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<main> |
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<article id="content"> |
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<header> |
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<h1 class="title">Module <code>pymskt.mesh.meshRegistration</code></h1> |
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</header> |
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<section id="section-intro"> |
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<details class="source"> |
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<summary> |
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<span>Expand source code</span> |
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</summary> |
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<pre><code class="python">import sys |
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import vtk |
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try: |
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import pyfocusr |
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except ModuleNotFoundError: |
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print('pyfocusr not found') |
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print('If you are not using the registration tools, you can ignore this message.') |
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print('install pyfocusr as described in the README: https://github.com/gattia/pymskt') |
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print('or visit the pyfocusr github repo: https://github.com/gattia/pyfocusr') |
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import numpy as np |
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def get_icp_transform(source, target, max_n_iter=1000, n_landmarks=1000, reg_mode='similarity'): |
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""" |
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Get the Interative Closest Point (ICP) transformation from the `source` mesh to the |
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`target` mesh. |
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Parameters |
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---------- |
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source : vtk.vtkPolyData |
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Source mesh that we want to transform onto the target mesh. |
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target : vtk.vtkPolyData |
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Target mesh that we want to transform the source mesh onto. |
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max_n_iter : int, optional |
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Max number of iterations for the registration algorithm to perform, by default 1000 |
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n_landmarks : int, optional |
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How many landmarks to sample when determining distance between meshes & |
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solving for the optimal transformation, by default 1000 |
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reg_mode : str, optional |
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The type of registration to perform. The options are: |
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- 'rigid': true rigid, translation only |
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- 'similarity': rigid + equal scale |
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by default 'similarity' |
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Returns |
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------- |
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vtk.vtkIterativeClosestPointTransform |
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The actual transform object after running the registration. |
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""" |
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icp = vtk.vtkIterativeClosestPointTransform() |
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icp.SetSource(source) |
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icp.SetTarget(target) |
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if reg_mode == 'rigid': |
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icp.GetLandmarkTransform().SetModeToRigidBody() |
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elif reg_mode == 'similarity': |
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icp.GetLandmarkTransform().SetModeToSimilarity() |
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icp.SetMaximumNumberOfIterations(max_n_iter) |
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icp.StartByMatchingCentroidsOn() |
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icp.Modified() |
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icp.Update() |
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icp.SetMaximumNumberOfLandmarks(n_landmarks) |
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return icp |
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def non_rigidly_register( |
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target_mesh=None, |
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source_mesh=None, |
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final_pt_location='weighted_average', # 'weighted_average' or 'nearest_neighbour' |
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icp_register_first=True, # Get bones/objects into roughly the same alignment first |
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icp_registration_mode='similarity', # similarity = rigid + scaling (isotropic), ("rigid", "similarity", "affine") |
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icp_reg_target_to_source=True, # For shape models, the source is usually the reference so we want target in its space (true) |
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n_spectral_features=3, |
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n_extra_spectral=3, # For ensuring we have the right spec coords - determined using wasserstein distances. |
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target_eigenmap_as_reference=True, |
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get_weighted_spectral_coords=False, |
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list_features_to_calc=['curvature'], # 'curvature', min_curvature' 'max_curvature' (other features for registration) |
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use_features_as_coords=True, # During registraiton - do we want to use curvature etc. |
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rigid_reg_max_iterations=100, |
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non_rigid_alpha=0.01, |
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non_rigid_beta=50, |
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non_rigid_n_eigens=100, # number of eigens for low rank CPD registration |
