Index

Symbols

--arrows moseq2-viz-plot-transition-graph command line option --cmap moseq2-viz-make-crowd-movies command line option --colors moseq2-viz-plot-scalar-summary command line option moseq2-viz-plot-stats command line option --count moseq2-viz-make-crowd-movies command line option moseq2-viz-plot-stats command line option moseq2-viz-plot-transition-graph command line option --ctrl-group moseq2-viz-plot-stats command line option --edge-scaling moseq2-viz-plot-transition-graph command line option --edge-threshold moseq2-viz-plot-transition-graph command line option --exact moseq2-viz-add-group command line option --exp-group moseq2-viz-plot-stats command line option --ext moseq2-viz-get-best-model command line option --figsize moseq2-viz-plot-stats command line option --fps moseq2-viz-get-best-model command line option --frame-path moseq2-viz-make-crowd-movies command line option --gaussfilter-space moseq2-viz-make-crowd-movies command line option --group moseq2-viz-add-group command line option moseq2-viz-plot-stats command line option moseq2-viz-plot-transition-graph command line option --input-dir moseq2-viz-copy-h5-metadata-to-yaml command line option --keep-orphans moseq2-viz-plot-transition-graph command line option --key moseq2-viz-add-group command line option --layout moseq2-viz-plot-transition-graph command line option --legacy-jitter-fix moseq2-viz-make-crowd-movies command line option --lowercase moseq2-viz-add-group command line option --max-dur moseq2-viz-make-crowd-movies command line option --max-examples moseq2-viz-make-crowd-movies command line option --max-height moseq2-viz-make-crowd-movies command line option --max-syllable moseq2-viz-make-crowd-movies command line option moseq2-viz-plot-stats command line option moseq2-viz-plot-transition-graph command line option --medfilter-space moseq2-viz-make-crowd-movies command line option --min-dur moseq2-viz-make-crowd-movies command line option --min-height moseq2-viz-make-crowd-movies command line option --negative moseq2-viz-add-group command line option --node-scaling moseq2-viz-plot-transition-graph command line option --normalize moseq2-viz-plot-group-position-heatmaps command line option moseq2-viz-plot-transition-graph command line option moseq2-viz-plot-verbose-position-heatmaps command line option --objective moseq2-viz-get-best-model command line option --ordering moseq2-viz-plot-stats command line option

--orphan-weight moseq2-viz-plot-transition-graph command line option --output-dir moseq2-viz-make-crowd-movies command line option --output-file moseq2-viz-plot-group-position-heatmaps command line option moseq2-viz-plot-scalar-summary command line option moseq2-viz-plot-stats command line option moseq2-viz-plot-transition-graph command line option moseq2-viz-plot-verbose-position-heatmaps command line option --pad moseq2-viz-make-crowd-movies command line option --plot-all moseq2-viz-get-best-model command line option --processes moseq2-viz-make-crowd-movies command line option --progress-bar moseq2-viz-make-crowd-movies command line option --raw-size moseq2-viz-make-crowd-movies command line option --scale moseq2-viz-make-crowd-movies command line option --scale-node-by-usage moseq2-viz-plot-transition-graph command line option --seed moseq2-viz-make-crowd-movies command line option --separate-by moseq2-viz-make-crowd-movies command line option --session-names moseq2-viz-make-crowd-movies command line option --sort moseq2-viz-make-crowd-movies command line option moseq2-viz-plot-stats command line option moseq2-viz-plot-transition-graph command line option --specific-syllable moseq2-viz-make-crowd-movies command line option --stat moseq2-viz-plot-stats command line option --usage-threshold moseq2-viz-plot-transition-graph command line option --value moseq2-viz-add-group command line option --version moseq2-viz command line option --width-per-group moseq2-viz-plot-transition-graph command line option -c moseq2-viz-plot-scalar-summary command line option moseq2-viz-plot-stats command line option -e moseq2-viz-add-group command line option -g moseq2-viz-add-group command line option moseq2-viz-plot-stats command line option moseq2-viz-plot-transition-graph command line option -i moseq2-viz-copy-h5-metadata-to-yaml command line option -k moseq2-viz-add-group command line option moseq2-viz-plot-transition-graph command line option -m moseq2-viz-make-crowd-movies command line option -n moseq2-viz-add-group command line option -o moseq2-viz-make-crowd-movies command line option moseq2-viz-plot-stats command line option -p moseq2-viz-make-crowd-movies command line option -s moseq2-viz-make-crowd-movies command line option -v moseq2-viz-add-group command line option

