`deepcinac.gui.cinac_gui`¶

Module Contents¶

Classes¶

`DataAndParam`
`MySessionButton`	Button widget.
`RawFormatOptionModule`	Frame widget which may contain other widgets and can have a 3D border.
`ChoiceRawFormatFrame`	Frame widget which may contain other widgets and can have a 3D border.
`ChoiceFormatFrame`	Frame widget which may contain other widgets and can have a 3D border.
`ChoiceNwbFormatFrame`	Frame widget which may contain other widgets and can have a 3D border.
`ChoiceCinacFormatFrame`	Frame widget which may contain other widgets and can have a 3D border.
`ManualAction`
`RemoveOnsetAction`
`RemovePeakAction`
`AgreePeakAction`
`DontAgreePeakAction`
`DontAgreeOnsetAction`
`AgreeOnsetAction`
`AddOnsetAction`
`AddThemAllAction`
`AddSegmentToSaveAction`
`RemoveSegmentToSaveAction`
`AddPeakAction`
`AddDoubtfulFramesAction`
`RemoveDoubtfulFramesAction`
`AddMvtFramesAction`
`RemoveMvtFramesAction`
`MyCanvas`	The canvas the figure renders into. Calls the draw and print fig
`ManualOnsetFrame`	Frame widget which may contain other widgets and can have a 3D border.

Functions¶

`event_lambda`(f, args, *kwds)
`raise_above_all`(window)	Take a window as argument (like tk.root()) and put it on front of all other
`set_menu_from_list`(keys, menu_tk, menu_variable, favorite_key)
`load_menu_from_file`(file_name, menu_tk, menu_variable, keyword_for_key=None)	Take a tkinter OptionMenu instance and load it using the fields of a matlab or npy file.
`load_data_from_npy_or_mat_file`(file_name, data_descr, attr_name=None)	Load data from a numpy or matlab file (.npz, .npz or .mat)
`display_loading_window`(message, fct_to_run, args_for_fct)
`get_file_name_and_path`(path_file)
`do_traces_smoothing`(traces)
`print_save`(text, file, to_write, no_print=False)
`merge_close_values`(raster, raster_to_fill, cell, merging_threshold)	param raster Raster is a 2d binary array, lines represents cells, columns binary values
`fusion_gui_selection`(path_data)
`launch_cinac_gui`()

deepcinac.gui.cinac_gui.NWB_PACKAGE_AVAILABLE = True¶

deepcinac.gui.cinac_gui.NWB_PACKAGE_AVAILABLE = False¶

deepcinac.gui.cinac_gui.event_lambda(f, *args, **kwds)¶

class deepcinac.gui.cinac_gui.DataAndParam(path_data=None)¶

class deepcinac.gui.cinac_gui.MySessionButton(master)¶

Bases: tkinter.Button

Button widget.

deepcinac.gui.cinac_gui.raise_above_all(window)¶

Take a window as argument (like tk.root()) and put it on front of all other :param window:

Returns:

deepcinac.gui.cinac_gui.set_menu_from_list(keys, menu_tk, menu_variable, favorite_key)¶

deepcinac.gui.cinac_gui.load_menu_from_file(file_name, menu_tk, menu_variable, keyword_for_key=None)¶

Take a tkinter OptionMenu instance and load it using the fields of a matlab or npy file. :param file_name: string :param menu_tk: OptionMenu instance :param menu_variable: Variable from the menu :param keyword_for_key: string, keyword, if found in one of the field, this field will be selected by default :param in the menu:

Returns: a list of string representing the options of the menu

class deepcinac.gui.cinac_gui.RawFormatOptionModule(button_text, label_text, with_file_dialog, file_dialog_filetypes, file_dialog_title, root, mandatory, with_only_label=False, with_check_box=False, label_check_box=None, check_box_active_by_default=True, active_label_text=None, with_option_menu=False, with_spin_box=False, menu_keyword_for_key=None, fct_to_call_at_update=None, last_path_open=None, height_button=3, command_fct=None, default_path=None, master=None)¶

Bases: Tkinter.Frame

Frame widget which may contain other widgets and can have a 3D border.

