process.py File Reference

Namespaces
namespace	process

Functions
	process.read_configuration (str configuration_file, str configuration)
	import a specified structure from a configuration file
	process.read_computation_settings (str settings_file, settings_name)
	process.read_sample (str structure_file, str configuration)
	import a specified sample range from a configuration file
	process.read_oineus_settings (str structure_file, str setting_name)
	import settings for kernel/image/cokernel
	process.sample_at (str file_path, str format, sample_index, int repeat_x, int repeat_y, int repeat_z, atom_list, radius_list)
	Sample a structure at a particular time, with cell repetitions.
	process.weighted_alpha_diode (points)
	Use diode to fill the weighted alpha shapes.
	process.convert_simps_to_oineus (list simplices)
	Diode is set to create simplices for dionysus, so we need to convert them to the correct type for oineus.
	process.oineus_compare (x, y)
	Comparison to compare list of simplicies to get them in the order for oineus.
	process.sub_complex (pandas.DataFrame points, float z_upper, float z_lower)
	Given the points, and the upper and lower thresholds in the 'z'-component.
	process.oineus_filtration (pandas.DataFrame points, oineus.ReductionParams params)
	Given a set of points, compute the oineus.filtration of the alpha complex.
	process.oineus_pair (pandas.DataFrame points, list sub)
	Given a set of points, and the points that are in the subset L, construct the complexes and map between them.
	process.oineus_process (pandas.DataFrame points, oineus.ReductionParams params)
	Given some points with weights, and the number of threads to use, obtain the persistent homology of the weighted alpha complex of these points, using oineus.
	process.oineus_kernel_image_cokernel (pandas.DataFrame points, oineus.ReductionParams params, float upper_threshold, float lower_threshold)
	Given points, and parameters for oineus, calculate the kernel/image/cokernel persistence as desired.
	process.calculate_APF (dgm)
	Calcualte the APF from a diagram.