Index

A

add_classification_to_vocals() (vocalpy.modules.list_of_vocals.ListOfVocals method) add_segmentation_masks_to_vocals() (vocalpy.modules.list_of_vocals.ListOfVocals method) add_spectrograms_to_vocals() (vocalpy.modules.list_of_vocals.ListOfVocals method) adjust_normalized_spectrogram() (vocalpy.pipelines.animal.Animal method) (vocalpy.pipelines.guineapig.Guineapig method)

Animal (class in vocalpy.pipelines.animal) apply_morphology() (vocalpy.pipelines.animal.Animal method) (vocalpy.pipelines.guineapig.Guineapig method) area (vocalpy.modules.vocal.Vocal property) avg_freq (vocalpy.modules.vocal.Vocal property) avg_intensity (vocalpy.modules.vocal.Vocal property)

B

bandwidth (vocalpy.modules.vocal.Vocal property) bg_intensity (vocalpy.modules.vocal.Vocal property) bin_number (vocalpy.modules.vocal.Vocal property) bradley_roth() (in module vocalpy.utils.image_processing) build_candidate_mask() (vocalpy.pipelines.animal.Animal method) build_vocal_from_prop() (vocalpy.pipelines.animal.Animal method)

butter_bandpass() (in module vocalpy.utils.signal_processing) butter_bandpass_filter() (in module vocalpy.utils.signal_processing) butter_highpass() (in module vocalpy.utils.signal_processing) butter_highpass_filter() (in module vocalpy.utils.signal_processing) butter_lowpass() (in module vocalpy.utils.signal_processing) butter_lowpass_filter() (in module vocalpy.utils.signal_processing)

C

centroid (vocalpy.modules.vocal.Vocal property) check_if_vocals_are_close() (vocalpy.pipelines.animal.Animal method) (vocalpy.pipelines.guineapig.Guineapig method) (vocalpy.pipelines.mouse.Mouse method) (vocalpy.pipelines.rat.Rat method) classify_vocalizations() (vocalpy.modules.recording.Recording method) (vocalpy.pipelines.animal.Animal method) (vocalpy.pipelines.guineapig.Guineapig method) cnn_mask (vocalpy.modules.vocal.Vocal property) combine_list_of_list_of_vocals() (vocalpy.modules.list_of_vocals.ListOfVocals method) combine_viz() (vocalpy.modules.viz.Viz method) combine_viz_dataframes() (vocalpy.modules.viz.Viz method) combine_vocals() (vocalpy.pipelines.animal.Animal method) compute_multitaper_spectrogram() (in module vocalpy.utils.signal_processing) compute_spectrogram() (in module vocalpy.utils.signal_processing)

connect_vocals() (vocalpy.pipelines.animal.Animal method) contrast_adjustment() (in module vocalpy.utils.image_processing) coords (vocalpy.modules.vocal.Vocal property) create_animal_pipeline() (vocalpy.modules.recording.Recording method) create_dataframe_from_list_of_vocals() (in module vocalpy.utils.misc) create_dataset() (vocalpy.modules.recording.Recording method) create_directory() (in module vocalpy.utils.io) create_group_viz() (vocalpy.modules.viz.Viz method) create_list_of_vocals() (vocalpy.modules.viz.SingleViz method) (vocalpy.pipelines.animal.Animal method) create_logger() (in module vocalpy.utils.misc) create_object_dataframe() (vocalpy.modules.viz.SingleViz method) create_output_directory_structure() (in module vocalpy.utils.io) create_paths() (vocalpy.modules.recording.Recording method) create_user_parameters_yaml() (vocalpy.modules.recording.Recording method) create_viz_for_each_recording() (vocalpy.modules.viz.Viz method)

D

duration (vocalpy.modules.vocal.Vocal property)

E

end (vocalpy.modules.vocal.Vocal property)

end_coord (vocalpy.modules.vocal.Vocal property) estimate_background_intensity() (vocalpy.pipelines.animal.Animal method)

F

filter_band_pass() (in module vocalpy.utils.signal_processing) filter_high_pass() (in module vocalpy.utils.signal_processing)

filter_low_pass() (in module vocalpy.utils.signal_processing) finalize_candidate_mask() (vocalpy.pipelines.animal.Animal method) (vocalpy.pipelines.guineapig.Guineapig method)

