Index

_

__call__() (demeter.metamorphosis.data_cost.DataCost method)

__init__() (demeter.metamorphosis.data_cost.DataCost method) __repr__() (demeter.metamorphosis.data_cost.DataCost method)

A

addGrid2im() (in module demeter.utils.torchbox)

annotate_heatmap() (in module demeter.utils.toolbox) append_to_csv_new() (in module demeter.utils.fill_saves_overview)

B

backtracking_search() (demeter.utils.optim.GradientDescent method)

BCH() (in module demeter.utils.torchbox) bspline_basis() (in module demeter.utils.bspline)

C

Cfm (class in demeter.metamorphosis.data_cost) checkDiffeo() (in module demeter.utils.torchbox) Combine_ssd_CFM (class in demeter.utils.cost_functions) complex_matmul() (in module demeter.utils.fft_conv) compose_fields() (in module demeter.utils.torchbox) compute_DICE() (demeter.metamorphosis.abstract.Optimize_geodesicShooting method) compute_field_sim() (demeter.metamorphosis.constrained.ConstrainedMetamorphosis_integrator method) compute_landmark_dist() (demeter.metamorphosis.abstract.Optimize_geodesicShooting method)

ConstrainedMetamorphosis_integrator (class in demeter.metamorphosis.constrained) ConstrainedMetamorphosis_Shooting (class in demeter.metamorphosis.constrained) cost() (demeter.metamorphosis.abstract.Optimize_geodesicShooting method) (demeter.metamorphosis.classic.Metamorphosis_Shooting method) (demeter.metamorphosis.constrained.ConstrainedMetamorphosis_Shooting method) (demeter.metamorphosis.constrained.Reduce_field_Optim method) (demeter.metamorphosis.joined.Weighted_joinedMask_Metamorphosis_Shooting method) (demeter.metamorphosis.simplex.Simplex_sqrt_Shooting method)

D

DataCost (class in demeter.metamorphosis.data_cost) deformation_show() (in module demeter.utils.torchbox) demeter module demeter.constants module demeter.metamorphosis module demeter.metamorphosis.abstract module demeter.metamorphosis.classic module demeter.metamorphosis.constrained module demeter.metamorphosis.data_cost module demeter.metamorphosis.joined module demeter.metamorphosis.load module demeter.metamorphosis.simplex module demeter.metamorphosis.wraps module demeter.utils module

demeter.utils.bspline module demeter.utils.cost_functions module demeter.utils.decorators module demeter.utils.fft_conv module demeter.utils.fill_saves_overview module demeter.utils.optim module demeter.utils.reproducing_kernels module demeter.utils.toolbox module demeter.utils.torchbox module demeter.utils.vector_field_to_flow module deprecated() (in module demeter.utils.decorators) derivative() (demeter.utils.torchbox.RandomGaussianImage method) detOfJacobian() (in module demeter.utils.torchbox) display_env_help() (in module demeter.constants) divergence() (demeter.utils.torchbox.RandomGaussianField method) dx_convention_handler() (in module demeter.utils.reproducing_kernels)

F

fft_conv() (in module demeter.utils.fft_conv) fft_filter() (in module demeter.utils.reproducing_kernels) field() (demeter.utils.torchbox.RandomGaussianField method) field2D_bspline() (in module demeter.utils.bspline) field2diffeo() (in module demeter.utils.torchbox) field3D_bspline() (in module demeter.utils.bspline) field_2d_hessian() (in module demeter.utils.torchbox) field_2d_jacobian() (in module demeter.utils.torchbox) Field_divergence (class in demeter.utils.torchbox) field_divergence() (in module demeter.utils.torchbox) FieldIntegrator (class in demeter.utils.vector_field_to_flow) fieldNorm2() (in module demeter.utils.torchbox) fig_to_image() (in module demeter.utils.toolbox) find_binary_center() (in module demeter.utils.torchbox) find_cuda() (in module demeter.constants) format_sigmas() (in module demeter.utils.torchbox)

