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Merge pull request #167 from ANTsX/fix-name-collisions
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FIX: remove name collisions
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Nicholas Cullen, PhD authored May 19, 2024
2 parents a72ea51 + f3debd6 commit 38c4f06
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Showing 30 changed files with 225 additions and 224 deletions.
1 change: 1 addition & 0 deletions .gitignore
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@@ -1,5 +1,6 @@
*.tgz
..Rcheck/
.vscode/

docs
/src/*.o
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112 changes: 56 additions & 56 deletions R/RcppExports.R
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Expand Up @@ -30,16 +30,16 @@ DenoiseImage <- function(r_args) {
.Call(`_ANTsRCore_DenoiseImage`, r_args)
}

fitBsplineDisplacementField <- function(r_dimensionality, r_displacementField, r_displacementFieldWeightImage, r_displacementOrigins, r_displacements, r_displacementWeights, r_origin, r_spacing, r_size, r_direction, r_numberOfFittingLevels, r_numberOfControlPoints, r_splineOrder, r_enforceStationaryBoundary, r_estimateInverse, r_rasterizePoints) {
.Call(`_ANTsRCore_fitBsplineDisplacementField`, r_dimensionality, r_displacementField, r_displacementFieldWeightImage, r_displacementOrigins, r_displacements, r_displacementWeights, r_origin, r_spacing, r_size, r_direction, r_numberOfFittingLevels, r_numberOfControlPoints, r_splineOrder, r_enforceStationaryBoundary, r_estimateInverse, r_rasterizePoints)
fitBsplineDisplacementFieldR <- function(r_dimensionality, r_displacementField, r_displacementFieldWeightImage, r_displacementOrigins, r_displacements, r_displacementWeights, r_origin, r_spacing, r_size, r_direction, r_numberOfFittingLevels, r_numberOfControlPoints, r_splineOrder, r_enforceStationaryBoundary, r_estimateInverse, r_rasterizePoints) {
.Call(`_ANTsRCore_fitBsplineDisplacementFieldR`, r_dimensionality, r_displacementField, r_displacementFieldWeightImage, r_displacementOrigins, r_displacements, r_displacementWeights, r_origin, r_spacing, r_size, r_direction, r_numberOfFittingLevels, r_numberOfControlPoints, r_splineOrder, r_enforceStationaryBoundary, r_estimateInverse, r_rasterizePoints)
}

fitBsplineObjectToScatteredData <- function(r_scatteredData, r_parametricData, r_dataWeights, r_parametricDomainOrigin, r_parametricDomainSpacing, r_parametricDomainSize, r_isParametricDimensionClosed, r_numberOfFittingLevels, r_numberOfControlPoints, r_splineOrder) {
.Call(`_ANTsRCore_fitBsplineObjectToScatteredData`, r_scatteredData, r_parametricData, r_dataWeights, r_parametricDomainOrigin, r_parametricDomainSpacing, r_parametricDomainSize, r_isParametricDimensionClosed, r_numberOfFittingLevels, r_numberOfControlPoints, r_splineOrder)
fitBsplineObjectToScatteredDataR <- function(r_scatteredData, r_parametricData, r_dataWeights, r_parametricDomainOrigin, r_parametricDomainSpacing, r_parametricDomainSize, r_isParametricDimensionClosed, r_numberOfFittingLevels, r_numberOfControlPoints, r_splineOrder) {
.Call(`_ANTsRCore_fitBsplineObjectToScatteredDataR`, r_scatteredData, r_parametricData, r_dataWeights, r_parametricDomainOrigin, r_parametricDomainSpacing, r_parametricDomainSize, r_isParametricDimensionClosed, r_numberOfFittingLevels, r_numberOfControlPoints, r_splineOrder)
}

fitThinPlateSplineDisplacementField <- function(r_dimensionality, r_displacementOrigins, r_displacements, r_origin, r_spacing, r_size, r_direction) {
.Call(`_ANTsRCore_fitThinPlateSplineDisplacementField`, r_dimensionality, r_displacementOrigins, r_displacements, r_origin, r_spacing, r_size, r_direction)
fitThinPlateSplineDisplacementFieldR <- function(r_dimensionality, r_displacementOrigins, r_displacements, r_origin, r_spacing, r_size, r_direction) {
.Call(`_ANTsRCore_fitThinPlateSplineDisplacementFieldR`, r_dimensionality, r_displacementOrigins, r_displacements, r_origin, r_spacing, r_size, r_direction)
}

