meanap.params

Pipeline parameter definitions, mirroring the MATLAB Params struct.

Classes

Params(home_dir, raw_data, ...)

class meanap.params.Params(home_dir: str = '', raw_data: str = '', output_data_folder: str = '', output_data_folder_name: str = '', spreadsheet_file_name: str = '', spreadsheet_range: str = 'A2:A100000', spike_detected_data: str = '', prior_analysis_path: str = '', fs: float = 25000.0, d_samp_f: float = 1000.0, potential_difference_unit: str = 'uV', channel_layout: str = 'MCS60', detect_spikes: bool = True, run_spike_check_on_prev_spike_data: bool = False, thresholds: list[float] = <factory>, abs_thresholds: list[float] = <factory>, wname_list: list[str] = <factory>, cost_list: float = -0.12, spikes_method: str = 'bior1p5', filter_low_pass: float = 600.0, filter_high_pass: float = 8000.0, ref_period: float = 2.0, get_template_ref_period: float = 2.0, min_peak_thr_multiplier: float = -5.0, max_peak_thr_multiplier: float = -100.0, pos_peak_thr_multiplier: float = 40.0, n_spikes: int = 100, multiple_templates: bool = False, multi_template_method: str = 'PCA', min_activity_level: float = 0.0, remove_inactive_nodes: bool = False, remove_artifacts: bool = False, func_con_lag_val: list[int] = <factory>, trunc_rec: bool = False, trunc_length: float = 120.0, adj_m_type: Literal['weighted', 'binary'] = 'weighted', prob_thresh_rep_num: int = 200, prob_thresh_tail: float = 0.05, prob_thresh_plot_checks: bool = False, prob_thresh_plot_checks_n: int = 5, network_burst_detection_method: str = 'Bakkum', min_spike_network_burst: int = 10, min_channel_network_burst: int = 3, bakkum_network_burst_isi_n_threshold: str | float = 'automatic', single_channel_burst_detection_method: str = 'Bakkum', single_channel_burst_min_spike: int = 5, single_channel_isi_threshold: str | float = 'automatic', net_met_to_cal: list[str] = <factory>, recompute_metrics: bool = False, min_number_of_nodes_to_cal_net_met: int = 3, exclude_edges_below_threshold: bool = True, auto_set_cartography_boundaries: bool = True, auto_set_cartography_boundaries_per_lag: bool = False, cartography_lag_val: list[int] = <factory>, hub_boundary_wm_d_deg: float = 2.5, peri_part_coef: float = 0.625, pro_hub_part_coef: float = 0.3, non_hub_connector_part_coef: float = 0.8, connector_hub_part_coef: float = 0.75, eff_rank_cal_method: str = 'ordinary', eff_rank_downsample_freq: float = 10.0, nmf_downsample_freq: float = 10.0, include_nmf_components: bool = False, fig_ext: list[str] = <factory>, show_one_fig: bool = True, full_svg: bool = False, raster_plot_upper_percentile: float = 99.0, include_not_box_plots: bool = False, include_channel_number_in_plots: bool = False, use_theoretical_bounds: bool = True, use_min_max_all_recording_bounds: bool = False, use_min_max_per_genotype_bounds: bool = False, min_node_size: float = 0.01, max_node_size: float = 0.06, node_scaling_method: str = 'degree', node_scaling_power: float = 1.0, kde_height: float = 0.3, kde_width_for_one_point: float = 0.5, raster_colormap: str = 'parula', line_plot_shade_metric: str = 'sem', custom_grp_order: list[str] = <factory>, network_plot_edge_threshold_method: str = 'percentile', network_plot_edge_threshold_percentile: float = 90.0, network_plot_edge_threshold: float = 0.1, max_num_edges_to_plot: int = 500, edge_subsampling_method: str = 'random', node_layout: str = 'MEA', start_analysis_step: int = 1, stop_analysis_step: int = 4, optional_steps_to_run: list[str] = <factory>, prior_analysis: bool = False, verbose_level: str = 'Normal', time_processes: bool = False, output_spreadsheet_file_type: str = 'csv', twop_activity: str = 'peaks', twop_redo_denoising: bool = False, remove_nodes_with_no_peaks: bool = False, num_2p_traces: int = 3, twop_denoising_threshold: float = 1.3, twop_denoising_time_before_peak: float = 1.0, twop_denoising_time_after_peak: float = 2.05, python_path: str = '', stimulation_mode: bool = False, automatic_stim_detection: bool = False, stim_detection_method: str = 'threshold', stim_detection_val: float = 2.5, stim_refractory_period: float = 0.5, stim_duration: float = 0.002, stim_duration_for_plotting: float = 0.01)

