controllers

Module Contents

Classes

IntController
LifetimeController
GroupingController
SpectraController
myPlotROI
MyCrosshairOverlay
RasterScanController
AntibunchingController
PlotFeature
FilteringController

Functions

export_plot_item(plot_item, path[, text])

Attributes

__docformat__
EXPORT_WIDTH
EXPORT_MPL_WIDTH
EXPORT_MPL_HEIGHT
EXPORT_MPL_DPI
SIG_ROI_CHANGE_THRESHOLD
logger

controllers.__docformat__ = "'NumPy'"

controllers.EXPORT_WIDTH = '1500'

controllers.EXPORT_MPL_WIDTH = '10'

controllers.EXPORT_MPL_HEIGHT = '4.5'

controllers.EXPORT_MPL_DPI = '300'

controllers.SIG_ROI_CHANGE_THRESHOLD = '0.1'

controllers.logger = "'controllers'"

controllers.export_plot_item(plot_item: pyqtgraph.PlotItem, path: str, text: str = None)

class controllers.IntController(main_window: main.MainWindow)

Bases: PyQt5.QtCore.QObject

main_window

resolve_mode = 'None'

results_gathered = 'False'

int_widget

int_plot

int_hist_container

show_int_hist

int_hist_line

int_hist_widget

int_hist_plot

lifetime_widget

lifetime_plot

group_int_widget

groups_int_plot

groups_hist_widget

groups_hist_plot

int_level_info_container

level_info_text

int_level_line

show_level_info

show_exp_trace

temp_fig = 'None'

temp_ax = 'None'

temp_bins = 'None'

int_ROI

confidence_index

setup_plot(plot_item: pyqtgraph.PlotItem, is_int_hist: bool = False, is_group_hist: bool = False, is_lifetime: bool = False)

static setup_widget(plot_widget: pyqtgraph.PlotWidget)

hide_show_chb(chb_obj: PyQt5.QtWidgets.QCheckBox, show: bool)

roi_chb_changed()

roi_region_changed()

hist_chb_changed()

level_info_chb_changed()

exp_trace_chb_changed()

gui_apply_bin()

Changes the bin size of the data of the current particle and then displays the new trace.

gui_chb_show_groups()

gui_chb_show_global_groups()

get_bin() → int

Returns current GUI value for bin size in ms.

Returns:

The value of the bin size on the GUI in spbBinSize.

Return type:

int

set_bin(new_bin: int)

Sets the GUI value for the bin size in ms

Parameters:

new_bin (int) – Value to set bin size to, in ms.

gui_apply_bin_all()

Changes the bin size of the data of all the particles and then displays the new trace of the current particle.

start_binall_thread(bin_size) → None

Parameters:

bin_size

binall_thread_complete()

gui_resolve()

Resolves the levels of the current particle and displays it.

gui_resolve_selected()

Resolves the levels of the selected particles and displays the levels of the current particle.

gui_resolve_all()

Resolves the levels of the all the particles and then displays the levels of the current particle.

plot_trace(particle: smsh5.Particle = None, for_export: bool = False, export_path: str = None, lock: bool = False) → None

Used to display the trace from the absolute arrival time data of the current particle.

plot_levels(particle: smsh5.Particle = None, for_export: bool = False, export_path: str = None, lock: bool = False)

Used to plot the resolved intensity levels of the current particle.

plot_hist(particle: smsh5.Particle = None, for_export: bool = False, export_path: str = None, for_levels: bool = False, for_groups: bool = False)

update_level_info(particle: smsh5.Particle = None)

plot_group_bounds(particle: smsh5.Particle = None, for_export: bool = False, export_path: str = None, lock: bool = False)

plot_all()

start_resolve_thread(mode: str = 'current', thread_finished=None, end_time_s=None) → None

Creates a worker to resolve levels.

Depending on the current_selected_all parameter the worker will be given the necessary parameter to fit the current, selected or all particles.

Parameters:

• end_time_s (float)

• thread_finished

• mode ({'current', 'selected', 'all'}) – Possible values are ‘current’ (default), ‘selected’, and ‘all’.

gather_replace_results(results: List[threads.ProcessTaskResult] | threads.ProcessTaskResult)

resolve_thread_complete(thread: threads.ProcessThread)

get_gui_confidence()

Return current GUI value for confidence percentage.

gui_quick_roi(mode: str)

any_int_plot_double_click(event: pyqtgraph.GraphicsScene.mouseEvents.MouseClickEvent)

error(e)

class controllers.LifetimeController(main_window: main.MainWindow)

Bases: PyQt5.QtCore.QObject

all_should_apply = 'None'

main_window

lifetime_hist_widget

life_hist_plot

residual_widget

residual_plot

fitparamdialog

fitparam

irf_loaded = 'False'

first = '0'

startpoint = 'None'

tmin = '0'

temp_fig = 'None'

temp_ax = 'None'

setup_plot(plot: pyqtgraph.PlotItem, is_residuals: bool = False)

static setup_widget(plot_widget: pyqtgraph.PlotWidget)

gui_prev_lev()