HausdorffDistanceR <- function(r_inputImage1, r_inputImage2) {
Expand All @@ -50,12 +50,12 @@ histogramMatchImageR <- function(r_sourceImage, r_referenceImage, r_numberOfHist
.Call(`_ANTsRCore_histogramMatchImageR`, r_sourceImage, r_referenceImage, r_numberOfHistogramBins, r_numberOfMatchPoints, r_useThresholdAtMeanIntensity)
}

integrateVelocityField <- function(r_dimensionality, r_velocityField, r_lowerBound, r_upperBound, r_numberOfIntegrationSteps) {
.Call(`_ANTsRCore_integrateVelocityField`, r_dimensionality, r_velocityField, r_lowerBound, r_upperBound, r_numberOfIntegrationSteps)
integrateVelocityFieldR <- function(r_dimensionality, r_velocityField, r_lowerBound, r_upperBound, r_numberOfIntegrationSteps) {
.Call(`_ANTsRCore_integrateVelocityFieldR`, r_dimensionality, r_velocityField, r_lowerBound, r_upperBound, r_numberOfIntegrationSteps)
}

invertDisplacementField <- function(r_dimensionality, r_displacementField, r_inverseFieldInitialEstimate, r_maxNumberOfIterations, r_meanErrorToleranceThreshold, r_maxErrorToleranceThreshold, r_enforceBoundaryCondition) {
.Call(`_ANTsRCore_invertDisplacementField`, r_dimensionality, r_displacementField, r_inverseFieldInitialEstimate, r_maxNumberOfIterations, r_meanErrorToleranceThreshold, r_maxErrorToleranceThreshold, r_enforceBoundaryCondition)
invertDisplacementFieldR <- function(r_dimensionality, r_displacementField, r_inverseFieldInitialEstimate, r_maxNumberOfIterations, r_meanErrorToleranceThreshold, r_maxErrorToleranceThreshold, r_enforceBoundaryCondition) {
.Call(`_ANTsRCore_invertDisplacementFieldR`, r_dimensionality, r_displacementField, r_inverseFieldInitialEstimate, r_maxNumberOfIterations, r_meanErrorToleranceThreshold, r_maxErrorToleranceThreshold, r_enforceBoundaryCondition)
}

KellyKapowski <- function(r_args) {
Expand Down Expand Up @@ -94,16 +94,16 @@ ThresholdImage <- function(r_args) {
.Call(`_ANTsRCore_ThresholdImage`, r_args)
}

antsAffineInitializer <- function(r_args) {
.Call(`_ANTsRCore_antsAffineInitializer`, r_args)
AntsAffineInitializer <- function(r_args) {
.Call(`_ANTsRCore_AntsAffineInitializer`, r_args)
}

antsApplyTransforms <- function(r_args) {
.Call(`_ANTsRCore_antsApplyTransforms`, r_args)
AntsApplyTransforms <- function(r_args) {
.Call(`_ANTsRCore_AntsApplyTransforms`, r_args)
}

antsApplyTransformsToPoints <- function(r_args) {
.Call(`_ANTsRCore_antsApplyTransformsToPoints`, r_args)
AntsApplyTransformsToPoints <- function(r_args) {
.Call(`_ANTsRCore_AntsApplyTransformsToPoints`, r_args)
}

antsImage <- function(r_pixeltype, r_dimension, r_components) {
Expand Down Expand Up @@ -202,8 +202,8 @@ antsImageArithImageImage <- function(r_antsimage1, r_antsimage2, r_operator) {
.Call(`_ANTsRCore_antsImageArithImageImage`, r_antsimage1, r_antsimage2, r_operator)
}

antsImageClone <- function(r_in_image, r_out_pixeltype) {
.Call(`_ANTsRCore_antsImageClone`, r_in_image, r_out_pixeltype)
AntsImageClone <- function(r_in_image, r_out_pixeltype) {
.Call(`_ANTsRCore_AntsImageClone`, r_in_image, r_out_pixeltype)
}

