VocalPy
Documentation
Getting started
Installation
Running the CLI
CLI options
Species defaults
Output
CSV columns
Autoencoder-based segmentation
Serialized outputs
Packaging notes
Example fixtures
Maintained audio fixtures
Maintained notebooks
Archived notebooks
Legacy demo data
Operational checks
Bundled models
Validate bundled models
Validate example fixtures
Rewrite fixtures
Reference
vocalpy package
Subpackages
vocalpy.modules package
Submodules
vocalpy.modules.list_of_vocals module
vocalpy.modules.recording module
vocalpy.modules.viz module
vocalpy.modules.vocal module
Module contents
vocalpy.pipelines package
Submodules
vocalpy.pipelines.animal module
vocalpy.pipelines.guineapig module
vocalpy.pipelines.mouse module
vocalpy.pipelines.rat module
Module contents
vocalpy.utils package
Submodules
vocalpy.utils.image_processing module
vocalpy.utils.io module
vocalpy.utils.misc module
vocalpy.utils.signal_processing module
Module contents
Module contents
VocalPy
Index
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
V
|
W
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)