main

Module for analysis of SMS data from HDF5 files

Bertus van Heerden and Joshua Botha University of Pretoria 2020

Module Contents

Classes

MainWindow

Class for Full SMS application that returns QMainWindow object.

Functions

display_on()
display_reset()
main()	Creates QApplication and runs MainWindow().

Attributes

__docformat__
SMS_VERSION
main_window_file
logger

main.__docformat__ = "'NumPy'"

main.SMS_VERSION = "'0.7.7'"

main.main_window_file

main.logger = "'main'"

class main.MainWindow

Bases: PyQt5.QtWidgets.QMainWindow, UI_Main_Window

Class for Full SMS application that returns QMainWindow object.

This class uses a *.ui that is automatically converted to a *.py script upon exectution.

threadpool

active_threads = '[]'

confidence_index

settings_dialog

settings

intensity_controller

lifetime_controller

grouping_controller

spectra_controller

raster_scan_controller

antibunch_controller

filtering_controller

treemodel

_root_was_checked = 'False'

part_nodes = '[]'

part_index = '[]'

tauparam = 'None'

ampparam = 'None'

shift = 'None'

decaybg = 'None'

irfbg = 'None'

start = 'None'

end = 'None'

addopt = 'None'

progress

current_progress

data_loaded = 'False'

irf_loaded = 'False'

current_dataset = 'None'

current_particle = 'None'

lock = 'None'

after_show()

sums_file_check() → bool

calc_store_sums() → None

Check if the all_sums.pickle file exists, and if it doesn’t creates it

gui_export_current()

gui_export_selected()

gui_export_all()

gui_select_groups_changed(chb_changed)

act_detect_remove_bursts_current()

act_detect_remove_bursts_selected()

act_detect_remove_bursts_all()

act_remove_bursts_current()

act_remove_bursts_selected()

act_remove_bursts_all()

act_restore_bursts_current()

act_restore_bursts_selected()

act_restore_bursts_all()

set_bin_size(bin_size: int)

act_open_settings_dialog()

act_filtering_and_normalization_dialog()

gui_group_use_roi()

act_open_h5()

Allows the user to point to a h5 file and then starts a thread that reads and loads the file.

act_save_selected()

“ Saves selected particles into a new HDF5 file.

act_save_analysis()

act_trim()

Used to trim the ‘dead’ part of a trace as defined by two parameters.

act_switch_all()

act_switch_selected()

act_set_startpoint()

set_startpoint(irf_data=None, start=None)

add_dataset(dataset_node)

add_node(particle_node, num)

add_all_nodes(all_nodes)

tree_view_clicked(model_index)

tree_view_key_press(event)

act_select_all(*args, **kwargs)

act_invert_selection(*args, **kwargs)

act_deselect_all(*args, **kwargs)

tab_change(active_tab_index: int)

update_int_gui()

card_selected() → None

selection_changed() → None

display_data(current=None, prev=None, combocard=False, is_global_group=False) → None

Displays the intensity trace and the histogram of the current particle.

Directly called by the tree signal currentChanged, thus the two arguments.

Parameters:

• current (QtCore.QModelIndex) – The index of the current selected particle as defined by QtCore.QModelIndex.

• prev (QtCore.QModelIndex) – The index of the previous selected particle as defined by QtCore.QModelIndex.

• combocard (bool) – True if called due to selecting other TCSPC card.

status_message(message: str) → None

Updates the status bar with the provided message argument.

Parameters:

message (str) – The message that is to be displayed in the status bar.

start_progress(max_num: int = None) → None

Sets the maximum value of the progress bar before use.

reset parameter can be optionally set to False to prevent the setting of the progress bar value to 0.

Parameters:

max_num (int) – The number of iterations or steps that the complete process is made up of.

set_progress(progress_value: int) → None

Sets the maximum value of the progress bar before use.

reset parameter can be optionally set to False to prevent the setting of the progress bar value to 0.

Parameters:

progress_value (int) – The number of iterations or steps that the complete process is made up of.

update_progress(value: int | float = None) → None

Used to update the progress bar by an increment of one. If at maximum sets progress bars visibility to False

end_progress()

tree2particle(identifier)

Returns the particle dataset for the identifier given. The identifier could be the number of the particle of the datasetnode value.

Parameters:

identifier – The integer number or a datasetnode object of the particle in question.

tree2dataset() → smsh5.H5dataset

Returns the H5dataset object of the file loaded.

Return type:

smsh5.H5dataset

set_data_loaded()

open_save_file_version_outdated()

open_file_thread_complete(thread: threads.ProcessThread = None, irf=False) → None

Is called as soon as all of the threads have finished.

set_export_options()

select_all_export_options()

select_all_plots_export_options()

select_all_dataframes_export_options()

open_file_error(err: Exception)

detect_remove_bursts(mode: str = None) → None

remove_bursts(mode: str = None, confirm: bool = True) → None

restore_bursts(mode: str = None) → None

run_parallel_cpa(particle)

switching_frequency(all_selected: str = None)

Calculates and exports the accumulated switching frequency of either all the particles, or only the selected.

Parameters:

all_selected ({'all', 'selected'}) – Possible values are ‘all’ (default) or ‘selected’.

get_checked()

get_checked_nums()

get_checked_particles()

set_particle_check_state(particle_number: int, set_checked: bool)

set_level_resolved()

gui_plot_intensity_clicked(new_value)

gui_plot_lifetime_clicked(new_value)

gui_export(mode: str = None)

convert_file_dialog()

range_selection()

reset_gui()

Sets the GUI elements to enabled if it should be accessible.

close_file()

error_handler(e: Exception)

main.display_on()

main.display_reset()

main.main()

Creates QApplication and runs MainWindow().