From aaf8ccbb7df19196af8ed1af8d1693071d6c8b96 Mon Sep 17 00:00:00 2001 From: Vincent Dumoulin Date: Wed, 16 Aug 2023 10:12:48 -0700 Subject: [PATCH] Update beam and pandas dependencies, and add instructions to download and prepare the BIRB evaluation data PiperOrigin-RevId: 557524484 --- README.md | 18 +- chirp/data/bird_taxonomy/bird_taxonomy.py | 54 +- chirp/data/soundscapes/soundscapes.py | 7 +- chirp/tests/bird_taxonomy_test.py | 12 +- chirp/tests/filter_scrub_test.py | 5 +- poetry.lock | 2117 ++++++++++++++++----- pyproject.toml | 4 +- 7 files changed, 1697 insertions(+), 520 deletions(-) diff --git a/README.md b/README.md index 09b70e9a..21e442a6 100644 --- a/README.md +++ b/README.md @@ -12,8 +12,8 @@ You might need the following dependencies. # Install Poetry for package management curl -sSL https://install.python-poetry.org | python3 - -# Install dependencies for librosa (required for testing only) -sudo apt-get install libsndfile1 +# Install dependencies for librosa +sudo apt-get install libsndfile1 ffmpeg # Install all dependencies specified in the poetry configs. poetry install @@ -26,4 +26,18 @@ dependencies, in which you can run the Chirp codebase. To run the tests, try poetry run python -m unittest discover -s chirp/tests -p "*test.py" ``` +## BIRB data preparation + +### Evaluation data + +After [installing](#installation) the `chirp` package, run the following command from the repository's root directory: + +```bash +poetry run tfds build -i chirp.data.bird_taxonomy,chirp.data.soundscapes \ + soundscapes/{ssw,hawaii,coffee_farms,sierras_kahl,high_sierras,peru}_full_length \ + bird_taxonomy/{downstream_full_length,class_representatives_slice_peaked} +``` + +The process should take 36 to 48 hours to complete and use around 256 GiB of disk space. + *This is not an officially supported Google product.* diff --git a/chirp/data/bird_taxonomy/bird_taxonomy.py b/chirp/data/bird_taxonomy/bird_taxonomy.py index 358f2326..c0722b6a 100644 --- a/chirp/data/bird_taxonomy/bird_taxonomy.py +++ b/chirp/data/bird_taxonomy/bird_taxonomy.py @@ -17,6 +17,7 @@ import dataclasses import functools +import resource import tempfile from typing import Any, Callable import warnings @@ -27,6 +28,7 @@ from chirp.data.bird_taxonomy import premade_queries from chirp.taxonomy import namespace_db from etils import epath +import jax from jax import numpy as jnp import numpy as np import pandas as pd @@ -50,6 +52,10 @@ be retrieved from the 'filename' feature: 'XC{xeno_canto_id}.mp3'. """ +# The maximum audio sequence length to consider if a localization function is +# provided. This is 5 * 60 seconds = 5 minutes. +_MAX_LOCALIZATION_LENGTH_S = 5 * 60 + LocalizationFn = Callable[[Any, int, float], jnp.ndarray] @@ -335,6 +341,11 @@ def _info(self) -> tfds.core.DatasetInfo: ) def _split_generators(self, dl_manager: tfds.download.DownloadManager): + # Increase the file handle resource soft limit to the hard limit. The + # dataset is large enough that it causes TFDS to hit the soft limit. + _low, _high = resource.getrlimit(resource.RLIMIT_NOFILE) + resource.setrlimit(resource.RLIMIT_NOFILE, (_high, _high)) + # No checksum is found for the new taxonomy_info. dl_manager may raise # an error when removing the line below. dl_manager._force_checksums_validation = ( @@ -435,6 +446,9 @@ def _process_example(row): # Resampling can introduce artifacts that push the signal outside the # [-1, 1) interval. audio = np.clip(audio, -1.0, 1.0 - (1.0 / float(1 << 15))) + # Skip empty audio files. + if audio.shape[0] == 0 or np.max(np.abs(audio)) == 0.0: + return None # The scrubbed foreground annotations are replaced by ''. When this is the # case, we translate this annotation into [] rather than ['']. foreground_label = ( @@ -463,19 +477,24 @@ def _process_example(row): 