G

generate_group_names() (vocalpy.modules.viz.Viz method) get_background_window_radius() (vocalpy.pipelines.animal.Animal method) (vocalpy.pipelines.guineapig.Guineapig method) get_centered_window_bounds() (vocalpy.pipelines.animal.Animal method) get_component_min_area() (vocalpy.pipelines.animal.Animal method) (vocalpy.pipelines.guineapig.Guineapig method) get_duration_limits_in_frames() (vocalpy.pipelines.animal.Animal method) get_median_filter_size() (vocalpy.pipelines.animal.Animal method) (vocalpy.pipelines.guineapig.Guineapig method) get_output_directory_for_audio_file() (in module vocalpy.utils.io) get_output_spectrogram_range() (vocalpy.pipelines.animal.Animal method) (vocalpy.pipelines.guineapig.Guineapig method) (vocalpy.pipelines.mouse.Mouse method) (vocalpy.pipelines.rat.Rat method)

get_region_intensity_stats() (vocalpy.pipelines.animal.Animal method) get_sorted_regionprops() (vocalpy.pipelines.animal.Animal method) get_spectrogram_kwargs() (vocalpy.pipelines.animal.Animal method) (vocalpy.pipelines.guineapig.Guineapig method) (vocalpy.pipelines.rat.Rat method) get_time_range_label() (vocalpy.pipelines.animal.Animal method) get_vocal_times() (vocalpy.pipelines.animal.Animal method) get_vocalpy_file_path() (in module vocalpy.utils.io) group_name (vocalpy.modules.recording.Recording property) group_pointplot() (vocalpy.modules.viz.Viz method) GroupViz (class in vocalpy.modules.viz) Guineapig (class in vocalpy.pipelines.guineapig)

H

has_cnn_masks() (vocalpy.modules.list_of_vocals.ListOfVocals method)

has_list_of_vocals (vocalpy.modules.recording.Recording property) has_minimum_contrast() (vocalpy.pipelines.animal.Animal method)

I

identifier() (vocalpy.pipelines.animal.Animal method) identify_vocalizations() (vocalpy.modules.recording.Recording method) (vocalpy.pipelines.animal.Animal method)

identify_vocalizations_finished() (vocalpy.modules.recording.Recording method) interval (vocalpy.modules.vocal.Vocal property)

L

list_of_groups (vocalpy.modules.viz.Viz property) list_of_vocals (vocalpy.modules.recording.Recording property) ListOfVocals (class in vocalpy.modules.list_of_vocals) load_checkpoint() (in module vocalpy.utils.io)

load_list_of_vocals() (vocalpy.modules.recording.Recording method) load_model() (in module vocalpy.utils.io) load_pickle_file() (in module vocalpy.utils.io) load_recording_data() (in module vocalpy.utils.io) load_vocalpy_file() (in module vocalpy.utils.io)

M

mask (vocalpy.modules.vocal.Vocal property) max_freq (vocalpy.modules.vocal.Vocal property) max_freq_coord (vocalpy.modules.vocal.Vocal property) max_intensity (vocalpy.modules.vocal.Vocal property) min_freq (vocalpy.modules.vocal.Vocal property) min_freq_coord (vocalpy.modules.vocal.Vocal property) min_intensity (vocalpy.modules.vocal.Vocal property) module vocalpy vocalpy.modules vocalpy.modules.list_of_vocals vocalpy.modules.recording vocalpy.modules.viz vocalpy.modules.vocal vocalpy.pipelines vocalpy.pipelines.animal vocalpy.pipelines.guineapig vocalpy.pipelines.mouse vocalpy.pipelines.rat vocalpy.utils vocalpy.utils.image_processing vocalpy.utils.io vocalpy.utils.misc vocalpy.utils.signal_processing

Mouse (class in vocalpy.pipelines.mouse)

N

normalize() (in module vocalpy.utils.image_processing)

numpy_to_grayscale_image() (in module vocalpy.utils.image_processing)

O

orientation (vocalpy.modules.vocal.Vocal property)

P

parse_chunk() (vocalpy.pipelines.animal.Animal method) parse_input_path() (in module vocalpy.utils.io) plot() (vocalpy.modules.viz.Viz method)

plot_group() (vocalpy.modules.viz.Viz method) plot_individual() (vocalpy.modules.viz.Viz method) probabilities (vocalpy.modules.vocal.Vocal property)

