vocalpy.pipelines package¶

Submodules¶

vocalpy.pipelines.animal module¶

VocalPy - Vocal analysis framework

class vocalpy.pipelines.animal.Animal(animal, params)¶

Bases: ABC

Animal class calls apropriate pipeline functions

adjust_normalized_spectrogram(normalized_spectrogram)¶

apply_morphology(binary_spectrogram)¶

build_candidate_mask(spectrogram)¶

build_vocal_from_prop(prop, spectrogram, time_res, freq_res, this_bin, bin_size, lower_frequency_cutoff)¶

abstractmethod check_if_vocals_are_close(first_vocal, second_vocal)¶

classify_vocalizations(network_type, list_of_vocals, source=None)¶

combine_vocals(first_vocal, second_vocal)¶

Combines two vocals

Parameters:

first_vocal (Vocal)
second_vocal (Vocal) – vocals to be combined

connect_vocals(list_of_vocals)¶

Checks segmentation and combines segments that belong to the same vocalization. Uses predefined constraints. Can have different contrainsts for different animal pipelines

Parameters:: list_of_vocals (ListOfVocals) – list of vocal candidates to be connected

create_list_of_vocals(props, spectrogram, candidate_mask, time_res, freq_res, this_bin, bin_size)¶

estimate_background_intensity(spectrogram, center, window_radius)¶: Estimate local background intensity around a candidate vocalization.

finalize_candidate_mask(candidate_mask)¶

get_background_window_radius()¶

get_centered_window_bounds(center, window_radius, max_width)¶: Clamp a centered window to valid bounds while preserving width when possible.

get_component_min_area()¶

get_duration_limits_in_frames(time_resolution_ms)¶

Resolve duration thresholds to spectrogram-frame counts.

Legacy configs used min_vocal_duration / max_vocal_duration as frame counts despite the ambiguous name. Preserve that behavior while allowing explicit frame or millisecond keys going forward.

get_median_filter_size()¶

get_output_spectrogram_range()¶

get_region_intensity_stats(prop)¶: Read intensity statistics across skimage regionprops API versions.

get_sorted_regionprops(candidate_mask, spectrogram)¶

get_spectrogram_kwargs()¶

get_time_range_label(sample_range, sample_rate, start_range, end_range)¶

get_vocal_times(start, end, time_res, this_bin, bin_size)¶

has_minimum_contrast(signal_intensity, background_intensity)¶: Compare signal and background in dB space.

identifier(chunk)¶

identify_vocalizations(chunk)¶

parse_chunk(chunk)¶: Convert the mixed-type chunk payload back into typed values.

segment_vocalizations(list_of_vocals, source=None, path_to_model=None, threshold=None)¶

vocalpy.pipelines.guineapig module¶

VocalPy - Vocal analysis framework

class vocalpy.pipelines.guineapig.Guineapig(animal, params)¶

Bases: Animal

adjust_normalized_spectrogram(normalized_spectrogram)¶

apply_morphology(binary_spectrogram)¶

check_if_vocals_are_close(base_vocal, next_vocal)¶

classify_vocalizations(network_type, list_of_vocals, source=None)¶

finalize_candidate_mask(candidate_mask)¶

get_background_window_radius()¶

get_component_min_area()¶

get_median_filter_size()¶

get_output_spectrogram_range()¶

get_spectrogram_kwargs()¶

vocalpy.pipelines.mouse module¶

VocalPy - Vocal analysis framework

class vocalpy.pipelines.mouse.Mouse(animal, params)¶

Bases: Animal

check_if_vocals_are_close(first_vocal, second_vocal)¶

get_output_spectrogram_range()¶

vocalpy.pipelines.rat module¶

VocalPy - Vocal analysis framework

class vocalpy.pipelines.rat.Rat(animal, params)¶

Bases: Animal

check_if_vocals_are_close(first_vocal, second_vocal)¶

get_output_spectrogram_range()¶

get_spectrogram_kwargs()¶

Module contents¶

animals module

methods for each animal pipeline