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WIP: Convert "parameters.*.toml" files from elastix txt to TOML
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| // This parameter file is used to register the images | ||
| // 2D_square_object_at_(1,3) and 2D_square_object_at_(2,1). | ||
| # This parameter file is used to register the images | ||
| # 2D_square_object_at_(1,3) and 2D_square_object_at_(2,1). | ||
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| (FixedInternalImagePixelType "float") | ||
| (FixedImageDimension 2) | ||
| (MovingInternalImagePixelType "float") | ||
| (MovingImageDimension 2) | ||
| FixedInternalImagePixelType = "float" | ||
| FixedImageDimension = 2 | ||
| MovingInternalImagePixelType = "float" | ||
| MovingImageDimension = 2 | ||
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| (Metric "AdvancedNormalizedCorrelation") | ||
| (Optimizer "AdaptiveStochasticGradientDescent") | ||
| (Transform "TranslationTransform") | ||
| (MaximumNumberOfIterations 2) | ||
| (ImageSampler "Full") | ||
| Metric = "AdvancedNormalizedCorrelation" | ||
| Optimizer = "AdaptiveStochasticGradientDescent" | ||
| Transform = "TranslationTransform" | ||
| MaximumNumberOfIterations = 2 | ||
| ImageSampler = "Full" |
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| @@ -1,88 +1,88 @@ | ||
| // This parameter file has kind of realistic values. | ||
| // In most other parameter files for testing, the number of samples and iterations is rather low, to allow fast testing. | ||
| # This parameter file has kind of realistic values. | ||
| # In most other parameter files for testing, the number of samples and iterations is rather low, to allow fast testing. | ||
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| // ********** Image Types | ||
| # ********** Image Types | ||
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| (FixedInternalImagePixelType "float") | ||
| (FixedImageDimension 3) | ||
| (MovingInternalImagePixelType "float") | ||
| (MovingImageDimension 3) | ||
| FixedInternalImagePixelType = "float" | ||
| FixedImageDimension = 3 | ||
| MovingInternalImagePixelType = "float" | ||
| MovingImageDimension = 3 | ||
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| // ********** Components | ||
| # ********** Components | ||
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| (Registration "MultiResolutionRegistration") | ||
| (FixedImagePyramid "FixedRecursiveImagePyramid") | ||
| (MovingImagePyramid "MovingRecursiveImagePyramid") | ||
| (Interpolator "NearestNeighborInterpolator") | ||
| (Metric "AdvancedKappaStatistic") | ||
| (Optimizer "AdaptiveStochasticGradientDescent") | ||
| (ResampleInterpolator "FinalBSplineInterpolator") | ||
| (Resampler "DefaultResampler") | ||
| (Transform "BSplineTransform") | ||
| Registration = "MultiResolutionRegistration" | ||
| FixedImagePyramid = "FixedRecursiveImagePyramid" | ||
| MovingImagePyramid = "MovingRecursiveImagePyramid" | ||
| Interpolator = "NearestNeighborInterpolator" | ||
| Metric = "AdvancedKappaStatistic" | ||
| Optimizer = "AdaptiveStochasticGradientDescent" | ||
| ResampleInterpolator = "FinalBSplineInterpolator" | ||
| Resampler = "DefaultResampler" | ||
| Transform = "BSplineTransform" | ||
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| // ********** Pyramid | ||
| # ********** Pyramid | ||
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| // Total number of resolutions | ||
| (NumberOfResolutions 3) | ||
| (ImagePyramidSchedule 4 4 4 2 2 2 1 1 1) | ||
| # Total number of resolutions | ||
| NumberOfResolutions = 3 | ||
| ImagePyramidSchedule = [4, 4, 4, 2, 2, 2, 1, 1, 1] | ||
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| // ********** Transform | ||
| # ********** Transform | ||
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| (FinalGridSpacingInPhysicalUnits 10.0 10.0 10.0) | ||
| (GridSpacingSchedule 4.0 2.0 1.0) | ||
| (HowToCombineTransforms "Compose") | ||
| FinalGridSpacingInPhysicalUnits = [10.0, 10.0, 10.0] | ||
| GridSpacingSchedule = [4.0, 2.0, 1.0] | ||
| HowToCombineTransforms = "Compose" | ||
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| // ********** Optimizer | ||
| # ********** Optimizer | ||
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| // Maximum number of iterations in each resolution level: | ||
| (MaximumNumberOfIterations 100) | ||
| # Maximum number of iterations in each resolution level: | ||
| MaximumNumberOfIterations = 100 | ||
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| (AutomaticParameterEstimation "true") | ||
| (UseAdaptiveStepSizes "true") | ||
| AutomaticParameterEstimation = true | ||
| UseAdaptiveStepSizes = true | ||
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| // ********** Metric | ||
