Autoría: Fabricio Quirós Corella, M.Sc.
Contacto: fquiros@cenat.ac.cr (fabisqc0207@gmail.com)
Fecha: 09/09/2024
Tarea: Análisis Exploratorio de los Datos y Modelos de Clasificación
Referencia: Holger Klinck, Maggie, Sohier Dane, Stefan Kahl, Tom Denton, Vijay Ramesh. (2024). BirdCLEF 2024. Kaggle. https://kaggle.com/competitions/birdclef-2024.
Descripción general¶
Los pájaros son excelentes indicadores del cambio de biodiversidad debido a que son altamente móviles and poseen diversos requisitos en sus hábitas. Las modificaciones en los cojuntos de especies y la cantidad de pájaros por ello pueden indicar exitosamente la razón de éxito de un proyecto de restuaración de hábitats. No obstante, los métodos tradicionales frecuentemente empleados para estudiar pájaros en áreas extensas son logísticamente complejas y altamente exhaustivos.
En comparación, el monitoreo acústico pasivo (passive acoustic monitoring, PAM) combinado con herramientas analíticas novedosas basadas en aprendizaje automático (machine learning, ML) facilitan a los conservacionistas muestrar a mayor escala espacial y resolución temporal, así como explorar la relación entre las interveciones de resturación y la consevación de biodiversidad en profundidad.
Objetivo principal¶
Utilizaremos métodos de aprendizaje automático para la identificación de especies de aves de la Indian gracias a bio-sonidos. Específicamente, desarrollaremos una solución computacional que procese datos de audio continuos y reconozca las especies por sus llamados con datos de entrenamiento limitados. Apoyar el avance en esfuerzos para proteger la biodiversidad aviar en las Ghats occidentales, India, incluyendo aquellos liderados por V.V. Robin's Lab at IISER Tirupati.
Configuración inicial¶
Verifiquemos el directorio del sistema de archivos en el clúster Kabré.
In [1]:
%pwd
Out[1]:
'/home/fquiros/ondemand'
Exploremos el conjunto de datos disponible con respecto a la competición del BirdCLEF24 challenge.
In [2]:
!ls /data/fquiros/projects/birdCLEF24/datasets
20240910-200736_train.csv findsounds.tar.gz train_img_metadata.csv 20240910-200919_train_imgs.csv sample_submission.csv train_imgs birdclef-2024.zip test_audio train_metadata.csv eBird_Taxonomy_v2021.csv test_soundscapes findsounds train_audio
Enlistemos las librerías disponibles dentro de nuestro ambiente de esta sesión de Jupyter.
NOTA: el siguiente comando podría variar en la plataforma computacional utilizada.
In [3]:
!conda list
# packages in environment at /opt/python/miniconda3/envs/python-ml-dl: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge absl-py 2.1.0 pypi_0 pypi alsa-lib 1.2.12 h4ab18f5_0 conda-forge asttokens 2.4.1 pyhd8ed1ab_0 conda-forge astunparse 1.6.3 pypi_0 pypi attrs 24.2.0 pyh71513ae_0 conda-forge audioread 3.0.1 pypi_0 pypi bzip2 1.0.8 h5eee18b_6 ca-certificates 2024.7.4 hbcca054_0 conda-forge cachetools 5.4.0 pypi_0 pypi cairo 1.18.0 hebfffa5_3 conda-forge certifi 2024.7.4 pypi_0 pypi cffi 1.16.0 pypi_0 pypi charset-normalizer 3.3.2 pypi_0 pypi