reeb_aux Namespace Reference

Functions
	thread_safe_numba_call (func, *args, **kwargs)
	safe_dist_from_pts_periodic_boundaries_numba (A_, B_, M, m, axes, dim=3)
	safe_point_cloud_frechet_mean_numba (D, M, m, subsample=10, tol=0.001, maxiter=50)
	safe_flow_to_fmean_dist (flow, backbone, M, m)
	circular_max_flow (reeb)
	sphere_sample (n=100, seed=0)
	sample_matrix_grid (n=100, seed=0)
	canonical_matrix_grid ()
	gramschmidt (A)
	make_cubic_to_res (cubic_grid, res_grid, nx, ny, nz)
	make_graph (grid, res_grid, nx, ny, nz, dim, M, m)
	make_graph_fast (grid, res_idxs, res_to_grid, grid_to_res, grid_to_cubic, cubic_to_grid, nx, ny, nz, dim, M, m)
	match_grids (new_grid, old_grid)
	match_graphs (old_to_new, old_graph)
	dist_from_pts_periodic_boundaries_pool (LIST)
	numba_dist (a, b)
	dist_from_pts_periodic_boundaries_numba (A_, B_, M, m, axes, dim=3)
	numba_dist_print (a, b)
	dist_from_pts_periodic_boundaries_numba_print (A_, B_, M, m, axes, dim=3)
	point_cloud_frechet_mean_numba (D, M, m, subsample=10, tol=0.001, maxiter=50)
	procustes_mean (p, D, M, m, tol=0.001, maxiter=50)
	frechet_mean_numba (D, initial_points, M, m, tol=0.001, maxiter=50)
	point_cloud_frechet_mean (D, M, m, subsample=10, tol=0.0001, maxiter=50)
	frechet_mean (D, initial_points, M, m, tol=0.0001, maxiter=50)
	estimate_radius (inputfile, backbone_atoms, flow_atoms, n_tmp_grid)
	Li_to_backbone_dist (Li, P, S, M, m)
	flow_to_fmean_dist (flow, backbone, M, m)
	preprocess_ions (fmean, backbone_t, ions, M, m)
	preprocess_PATHS (fmean, BACKBONE, PATHS, M, m)
	make_neigh (grid, p_graph, i_graph, f)
	make_neigh_ (grid, p_graph, i_graph, f)
	connect_lvl_sets_aux (i, n_c, C, grid, lvl_to_grid, REEB_GRAPH, norm, count)

Variables
	_numba_lock = threading.Lock()

Function Documentation

canonical_matrix_grid()

reeb_aux.canonical_matrix_grid

(

)

circular_max_flow()

reeb_aux.circular_max_flow

(

reeb

)

connect_lvl_sets_aux()

reeb_aux.connect_lvl_sets_aux	(		i,
			n_c,
			C,
			grid,
			lvl_to_grid,
			REEB_GRAPH,
			norm,
			count )

dist_from_pts_periodic_boundaries_numba()

reeb_aux.dist_from_pts_periodic_boundaries_numba	(		A_,
			B_,
			M,
			m,
			axes,
			dim = 3 )

A,B -> array of pts (npts,dim), calcolo distanza d(a,b) per ogni a in A e b in B
M -> array with upper bounds of the box (dim,)
m -> array with lower bound of the box (dim,)
axes -> array with the axes in which the boundary condition is applied
dim -> dimension of the dataset

dist_from_pts_periodic_boundaries_numba_print()

reeb_aux.dist_from_pts_periodic_boundaries_numba_print	(		A_,
			B_,
			M,
			m,
			axes,
			dim = 3 )

A,B -> array of pts (npts,dim), calcolo distanza d(a,b) per ogni a in A e b in B
M -> array with upper bounds of the box (dim,)
m -> array with lower bound of the box (dim,)
axes -> array with the axes in which the boundary condition is applied
dim -> dimension of the dataset

dist_from_pts_periodic_boundaries_pool()

reeb_aux.dist_from_pts_periodic_boundaries_pool

(

LIST

)

estimate_radius()

reeb_aux.estimate_radius	(		inputfile,
			backbone_atoms,
			flow_atoms,
			n_tmp_grid )

flow_to_fmean_dist()

reeb_aux.flow_to_fmean_dist	(		flow,
			backbone,
			M,
			m )

frechet_mean()

reeb_aux.frechet_mean	(		D,
			initial_points,
			M,
			m,
			tol = 0.0001,
			maxiter = 50 )

frechet_mean_numba()

reeb_aux.frechet_mean_numba	(		D,
			initial_points,
			M,
			m,
			tol = 0.001,
			maxiter = 50 )

gramschmidt()

reeb_aux.gramschmidt

(

A

)

Applies the Gram-Schmidt method to A
and returns Q and R, so Q*R = A.