'sound_type': source['sound_type'], } - pipeline = beam.Create(source_info.iterrows()) | beam.Map(_process_example) - if self.builder_config.localization_fn: - def _localize_intervals(args): + def localize_intervals_fn(args): key, example = args sample_rate_hz = self.builder_config.sample_rate_hz interval_length_s = self.builder_config.interval_length_s target_length = int(sample_rate_hz * interval_length_s) - audio = audio_utils.pad_to_length_if_shorter( - example['audio'], target_length - ) + audio = example['audio'] + + # We limit audio sequence length to _MAX_LOCALIZATION_LENGTH_S when + # localizing intervals because the localization function can result in + # very large memory consumption for long audio sequences. + max_length = sample_rate_hz * _MAX_LOCALIZATION_LENGTH_S + if audio.shape[0] > max_length: + audio = audio[:max_length] + + audio = audio_utils.pad_to_length_if_shorter(audio, target_length) # Pass padded audio to avoid localization_fn having to pad again audio_intervals = self.builder_config.localization_fn( audio, sample_rate_hz, interval_length_s @@ -499,6 +518,23 @@ def _localize_intervals(args): )) return interval_examples - pipeline = pipeline | beam.FlatMap(_localize_intervals) - - return pipeline + else: + localize_intervals_fn = None + + for i, key_and_example in enumerate( + map(_process_example, source_info.iterrows()) + ): + # Since the audio files have variable length, the JAX compilation cache + # can use up a large amount of memory after a while. + if i % 100 == 0: + jax.clear_caches() + + # Skip empty audio files. + if key_and_example is None: + continue + + if localize_intervals_fn: + for key_and_example in localize_intervals_fn(key_and_example): + yield key_and_example + else: + yield key_and_example diff --git a/chirp/data/soundscapes/soundscapes.py b/chirp/data/soundscapes/soundscapes.py index 74a098e1..7a5300bf 100644 --- a/chirp/data/soundscapes/soundscapes.py +++ b/chirp/data/soundscapes/soundscapes.py @@ -604,7 +604,6 @@ def _process_group( beam.metrics.Metrics.counter('soundscapes', 'examples').inc() return valid_segments - pipeline = beam.Create( - enumerate(segments.groupby('filename')) - ) | beam.FlatMap(_process_group) - return pipeline + for group in enumerate(segments.groupby('filename')): + for key, example in _process_group(group): + yield key, example diff --git a/chirp/tests/bird_taxonomy_test.py b/chirp/tests/bird_taxonomy_test.py index 1745e995..4a1edc1c 100644 --- a/chirp/tests/bird_taxonomy_test.py +++ b/chirp/tests/bird_taxonomy_test.py @@ -76,9 +76,15 @@ def setUpClass(cls): subdir = epath.Path(cls.tempdir) / 'audio-data' / 'comter' subdir.mkdir(parents=True) for i in range(4): - tfds.core.lazy_imports.pydub.AudioSegment.silent(duration=10000).export( - subdir / f'XC{i:05d}.mp3', format='mp3' - ) + tfds.core.lazy_imports.pydub.AudioSegment( + b'\0\1' * int(10_000 * 10), + metadata={ + 'channels': 1, + 'sample_width': 2, + 'frame_rate': 10_000, + 'frame_width': 2, + }, + ).export(subdir / f'XC{i:05d}.mp3', format='mp3') @classmethod def tearDownClass(cls): diff --git a/chirp/tests/filter_scrub_test.py b/chirp/tests/filter_scrub_test.py index 23d5f81b..f7a7ec1b 100644 --- a/chirp/tests/filter_scrub_test.py +++ b/chirp/tests/filter_scrub_test.py @@ -458,7 +458,10 @@ def test_merge_concat_no_duplicates(self): # of .to_dict(). self.assertTrue( fsu.apply_parallel(self.toy_df, query_parallel).equals( - self.toy_df.loc[[0]].append([scrubbed_r0, self.toy_df.loc[1]]) + pd.concat([ + self.toy_df.loc[[0]], + pd.DataFrame([scrubbed_r0, self.toy_df.loc[1]]), + ]) ) ) diff --git a/poetry.lock b/poetry.lock index b8d79e36..09048be8 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.5.0 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. 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