check_box_action(self)¶

button_action(self)¶

activate_only_label(self, enabling_button=False)¶

activate_spin_box(self)¶

set_file_value(self, with_file_dialog=True, file_name=None)¶

deactivate(self, disabling_button=False)¶: Deactivate the module Returns:

add_exclusive_modules(self, exclusive_modules)¶

Means that only one among self and exclusive_modules can be activated at once. When one is activated, the other are deactivated :param exclusive_modules: list of instance of RawFormatOptionModule

Returns:

get_config_as_dict(self)¶: From the data gui in widgets, build a dictionnary used to save the parameters Returns:

set_config_from_dict(self, config_dict)¶: From the data gui in widgets, build a dictionnary used to save the parameters Returns:

class deepcinac.gui.cinac_gui.ChoiceRawFormatFrame(default_path=None, master=None)¶

Bases: Tkinter.Frame

Frame widget which may contain other widgets and can have a 3D border.

__configure(self, event)¶

create_buttons(self)¶: Create buttons Returns:

display_only_raw_traces_check_box_action(self)¶

launch_exploratory_gui(self)¶: Returns:

load_last_used_config(self)¶

load_config(self)¶: Returns: None

save_config(self, file_name=None)¶

get_config_as_dict(self)¶: From the data gui in widgets, build a dictionnary used to save the paramters Returns:

set_config_from_dict(self, config_dict)¶: From the data gui in widgets, build a dictionnary used to save the parameters Returns:

update_launch_gui_button(self)¶: Update the launch gui button depending on the file being selected Returns:

deepcinac.gui.cinac_gui.load_data_from_npy_or_mat_file(file_name, data_descr, attr_name=None)¶

Load data from a numpy or matlab file (.npz, .npz or .mat) :param file_name: :param data_descr: string used to display error message if the file is not in the good format :param attr_name:

Returns:

class deepcinac.gui.cinac_gui.ChoiceFormatFrame(default_path=None, master=None)¶

Bases: Tkinter.Frame

Frame widget which may contain other widgets and can have a 3D border.

create_buttons(self)¶

open_option_format_frame(self, format_str)¶

deepcinac.gui.cinac_gui.display_loading_window(message, fct_to_run, args_for_fct)¶

class deepcinac.gui.cinac_gui.ChoiceNwbFormatFrame(default_path=None, master=None)¶

Bases: Tkinter.Frame

Frame widget which may contain other widgets and can have a 3D border.

neuronal_data_check_box_action(self)¶

activate_all_buttons(self)¶

deactivate_all_buttons(self)¶

__configure(self, event)¶

select_nwb_file(self)¶: Open a file dialog to select to cinac file to open and then change the GUI accordingly Returns:

_get_segmentations(self)¶: Returns: a dict that for each step till plane_segmentation represents the different option. First dict will have as keys the name of the modules, then for each modules the value will be a new dict with keys the ImageSegmentation names and then the value will be a list representing the segmentation plane

get_pixel_mask(self, segmentation_info)¶

Return pixel_mask which is a list of list of pair of integers representing the pixels coordinate (x, y) for each cell. the list length is the same as the number of cells. :param segmentation_info: a list of 3 elements: first one being the name of the module, then the name :param of image_segmentation and then the name of the segmentation plane.:

Returns:

_get_roi_response_serie_data(self, keys)¶

Parameters: keys – lsit of string allowing to get the roi repsonse series wanted

Returns:

_get_roi_response_series(self, keywords_to_exclude=None)¶

param: keywords_to_exclude: if not None, list of str, if one of neuronal data has this keyword, then we don’t add it to the choices

Returns: a list or dict of objects representing all roi response series (rrs) names rrs could represents raw traces, or binary raster, and its link to a given segmentation. The results returned should allow to identify the segmentation associated. Object could be strings, or a list of strings, that identify a rrs and give information how to get there.

launch_exploratory_gui(self)¶: Returns:

class deepcinac.gui.cinac_gui.ChoiceCinacFormatFrame(default_path=None, master=None)¶

Bases: Tkinter.Frame

Frame widget which may contain other widgets and can have a 3D border.

launch_exploratory_gui_for_a_segment(self, segment_selected)¶

Launch the exploratory GUI for a given segment :param segment_selected: tuple of 3 int representing the cell, first_frame and last_frame

