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Notes
Installation
Parameters
Mermaid configurations
TODOs
How to write your own registration model
Simple example
Step by step registration example
RDMM example on synthetic data
Example Gallery
Jupyter notebook examples
Demonstration of mermaid’s simple registration interface
Package reference
Simple interface
Registration models
Similarity measures
Basic Numerics
Optimizers
Visualization
Configurations
Image IO
Regularization and Smoothing
Utilities and Extensions
Deep networks
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B
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P
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R
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W
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X
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Z
A
Ab (mermaid.registration_networks.AffineMapLoss attribute)
adaptive_padding (mermaid.fileio.ImageIO attribute)
AdaptiveMultiGaussianFourierSmoother (class in mermaid.smoother_factory)
AdaptiveSingleGaussianFourierSmoother (class in mermaid.smoother_factory)
AdaptiveSmootherMomentumMapBasicLoss (class in mermaid.registration_networks)
AdaptiveSmootherMomentumMapBasicNet (class in mermaid.registration_networks)
AdaptVal() (in module mermaid.data_wrapper)
add_axes_event() (mermaid.viewers.FigureEventHandler method)
add_model() (mermaid.model_factory.ModelFactory method)
(mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SingleScaleBatchRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SingleScaleConsensusRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
add_model_lossClass (mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer attribute)
add_model_name (mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer attribute)
add_model_networkClass (mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer attribute)
add_similarity_measure() (mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SingleScaleBatchRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SingleScaleConsensusRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
(mermaid.registration_networks.RegistrationLoss method)
(mermaid.similarity_measure_factory.SimilarityMeasureFactory method)
addSimMeasure (mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer attribute)
addSimName (mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer attribute)
AdpSmoother (class in mermaid.utils)
AdvectImage (class in mermaid.forward_models)
AdvectMap (class in mermaid.forward_models)
AffineMapLoss (class in mermaid.registration_networks)
AffineMapNet (class in mermaid.registration_networks)
alpha (mermaid.custom_pytorch_extensions.InverseFourierConvolution attribute)
(mermaid.regularizer_factory.HelmholtzRegularizer attribute)
analysis() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
apply_affine_transform_to_map() (in module mermaid.utils)
apply_affine_transform_to_map_multiNC() (in module mermaid.utils)
apply_dropout() (mermaid.deep_networks.decoder_block_2d method)
(mermaid.deep_networks.Simple_consistent method)
(mermaid.deep_networks.encoder_block_2d method)
apply_smooth() (mermaid.smoother_factory.AdaptiveMultiGaussianFourierSmoother method)
(mermaid.smoother_factory.AdaptiveSingleGaussianFourierSmoother method)
(mermaid.smoother_factory.DiffusionSmoother method)
(mermaid.smoother_factory.GaussianFourierSmoother method)
(mermaid.smoother_factory.GaussianSpatialSmoother method)
(mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother method)
(mermaid.smoother_factory.LocalFourierSmoother method)
(mermaid.smoother_factory.Smoother method)
are_indices_close() (in module mermaid.custom_pytorch_extensions)
associate_parameters_with_module() (mermaid.registration_networks.ShootingVectorMomentumNet method)
(mermaid.smoother_factory.AdaptiveMultiGaussianFourierSmoother method)
(mermaid.smoother_factory.AdaptiveSingleGaussianFourierSmoother method)
(mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother method)
(mermaid.smoother_factory.Smoother method)
AvailableModels (class in mermaid.model_factory)
AvailableSmoothers (class in mermaid.smoother_factory)
ax_events (mermaid.viewers.FigureEventHandler attribute)
B
backward() (mermaid.custom_pytorch_extensions.FourierConvolution method)
(mermaid.custom_pytorch_extensions.FourierMultiGaussianConvolution method)
(mermaid.custom_pytorch_extensions.FourierSetOfGaussianConvolutions method)
(mermaid.custom_pytorch_extensions.FourierSingleGaussianConvolution method)
(mermaid.custom_pytorch_extensions.InverseFourierConvolution method)
(mermaid.libraries.functions.stn_nd.STNFunction_ND_BCXYZ_Compile method)
(mermaid.similarity_helper_omt.OTSimilarityHelper static method)
(mermaid.spline_interpolation.PerformSplineInterpolationHelper method)
backward_stn() (mermaid.libraries.functions.stn_nd.STNFunction_ND_BCXYZ_Compile method)
batch_size (mermaid.multiscale_optimizer.SingleScaleBatchRegistrationOptimizer attribute)
(mermaid.multiscale_optimizer.SingleScaleConsensusRegistrationOptimizer attribute)
(mermaid.smoother_factory.Smoother attribute)
bcDirichletZero (mermaid.finite_differences.FD attribute)
bh() (in module mermaid.utils)
bias (mermaid.noisy_convolution.NoisyConv1d attribute)
(mermaid.noisy_convolution.NoisyConv2d attribute)
(mermaid.noisy_convolution.NoisyConv3d attribute)
(mermaid.noisy_convolution.NoisyConvTranspose1d attribute)
(mermaid.noisy_convolution.NoisyConvTranspose2d attribute)
(mermaid.noisy_convolution.NoisyConvTranspose3d attribute)
(mermaid.noisy_convolution.NoisyLinear attribute)
build_kernel_matrix() (mermaid.similarity_helper_omt.OTSimilarityGradient method)
build_kernel_matrix_gradient() (mermaid.similarity_helper_omt.OTSimilarityGradient method)
C
cal_weights_for_omt() (mermaid.deep_networks.OMTLoss method)
cal_weights_for_weightrange() (mermaid.deep_networks.WeightRangeLoss method)
centered_identity_map() (in module mermaid.utils)
centered_identity_map_multiN() (in module mermaid.utils)
check_fourier_conv() (in module mermaid.custom_pytorch_extensions)
check_run_forward_and_backward() (in module mermaid.custom_pytorch_extensions)
checkerboard_2d() (in module mermaid.visualize_registration_results)
checkNan() (in module mermaid.utils)
checkpoint_interval (mermaid.multiscale_optimizer.SingleScaleBatchRegistrationOptimizer attribute)
checkpoint_output_directory (mermaid.multiscale_optimizer.SingleScaleConsensusRegistrationOptimizer attribute)
ClusteredWeightedSmoothingModel (class in mermaid.deep_smoothers)
ClusteringLoss (class in mermaid.deep_networks)
combine_dict() (in module mermaid.utils)
compute_diffusion() (mermaid.deep_smoothers.DeepSmoothingModel method)
compute_gradient() (mermaid.similarity_helper_omt.OTSimilarityGradient method)
compute_inverse_map (mermaid.forward_models.AdvectMap attribute)
(mermaid.forward_models.EPDiffAdaptMap attribute)
(mermaid.forward_models.EPDiffMap attribute)
(mermaid.forward_models.EPDiffScalarMomentumMap attribute)
(mermaid.multiscale_optimizer.Optimizer attribute)
(mermaid.registration_networks.AdaptiveSmootherMomentumMapBasicNet attribute)
(mermaid.registration_networks.LDDMMShootingScalarMomentumMapNet attribute)
(mermaid.registration_networks.LDDMMShootingVectorMomentumMapNet attribute)
(mermaid.registration_networks.OneStepMapNet attribute)
(mermaid.registration_networks.SVFMapNet attribute)
(mermaid.registration_networks.SVFScalarMomentumMapNet attribute)
(mermaid.registration_networks.SVFVectorAdaptiveSmootherMomentumMapNet attribute)
(mermaid.registration_networks.SVFVectorMomentumMapNet attribute)
compute_l2_parameter_weight_penalty() (mermaid.deep_smoothers.ClusteredWeightedSmoothingModel method)
(mermaid.deep_smoothers.DeepSmoothingModel method)
(mermaid.deep_smoothers.GeneralNetworkWeightedSmoothingModel method)
compute_local_weighted_tv_norm() (mermaid.deep_networks.TotalVariationLoss method)
compute_localized_edge_penalty() (in module mermaid.deep_smoothers)
compute_low_res_image_if_needed() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
compute_normalized_gaussian() (in module mermaid.utils)
compute_omt_penalty() (mermaid.deep_networks.OMTLoss method)
compute_optimizer_parameter_loss() (mermaid.multiscale_optimizer.Optimizer method)
compute_penalty() (mermaid.smoother_factory.LocalFourierSmoother method)
compute_regularization_energy() (mermaid.registration_networks.AdaptiveSmootherMomentumMapBasicLoss method)
(mermaid.registration_networks.AffineMapLoss method)
(mermaid.registration_networks.CurvatureMapLoss method)
(mermaid.registration_networks.DiffusionMapLoss method)
(mermaid.registration_networks.LDDMMShootingScalarMomentumImageLoss method)
(mermaid.registration_networks.LDDMMShootingScalarMomentumMapLoss method)
(mermaid.registration_networks.LDDMMShootingVectorMomentumImageLoss method)
(mermaid.registration_networks.LDDMMShootingVectorMomentumMapLoss method)
(mermaid.registration_networks.OneStepMapLoss method)
(mermaid.registration_networks.RegistrationLoss method)
(mermaid.registration_networks.SVFImageLoss method)
(mermaid.registration_networks.SVFMapLoss method)
(mermaid.registration_networks.SVFQuasiMomentumImageLoss method)
(mermaid.registration_networks.SVFScalarMomentumImageLoss method)
(mermaid.registration_networks.SVFScalarMomentumMapLoss method)
(mermaid.registration_networks.SVFVectorMomentumImageLoss method)
(mermaid.registration_networks.SVFVectorMomentumMapLoss method)
(mermaid.registration_networks.TotalVariationMapLoss method)
compute_regularizer_multiN() (mermaid.regularizer_factory.Regularizer method)
compute_similarity() (mermaid.similarity_helper_omt.OTSimilarityGradient method)
(mermaid.similarity_measure_factory.LNCCSimilarity method)
(mermaid.similarity_measure_factory.LocalizedNCCSimilarity method)
(mermaid.similarity_measure_factory.NCCNegativeSimilarity method)
(mermaid.similarity_measure_factory.NCCPositiveSimilarity method)
(mermaid.similarity_measure_factory.NCCSimilarity method)
(mermaid.similarity_measure_factory.OptimalMassTransportSimilarity method)
(mermaid.similarity_measure_factory.SSDSimilarity method)
(mermaid.similarity_measure_factory.SimilarityMeasure method)
compute_similarity_energy() (mermaid.registration_networks.RegistrationLoss method)
compute_similarity_multiC() (mermaid.similarity_measure_factory.SimilarityMeasure method)
compute_similarity_multiNC() (mermaid.similarity_measure_factory.SimilarityMeasure method)
compute_vector_momentum_from_scalar_momentum_multiN() (in module mermaid.utils)
compute_vector_momentum_from_scalar_momentum_multiNC() (in module mermaid.utils)
compute_warped_image() (in module mermaid.utils)
compute_warped_image_multiNC() (in module mermaid.utils)
compute_weighted_multi_smooth_v() (in module mermaid.deep_smoothers)
computed_pre_weights (mermaid.deep_smoothers.DeepSmoothingModel attribute)
computed_weights (mermaid.deep_smoothers.DeepSmoothingModel attribute)
connect() (mermaid.viewers.FigureEventHandler method)
continue_from_last_checkpoint (mermaid.multiscale_optimizer.SingleScaleConsensusRegistrationOptimizer attribute)
conv_norm_in_rel (class in mermaid.deep_networks)
ConvBnRel (class in mermaid.utils)
create_complex_fourier_filter() (in module mermaid.custom_pytorch_extensions)