R

Rat (class in vocalpy.pipelines.rat) read_audio() (in module vocalpy.utils.io) read_audio_information() (in module vocalpy.utils.io) read_yaml() (in module vocalpy.utils.io) Recording (class in vocalpy.modules.recording) remove_cnn_masks() (vocalpy.modules.list_of_vocals.ListOfVocals method) remove_directory() (in module vocalpy.utils.io)

remove_masks() (vocalpy.modules.list_of_vocals.ListOfVocals method) remove_spectrograms() (vocalpy.modules.list_of_vocals.ListOfVocals method) remove_spectrograms_and_masks_from_object() (vocalpy.modules.recording.Recording method) remove_visual_data() (vocalpy.modules.list_of_vocals.ListOfVocals method) remove_vocals_classified_as_noise() (vocalpy.modules.list_of_vocals.ListOfVocals method) remove_vocals_classified_as_noise_from_list_of_vocals() (vocalpy.modules.recording.Recording method) rewrite_vocalpy_file() (in module vocalpy.utils.io)

S

save_cnn_mask_as_image() (vocalpy.modules.vocal.Vocal method) save_cnn_masks() (vocalpy.modules.list_of_vocals.ListOfVocals method) (vocalpy.modules.recording.Recording method) save_dataframe_as_csv() (in module vocalpy.utils.io) save_image_to_disk() (in module vocalpy.utils.io) save_list_of_vocals_object() (vocalpy.modules.list_of_vocals.ListOfVocals method) save_mask_as_image() (vocalpy.modules.vocal.Vocal method) save_masks() (vocalpy.modules.list_of_vocals.ListOfVocals method) save_outputs() (vocalpy.modules.recording.Recording method) save_recording_data_to_csv() (vocalpy.modules.recording.Recording method) save_recording_object() (vocalpy.modules.recording.Recording method) save_spectrogram_as_image() (vocalpy.modules.vocal.Vocal method)

save_spectrogram_with_segmentation_as_image() (vocalpy.modules.vocal.Vocal method) save_spectrograms() (vocalpy.modules.list_of_vocals.ListOfVocals method) (vocalpy.modules.recording.Recording method) save_spectrograms_and_masks() (vocalpy.modules.recording.Recording method) save_validation_images() (vocalpy.modules.list_of_vocals.ListOfVocals method) (vocalpy.modules.recording.Recording method) scatter_over_spectrogram() (in module vocalpy.utils.image_processing) segment_vocalizations() (vocalpy.modules.recording.Recording method) (vocalpy.pipelines.animal.Animal method) SingleViz (class in vocalpy.modules.viz) spectrogram (vocalpy.modules.vocal.Vocal property) start (vocalpy.modules.vocal.Vocal property) start_coord (vocalpy.modules.vocal.Vocal property)

T

top1 (vocalpy.modules.vocal.Vocal property)

top2 (vocalpy.modules.vocal.Vocal property)

U

update_centroids() (vocalpy.modules.list_of_vocals.ListOfVocals method) update_coords() (vocalpy.modules.list_of_vocals.ListOfVocals method)

update_intervals() (vocalpy.modules.list_of_vocals.ListOfVocals method) update_vocals_with_class_classification() (vocalpy.modules.recording.Recording method) update_vocals_with_segmentation_masks() (vocalpy.modules.recording.Recording method)

V

validate_animal() (in module vocalpy.utils.misc) validate_arguments() (in module vocalpy.utils.misc) validate_bin_size() (in module vocalpy.utils.misc) validate_frequency_range() (in module vocalpy.utils.misc) validate_segmentation_arguments() (in module vocalpy.utils.misc) validate_thread_count() (in module vocalpy.utils.misc) Viz (class in vocalpy.modules.viz) Vocal (class in vocalpy.modules.vocal) vocalpy module vocalpy.modules module vocalpy.modules.list_of_vocals module vocalpy.modules.recording module vocalpy.modules.viz module vocalpy.modules.vocal module

vocalpy.pipelines module vocalpy.pipelines.animal module vocalpy.pipelines.guineapig module vocalpy.pipelines.mouse module vocalpy.pipelines.rat module vocalpy.utils module vocalpy.utils.image_processing module vocalpy.utils.io module vocalpy.utils.misc module vocalpy.utils.signal_processing module

W

write_pickle_file() (in module vocalpy.utils.io)

write_vocalpy_file() (in module vocalpy.utils.io) write_yaml() (in module vocalpy.utils.io)