Bases: object

Parameters:

• home_dir (str)

• raw_data (str)

• output_data_folder (str)

• output_data_folder_name (str)

• spreadsheet_file_name (str)

• spreadsheet_range (str)

• spike_detected_data (str)

• prior_analysis_path (str)

• fs (float)

• d_samp_f (float)

• potential_difference_unit (str)

• channel_layout (str)

• detect_spikes (bool)

• run_spike_check_on_prev_spike_data (bool)

• thresholds (list[float])

• abs_thresholds (list[float])

• wname_list (list[str])

• cost_list (float)

• spikes_method (str)

• filter_low_pass (float)

• filter_high_pass (float)

• ref_period (float)

• get_template_ref_period (float)

• min_peak_thr_multiplier (float)

• max_peak_thr_multiplier (float)

• pos_peak_thr_multiplier (float)

• n_spikes (int)

• multiple_templates (bool)

• multi_template_method (str)

• min_activity_level (float)

• remove_inactive_nodes (bool)

• remove_artifacts (bool)

• func_con_lag_val (list[int])

• trunc_rec (bool)

• trunc_length (float)

• adj_m_type (Literal['weighted', 'binary'])

• prob_thresh_rep_num (int)

• prob_thresh_tail (float)

• prob_thresh_plot_checks (bool)

• prob_thresh_plot_checks_n (int)

• network_burst_detection_method (str)

• min_spike_network_burst (int)

• min_channel_network_burst (int)

• bakkum_network_burst_isi_n_threshold (str | float)

• single_channel_burst_detection_method (str)

• single_channel_burst_min_spike (int)

• single_channel_isi_threshold (str | float)

• net_met_to_cal (list[str])

• recompute_metrics (bool)

• min_number_of_nodes_to_cal_net_met (int)

• exclude_edges_below_threshold (bool)

• auto_set_cartography_boundaries (bool)

• auto_set_cartography_boundaries_per_lag (bool)

• cartography_lag_val (list[int])

• hub_boundary_wm_d_deg (float)

• peri_part_coef (float)

• pro_hub_part_coef (float)

• non_hub_connector_part_coef (float)

• connector_hub_part_coef (float)

• eff_rank_cal_method (str)

• eff_rank_downsample_freq (float)

• nmf_downsample_freq (float)

• include_nmf_components (bool)

• fig_ext (list[str])

• show_one_fig (bool)

• full_svg (bool)

• raster_plot_upper_percentile (float)

• include_not_box_plots (bool)

• include_channel_number_in_plots (bool)

• use_theoretical_bounds (bool)

• use_min_max_all_recording_bounds (bool)

• use_min_max_per_genotype_bounds (bool)

• min_node_size (float)

• max_node_size (float)

• node_scaling_method (str)

• node_scaling_power (float)

• kde_height (float)

• kde_width_for_one_point (float)

• raster_colormap (str)

• line_plot_shade_metric (str)

• custom_grp_order (list[str])

• network_plot_edge_threshold_method (str)

• network_plot_edge_threshold_percentile (float)

• network_plot_edge_threshold (float)

• max_num_edges_to_plot (int)

• edge_subsampling_method (str)

• node_layout (str)

• start_analysis_step (int)

• stop_analysis_step (int)

• optional_steps_to_run (list[str])

• prior_analysis (bool)

• verbose_level (str)

• time_processes (bool)

• output_spreadsheet_file_type (str)

• twop_activity (str)

• twop_redo_denoising (bool)

• remove_nodes_with_no_peaks (bool)

• num_2p_traces (int)

• twop_denoising_threshold (float)

• twop_denoising_time_before_peak (float)

• twop_denoising_time_after_peak (float)

• python_path (str)

• stimulation_mode (bool)

• automatic_stim_detection (bool)

• stim_detection_method (str)

• stim_detection_val (float)

• stim_refractory_period (float)

• stim_duration (float)