Returns:

launch_exploratory_gui(self)¶: Returns:

select_ci_movie(self)¶: Open a file dialog to select to calcium imagine movie Returns:

activate_all_buttons(self)¶

deactivate_all_buttons(self)¶

select_cinac_file(self)¶: Open a file dialog to select to cinac file to open and then change the GUI accordingly Returns:

__configure(self, event)¶

class deepcinac.gui.cinac_gui.ManualAction(session_frame, neuron, is_saved, x_limits=None, y_limits=None)¶

undo(self)¶

redo(self)¶

class deepcinac.gui.cinac_gui.RemoveOnsetAction(removed_times, **kwargs)¶

Bases: deepcinac.gui.cinac_gui.ManualAction

undo(self)¶

redo(self)¶

class deepcinac.gui.cinac_gui.RemovePeakAction(removed_times, amplitudes, removed_onset_action=None, **kwargs)¶

Bases: deepcinac.gui.cinac_gui.ManualAction

undo(self)¶

redo(self)¶

class deepcinac.gui.cinac_gui.AgreePeakAction(agreed_peaks_index, agree_onset_action, agreed_peaks_values, peaks_added, **kwargs)¶

Bases: deepcinac.gui.cinac_gui.ManualAction

undo(self)¶

redo(self)¶

class deepcinac.gui.cinac_gui.DontAgreePeakAction(not_agreed_peaks_index, dont_agree_onset_action, not_agreed_peaks_values, **kwargs)¶

Bases: deepcinac.gui.cinac_gui.ManualAction

undo(self)¶

redo(self)¶

class deepcinac.gui.cinac_gui.DontAgreeOnsetAction(not_agreed_onsets_index, not_agreed_onsets_values, **kwargs)¶

Bases: deepcinac.gui.cinac_gui.ManualAction

undo(self)¶

redo(self)¶

class deepcinac.gui.cinac_gui.AgreeOnsetAction(agreed_onsets_index, agreed_onsets_values, onsets_added, **kwargs)¶

Bases: deepcinac.gui.cinac_gui.ManualAction

undo(self)¶

redo(self)¶

class deepcinac.gui.cinac_gui.AddOnsetAction(added_time, add_peak_action=None, **kwargs)¶

Bases: deepcinac.gui.cinac_gui.ManualAction

undo(self)¶

redo(self)¶

class deepcinac.gui.cinac_gui.AddThemAllAction(first_frame, last_frame, old_peak_values, new_peak_values, old_onset_values, new_onset_values, **kwargs)¶

Bases: deepcinac.gui.cinac_gui.ManualAction

undo(self)¶

redo(self)¶

class deepcinac.gui.cinac_gui.AddSegmentToSaveAction(segment_list, segment_added, **kwargs)¶

Bases: deepcinac.gui.cinac_gui.ManualAction

undo(self)¶

redo(self)¶

class deepcinac.gui.cinac_gui.RemoveSegmentToSaveAction(segment_list, segment_added, index_to_remove, **kwargs)¶

Bases: deepcinac.gui.cinac_gui.ManualAction

undo(self)¶

redo(self)¶

class deepcinac.gui.cinac_gui.AddPeakAction(added_time, amplitude, **kwargs)¶

Bases: deepcinac.gui.cinac_gui.ManualAction

undo(self)¶

redo(self)¶

class deepcinac.gui.cinac_gui.AddDoubtfulFramesAction(x_from, x_to, backup_values, **kwargs)¶

Bases: deepcinac.gui.cinac_gui.ManualAction

undo(self)¶

redo(self)¶

class deepcinac.gui.cinac_gui.RemoveDoubtfulFramesAction(removed_times, **kwargs)¶

Bases: deepcinac.gui.cinac_gui.ManualAction

undo(self)¶

redo(self)¶

class deepcinac.gui.cinac_gui.AddMvtFramesAction(x_from, x_to, backup_values, **kwargs)¶