antsImageComparisonImageNumeric <- function(r_antsimage, r_numeric, r_operator) {
Expand All @@ -214,12 +214,12 @@ antsImageComparisonImageImage <- function(r_antsimage1, r_antsimage2, r_operator
.Call(`_ANTsRCore_antsImageComparisonImageImage`, r_antsimage1, r_antsimage2, r_operator)
}

antsImageHeaderInfo <- function(r_filename) {
.Call(`_ANTsRCore_antsImageHeaderInfo`, r_filename)
AntsImageHeaderInfo <- function(r_filename) {
.Call(`_ANTsRCore_AntsImageHeaderInfo`, r_filename)
}

antsImageIterator <- function(r_antsimage) {
.Call(`_ANTsRCore_antsImageIterator`, r_antsimage)
AntsImageIterator <- function(r_antsimage) {
.Call(`_ANTsRCore_AntsImageIterator`, r_antsimage)
}

antsImageIterator_Get <- function(r_antsimageiterator) {
Expand Down Expand Up @@ -282,16 +282,16 @@ antsImageMutualInformation <- function(r_in_image1, r_in_image2) {
.Call(`_ANTsRCore_antsImageMutualInformation`, r_in_image1, r_in_image2)
}

antsImageRead <- function(r_filename, r_pixeltype, r_dimension, r_components) {
.Call(`_ANTsRCore_antsImageRead`, r_filename, r_pixeltype, r_dimension, r_components)
AntsImageRead <- function(r_filename, r_pixeltype, r_dimension, r_components) {
.Call(`_ANTsRCore_AntsImageRead`, r_filename, r_pixeltype, r_dimension, r_components)
}

antsImageStats <- function(r_antsimage, r_mask, r_narm) {
.Call(`_ANTsRCore_antsImageStats`, r_antsimage, r_mask, r_narm)
AntsImageStats <- function(r_antsimage, r_mask, r_narm) {
.Call(`_ANTsRCore_AntsImageStats`, r_antsimage, r_mask, r_narm)
}

antsImageWrite <- function(r_img, r_filename, r_asTensor) {
.Call(`_ANTsRCore_antsImageWrite`, r_img, r_filename, r_asTensor)
AntsImageWrite <- function(r_img, r_filename, r_asTensor) {
.Call(`_ANTsRCore_AntsImageWrite`, r_img, r_filename, r_asTensor)
}

antsJointFusion <- function(r_args) {
Expand All @@ -310,16 +310,16 @@ antsMatrix_asantsMatrix <- function(r_list, r_elementtype) {
.Call(`_ANTsRCore_antsMatrix_asantsMatrix`, r_list, r_elementtype)
}

antsMotionCorr <- function(r_args) {
.Call(`_ANTsRCore_antsMotionCorr`, r_args)
AntsMotionCorr <- function(r_args) {
.Call(`_ANTsRCore_AntsMotionCorr`, r_args)
}

antsMotionCorrStats <- function(r_tsimg, r_mask, r_moco, r_stupidoffset) {
.Call(`_ANTsRCore_antsMotionCorrStats`, r_tsimg, r_mask, r_moco, r_stupidoffset)
}

antsRegistration <- function(r_args) {
.Call(`_ANTsRCore_antsRegistration`, r_args)
AntsRegistration <- function(r_args) {
.Call(`_ANTsRCore_AntsRegistration`, r_args)
}

antsrMetric <- function(r_pixeltype, r_dimension, r_type, r_isVector, r_fixed, r_moving) {
Expand Down Expand Up @@ -418,20 +418,20 @@ antsrTransform_Write <- function(r_transform, filename_) {
.Call(`_ANTsRCore_antsrTransform_Write`, r_transform, filename_)
}

cropImage <- function(r_in_image1, r_in_image2, r_label, r_decrop, r_loind, r_upind) {
.Call(`_ANTsRCore_cropImage`, r_in_image1, r_in_image2, r_label, r_decrop, r_loind, r_upind)
CropImage <- function(r_in_image1, r_in_image2, r_label, r_decrop, r_loind, r_upind) {
.Call(`_ANTsRCore_CropImage`, r_in_image1, r_in_image2, r_label, r_decrop, r_loind, r_upind)
}

