diffusion_utils Namespace Reference

Functions
	row_reduce_matrix (A, GF)
	solve_linear_system_with_boundary (B, v, A, A_red, V, GF)
	solve_linear_system (B, v)
	cut_path_from_bottom (path, h, grid, axis=-1)
	cut_path_from_top (path, h, grid, axis=-1)
	get_cmap (n, name='hsv')
	get_box_from_cell (cell_file)
	out_to_atoms (inputfile, backbone_atoms, flow_atoms)
	DEPRECATED?
	clean_Li (Li, m, M)
	make_geodesics (grid, r, M, m, axes, dim, D_=None, D_force_graph_=None, verbose=False)
	find_geod (idx0, idx1, geodesics, pts, D, maxiter=np.inf)
	dist_periodic_boundaries (grid_, M, m, axes, dim=3)
	dist_from_pts_periodic_boundaries (pts_, grid_, M, m, axes, dim=3)
	append_tr (ITRIS, B, edge_idxs, ia, ib, ic)
	check_tr (p0, p1, p2, res_grid, grid, cubic_to_res, ITRIS, B, edge_idxs)
	r_squared (px, py, pz, balls_centres, balls_radii)
	aux_fn (px, py, pz, xc, yc, zc, r, eps, p=4)
	grad_r2 (pt, balls_centres, balls_radii, p=2, eps=1)
	sample_path (idx, N, res_grid, z_1, maxiter=100000)
	smooth_path (path, geod, res_grid, D)
	close_paths (p_0, p_1, grid, geod, D)
	homological_simplification_of_path_pts (idx0, idx1, path, grid, geod, V, rank, GF, D, N, edge_idxs, r_graph)
	homological_simplification_of_path (path, grid, geod, V, rank, GF, D, N, edge_idxs, r_graph)
	close_paths_A_0_A_1 (p_0, p_1, D, A_0, A_1, res_to_A_0, res_to_A_1, A_0_to_res, A_1_to_res, geod_A_0, geod_A_1)
	join_points_boundary_conditions (p_, q_, M, m, axes, dim, n=20)
	close_paths_boundary_conditions (p_0, p_1, res_grid, geod, M, m, D, axes, dim)
	close_deadlocks (p_0, p_1, res_grid, geod, res_to_A_0, A_0_to_res, geod_A_0, A_0)
	simplify_path (path_)
	path_to_vec (path, D, N_1, edge_idxs, r_graph, verbose=False)
	equivalence (A, v_path, rank)
	project_path (path_coords, grid)
	project_path_periodic (path_coords, grid, M, m, axes, dim=3, D_=None)
	project_timeseries_array (A, grid, M, m, axes, dim=3)
	cluster_deadlocks (PATHS, res_grid, geod, res_to_A_0, geod_A_0, A_0)
	save_paths (LIST, name, folder_path)
	compute_all (LIST)
	compute_penalties (LIST)
	compute_direction (LIST)
	compute_repulsion (LIST)
	find_geod_wrap (LIST)
	rank_mod_p (LIST)

Function Documentation

append_tr()

diffusion_utils.append_tr	(		ITRIS,
			B,
			edge_idxs,
			ia,
			ib,
			ic )

N.B. ia<ib<ic

aux_fn()

diffusion_utils.aux_fn	(		px,
			py,
			pz,
			xc,
			yc,
			zc,
			r,
			eps,
			p = 4 )

check_tr()

diffusion_utils.check_tr	(		p0,
			p1,
			p2,
			res_grid,
			grid,
			cubic_to_res,
			ITRIS,
			B,
			edge_idxs )

clean_Li()

diffusion_utils.clean_Li	(		Li,
			m,
			M )

Remove Lithium Atoms Outside the Box

close_deadlocks()

diffusion_utils.close_deadlocks	(		p_0,
			p_1,
			res_grid,
			geod,
			res_to_A_0,
			A_0_to_res,
			geod_A_0,
			A_0 )

close_paths()

diffusion_utils.close_paths	(		p_0,
			p_1,
			grid,
			geod,
			D )

close_paths_A_0_A_1()

diffusion_utils.close_paths_A_0_A_1	(		p_0,
			p_1,
			D,
			A_0,
			A_1,
			res_to_A_0,
			res_to_A_1,
			A_0_to_res,
			A_1_to_res,
			geod_A_0,
			geod_A_1 )

close_paths_boundary_conditions()

diffusion_utils.close_paths_boundary_conditions	(		p_0,
			p_1,
			res_grid,
			geod,
			M,
			m,
			D,
			axes,
			dim )

cluster_deadlocks()

diffusion_utils.cluster_deadlocks	(		PATHS,
			res_grid,
			geod,
			res_to_A_0,
			geod_A_0,
			A_0 )

compute_all()

diffusion_utils.compute_all

(

LIST

)

compute_direction()

diffusion_utils.compute_direction

(

LIST

)

compute_penalties()