Moves to the previous resolves level and displays its decay curve.

gui_next_lev()

Moves to the next resolves level and displays its decay curve.

gui_whole_trace()

Unselects selected level and shows whole trace’s decay curve

gui_jump_to_groups()

gui_show_hide_residuals()

gui_load_irf()

Allow the user to load a IRF instead of the IRF that has already been loaded.

add_irf(decay, t)

gui_fit_param()

Opens a dialog to choose the setting with which the decay curve will be fitted.

gui_fit_current()

Fits the currently selected level’s decay curve using the provided settings.

gui_fit_selected()

Fits the all the levels decay curves in the all the selected particles using the provided settings.

gui_fit_all()

Fits the all the levels decay curves in the all the particles using the provided settings.

gui_fit_levels()

Fits the all the levels decay curves for the current particle.

gui_use_roi_changed()

test_need_roi_apply(particle: smsh5.Particle = None, update_buttons: bool = True)

update_apply_roi_button_colors()

apply_roi(particles: list)

gui_apply_roi_current()

gui_apply_roi_selected()

gui_apply_roi_all()

plot_all()

update_plot_log()

update_results(use_selected: bool = False, selected_level_or_group: change_point.Level | grouping.GlobalLevel | grouping.Group = None, particle: smsh5.Particle = None, for_export: bool = False, str_return: bool = False) → str | None

plot_decay_and_convd(particle: smsh5.Particle, export_path: str, has_groups: bool, only_groups: bool = False, lock: bool = False)

plot_decay_convd_and_hist(particle: smsh5.Particle, export_path: str, has_groups: bool, only_groups: bool = False, lock: bool = False)

plot_decay(selected_level_or_group: None | change_point.Level | grouping.GlobalLevel | grouping.Group = None, use_selected: bool = False, particle: smsh5.Particle = None, remove_empty: bool = False, for_export: bool = False, export_path: str = None, lock: bool = False) → None

Used to display the histogram of the decay data of the current particle.

plot_convd(selected_level_or_group: change_point.Level | grouping.GlobalLevel | grouping.Group = None, use_selected: bool = False, particle: smsh5.Particle = None, remove_empty: bool = False, for_export: bool = False, export_path: str = None, lock: bool = False) → None

Used to display the histogram of the decay data of the current particle.

plot_residuals(selected_level_or_group: change_point.Level | grouping.GlobalLevel | grouping.Group = None, use_selected: bool = False, particle: smsh5.Particle = None, for_export: bool = False, export_path: str = None, lock: bool = False) → None

Used to display the histogram of the decay data of the current particle.

start_fitting_thread(mode: str = 'current') → None

For now, doesn’t actually use threads. This is due to high memory consumption.

Depending on the current_selected_all parameter the worker will be given the necessary parameter to fit the current, selected or all particles.

Parameters:

mode ({'current', 'selected', 'all'}) – Possible values are ‘current’ (default), ‘selected’, and ‘all’.

gather_replace_results(results: List[threads.ProcessTaskResult] | threads.ProcessTaskResult)

fitting_thread_complete(mode: str = None)

change_irf_start(start, irf_data)

set_tmin(tmin=0)

show_residuals_widget(show: bool = True, lock: bool = None)

error(e)

class controllers.GroupingController(main_widow: main.MainWindow)

Bases: PyQt5.QtCore.QObject

main_window

bic_plot_widget

bic_scatter_plot

all_bic_plots = 'None'

all_last_solutions = 'None'

temp_dir = 'None'

temp_fig = 'None'

temp_ax = 'None'

clear_bic()

solution_clicked(plot, points)

plot_group_bic(particle: smsh5.Particle = None, for_export: bool = False, export_path: str = None, lock: bool = False, is_global_group=False)

gui_group_current()

gui_group_selected()

gui_group_all()

gui_apply_groups_current()

gui_apply_groups_selected()

gui_apply_groups_all()

start_grouping_thread(mode: str = 'current') → None

Creates a worker to resolve levels.

Depending on the current_selected_all parameter the worker will be given the necessary parameter to fit the current, selected or all particles.

Parameters:

• thread_finished

• mode ({'current', 'selected', 'all'}) – Possible values are ‘current’ (default), ‘selected’, and ‘all’.

gather_replace_results(results: List[threads.ProcessTaskResult] | threads.ProcessTaskResult)

grouping_thread_complete(mode)

check_rois_and_set_label()

apply_groups(mode: str = 'current', particles=None)

build_global()

global_gather_replace_results(result: threads.ProcessTaskResult)

global_grouping_thread_complete()

start_global_grouping_thread()

gui_group_global()

error(e: Exception)

class controllers.SpectraController(main_window: main.MainWindow)

Bases: PyQt5.QtCore.QObject

main_window

spectra_image_view

temp_fig = 'None'

temp_ax = 'None'

roi_rotated = 'False'

gui_sub_bkg()