extractSlice <- function(r_in_image1, r_slice, r_direction, r_collapseStrategy) {
.Call(`_ANTsRCore_extractSlice`, r_in_image1, r_slice, r_direction, r_collapseStrategy)
ExtractSlice <- function(r_in_image1, r_slice, r_direction, r_collapseStrategy) {
.Call(`_ANTsRCore_ExtractSlice`, r_in_image1, r_slice, r_direction, r_collapseStrategy)
}

fastMarchingExtension <- function(r_speedImage, r_labelImage, r_valueImage) {
.Call(`_ANTsRCore_fastMarchingExtension`, r_speedImage, r_labelImage, r_valueImage)
}

fsl2antsrTransform <- function(r_matrix, r_reference, r_moving, r_flag) {
.Call(`_ANTsRCore_fsl2antsrTransform`, r_matrix, r_reference, r_moving, r_flag)
fsl2antsrTransformR <- function(r_matrix, r_reference, r_moving, r_flag) {
.Call(`_ANTsRCore_fsl2antsrTransformR`, r_matrix, r_reference, r_moving, r_flag)
}

iMathInterface <- function(r_args) {
Expand All @@ -446,8 +446,8 @@ iMathInterface2 <- function(r_args) {
.Call(`_ANTsRCore_iMathInterface2`, r_args)
}

imagesToMatrix <- function(r_fns, r_mask, r_n) {
.Call(`_ANTsRCore_imagesToMatrix`, r_fns, r_mask, r_n)
imagesToMatrixR <- function(r_fns, r_mask, r_n) {
.Call(`_ANTsRCore_imagesToMatrixR`, r_fns, r_mask, r_n)
}

invariantImageSimilarity <- function(r_in_image1, r_in_image2, thetas, thetas2, thetas3, localSearchIterations, whichMetric, r_scale, r_doref, txfn, whichTransform, r_mask) {
Expand All @@ -458,16 +458,16 @@ itkConvolveImage <- function(r_in_image1, r_in_image2) {
.Call(`_ANTsRCore_itkConvolveImage`, r_in_image1, r_in_image2)
}

labelStats <- function(r_image, r_labelImage) {
.Call(`_ANTsRCore_labelStats`, r_image, r_labelImage)
labelStatsR <- function(r_image, r_labelImage) {
.Call(`_ANTsRCore_labelStatsR`, r_image, r_labelImage)
}

makeImage <- function(r_pixeltype, r_size, r_spacing, r_origin, r_direction, r_components) {
.Call(`_ANTsRCore_makeImage`, r_pixeltype, r_size, r_spacing, r_origin, r_direction, r_components)
makeImageR <- function(r_pixeltype, r_size, r_spacing, r_origin, r_direction, r_components) {
.Call(`_ANTsRCore_makeImageR`, r_pixeltype, r_size, r_spacing, r_origin, r_direction, r_components)
}

mergeChannels <- function(r_imageList) {
.Call(`_ANTsRCore_mergeChannels`, r_imageList)
mergeChannelsR <- function(r_imageList) {
.Call(`_ANTsRCore_mergeChannelsR`, r_imageList)
}

blobAnalysis <- function(r_inimg, r_outimg, r_numberOfBlobsToExtract, r_minScale, r_maxScale, r_stepsPerOctave) {
Expand All @@ -486,12 +486,12 @@ rcpp_hello_world33 <- function() {
.Call(`_ANTsRCore_rcpp_hello_world33`)
}

reflectionMatrix <- function(r_image, r_axis, r_filename) {
.Call(`_ANTsRCore_reflectionMatrix`, r_image, r_axis, r_filename)
reflectionMatrixR <- function(r_image, r_axis, r_filename) {
.Call(`_ANTsRCore_reflectionMatrixR`, r_image, r_axis, r_filename)
}

reorientImage <- function(r_in_image1, r_txfn, r_axis1, r_axis2, rrfl, rscl) {
.Call(`_ANTsRCore_reorientImage`, r_in_image1, r_txfn, r_axis1, r_axis2, rrfl, rscl)
reorientImageR <- function(r_in_image1, r_txfn, r_axis1, r_axis2, rrfl, rscl) {
.Call(`_ANTsRCore_reorientImageR`, r_in_image1, r_txfn, r_axis1, r_axis2, rrfl, rscl)
}