create_cuda_filter() (in module mermaid.custom_pytorch_extensions)
create_deep_smoother() (mermaid.deep_smoothers.DeepSmootherFactory method)
create_image_pair() (mermaid.example_generation.CreateExample method)
(mermaid.example_generation.CreateRealExampleImages method)
(mermaid.example_generation.CreateSquares method)
create_integrator() (mermaid.registration_networks.LDDMMAdaptiveSmootherMomentumMapNet method)
(mermaid.registration_networks.LDDMMShootingScalarMomentumImageNet method)
(mermaid.registration_networks.LDDMMShootingScalarMomentumMapNet method)
(mermaid.registration_networks.LDDMMShootingVectorMomentumImageNet method)
(mermaid.registration_networks.LDDMMShootingVectorMomentumMapNet method)
(mermaid.registration_networks.OneStepMapNet method)
(mermaid.registration_networks.RegistrationNetTimeIntegration method)
(mermaid.registration_networks.SVFImageNet method)
(mermaid.registration_networks.SVFMapNet method)
(mermaid.registration_networks.SVFQuasiMomentumImageNet method)
(mermaid.registration_networks.SVFScalarMomentumImageNet method)
(mermaid.registration_networks.SVFScalarMomentumMapNet method)
(mermaid.registration_networks.SVFVectorAdaptiveSmootherMomentumMapNet method)
(mermaid.registration_networks.SVFVectorMomentumImageNet method)
(mermaid.registration_networks.SVFVectorMomentumMapNet method)
create_local_filter_weights_parameter_multiN() (in module mermaid.utils)
create_local_filter_weights_parameters() (mermaid.registration_networks.AdaptiveSmootherMomentumMapBasicNet method)
create_ND_scalar_field_parameter_multiNC() (in module mermaid.utils)
create_ND_vector_field_parameter_multiN() (in module mermaid.utils)
create_ND_vector_field_variable() (in module mermaid.utils)
create_ND_vector_field_variable_multiN() (in module mermaid.utils)
create_numpy_filter() (in module mermaid.custom_pytorch_extensions)
create_registration_model() (mermaid.model_factory.ModelFactory method)
create_registration_parameters() (mermaid.registration_networks.AffineMapNet method)
(mermaid.registration_networks.RegistrationNet method)
(mermaid.registration_networks.RegistrationNetDisplacement method)
(mermaid.registration_networks.SVFNet method)
(mermaid.registration_networks.SVFQuasiMomentumNet method)
(mermaid.registration_networks.ShootingScalarMomentumNet method)
(mermaid.registration_networks.ShootingVectorMomentumNet method)
create_regularizer() (mermaid.regularizer_factory.RegularizerFactory method)
create_regularizer_by_name() (mermaid.regularizer_factory.RegularizerFactory method)
create_similarity_measure() (mermaid.similarity_measure_factory.SimilarityMeasureFactory method)
create_single_local_smoother() (mermaid.registration_networks.AdaptiveSmootherMomentumMapBasicNet method)
create_smoother() (mermaid.smoother_factory.SmootherFactory method)
create_smoother_by_name() (mermaid.smoother_factory.SmootherFactory method)
create_symlink_with_correct_ext() (in module mermaid.utils)
create_vector_parameter() (in module mermaid.utils)
create_zero_array() (mermaid.finite_differences.FD method)
(mermaid.finite_differences.FD_np method)
(mermaid.finite_differences.FD_torch method)
CreateExample (class in mermaid.example_generation)
CreateRealExampleImages (class in mermaid.example_generation)
CreateSquares (class in mermaid.example_generation)
criterion (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer attribute)
CUDA_ON (in module mermaid.config_parser)
current_epoch (mermaid.multiscale_optimizer.ImageRegistrationOptimizer attribute)
current_penalty (mermaid.deep_smoothers.DeepSmoothingModel attribute)
CurvatureMapLoss (class in mermaid.registration_networks)
CurvatureRegularizer (class in mermaid.regularizer_factory)
cxyz_to_xyzc() (in module mermaid.utils)
D
d (mermaid.registration_networks.CurvatureMapLoss attribute)
(mermaid.registration_networks.DiffusionMapLoss attribute)
(mermaid.registration_networks.RegistrationNetDisplacement attribute)
(mermaid.registration_networks.TotalVariationMapLoss attribute)
datatype_conversion (mermaid.fileio.FileIO attribute)
ddXc() (mermaid.finite_differences.FD method)
ddYc() (mermaid.finite_differences.FD method)
ddZc() (mermaid.finite_differences.FD method)
debug_distrib() (mermaid.forward_models.EPDiffAdaptMap method)
(mermaid.registration_networks.AdaptiveSmootherMomentumMapBasicNet method)
debug_nan() (mermaid.forward_models.EPDiffAdaptMap method)
debugging() (mermaid.forward_models.EPDiffMap method)
(mermaid.rungekutta_integrators.RK4 method)
(mermaid.smoother_factory.LocalFourierSmoother method)
decoder_block_2d (class in mermaid.deep_networks)
deep_network_local_weight_smoothing (mermaid.deep_smoothers.DeepSmoothingModel attribute)
deep_network_weight_smoother (mermaid.deep_smoothers.DeepSmoothingModel attribute)
DeepNetwork (class in mermaid.deep_networks)
DeepSmootherFactory (class in mermaid.deep_smoothers)
DeepSmoothingModel (class in mermaid.deep_smoothers)
default_intensity_normalization() (mermaid.image_manipulations.IntensityNormalizeImage method)
default_learning_rate (mermaid.multiscale_optimizer.Optimizer attribute)
default_normalization_mode (mermaid.image_manipulations.IntensityNormalizeImage attribute)
default_regularizer_type (mermaid.regularizer_factory.RegularizerFactory attribute)
default_smoother_type (mermaid.smoother_factory.SmootherFactory attribute)
develop_smoother (mermaid.registration_networks.LDDMMShootingScalarMomentumImageLoss attribute)
(mermaid.registration_networks.LDDMMShootingScalarMomentumMapLoss attribute)
(mermaid.registration_networks.SVFScalarMomentumImageLoss attribute)
(mermaid.registration_networks.SVFScalarMomentumMapLoss attribute)
DiffusionMapLoss (class in mermaid.registration_networks)
DiffusionRegularizer (class in mermaid.regularizer_factory)
DiffusionSmoother (class in mermaid.smoother_factory)
dim (mermaid.custom_pytorch_extensions.GaussianFourierFilterGenerator attribute)
(mermaid.deep_smoothers.DeepSmootherFactory attribute)
(mermaid.example_generation.CreateExample attribute)
(mermaid.finite_differences.FD attribute)
(mermaid.forward_models.ForwardModel attribute)
(mermaid.forward_models.RHSLibrary attribute)
(mermaid.model_factory.ModelFactory attribute)
(mermaid.registration_networks.RegistrationNet attribute)
(mermaid.regularizer_factory.Regularizer attribute)
(mermaid.regularizer_factory.RegularizerFactory attribute)
(mermaid.similarity_measure_factory.SimilarityMeasure attribute)
(mermaid.similarity_measure_factory.SimilarityMeasureFactory attribute)
(mermaid.smoother_factory.Smoother attribute)
(mermaid.smoother_factory.SmootherFactory attribute)
dim_info (mermaid.forward_models_wrap.ODEWrapFunc attribute)
(mermaid.forward_models_wrap.ODEWrapFunc_tuple attribute)
DimBatchNorm() (in module mermaid.deep_networks)
DimConv() (in module mermaid.deep_networks)
DimConvTranspose() (in module mermaid.deep_networks)
DimInstanceNorm() (in module mermaid.deep_networks)
DimMaxPool() (in module mermaid.deep_networks)
DimNoisyConv() (in module mermaid.deep_networks)
DimNoisyConvTranspose() (in module mermaid.deep_networks)
DimNormalization() (in module mermaid.deep_networks)
disable_penalty_computation() (mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother method)
(mermaid.smoother_factory.LocalFourierSmoother method)
disconnect() (mermaid.viewers.FigureEventHandler method)
display_title() (mermaid.viewers.ImageViewer method)
(mermaid.viewers.ImageViewer3D_Sliced method)
downsample_image_by_factor() (mermaid.image_sampling.ResampleImage method)
downsample_image_to_size() (mermaid.image_sampling.ResampleImage method)
downsample_model_parameters() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
downsample_registration_parameters() (mermaid.registration_networks.AdaptiveSmootherMomentumMapBasicNet method)
(mermaid.registration_networks.AffineMapNet method)
(mermaid.registration_networks.RegistrationNet method)
(mermaid.registration_networks.RegistrationNetDisplacement method)
(mermaid.registration_networks.SVFNet method)
(mermaid.registration_networks.SVFQuasiMomentumNet method)
(mermaid.registration_networks.ShootingScalarMomentumNet method)
(mermaid.registration_networks.ShootingVectorMomentumNet method)
downsample_vector_field_by_factor() (mermaid.image_sampling.ResampleImage method)
dXb() (mermaid.finite_differences.FD method)
dXc() (mermaid.finite_differences.FD method)
dXf() (mermaid.finite_differences.FD method)
dYb() (mermaid.finite_differences.FD method)
dYc() (mermaid.finite_differences.FD method)
dYf() (mermaid.finite_differences.FD method)
dZb() (mermaid.finite_differences.FD method)
dZc() (mermaid.finite_differences.FD method)
dZf() (mermaid.finite_differences.FD method)
E
embedded_smoother (mermaid.forward_models.EPDiffAdaptMap attribute)
enable_accumulated_penalty() (mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother method)
(mermaid.smoother_factory.LocalFourierSmoother method)
enable_penalty_computation() (mermaid.smoother_factory.LocalFourierSmoother method)
encoder_block_2d (class in mermaid.deep_networks)
Encoder_decoder (class in mermaid.deep_networks)
env (mermaid.registration_networks.RegistrationLoss attribute)
(mermaid.registration_networks.RegistrationNetTimeIntegration attribute)
EPDiffAdaptMap (class in mermaid.forward_models)
EPDiffImage (class in mermaid.forward_models)
EPDiffMap (class in mermaid.forward_models)
EPDiffScalarMomentum (class in mermaid.forward_models)
EPDiffScalarMomentumImage (class in mermaid.forward_models)
EPDiffScalarMomentumMap (class in mermaid.forward_models)
EulerForward (class in mermaid.rungekutta_integrators)
evaluate_but_do_not_optimize_over_shared_registration_parameters (mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother attribute)
evaluate_model() (in module mermaid.model_evaluation)
evaluate_model_low_level_interface() (in module mermaid.model_evaluation)
extra_var (mermaid.forward_models_wrap.ODEWrapFunc attribute)
(mermaid.forward_models_wrap.ODEWrapFunc_tuple attribute)
F
f (mermaid.rungekutta_integrators.RKIntegrator attribute)
f() (mermaid.forward_models.AdvectImage method)
(mermaid.forward_models.AdvectMap method)
(mermaid.forward_models.EPDiffAdaptMap method)
(mermaid.forward_models.EPDiffImage method)
(mermaid.forward_models.EPDiffMap method)
(mermaid.forward_models.EPDiffScalarMomentumImage method)
(mermaid.forward_models.EPDiffScalarMomentumMap method)
(mermaid.forward_models.ForwardModel method)
factor_input() (mermaid.forward_models_wrap.ODEWrapFunc method)
(mermaid.forward_models_wrap.ODEWrapFunc_tuple method)
factor_res() (mermaid.forward_models_wrap.ODEWrapFunc static method)
(mermaid.forward_models_wrap.ODEWrapFunc_tuple static method)
FcRel (class in mermaid.utils)
FD (class in mermaid.finite_differences)
FD_np (class in mermaid.finite_differences)
FD_torch (class in mermaid.finite_differences)
fdt (mermaid.regularizer_factory.Regularizer attribute)
(mermaid.smoother_factory.Smoother attribute)
fdt_di (mermaid.forward_models.RHSLibrary attribute)
fdt_le (mermaid.forward_models.RHSLibrary attribute)
fdt_ne (mermaid.forward_models.RHSLibrary attribute)
FFilter (mermaid.smoother_factory.GaussianFourierSmoother attribute)
FFTVal() (in module mermaid.data_wrapper)
fig (mermaid.viewers.FigureEventHandler attribute)
FigureEventHandler (class in mermaid.viewers)
FileIO (class in mermaid.fileio)
