demeter package

Subpackages

Demeter is made of two main subpackages: metamorphosis and utils. demeter.metamorphosis contains the main classes and functions to perform the optimization. demeter.utils contains utility functions and classes that are used in the optimization process.

• demeter.metamorphosis package
  • Submodules
  • demeter.metamorphosis.abstract module
    • Geodesic_integrator
      • Geodesic_integrator.forward()
      • Geodesic_integrator.get_deformation()
      • Geodesic_integrator.get_deformator()
      • Geodesic_integrator.plot()
      • Geodesic_integrator.plot_deform()
      • Geodesic_integrator.step()
      • Geodesic_integrator.to_device()
    • Optimize_geodesicShooting
      • Optimize_geodesicShooting.compute_DICE()
      • Optimize_geodesicShooting.compute_landmark_dist()
      • Optimize_geodesicShooting.cost()
      • Optimize_geodesicShooting.forward()
      • Optimize_geodesicShooting.forward_safe_mode()
      • Optimize_geodesicShooting.get_DICE()
      • Optimize_geodesicShooting.get_all_arguments()
      • Optimize_geodesicShooting.get_geodesic_distance()
      • Optimize_geodesicShooting.get_landmark_dist()
      • Optimize_geodesicShooting.get_ssd_def()
      • Optimize_geodesicShooting.get_total_cost()
      • Optimize_geodesicShooting.plot()
      • Optimize_geodesicShooting.plot_cost()
      • Optimize_geodesicShooting.plot_deform()
      • Optimize_geodesicShooting.plot_imgCmp()
      • Optimize_geodesicShooting.save()
      • Optimize_geodesicShooting.save_to_gif()
      • Optimize_geodesicShooting.to_device()
  • demeter.metamorphosis.classic module
    • Metamorphosis_Shooting
      • Metamorphosis_Shooting.cost()
      • Metamorphosis_Shooting.get_all_arguments()
    • Metamorphosis_integrator
      • Metamorphosis_integrator.step()
  • demeter.metamorphosis.constrained module
    • ConstrainedMetamorphosis_Shooting
      • ConstrainedMetamorphosis_Shooting.cost()
      • ConstrainedMetamorphosis_Shooting.forward()
      • ConstrainedMetamorphosis_Shooting.get_all_arguments()
      • ConstrainedMetamorphosis_Shooting.get_total_cost()
      • ConstrainedMetamorphosis_Shooting.plot_cost()
      • ConstrainedMetamorphosis_Shooting.to_device()
    • ConstrainedMetamorphosis_integrator
      • ConstrainedMetamorphosis_integrator.compute_field_sim()
      • ConstrainedMetamorphosis_integrator.plot_field_sim()
      • ConstrainedMetamorphosis_integrator.step()
      • ConstrainedMetamorphosis_integrator.step_deprecated()
      • ConstrainedMetamorphosis_integrator.to_device()
    • Reduce_field_Optim
      • Reduce_field_Optim.cost()
      • Reduce_field_Optim.forward()
      • Reduce_field_Optim.get_total_cost()
      • Reduce_field_Optim.plot_cost()
      • Reduce_field_Optim.to_device()
  • demeter.metamorphosis.data_cost module
    • Cfm
    • DataCost
      • DataCost.__init__()
      • DataCost.__repr__()
      • DataCost.set_optimizer()
      • DataCost.to_device()
      • DataCost.__call__()
      • DataCost.set_optimizer()
      • DataCost.to_device()
    • Longitudinal_DataCost
      • Longitudinal_DataCost.set_optimizer()
      • Longitudinal_DataCost.to_device()
    • Mutlimodal_ssd_cfm
      • Mutlimodal_ssd_cfm.set_optimizer()
      • Mutlimodal_ssd_cfm.to_device()
    • Mutual_Information
      • Mutual_Information.to_device()
    • SimiliSegs
      • SimiliSegs.set_optimizer()
      • SimiliSegs.to_device()
    • Ssd
      • Ssd.to_device()
    • Ssd_normalized
      • Ssd_normalized.to_device()
  • demeter.metamorphosis.joined module
    • Weighted_joinedMask_Metamorphosis_Shooting
      • Weighted_joinedMask_Metamorphosis_Shooting.cost()
      • Weighted_joinedMask_Metamorphosis_Shooting.get_all_arguments()
      • Weighted_joinedMask_Metamorphosis_Shooting.get_ssd_def()
      • Weighted_joinedMask_Metamorphosis_Shooting.plot_cost()
      • Weighted_joinedMask_Metamorphosis_Shooting.plot_imgCmp()
    • Weighted_joinedMask_Metamorphosis_integrator
      • Weighted_joinedMask_Metamorphosis_integrator.forward()
      • Weighted_joinedMask_Metamorphosis_integrator.plot()
      • Weighted_joinedMask_Metamorphosis_integrator.step()
      • Weighted_joinedMask_Metamorphosis_integrator.step_sharp()
      • Weighted_joinedMask_Metamorphosis_integrator.to_device()
  • demeter.metamorphosis.load module
    • load_optimize_geodesicShooting()
  • demeter.metamorphosis.simplex module
