Index

_

__init__ (pypore.event_finder.Parameters attribute) (pypore.i_o.abstract_reader.AbstractReader attribute) (pypore.strategies.absolute_change_threshold_strategy.AbsoluteChangeThresholdStrategy attribute) (pypore.strategies.adaptive_baseline_strategy.AdaptiveBaselineStrategy attribute) (pypore.strategies.baseline_strategy.BaselineStrategy attribute) (pypore.strategies.noise_based_threshold_strategy.NoiseBasedThresholdStrategy attribute) (pypore.strategies.percent_change_threshold_strategy.PercentChangeThresholdStrategy attribute)

__init__() (pyporegui.file_items.DataFileListItem method) (pyporegui.file_items.FileListItem method) (pyporegui.file_items.FilterListItem method) (pyporegui.graphicsItems.histogram_item.HistogramItem method) (pyporegui.graphicsItems.my_plot_item.MyPlotItem method) (pyporegui.graphicsItems.path_item.PathItem method) (pyporegui.graphicsItems.scatter_plot_item.ScatterPlotItem method) (pyporegui.graphicsItems.spot_item.SpotItem method) (pyporegui.gui.MyMainWindow method) (pyporegui.my_threads.AnalyzeDataThread method) (pyporegui.my_threads.PlotThread method) (pyporegui.widgets.base_tabs.BaseQSplitter method) (pyporegui.widgets.base_tabs.BaseQSplitterDataFile method) (pyporegui.widgets.event_analysis_plot_widget.EventAnalysisPlotWidget method) (pyporegui.widgets.event_analysis_tab.EventAnalysisTab method) (pyporegui.widgets.event_finding_tab.EventFindingTab method) (pyporegui.widgets.event_viewing_tab.EventViewingTab method) (pyporegui.widgets.file_viewer_tab.FileViewerTab method) (pyporegui.widgets.plot_tool_bar.PlotToolBar method)

A

AbsoluteChangeThresholdStrategy (class in pypore.strategies.absolute_change_threshold_strategy) AbstractReader (class in pypore.i_o.abstract_reader) AdaptiveBaselineStrategy (class in pypore.strategies.adaptive_baseline_strategy) adc_bits (pypore.i_o.chimera_reader.ChimeraReader attribute) adc_v_ref (pypore.i_o.chimera_reader.ChimeraReader attribute) add_actions() (pyporegui.gui.MyMainWindow static method) add_event_item() (pyporegui.graphicsItems.my_plot_item.MyPlotItem method) add_filter_clicked() (pyporegui.widgets.event_analysis_tab.EventAnalysisTab method) add_histogram() (pyporegui.graphicsItems.histogram_item.HistogramItem method)

add_selections() (pyporegui.widgets.event_analysis_plot_widget.EventAnalysisPlotWidget method) addItem() (pyporegui.graphicsItems.my_plot_item.MyPlotItem method) addWidget() (pyporegui.widgets.plot_tool_bar.PlotToolBar method) AnalyzeDataThread (class in pyporegui.my_threads) append_event() (pypore.filetypes.event_database.EventDatabase method) append_level_lengths() (pypore.filetypes.event_database.EventDatabase method) append_levels() (pypore.filetypes.event_database.EventDatabase method) append_raw_data() (pypore.filetypes.event_database.EventDatabase method)

B

baseline (pypore.strategies.baseline_strategy.BaselineStrategy attribute) baseline_filter_parameter (pypore.strategies.adaptive_baseline_strategy.AdaptiveBaselineStrategy attribute) baseline_strategy (pypore.event_finder.Parameters attribute) BaselineStrategy (class in pypore.strategies.baseline_strategy)

BaseQSplitter (class in pyporegui.widgets.base_tabs) BaseQSplitterDataFile (class in pyporegui.widgets.base_tabs) bit_mask (pypore.i_o.chimera_reader.ChimeraReader attribute) boundingRect() (pyporegui.graphicsItems.path_item.PathItem method)