filter (mermaid.smoother_factory.GaussianSpatialSmoother attribute)
forward() (mermaid.custom_pytorch_extensions.FourierConvolution method)
(mermaid.custom_pytorch_extensions.FourierMultiGaussianConvolution method)
(mermaid.custom_pytorch_extensions.FourierSetOfGaussianConvolutions method)
(mermaid.custom_pytorch_extensions.FourierSingleGaussianConvolution method)
(mermaid.custom_pytorch_extensions.InverseFourierConvolution method)
(mermaid.deep_networks.ClusteringLoss method)
(mermaid.deep_networks.Encoder_decoder method)
(mermaid.deep_networks.GlobalHLoss method)
(mermaid.deep_networks.HLoss method)
(mermaid.deep_networks.OMTLoss method)
(mermaid.deep_networks.Simple_Unet method)
(mermaid.deep_networks.Simple_consistent method)
(mermaid.deep_networks.TotalVariationLoss method)
(mermaid.deep_networks.Unet method)
(mermaid.deep_networks.Unet_no_skip method)
(mermaid.deep_networks.WeightInputRangeLoss method)
(mermaid.deep_networks.WeightRangeLoss method)
(mermaid.deep_networks.conv_norm_in_rel method)
(mermaid.deep_networks.decoder_block_2d method)
(mermaid.deep_networks.encoder_block_2d method)
(mermaid.deep_smoothers.DeepSmoothingModel method)
(mermaid.deep_smoothers.LinearSoftmax method)
(mermaid.deep_smoothers.LinearSoftnorm method)
(mermaid.deep_smoothers.StableSoftmax method)
(mermaid.deep_smoothers.WeightedLinearSoftmax method)
(mermaid.deep_smoothers.WeightedLinearSoftnorm method)
(mermaid.deep_smoothers.WeightedSoftmax method)
(mermaid.deep_smoothers.WeightedSqrtSoftmax method)
(mermaid.forward_models_wrap.ODEWrapFunc method)
(mermaid.forward_models_wrap.ODEWrapFunc_tuple method)
(mermaid.libraries.functions.stn_nd.STNFunction_ND_BCXYZ method)
(mermaid.libraries.functions.stn_nd.STNFunction_ND_BCXYZ_Compile method)
(mermaid.libraries.modules.stn_nd.STN_ND_BCXYZ method)
(mermaid.noisy_convolution.NoisyConv1d method)
(mermaid.noisy_convolution.NoisyConv2d method)
(mermaid.noisy_convolution.NoisyConv3d method)
(mermaid.noisy_convolution.NoisyConvTranspose1d method)
(mermaid.noisy_convolution.NoisyConvTranspose2d method)
(mermaid.noisy_convolution.NoisyConvTranspose3d method)
(mermaid.noisy_convolution.NoisyLayer method)
(mermaid.noisy_convolution.NoisyLinear method)
(mermaid.registration_networks.AdaptiveSmootherMomentumMapBasicNet method)
(mermaid.registration_networks.AffineMapNet method)
(mermaid.registration_networks.LDDMMAdaptiveSmootherMomentumMapNet method)
(mermaid.registration_networks.LDDMMShootingScalarMomentumImageNet method)
(mermaid.registration_networks.LDDMMShootingScalarMomentumMapNet method)
(mermaid.registration_networks.LDDMMShootingVectorMomentumImageNet method)
(mermaid.registration_networks.LDDMMShootingVectorMomentumMapNet method)
(mermaid.registration_networks.OneStepMapNet method)
(mermaid.registration_networks.RegistrationImageLoss method)
(mermaid.registration_networks.RegistrationMapLoss method)
(mermaid.registration_networks.RegistrationNetDisplacement method)
(mermaid.registration_networks.SVFImageNet method)
(mermaid.registration_networks.SVFMapNet method)
(mermaid.registration_networks.SVFQuasiMomentumImageNet method)
(mermaid.registration_networks.SVFScalarMomentumImageNet method)
(mermaid.registration_networks.SVFScalarMomentumMapNet method)
(mermaid.registration_networks.SVFVectorAdaptiveSmootherMomentumMapNet method)
(mermaid.registration_networks.SVFVectorMomentumImageNet method)
(mermaid.registration_networks.SVFVectorMomentumMapNet method)
(mermaid.similarity_helper_omt.OTSimilarityHelper static method)
(mermaid.spline_interpolation.PerformSplineInterpolationHelper method)
(mermaid.spline_interpolation.SplineInterpolation_ND_BCXYZ method)
(mermaid.utils.AdpSmoother method)
(mermaid.utils.ConvBnRel method)
(mermaid.utils.FcRel method)
forward_stn() (mermaid.libraries.functions.stn_nd.STNFunction_ND_BCXYZ method)
(mermaid.libraries.functions.stn_nd.STNFunction_ND_BCXYZ_Compile method)
forward_with_normalization() (mermaid.deep_networks.decoder_block_2d method)
(mermaid.deep_networks.encoder_block_2d method)
forward_without_normalization() (mermaid.deep_networks.decoder_block_2d method)
(mermaid.deep_networks.encoder_block_2d method)
ForwardModel (class in mermaid.forward_models)
fourier_convolution() (in module mermaid.custom_pytorch_extensions)
fourier_multi_gaussian_convolution() (in module mermaid.custom_pytorch_extensions)
fourier_set_of_gaussian_convolutions() (in module mermaid.custom_pytorch_extensions)
fourier_single_gaussian_convolution() (in module mermaid.custom_pytorch_extensions)
FourierConvolution (class in mermaid.custom_pytorch_extensions)
FourierGaussianConvolution (class in mermaid.custom_pytorch_extensions)
FourierMultiGaussianConvolution (class in mermaid.custom_pytorch_extensions)
FourierSetOfGaussianConvolutions (class in mermaid.custom_pytorch_extensions)
FourierSingleGaussianConvolution (class in mermaid.custom_pytorch_extensions)
freeze_adaptive_regularizer_param() (mermaid.registration_networks.AdaptiveSmootherMomentumMapBasicNet method)
freeze_momentum() (mermaid.registration_networks.AdaptiveSmootherMomentumMapBasicNet method)
freeze_parameters (mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother attribute)
G
gamma (mermaid.regularizer_factory.HelmholtzRegularizer attribute)
gaussian_fourier_filter_generator (mermaid.smoother_factory.AdaptiveMultiGaussianFourierSmoother attribute)
gaussian_std (mermaid.similarity_measure_factory.LocalizedNCCSimilarity attribute)
gaussian_stds (mermaid.deep_smoothers.DeepSmootherFactory attribute)
GaussianFourierFilterGenerator (class in mermaid.custom_pytorch_extensions)
GaussianFourierSmoother (class in mermaid.smoother_factory)
GaussianSmoother (class in mermaid.smoother_factory)
GaussianSpatialSmoother (class in mermaid.smoother_factory)
gaussianStd (mermaid.smoother_factory.AdaptiveSingleGaussianFourierSmoother attribute)
(mermaid.smoother_factory.SingleGaussianFourierSmoother attribute)
gaussianStd_min (mermaid.smoother_factory.AdaptiveMultiGaussianFourierSmoother attribute)
(mermaid.smoother_factory.AdaptiveSingleGaussianFourierSmoother attribute)
(mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother attribute)
(mermaid.smoother_factory.SingleGaussianFourierSmoother attribute)
gaussianWeight_min (mermaid.deep_smoothers.DeepSmoothingModel attribute)
(mermaid.smoother_factory.AdaptiveMultiGaussianFourierSmoother attribute)
(mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother attribute)
GeneralNetworkWeightedSmoothingModel (class in mermaid.deep_smoothers)
GenericIO (class in mermaid.fileio)
get_algconf_settings() (in module mermaid.config_parser)
get_alpha() (mermaid.custom_pytorch_extensions.InverseFourierConvolution method)
(mermaid.regularizer_factory.HelmholtzRegularizer method)
get_available_models() (mermaid.simple_interface.RegisterImagePair static method)
get_baseconf_settings() (in module mermaid.config_parser)
get_checkpoint_dict() (mermaid.multiscale_optimizer.Optimizer method)
(mermaid.multiscale_optimizer.SingleScaleBatchRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SingleScaleConsensusRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
get_compatible_state_dict_for_module() (in module mermaid.smoother_factory)
get_computed_pre_weights() (mermaid.deep_smoothers.DeepSmoothingModel method)
get_computed_weights() (mermaid.deep_smoothers.DeepSmoothingModel method)
get_current_epoch() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
get_current_penalty() (mermaid.deep_smoothers.DeepSmoothingModel method)
get_custom_optimizer_output_string() (mermaid.registration_networks.RegistrationNet method)
(mermaid.registration_networks.SVFQuasiMomentumNet method)
(mermaid.registration_networks.ShootingScalarMomentumNet method)
(mermaid.registration_networks.ShootingVectorMomentumNet method)
(mermaid.smoother_factory.AdaptiveMultiGaussianFourierSmoother method)
(mermaid.smoother_factory.AdaptiveSingleGaussianFourierSmoother method)
(mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother method)
(mermaid.smoother_factory.LocalFourierSmoother method)
(mermaid.smoother_factory.Smoother method)
get_custom_optimizer_output_values() (mermaid.registration_networks.RegistrationNet method)
(mermaid.registration_networks.SVFQuasiMomentumNet method)
(mermaid.registration_networks.ShootingScalarMomentumNet method)
(mermaid.registration_networks.ShootingVectorMomentumNet method)
(mermaid.smoother_factory.AdaptiveMultiGaussianFourierSmoother method)
(mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother method)
(mermaid.smoother_factory.LocalFourierSmoother method)
(mermaid.smoother_factory.Smoother method)
get_custom_optimizer_values() (mermaid.smoother_factory.AdaptiveSingleGaussianFourierSmoother method)
get_custom_output_values() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
get_debug_computed_local_pre_weights() (mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother method)
get_debug_computed_local_weights() (mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother method)
get_deep_smoother_preweights() (mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother method)
get_deep_smoother_weights() (mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother method)
get_default_algconf_settings_filenames() (in module mermaid.config_parser)
get_default_baseconf_settings_filenames() (in module mermaid.config_parser)
get_default_compute_settings_filenames() (in module mermaid.config_parser)
get_default_datatype() (mermaid.fileio.FileIO method)
get_default_democonf_settings_filenames() (in module mermaid.config_parser)
get_default_multi_gaussian_weights() (mermaid.smoother_factory.AdaptiveMultiGaussianFourierSmoother method)
(mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother method)
(mermaid.smoother_factory.LocalFourierSmoother method)
get_default_respro_settings_filenames() (in module mermaid.config_parser)
get_democonf_settings() (in module mermaid.config_parser)
get_dim_of_affine_transform() (in module mermaid.utils)
get_dimension() (mermaid.custom_pytorch_extensions.GaussianFourierFilterGenerator method)
get_dt() (mermaid.rungekutta_integrators.RKIntegrator method)
get_energy() (mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SimpleRegistration method)
(mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
(mermaid.registration_networks.RegistrationImageLoss method)
(mermaid.registration_networks.RegistrationMapLoss method)
(mermaid.simple_interface.RegisterImagePair method)
get_expr_name() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
get_external_optimizer_parameter_loss() (mermaid.multiscale_optimizer.Optimizer method)
get_gamma() (mermaid.regularizer_factory.HelmholtzRegularizer method)
get_gaussian_filters() (mermaid.custom_pytorch_extensions.GaussianFourierFilterGenerator method)
get_gaussian_std() (mermaid.smoother_factory.AdaptiveSingleGaussianFourierSmoother method)
(mermaid.smoother_factory.SingleGaussianFourierSmoother method)
get_gaussian_stds() (mermaid.smoother_factory.AdaptiveMultiGaussianFourierSmoother method)
(mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother method)
(mermaid.smoother_factory.LocalFourierSmoother method)
get_gaussian_weights() (mermaid.smoother_factory.AdaptiveMultiGaussianFourierSmoother method)
(mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother method)
(mermaid.smoother_factory.LocalFourierSmoother method)
get_gaussian_xsqr_filters() (mermaid.custom_pytorch_extensions.GaussianFourierFilterGenerator method)
get_history() (mermaid.multiscale_optimizer.Optimizer method)
(mermaid.multiscale_optimizer.SimpleRegistration method)
(mermaid.simple_interface.RegisterImagePair method)
get_individual_model_parameters() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
get_individual_registration_parameters() (mermaid.registration_networks.RegistrationNet method)
get_initial_inverse_map() (mermaid.multiscale_optimizer.SimpleRegistration method)
(mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
(mermaid.simple_interface.RegisterImagePair method)
get_initial_map() (mermaid.multiscale_optimizer.SimpleRegistration method)
(mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
(mermaid.simple_interface.RegisterImagePair method)
get_integraton_tfrom() (mermaid.registration_networks.RegistrationNetTimeIntegration method)
get_integraton_tto() (mermaid.registration_networks.RegistrationNetTimeIntegration method)
get_intensity_normalization() (mermaid.fileio.ImageIO method)
get_inverse_affine_param() (in module mermaid.utils)
get_inverse_map() (mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SimpleRegistration method)
(mermaid.multiscale_optimizer.SingleScaleBatchRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
(mermaid.simple_interface.RegisterImagePair method)
get_iter() (mermaid.image_sampling.ResampleImage method)
(mermaid.smoother_factory.DiffusionSmoother method)
get_k_sz_h() (mermaid.smoother_factory.GaussianSpatialSmoother method)
get_last_kernel_size() (mermaid.deep_networks.ClusteringLoss method)
(mermaid.deep_networks.DeepNetwork method)
(mermaid.deep_networks.Encoder_decoder method)
(mermaid.deep_networks.Simple_Unet method)
(mermaid.deep_networks.Simple_consistent method)
(mermaid.deep_networks.Unet method)
(mermaid.deep_networks.Unet_no_skip method)
(mermaid.deep_smoothers.ClusteredWeightedSmoothingModel method)
(mermaid.deep_smoothers.DeepSmoothingModel method)
(mermaid.deep_smoothers.GeneralNetworkWeightedSmoothingModel method)
get_last_successful_step_size_taken() (mermaid.multiscale_optimizer.Optimizer method)
get_map() (mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SimpleRegistration method)
(mermaid.multiscale_optimizer.SingleScaleBatchRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SingleScaleConsensusRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
(mermaid.simple_interface.RegisterImagePair method)
get_model_parameters() (mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SimpleRegistration method)
(mermaid.multiscale_optimizer.SingleScaleBatchRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SingleScaleConsensusRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
(mermaid.simple_interface.RegisterImagePair method)
get_model_state_dict() (mermaid.multiscale_optimizer.SimpleRegistration method)
(mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
get_models() (mermaid.model_factory.AvailableModels method)
(mermaid.model_factory.ModelFactory method)
get_net_sched() (mermaid.utils.AdpSmoother method)
get_normalize_spacing() (mermaid.fileio.ImageIO method)
get_nr_of_gaussians() (mermaid.smoother_factory.LocalFourierSmoother method)
get_number_of_currently_stored_gaussians() (mermaid.custom_pytorch_extensions.GaussianFourierFilterGenerator method)
get_number_of_image_channels_from_state_dict() (mermaid.deep_smoothers.DeepSmoothingModel method)
get_number_of_input_channels() (mermaid.deep_smoothers.DeepSmoothingModel method)
get_number_of_iterations() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
get_number_of_slots() (mermaid.custom_pytorch_extensions.GaussianFourierFilterGenerator method)
get_number_of_time_steps() (mermaid.rungekutta_integrators.RKIntegrator method)
get_omt_power() (mermaid.deep_smoothers.DeepSmoothingModel method)
get_omt_weight_penalty() (mermaid.deep_smoothers.DeepSmoothingModel method)
get_opt() (mermaid.simple_interface.RegisterImagePair method)
get_opt_par_energy() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
get_optimization_parameters() (mermaid.smoother_factory.AdaptiveSingleGaussianFourierSmoother method)
(mermaid.smoother_factory.Smoother method)
get_optimizer() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SimpleRegistration method)
get_optimizer_by_name() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
get_pair_name() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
get_parameter_image_and_name_to_visualize() (mermaid.registration_networks.AdaptiveSmootherMomentumMapBasicNet method)
(mermaid.registration_networks.AffineMapNet method)
(mermaid.registration_networks.RegistrationNet method)
(mermaid.registration_networks.RegistrationNetDisplacement method)
(mermaid.registration_networks.SVFNet method)
(mermaid.registration_networks.SVFQuasiMomentumNet method)
(mermaid.registration_networks.ShootingScalarMomentumNet method)
(mermaid.registration_networks.ShootingVectorMomentumNet method)
get_parameter_list_and_par_to_name_dict_from_parameter_dict() (in module mermaid.utils)
get_parameter_list_from_parameter_dict() (in module mermaid.utils)
get_params() (mermaid.simple_interface.RegisterImagePair method)
get_penalty() (mermaid.smoother_factory.AdaptiveMultiGaussianFourierSmoother method)
(mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother method)
(mermaid.smoother_factory.LocalFourierSmoother method)
(mermaid.smoother_factory.Smoother method)
get_phi_slice_at_dimension() (mermaid.viewers.ImageViewer3D_Sliced_Contour method)
get_pnorm() (mermaid.regularizer_factory.TotalVariationRegularizer method)
get_pre_weights() (mermaid.deep_smoothers.DeepSmoothingModel method)
get_print_settings() (mermaid.module_parameters.ParameterDict method)
get_registration_parameters() (mermaid.registration_networks.RegistrationNet method)
get_registration_parameters_and_buffers() (mermaid.registration_networks.RegistrationNet method)
get_rel_ftol() (mermaid.multiscale_optimizer.Optimizer method)
get_respro_settings() (in module mermaid.config_parser)
get_save_fig() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
get_save_fig_num() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
get_save_fig_path() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
get_scalar() (in module mermaid.utils)
get_scale_vectors_on_read_and_write() (mermaid.fileio.ImageIO method)
get_scheduler_patience() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
get_sgd_individual_model_parameters_and_optimizer_states() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
get_sgd_shared_model_parameters() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
get_sgd_split_indvidual() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
get_sgd_split_shared() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
get_shared_model_parameters() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
get_shared_model_parameters_and_buffers() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
get_shared_registration_parameters() (mermaid.registration_networks.RegistrationNet method)
get_shared_registration_parameters_and_buffers() (mermaid.registration_networks.RegistrationNet method)
get_sigma() (mermaid.similarity_measure_factory.SimilarityMeasure method)
get_single_gaussian_smoother() (in module mermaid.utils)
get_size_of_array() (mermaid.finite_differences.FD method)
(mermaid.finite_differences.FD_np method)
(mermaid.finite_differences.FD_torch method)
get_smoothers() (mermaid.smoother_factory.AvailableSmoothers method)
(mermaid.smoother_factory.SmootherFactory method)
get_source_label() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
get_squeeze_image() (mermaid.fileio.ImageIO method)
get_state_dict() (mermaid.smoother_factory.Smoother method)
get_state_dict_for_module() (in module mermaid.smoother_factory)
get_synchronize() (mermaid.viewers.ImageViewer3D method)
(mermaid.viewers.ImageViewer3D_Sliced method)
get_target_label() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
get_variables_to_transfer_to_loss_function() (mermaid.registration_networks.RegistrationNet method)
(mermaid.registration_networks.ShootingScalarMomentumNet method)
(mermaid.registration_networks.ShootingVectorMomentumNet method)
get_visualization() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
get_visualize_step() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
get_warped_image() (mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SimpleRegistration method)
(mermaid.multiscale_optimizer.SingleScaleBatchRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SingleScaleConsensusRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
(mermaid.simple_interface.RegisterImagePair method)
get_warped_label() (mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SimpleRegistration method)
(mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
(mermaid.simple_interface.RegisterImagePair method)
get_warped_label_map() (in module mermaid.utils)
get_weighting_type() (mermaid.deep_smoothers.DeepSmoothingModel method)
get_weights() (mermaid.deep_smoothers.DeepSmoothingModel method)
getdimension() (mermaid.finite_differences.FD method)
(mermaid.finite_differences.FD_np method)
(mermaid.finite_differences.FD_torch method)
global_parameter_scaling_factor (mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother attribute)
GlobalHLoss (class in mermaid.deep_networks)
grad_norm_sqr_b() (mermaid.finite_differences.FD method)
grad_norm_sqr_c() (mermaid.finite_differences.FD method)
grad_norm_sqr_f() (mermaid.finite_differences.FD method)
H
has_combined_input (mermaid.forward_models_wrap.ODEWrapFunc attribute)
(mermaid.forward_models_wrap.ODEWrapFunc_tuple attribute)
has_key() (mermaid.module_parameters.ParameterDict method)
HelmholtzRegularizer (class in mermaid.regularizer_factory)
HLoss (class in mermaid.deep_networks)
I
identity_map() (in module mermaid.utils)
identity_map_multiN() (in module mermaid.utils)
ifftn (mermaid.custom_pytorch_extensions.FourierConvolution attribute)
(mermaid.custom_pytorch_extensions.InverseFourierConvolution attribute)
im_sz (mermaid.deep_smoothers.DeepSmootherFactory attribute)
ImageIO (class in mermaid.fileio)
ImageRegistrationOptimizer (class in mermaid.multiscale_optimizer)
ImageViewer (class in mermaid.viewers)
ImageViewer3D (class in mermaid.viewers)
ImageViewer3D_Sliced (class in mermaid.viewers)
ImageViewer3D_Sliced_Contour (class in mermaid.viewers)
import_outside_var() (mermaid.smoother_factory.LocalFourierSmoother method)
index (mermaid.viewers.ImageViewer3D_Sliced attribute)
individual_parameters_to_model_parameters() (in module mermaid.utils)
individual_state_dict() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
(mermaid.registration_networks.RegistrationNet method)
init_analysis_params() (mermaid.simple_interface.RegisterImagePair method)
init_velocity_mask() (mermaid.forward_models.EPDiffAdaptMap method)
init_weights() (in module mermaid.utils)
init_zero_sm_weight() (mermaid.forward_models.EPDiffAdaptMap method)
initial_velocity (mermaid.registration_networks.ShootingVectorMomentumNet attribute)
initialInverseMap (mermaid.multiscale_optimizer.ImageRegistrationOptimizer attribute)
(mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer attribute)
initialize_network_weights() (mermaid.deep_networks.DeepNetwork method)
initialMap (mermaid.multiscale_optimizer.ImageRegistrationOptimizer attribute)
(mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer attribute)
integrator (mermaid.registration_networks.LDDMMAdaptiveSmootherMomentumMapNet attribute)
(mermaid.registration_networks.LDDMMShootingVectorMomentumImageNet attribute)
(mermaid.registration_networks.LDDMMShootingVectorMomentumMapNet attribute)
(mermaid.registration_networks.OneStepMapNet attribute)
(mermaid.registration_networks.SVFNet attribute)
(mermaid.registration_networks.SVFQuasiMomentumNet attribute)
(mermaid.registration_networks.SVFVectorAdaptiveSmootherMomentumMapNet attribute)
(mermaid.registration_networks.SVFVectorMomentumImageNet attribute)
(mermaid.registration_networks.SVFVectorMomentumMapNet attribute)
(mermaid.registration_networks.ShootingScalarMomentumNet attribute)
(mermaid.registration_networks.ShootingVectorMomentumNet attribute)
intensity_normalize_image (mermaid.fileio.ImageIO attribute)
IntensityNormalizeImage (class in mermaid.image_manipulations)
interoplate_boundary_right() (in module mermaid.utils)
inverse_fourier_convolution() (in module mermaid.custom_pytorch_extensions)
InverseFourierConvolution (class in mermaid.custom_pytorch_extensions)
is_datatype_conversion_on() (mermaid.fileio.FileIO method)
is_turn_nan_to_zero_conversion_on() (mermaid.fileio.FileIO method)
isempty() (mermaid.module_parameters.ParameterDict method)
ISource (mermaid.multiscale_optimizer.ImageRegistrationOptimizer attribute)
(mermaid.smoother_factory.Smoother attribute)
ITarget (mermaid.multiscale_optimizer.ImageRegistrationOptimizer attribute)
iter (mermaid.smoother_factory.DiffusionSmoother attribute)
iter_count (mermaid.multiscale_optimizer.ImageRegistrationOptimizer attribute)
K
k_sz_h (mermaid.smoother_factory.GaussianSpatialSmoother attribute)
kernel_multiplication() (mermaid.similarity_helper_omt.OTSimilarityGradient method)
kernel_multiplication_gradient_helper() (mermaid.similarity_helper_omt.OTSimilarityGradient method)
L
lam (mermaid.registration_networks.LDDMMShootingScalarMomentumImageLoss attribute)
(mermaid.registration_networks.LDDMMShootingScalarMomentumMapLoss attribute)
(mermaid.registration_networks.SVFScalarMomentumImageLoss attribute)
(mermaid.registration_networks.SVFScalarMomentumMapLoss attribute)
(mermaid.registration_networks.ShootingScalarMomentumNet attribute)
lap() (mermaid.finite_differences.FD method)
last_step_size_taken() (mermaid.custom_optimizers.LBFGS_LS method)
last_successful_step_size_taken (mermaid.multiscale_optimizer.Optimizer attribute)
LBFGS_LS (class in mermaid.custom_optimizers)
LDDMMAdaptiveSmootherMomentumMapLoss (class in mermaid.registration_networks)
LDDMMAdaptiveSmootherMomentumMapNet (class in mermaid.registration_networks)
LDDMMShootingScalarMomentumImageLoss (class in mermaid.registration_networks)
LDDMMShootingScalarMomentumImageNet (class in mermaid.registration_networks)
LDDMMShootingScalarMomentumMapLoss (class in mermaid.registration_networks)
LDDMMShootingScalarMomentumMapNet (class in mermaid.registration_networks)
LDDMMShootingVectorMomentumImageLoss (class in mermaid.registration_networks)
LDDMMShootingVectorMomentumImageNet (class in mermaid.registration_networks)
LDDMMShootingVectorMomentumMapLoss (class in mermaid.registration_networks)
LDDMMShootingVectorMomentumMapNet (class in mermaid.registration_networks)
LearnedMultiGaussianCombinationFourierSmoother (class in mermaid.smoother_factory)
lift_to_dimension() (in module mermaid.utils)
linear_softmax() (in module mermaid.deep_smoothers)
linear_softnorm() (in module mermaid.deep_smoothers)
LinearSoftmax (class in mermaid.deep_smoothers)
LinearSoftnorm (class in mermaid.deep_smoothers)
LNCCSimilarity (class in mermaid.similarity_measure_factory)
load_checkpoint() (mermaid.multiscale_optimizer.Optimizer method)
load_checkpoint_dict() (mermaid.multiscale_optimizer.Optimizer method)
(mermaid.multiscale_optimizer.SingleScaleBatchRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SingleScaleConsensusRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
load_dnn_parameters_from_this_file (mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother attribute)
load_individual_state_dict() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
load_JSON() (mermaid.module_parameters.ParameterDict method)
load_optimizer_state_from_checkpoint (mermaid.multiscale_optimizer.SingleScaleConsensusRegistrationOptimizer attribute)
load_shared_state_dict() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
(mermaid.registration_networks.RegistrationNet method)
local_pre_weight_max (mermaid.deep_smoothers.DeepSmoothingModel attribute)
LocalFourierSmoother (class in mermaid.smoother_factory)
LocalizedNCCSimilarity (class in mermaid.similarity_measure_factory)
lowResInitialInverseMap (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer attribute)
lowResInitialMap (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer attribute)
lowResISource (mermaid.multiscale_optimizer.ImageRegistrationOptimizer attribute)
lowResITarget (mermaid.multiscale_optimizer.ImageRegistrationOptimizer attribute)
lowResLSource (mermaid.multiscale_optimizer.ImageRegistrationOptimizer attribute)
lowResLTarget (mermaid.multiscale_optimizer.ImageRegistrationOptimizer attribute)
lowResSize (mermaid.multiscale_optimizer.Optimizer attribute)
lowResSpacing (mermaid.multiscale_optimizer.Optimizer attribute)
LSource (mermaid.multiscale_optimizer.ImageRegistrationOptimizer attribute)
LTarget (mermaid.multiscale_optimizer.ImageRegistrationOptimizer attribute)
M
m (mermaid.registration_networks.AdaptiveSmootherMomentumMapBasicLoss attribute)
(mermaid.registration_networks.LDDMMShootingVectorMomentumImageLoss attribute)
(mermaid.registration_networks.LDDMMShootingVectorMomentumMapLoss attribute)
(mermaid.registration_networks.OneStepMapLoss attribute)
(mermaid.registration_networks.SVFQuasiMomentumImageLoss attribute)
(mermaid.registration_networks.SVFQuasiMomentumNet attribute)
(mermaid.registration_networks.SVFVectorMomentumImageLoss attribute)
(mermaid.registration_networks.SVFVectorMomentumMapLoss attribute)
map0_external (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer attribute)
map0_inverse_external (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer attribute)
MapIO (class in mermaid.fileio)
mapLowResFactor (mermaid.multiscale_optimizer.Optimizer attribute)
MATPLOTLIB_AGG (in module mermaid.config_parser)
max_normalization() (mermaid.image_manipulations.IntensityNormalizeImage method)
mermaid.config_parser (module)
mermaid.custom_optimizers (module)
mermaid.custom_pytorch_extensions (module)
mermaid.data_wrapper (module)
mermaid.deep_networks (module)
mermaid.deep_smoothers (module)
mermaid.example_generation (module)
mermaid.fileio (module)
mermaid.finite_differences (module)
mermaid.forward_models (module)
mermaid.forward_models_wrap (module)
mermaid.image_manipulations (module)
mermaid.image_sampling (module)
mermaid.libraries.functions.stn_nd (module)
mermaid.libraries.modules.stn_nd (module)
mermaid.load_default_settings (module)
mermaid.model_evaluation (module)
mermaid.model_factory (module)
mermaid.module_parameters (module)
mermaid.multiscale_optimizer (module)
mermaid.noisy_convolution (module)
mermaid.optimizer_data_loaders (module)
mermaid.registration_networks (module)
mermaid.regularizer_factory (module)
mermaid.rungekutta_integrators (module)
mermaid.similarity_helper_omt (module)
mermaid.similarity_measure_factory (module)
mermaid.simple_interface (module)
mermaid.smoother_factory (module)
mermaid.spline_interpolation (module)
mermaid.utils (module)
mermaid.viewers (module)
mermaid.visualize_registration_results (module)
model (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer attribute)
model_name (mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer attribute)
ModelFactory (class in mermaid.model_factory)
models (mermaid.model_factory.AvailableModels attribute)
momentum_boundary_weight_mask() (in module mermaid.utils)
multi_gaussian_optimizer_params (mermaid.smoother_factory.Smoother attribute)
multi_gaussian_stds (mermaid.smoother_factory.AdaptiveMultiGaussianFourierSmoother attribute)
(mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother attribute)
multi_gaussian_weights (mermaid.smoother_factory.AdaptiveMultiGaussianFourierSmoother attribute)
(mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother attribute)
(mermaid.smoother_factory.MultiGaussianFourierSmoother attribute)
multi_scale_info_dic (mermaid.multiscale_optimizer.ImageRegistrationOptimizer attribute)
MultiGaussianFourierSmoother (class in mermaid.smoother_factory)
MultiScaleRegistrationOptimizer (class in mermaid.multiscale_optimizer)
my_dot() (mermaid.similarity_helper_omt.OTSimilarityGradient method)
my_hasnan() (in module mermaid.utils)
my_sum() (mermaid.similarity_helper_omt.OTSimilarityGradient method)
N
NCCNegativeSimilarity (class in mermaid.similarity_measure_factory)
NCCPositiveSimilarity (class in mermaid.similarity_measure_factory)
NCCSimilarity (class in mermaid.similarity_measure_factory)
nested_class (mermaid.forward_models_wrap.ODEWrapFunc attribute)
(mermaid.forward_models_wrap.ODEWrapFunc_tuple attribute)
network_penalty (mermaid.deep_smoothers.DeepSmoothingModel attribute)
next_slice() (mermaid.viewers.ImageViewer3D method)
(mermaid.viewers.ImageViewer3D_Sliced method)
(mermaid.viewers.ImageViewer3D_Sliced_Contour method)
NoisyConv1d (class in mermaid.noisy_convolution)
NoisyConv2d (class in mermaid.noisy_convolution)
NoisyConv3d (class in mermaid.noisy_convolution)
NoisyConvTranspose1d (class in mermaid.noisy_convolution)
NoisyConvTranspose2d (class in mermaid.noisy_convolution)
NoisyConvTranspose3d (class in mermaid.noisy_convolution)
NoisyLayer (class in mermaid.noisy_convolution)
NoisyLinear (class in mermaid.noisy_convolution)
noramlized_spacing_to_smallest() (in module mermaid.utils)
normalize_spacing (mermaid.fileio.ImageIO attribute)
nr_of_epochs (mermaid.multiscale_optimizer.SingleScaleBatchRegistrationOptimizer attribute)
(mermaid.multiscale_optimizer.SingleScaleConsensusRegistrationOptimizer attribute)
nr_of_gaussians (mermaid.deep_smoothers.DeepSmootherFactory attribute)
(mermaid.smoother_factory.AdaptiveMultiGaussianFourierSmoother attribute)
(mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother attribute)
nr_of_image_channels (mermaid.deep_smoothers.DeepSmootherFactory attribute)
nr_of_slots (mermaid.custom_pytorch_extensions.GaussianFourierFilterGenerator attribute)
nr_of_threads (in module mermaid.config_parser)
nrOfChannels (mermaid.registration_networks.RegistrationNet attribute)
nrOfImages (mermaid.registration_networks.RegistrationNet attribute)
nrOfIterations (mermaid.multiscale_optimizer.ImageRegistrationOptimizer attribute)
nrOfTimeSteps_perUnitTimeInterval (mermaid.rungekutta_integrators.RKIntegrator attribute)
num_workers (mermaid.multiscale_optimizer.SingleScaleBatchRegistrationOptimizer attribute)
O
ODEWrapFunc (class in mermaid.forward_models_wrap)
ODEWrapFunc_tuple (class in mermaid.forward_models_wrap)
