depracated_single_mode.py File Reference

Namespaces
namespace	depracated_single_mode

Functions
	depracated_single_mode.read_configuration (str configuration_file, str configuration)
	import a specified structure from a configuration file
	depracated_single_mode.read_computation_settings (str settings_file, settings_name)
	depracated_single_mode.read_sample (str structure_file, str configuration)
	import a specified sample range from a configuration file
	depracated_single_mode.read_oineus_settings (str structure_file, str setting_name)
	import settings for kernel/image/cokernel
	depracated_single_mode.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.
	depracated_single_mode.weighted_alpha_diode (points)
	Use diode to fill the weighted alpha shapes.
	depracated_single_mode.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.
	depracated_single_mode.oineus_compare (x, y)
	Comparison to compare list of simplicies to get them in the order for oineus.
	depracated_single_mode.sub_complex (pd.DataFrame points, float z_upper, float z_lower)
	Given the points, and the upper and lower thresholds in the 'z'-component.
	depracated_single_mode.oineus_filtration (pd.DataFrame points, oineus.ReductionParams params)
	Given a set of points, compute the oineus.filtration of the alpha complex.
	depracated_single_mode.oineus_pair (pd.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.
	depracated_single_mode.oineus_process (pd.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.
	depracated_single_mode.oineus_kernel_image_cokernel (pd.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.
	depracated_single_mode.calculate_APF (dgm)
	Calcualte the APF from a diagram.
	depracated_single_mode.load_configuration_settings ()
	depracated_single_mode.load_computation_settings ()
	depracated_single_mode.compute ()

Variables
	depracated_single_mode.params
	depracated_single_mode.loaded
	depracated_single_mode.processed
	depracated_single_mode.plotted
	depracated_single_mode.file_path = st.text_input("Intial structure file:",key="file_path")
	depracated_single_mode.file_format = st.text_input("File format:", key="file_format",placeholder="Auto")
	depracated_single_mode.manual_config = st.checkbox("Manually specify configuration", key="manual_config")
	depracated_single_mode.config_file
	depracated_single_mode.key
	depracated_single_mode.config_name
	depracated_single_mode.atoms
	depracated_single_mode.radii
	depracated_single_mode.sample_index
	depracated_single_mode.repeat_x
	depracated_single_mode.repeat_y
	depracated_single_mode.repeat_z
	depracated_single_mode.manual_compute = st.checkbox("Manually specify settings for the computations (i.e number of threds, and if you want to compute kernel/image/cokernel)", key="maual_comp_config")
	depracated_single_mode.same_config_file = st.checkbox("The computation settings are in the same configuration file.", key="same_config_file")
	depracated_single_mode.comp_file
	depracated_single_mode.comp_name
	depracated_single_mode.kernel
	depracated_single_mode.image
	depracated_single_mode.cokernel
	depracated_single_mode.placeholder
	depracated_single_mode.n_threads
	depracated_single_mode.thickness
	depracated_single_mode.pd_checks = st.columns(3)
	depracated_single_mode.pd0 = st.session_state["pd0"]
	depracated_single_mode.pd1 = st.session_state["pd1"]
	depracated_single_mode.pd2 = st.session_state["pd2"]
	depracated_single_mode.apf_checks = st.columns(3)
	depracated_single_mode.apf0 = st.session_state["apf0"]
	depracated_single_mode.apf1 = st.session_state["apf1"]
	depracated_single_mode.apf2 = st.session_state["apf2"]
	depracated_single_mode.on_click