vocalpy.pipelines package
Submodules
vocalpy.pipelines.animal module
VocalPy - Vocal analysis framework
- class vocalpy.pipelines.animal.Animal(animal, params)
Bases:
ABCAnimal 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
vocalpy.pipelines.rat module
VocalPy - Vocal analysis framework
Module contents
animals module
methods for each animal pipeline