omt_boundary_weight_mask() (in module mermaid.utils)
omt_power (mermaid.smoother_factory.AdaptiveMultiGaussianFourierSmoother attribute)
(mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother attribute)
omt_use_log_transformed_std (mermaid.smoother_factory.AdaptiveMultiGaussianFourierSmoother attribute)
(mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother attribute)
omt_weight_penalty (mermaid.smoother_factory.AdaptiveMultiGaussianFourierSmoother attribute)
(mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother attribute)
OMTLoss (class in mermaid.deep_networks)
on_mouse_press() (mermaid.viewers.ImageViewer3D method)
OneStepMapLoss (class in mermaid.registration_networks)
OneStepMapNet (class in mermaid.registration_networks)
OptimalMassTransportSimilarity (class in mermaid.similarity_measure_factory)
optimize() (mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer method)
(mermaid.multiscale_optimizer.Optimizer method)
(mermaid.multiscale_optimizer.SingleScaleBatchRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SingleScaleConsensusRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
optimize_over_deep_network (mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother attribute)
optimize_over_smoother_parameters (mermaid.smoother_factory.AdaptiveSingleGaussianFourierSmoother attribute)
optimize_over_smoother_stds (mermaid.smoother_factory.AdaptiveMultiGaussianFourierSmoother attribute)
(mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother attribute)
optimize_over_smoother_weights (mermaid.smoother_factory.AdaptiveMultiGaussianFourierSmoother attribute)
(mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother attribute)
Optimizer (class in mermaid.multiscale_optimizer)
optimizer (mermaid.multiscale_optimizer.ImageRegistrationOptimizer attribute)
optimizer_has_been_initialized (mermaid.multiscale_optimizer.Optimizer attribute)
optimizer_instance (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer attribute)
optimizer_name (mermaid.multiscale_optimizer.ImageRegistrationOptimizer attribute)
optimizer_parameter_loss() (mermaid.multiscale_optimizer.Optimizer method)
optimizer_params (mermaid.multiscale_optimizer.ImageRegistrationOptimizer attribute)
organize_data() (in module mermaid.utils)
OTSimilarityGradient (class in mermaid.similarity_helper_omt)
OTSimilarityHelper (class in mermaid.similarity_helper_omt)
P
pair_name (mermaid.multiscale_optimizer.ImageRegistrationOptimizer attribute)
PairwiseRegistrationDataset (class in mermaid.optimizer_data_loaders)
parameter_output_dir (mermaid.multiscale_optimizer.SingleScaleBatchRegistrationOptimizer attribute)
ParameterDict (class in mermaid.module_parameters)
params (mermaid.deep_networks.ClusteringLoss attribute)
(mermaid.deep_networks.TotalVariationLoss attribute)
(mermaid.forward_models.ForwardModel attribute)
(mermaid.multiscale_optimizer.Optimizer attribute)
(mermaid.registration_networks.RegistrationLoss attribute)
(mermaid.registration_networks.RegistrationNet attribute)
(mermaid.regularizer_factory.Regularizer attribute)
(mermaid.similarity_measure_factory.SimilarityMeasure attribute)
(mermaid.smoother_factory.Smoother attribute)
pars (mermaid.forward_models_wrap.ODEWrapFunc attribute)
(mermaid.forward_models_wrap.ODEWrapFunc_tuple attribute)
(mermaid.rungekutta_integrators.RKIntegrator attribute)
percentile_normalization() (mermaid.image_manipulations.IntensityNormalizeImage method)
perform_spline_interpolation_helper() (in module mermaid.spline_interpolation)
PerformSplineInterpolationHelper (class in mermaid.spline_interpolation)
phi (mermaid.viewers.ImageViewer3D_Sliced_Contour attribute)
prepare_data() (mermaid.utils.AdpSmoother method)
previous_slice() (mermaid.viewers.ImageViewer3D method)
(mermaid.viewers.ImageViewer3D_Sliced method)
(mermaid.viewers.ImageViewer3D_Sliced_Contour method)
print_available_models() (mermaid.model_factory.AvailableModels method)
(mermaid.model_factory.ModelFactory method)
(mermaid.simple_interface.RegisterImagePair static method)
print_available_similarity_measures() (mermaid.similarity_measure_factory.SimilarityMeasureFactory method)
print_available_smoothers() (mermaid.smoother_factory.AvailableSmoothers method)
(mermaid.smoother_factory.SmootherFactory method)
print_settings_off() (mermaid.module_parameters.ParameterDict method)
print_settings_on() (mermaid.module_parameters.ParameterDict method)
R
randomly_initialize_network (mermaid.deep_smoothers.GeneralNetworkWeightedSmoothingModel attribute)
read() (mermaid.fileio.FileIO method)
(mermaid.fileio.GenericIO method)
(mermaid.fileio.ImageIO method)
read_batch_to_nc_format() (mermaid.fileio.ImageIO method)
read_from_validation_map_format() (mermaid.fileio.MapIO method)
read_to_map_compatible_format() (mermaid.fileio.ImageIO method)
read_to_nc_format() (mermaid.fileio.ImageIO method)
rec_custom_optimizer_output_string (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer attribute)
recording_step (mermaid.multiscale_optimizer.ImageRegistrationOptimizer attribute)
register() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SimpleMultiScaleRegistration method)
(mermaid.multiscale_optimizer.SimpleRegistration method)
(mermaid.multiscale_optimizer.SimpleSingleScaleBatchRegistration method)
(mermaid.multiscale_optimizer.SimpleSingleScaleConsensusRegistration method)
(mermaid.multiscale_optimizer.SimpleSingleScaleRegistration method)
register_images() (mermaid.simple_interface.RegisterImagePair method)
register_images_from_files() (mermaid.simple_interface.RegisterImagePair method)
RegisterImagePair (class in mermaid.simple_interface)
RegistrationImageLoss (class in mermaid.registration_networks)
RegistrationLoss (class in mermaid.registration_networks)
RegistrationMapLoss (class in mermaid.registration_networks)
RegistrationNet (class in mermaid.registration_networks)
RegistrationNetDisplacement (class in mermaid.registration_networks)
RegistrationNetTimeIntegration (class in mermaid.registration_networks)
Regularizer (class in mermaid.regularizer_factory)
regularizer (mermaid.registration_networks.CurvatureMapLoss attribute)
(mermaid.registration_networks.DiffusionMapLoss attribute)
(mermaid.registration_networks.SVFImageLoss attribute)
(mermaid.registration_networks.SVFMapLoss attribute)
(mermaid.registration_networks.SVFQuasiMomentumImageLoss attribute)
(mermaid.registration_networks.TotalVariationMapLoss attribute)
RegularizerFactory (class in mermaid.regularizer_factory)
rel_ftol (mermaid.multiscale_optimizer.Optimizer attribute)
remove_axes_event() (mermaid.viewers.FigureEventHandler method)
remove_infs_from_variable() (in module mermaid.utils)
replace_nans_with_zeros (mermaid.fileio.FileIO attribute)
ResampleImage (class in mermaid.image_sampling)
reset_parameters() (mermaid.noisy_convolution.NoisyLinear method)
reset_penalty() (mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother method)
(mermaid.smoother_factory.LocalFourierSmoother method)
reset_synchronize() (mermaid.viewers.FigureEventHandler method)
rhs (mermaid.forward_models.ForwardModel attribute)
rhs_adapt_epdiff_wkw_multiNC() (mermaid.forward_models.RHSLibrary method)
rhs_advect_image_multiNC() (mermaid.forward_models.RHSLibrary method)
rhs_advect_map_multiNC() (mermaid.forward_models.RHSLibrary method)
rhs_epdiff_multiNC() (mermaid.forward_models.RHSLibrary method)
rhs_lagrangian_evolve_map_multiNC() (mermaid.forward_models.RHSLibrary method)
rhs_scalar_conservation_multiNC() (mermaid.forward_models.RHSLibrary method)
RHSLibrary (class in mermaid.forward_models)
RK4 (class in mermaid.rungekutta_integrators)
RKIntegrator (class in mermaid.rungekutta_integrators)
S
save_checkpoint() (mermaid.multiscale_optimizer.Optimizer method)
save_consensus_state_checkpoints (mermaid.multiscale_optimizer.SingleScaleConsensusRegistrationOptimizer attribute)
save_fig (mermaid.multiscale_optimizer.ImageRegistrationOptimizer attribute)
save_fig_num (mermaid.multiscale_optimizer.ImageRegistrationOptimizer attribute)
save_fig_path (mermaid.multiscale_optimizer.ImageRegistrationOptimizer attribute)
save_intermediate_checkpoints (mermaid.multiscale_optimizer.SingleScaleConsensusRegistrationOptimizer attribute)
scale_global_parameters (mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother attribute)
scale_noise() (mermaid.noisy_convolution.NoisyLinear method)
scale_vectors_on_read_and_write (mermaid.fileio.ImageIO attribute)
scaleFactors (mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer attribute)
scaleIterations (mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer attribute)
sel_fftn() (in module mermaid.custom_pytorch_extensions)
sel_ifftn() (in module mermaid.custom_pytorch_extensions)
set_adaptive_padding() (mermaid.fileio.ImageIO method)
set_affine_transform_to_identity() (in module mermaid.utils)
set_affine_transform_to_identity_multiN() (in module mermaid.utils)
set_alpha() (mermaid.custom_pytorch_extensions.InverseFourierConvolution method)
(mermaid.regularizer_factory.HelmholtzRegularizer method)
set_choice_kernel_gibbs() (mermaid.similarity_helper_omt.OTSimilarityGradient method)
set_cur_epoch() (mermaid.deep_smoothers.DeepSmoothingModel method)
set_current_epoch() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
set_debug_mode_on() (mermaid.forward_models_wrap.ODEWrapFunc method)
(mermaid.forward_models_wrap.ODEWrapFunc_tuple method)
set_debug_retain_computed_local_weights() (mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother method)
(mermaid.smoother_factory.LocalFourierSmoother method)
set_default_datatype() (mermaid.fileio.FileIO method)
set_default_regularizer_type_to_curvature() (mermaid.regularizer_factory.RegularizerFactory method)
set_default_regularizer_type_to_diffusion() (mermaid.regularizer_factory.RegularizerFactory method)
set_default_regularizer_type_to_helmholtz() (mermaid.regularizer_factory.RegularizerFactory method)
set_default_regularizer_type_to_total_variation() (mermaid.regularizer_factory.RegularizerFactory method)
set_default_smoother_type_to_diffusion() (mermaid.smoother_factory.SmootherFactory method)
set_default_smoother_type_to_gaussian() (mermaid.smoother_factory.SmootherFactory method)
set_default_smoother_type_to_gaussianSpatial() (mermaid.smoother_factory.SmootherFactory method)
set_dictionary_to_pass_to_integrator() (mermaid.registration_networks.RegistrationNet method)
set_dictionary_to_pass_to_smoother() (mermaid.registration_networks.RegistrationLoss method)
set_dim_info() (mermaid.forward_models_wrap.ODEWrapFunc method)
(mermaid.forward_models_wrap.ODEWrapFunc_tuple method)
set_epoch() (mermaid.smoother_factory.LocalFourierSmoother method)
set_expr_name() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
set_external_optimizer_parameter_loss() (mermaid.multiscale_optimizer.Optimizer method)
set_gamma() (mermaid.regularizer_factory.HelmholtzRegularizer method)
set_gaussian_std() (mermaid.smoother_factory.AdaptiveSingleGaussianFourierSmoother method)
(mermaid.smoother_factory.SingleGaussianFourierSmoother method)
set_gaussian_stds() (mermaid.smoother_factory.AdaptiveMultiGaussianFourierSmoother method)
(mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother method)
set_gaussian_weights() (mermaid.smoother_factory.AdaptiveMultiGaussianFourierSmoother method)
(mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother method)
set_individual_model_parameters() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
set_individual_registration_parameters() (mermaid.registration_networks.RegistrationNet method)
set_initial_map() (mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SimpleRegistration method)
(mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
(mermaid.simple_interface.RegisterImagePair method)
set_initial_weight_map() (mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
set_integration_tfrom() (mermaid.registration_networks.RegistrationNetTimeIntegration method)
set_integration_tto() (mermaid.registration_networks.RegistrationNetTimeIntegration method)
set_intensity_normalization() (mermaid.fileio.ImageIO method)
set_iter() (mermaid.image_sampling.ResampleImage method)
(mermaid.smoother_factory.DiffusionSmoother method)
set_k_sz_h() (mermaid.smoother_factory.GaussianSpatialSmoother method)
set_last_successful_step_size_taken() (mermaid.multiscale_optimizer.Optimizer method)
set_model() (mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer method)
(mermaid.multiscale_optimizer.Optimizer method)
(mermaid.multiscale_optimizer.SingleScaleBatchRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SingleScaleConsensusRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
set_model_parameters() (mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SimpleRegistration method)
(mermaid.multiscale_optimizer.SingleScaleBatchRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SingleScaleConsensusRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
(mermaid.simple_interface.RegisterImagePair method)
set_model_parameters_to_zero() (mermaid.simple_interface.RegisterImagePair method)
set_model_state_dict() (mermaid.multiscale_optimizer.SimpleRegistration method)
(mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
set_multi_scale_info() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
set_n_scale() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
set_normalize_spacing() (mermaid.fileio.ImageIO method)
set_number_of_iterations() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
set_number_of_iterations_per_scale() (mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer method)
set_number_of_time_steps() (mermaid.rungekutta_integrators.RKIntegrator method)
set_opt() (mermaid.simple_interface.RegisterImagePair method)
set_opt_param() (mermaid.forward_models_wrap.ODEWrapFunc method)
(mermaid.forward_models_wrap.ODEWrapFunc_tuple method)
set_optimizer() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
set_optimizer_by_name() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
set_optimizer_params() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
set_over_scale_iter_count() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
set_pair_name() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
(mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer method)
set_pars() (mermaid.rungekutta_integrators.RKIntegrator method)
set_pnorm() (mermaid.regularizer_factory.TotalVariationRegularizer method)
set_print_settings() (mermaid.module_parameters.ParameterDict method)
set_recording_step() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
set_registration_parameters() (mermaid.registration_networks.RegistrationNet method)
set_rel_ftol() (mermaid.multiscale_optimizer.Optimizer method)
set_save_fig() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
set_save_fig_num() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
set_save_fig_path() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
(mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer method)
set_scale_factors() (mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer method)
set_scale_vectors_on_read_and_write() (mermaid.fileio.ImageIO method)
set_scheduler_patience() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
set_scheduler_patience_silent() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
set_sgd_individual_model_parameters_and_optimizer_states() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
set_sgd_shared_model_parameters_and_optimizer_states() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
set_shared_model_parameters() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
set_shared_registration_parameters() (mermaid.registration_networks.RegistrationNet method)
set_sigma() (mermaid.similarity_measure_factory.SimilarityMeasure method)
set_similarity_measure_default_type_to_lncc() (mermaid.similarity_measure_factory.SimilarityMeasureFactory method)
set_similarity_measure_default_type_to_ncc() (mermaid.similarity_measure_factory.SimilarityMeasureFactory method)
set_similarity_measure_default_type_to_ncc_negative() (mermaid.similarity_measure_factory.SimilarityMeasureFactory method)
set_similarity_measure_default_type_to_ncc_positive() (mermaid.similarity_measure_factory.SimilarityMeasureFactory method)
set_similarity_measure_default_type_to_omt() (mermaid.similarity_measure_factory.SimilarityMeasureFactory method)
set_similarity_measure_default_type_to_ssd() (mermaid.similarity_measure_factory.SimilarityMeasureFactory method)
set_source_image() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
(mermaid.smoother_factory.Smoother method)
set_source_label() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
set_squeeze_image() (mermaid.fileio.ImageIO method)
set_state_dict() (mermaid.smoother_factory.AdaptiveMultiGaussianFourierSmoother method)
(mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother method)
(mermaid.smoother_factory.Smoother method)
set_synchronize() (mermaid.viewers.ImageViewer3D method)
(mermaid.viewers.ImageViewer3D_Sliced method)
(mermaid.viewers.ImageViewer3D_Sliced_Contour method)
set_target_image() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
set_target_label() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
set_visualization() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
set_visualize_step() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
set_weight_map() (mermaid.multiscale_optimizer.SimpleRegistration method)
(mermaid.simple_interface.RegisterImagePair method)
shared_state_dict() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
(mermaid.registration_networks.RegistrationNet method)
ShootingScalarMomentumNet (class in mermaid.registration_networks)
ShootingVectorMomentumNet (class in mermaid.registration_networks)
show() (mermaid.viewers.ImageViewer method)
(mermaid.viewers.ImageViewer3D_Sliced method)
(mermaid.viewers.ImageViewer3D_Sliced_Contour method)
show_contours() (mermaid.viewers.ImageViewer3D_Sliced_Contour method)
show_current_images() (in module mermaid.visualize_registration_results)
show_sample_optimizer_output (mermaid.multiscale_optimizer.SingleScaleBatchRegistrationOptimizer attribute)
showColorbar (mermaid.viewers.ImageViewer3D_Sliced attribute)
shuffle (mermaid.multiscale_optimizer.SingleScaleBatchRegistrationOptimizer attribute)
sigma (mermaid.multiscale_optimizer.SingleScaleConsensusRegistrationOptimizer attribute)
(mermaid.similarity_measure_factory.SimilarityMeasure attribute)
similarity_measure_default_type (mermaid.similarity_measure_factory.SimilarityMeasureFactory attribute)
SimilarityMeasure (class in mermaid.similarity_measure_factory)
similarityMeasure (mermaid.registration_networks.RegistrationLoss attribute)
SimilarityMeasureFactory (class in mermaid.similarity_measure_factory)
simMeasures (mermaid.similarity_measure_factory.SimilarityMeasureFactory attribute)
Simple_consistent (class in mermaid.deep_networks)
Simple_Unet (class in mermaid.deep_networks)
SimpleMultiScaleRegistration (class in mermaid.multiscale_optimizer)
SimpleRegistration (class in mermaid.multiscale_optimizer)
SimpleSingleScaleBatchRegistration (class in mermaid.multiscale_optimizer)
SimpleSingleScaleConsensusRegistration (class in mermaid.multiscale_optimizer)
SimpleSingleScaleRegistration (class in mermaid.multiscale_optimizer)
SingleGaussianFourierSmoother (class in mermaid.smoother_factory)
SingleScaleBatchRegistrationOptimizer (class in mermaid.multiscale_optimizer)
SingleScaleConsensusRegistrationOptimizer (class in mermaid.multiscale_optimizer)
SingleScaleRegistrationOptimizer (class in mermaid.multiscale_optimizer)
sliceDim (mermaid.viewers.ImageViewer3D_Sliced attribute)
smallest_gaussian_std (mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother attribute)
smFactory (mermaid.registration_networks.RegistrationLoss attribute)
smooth() (mermaid.smoother_factory.Smoother method)
Smoother (class in mermaid.smoother_factory)
smoother (mermaid.registration_networks.ShootingScalarMomentumNet attribute)
(mermaid.registration_networks.SVFQuasiMomentumImageLoss attribute)
(mermaid.registration_networks.SVFQuasiMomentumNet attribute)
(mermaid.registration_networks.ShootingVectorMomentumNet attribute)
SmootherFactory (class in mermaid.smoother_factory)
smoothers (mermaid.smoother_factory.AvailableSmoothers attribute)
solve() (mermaid.rungekutta_integrators.RKIntegrator method)
solve_one_step() (mermaid.rungekutta_integrators.EulerForward method)
(mermaid.rungekutta_integrators.RK4 method)
(mermaid.rungekutta_integrators.RKIntegrator method)
space_normal() (in module mermaid.utils)
spacing (mermaid.custom_pytorch_extensions.GaussianFourierFilterGenerator attribute)
(mermaid.deep_smoothers.DeepSmootherFactory attribute)
(mermaid.finite_differences.FD attribute)
(mermaid.forward_models.ForwardModel attribute)
(mermaid.forward_models.RHSLibrary attribute)
(mermaid.libraries.modules.stn_nd.STN_ND_BCXYZ attribute)
(mermaid.multiscale_optimizer.Optimizer attribute)
(mermaid.registration_networks.RegistrationNet attribute)
(mermaid.regularizer_factory.Regularizer attribute)
(mermaid.regularizer_factory.RegularizerFactory attribute)
(mermaid.similarity_measure_factory.SimilarityMeasure attribute)
(mermaid.similarity_measure_factory.SimilarityMeasureFactory attribute)
(mermaid.smoother_factory.Smoother attribute)
(mermaid.smoother_factory.SmootherFactory attribute)
(mermaid.spline_interpolation.SplineInterpolation_ND_BCXYZ attribute)
spacing_min (mermaid.forward_models.RHSLibrary attribute)
spacing_model (mermaid.model_factory.ModelFactory attribute)
(mermaid.registration_networks.RegistrationLoss attribute)
spacing_sim (mermaid.model_factory.ModelFactory attribute)
(mermaid.registration_networks.RegistrationLoss attribute)
sparams (mermaid.registration_networks.ShootingVectorMomentumNet attribute)
spatially_average() (mermaid.deep_smoothers.DeepSmoothingModel method)
spline_order (mermaid.multiscale_optimizer.Optimizer attribute)
(mermaid.registration_networks.RegistrationMapLoss attribute)
(mermaid.registration_networks.RegistrationNetDisplacement attribute)
(mermaid.registration_networks.SVFNet attribute)
(mermaid.registration_networks.SVFQuasiMomentumNet attribute)
(mermaid.registration_networks.ShootingScalarMomentumNet attribute)
(mermaid.registration_networks.ShootingVectorMomentumNet attribute)
(mermaid.similarity_measure_factory.OptimalMassTransportSimilarity attribute)
(mermaid.spline_interpolation.SplineInterpolation_ND_BCXYZ attribute)
SplineInterpolation_ND_BCXYZ (class in mermaid.spline_interpolation)