Bases: deepcinac.gui.cinac_gui.ManualAction

undo(self)¶

redo(self)¶

class deepcinac.gui.cinac_gui.RemoveMvtFramesAction(removed_times, **kwargs)¶

Bases: deepcinac.gui.cinac_gui.ManualAction

undo(self)¶

redo(self)¶

deepcinac.gui.cinac_gui.get_file_name_and_path(path_file)¶

deepcinac.gui.cinac_gui.do_traces_smoothing(traces)¶

class deepcinac.gui.cinac_gui.MyCanvas(figure, parent_frame, manual_onset_frame)¶

Bases: matplotlib.backends.backend_tkagg.FigureCanvasTkAgg

The canvas the figure renders into. Calls the draw and print fig methods, creates the renderers, etc…

figure¶

A high-level Figure instance

Type: matplotlib.figure.Figure

button_press_event(self, event, **args)¶

Backend derived classes should call this function on any mouse button press. x,y are the canvas coords: 0,0 is lower, left. button and key are as defined in MouseEvent.

This method will be call all functions connected to the ‘button_press_event’ with a MouseEvent instance.

class deepcinac.gui.cinac_gui.ManualOnsetFrame(data_and_param, default_path=None, segment_mode=False, parent=None, title=None)¶

Bases: Tkinter.Frame

Frame widget which may contain other widgets and can have a 3D border.

RAW_TRACE = Cell¶

RAW_TRACE_WITHOUT_OVERLAP = Cell no over¶

NEUROPIL_TRACE = Neuropil (Np)¶

RAW_M_NEUROPIL_TRACE = Cell no over - Np¶

neuron_entry_change(self, *args)¶

switch_michou(self)¶

_build_traces(self)¶: Build different fluorescence signal for each cell. Fill the self.traces_dict, each key is a trace description (str), and each value is a 2d array (n cells * n frames) Returns:

switch_movie_mode(self, from_movie_button=True)¶

switch_mvt_display(self)¶

switch_magnifier(self)¶

set_inter_neuron(self)¶

remove_cell(self)¶

clear_and_update_center_segment_entry_widget(self)¶

clear_and_update_entry_neuron_widget(self)¶

clear_and_update_entry_cell_type_widget(self)¶

update_uncertain_prediction_values(self, event=None)¶: Update the widget that contain the limit of the prediction we want to look at :param event: :return:

center_segment_button_action(self, event=None)¶

cell_type_action(self, event=None)¶

Action called when the entry widget for cell type is called :param event:

Returns:

go_to_neuron_button_action(self, event=None)¶

key_press_action(self, event)¶

key_release_action(self, event)¶

detect_onset_associated_to_peak(self, peak_times)¶: Return an array with the onset times (from trace time) associated to the peak_times. We look before each peak_time (1sec before), for current_neurons :param peak_times: :return:

update_onset_times(self)¶

numbers_of_onset(self)¶

numbers_of_peak(self)¶

numbers_of_onset_to_agree(self)¶

numbers_of_peak_to_agree(self)¶

swith_all_click_actions(self, initiator)¶

center_segment_swith_mode(self, from_center_segment_button=True)¶

switch_prediction_improvement_mode(self)¶: Allows to display a signal that might change a prediction according for ex to neuropil variation or transient correlation. Mode only active if predictions are available Returns:

compute_prediction_improvement_for_cell(self, cell)¶

COmpute prediction improvement only if predictions available for this cell :param cell:

Returns:

add_onset_switch_mode(self, with_peak=False, from_add_onset_button=True)¶

Parameters

with_peak – if True, then a peak after onset will be added automatically
from_add_onset_button –

Returns:

remove_onset_switch_mode(self, from_remove_onset_button=True)¶

add_doubtful_frames_switch_mode(self, from_add_doubtful_frames_button=True)¶

remove_doubtful_frames_switch_mode(self, from_remove_doubtful_frames_button=True)¶

add_mvt_frames_switch_mode(self, from_add_mvt_frames_button=True)¶

remove_mvt_frames_switch_mode(self, from_remove_mvt_frames_button=True)¶

update_transient_prediction_periods_to_check(self)¶

update_predictions_list_box(self, keep_same_selected_index=False)¶

update_segments_to_save_list_box(self, initial_loading=False)¶

segments_to_save_list_box_double_click(self, evt)¶

Called when a double click is done on segments to save list_box. It removes from the list the element that is double clicked :param evt:

Returns:

remove_segment_to_save(self, index_to_remove)¶

change_prediction_transient_to_look_at(self, period)¶: CHange the plot such as the period indicated is displayed :param period: a tuple of len 4: cell, x_left, x_right, pred :return:

predictions_list_box_click(self, evt)¶

segments_to_save_list_box_click(self, evt)¶

predictions_list_box_double_click(self, evt)¶

add_current_segment_to_save_list(self)¶: Add the current view as a segment. The view should have a minimum of 10 frames. The view should not be already added. Returns:

update_contour_for_cell(self, cell)¶

agree_switch_mode(self, from_agree_button=True)¶

dont_agree_switch_mode(self, from_dont_agree_button=True)¶

remove_peak_switch_mode(self, from_remove_peak_button=True)¶

remove_all_switch_mode(self, from_remove_all_button=True)¶

onrelease_map(self, event)¶: Action when a mouse button is released on cell map :param event: :return:

onrelease(self, event)¶: Action when a mouse button is released :param event: :return:

motion(self, event)¶: Action when the mouse is moved :param event: :return:

onclick(self, event)¶: Action when a mouse button is pressed :param event: :return:

remove_onset(self, x_from, x_to)¶

dont_agree_on_fusion(self, x_from, x_to)¶

agree_on_fusion(self, x_from, x_to)¶

remove_all(self, x_from, x_to)¶

remove_peaks_under_threshold(self)¶

remove_peak(self, x_from, x_to)¶

switch_trace_to_be_displayed(self, trace_str)¶

Called when one of the trace checkbox change selection. Allows to change the trace displayed

Returns:

switch_source_profile_mode(self, from_check_box=True, from_key_shortcut=False, from_magnifier=False)¶

activate_movie_zoom(self, from_check_box=True)¶

set_transient_classifier_prediction_for_cell(self, cell)¶

transient_classifier_check_box_action(self)¶

set_cell_type_classifier_prediction_for_cell(self, cell)¶

cell_type_classifier_button_action(self)¶: Method called when pushing cell type classification button Returns:

display_cell_type_predictions(self)¶: Display in the cell type labels the predictions for the current_neuron Returns:

correlation_check_box_action(self, from_std_treshold=False)¶

threshold_check_box_action(self, from_correlation=False)¶

spin_box_pixels_around_cell_update(self)¶

spin_box_transient_classifier_update(self)¶

spin_box_threshold_update(self)¶

spin_box_correlation_update(self)¶

unsaved(self)¶: means a changed has been done, and the actual plot is not saved

update_doubtful_frames_periods(self, cell)¶

update_mvt_frames_periods(self, cell)¶

normalize_traces(self)¶: Normalize the fluorescence signal using z-score and change the value of smooth smooth_traces so there are displayed under the raw smooth_traces Returns:

add_onset(self, at_time)¶

add_peak(self, at_time, amplitude=0)¶

update_last_action(self, new_action, from_redo_action=False)¶: Keep the size of the last_actions up to five actions :param new_action: :return:

add_peak_switch_mode(self, from_add_peak_button=True)¶

Parameters: from_add_peak_button – indicate the user click on the add_peak button, otherwise it means the

function has been called after another button has been clicked :return:

remove_doubtful_frames(self, x_from, x_to)¶

add_doubtful_frames(self, x_from, x_to)¶

remove_mvt_frames(self, x_from, x_to)¶

add_mvt_frames(self, x_from, x_to)¶

validation_before_closing(self)¶

redo_action(self)¶

undo_action(self)¶: Revoke the last action :return:

save_sources_profile_map(self, key_cmap=None)¶

get_square_coord_around_cell(self, cell, x_len_max, y_len_max, square_size)¶

Parameters

cell –
x_len_max – max x value (border of the movie)
y_len_max – max y value (border of the movie)
square_size – number of pixels that compose the border of the square