• stim_duration_for_plotting (float)

abs_thresholds: list[float]

adj_m_type: Literal['weighted', 'binary'] = 'weighted'

auto_set_cartography_boundaries: bool = True

auto_set_cartography_boundaries_per_lag: bool = False

automatic_stim_detection: bool = False

bakkum_network_burst_isi_n_threshold: str | float = 'automatic'

cartography_lag_val: list[int]

channel_layout: str = 'MCS60'

connector_hub_part_coef: float = 0.75

cost_list: float = -0.12

custom_grp_order: list[str]

d_samp_f: float = 1000.0

detect_spikes: bool = True

edge_subsampling_method: str = 'random'

eff_rank_cal_method: str = 'ordinary'

eff_rank_downsample_freq: float = 10.0

exclude_edges_below_threshold: bool = True

fig_ext: list[str]

filter_high_pass: float = 8000.0

filter_low_pass: float = 600.0

fs: float = 25000.0

full_svg: bool = False

func_con_lag_val: list[int]

get_template_ref_period: float = 2.0

home_dir: str = ''

hub_boundary_wm_d_deg: float = 2.5

include_channel_number_in_plots: bool = False

include_nmf_components: bool = False

include_not_box_plots: bool = False

kde_height: float = 0.3

kde_width_for_one_point: float = 0.5

line_plot_shade_metric: str = 'sem'

max_node_size: float = 0.06

max_num_edges_to_plot: int = 500

max_peak_thr_multiplier: float = -100.0

min_activity_level: float = 0.0

min_channel_network_burst: int = 3

min_node_size: float = 0.01

min_number_of_nodes_to_cal_net_met: int = 3

min_peak_thr_multiplier: float = -5.0

min_spike_network_burst: int = 10

multi_template_method: str = 'PCA'

multiple_templates: bool = False

n_spikes: int = 100

net_met_to_cal: list[str]

network_burst_detection_method: str = 'Bakkum'

network_plot_edge_threshold: float = 0.1

network_plot_edge_threshold_method: str = 'percentile'

network_plot_edge_threshold_percentile: float = 90.0

nmf_downsample_freq: float = 10.0

node_layout: str = 'MEA'

node_scaling_method: str = 'degree'

node_scaling_power: float = 1.0

non_hub_connector_part_coef: float = 0.8

num_2p_traces: int = 3

optional_steps_to_run: list[str]

output_data_folder: str = ''

output_data_folder_name: str = ''

output_spreadsheet_file_type: str = 'csv'

peri_part_coef: float = 0.625

pos_peak_thr_multiplier: float = 40.0

potential_difference_unit: str = 'uV'

prior_analysis: bool = False

prior_analysis_path: str = ''

pro_hub_part_coef: float = 0.3

prob_thresh_plot_checks: bool = False

prob_thresh_plot_checks_n: int = 5

prob_thresh_rep_num: int = 200

prob_thresh_tail: float = 0.05

python_path: str = ''

raster_colormap: str = 'parula'

raster_plot_upper_percentile: float = 99.0

raw_data: str = ''

recompute_metrics: bool = False

ref_period: float = 2.0

remove_artifacts: bool = False

remove_inactive_nodes: bool = False

remove_nodes_with_no_peaks: bool = False

run_spike_check_on_prev_spike_data: bool = False

show_one_fig: bool = True

single_channel_burst_detection_method: str = 'Bakkum'

single_channel_burst_min_spike: int = 5

single_channel_isi_threshold: str | float = 'automatic'

spike_detected_data: str = ''

spikes_method: str = 'bior1p5'

spreadsheet_file_name: str = ''

spreadsheet_range: str = 'A2:A100000'

start_analysis_step: int = 1

stim_detection_method: str = 'threshold'

stim_detection_val: float = 2.5

stim_duration: float = 0.002

stim_duration_for_plotting: float = 0.01

stim_refractory_period: float = 0.5

stimulation_mode: bool = False

stop_analysis_step: int = 4

thresholds: list[float]

time_processes: bool = False

trunc_length: float = 120.0

trunc_rec: bool = False

twop_activity: str = 'peaks'

twop_denoising_threshold: float = 1.3

twop_denoising_time_after_peak: float = 2.05

twop_denoising_time_before_peak: float = 1.0

twop_redo_denoising: bool = False

use_min_max_all_recording_bounds: bool = False

use_min_max_per_genotype_bounds: bool = False

use_theoretical_bounds: bool = True

verbose_level: str = 'Normal'

wname_list: list[str]