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non_rigid_max_iterations=500, |
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rigid_before_non_rigid_reg=False, # This is of the spectral coordinates - not the x/y/z used in icp_register_first |
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projection_smooth_iterations=30, # Used for distributing registered points onto target surface - helps preserve diffeomorphism |
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graph_smoothing_iterations=300, # For smoothing the target mesh before final point correspondence |
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feature_smoothing_iterations=30, # how much should features (curvature) be smoothed before registration |
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include_points_as_features=False, # Do we want to incldue x/y/z positions in registration? |
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norm_physical_and_spectral=True, # set standardized mean and variance for each feature |
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feature_weights=np.diag([.1,.1]), # should we weight the extra features (curvature) more/less than spectral |
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n_coords_spectral_ordering=20000, # How many points on mesh to use for ordering spectral coordinates () |
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n_coords_spectral_registration=1000, # How many points to use for spectral registrtaion (usually random subsample) |
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initial_correspondence_type='kd', # kd = nearest neightbor, hungarian = minimum cost of assigning between graphs (more compute heavy) |
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final_correspondence_type='kd' # kd = nearest neightbor, hungarian = minimum cost of assigning between graphs (more compute heavy) |
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): |
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if 'pyfocusr' not in sys.modules: |
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raise ModuleNotFoundError('pyfocusr is not installed & is necessary for non-rigid registration.') |
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if final_pt_location not in ['weighted_average', 'nearest_neighbour']: |
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raise Exception('Did not specify appropriate final_pt_location, must be either "weighted_average", or "nearest_neighbour"') |
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# Test if mesh is a vtk mesh, or a pymsky.Mesh object. |
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if isinstance(target_mesh, vtk.vtkPolyData): |
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vtk_mesh_target = target_mesh |
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else: |
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try: |
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vtk_mesh_target = target_mesh.mesh |
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except: |
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raise Exception(f'expected type vtk.vtkPolyData or pymskt.mesh.Mesh, got: {type(target_mesh)}') |
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if isinstance(source_mesh, vtk.vtkPolyData): |
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vtk_mesh_source = source_mesh |
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else: |
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try: |
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vtk_mesh_source = source_mesh.mesh |
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except: |
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raise Exception(f'expected type vtk.vtkPolyData or pymskt.mesh.Mesh, got: {type(target_mesh)}') |
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reg = pyfocusr.Focusr( |
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vtk_mesh_target=vtk_mesh_target, |
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vtk_mesh_source=vtk_mesh_source, |
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icp_register_first=icp_register_first, |
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icp_registration_mode=icp_registration_mode, |
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icp_reg_target_to_source=icp_reg_target_to_source, |
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n_spectral_features=n_spectral_features, |
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n_extra_spectral=n_extra_spectral, |
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target_eigenmap_as_reference=target_eigenmap_as_reference, |
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get_weighted_spectral_coords=get_weighted_spectral_coords, |
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list_features_to_calc=list_features_to_calc, |
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use_features_as_coords=use_features_as_coords, |
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rigid_reg_max_iterations=rigid_reg_max_iterations, |
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non_rigid_alpha=non_rigid_alpha, |
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non_rigid_beta=non_rigid_beta, |
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non_rigid_n_eigens=non_rigid_n_eigens, |
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non_rigid_max_iterations=non_rigid_max_iterations, |
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rigid_before_non_rigid_reg=rigid_before_non_rigid_reg, |
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projection_smooth_iterations=projection_smooth_iterations, |
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graph_smoothing_iterations=graph_smoothing_iterations, |
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feature_smoothing_iterations=feature_smoothing_iterations, |
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include_points_as_features=include_points_as_features, |
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norm_physical_and_spectral=norm_physical_and_spectral, |
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feature_weights=feature_weights, |
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n_coords_spectral_ordering=n_coords_spectral_ordering, |
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n_coords_spectral_registration=n_coords_spectral_registration, |
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initial_correspondence_type=initial_correspondence_type, |
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final_correspondence_type=final_correspondence_type |
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) |
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reg.align_maps() |
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if final_pt_location == 'weighted_average': |
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reg.get_source_mesh_transformed_weighted_avg() |