centerOfMass <- function(r_in_image1) {
Expand All @@ -514,19 +514,19 @@ sccanCpp <- function(r_X, r_Y, r_maskx, r_masky, r_sparsenessx, r_sparsenessy, r
.Call(`_ANTsRCore_sccanCpp`, r_X, r_Y, r_maskx, r_masky, r_sparsenessx, r_sparsenessy, r_nvecs, r_its, r_cthreshx, r_cthreshy, r_z, r_smooth, r_initializationListx, r_initializationListy, r_mycoption, r_ell1, r_verbose, r_priorWeight, r_maxBasedThresh)
}

smoothImage <- function(r_inimg, r_outimg, r_sigma, sigmaInPhysicalCoordinates, r_kernelwidth) {
.Call(`_ANTsRCore_smoothImage`, r_inimg, r_outimg, r_sigma, sigmaInPhysicalCoordinates, r_kernelwidth)
smoothImageR <- function(r_inimg, r_outimg, r_sigma, sigmaInPhysicalCoordinates, r_kernelwidth) {
.Call(`_ANTsRCore_smoothImageR`, r_inimg, r_outimg, r_sigma, sigmaInPhysicalCoordinates, r_kernelwidth)
}

splitChannels <- function(r_antsimage) {
.Call(`_ANTsRCore_splitChannels`, r_antsimage)
splitChannelsR <- function(r_antsimage) {
.Call(`_ANTsRCore_splitChannelsR`, r_antsimage)
}

timeSeriesSubtraction <- function(r_antsimage, method) {
.Call(`_ANTsRCore_timeSeriesSubtraction`, r_antsimage, method)
}

weingartenImageCurvature <- function(r_antsimage, r_sigma, r_opt, r_labeled) {
.Call(`_ANTsRCore_weingartenImageCurvature`, r_antsimage, r_sigma, r_opt, r_labeled)
weingartenImageCurvatureR <- function(r_antsimage, r_sigma, r_opt, r_labeled) {
.Call(`_ANTsRCore_weingartenImageCurvatureR`, r_antsimage, r_sigma, r_opt, r_labeled)
}

2 changes: 1 addition & 1 deletion src/FitBSplineDisplacementField.cpp
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Expand Up @@ -305,7 +305,7 @@ SEXP fitBSplineVectorImageHelper(
}

// [[Rcpp::export]]
SEXP fitBsplineDisplacementField(
SEXP fitBsplineDisplacementFieldR(
SEXP r_dimensionality,
SEXP r_displacementField,
SEXP r_displacementFieldWeightImage,
Expand Down
2 changes: 1 addition & 1 deletion src/FitBSplineObjectToScatteredData.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -349,7 +349,7 @@ SEXP fitBSplineVectorImageHelper(
}

// [[Rcpp::export]]
SEXP fitBsplineObjectToScatteredData(
SEXP fitBsplineObjectToScatteredDataR(
SEXP r_scatteredData,
SEXP r_parametricData,
SEXP r_dataWeights,
Expand Down
2 changes: 1 addition & 1 deletion src/FitThinPlateSplineDisplacementField.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -132,7 +132,7 @@ SEXP fitThinPlateSplineVectorImageHelper(
}

// [[Rcpp::export]]
SEXP fitThinPlateSplineDisplacementField(
SEXP fitThinPlateSplineDisplacementFieldR(
SEXP r_dimensionality,
SEXP r_displacementOrigins,
SEXP r_displacements,
Expand Down
2 changes: 1 addition & 1 deletion src/IntegrateVelocityField.cpp
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Expand Up @@ -93,7 +93,7 @@ SEXP integrateVelocityFieldHelper(
}

// [[Rcpp::export]]
SEXP integrateVelocityField(
SEXP integrateVelocityFieldR(
SEXP r_dimensionality,
SEXP r_velocityField,
SEXP r_lowerBound,
Expand Down
2 changes: 1 addition & 1 deletion src/InvertDisplacementField.cpp
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Expand Up @@ -103,7 +103,7 @@ SEXP invertDisplacementFieldHelper(
}

// [[Rcpp::export]]
SEXP invertDisplacementField(
SEXP invertDisplacementFieldR(
SEXP r_dimensionality,
SEXP r_displacementField,
SEXP r_inverseFieldInitialEstimate,
Expand Down
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