and Mac + * New multi-level analysis feature in ShapeWorks Studio ([details here](http://sciinstitute.github.io/ShapeWorks/6.4/studio/studio-analyze.html#multi-level-pca)) + * Added ability to hide/show particles per domain + * Added feature to compare origina vs groomed vs reconstructed shapes + * Added feature to show the difference to the mean for any given mesh (subjects or generated PCA mode positions) * **User's Support** + * Hip Use Case: The use case uses the hip joint to demonstrate the capability of ShapeWorks + to capture inter-domain correlations and interactions directly on triangular surface meshes. + The use case showcases calculating the alignment options available for multiple organ anatomies. + ([details here](http://sciinstitute.github.io/ShapeWorks/6.4/use-cases/mesh-based/hip.html)) + * Added options to the incremental use case when run in --interactive mode, including sorting method, + initial model size, and incremental batch size. The sorting method determines how the shapes are sorted + to be added incrementally. There are three options: random, median, distribution. + * [Python API documentation](http://sciinstitute.github.io/ShapeWorks/6.4/python/python-api.html) has been added to the ShapeWorks documentation site + + ### Fixes * Fix Studio python problem causing crash on group differences (#1781) * Fix Studio slow/hanging on certain free form constraints (#1817, #1801) * Fix crashes on certain projects (#1800, #1815) - * Fix Stud + * Fix procrustes with multi-domain models (#1755) + * Fixed crashes in groom due to multi-threading (#1944) ## ShapeWorks 6.3.2 - 2022-10-04 ### Fixes diff --git a/docs/studio/studio-analyze.md b/docs/studio/studio-analyze.md index 129f5dfa2e..464f9069ee 100644 --- a/docs/studio/studio-analyze.md +++ b/docs/studio/studio-analyze.md @@ -34,6 +34,8 @@ The PCA tab of the View panel shows reconstructed shapes (surface meshes) along ![ShapeWorks Studio Analysis View Panel PCA Display](../img/studio/studio_analyze_view_pca.png) +### Multi-Level PCA + The PCA tab of the View panel shows options to select modes of variation in different subspaces when a multiple domain shape model is loaded: ![ShapeWorks Studio Analysis View Panel PCA Display for Multiple-Domain Shape Model](../img/studio/studio_analyze_view_pca_multiple_domain.png) From 1bd80aee95b898b5803ade459d2ef43e856dcb56 Mon Sep 17 00:00:00 2001 From: Alan Morris Date: Sat, 18 Mar 2023 10:40:40 -0600 Subject: [PATCH 3/9] Switch links to relative md --- docs/about/release-notes.md | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/docs/about/release-notes.md b/docs/about/release-notes.md index 03dacce092..a22fc8e2cb 100644 --- a/docs/about/release-notes.md +++ b/docs/about/release-notes.md @@ -6,7 +6,7 @@ * New shapeworks 'analyze' command for offline analysis of shape models * Improved free form constraints that now support doubly connected areas (e.g. donut-like) * Data Portal migrated to new ShapeWorks Cloud and swcc (ShapeWorks Cloud Client) tool - * ShapeWorks can now be used as a 3rd party library ([details here](http://sciinstitute.github.io/ShapeWorks/6.4/dev/shapeworks-library.html)) + * ShapeWorks can now be used as a 3rd party library ([details here](../dev/shapeworks-library.md)) * Added support for 'save_init_splits' and 'checkpointing_interval' parameters in the project spreadsheet formats * Added new JSON based file format for storing ShapeWorks projects (swproj) * Added a unified logging library for ShapeWorks (spdlog) @@ -16,19 +16,20 @@ * Improved progress bar in ShapeWorks Studio that shows time remaining * Added ability to scale difference arrows in ShapeWorks Studio * Added file association support for swproj file extension on Windows and Mac - * New multi-level analysis feature in ShapeWorks Studio ([details here](http://sciinstitute.github.io/ShapeWorks/6.4/studio/studio-analyze.html#multi-level-pca)) + * New multi-level analysis feature in ShapeWorks Studio ([details here](../studio/studio-analyze.md#multi-level-pca)) * Added ability to hide/show particles per domain - * Added feature to compare origina vs groomed vs reconstructed shapes + * Added feature to compare original vs groomed vs reconstructed shapes * Added feature to show the difference to the mean for any given mesh (subjects or generated PCA mode positions) * **User's Support** * Hip Use Case: The use case uses the hip joint to demonstrate the capability of ShapeWorks to capture inter-domain correlations and interactions directly on triangular surface meshes. The use case showcases calculating the alignment options available for multiple organ anatomies. - ([details here](http://sciinstitute.github.io/ShapeWorks/6.4/use-cases/mesh-based/hip.html)) + ([details here](../use-cases/mesh-based/hip.md)) * Added options to the incremental use case when run in --interactive mode, including sorting method, initial model size, and incremental batch size. The sorting method determines how the shapes are sorted to be added incrementally. There are three options: random, median, distribution. - * [Python API documentation](http://sciinstitute.github.io/ShapeWorks/6.4/python/python-api.html) has been added to the ShapeWorks documentation site + ([detauls here](../use-cases/multistep/incremental_supershapes.md)) + * [Python API documentation](../python/python-api.md) has been added to the ShapeWorks documentation site ### Fixes From c4993c024addc27c2860a1e192a5ea898fc3894f Mon Sep 17 