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mesh_transformed_to_target = reg.weighted_avg_transformed_mesh |
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elif final_pt_location == 'nearest_neighbour': |
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reg.get_source_mesh_transformed_nearest_neighbour() |
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mesh_transformed_to_target = reg.nearest_neighbour_transformed_mesh |
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return mesh_transformed_to_target </code></pre> |
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</details> |
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</section> |
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<section> |
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</section> |
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<section> |
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</section> |
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<section> |
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<h2 class="section-title" id="header-functions">Functions</h2> |
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<dl> |
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<dt id="pymskt.mesh.meshRegistration.get_icp_transform"><code class="name flex"> |
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<span>def <span class="ident">get_icp_transform</span></span>(<span>source, target, max_n_iter=1000, n_landmarks=1000, reg_mode='similarity')</span> |
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</code></dt> |
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<dd> |
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<div class="desc"><p>Get the Interative Closest Point (ICP) transformation from the <code>source</code> mesh to the |
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<code>target</code> mesh. </p> |
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<h2 id="parameters">Parameters</h2> |
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<dl> |
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<dt><strong><code>source</code></strong> : <code>vtk.vtkPolyData</code></dt> |
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<dd>Source mesh that we want to transform onto the target mesh.</dd> |
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<dt><strong><code>target</code></strong> : <code>vtk.vtkPolyData</code></dt> |
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<dd>Target mesh that we want to transform the source mesh onto.</dd> |
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<dt><strong><code>max_n_iter</code></strong> : <code>int</code>, optional</dt> |
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<dd>Max number of iterations for the registration algorithm to perform, by default 1000</dd> |
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<dt><strong><code>n_landmarks</code></strong> : <code>int</code>, optional</dt> |
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<dd>How many landmarks to sample when determining distance between meshes & |
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solving for the optimal transformation, by default 1000</dd> |
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<dt><strong><code>reg_mode</code></strong> : <code>str</code>, optional</dt> |
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<dd>The type of registration to perform. The options are: |
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- 'rigid': true rigid, translation only |
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- 'similarity': rigid + equal scale |
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by default 'similarity'</dd> |
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</dl> |
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<h2 id="returns">Returns</h2> |
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<dl> |
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<dt><code>vtk.vtkIterativeClosestPointTransform</code></dt> |
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<dd>The actual transform object after running the registration.</dd> |
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</dl></div> |
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<details class="source"> |
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<summary> |
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<span>Expand source code</span> |
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</summary> |
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<pre><code class="python">def get_icp_transform(source, target, max_n_iter=1000, n_landmarks=1000, reg_mode='similarity'): |
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""" |
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Get the Interative Closest Point (ICP) transformation from the `source` mesh to the |
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`target` mesh. |
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Parameters |
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---------- |
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source : vtk.vtkPolyData |
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Source mesh that we want to transform onto the target mesh. |
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target : vtk.vtkPolyData |
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Target mesh that we want to transform the source mesh onto. |
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max_n_iter : int, optional |
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Max number of iterations for the registration algorithm to perform, by default 1000 |
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n_landmarks : int, optional |
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How many landmarks to sample when determining distance between meshes & |
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solving for the optimal transformation, by default 1000 |
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reg_mode : str, optional |
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The type of registration to perform. The options are: |
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- 'rigid': true rigid, translation only |
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- 'similarity': rigid + equal scale |
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by default 'similarity' |
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Returns |
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------- |
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vtk.vtkIterativeClosestPointTransform |
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The actual transform object after running the registration. |
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""" |
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icp = vtk.vtkIterativeClosestPointTransform() |
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icp.SetSource(source) |
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icp.SetTarget(target) |