| # ********** Metric | ||
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| (UseComplement "true") | ||
| (UseForegroundValue "false") | ||
| (ForegroundValue 1) | ||
| UseComplement = true | ||
| UseForegroundValue = false | ||
| ForegroundValue = 1 | ||
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| // ********** Several | ||
| # ********** Several | ||
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| (WriteTransformParametersEachIteration "false") | ||
| (WriteTransformParametersEachResolution "true") | ||
| (WriteResultImageAfterEachResolution "false") | ||
| (WritePyramidImagesAfterEachResolution "false") | ||
| (WriteResultImage "false") | ||
| (ShowExactMetricValue "false") | ||
| (ErodeMask "false") | ||
| (UseDirectionCosines "true") | ||
| WriteTransformParametersEachIteration = false | ||
| WriteTransformParametersEachResolution = true | ||
| WriteResultImageAfterEachResolution = false | ||
| WritePyramidImagesAfterEachResolution = false | ||
| WriteResultImage = false | ||
| ShowExactMetricValue = false | ||
| ErodeMask = false | ||
| UseDirectionCosines = true | ||
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| // ********** ImageSampler | ||
| # ********** ImageSampler | ||
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| //Number of spatial samples used to compute the mutual information in each resolution level: | ||
| (ImageSampler "Random") | ||
| (NumberOfSpatialSamples 2000) | ||
| (NewSamplesEveryIteration "true") | ||
| (UseRandomSampleRegion "false") | ||
| //(SampleRegionSize 50.0 50.0 50.0) | ||
| (MaximumNumberOfSamplingAttempts 5) | ||
| #Number of spatial samples used to compute the mutual information in each resolution level: | ||
| ImageSampler = "Random" | ||
| NumberOfSpatialSamples = 2000 | ||
| NewSamplesEveryIteration = true | ||
| UseRandomSampleRegion = false | ||
| #(SampleRegionSize 50.0 50.0 50.0) | ||
| MaximumNumberOfSamplingAttempts = 5 | ||
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| // ********** Interpolator and Resampler | ||
| # ********** Interpolator and Resampler | ||
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| //Order of B-Spline interpolation used in each resolution level: | ||
| (BSplineInterpolationOrder 1) | ||
| #Order of B-Spline interpolation used in each resolution level: | ||
| BSplineInterpolationOrder = 1 | ||
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| //Order of B-Spline interpolation used for applying the final deformation: | ||
| (FinalBSplineInterpolationOrder 0) | ||
| #Order of B-Spline interpolation used for applying the final deformation: | ||
| FinalBSplineInterpolationOrder = 0 | ||
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| //Default pixel value for pixels that come from outside the picture: | ||
| (DefaultPixelValue 0) | ||
| #Default pixel value for pixels that come from outside the picture: | ||
| DefaultPixelValue = 0 | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,90 +1,90 @@ | ||
| // This parameter file has kind of realistic values. | ||
| // In most other parameter files for testing, the number of samples and iterations is rather low, to allow fast testing. | ||
| # This parameter file has kind of realistic values. | ||
| # In most other parameter files for testing, the number of samples and iterations is rather low, to allow fast testing. | ||
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| // ********** Image Types | ||
| # ********** Image Types | ||
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| (FixedInternalImagePixelType "float") | ||
| (FixedImageDimension 3) | ||
| (MovingInternalImagePixelType "float") | ||
| (MovingImageDimension 3) | ||
| FixedInternalImagePixelType = "float" | ||
| FixedImageDimension = 3 | ||
| MovingInternalImagePixelType = "float" | ||
| MovingImageDimension = 3 | ||
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| // ********** Components | ||
| # ********** Components | ||
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| (Registration "MultiResolutionRegistration") | ||
| (FixedImagePyramid "FixedRecursiveImagePyramid") | ||
| (MovingImagePyramid "MovingRecursiveImagePyramid") | ||
| (Interpolator "BSplineInterpolator") | ||
| (Metric "AdvancedMattesMutualInformation") | ||
| (Optimizer "AdaptiveStochasticGradientDescent") | ||
| (ResampleInterpolator "FinalBSplineInterpolator") | ||
| (Resampler "DefaultResampler") | ||
| (Transform "BSplineTransform") | ||
| Registration = "MultiResolutionRegistration" | ||
| FixedImagePyramid = "FixedRecursiveImagePyramid" | ||
| MovingImagePyramid = "MovingRecursiveImagePyramid" | ||
| Interpolator = "BSplineInterpolator" | ||
| Metric = "AdvancedMattesMutualInformation" | ||
| Optimizer = "AdaptiveStochasticGradientDescent" | ||