format_time() (in module demeter.utils.toolbox) forward() (demeter.metamorphosis.abstract.Geodesic_integrator method) (demeter.metamorphosis.abstract.Optimize_geodesicShooting method) (demeter.metamorphosis.constrained.ConstrainedMetamorphosis_Shooting method) (demeter.metamorphosis.constrained.Reduce_field_Optim method) (demeter.metamorphosis.joined.Weighted_joinedMask_Metamorphosis_integrator method) (demeter.metamorphosis.simplex.Simplex_sqrt_Metamorphosis_integrator method) (demeter.utils.cost_functions.Mutual_Information method) (demeter.utils.cost_functions.SoftHistogram1D method) (demeter.utils.cost_functions.SoftHistogram2D method) (demeter.utils.reproducing_kernels.GaussianRKHS method) (demeter.utils.reproducing_kernels.VolNormalizedGaussianRKHS method) (demeter.utils.torchbox.Field_divergence method) forward_safe_mode() (demeter.metamorphosis.abstract.Optimize_geodesicShooting method) full_ellipse() (in module demeter.utils.toolbox) function() (demeter.utils.cost_functions.SumSquaredDifference method)

G

gaussian() (demeter.utils.torchbox.RandomGaussianImage method) GaussianRKHS (class in demeter.utils.reproducing_kernels) geodesic_3d_slider() (in module demeter.utils.torchbox) Geodesic_integrator (class in demeter.metamorphosis.abstract) get_all_arguments() (demeter.metamorphosis.abstract.Optimize_geodesicShooting method) (demeter.metamorphosis.classic.Metamorphosis_Shooting method) (demeter.metamorphosis.constrained.ConstrainedMetamorphosis_Shooting method) (demeter.metamorphosis.joined.Weighted_joinedMask_Metamorphosis_Shooting method) (demeter.metamorphosis.simplex.Simplex_sqrt_Shooting method) (demeter.utils.reproducing_kernels.GaussianRKHS method) (demeter.utils.reproducing_kernels.Multi_scale_GaussianRKHS method) (demeter.utils.reproducing_kernels.VolNormalizedGaussianRKHS method) get_deformation() (demeter.metamorphosis.abstract.Geodesic_integrator method) get_deformator() (demeter.metamorphosis.abstract.Geodesic_integrator method) get_DICE() (demeter.metamorphosis.abstract.Optimize_geodesicShooting method) get_freer_gpu() (in module demeter.constants) (in module demeter.utils.toolbox) get_gaussian_kernel1d() (in module demeter.utils.reproducing_kernels)

get_gaussian_kernel2d() (in module demeter.utils.reproducing_kernels) get_gaussian_kernel3d() (in module demeter.utils.reproducing_kernels) get_geodesic_distance() (demeter.metamorphosis.abstract.Optimize_geodesicShooting method) get_landmark_dist() (demeter.metamorphosis.abstract.Optimize_geodesicShooting method) get_sigma_from_img_ratio() (in module demeter.utils.reproducing_kernels) get_size() (in module demeter.utils.toolbox) get_sobel_kernel_2d() (in module demeter.utils.torchbox) get_sobel_kernel_3d() (in module demeter.utils.torchbox) get_ssd_def() (demeter.metamorphosis.abstract.Optimize_geodesicShooting method) (demeter.metamorphosis.joined.Weighted_joinedMask_Metamorphosis_Shooting method) get_total_cost() (demeter.metamorphosis.abstract.Optimize_geodesicShooting method) (demeter.metamorphosis.constrained.ConstrainedMetamorphosis_Shooting method) (demeter.metamorphosis.constrained.Reduce_field_Optim method) getCMS_allcombinaision() (in module demeter.utils.bspline) getCMS_turn() (in module demeter.utils.bspline) GradientDescent (class in demeter.utils.optim) grid2im() (in module demeter.utils.torchbox) gridDef_plot() (in module demeter.utils.torchbox) gridDef_plot_2d() (in module demeter.utils.torchbox)

H

heatmap() (in module demeter.utils.toolbox)

I

im2grid() (in module demeter.utils.torchbox) image() (demeter.utils.torchbox.RandomGaussianImage method) image_slice() (in module demeter.utils.torchbox) imCmp() (in module demeter.utils.toolbox) (in module demeter.utils.torchbox) imgDeform() (in module demeter.utils.torchbox)

imgShow() (demeter.utils.cost_functions.SumSquaredDifference method) independence_plot() (demeter.utils.cost_functions.Mutual_Information method) init_kernel() (demeter.utils.reproducing_kernels.GaussianRKHS method) (demeter.utils.reproducing_kernels.Multi_scale_GaussianRKHS method) (demeter.utils.reproducing_kernels.VolNormalizedGaussianRKHS method) is_tensor() (in module demeter.utils.torchbox)