diffusion_utils.compute_penalties

(

LIST

)

compute_repulsion()

diffusion_utils.compute_repulsion

(

LIST

)

cut_path_from_bottom()

diffusion_utils.cut_path_from_bottom	(		path,
			h,
			grid,
			axis = -1 )

cut_path_from_top()

diffusion_utils.cut_path_from_top	(		path,
			h,
			grid,
			axis = -1 )

dist_from_pts_periodic_boundaries()

diffusion_utils.dist_from_pts_periodic_boundaries	(		pts_,
			grid_,
			M,
			m,
			axes,
			dim = 3 )

pts -> punti da proiettare
grid -> array of pts (npts,dim)
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_periodic_boundaries()

diffusion_utils.dist_periodic_boundaries	(		grid_,
			M,
			m,
			axes,
			dim = 3 )

Makes a 

grid -> array of pts (npts,dim)
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

equivalence()

diffusion_utils.equivalence	(		A,
			v_path,
			rank )

Broken!

find_geod()

diffusion_utils.find_geod	(		idx0,
			idx1,
			geodesics,
			pts,
			D,
			maxiter = np.inf )

find_geod_wrap()

diffusion_utils.find_geod_wrap

(

LIST

)

get_box_from_cell()

diffusion_utils.get_box_from_cell

(

cell_file

)

get_cmap()

diffusion_utils.get_cmap	(		n,
			name = 'hsv' )

Returns a function that maps each index in 0, 1, ..., n-1 to a distinct 
RGB color; the keyword argument name must be a standard mpl colormap name.

grad_r2()

diffusion_utils.grad_r2	(		pt,
			balls_centres,
			balls_radii,
			p = 2,
			eps = 1 )

homological_simplification_of_path()

diffusion_utils.homological_simplification_of_path	(		path,
			grid,
			geod,
			V,
			rank,
			GF,
			D,
			N,
			edge_idxs,
			r_graph )

homological_simplification_of_path_pts()

diffusion_utils.homological_simplification_of_path_pts	(		idx0,
			idx1,
			path,
			grid,
			geod,
			V,
			rank,
			GF,
			D,
			N,
			edge_idxs,
			r_graph )

idx0,idx1 (p0,p1) -> are indexes to sample from the path
q0,q1 -> are the indexes sampled from the paths and refer to pts in the grid

join_points_boundary_conditions()

diffusion_utils.join_points_boundary_conditions	(		p_,
			q_,
			M,
			m,
			axes,
			dim,
			n = 20 )

make_geodesics()

diffusion_utils.make_geodesics	(		grid,
			r,
			M,
			m,
			axes,
			dim,
			D_ = None,
			D_force_graph_ = None,
			verbose = False )

out_to_atoms()

diffusion_utils.out_to_atoms	(		inputfile,
			backbone_atoms,
			flow_atoms )

DEPRECATED?

def read_data(path, backbone_atoms, flow_atoms): """ Read an xyz file and extract the molecule's geometry.

Read the .xyz file and returns atoms coordinates by type, cardinalities and box boundaries

path_to_vec()

diffusion_utils.path_to_vec	(		path,
			D,
			N_1,
			edge_idxs,
			r_graph,
			verbose = False )

project_path()

diffusion_utils.project_path	(		path_coords,
			grid )

project_path_periodic()

diffusion_utils.project_path_periodic	(		path_coords,
			grid,
			M,
			m,
			axes,
			dim = 3,
			D_ = None )

path_coords -> coordinates of the points of the path
grid -> array of pts to project the path on (npts,dim)
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
D_ -> distance matrix if already computed

project_timeseries_array()

diffusion_utils.project_timeseries_array	(		A,
			grid,
			M,
			m,
			axes,
			dim = 3 )

r_squared()

diffusion_utils.r_squared	(		px,
			py,
			pz,
			balls_centres,
			balls_radii )

rank_mod_p()

diffusion_utils.rank_mod_p

(

LIST

)

row_reduce_matrix()

diffusion_utils.row_reduce_matrix	(		A,
			GF )

sample_path()

diffusion_utils.sample_path	(		idx,
			N,
			res_grid,
			z_1,
			maxiter = 100000 )

save_paths()

diffusion_utils.save_paths	(		LIST,
			name,
			folder_path )

simplify_path()

diffusion_utils.simplify_path

(

path_

)

smooth_path()

diffusion_utils.smooth_path	(		path,
			geod,
			res_grid,
			D )

solve_linear_system()

diffusion_utils.solve_linear_system	(		B,
			v )

Finds a solution - if it exists - of B*x = v

B is row-reduced form

solve_linear_system_with_boundary()

diffusion_utils.solve_linear_system_with_boundary	(		B,
			v,
			A,
			A_red,
			V,
			GF )

Finds a solution - if it exists - of B*x = v + A*mu

B is row-reduced form
A generates the boundary subspace
A_red is A[rank(B):,:] in row reduced form via the matrix V
tmp tells if the solution is exact