A

add_duration_column() (in module moseq2_viz.model.util) add_group() (in module moseq2_viz.gui)

add_group_wrapper() (in module moseq2_viz.helpers.wrappers) assert_model_and_index_uuids_match() (in module moseq2_viz.util)

B

bootstrap_group_means() (in module moseq2_viz.model.stat)

bootstrap_me() (in module moseq2_viz.model.stat)

C

camel_to_snake() (in module moseq2_viz.util) check_video_parameters() (in module moseq2_viz.io.video) classifier_fingerprint() (in module moseq2_viz.model.fingerprint_classifier) clean_dict() (in module moseq2_viz.util) clean_frames() (in module moseq2_viz.viz) compute_all_pdf_data() (in module moseq2_viz.scalars.util) compute_and_graph_grouped_TMs() (in module moseq2_viz.model.trans_graph) compute_behavioral_statistics() (in module moseq2_viz.model.util) compute_mean_syll_scalar() (in module moseq2_viz.scalars.util) compute_mouse_dist_to_center() (in module moseq2_viz.scalars.util) compute_pvalues_for_group_pairs() (in module moseq2_viz.model.stat)

compute_syllable_explained_variance() (in module moseq2_viz.model.util) compute_syllable_onset() (in module moseq2_viz.model.util) compute_syllable_position_heatmaps() (in module moseq2_viz.scalars.util) convert_ebunch_to_graph() (in module moseq2_viz.model.trans_graph) convert_legacy_scalars() (in module moseq2_viz.scalars.util) convert_pxs_to_mm() (in module moseq2_viz.scalars.util) convert_transition_matrix_to_ebunch() (in module moseq2_viz.model.trans_graph) copy_h5_metadata_to_yaml_wrapper() (in module moseq2_viz.helpers.wrappers) CP_PATH moseq2-viz-get-best-model command line option create_fingerprint_dataframe() (in module moseq2_viz.model.fingerprint_classifier)

D

draw_graph() (in module moseq2_viz.model.trans_graph)

dunns_z_test_permute_within_group_pairs() (in module moseq2_viz.model.stat)

E

entropy() (in module moseq2_viz.info.util)

entropy_rate() (in module moseq2_viz.info.util)

G

generate_empty_feature_dict() (in module moseq2_viz.scalars.util) get_behavioral_distance() (in module moseq2_viz.model.dist) get_behavioral_distance_ar() (in module moseq2_viz.model.dist) get_best_fit() (in module moseq2_viz.model.util) get_best_fit_model() (in module moseq2_viz.gui) get_best_fit_model_wrapper() (in module moseq2_viz.helpers.wrappers) get_group_trans_mats() (in module moseq2_viz.model.trans_graph) get_groups_command() (in module moseq2_viz.gui) get_index_hits() (in module moseq2_viz.util) get_init_points() (in module moseq2_viz.model.dist) get_metadata_path() (in module moseq2_viz.util) get_mouse_syllable_slices() (in module moseq2_viz.model.util) get_normalized_syllable_usages() (in module moseq2_viz.model.util) get_pos() (in module moseq2_viz.model.trans_graph) get_scalar_map() (in module moseq2_viz.scalars.util)

get_scalar_triggered_average() (in module moseq2_viz.scalars.util) get_session_mean_df() (in module moseq2_viz.model.stat) get_sig_syllables() (in module moseq2_viz.model.stat) get_sorted_index() (in module moseq2_viz.util) get_syllable_pdfs() (in module moseq2_viz.scalars.util) get_syllable_slices() (in module moseq2_viz.model.util) get_syllable_statistics() (in module moseq2_viz.model.util) get_syllable_usages() (in module moseq2_viz.model.util) get_tie_correction() (in module moseq2_viz.model.stat) get_timestamps_from_h5() (in module moseq2_viz.util) get_trans_graph_groups() (in module moseq2_viz.model.trans_graph) get_transition_matrix() (in module moseq2_viz.model.trans_graph) get_transitions() (in module moseq2_viz.model.trans_graph) get_Xy_values() (in module moseq2_viz.model.util) graph_transition_matrix() (in module moseq2_viz.model.trans_graph)

