ENH: Improve radius estimation and refactor tube-to-image registratio…

…n framework (#82)

Radius estimation is now performed by fitting a sigmoid to the radius-vs-intensity profile.

TubeToImageRegistration framework is an adaption of the ImageToImageRegistration framework used by TubeTK. It is easily extended to support additional transforms and metrics.

.github/workflows/build-test-package.yml

@@ -5,7 +5,7 @@ on: [push,pull_request]
 env:
   ITKMinimalPathExtraction-git-tag: v1.2.0
   vtk-git-tag: "1681cee3489800373c2e183af2d3ca8552e05940"
-  itk-git-tag: v5.2.0
+  itk-git-tag: v5.2.1
 
 jobs:
   build-test-cxx:
@@ -203,7 +203,7 @@ jobs:
       matrix:
         python-version: [36, 37, 38, 39]
         include:
-          - itk-python-git-tag: "v5.2.0.post2"
+          - itk-python-git-tag: "v5.2.1.post1"
             c-compiler: "gcc"
             cxx-compiler: "g++"
             cmake-build-type: "Release"
@@ -312,7 +312,7 @@ jobs:
       max-parallel: 1
       matrix:
         include:
-          - itk-python-git-tag: "v5.2.0.post2"
+          - itk-python-git-tag: "v5.2.1.post1"
             c-compiler: "clang"
             cxx-compiler: "clang++"
             cmake-build-type: "Release"
@@ -395,7 +395,7 @@ jobs:
       matrix:
         python-version-minor: [6, 7, 8, 9]
         include:
-          - itk-python-git-tag: "v5.2.0.post2"
+          - itk-python-git-tag: "v5.2.1.post1"
             c-compiler: "cl.exe"
             cxx-compiler: "cl.exe"
             cmake-build-type: "Release"

examples/Applications/CMakeLists.txt

@@ -53,7 +53,6 @@ add_subdirectory( AtlasBuilderUsingIntensity )
 add_subdirectory( ComputeBinaryImageSimilarityMetrics )
 add_subdirectory( ComputeImageSimilarityMetrics )
 add_subdirectory( ComputeImageStatistics )
-add_subdirectory( ComputeImageToTubeRigidMetricImage )
 add_subdirectory( ComputeTrainingMask )
 add_subdirectory( ComputeTubeFlyThroughImage )
 add_subdirectory( ComputeTubeGraphProbability )
@@ -83,14 +82,13 @@ add_subdirectory( EnhanceTubesUsingDiffusion )
 add_subdirectory( EnhanceTubesUsingDiscriminantAnalysis )
 add_subdirectory( EnhanceUsingDiscriminantAnalysis )
 add_subdirectory( EnhanceUsingNJetDiscriminantAnalysis )
-add_subdirectory( ExtractMetricImageSlice )
 add_subdirectory( ImageMath )
 add_subdirectory( MergeAdjacentImages )
 add_subdirectory( MergeTubeGraphs )
 add_subdirectory( ResampleImage )
 add_subdirectory( ResampleTubes )
 add_subdirectory( RegisterImages )
-add_subdirectory( RegisterImageToTubesUsingRigidTransform )
+add_subdirectory( RegisterSpatialObjectsToImage )
 add_subdirectory( SampleCLIApplication )
 add_subdirectory( SegmentBinaryImageSkeleton3D )
 add_subdirectory( SegmentConnectedComponents )