squeeze_image (mermaid.fileio.ImageIO attribute)
SSDSimilarity (class in mermaid.similarity_measure_factory)
ssOpt (mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer attribute)
stable_softmax() (in module mermaid.deep_smoothers)
StableSoftmax (class in mermaid.deep_smoothers)
standardize_display_standardization (mermaid.deep_smoothers.DeepSmoothingModel attribute)
standardize_divide_input_images (mermaid.deep_smoothers.DeepSmoothingModel attribute)
standardize_divide_input_momentum (mermaid.deep_smoothers.DeepSmoothingModel attribute)
standardize_input_images (mermaid.deep_smoothers.DeepSmoothingModel attribute)
standardize_input_momentum (mermaid.deep_smoothers.DeepSmoothingModel attribute)
standardize_subtract_from_input_images (mermaid.deep_smoothers.DeepSmoothingModel attribute)
standardize_subtract_from_input_momentum (mermaid.deep_smoothers.DeepSmoothingModel attribute)
start_from_previously_saved_parameters (mermaid.multiscale_optimizer.SingleScaleBatchRegistrationOptimizer attribute)
start_optimize_over_nn_smoother_parameters_at_iteration (mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother attribute)
start_optimize_over_smoother_parameters_at_iteration (mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother attribute)
step() (mermaid.custom_optimizers.LBFGS_LS method)
STN_ND_BCXYZ (class in mermaid.libraries.modules.stn_nd)
STNFunction_ND_BCXYZ (class in mermaid.libraries.functions.stn_nd)
STNFunction_ND_BCXYZ_Compile (class in mermaid.libraries.functions.stn_nd)
STNVal() (in module mermaid.data_wrapper)
supported_events (mermaid.viewers.FigureEventHandler attribute)
SVFImageLoss (class in mermaid.registration_networks)
SVFImageNet (class in mermaid.registration_networks)
SVFMapLoss (class in mermaid.registration_networks)
SVFMapNet (class in mermaid.registration_networks)
SVFNet (class in mermaid.registration_networks)
SVFQuasiMomentumImageLoss (class in mermaid.registration_networks)
SVFQuasiMomentumImageNet (class in mermaid.registration_networks)
SVFQuasiMomentumNet (class in mermaid.registration_networks)
SVFScalarMomentumImageLoss (class in mermaid.registration_networks)
SVFScalarMomentumImageNet (class in mermaid.registration_networks)
SVFScalarMomentumMapLoss (class in mermaid.registration_networks)
SVFScalarMomentumMapNet (class in mermaid.registration_networks)
SVFVectorAdaptiveSmootherMomentumMapLoss (class in mermaid.registration_networks)
SVFVectorAdaptiveSmootherMomentumMapNet (class in mermaid.registration_networks)
SVFVectorMomentumImageLoss (class in mermaid.registration_networks)
SVFVectorMomentumImageNet (class in mermaid.registration_networks)
SVFVectorMomentumMapLoss (class in mermaid.registration_networks)
SVFVectorMomentumMapNet (class in mermaid.registration_networks)
symmetrize_filter_center_at_zero() (in module mermaid.custom_pytorch_extensions)
sync_d (mermaid.viewers.FigureEventHandler attribute)
synchronize() (mermaid.viewers.FigureEventHandler method)
sz (mermaid.custom_pytorch_extensions.GaussianFourierFilterGenerator attribute)
(mermaid.forward_models.ForwardModel attribute)
(mermaid.multiscale_optimizer.Optimizer attribute)
(mermaid.registration_networks.RegistrationNet attribute)
(mermaid.smoother_factory.Smoother attribute)
(mermaid.smoother_factory.SmootherFactory attribute)
sz_model (mermaid.model_factory.ModelFactory attribute)
(mermaid.registration_networks.RegistrationLoss attribute)
sz_sim (mermaid.model_factory.ModelFactory attribute)
(mermaid.registration_networks.RegistrationLoss attribute)
T
t2np() (in module mermaid.utils)
test_me() (in module mermaid.image_sampling)
(in module mermaid.spline_interpolation)
test_me_2() (in module mermaid.image_sampling)
test_parameter_dict() (in module mermaid.module_parameters)
test_viewer() (in module mermaid.viewers)
textStr (mermaid.viewers.ImageViewer3D_Sliced attribute)
tFrom (mermaid.registration_networks.RegistrationNetTimeIntegration attribute)
time_warped_function() (in module mermaid.utils)
TotalVariationLoss (class in mermaid.deep_networks)
TotalVariationMapLoss (class in mermaid.registration_networks)
TotalVariationRegularizer (class in mermaid.regularizer_factory)
tTo (mermaid.registration_networks.RegistrationNetTimeIntegration attribute)
turn_datatype_conversion_off() (mermaid.fileio.FileIO method)
turn_datatype_conversion_on() (mermaid.fileio.FileIO method)
turn_intensity_normalization_off() (mermaid.fileio.ImageIO method)
turn_intensity_normalization_on() (mermaid.fileio.ImageIO method)
turn_iteration_output_off() (mermaid.multiscale_optimizer.Optimizer method)
turn_iteration_output_on() (mermaid.multiscale_optimizer.Optimizer method)
turn_nan_to_zero_conversion_off() (mermaid.fileio.FileIO method)
turn_nan_to_zero_conversion_on() (mermaid.fileio.FileIO method)
turn_normalize_spacing_off() (mermaid.fileio.ImageIO method)
turn_normalize_spacing_on() (mermaid.fileio.ImageIO method)
turn_scale_vectors_on_read_and_write_off() (mermaid.fileio.ImageIO method)
turn_scale_vectors_on_read_and_write_on() (mermaid.fileio.ImageIO method)
turn_squeeze_image_off() (mermaid.fileio.ImageIO method)
turn_squeeze_image_on() (mermaid.fileio.ImageIO method)
turn_visualization_off() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
turn_visualization_on() (mermaid.multiscale_optimizer.ImageRegistrationOptimizer method)
U
u (mermaid.rungekutta_integrators.RKIntegrator attribute)
u() (mermaid.forward_models.AdvectImage method)
(mermaid.forward_models.AdvectMap method)
(mermaid.forward_models.ForwardModel method)
Unet (class in mermaid.deep_networks)
Unet_no_skip (class in mermaid.deep_networks)
unfreeze_adaptive_regularizer_param() (mermaid.registration_networks.AdaptiveSmootherMomentumMapBasicNet method)
unfreeze_momentum() (mermaid.registration_networks.AdaptiveSmootherMomentumMapBasicNet method)
update_affine_param() (in module mermaid.utils)
upsample_image_by_factor() (mermaid.image_sampling.ResampleImage method)
upsample_image_to_size() (mermaid.image_sampling.ResampleImage method)
upsample_model_parameters() (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
upsample_registration_parameters() (mermaid.registration_networks.AdaptiveSmootherMomentumMapBasicNet method)
(mermaid.registration_networks.AffineMapNet method)
(mermaid.registration_networks.RegistrationNet method)
(mermaid.registration_networks.RegistrationNetDisplacement method)
(mermaid.registration_networks.SVFNet method)
(mermaid.registration_networks.SVFQuasiMomentumNet method)
(mermaid.registration_networks.ShootingScalarMomentumNet method)
(mermaid.registration_networks.ShootingVectorMomentumNet method)
upsample_vector_field_by_factor() (mermaid.image_sampling.ResampleImage method)
use_CFL_clamping (mermaid.registration_networks.RegistrationNetTimeIntegration attribute)
USE_FLOAT16 (in module mermaid.config_parser)
use_multi_gaussian_regularization (mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother attribute)
use_neumann_BC_for_map (mermaid.forward_models.RHSLibrary attribute)
useMap (mermaid.multiscale_optimizer.Optimizer attribute)
V
v (mermaid.registration_networks.SVFImageLoss attribute)
(mermaid.registration_networks.SVFMapLoss attribute)
(mermaid.registration_networks.SVFNet attribute)
(mermaid.registration_networks.SVFQuasiMomentumNet attribute)
variables_from_optimizer (mermaid.forward_models_wrap.ODEWrapFunc attribute)
(mermaid.forward_models_wrap.ODEWrapFunc_tuple attribute)
velocity_mask (mermaid.registration_networks.ShootingVectorMomentumNet attribute)
visualize (mermaid.multiscale_optimizer.ImageRegistrationOptimizer attribute)
visualize_step (mermaid.multiscale_optimizer.ImageRegistrationOptimizer attribute)
volumeElement (mermaid.custom_pytorch_extensions.GaussianFourierFilterGenerator attribute)
(mermaid.regularizer_factory.Regularizer attribute)
(mermaid.similarity_measure_factory.SimilarityMeasure attribute)
(mermaid.smoother_factory.Smoother attribute)
W
weight (mermaid.noisy_convolution.NoisyConv1d attribute)
(mermaid.noisy_convolution.NoisyConv2d attribute)
(mermaid.noisy_convolution.NoisyConv3d attribute)
(mermaid.noisy_convolution.NoisyConvTranspose1d attribute)
(mermaid.noisy_convolution.NoisyConvTranspose2d attribute)
(mermaid.noisy_convolution.NoisyConvTranspose3d attribute)
(mermaid.noisy_convolution.NoisyLinear attribute)
weight_clipping_type (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer attribute)
weight_clipping_value (mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer attribute)
weight_map (mermaid.multiscale_optimizer.ImageRegistrationOptimizer attribute)
(mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer attribute)
weighted_linear_softmax() (in module mermaid.deep_smoothers)
weighted_linear_softnorm() (in module mermaid.deep_smoothers)
weighted_softmax() (in module mermaid.deep_smoothers)
weighted_sqrt_softmax() (in module mermaid.deep_smoothers)
WeightedLinearSoftmax (class in mermaid.deep_smoothers)
WeightedLinearSoftnorm (class in mermaid.deep_smoothers)
WeightedSoftmax (class in mermaid.deep_smoothers)
WeightedSqrtSoftmax (class in mermaid.deep_smoothers)
WeightInputRangeLoss (class in mermaid.deep_networks)
WeightRangeLoss (class in mermaid.deep_networks)
weights_init_kaiming() (in module mermaid.utils)
weights_init_normal() (in module mermaid.utils)
weights_init_orthogonal() (in module mermaid.utils)
weights_init_rd_normal() (in module mermaid.utils)
weights_init_uniform() (in module mermaid.utils)
weights_init_xavier() (in module mermaid.utils)
write() (mermaid.fileio.FileIO method)
(mermaid.fileio.GenericIO method)
(mermaid.fileio.ImageIO method)
(mermaid.fileio.MapIO method)
write_batch_to_individual_files() (mermaid.fileio.ImageIO method)
write_JSON() (mermaid.module_parameters.ParameterDict method)
write_JSON_and_JSON_comments() (mermaid.module_parameters.ParameterDict method)
write_JSON_comments() (mermaid.module_parameters.ParameterDict method)
write_parameters_to_settings() (mermaid.multiscale_optimizer.MultiScaleRegistrationOptimizer method)
(mermaid.multiscale_optimizer.Optimizer method)
(mermaid.multiscale_optimizer.SimpleRegistration method)
(mermaid.multiscale_optimizer.SingleScaleBatchRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SingleScaleConsensusRegistrationOptimizer method)
(mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer method)
(mermaid.registration_networks.RegistrationNet method)
(mermaid.registration_networks.SVFQuasiMomentumNet method)
(mermaid.registration_networks.ShootingScalarMomentumNet method)
(mermaid.registration_networks.ShootingVectorMomentumNet method)
(mermaid.smoother_factory.AdaptiveMultiGaussianFourierSmoother method)
(mermaid.smoother_factory.AdaptiveSingleGaussianFourierSmoother method)
(mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother method)
(mermaid.smoother_factory.Smoother method)
write_to_validation_map_format() (mermaid.fileio.MapIO method)
ws (mermaid.smoother_factory.LearnedMultiGaussianCombinationFourierSmoother attribute)
X
xm() (mermaid.finite_differences.FD method)
xp() (mermaid.finite_differences.FD method)
Y
ym() (mermaid.finite_differences.FD method)
yp() (mermaid.finite_differences.FD method)
Z
zm() (mermaid.finite_differences.FD method)
zp() (mermaid.finite_differences.FD method)
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