H

h5_filepath_from_sorted() (in module moseq2_viz.util)

h5_to_dict() (in module moseq2_viz.util)

I

INDEX_FILE moseq2-viz-add-group command line option moseq2-viz-make-crowd-movies command line option moseq2-viz-plot-group-position-heatmaps command line option moseq2-viz-plot-scalar-summary command line option moseq2-viz-plot-stats command line option moseq2-viz-plot-transition-graph command line option moseq2-viz-plot-verbose-position-heatmaps command line option

init_wrapper_function() (in module moseq2_viz.helpers.wrappers) is_legacy() (in module moseq2_viz.scalars.util)

L

labels_to_changepoints() (in module moseq2_viz.model.util)

load_changepoint_distribution() (in module moseq2_viz.util) load_timestamps() (in module moseq2_viz.util)

M

make_crowd_matrix() (in module moseq2_viz.viz) make_crowd_movies_wrapper() (in module moseq2_viz.helpers.wrappers) make_difference_graphs() (in module moseq2_viz.model.trans_graph) make_separate_crowd_movies() (in module moseq2_viz.model.util) make_transition_graphs() (in module moseq2_viz.model.trans_graph) mann_whitney() (in module moseq2_viz.model.stat) merge_models() (in module moseq2_viz.model.util) MODEL_DIR moseq2-viz-get-best-model command line option MODEL_FIT moseq2-viz-plot-stats command line option moseq2-viz-plot-transition-graph command line option MODEL_PATH moseq2-viz-make-crowd-movies command line option module moseq2_viz.gui moseq2_viz.helpers.wrappers moseq2_viz.info.util moseq2_viz.io.video moseq2_viz.model.dist moseq2_viz.model.embed moseq2_viz.model.fingerprint_classifier moseq2_viz.model.stat moseq2_viz.model.trans_graph moseq2_viz.model.util moseq2_viz.scalars.util moseq2_viz.util moseq2_viz.viz moseq2-viz command line option --version moseq2-viz-add-group command line option --exact --group --key --lowercase --negative --value -e -g -k -n -v INDEX_FILE moseq2-viz-copy-h5-metadata-to-yaml command line option --input-dir -i moseq2-viz-get-best-model command line option --ext --fps --objective --plot-all CP_PATH MODEL_DIR OUTPUT_FILE moseq2-viz-make-crowd-movies command line option --cmap --count --frame-path --gaussfilter-space --legacy-jitter-fix --max-dur --max-examples --max-height --max-syllable --medfilter-space --min-dur --min-height --output-dir --pad --processes --progress-bar --raw-size --scale --seed --separate-by --session-names --sort --specific-syllable -m -o -p -s INDEX_FILE MODEL_PATH

moseq2-viz-plot-group-position-heatmaps command line option --normalize --output-file INDEX_FILE moseq2-viz-plot-scalar-summary command line option --colors --output-file -c INDEX_FILE moseq2-viz-plot-stats command line option --colors --count --ctrl-group --exp-group --figsize --group --max-syllable --ordering --output-file --sort --stat -c -g -o INDEX_FILE MODEL_FIT moseq2-viz-plot-transition-graph command line option --arrows --count --edge-scaling --edge-threshold --group --keep-orphans --layout --max-syllable --node-scaling --normalize --orphan-weight --output-file --scale-node-by-usage --sort --usage-threshold --width-per-group -g -k INDEX_FILE MODEL_FIT moseq2-viz-plot-verbose-position-heatmaps command line option --normalize --output-file INDEX_FILE moseq2_viz.gui module moseq2_viz.helpers.wrappers module moseq2_viz.info.util module moseq2_viz.io.video module moseq2_viz.model.dist module moseq2_viz.model.embed module moseq2_viz.model.fingerprint_classifier module moseq2_viz.model.stat module moseq2_viz.model.trans_graph module moseq2_viz.model.util module moseq2_viz.scalars.util module moseq2_viz.util module moseq2_viz.viz module