| ResampleInterpolator = "FinalBSplineInterpolator" | ||
| Resampler = "DefaultResampler" | ||
| Transform = "BSplineTransform" | ||
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| // ********** Pyramid | ||
| # ********** Pyramid | ||
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| // Total number of resolutions | ||
| (NumberOfResolutions 3) | ||
| (ImagePyramidSchedule 4 4 4 2 2 2 1 1 1) | ||
| # Total number of resolutions | ||
| NumberOfResolutions = 3 | ||
| ImagePyramidSchedule = [4, 4, 4, 2, 2, 2, 1, 1, 1] | ||
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| // ********** Transform | ||
| # ********** Transform | ||
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| (FinalGridSpacingInPhysicalUnits 10.0 10.0 10.0) | ||
| (GridSpacingSchedule 4.0 2.0 1.0) | ||
| (HowToCombineTransforms "Compose") | ||
| FinalGridSpacingInPhysicalUnits = [10.0, 10.0, 10.0] | ||
| GridSpacingSchedule = [4.0, 2.0, 1.0] | ||
| HowToCombineTransforms = "Compose" | ||
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| // ********** Optimizer | ||
| # ********** Optimizer | ||
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| // Maximum number of iterations in each resolution level: | ||
| (MaximumNumberOfIterations 500) | ||
| # Maximum number of iterations in each resolution level: | ||
| MaximumNumberOfIterations = 500 | ||
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| (AutomaticParameterEstimation "true") | ||
| (UseAdaptiveStepSizes "true") | ||
| AutomaticParameterEstimation = true | ||
| UseAdaptiveStepSizes = true | ||
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| // ********** Metric | ||
| # ********** Metric | ||
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| (NumberOfHistogramBins 32) | ||
| (FixedKernelBSplineOrder 0) | ||
| (MovingKernelBSplineOrder 3) | ||
| (UseFastAndLowMemoryVersion "true") | ||
| NumberOfHistogramBins = 32 | ||
| FixedKernelBSplineOrder = 0 | ||
| MovingKernelBSplineOrder = 3 | ||
| UseFastAndLowMemoryVersion = true | ||
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| // ********** Several | ||
| # ********** Several | ||
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| (WriteTransformParametersEachIteration "false") | ||
| (WriteTransformParametersEachResolution "true") | ||
| (WriteResultImageAfterEachResolution "false") | ||
| (WritePyramidImagesAfterEachResolution "false") | ||
| (WriteResultImage "false") | ||
| (ShowExactMetricValue "false") | ||
| (ErodeMask "false") | ||
| (UseDirectionCosines "true") | ||
| WriteTransformParametersEachIteration = false | ||
| WriteTransformParametersEachResolution = true | ||
| WriteResultImageAfterEachResolution = false | ||
| WritePyramidImagesAfterEachResolution = false | ||
| WriteResultImage = false | ||
| ShowExactMetricValue = false | ||
| ErodeMask = false | ||
| UseDirectionCosines = true | ||
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| // ********** ImageSampler | ||
| # ********** ImageSampler | ||
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| //Number of spatial samples used to compute the mutual information in each resolution level: | ||
| (ImageSampler "Random") | ||
| (NumberOfSpatialSamples 2000) | ||
| (NewSamplesEveryIteration "true") | ||
| (UseRandomSampleRegion "false") | ||
| //(SampleRegionSize 50.0 50.0 50.0) | ||
| (MaximumNumberOfSamplingAttempts 5) | ||
| #Number of spatial samples used to compute the mutual information in each resolution level: | ||
| ImageSampler = "Random" | ||
| NumberOfSpatialSamples = 2000 | ||
| NewSamplesEveryIteration = true | ||
| UseRandomSampleRegion = false | ||
| #(SampleRegionSize 50.0 50.0 50.0) | ||
| MaximumNumberOfSamplingAttempts = 5 | ||
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| // ********** Interpolator and Resampler | ||
| # ********** Interpolator and Resampler | ||
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| //Order of B-Spline interpolation used in each resolution level: | ||
| (BSplineInterpolationOrder 1) | ||
| #Order of B-Spline interpolation used in each resolution level: | ||
| BSplineInterpolationOrder = 1 | ||
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| //Order of B-Spline interpolation used for applying the final deformation: | ||
| (FinalBSplineInterpolationOrder 3) | ||
| #Order of B-Spline interpolation used for applying the final deformation: | ||
| FinalBSplineInterpolationOrder = 3 | ||
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| //Default pixel value for pixels that come from outside the picture: | ||
| (DefaultPixelValue 0) | ||
| #Default pixel value for pixels that come from outside the picture: | ||
| DefaultPixelValue = 0 | ||
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