J

joined_metamorphosis() (in module demeter.metamorphosis.wraps)

L

leviCivita_2Dderivative() (in module demeter.utils.torchbox) lieBracket() (in module demeter.utils.torchbox)

load_optimize_geodesicShooting() (in module demeter.metamorphosis.load) Longitudinal_DataCost (class in demeter.metamorphosis.data_cost)

M

make_3d_flat() (in module demeter.utils.torchbox) make_ball_at_shape_center() (in module demeter.utils.torchbox) make_regular_grid() (in module demeter.utils.torchbox) memo() (in module demeter.utils.bspline) Metamorphosis_integrator (class in demeter.metamorphosis.classic) Metamorphosis_Shooting (class in demeter.metamorphosis.classic) module demeter demeter.constants demeter.metamorphosis demeter.metamorphosis.abstract demeter.metamorphosis.classic demeter.metamorphosis.constrained demeter.metamorphosis.data_cost demeter.metamorphosis.joined demeter.metamorphosis.load demeter.metamorphosis.simplex demeter.metamorphosis.wraps demeter.utils demeter.utils.bspline demeter.utils.cost_functions demeter.utils.decorators demeter.utils.fft_conv demeter.utils.fill_saves_overview demeter.utils.optim demeter.utils.reproducing_kernels demeter.utils.toolbox demeter.utils.torchbox demeter.utils.vector_field_to_flow

Multi_scale_GaussianRKHS (class in demeter.utils.reproducing_kernels) Multi_scale_GaussianRKHS_notAverage (class in demeter.utils.reproducing_kernels) Mutlimodal_ssd_cfm (class in demeter.metamorphosis.data_cost) Mutual_Information (class in demeter.metamorphosis.data_cost) (class in demeter.utils.cost_functions)

O

Optimize_geodesicShooting (class in demeter.metamorphosis.abstract)

P

pad_to_same_size() (in module demeter.utils.torchbox) pixel_to_2square_convention() (in module demeter.utils.torchbox) pixel_to_square_convention() (in module demeter.utils.torchbox) plot() (demeter.metamorphosis.abstract.Geodesic_integrator method) (demeter.metamorphosis.abstract.Optimize_geodesicShooting method) (demeter.metamorphosis.joined.Weighted_joinedMask_Metamorphosis_integrator method) (demeter.utils.reproducing_kernels.GaussianRKHS method) (demeter.utils.reproducing_kernels.Multi_scale_GaussianRKHS method) (demeter.utils.reproducing_kernels.VolNormalizedGaussianRKHS method) plot_cost() (demeter.metamorphosis.abstract.Optimize_geodesicShooting method) (demeter.metamorphosis.constrained.ConstrainedMetamorphosis_Shooting method) (demeter.metamorphosis.constrained.Reduce_field_Optim method) (demeter.metamorphosis.joined.Weighted_joinedMask_Metamorphosis_Shooting method)

plot_deform() (demeter.metamorphosis.abstract.Geodesic_integrator method) (demeter.metamorphosis.abstract.Optimize_geodesicShooting method) plot_field_sim() (demeter.metamorphosis.constrained.ConstrainedMetamorphosis_integrator method) plot_gaussian_kernel_1d() (in module demeter.utils.reproducing_kernels) plot_gaussian_kernel_2d() (in module demeter.utils.reproducing_kernels) plot_gaussian_kernel_3d() (in module demeter.utils.reproducing_kernels) plot_imgCmp() (demeter.metamorphosis.abstract.Optimize_geodesicShooting method) (demeter.metamorphosis.joined.Weighted_joinedMask_Metamorphosis_Shooting method) plot_kernel_on_image() (in module demeter.utils.reproducing_kernels)

Q

quiver_plot() (in module demeter.utils.torchbox)

R

RandomGaussianField (class in demeter.utils.torchbox) RandomGaussianImage (class in demeter.utils.torchbox) rec() (in module demeter.utils.fill_saves_overview)

Reduce_field_Optim (class in demeter.metamorphosis.constrained) reg_open() (in module demeter.utils.torchbox) resize_image() (in module demeter.utils.torchbox) rgb2gray() (in module demeter.utils.toolbox)