C

cancel() (pyporegui.my_threads.AnalyzeDataThread method) cancelled (pyporegui.my_threads.AnalyzeDataThread attribute) (pyporegui.my_threads.PlotThread attribute) change_end (pypore.strategies.absolute_change_threshold_strategy.AbsoluteChangeThresholdStrategy attribute) change_start (pypore.strategies.absolute_change_threshold_strategy.AbsoluteChangeThresholdStrategy attribute) ChimeraReader (class in pypore.i_o.chimera_reader) clean_database() (pypore.filetypes.data_file.DataFile method) (pypore.filetypes.event_database.EventDatabase method) clean_threads() (pyporegui.gui.MyMainWindow method) clear() (pyporegui.graphicsItems.my_plot_item.MyPlotItem method) clear_event_items() (pyporegui.graphicsItems.my_plot_item.MyPlotItem method) close() (pypore.i_o.abstract_reader.AbstractReader method)

color_picker_btn_clicked() (pyporegui.widgets.event_analysis_tab.EventAnalysisTab method) compute_baseline() (pypore.strategies.baseline_strategy.BaselineStrategy method) compute_ending_threshold() (pypore.strategies.threshold_strategy.ThresholdStrategy method) compute_starting_threshold() (pypore.strategies.threshold_strategy.ThresholdStrategy method) compute_variance() (pypore.strategies.baseline_strategy.BaselineStrategy method) convert_file() (in module pypore.file_converter) create_action() (pyporegui.gui.MyMainWindow method) create_random_data() (in module pypore.sampledata.creator) create_specified_data() (in module pypore.sampledata.creator) current_offset (pypore.i_o.chimera_reader.ChimeraReader attribute)

D

DataFile (class in pypore.filetypes.data_file) datafile (pypore.i_o.chimera_reader.ChimeraReader attribute) DataFileListItem (class in pyporegui.file_items) DataFileReader (class in pypore.i_o.data_file_reader) dataReady (pyporegui.my_threads.AnalyzeDataThread attribute) (pyporegui.my_threads.PlotThread attribute)

decimate_sample_rate (pypore.i_o.chimera_reader.ChimeraReader attribute) DEFAULT_MAX_EVENT_LENGTH (pypore.filetypes.event_database.EventDatabase attribute) detect_negative_events (pypore.event_finder.Parameters attribute) detect_positive_events (pypore.event_finder.Parameters attribute)

E

end_std_dev (pypore.strategies.noise_based_threshold_strategy.NoiseBasedThresholdStrategy attribute) event_position (pyporegui.graphicsItems.spot_item.SpotItem attribute) event_row (pypore.filetypes.event_database.EventDatabase attribute) EventAnalysisPlotWidget (class in pyporegui.widgets.event_analysis_plot_widget)

EventAnalysisTab (class in pyporegui.widgets.event_analysis_tab) EventDatabase (class in pypore.filetypes.event_database) EventFindingTab (class in pyporegui.widgets.event_finding_tab) EventViewingTab (class in pyporegui.widgets.event_viewing_tab)

F

FileListItem (class in pyporegui.file_items) FileViewerTab (class in pyporegui.widgets.file_viewer_tab) filter_file() (in module pypore.file_converter)

FilterListItem (class in pyporegui.file_items) find_events() (in module pypore.event_finder) FixedBaselineStrategy (class in pypore.strategies.fixed_baseline_strategy)

G

get_all_data() (pypore.i_o.abstract_reader.AbstractReader method) get_baseline() (pypore.strategies.baseline_strategy.BaselineStrategy method) get_current_analysis_parameters() (pyporegui.widgets.event_finding_tab.EventFindingTab method) get_data_length() (pypore.filetypes.data_file.DataFile method) get_directory() (pyporegui.file_items.FileListItem method) get_event_count() (pypore.filetypes.event_database.EventDatabase method) get_event_data_at() (pypore.filetypes.event_database.EventDatabase method) get_event_row() (pypore.filetypes.event_database.EventDatabase method) get_event_table() (pypore.filetypes.event_database.EventDatabase method) get_event_table_row() (pypore.filetypes.event_database.EventDatabase method) get_events_group() (pypore.filetypes.event_database.EventDatabase method) get_file_name() (pyporegui.file_items.FileListItem method) get_file_name_at() (pyporegui.file_items.FilterListItem method) get_file_name_from_position() (pyporegui.graphicsItems.scatter_plot_item.ScatterPlotItem method) get_file_names() (pyporegui.file_items.FilterListItem method)

