def compute_geom(self, diffusion_time, n_neighbors): data = self.data dim = self.dim #set radius according to paper (i think this is dim not d) radius = (diffusion_time * (diffusion_time * np.pi * 4)**(dim/2))**(0.5) #set adjacency radius large enough that points beyond it have affinity close to zero bigradius = 3 * radius adjacency_method = 'cyflann' cyflann_kwds = {'index_type':'kdtrees', 'num_trees':10, 'num_checks':n_neighbors} adjacency_kwds = {'radius':bigradius, 'cyflann_kwds':cyflann_kwds} affinity_method = 'gaussian' affinity_kwds = {'radius':radius} laplacian_method = 'geometric' laplacian_kwds = {'scaling_epps':radius} geom = Geometry(adjacency_method=adjacency_method, adjacency_kwds=adjacency_kwds, affinity_method=affinity_method, affinity_kwds=affinity_kwds, laplacian_method=laplacian_method, laplacian_kwds=laplacian_kwds) geom.set_data_matrix(data) adjacency_matrix = geom.compute_adjacency_matrix() laplacian_matrix = geom.compute_laplacian_matrix() return(geom)
adjacency_method = 'cyflann' adjacency_kwds = {'radius': radius} affinity_method = 'gaussian' affinity_kwds = {'radius': radius} laplacian_method = 'symmetricnormalized' laplacian_kwds = {'scaling_epps': radius} dataname = workingdirectory + '/untracked_data/chemistry_data/tolueneangles020619_pca50' #dataname = '/Users/samsonkoelle/Downloads/manigrad-100818/mani-samk-gradients/untracked_data/chemistry_data/ethanolangles022119_pca50' data = np.load(dataname + '.npy') geom = Geometry(adjacency_method=adjacency_method, adjacency_kwds=adjacency_kwds, affinity_method=affinity_method, affinity_kwds=affinity_kwds, laplacian_method=laplacian_method, laplacian_kwds=laplacian_kwds) geom.set_data_matrix(data) geom.laplacian_method = 'geometric' geom.laplacian_kwds = {'scaling_epps': radius} laplacian_matrix = geom.compute_laplacian_matrix() geom.compute_laplacian_matrix() sample = np.arange(0, data.shape[0], 1000) distorion_vs_rad_dim2 = run_estimate_radius(data, geom.adjacency_matrix, sample=sample, d=1, rmin=1, rmax=10, ntry=50, run_parallel=True, search_space='logspace') np.save(dataname + '_distortionradius', distorion_vs_rad_dim2)
compute the Laplacian for best results you should use laplacian_method = 'geometric' and set the keyword parameter 'scaling_epps' to the 'radius' that was used in the affinity method. First import the class: ''' from megaman.geometry.rmetric import RiemannMetric ''' We can then estimate the R metric on each embedding with: ''' geom.laplacian_method = 'geometric' geom.laplacian_kwds = {'scaling_epps':radius} # scaling ensures convergence to Laplace-Beltrami operator laplacian_matrix = geom.compute_laplacian_matrix() rmetric_spectral = RiemannMetric(embed_spectral, geom.laplacian_matrix) H_spectral = rmetric_spectral.get_dual_rmetric() rmetric_ltsa = RiemannMetric(embed_ltsa, geom.laplacian_matrix) H_ltsa = rmetric_ltsa.get_dual_rmetric() rmetric_lle = RiemannMetric(embed_lle, geom.laplacian_matrix) H_lle = rmetric_lle.get_dual_rmetric() rmetric_isomap = RiemannMetric(embed_isomap, geom.laplacian_matrix) H_isomap = rmetric_isomap.get_dual_rmetric() '''