SuperElastix/elastix: 5.3.0

Preliminary Release Notes Major improvements of this release IMPACT metric van Valentin Boussot TOML support parameter files Fixed width types ("int8", "float64", etc) for ResultImagePixelType Support registering a 3D slice on a 3D volume "-def": Transform VTK files in accordance with their format and floating point precision (rather than always ASCII 64-bit) Library enhancements: Add SetFixedPoints, SetMovingPoints to ElastixRegistrationMethod Random numbers multithreading registrations deterministic What's Changed BUG: Replace Doxygen "Modules" with "Topics" in pull request #1204 Append "Flat" to "OriginalFixedImage/fixedImageOriginal" Direction identifiers, replace some this-> in pull request #1206 STYLE: Remove warning when UseDirectionCosines is unspecified in pull request #1210 DOC: Fix documentation about order of matrix elements Rigid3DTransform in pull request #1211 Declare AdvancedBSplineDeformableTransform data members as C-style array, remove this-> in pull request #1212 Remove ValidRegion properties from BSpline Transforms in pull request #1213 Simplify offset estimations for AdvancedBSplineDeformableTransform::SetGridRegion in pull request #1214 Add notes on the order of matrix elements of Direction and GridDirection parameters in pull request #1208 DOC: Add references to Zenodo to README, for software DOIs in pull request #1217 Remove GoToBegin() calls after iterator construction, move iterator variable declarations into init-statement of for in pull request #1218 COMP: Remove ITK_DISALLOW_COPY_AND_MOVE from UserData struct's by @thewtex in pull request #1202 STYLE: Remove commented out ITK_DISALLOW_COPY_AND_MOVE call in pull request #1220 STYLE: Use auto more extensively, by clang-tidy modernize-use-auto in pull request #1219 STYLE: Use "typename" for template parameters in pull request #1221 PERF: itkGPUShrinkImageFilter use faster TransformPhysicalPointToIndex in pull request #1223 COMP: Make itkUseMevisDicomTiff.cxx compile with ITK >= 5.1 in pull request #1222 STYLE: Use modern C++ range-based for loops in Core/Main and Common in pull request #1225 COMP: Add missing semicolons to ITK macro calls in pull request #1227 COMP: Add missing semicolons to ElastixRegistrationMethod and OpenCL in pull request #1228 Improve elastix SplineKernelTransform handling "-ipp"/"-fp" landmark file parameter in pull request #1229 Declare check variables const, rename them to "commandLineArgument" in pull request #1230 Remove std::ostringstream{} << when logging a literal string or a command-line argument in pull request #1231 Remove ReadLandmarks from StatisticalShapePenalty, make it private in CorrespondingPointsEuclideanDistanceMetric in pull request #1232 Use GetFixedPoints, GetMovingPoints in CorrespondingPointsEuclideanDistanceMetric and other style improvements in pull request #1233 STYLE: Use GetFixedPoints() in StatisticalShapePointPenalty in pull request #1234 Add CorrespondingPointsEuclideanDistancePointMetric GoogleTest unit tests in pull request #1235 COMP: Upgrade clang-format-lint-action to v0.18.2 in pull request #1236 PERF: EuclideanDistanceMetric get vector norm without GetVnlVector() in pull request #1237 STYLE: Remove TElementIdentifier parameter from VectorDataContainer in pull request #1241 ENH: Add ElastixRegistrationMethod::ImageDimension in pull request #1240 ENH: EuclideanDistanceMetric check that point sets are specified in pull request #1243 STYLE: Declare local point sets in EuclideanDistanceMetric "const" in pull request #1244 PERF: Make GPUImageDataManager->m_Image a weak pointer by @Sager611 in pull request #1242 Use modern C++ range-based for loops in OpenCL/GPU based code in pull request #1226 COMP: remove __write_only from all OpenCL*.cl kernels by @dpshamonin in pull request #1246 Itk OpenCLImage test fixes by @dpshamonin in pull request #1247 COMP: Add missing semicolon to macro call itkOpenCLVector.hxx line 113 in pull request #1249 STYLE: Remove top level const from GetDefaultParameterMap return type in pull request #1251 STYLE: Clean up AdvancedCombinationTransform::GetNthTransform in pull request #1252 Add itkElastixRegistrationMethod Similarity transform unit tests in pull request #1254 Transform VTK files in accordance with their format and floating point precision in pull request #1253 STYLE: Replace Fill(0) on local variables with {} initialization in pull request #1257 STYLE: Replace Fill(0U) and Fill(0.0f) on local variables with {} in pull request #1259 Replace itkTypeMacroNoParent, itkTypeMacro with itkVirtualGetNameOfClassMacro, itkOverrideGetNameOfClassMacro in pull request #1262 Remove unused PointDataIterator and PointSetPixelType typedefs in pull request #1263 Clean-up using-declarations and typedef's CorrespondingPointsEuclideanDistancePoint and other metrics in pull request #1265 COMP: Upgrade GitHub actions/upload-artifact from v3 to v4.4.3 in pull request #1264 Add