00:00:00 2001 From: Alan Morris Date: Sat, 18 Mar 2023 10:43:32 -0600 Subject: [PATCH 4/9] ShapeWorks Studio -> Studio --- docs/about/release-notes.md | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/docs/about/release-notes.md b/docs/about/release-notes.md index a22fc8e2cb..f0d2689832 100644 --- a/docs/about/release-notes.md +++ b/docs/about/release-notes.md @@ -12,11 +12,11 @@ * Added a unified logging library for ShapeWorks (spdlog) * Uniform numerical computation of specificity across platforms * **ShapeWorks Front-end** - * ShapeWorks Studio can now automatically check for updates and prompt the user to download them - * Improved progress bar in ShapeWorks Studio that shows time remaining - * Added ability to scale difference arrows in ShapeWorks Studio + * Studio can now automatically check for updates and prompt the user to download them + * Improved progress bar in Studio is more representative and also estimates time remaining + * Added ability to arbitrarily scale difference arrows in Studio * Added file association support for swproj file extension on Windows and Mac - * New multi-level analysis feature in ShapeWorks Studio ([details here](../studio/studio-analyze.md#multi-level-pca)) + * New multi-level analysis feature in Studio ([details here](../studio/studio-analyze.md#multi-level-pca)) * Added ability to hide/show particles per domain * Added feature to compare original vs groomed vs reconstructed shapes * Added feature to show the difference to the mean for any given mesh (subjects or generated PCA mode positions) @@ -31,7 +31,6 @@ ([detauls here](../use-cases/multistep/incremental_supershapes.md)) * [Python API documentation](../python/python-api.md) has been added to the ShapeWorks documentation site - ### Fixes * Fix Studio python problem causing crash on group differences (#1781) * Fix Studio slow/hanging on certain free form constraints (#1817, #1801) From c0d9dc040a7d5e5a549598a09027cd43f51a2484 Mon Sep 17 00:00:00 2001 From: Alan Morris Date: Sat, 18 Mar 2023 10:47:35 -0600 Subject: [PATCH 5/9] Removed items that were already in 6.3 --- docs/about/release-notes.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/about/release-notes.md b/docs/about/release-notes.md index f0d2689832..7c6cd8c5b0 100644 --- a/docs/about/release-notes.md +++ b/docs/about/release-notes.md @@ -18,8 +18,6 @@ * Added file association support for swproj file extension on Windows and Mac * New multi-level analysis feature in Studio ([details here](../studio/studio-analyze.md#multi-level-pca)) * Added ability to hide/show particles per domain - * Added feature to compare original vs groomed vs reconstructed shapes - * Added feature to show the difference to the mean for any given mesh (subjects or generated PCA mode positions) * **User's Support** * Hip Use Case: The use case uses the hip joint to demonstrate the capability of ShapeWorks to capture inter-domain correlations and interactions directly on triangular surface meshes. From 5574e251c916a7c612b86c3387a15e9f74ade4df Mon Sep 17 00:00:00 2001 From: Alan Morris Date: Tue, 21 Mar 2023 13:27:56 -0600 Subject: [PATCH 6/9] Empty commit to trigger GitHub Actions From e21a0edb198bea20faff7235b441bbce678bbdab Mon Sep 17 00:00:00 2001 From: Alan Morris Date: Fri, 24 Mar 2023 01:24:08 -0600 Subject: [PATCH 7/9] Empty commit to trigger GitHub Actions From c41de6dc1249837e472adf82c936ad646eec84a4 Mon Sep 17 00:00:00 2001 From: Alan Morris Date: Tue, 18 Apr 2023 00:59:17 -0600 Subject: [PATCH 8/9] Fix typo, update month --- docs/about/release-notes.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/about/release-notes.md b/docs/about/release-notes.md index 7c6cd8c5b0..5eed30b2cd 100644 --- a/docs/about/release-notes.md +++ b/docs/about/release-notes.md @@ -1,6 +1,6 @@ # Release Notes -## ShapeWorks 6.4.0 - 2023-03-?? +## ShapeWorks 6.4.0 - 2023-04-?? ### What is new? * **ShapeWorks Back-end** * New shapeworks 'analyze' command for offline analysis of shape models @@ -26,7 +26,7 @@ * Added options to the incremental use case when run in --interactive mode, including sorting method, initial model size, and incremental batch size. The sorting method determines how the shapes are sorted to be added incrementally. There are three options: random, median, distribution. - ([detauls here](../use-cases/multistep/incremental_supershapes.md)) + ([details here](../use-cases/multistep/incremental_supershapes.md)) * [Python API documentation](../python/python-api.md) has been added to the ShapeWorks documentation site ### Fixes From 664f378c37350cba7a059fa49292ddd321160884 Mon Sep 17 00:00:00 2001 From: Alan Morris Date: Tue, 18 Apr 2023 01:02:17 -0600 Subject: [PATCH 9/9] List major library version upgrades. --- docs/about/release-notes.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/about/release-notes.md b/docs/about/release-notes.md index 5eed30b2cd..d03f470413 100644 --- a/docs/about/release-notes.md +++ b/docs/about/release-notes.md @@ -11,6 +11,7 @@ * Added new JSON based file format for storing ShapeWorks projects (swproj) * Added a unified logging library for ShapeWorks (spdlog) * Uniform numerical computation of specificity across platforms + * Updated dependencies. Python now at 3.9, PyTorch 1.11.0, VTK 9.1, ITK 5.2.1 * **ShapeWorks Front-end** * Studio can now automatically check for updates and prompt the user to download them * Improved progress bar in Studio is more representative and also estimates time remaining