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if reg_mode == 'rigid': |
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icp.GetLandmarkTransform().SetModeToRigidBody() |
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elif reg_mode == 'similarity': |
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icp.GetLandmarkTransform().SetModeToSimilarity() |
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icp.SetMaximumNumberOfIterations(max_n_iter) |
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icp.StartByMatchingCentroidsOn() |
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icp.Modified() |
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icp.Update() |
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icp.SetMaximumNumberOfLandmarks(n_landmarks) |
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return icp</code></pre> |
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</details> |
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</dd> |
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<dt id="pymskt.mesh.meshRegistration.non_rigidly_register"><code class="name flex"> |
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<span>def <span class="ident">non_rigidly_register</span></span>(<span>target_mesh=None, source_mesh=None, final_pt_location='weighted_average', icp_register_first=True, icp_registration_mode='similarity', icp_reg_target_to_source=True, n_spectral_features=3, n_extra_spectral=3, target_eigenmap_as_reference=True, get_weighted_spectral_coords=False, list_features_to_calc=['curvature'], use_features_as_coords=True, rigid_reg_max_iterations=100, non_rigid_alpha=0.01, non_rigid_beta=50, non_rigid_n_eigens=100, non_rigid_max_iterations=500, rigid_before_non_rigid_reg=False, projection_smooth_iterations=30, graph_smoothing_iterations=300, feature_smoothing_iterations=30, include_points_as_features=False, norm_physical_and_spectral=True, feature_weights=array([[0.1, 0. ], |
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[0. , 0.1]]), n_coords_spectral_ordering=20000, n_coords_spectral_registration=1000, initial_correspondence_type='kd', final_correspondence_type='kd')</span> |
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</code></dt> |
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<dd> |
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<div class="desc"></div> |
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<details class="source"> |
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<summary> |
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<span>Expand source code</span> |
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</summary> |
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<pre><code class="python">def non_rigidly_register( |
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target_mesh=None, |
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source_mesh=None, |
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final_pt_location='weighted_average', # 'weighted_average' or 'nearest_neighbour' |
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icp_register_first=True, # Get bones/objects into roughly the same alignment first |
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icp_registration_mode='similarity', # similarity = rigid + scaling (isotropic), ("rigid", "similarity", "affine") |
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icp_reg_target_to_source=True, # For shape models, the source is usually the reference so we want target in its space (true) |
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n_spectral_features=3, |
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n_extra_spectral=3, # For ensuring we have the right spec coords - determined using wasserstein distances. |
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target_eigenmap_as_reference=True, |
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get_weighted_spectral_coords=False, |
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list_features_to_calc=['curvature'], # 'curvature', min_curvature' 'max_curvature' (other features for registration) |
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use_features_as_coords=True, # During registraiton - do we want to use curvature etc. |
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rigid_reg_max_iterations=100, |
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non_rigid_alpha=0.01, |
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non_rigid_beta=50, |
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non_rigid_n_eigens=100, # number of eigens for low rank CPD registration |
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non_rigid_max_iterations=500, |
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rigid_before_non_rigid_reg=False, # This is of the spectral coordinates - not the x/y/z used in icp_register_first |
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projection_smooth_iterations=30, # Used for distributing registered points onto target surface - helps preserve diffeomorphism |
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graph_smoothing_iterations=300, # For smoothing the target mesh before final point correspondence |
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feature_smoothing_iterations=30, # how much should features (curvature) be smoothed before registration |
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include_points_as_features=False, # Do we want to incldue x/y/z positions in registration? |
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norm_physical_and_spectral=True, # set standardized mean and variance for each feature |
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feature_weights=np.diag([.1,.1]), # should we weight the extra features (curvature) more/less than spectral |
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n_coords_spectral_ordering=20000, # How many points on mesh to use for ordering spectral coordinates () |
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n_coords_spectral_registration=1000, # How many points to use for spectral registrtaion (usually random subsample) |
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initial_correspondence_type='kd', # kd = nearest neightbor, hungarian = minimum cost of assigning between graphs (more compute heavy) |
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final_correspondence_type='kd' # kd = nearest neightbor, hungarian = minimum cost of assigning between graphs (more compute heavy) |
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): |
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300 |
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if 'pyfocusr' not in sys.modules: |
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raise ModuleNotFoundError('pyfocusr is not installed & is necessary for non-rigid registration.') |
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if final_pt_location not in ['weighted_average', 'nearest_neighbour']: |