Returns: Two int representing the minx and miny of the square that will be used to train the classifier

save_segments(self, and_close=False)¶

save_segments_as(self, and_close=False)¶: Open a filedialog to save the data in a .cinac extension (hdf5 format). The data saved correspond to the onset and peak for the cells and frames displayed over the smooth_traces. Returns: None

get_threshold(self)¶

plot_magnifier(self, first_time=False, mouse_x_position=None, mouse_y_position=None)¶: Plot the magnifier :param first_time: if True, means the function is called for the first time, allow sto initialize some variables. :param mouse_x_position: indicate the x position of the mouse cursor :param mouse_y_position: indicate the y position of the mouse cursor :return: None

draw_magnifier_marker(self, mouse_x_position=None, mouse_y_position=None)¶

corr_between_source_and_transient(self, cell, transient, pixels_around=1, redo_computation=False)¶

Parameters

cell – int
transient – (int, int) first_frame and last_frame
pixels_around –
redo_computation – if True, means that even if the correlation has been done before for the peak,

it will be redo (useful if the onset has changed for exemple :return:

compute_source_and_transients_correlation(self, main_cell, redo_computation=False, with_overlapping_cells=True)¶: Compute the source and transient profiles of a given cell. Should be call for each new neuron displayed :param cell: :param redo_computation: if True, means that even if the correlation has been done before for this cell, it will be redo (useful if the onsets or peaks has changed for exemple) :return:

plot_source_transient(self, transient)¶

get_source_profile(self, cell, pixels_around=0, bounds=None, buffer=None, with_full_frame=False)¶

Parameters

cell –
pixels_around –
bounds –
buffer –
with_full_frame – Average the full frame

Returns

get_transient_profile(self, cell, transient, pixels_around=0, bounds=None)¶

get_cell_new_coord_in_source(self, cell, minx, miny)¶

update_plot_magnifier(self, mouse_x_position, mouse_y_position, change_frame_ref)¶

start_playing_movie(self, x_from, x_to)¶

square_coord_around_cell(self, cell, size_square, x_len_max, y_len_max)¶

For a given cell, give the coordinates of the square surrounding the cell.

Parameters

cell –
size_square –
x_len_max –
y_len_max –

Returns

(x_beg, x_end, y_beg, y_end)

animate_movie(self, i)¶

plot_map_img(self, first_time=True, after_movie=False)¶

draw_cell_contour(self)¶

update_plot_map_img(self, after_michou=False, after_movie=False)¶

plot_graph(self, first_time=False)¶

Parameters: first_time –
Returns

current_max_amplitude(self)¶: Ceiling value :return:

move_zoom(self, to_the_left)¶

add_them_all(self)¶: Add all possible onset and peaks based on change of derivative in the smooth trace Returns:

update_plot(self, new_neuron=False, amplitude_zoom_fit=True, new_x_limit=None, new_y_limit=None, changing_face_color=False, new_trace=False, raw_trace_display_action=False)¶

Parameters

new_neuron –
amplitude_zoom_fit –
new_x_limit –
new_y_limit –
changing_face_color –
new_trace – if True, means the trace has changed, and so we want to adapt the y-axis limit
raw_trace_display_action –

Returns:

update_to_agree_label(self)¶

update_after_onset_change(self, new_neuron=- 1, new_x_limit=None, new_y_limit=None)¶: Update the frame if an onset change has been made :param new_neuron: if -1, then the neuron hasn’t changed, neuron might change if undo or redo are done. :return:

select_previous_neuron(self)¶

select_next_neuron(self)¶

go_to_next_cell_with_same_type(self)¶: If cell typeis know, allows to display the next cell from the cell type as the cell actualy displayed Returns:

update_neuron(self, new_neuron, new_x_limit=None, new_y_limit=None, amplitude_zoom_fit=True)¶: Call when the neuron number has changed :return:

deepcinac.gui.cinac_gui.print_save(text, file, to_write, no_print=False)¶

deepcinac.gui.cinac_gui.merge_close_values(raster, raster_to_fill, cell, merging_threshold)¶

Parameters

raster – Raster is a 2d binary array, lines represents cells, columns binary values
cell – which cell to merge
merging_threshold – times separation between two values under which to merge them

Returns

deepcinac.gui.cinac_gui.fusion_gui_selection(path_data)¶

deepcinac.gui.cinac_gui.launch_cinac_gui()¶

deepcinac.gui.cinac_gui¶

Module Contents¶

Classes¶

Functions¶

`deepcinac.gui.cinac_gui`¶