Itk-tubetk

What's Changed
* ENH: Update to use ITKv53rc4.post2 and MinimalPathExtractionv1.2.2 by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/122


**Full Changelog**: https://github.com/InsightSoftwareConsortium/ITKTubeTK/compare/v1.3...v1.3.1

v1.3-fix
Major fix to RidgeSeedFilter, PDFSegmenter, and VesselEnhancement filters via improvements to LDA and PCA basis feature computation.

Improvements include:

1. Ability to include the addition, subtraction, multiplication, and ratio of features when computing an LDA/PCA basis of a collection of features
2. Correct computation of intensity values at multiple scales as features. The prior code stopped working with updates to ITKv5that changed how GenerateData and DynamicMultiThreadedGenerateData are used.
3. Update file format for MetaIO RidgeSeed and LDA (and PCA) reading/writing. Now correctly reads/writes statistical whitening values for basis features.
4. Corrected and accelerated computation of statistical whitening values for basis features using variables computed during basis computation.
ENH: Can specify MinLength for vessel extraction - useful for extracting initial vessels used as training examples for vesselenhancement filters.

What's Changed
* ENH: Revert to ITKrc03 and update TubeTK to v1.2.2 by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/115
* Revert "ENH: Revert to ITKrc03 and update TubeTK to v1.2.2" by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/116
* ENH: Update http to https links where valid by tbirdso in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/117
* ENH: and BUG: Fixed RidgeSeedFilter and the classes it uses by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/118
* ENH: Bump version to 1.3 by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/119

New Contributors
* tbirdso made their first contribution in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/117

**Full Changelog**: https://github.com/InsightSoftwareConsortium/ITKTubeTK/compare/v1.2.1-Fix...v1.3-fix

v1.2.1-Fix
What's Changed
* COMP: Specify dependency on ITKThreshold by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/112
* ENH: Support for official release of ITKv5.3 by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/113
* ENH: Bump version to 1.2.1 by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/114


**Full Changelog**: https://github.com/InsightSoftwareConsortium/ITKTubeTK/compare/v1.2...v1.2.1-Fix

Minor bug fixes and updated to support ITKv5.3rc04.

What's Changed
* COMP: Resolved several compiler warnings generated when building VIA ITK. by kian-weimer in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/98
* ENH: Provide a more complete PyPI description by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/106
* ENH: ITK ResolveTimeStep-ValidTimeStep is back to being a bool by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/107
* ENH: Updates to work with ITKv5.3rc04 by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/108
* ENH: Enable specification of target Size for image resampling by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/109
* BUG: Update Write4D python API to support python ITK Image args by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/110
* ENH: TubeTK v1.2 by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/111

New Contributors
* kian-weimer made their first contribution in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/98

**Full Changelog**: https://github.com/InsightSoftwareConsortium/ITKTubeTK/compare/v1.1...v1.2

Supports CTP processing as used by https://github.com/KitwareMedical/ITKTubeTK-StrokeCollateralVessels

- Supports ITK 5.3rc03
- Improved radius estimation for vessels
- Vessel-based registration framework completed
- Had to refactor the ImageMath API due to memory constraints during wheel building. ImageMath in python is now only templated over Input Image Type. It is no longer has a second template argument for Output Image type.
- Python wrapping now supports 2D image registration (RegisterImages function)

What's Changed
* ENH: Upgrade wheels to use ITK53rc02 by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/92
* ENH: Provide a demo of manipulating the radius of tubes in python by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/91
* ENH: Add support for 2D images in the python wrapped RegisterImages by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/93
* COMP: Modules need updated version of ITK by hjmjohnson in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/95
* COMP: Remove inclusion of .hxx files as headers by hjmjohnson in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/94
* ENH: Improved methods and examples for CTA processing by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/96
* COMP: Updating to match API change in ITK for ValidTimeStep by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/99
* BUG: SlicerExecutionModel not finding ITK - verifying by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/100
* ENH: Update baselines for ITKv53rc03 by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/103
* COMP: Reduce the templating of ImageMath python wrapping to save memory by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/101
* ENH: Include documentation file for pypi wheels by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/102

New Contributors
* hjmjohnson made their first contribution in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/95

**Full Changelog**: https://github.com/InsightSoftwareConsortium/ITKTubeTK/compare/v1.0.0...v1.1rc01

Supports CTP processing as used by https://github.com/KitwareMedical/ITKTubeTK-StrokeCollateralVessels

- Supports ITK 5.3rc03
- Improved radius estimation for vessels
- Vessel-based registration framework completed
- Had to refactor the ImageMath API due to memory constraints during wheel building. ImageMath in python is now only templated over Input Image Type. It is no longer has a second template argument for Output Image type.
- Python wrapping now supports 2D image registration (RegisterImages function)

What's Changed
* ENH: Upgrade wheels to use ITK53rc02 by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/92
* ENH: Provide a demo of manipulating the radius of tubes in python by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/91
* ENH: Add support for 2D images in the python wrapped RegisterImages by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/93
* COMP: Modules need updated version of ITK by hjmjohnson in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/95
* COMP: Remove inclusion of .hxx files as headers by hjmjohnson in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/94
* ENH: Improved methods and examples for CTA processing by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/96
* COMP: Updating to match API change in ITK for ValidTimeStep by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/99
* BUG: SlicerExecutionModel not finding ITK - verifying by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/100
* ENH: Update baselines for ITKv53rc03 by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/103
* COMP: Reduce the templating of ImageMath python wrapping to save memory by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/101
* ENH: Include documentation file for pypi wheels by aylward in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/102

New Contributors
* hjmjohnson made their first contribution in https://github.com/InsightSoftwareConsortium/ITKTubeTK/pull/95

**Full Changelog**: https://github.com/InsightSoftwareConsortium/ITKTubeTK/compare/v1.0.0...v1.1rc01

Major changes:
* Supports (requires) ITKv5.3rc01 or greater
* Changed radius estimation method to a 1D optimization problem (fitting a sigmoid to intensity profile around a centerline)
* Refactored spatialObject-to-image registration framework to mimic the image-to-image registration framework used in TubeTK
- Uses evolutionary optimization followed by gradient descent to facilitate a larger capture range for registration
- Uses a image intensity along subsampled points (e.g., centerline points) as a metric
- Supports rigid and affine registration in sequence. Can be easily updated to bspline and other transforms
- Uses tube orientation to remove bias in global updates during registration
* Provides additional examples (jupyter notebooks) for segmentation of organs and vessels from CT and MRI and generation of PDF reports
- Segment tubes from CT perfusion data
- Generate CTA from CT perfusion
- Segment tubes from binary images
- Create tube-enhanced images, and many more
* Supports python wrapping of functions that require VTK (e.g., writeTubesAsPolyData)
* Applications provided as examples (and providing many additional tests). Required VTK and SlicerExecutionModel integration into python wrapping. Application executables still need to be bundled in pypi package.
* Improved tangent and normal computation for 2D and 3D spatial objects (contributed to ITK core)

* Jupyter notebooks as examples
* More methods available in python
* Applications now published as examples - requires SlicerExecutionModel
* TubeTK_USE_VTK now on by default
* Github actions/CI publishes wheels automatically
* Github actions/CI includes VTK (static build) and SlicerExecutionModel