Used to subtract the background

slot_plot_spectra(event)

gui_rot_roi()

Used to rotate the ROI

set_roi_plot_ticks(wl, times)

plot_spectra(particle: smsh5.Particle = None, for_export: bool = False, export_path: str = None, lock: bool = False)

class controllers.myPlotROI(size)

Bases: pyqtgraph.ROI

rotateSnapAngle = '90'

class controllers.MyCrosshairOverlay(pos=None, size=None, **kargs)

Bases: pyqtgraph.CrosshairROI

_shape = 'None'

aspectLocked = 'True'

class controllers.RasterScanController(main_window: main.MainWindow)

Bases: PyQt5.QtCore.QObject

main_window

raster_scan_image_view

list_text

_crosshair_item = 'None'

_text_item = 'None'

temp_fig = 'None'

temp_ax = 'None'

static create_crosshair_item(pos: Tuple[int, int], pixelsize) → MyCrosshairOverlay

static create_text_item(text: str, pos: Tuple[int, int]) → pyqtgraph.TextItem

plot_raster_scan(particle: smsh5.Particle = None, raster_scan: smsh5.RasterScan = None, for_export: bool = False, export_path: str = None, lock: bool = False)

class controllers.AntibunchingController(mainwindow: main.MainWindow, corr_widget: pyqtgraph.PlotWidget, corr_sum_widget: pyqtgraph.PlotWidget)

Bases: PyQt5.QtCore.QObject

property difftime

main_window

resolve_mode = 'None'

results_gathered = 'False'

corr_widget

corr_plot

corr_sum_widget

corr_sum_plot

temp_fig = 'None'

temp_ax = 'None'

corr = 'None'

bins = 'None'

irfdiff = '0'

setup_plot(plot_item: pyqtgraph.PlotItem)

static setup_widget(plot_widget: pyqtgraph.PlotWidget)

gui_correlate_current()

gui_correlate_selected()

gui_correlate_all()

plot_corr(particle: smsh5.Particle = None, for_export: bool = False, export_path: str = None, lock: bool = False) → None

plot_corr_sum()

gui_curr_chb(checked)

start_corr_thread(mode: str = 'current') → None

Creates a worker to calculate correlations.

Depending on the current_selected_all parameter the worker will be given the necessary parameter to correlate the current, selected or all particles.

Parameters:

mode ({'current', 'selected', 'all'}) – Possible values are ‘current’ (default), ‘selected’, and ‘all’.

gather_replace_results(results: List[threads.ProcessTaskResult] | threads.ProcessTaskResult)

corr_thread_complete(mode: str = None)

rebin_corrs()

error(e)

class controllers.PlotFeature

PhotonNumber = "'Photon Number'"

Intensity = "'Intensity'"

Lifetime = "'Lifetime'"

DW = "'DW'"

ChiSquared = "'Chi-Squared'"

IRFShift = "'IRF Shift'"

classmethod get_list() → list

classmethod get_dict() → dict

class controllers.FilteringController(main_window: main.MainWindow)

Bases: PyQt5.QtCore.QObject

main_window

plot_widget

plot

option_linker

current_plot_type = '(None, None)'

current_particles_to_use = 'None'

current_data_points_to_use = 'None'

current_particles = '[]'

levels_to_use = 'None'

fit_result = 'None'

has_fit = 'False'

is_normalized = 'False'

plot_pen

distribution_item

two_feature_item

plot_fit_pen

int_lifetime_fit_item

filter_settings = 'None'

static _get_label(feature: PlotFeature = None) → tuple

setup_plot(feature_x: PlotFeature, feature_y: PlotFeature = None, clear_plot: bool = True, is_first_setup: bool = False)

filter_option_changed(option: str)

auto_num_bins_changed()

get_two_features() → tuple

change_plot_type(feature_x: PlotFeature | str = None, feature_y: PlotFeature | str = None)

set_levels_to_use()

get_data() → tuple

two_features_changed(x_changed: bool = None)

switch_two_features()

plot_features(feature_x: PlotFeature | str = None, feature_y: PlotFeature | str = None, use_current_plot: bool = False, use_selected_two_features: bool = False)

static _filter_numeric_data(feature_data: numpy.ndarray, are_used_flags: List[bool], test_min: bool = False, test_max: bool = False, min_value=None, max_value=None)

get_feature_data(feature: PlotFeature | str) → tuple

get_all_feature_data() → tuple[dict[Any, dict[str, Any]], list[bool] | Any, list[bool] | Any]

get_all_filter() → numpy.ndarray

set_limits(feature_x: PlotFeature | str = None, feature_y: PlotFeature | str = None)

plot_distribution()

plot_two_features()

prepare_plot_for_int_lifetime_fit()

plot_fit_result()

fit_intensity_lifetime()

get_filter_settings() → dict

static _block_change(obj, change_method_name, value)

set_filter_settings(filter_settings: dict)

apply_filters()

reset_filters()

reset_dataset_filter()

get_all_levels_with_lifetime() → list

reset_normalization()

apply_normalization()