get_filename() (pypore.i_o.abstract_reader.AbstractReader method) get_level_lengths_at() (pypore.filetypes.event_database.EventDatabase method) get_levels_at() (pypore.filetypes.event_database.EventDatabase method) get_next_blocks() (in module pypore.data_file_opener) (pypore.i_o.abstract_reader.AbstractReader method) get_param() (pyporegui.file_items.DataFileListItem method) get_params() (pyporegui.file_items.DataFileListItem method) (pyporegui.file_items.FilterListItem method) get_points_per_channel_total() (pypore.i_o.abstract_reader.AbstractReader method) get_raw_data_at() (pypore.filetypes.event_database.EventDatabase method) get_reader_from_filename() (in module pypore.i_o) get_sample_rate() (pypore.filetypes.data_file.DataFile method) (pypore.filetypes.event_database.EventDatabase method) (pypore.i_o.abstract_reader.AbstractReader method) get_simple_name() (pyporegui.file_items.FileListItem method) get_simple_name_at() (pyporegui.file_items.FilterListItem method) get_simple_names() (pyporegui.file_items.FilterListItem method) get_variance() (pypore.strategies.baseline_strategy.BaselineStrategy method) get_widget_list() (pyporegui.widgets.plot_tool_bar.PlotToolBar method)

H

HistogramItem (class in pyporegui.graphicsItems.histogram_item)

I

initialize() (pypore.strategies.baseline_strategy.BaselineStrategy method) initialize_database() (pypore.filetypes.data_file.DataFile method) (pypore.filetypes.event_database.EventDatabase method) is_debug() (pypore.filetypes.event_database.EventDatabase method)

is_decimate_checked() (pyporegui.widgets.plot_tool_bar.PlotToolBar method) is_plot_during_checked() (pyporegui.widgets.plot_tool_bar.PlotToolBar method)

M

max_event_length (pypore.event_finder.Parameters attribute) (pypore.filetypes.event_database.EventDatabase attribute) min_event_length (pypore.event_finder.Parameters attribute) move_event_display_by() (pyporegui.widgets.event_viewing_tab.EventViewingTab method)

MyMainWindow (class in pyporegui.gui) MyPlotItem (class in pyporegui.graphicsItems.my_plot_item)

N

next_clicked() (pyporegui.widgets.event_viewing_tab.EventViewingTab method)

NoiseBasedThresholdStrategy (class in pypore.strategies.noise_based_threshold_strategy)

O

on_scatter_points_clicked() (pyporegui.widgets.event_analysis_plot_widget.EventAnalysisPlotWidget method) open_data() (in module pypore.data_file_opener) open_data_files() (pyporegui.gui.MyMainWindow method) (pyporegui.widgets.base_tabs.BaseQSplitterDataFile method) (pyporegui.widgets.event_finding_tab.EventFindingTab method)

open_event_databases() (pyporegui.gui.MyMainWindow method) (pyporegui.widgets.event_analysis_tab.EventAnalysisTab method) (pyporegui.widgets.event_viewing_tab.EventViewingTab method) open_file() (in module pypore.filetypes.data_file) (in module pypore.filetypes.event_database)

P

Parameters (class in pypore.event_finder) PathItem (class in pyporegui.graphicsItems.path_item) percent_change_end (pypore.strategies.percent_change_threshold_strategy.PercentChangeThresholdStrategy attribute) percent_change_start (pypore.strategies.percent_change_threshold_strategy.PercentChangeThresholdStrategy attribute) PercentChangeThresholdStrategy (class in pypore.strategies.percent_change_threshold_strategy) periodic_call() (pyporegui.my_threads.AnalyzeDataThread method) plot_data() (pyporegui.widgets.event_finding_tab.EventFindingTab method) plot_debug() (pyporegui.widgets.event_viewing_tab.EventViewingTab method) plot_single_event() (pyporegui.widgets.event_viewing_tab.EventViewingTab method) plot_single_events() (pyporegui.widgets.event_viewing_tab.EventViewingTab method) PlotThread (class in pyporegui.my_threads) PlotToolBar (class in pyporegui.widgets.plot_tool_bar) points() (pyporegui.graphicsItems.scatter_plot_item.ScatterPlotItem method) points_per_channel_total (pypore.i_o.abstract_reader.AbstractReader attribute) pre_adc_gain (pypore.i_o.chimera_reader.ChimeraReader attribute) prepare_data_file() (in module pypore.data_file_opener) previous_clicked() (pyporegui.widgets.event_viewing_tab.EventViewingTab method) pypore (module) pypore.data_file_opener (module) pypore.event_finder (module) pypore.file_converter (module) pypore.filetypes (module) pypore.filetypes.data_file (module) pypore.filetypes.event_database (module) pypore.i_o (module) pypore.i_o.abstract_reader (module) pypore.i_o.chimera_reader (module) pypore.i_o.data_file_reader (module) pypore.sampledata (module)