N

n_gram_transition_matrix() (in module moseq2_viz.model.trans_graph) nanzscore() (in module moseq2_viz.scalars.util)

normalize_pcs() (in module moseq2_viz.model.util) normalize_transition_matrix() (in module moseq2_viz.model.trans_graph) normalize_usages() (in module moseq2_viz.model.util)

O

OUTPUT_FILE moseq2-viz-get-best-model command line option

P

parse_batch_modeling() (in module moseq2_viz.model.util) parse_index() (in module moseq2_viz.util) parse_model_results() (in module moseq2_viz.model.util) plot_cm() (in module moseq2_viz.model.fingerprint_classifier) plot_cp_comparison() (in module moseq2_viz.viz) plot_embedding() (in module moseq2_viz.model.embed) plot_H_stat_significance() (in module moseq2_viz.model.stat) plot_mean_group_heatmap() (in module moseq2_viz.viz) plot_mean_group_position_pdf_wrapper() (in module moseq2_viz.helpers.wrappers)

plot_scalar_summary_wrapper() (in module moseq2_viz.helpers.wrappers) plot_syll_stats_with_sem() (in module moseq2_viz.viz) plot_syllable_stat_wrapper() (in module moseq2_viz.helpers.wrappers) plot_transition_graph_wrapper() (in module moseq2_viz.helpers.wrappers) plot_verbose_heatmap() (in module moseq2_viz.viz) plot_verbose_pdfs_wrapper() (in module moseq2_viz.helpers.wrappers) plotting_fingerprint() (in module moseq2_viz.model.fingerprint_classifier) position_plot() (in module moseq2_viz.viz) prepare_model_dataframe() (in module moseq2_viz.model.util) process_scalars() (in module moseq2_viz.scalars.util)

R

read_yaml() (in module moseq2_viz.util) recursive_find_h5s() (in module moseq2_viz.util) reformat_dtw_distances() (in module moseq2_viz.model.dist) relabel_by_usage() (in module moseq2_viz.model.util) retrieve_pcs_from_slices() (in module moseq2_viz.model.util) robust_max() (in module moseq2_viz.model.fingerprint_classifier)

robust_min() (in module moseq2_viz.model.fingerprint_classifier) run_2d_embedding() (in module moseq2_viz.model.embed) run_2d_scalar_embedding() (in module moseq2_viz.model.embed) run_kruskal() (in module moseq2_viz.model.stat) run_manual_KW_test() (in module moseq2_viz.model.stat) run_pairwise_stats() (in module moseq2_viz.model.stat)

S

save_fig() (in module moseq2_viz.viz) scalar_plot() (in module moseq2_viz.viz) scalars_to_dataframe() (in module moseq2_viz.scalars.util) simulate_ar_trajectory() (in module moseq2_viz.model.util) sort_batch_results() (in module moseq2_viz.model.util) sort_syllables_by_stat() (in module moseq2_viz.model.util) sort_syllables_by_stat_difference() (in module moseq2_viz.model.util)

star() (in module moseq2_viz.util) star_valmap() (in module moseq2_viz.scalars.util) strided_app() (in module moseq2_viz.util) syll_duration() (in module moseq2_viz.model.util) syll_id() (in module moseq2_viz.model.util) syll_onset() (in module moseq2_viz.model.util) syllable_slices_from_dict() (in module moseq2_viz.model.util)

T

transition_entropy() (in module moseq2_viz.info.util)

ttest() (in module moseq2_viz.model.stat)

W

whiten_pcs() (in module moseq2_viz.model.util) write_crowd_movie_info_file() (in module moseq2_viz.io.video)

write_crowd_movies() (in module moseq2_viz.io.video) write_frames_preview() (in module moseq2_viz.io.video)

Z

ztest() (in module moseq2_viz.model.stat)

ztest_vect() (in module moseq2_viz.model.stat)