vocalpy package

Subpackages

• vocalpy.modules package
  • Submodules
  • vocalpy.modules.list_of_vocals module
    • ListOfVocals
      • ListOfVocals.add_classification_to_vocals()
      • ListOfVocals.add_segmentation_masks_to_vocals()
      • ListOfVocals.add_spectrograms_to_vocals()
      • ListOfVocals.combine_list_of_list_of_vocals()
      • ListOfVocals.has_cnn_masks()
      • ListOfVocals.remove_cnn_masks()
      • ListOfVocals.remove_masks()
      • ListOfVocals.remove_spectrograms()
      • ListOfVocals.remove_visual_data()
      • ListOfVocals.remove_vocals_classified_as_noise()
      • ListOfVocals.save_cnn_masks()
      • ListOfVocals.save_list_of_vocals_object()
      • ListOfVocals.save_masks()
      • ListOfVocals.save_spectrograms()
      • ListOfVocals.save_validation_images()
      • ListOfVocals.update_centroids()
      • ListOfVocals.update_coords()
      • ListOfVocals.update_intervals()
  • vocalpy.modules.recording module
    • Recording
      • Recording.classify_vocalizations()
      • Recording.create_animal_pipeline()
      • Recording.create_dataset()
      • Recording.create_paths()
      • Recording.create_user_parameters_yaml()
      • Recording.group_name
      • Recording.has_list_of_vocals
      • Recording.identify_vocalizations()
      • Recording.identify_vocalizations_finished()
      • Recording.list_of_vocals
      • Recording.load_list_of_vocals()
      • Recording.remove_spectrograms_and_masks_from_object()
      • Recording.remove_vocals_classified_as_noise_from_list_of_vocals()
      • Recording.save_cnn_masks()
      • Recording.save_outputs()
      • Recording.save_recording_data_to_csv()
      • Recording.save_recording_object()
      • Recording.save_spectrograms()
      • Recording.save_spectrograms_and_masks()
      • Recording.save_validation_images()
      • Recording.segment_vocalizations()
      • Recording.update_vocals_with_class_classification()
      • Recording.update_vocals_with_segmentation_masks()
  • vocalpy.modules.viz module
    • GroupViz
    • SingleViz
      • SingleViz.create_list_of_vocals()
      • SingleViz.create_object_dataframe()
    • Viz
      • Viz.combine_viz()
      • Viz.combine_viz_dataframes()
      • Viz.create_group_viz()
      • Viz.create_viz_for_each_recording()
      • Viz.generate_group_names()
      • Viz.group_pointplot()
      • Viz.list_of_groups
      • Viz.plot()
      • Viz.plot_group()
      • Viz.plot_individual()
  • vocalpy.modules.vocal module
    • Vocal
      • Vocal.area
      • Vocal.avg_freq
      • Vocal.avg_intensity
      • Vocal.bandwidth
      • Vocal.bg_intensity
      • Vocal.bin_number
      • Vocal.centroid
      • Vocal.cnn_mask
      • Vocal.coords
      • Vocal.duration
      • Vocal.end
      • Vocal.end_coord
      • Vocal.interval
      • Vocal.mask
      • Vocal.max_freq
      • Vocal.max_freq_coord
      • Vocal.max_intensity
      • Vocal.min_freq
      • Vocal.min_freq_coord
      • Vocal.min_intensity
      • Vocal.orientation
      • Vocal.probabilities
      • Vocal.save_cnn_mask_as_image()
      • Vocal.save_mask_as_image()
      • Vocal.save_spectrogram_as_image()
      • Vocal.save_spectrogram_with_segmentation_as_image()
      • Vocal.spectrogram
      • Vocal.start
      • Vocal.start_coord
      • Vocal.top1
      • Vocal.top2
  • Module contents
• vocalpy.pipelines package
  • Submodules
  • vocalpy.pipelines.animal module
    • Animal
      • Animal.adjust_normalized_spectrogram()
      • Animal.apply_morphology()
      • Animal.build_candidate_mask()
      • Animal.build_vocal_from_prop()
      • Animal.check_if_vocals_are_close()
      • Animal.classify_vocalizations()
      • Animal.combine_vocals()
      • Animal.connect_vocals()
      • Animal.create_list_of_vocals()
      • Animal.estimate_background_intensity()
      • Animal.finalize_candidate_mask()
      • Animal.get_background_window_radius()
      • Animal.get_centered_window_bounds()
      • Animal.get_component_min_area()
      • Animal.get_duration_limits_in_frames()
      • Animal.get_median_filter_size()
      • Animal.get_output_spectrogram_range()
      • Animal.get_region_intensity_stats()
      • Animal.get_sorted_regionprops()
      • Animal.get_spectrogram_kwargs()
      • Animal.get_time_range_label()
      • Animal.get_vocal_times()
      • Animal.has_minimum_contrast()
      • Animal.identifier()
      • Animal.identify_vocalizations()
      • Animal.parse_chunk()
      • Animal.segment_vocalizations()
  • vocalpy.pipelines.guineapig module
    • Guineapig
      • Guineapig.adjust_normalized_spectrogram()
      • Guineapig.apply_morphology()
      • Guineapig.check_if_vocals_are_close()
      • Guineapig.classify_vocalizations()
      • Guineapig.finalize_candidate_mask()
      • Guineapig.get_background_window_radius()
      • Guineapig.get_component_min_area()
      • Guineapig.get_median_filter_size()
      • Guineapig.get_output_spectrogram_range()
      • Guineapig.get_spectrogram_kwargs()
  • vocalpy.pipelines.mouse module
    • Mouse
      • Mouse.check_if_vocals_are_close()
      • Mouse.get_output_spectrogram_range()
  • vocalpy.pipelines.rat module
    • Rat
      • Rat.check_if_vocals_are_close()
      • Rat.get_output_spectrogram_range()
      • Rat.get_spectrogram_kwargs()
  • Module contents
• vocalpy.utils package
  • Submodules
  • vocalpy.utils.image_processing module
    • bradley_roth()
    • contrast_adjustment()
    • normalize()
    • numpy_to_grayscale_image()
    • scatter_over_spectrogram()
  • vocalpy.utils.io module
    • create_directory()
    • create_output_directory_structure()
    • get_output_directory_for_audio_file()
    • get_vocalpy_file_path()
    • load_checkpoint()
    • load_model()
    • load_pickle_file()
    • load_recording_data()
    • load_vocalpy_file()
    • parse_input_path()
    • read_audio()
    • read_audio_information()
    • read_yaml()
    • remove_directory()
    • rewrite_vocalpy_file()
    • save_dataframe_as_csv()
    • save_image_to_disk()
    • write_pickle_file()
    • write_vocalpy_file()
    • write_yaml()
  • vocalpy.utils.misc module
    • create_dataframe_from_list_of_vocals()
    • create_logger()
    • validate_animal()
    • validate_arguments()
    • validate_bin_size()
    • validate_frequency_range()
    • validate_segmentation_arguments()
    • validate_thread_count()
  • vocalpy.utils.signal_processing module
    • butter_bandpass()
    • butter_bandpass_filter()
    • butter_highpass()
    • butter_highpass_filter()
    • butter_lowpass()
    • butter_lowpass_filter()
    • compute_multitaper_spectrogram()
    • compute_spectrogram()
    • filter_band_pass()
    • filter_high_pass()
    • filter_low_pass()
  • Module contents

Module contents

VocalPy - Vocal analysis framework