SuperElastix/elastix: 5.3.0
Zenodo (CERN European Organization for Nuclear Research)
Abstract
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 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 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 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
Authors 30
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Niels Dekker Aachen
Leiden University Medical Center
Affiliation as printed
LKEB, Leiden University Medical Center
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Marius Staring Aachen
Leiden University Medical Center
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Leiden University Medical Center
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Erasmus MC
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Division of Image Processing (LKEB)
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@fideus-labs
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ISO - horti innovators
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Laboratoire Traitement du Signal et de l'Image
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LTSI
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@KitwareMedical
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Stoppels Consulting
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PerkLab, Queen's University
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Brigham and Women's Hospital
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@EBATINCA @pixelmedical
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