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raise Exception('Did not specify appropriate final_pt_location, must be either "weighted_average", or "nearest_neighbour"') |
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# Test if mesh is a vtk mesh, or a pymsky.Mesh object. |
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if isinstance(target_mesh, vtk.vtkPolyData): |
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vtk_mesh_target = target_mesh |
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else: |
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try: |
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vtk_mesh_target = target_mesh.mesh |
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except: |
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raise Exception(f'expected type vtk.vtkPolyData or pymskt.mesh.Mesh, got: {type(target_mesh)}') |
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315 |
|
|
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if isinstance(source_mesh, vtk.vtkPolyData): |
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vtk_mesh_source = source_mesh |
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else: |
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319 |
try: |
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|
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vtk_mesh_source = source_mesh.mesh |
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except: |
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raise Exception(f'expected type vtk.vtkPolyData or pymskt.mesh.Mesh, got: {type(target_mesh)}') |
|
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323 |
|
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|
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reg = pyfocusr.Focusr( |
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|
325 |
vtk_mesh_target=vtk_mesh_target, |
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vtk_mesh_source=vtk_mesh_source, |
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|
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icp_register_first=icp_register_first, |
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|
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icp_registration_mode=icp_registration_mode, |
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icp_reg_target_to_source=icp_reg_target_to_source, |
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n_spectral_features=n_spectral_features, |
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n_extra_spectral=n_extra_spectral, |
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target_eigenmap_as_reference=target_eigenmap_as_reference, |
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get_weighted_spectral_coords=get_weighted_spectral_coords, |
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|
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list_features_to_calc=list_features_to_calc, |
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|
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use_features_as_coords=use_features_as_coords, |
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336 |
rigid_reg_max_iterations=rigid_reg_max_iterations, |
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|
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non_rigid_alpha=non_rigid_alpha, |
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|
338 |
non_rigid_beta=non_rigid_beta, |
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|
339 |
non_rigid_n_eigens=non_rigid_n_eigens, |
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non_rigid_max_iterations=non_rigid_max_iterations, |
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341 |
rigid_before_non_rigid_reg=rigid_before_non_rigid_reg, |
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|
342 |
projection_smooth_iterations=projection_smooth_iterations, |
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343 |
graph_smoothing_iterations=graph_smoothing_iterations, |
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344 |
feature_smoothing_iterations=feature_smoothing_iterations, |
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345 |
include_points_as_features=include_points_as_features, |
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346 |
norm_physical_and_spectral=norm_physical_and_spectral, |
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347 |
feature_weights=feature_weights, |
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348 |
n_coords_spectral_ordering=n_coords_spectral_ordering, |
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349 |
n_coords_spectral_registration=n_coords_spectral_registration, |
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|
350 |
initial_correspondence_type=initial_correspondence_type, |
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|
351 |
final_correspondence_type=final_correspondence_type |
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352 |
) |
|
|
353 |
reg.align_maps() |
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|
354 |
|
|
|
355 |
if final_pt_location == 'weighted_average': |
|
|
356 |
reg.get_source_mesh_transformed_weighted_avg() |
|
|
357 |
mesh_transformed_to_target = reg.weighted_avg_transformed_mesh |
|
|
358 |
elif final_pt_location == 'nearest_neighbour': |
|
|
359 |
reg.get_source_mesh_transformed_nearest_neighbour() |
|
|
360 |
mesh_transformed_to_target = reg.nearest_neighbour_transformed_mesh |
|
|
361 |
|
|
|
362 |
return mesh_transformed_to_target </code></pre> |
|
|
363 |
</details> |
|
|
364 |
</dd> |
|
|
365 |
</dl> |
|
|
366 |
</section> |
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|
367 |
<section> |
|
|
368 |
</section> |
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|
369 |
</article> |
|
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370 |
<nav id="sidebar"> |
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|
371 |
<h1>Index</h1> |
|
|
372 |
<div class="toc"> |
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373 |
<ul></ul> |
|
|
374 |
</div> |
|
|
375 |
<ul id="index"> |
|
|
376 |
<li><h3>Super-module</h3> |
|
|
377 |
<ul> |
|
|
378 |
<li><code><a title="pymskt.mesh" href="index.html">pymskt.mesh</a></code></li> |
|
|
379 |
</ul> |
|
|
380 |
</li> |
|
|
381 |
<li><h3><a href="#header-functions">Functions</a></h3> |
|
|
382 |
<ul class=""> |
|
|
383 |
<li><code><a title="pymskt.mesh.meshRegistration.get_icp_transform" href="#pymskt.mesh.meshRegistration.get_icp_transform">get_icp_transform</a></code></li> |
|
|
384 |
<li><code><a title="pymskt.mesh.meshRegistration.non_rigidly_register" href="#pymskt.mesh.meshRegistration.non_rigidly_register">non_rigidly_register</a></code></li> |
|
|
385 |
</ul> |
|
|
386 |
</li> |
|
|
387 |
</ul> |
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388 |
</nav> |
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</main> |
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<footer id="footer"> |
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