Li_to_backbone_dist()

reeb_aux.Li_to_backbone_dist	(		Li,
			P,
			S,
			M,
			m )

make_cubic_to_res()

reeb_aux.make_cubic_to_res	(		cubic_grid,
			res_grid,
			nx,
			ny,
			nz )

make_graph()

reeb_aux.make_graph	(		grid,
			res_grid,
			nx,
			ny,
			nz,
			dim,
			M,
			m )

make_graph_fast()

reeb_aux.make_graph_fast	(		grid,
			res_idxs,
			res_to_grid,
			grid_to_res,
			grid_to_cubic,
			cubic_to_grid,
			nx,
			ny,
			nz,
			dim,
			M,
			m )

make_neigh()

reeb_aux.make_neigh	(		grid,
			p_graph,
			i_graph,
			f )

make_neigh_()

reeb_aux.make_neigh_	(		grid,
			p_graph,
			i_graph,
			f )

match_graphs()

reeb_aux.match_graphs	(		old_to_new,
			old_graph )

match_grids()

reeb_aux.match_grids	(		new_grid,
			old_grid )

numba_dist()

reeb_aux.numba_dist	(		a,
			b )

A,B -> array of pts (npts,dim), calcolo distanza d(a_i,b_j) per ogni a_i in a e b_j in b

numba_dist_print()

reeb_aux.numba_dist_print	(		a,
			b )

A,B -> array of pts (npts,dim), calcolo distanza d(a_i,b_j) per ogni a_i in a e b_j in b

point_cloud_frechet_mean()

reeb_aux.point_cloud_frechet_mean	(		D,
			M,
			m,
			subsample = 10,
			tol = 0.0001,
			maxiter = 50 )

point_cloud_frechet_mean_numba()

reeb_aux.point_cloud_frechet_mean_numba	(		D,
			M,
			m,
			subsample = 10,
			tol = 0.001,
			maxiter = 50 )

preprocess_ions()

reeb_aux.preprocess_ions	(		fmean,
			backbone_t,
			ions,
			M,
			m )

preprocess_PATHS()

reeb_aux.preprocess_PATHS	(		fmean,
			BACKBONE,
			PATHS,
			M,
			m )

procustes_mean()

reeb_aux.procustes_mean	(		p,
			D,
			M,
			m,
			tol = 0.001,
			maxiter = 50 )

safe_dist_from_pts_periodic_boundaries_numba()

reeb_aux.safe_dist_from_pts_periodic_boundaries_numba	(		A_,
			B_,
			M,
			m,
			axes,
			dim = 3 )

Thread-safe wrapper for dist_from_pts_periodic_boundaries_numba

safe_flow_to_fmean_dist()

reeb_aux.safe_flow_to_fmean_dist	(		flow,
			backbone,
			M,
			m )

Thread-safe wrapper for flow_to_fmean_dist

safe_point_cloud_frechet_mean_numba()

reeb_aux.safe_point_cloud_frechet_mean_numba	(		D,
			M,
			m,
			subsample = 10,
			tol = 0.001,
			maxiter = 50 )

Thread-safe wrapper for point_cloud_frechet_mean_numba

sample_matrix_grid()

reeb_aux.sample_matrix_grid	(		n = 100,
			seed = 0 )

sphere_sample()

reeb_aux.sphere_sample	(		n = 100,
			seed = 0 )

thread_safe_numba_call()

reeb_aux.thread_safe_numba_call	(		func,
		*	args,
		**	kwargs )

Wrapper to ensure thread-safe execution of Numba functions

Variable Documentation

_numba_lock

reeb_aux._numba_lock = threading.Lock()

protected