pypore.sampledata.creator (module) pypore.strategies (module) pypore.strategies.absolute_change_threshold_strategy (module) pypore.strategies.adaptive_baseline_strategy (module) pypore.strategies.baseline_strategy (module) pypore.strategies.fixed_baseline_strategy (module) pypore.strategies.noise_based_threshold_strategy (module) pypore.strategies.percent_change_threshold_strategy (module) pypore.strategies.threshold_strategy (module) pypore.version (module) pyporegui (module) pyporegui.file_items (module) pyporegui.graphicsItems (module) pyporegui.graphicsItems.histogram_item (module) pyporegui.graphicsItems.my_plot_item (module) pyporegui.graphicsItems.path_item (module) pyporegui.graphicsItems.scatter_plot_item (module) pyporegui.graphicsItems.spot_item (module) pyporegui.gui (module) pyporegui.my_threads (module) pyporegui.version (module) pyporegui.widgets (module) pyporegui.widgets.base_tabs (module) pyporegui.widgets.event_analysis_plot_widget (module) pyporegui.widgets.event_analysis_tab (module) pyporegui.widgets.event_finding_tab (module) pyporegui.widgets.event_viewing_tab (module) pyporegui.widgets.file_viewer_tab (module) pyporegui.widgets.plot_tool_bar (module)

R

readyForEvents (pyporegui.my_threads.AnalyzeDataThread attribute) remove_event() (pypore.filetypes.event_database.EventDatabase method) remove_events() (pypore.filetypes.event_database.EventDatabase method) remove_filter() (pyporegui.widgets.event_analysis_plot_widget.EventAnalysisPlotWidget method)

remove_filter_clicked() (pyporegui.widgets.event_analysis_tab.EventAnalysisTab method) remove_item_at() (pyporegui.graphicsItems.histogram_item.HistogramItem method) run() (pyporegui.my_threads.AnalyzeDataThread method) (pyporegui.my_threads.PlotThread method)

S

sample_rate (pypore.i_o.abstract_reader.AbstractReader attribute) ScatterPlotItem (class in pyporegui.graphicsItems.scatter_plot_item) set_on_status_update_callback() (pyporegui.widgets.base_tabs.BaseQSplitter method) set_process_events_callback() (pyporegui.widgets.base_tabs.BaseQSplitter method) set_status() (pyporegui.gui.MyMainWindow method)

specs_file (pypore.i_o.chimera_reader.ChimeraReader attribute) SpotItem (class in pyporegui.graphicsItems.spot_item) start() (in module pyporegui) (in module pyporegui.gui) start_std_dev (pypore.strategies.noise_based_threshold_strategy.NoiseBasedThresholdStrategy attribute) staticMetaObject (pyporegui.graphicsItems.histogram_item.HistogramItem attribute) (pyporegui.graphicsItems.my_plot_item.MyPlotItem attribute) (pyporegui.graphicsItems.scatter_plot_item.ScatterPlotItem attribute) (pyporegui.gui.MyMainWindow attribute) (pyporegui.my_threads.AnalyzeDataThread attribute) (pyporegui.my_threads.PlotThread attribute) (pyporegui.widgets.base_tabs.BaseQSplitter attribute) (pyporegui.widgets.base_tabs.BaseQSplitterDataFile attribute) (pyporegui.widgets.event_analysis_plot_widget.EventAnalysisPlotWidget attribute) (pyporegui.widgets.event_analysis_tab.EventAnalysisTab attribute) (pyporegui.widgets.event_finding_tab.EventFindingTab attribute) (pyporegui.widgets.event_viewing_tab.EventViewingTab attribute) (pyporegui.widgets.file_viewer_tab.FileViewerTab attribute) (pyporegui.widgets.plot_tool_bar.PlotToolBar attribute)

T

threshold_strategy (pypore.event_finder.Parameters attribute) ThresholdStrategy (class in pypore.strategies.threshold_strategy)

tia_gain (pypore.i_o.chimera_reader.ChimeraReader attribute)

U

update_gui() (pyporegui.my_threads.AnalyzeDataThread method)

V

variance (pypore.strategies.baseline_strategy.BaselineStrategy attribute) variance_baseline (pypore.strategies.adaptive_baseline_strategy.AdaptiveBaselineStrategy attribute)

variance_filter_parameter (pypore.strategies.adaptive_baseline_strategy.AdaptiveBaselineStrategy attribute)