S

save() (demeter.metamorphosis.abstract.Optimize_geodesicShooting method) save_gif_with_plt() (in module demeter.utils.toolbox) save_to_gif() (demeter.metamorphosis.abstract.Optimize_geodesicShooting method) set_optimizer() (demeter.metamorphosis.data_cost.DataCost method), [1] (demeter.metamorphosis.data_cost.Longitudinal_DataCost method) (demeter.metamorphosis.data_cost.Mutlimodal_ssd_cfm method) (demeter.metamorphosis.data_cost.SimiliSegs method) set_ticks_off() (in module demeter.constants) SimiliSegs (class in demeter.metamorphosis.data_cost) simplex_metamorphosis() (in module demeter.metamorphosis.wraps) Simplex_sqrt_Metamorphosis_integrator (class in demeter.metamorphosis.simplex) Simplex_sqrt_Shooting (class in demeter.metamorphosis.simplex) SoftHistogram1D (class in demeter.utils.cost_functions) SoftHistogram2D (class in demeter.utils.cost_functions) spatialGradient() (in module demeter.utils.torchbox) spatialGradient_2d() (in module demeter.utils.torchbox) spatialGradient_3d() (in module demeter.utils.torchbox)

square2_to_pixel_convention() (in module demeter.utils.torchbox) square2_to_square_convention() (in module demeter.utils.torchbox) square_to_2square_convention() (in module demeter.utils.torchbox) square_to_pixel_convention() (in module demeter.utils.torchbox) Ssd (class in demeter.metamorphosis.data_cost) Ssd_normalized (class in demeter.metamorphosis.data_cost) step() (demeter.metamorphosis.abstract.Geodesic_integrator method) (demeter.metamorphosis.classic.Metamorphosis_integrator method) (demeter.metamorphosis.constrained.ConstrainedMetamorphosis_integrator method) (demeter.metamorphosis.joined.Weighted_joinedMask_Metamorphosis_integrator method) (demeter.metamorphosis.simplex.Simplex_sqrt_Metamorphosis_integrator method) (demeter.utils.optim.GradientDescent method) step_deprecated() (demeter.metamorphosis.constrained.ConstrainedMetamorphosis_integrator method) step_sharp() (demeter.metamorphosis.joined.Weighted_joinedMask_Metamorphosis_integrator method) SumSquaredDifference (class in demeter.utils.cost_functions) surf_bspline() (in module demeter.utils.bspline) surf_bspline_3D() (in module demeter.utils.bspline)

T

temporal_img_cmp() (in module demeter.utils.torchbox) TestCuda() (in module demeter.utils.toolbox) thresholding() (in module demeter.utils.torchbox) time_it() (in module demeter.utils.decorators) to_device() (demeter.metamorphosis.abstract.Geodesic_integrator method) (demeter.metamorphosis.abstract.Optimize_geodesicShooting method) (demeter.metamorphosis.constrained.ConstrainedMetamorphosis_integrator method) (demeter.metamorphosis.constrained.ConstrainedMetamorphosis_Shooting method) (demeter.metamorphosis.constrained.Reduce_field_Optim method) (demeter.metamorphosis.data_cost.DataCost method), [1] (demeter.metamorphosis.data_cost.Longitudinal_DataCost method) (demeter.metamorphosis.data_cost.Mutlimodal_ssd_cfm method) (demeter.metamorphosis.data_cost.Mutual_Information method) (demeter.metamorphosis.data_cost.SimiliSegs method) (demeter.metamorphosis.data_cost.Ssd method) (demeter.metamorphosis.data_cost.Ssd_normalized method) (demeter.metamorphosis.joined.Weighted_joinedMask_Metamorphosis_integrator method)

to_ntuple() (in module demeter.utils.fft_conv)

U

update_csv() (in module demeter.utils.fill_saves_overview)

update_progress() (in module demeter.utils.toolbox)

V

vect_spline_diffeo() (in module demeter.utils.torchbox)

vectField_show() (in module demeter.utils.torchbox) VolNormalizedGaussianRKHS (class in demeter.utils.reproducing_kernels)

W

Weighted_joinedMask_Metamorphosis_integrator (class in demeter.metamorphosis.joined)

Weighted_joinedMask_Metamorphosis_Shooting (class in demeter.metamorphosis.joined)