SetFixedPoints and SetMovingPoints to ElastixRegistrationMethod, for point-to-point EuclideanDistanceMetric in pull request #1239 Replace T var; var.Fill with auto var = T::Filled, for both Index and Size in pull request #1266 Replace Fill calls with auto var = MakeFilled<T> in pull request #1268 STYLE: Replace T var; var = x with T var = x in pull request #1269 STYLE: Replace T::Pointer with auto when initializing variables by New() in pull request #1271 STYLE: Simplify PyramidImageFilter member SetRescaleScheduleToUnity() in pull request #1267 Let ComputeJacobianTerms::Compute return the terms, and other style improvements in "Common/itkCompute." in pull request #1272 Remove notfinished variables from ComputeJacobianTerms, and other style improvements in pull request #1273 COMP: Replace macos-12/macOS-12 with macos-13/macOS-13, in *.yml in pull request #1274 Simplify use of NonZeroJacobianIndices in Common/itkCompute*.hxx, let SampleFixedImageForJacobianTerms() return std::vector, etc in pull request #1275 Remove sampler typedefs from "Common/itkCompute*.h", let Compute...Distribution use their own template parameters in pull request #1276 Use vnl_sparse_matrix::get in ComputeJacobianTerms::Compute() in pull request #1277 COMP: Upgrade from ITK 5.4.0 to ITK 5.4.1 in pull request #1279 Replace "CoordRep" with "Coordinate" in pull request #1280 DOC: Add EOSS badge to README in pull request #1282 STYLE: Remove this-> when ParameterFileParser accesses its own data in pull request #1285 Make ReturnParameterFileAsString static, remove m_ParameterFileParser from Configuration in pull request #1286 Print the parameter map to log, when there is no parameter file in pull request #1287 Support the TOML file format for input parameter files in pull request #1288 ENH: Support OutputTransformParameterFileFormat parameter for TOML in pull request #1289 Upgrade clang-format from version 8.0.0 to 19.1.4 in pull request #1290 ENH: Add pre-commit and pixi configuration by @thewtex in pull request #1291 Remove dynamic_cast's from NDImageBase::NewNDImage, modernize NDImageTemplate, etc. in pull request #1294 pre commit action by @thewtex in pull request #1293 STYLE: Remove this-> when elx::TransformBase accesses its own data in pull request #1295 STYLE: Simplify creating string representation of stop conditions in pull request #1296 Document the OutputTransformParameterFileFormat parameter, extend its test, etc. in pull request #1297 STYLE: Simplify retrieval of line from TOML file in pull request #1299 ENH: Let ElastixBase print git revision info, also for library users in pull request #1300 Replace various std::pow calls in pull request #1301 DOC: Fix ModelZoo URL: https://lkeb.ml/modelzoo/ in pull request #1304 STYLE: Calculate centerOfRotationIndex StackTransform in 64-bit double in pull request #1307 Remove RandomIteratorType and "random" ITK #include's in pull request #1308 Remove unnecessary private m_NumberOfPixelsCounted data members in pull request #1310 Remove parameters from CheckNumberOfSamples, let AdvancedImageToImageMetric directly access its own data in pull request #1309 BUG: Fix calculation CenterOfRotationPoint in EulerStackTransform in pull request #1306 STYLE: Remove sigma4factor from StochasticGradientDescent Optimizers in pull request #1270 STYLE: Drop the index-based "CenterOfRotation" transform parameter in pull request #1305 Avoid lossy string-to-float conversion by ParameterObject::PrintSelf in pull request #1312 STYLE: Remove unused variables from InitializeTransform stack transforms in pull request #1302 Declare ReadCenterOfRotationPoint private and non-virtual, let InitializeTransform() call ReadCenterOfRotationPoint, etc. in pull request #1313 COMP: Upgrade Azure Pipelines CI from ubuntu-20.04 to ubuntu-22.04 in pull request #1315 InitializeTransform() style improvements, including adding local configuration variables in pull request #1314 ENH: Replace unsigned long with uint64_t for non-zero Jacobian indices in pull request #1316 Replace (long) with static_cast<int64_t> in CalcRayIntercepts(), and also replace other uses of long in pull request #1317 COMP: Upgrade GitHub Actions to Python 3.9 in pull request #1320 ENH: Make random numbers multithreading registrations deterministic in pull request #1323 Bring SetInitialCausalCoefficient in sync with ITK, remove static_cast<unsigned int> from dimension constants, etc. in pull request #1324 STYLE: Add local configuration variables to elxAdvancedAffineTransform in pull request #1325 ENH: Run tests both in Release and in Debug mode in pull request #1326 COMP: Add missing semicolons by @blowekamp in pull request #1327 Replace VectorDataContainer::Size() calls with std::vector::size(), use size_t in pull request #1328 Use local variable for infoChanger output in CreateItkResultImage, use lambda for resultImage in pull request #1330 STYLE: Improve const-correctness TransformImage interface (ABI change) in pul