toma_io Namespace Reference

Functions
	read_configuration (str configuration_file, str configuration)
	import a specified structure from a configuration file
	read_computation_settings (str settings_file, settings_name)
	import a specified settings from a file
	load_configuration_settings ()
	Load the configuration settings.
	load_computation_settings ()
	Load the computation settings.
	write_dgm_csv (dgm, file_path, plot_name="")
	Save a digram as a csv file, with the option to save a plot as well.
	save_plots ()
	Save plots to a directory.

Function Documentation

load_computation_settings()

toma_io.load_computation_settings

(

)

Load the computation settings.

Load computation settings from the session state

This function reads computation settings from st.session_state and loads them into the session state. It uses read_computation_settings() to parse the settings file and extract:

• n_threads: Number of threads for Oineus to use
• save_plots: Whether to save plots
• kernel: Whether to compute kernel persistence
• image: Whether to compute image persistence
• cokernel: Whether to compute cokernel persistence
• thickness: Thickness settings

load_configuration_settings()

toma_io.load_configuration_settings

(

)

Load the configuration settings.

Load configuration settings from the session state

This function reads configuration settings from st.session_state and loads them into the session state. It uses read_configuration() to parse the config file and extract:

• atoms: ASE Atoms object containing atomic positions and types
• radii: Dictionary mapping atom types to their radii
• repeat_x/y/z: Number of times to repeat the cell in each direction

The settings are read from:

• st.session_state["config_file"]: Path to configuration file
• st.session_state["config_name"]: Name of configuration section to use

The parsed settings are stored back in st.session_state as:

• st.session_state.atoms
• st.session_state.radii
  
• st.session_state.repeat_x/y/z

read_computation_settings()

toma_io.read_computation_settings	(	str	settings_file,
			settings_name )

import a specified settings from a file

Parameters

settings_file	path to the file to use for configurations
settings_name	name of the structure to use

Returns

n_threads, save_plots, kernel, image, cokernel, thickness the number of threads for Oineus to use, wether plots should be saved, compute kernel persistence, compute image persistence, compute cokernel persistence, thickness settings

read_configuration()

toma_io.read_configuration	(	str	configuration_file,
		str	configuration )

import a specified structure from a configuration file

Parameters

configuration_file	path to the file to use for configurations
configuration	name of the structure to use

Returns

atoms, radii, repeat_x, repeat_y, repeat_z the atom symbols, radii to use for the atoms, repetition in x-axis, repetition in y-axis, repetition in z-axis

save_plots()

toma_io.save_plots

(

)

Save plots to a directory.

Save plots to a directory

This function saves plots to a specified directory. It uses the following from st.session_state:

• st.session_state.file_path: Path to the file containing the data
• st.session_state.sample_indices: Indices of samples to process
• st.session_state.params: Computation settings

write_dgm_csv()

toma_io.write_dgm_csv	(		dgm,
			file_path,
			plot_name = "" )

Save a digram as a csv file, with the option to save a plot as well.

Parameters

dgm	the diagram to be saved, and plotted
dir	directory in which to save the files
name	name of the structure
save_plot	save the plots as well