moseq2_app.viz package
Submodules
Viz - Controller Module
Main syllable crowd movie viewing, comparing, and labeling functionality.
- class moseq2_app.viz.controller.CrowdMovieComparison(config_data, index_path, df_path, model_path, syll_info, output_dir, get_pdfs, load_parquet)
Bases:
CrowdMovieCompareWidgets- crowd_movie_preview(syllable, groupby, nexamples)
run the crowd_movie_wrapper function and creates the HTML divs containing the generated crowd movies.
Args: syllable (int or ipywidgets.DropDownMenu): Currently displayed syllable. nexamples (int or ipywidgets.IntSlider): Number of mice to display per crowd movie.
- generate_crowd_movie_divs(grouped_syll_dict)
Generate HTML divs containing crowd movies and syllable metadata tables from the given syllable dict file.
Returns: divs (list of Bokeh.models.Div): Divs of HTML videos and metadata tables. bk_plots (list): list of corresponding position heatmap figures.
- get_mean_group_dict(group_df)
Create a dict object to convert to a displayed table containing syllable scalars.
Args: group_df (pd.DataFrame): DataFrame containing mean syllable scalar data for each session and their groups
- get_pdf_plot(group_syllable_pdf, group_name)
create a bokeh plot with the given PDF heatmap and figure title.
Args: group_syllable_pdf (2D np.ndarray): Mean syllable position PDF heatmap. group_name (str): Name of group for generated syllable pdf
Returns: pdf_fig (bokeh.figure): Create bokeh figure.
- get_selected_session_syllable_info(sel_sessions)
Prepare dict of session-based syllable information to display.
Args: sel_sessions (list): list of selected session names.
- get_session_mean_syllable_info_df()
Populate session-based syllable information dict with usage and scalar information.
- set_default_cm_parameters()
set default parameter for rendering crowd movie parameters.
- class moseq2_app.viz.controller.SyllableLabeler(model_fit, model_path, index_file, config_file, max_sylls, select_median_duration_instances, max_examples, crowd_movie_dir, save_path)
Bases:
SyllableLabelerWidgets- get_crowd_movie_paths(index_path, model_path, config_data, crowd_movie_dir)
Populate the syllable information dict with the respective crowd movie paths.
Args: crowd_movie_dir (str): Path to directory containing all the generated crowd movies
- get_mean_group_dict(group_df)
Create a dict object to convert to a displayed table containing syllable scalars.
Args: group_df (pd.DataFrame): DataFrame containing mean syllable scalar data for each session and their groups
- get_mean_syllable_info()
Populate syllable information dict with usage and scalar information.
- interactive_syllable_labeler(syllables)
create a Bokeh Div object to display the current video path.
Args: syllables (int or ipywidgets.DropDownMenu): Current syllable to label
- set_default_cm_parameters(config_data)
Set default crowd movie generation parameters that may be manually updated.
Args: config_data (dict): Dict of main moseq configuration parameters.
Returns: config_data (dict): updated config parameter dictionary.
- set_group_info_widgets(group_info)
read the syllable information into a pandas DataFrame and display it as a table.
Args: group_info (dict): Dictionary of grouped current syllable information
- write_syll_info(curr_syll=None)
Write current syllable info data to a YAML file.
Viz - View Module
Function that displays a grid of crowd movies and plotted bokeh figures of position heatmaps.
- moseq2_app.viz.view.display_crowd_movies(widget_box, curr_name, desc, divs, bk_figs)
display the crowd movies in jupyter notebook.
Args: divs (list of bokeh.models.Div): list of HTML Div objects containing videos to display
Returns:
Viz - Widgets Module
Widgets module containing classes with components for each of the interactive syllable visualization tools
- class moseq2_app.viz.widgets.CrowdMovieCompareWidgets
Bases:
object- clear_on_click(b=None)
Clear the cell output
Args: b (buttion click)
- on_click_trigger_button(b=None)
Generate crowd movies and displays them when the user clicks the trigger button
Args: b (ipywidgets.Button click event): User clicks “Generate Movies” button
- select_session(event=None)
get the session scalar information.
Args: event (event): User clicks on multiple sessions in the SelectMultiple widget
- show_session_select(change)
change current view to show session selector.
Args: change (event): User switches their DropDownMenu selection
- class moseq2_app.viz.widgets.SyllableLabelerWidgets
Bases:
object- clear_on_click(b=None)
Clear the cell output
Args: b (button click)
- on_next(event=None)
trigger an view update when the user clicks the “Next” button.
Args: event (ipywidgets.ButtonClick): User clicks next button.
- on_prev(event=None)
trigger an view update when the user clicks the “Previous” button.
Args: event (ipywidgets.ButtonClick): User clicks ‘previous’ button.
- on_set(event=None)
save the dict to syllable information file.
Args: event (ipywidgets.ButtonClick): User clicks the ‘Save’ button.