    • Simplex_sqrt_Metamorphosis_integrator
      • Simplex_sqrt_Metamorphosis_integrator.forward()
      • Simplex_sqrt_Metamorphosis_integrator.step()
    • Simplex_sqrt_Shooting
      • Simplex_sqrt_Shooting.cost()
      • Simplex_sqrt_Shooting.get_all_arguments()
  • demeter.metamorphosis.wraps module
    • joined_metamorphosis()
    • simplex_metamorphosis()
  • Module contents
• demeter.utils package
  • Submodules
  • demeter.utils.bspline module
    • bspline_basis()
    • field2D_bspline()
    • field3D_bspline()
    • getCMS_allcombinaision()
    • getCMS_turn()
    • memo()
    • surf_bspline()
    • surf_bspline_3D()
  • demeter.utils.cost_functions module
    • Combine_ssd_CFM
    • Mutual_Information
      • Mutual_Information.forward()
      • Mutual_Information.independence_plot()
    • SoftHistogram1D
      • SoftHistogram1D.forward()
    • SoftHistogram2D
      • SoftHistogram2D.forward()
    • SumSquaredDifference
      • SumSquaredDifference.function()
      • SumSquaredDifference.imgShow()
  • demeter.utils.decorators module
    • deprecated()
    • time_it()
  • demeter.utils.fft_conv module
    • complex_matmul()
    • fft_conv()
    • to_ntuple()
  • demeter.utils.fill_saves_overview module
    • append_to_csv_new()
    • rec()
    • update_csv()
  • demeter.utils.image_3d_visualisation module
  • demeter.utils.optim module
    • GradientDescent
      • GradientDescent.backtracking_search()
      • GradientDescent.step()
  • demeter.utils.reproducing_kernels module
    • GaussianRKHS
      • GaussianRKHS.forward()
      • GaussianRKHS.get_all_arguments()
      • GaussianRKHS.init_kernel()
      • GaussianRKHS.plot()
    • Multi_scale_GaussianRKHS
      • Multi_scale_GaussianRKHS.get_all_arguments()
      • Multi_scale_GaussianRKHS.init_kernel()
      • Multi_scale_GaussianRKHS.plot()
    • Multi_scale_GaussianRKHS_notAverage
    • VolNormalizedGaussianRKHS
      • VolNormalizedGaussianRKHS.forward()
      • VolNormalizedGaussianRKHS.get_all_arguments()
      • VolNormalizedGaussianRKHS.init_kernel()
      • VolNormalizedGaussianRKHS.plot()
    • dx_convention_handler()
    • fft_filter()
    • get_gaussian_kernel1d()
    • get_gaussian_kernel2d()
    • get_gaussian_kernel3d()
    • get_sigma_from_img_ratio()
    • plot_gaussian_kernel_1d()
    • plot_gaussian_kernel_2d()
    • plot_gaussian_kernel_3d()
    • plot_kernel_on_image()
  • demeter.utils.toolbox module
    • TestCuda()
    • annotate_heatmap()
    • fig_to_image()
    • format_time()
    • full_ellipse()
    • get_freer_gpu()
    • get_size()
    • heatmap()
    • imCmp()
    • rgb2gray()
    • save_gif_with_plt()
    • update_progress()
  • demeter.utils.torchbox module
    • BCH()
    • Field_divergence
      • Field_divergence.forward()
    • RandomGaussianField
      • RandomGaussianField.divergence()
      • RandomGaussianField.field()
    • RandomGaussianImage
      • RandomGaussianImage.derivative()
      • RandomGaussianImage.gaussian()
      • RandomGaussianImage.image()
    • addGrid2im()
    • checkDiffeo()
    • compose_fields()
    • deformation_show()
    • detOfJacobian()
    • field2diffeo()
    • fieldNorm2()
    • field_2d_hessian()
    • field_2d_jacobian()
    • field_divergence()
    • find_binary_center()
    • format_sigmas()
    • geodesic_3d_slider()
    • get_sobel_kernel_2d()
    • get_sobel_kernel_3d()
    • grid2im()
    • gridDef_plot()
    • gridDef_plot_2d()
    • im2grid()
    • imCmp()
    • image_slice()
    • imgDeform()
    • is_tensor()
    • leviCivita_2Dderivative()
    • lieBracket()
    • make_3d_flat()
    • make_ball_at_shape_center()
    • make_regular_grid()
    • pad_to_same_size()
    • pixel_to_2square_convention()
    • pixel_to_square_convention()
    • quiver_plot()
    • reg_open()
    • resize_image()
    • spatialGradient()
    • spatialGradient_2d()
    • spatialGradient_3d()
    • square2_to_pixel_convention()
    • square2_to_square_convention()
    • square_to_2square_convention()
    • square_to_pixel_convention()
    • temporal_img_cmp()
    • thresholding()
    • vectField_show()
    • vect_spline_diffeo()
  • demeter.utils.vector_field_to_flow module
    • FieldIntegrator
  • Module contents

Submodules

demeter.constants module

demeter.constants.display_env_help()

demeter.constants.find_cuda(foo=True)

demeter.constants.get_freer_gpu()

demeter.constants.set_ticks_off(ax)

Module contents