comm 0.2.2 pyhd8ed1ab_0 conda-forge conda-pack 0.8.0 pypi_0 pypi contourpy 1.2.1 pypi_0 pypi cuda-cccl 11.7.58 hc415cf5_0 nvidia/label/cuda-11.7.0 cuda-command-line-tools 11.7.0 0 nvidia/label/cuda-11.7.0 cuda-compiler 11.7.0 0 nvidia/label/cuda-11.7.0 cuda-cudart 11.7.60 h9538e0e_0 nvidia/label/cuda-11.7.0 cuda-cudart-dev 11.7.60 h6a7c232_0 nvidia/label/cuda-11.7.0 cuda-cuobjdump 11.7.50 h28cc80a_0 nvidia/label/cuda-11.7.0 cuda-cupti 11.7.50 hb6f9eaf_0 nvidia/label/cuda-11.7.0 cuda-cuxxfilt 11.7.50 hb365495_0 nvidia/label/cuda-11.7.0 cuda-documentation 11.7.50 0 nvidia/label/cuda-11.7.0 cuda-driver-dev 11.7.60 0 nvidia/label/cuda-11.7.0 cuda-gdb 11.7.50 h4a0ac72_0 nvidia/label/cuda-11.7.0 cuda-libraries 11.7.0 0 nvidia/label/cuda-11.7.0 cuda-libraries-dev 11.7.0 0 nvidia/label/cuda-11.7.0 cuda-memcheck 11.7.50 hc446b2b_0 nvidia/label/cuda-11.7.0 cuda-nsight 11.7.50 0 nvidia/label/cuda-11.7.0 cuda-nsight-compute 11.7.0 0 nvidia/label/cuda-11.7.0 cuda-nvcc 11.7.64 0 nvidia/label/cuda-11.7.0 cuda-nvdisasm 11.7.50 h5bd0695_0 nvidia/label/cuda-11.7.0 cuda-nvml-dev 11.7.50 h3af1343_0 nvidia/label/cuda-11.7.0 cuda-nvprof 11.7.50 h7a2404d_0 nvidia/label/cuda-11.7.0 cuda-nvprune 11.7.50 h7add7b4_0 nvidia/label/cuda-11.7.0 cuda-nvrtc 11.7.50 hd0285e0_0 nvidia/label/cuda-11.7.0 cuda-nvrtc-dev 11.7.50 heada363_0 nvidia/label/cuda-11.7.0 cuda-nvtx 11.7.50 h05b0816_0 nvidia/label/cuda-11.7.0 cuda-nvvp 11.7.50 hd2289d5_0 nvidia/label/cuda-11.7.0 cuda-python 11.7.1 pypi_0 pypi cuda-sanitizer-api 11.7.50 hb424887_0 nvidia/label/cuda-11.7.0 cuda-toolkit 11.7.0 0 nvidia/label/cuda-11.7.0 cuda-tools 11.7.0 0 nvidia/label/cuda-11.7.0 cuda-visual-tools 11.7.0 0 nvidia/label/cuda-11.7.0 cudatoolkit 11.7.1 h4bc3d14_13 conda-forge cycler 0.12.1 pypi_0 pypi cython 3.0.10 pypi_0 pypi debugpy 1.8.2 py310h76e45a6_0 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge exceptiongroup 1.2.2 pyhd8ed1ab_0 conda-forge executing 2.0.1 pyhd8ed1ab_0 conda-forge expat 2.6.2 h59595ed_0 conda-forge flatbuffers 24.3.25 pypi_0 pypi font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 h77eed37_2 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fonttools 4.53.1 pypi_0 pypi freetype 2.12.1 h267a509_2 conda-forge gast 0.4.0 pypi_0 pypi gds-tools 1.3.0.44 0 nvidia/label/cuda-11.7.0 giflib 5.2.2 hd590300_0 conda-forge google-auth 2.32.0 pypi_0 pypi google-auth-oauthlib 1.0.0 pypi_0 pypi google-pasta 0.2.0 pypi_0 pypi googleapis-common-protos 1.63.2 pypi_0 pypi graphite2 1.3.13 h59595ed_1003 conda-forge grpcio 1.65.1 pypi_0 pypi grpcio-status 1.44.0 pypi_0 pypi h5py 3.11.0 pypi_0 pypi harfbuzz 9.0.0 hda332d3_1 conda-forge humanize 4.10.0 pypi_0 pypi icu 75.1 he02047a_0 conda-forge idna 3.7 pypi_0 pypi imbalanced-learn 0.12.3 pypi_0 pypi importlib-metadata 8.2.0 pyha770c72_0 conda-forge importlib_metadata 8.2.0 hd8ed1ab_0 conda-forge importlib_resources 6.4.4 pyhd8ed1ab_0 conda-forge ipykernel 6.29.5 pyh3099207_0 conda-forge ipython 8.26.0 pyh707e725_0 conda-forge jax 0.4.30 pypi_0 pypi jaxlib 0.4.30 pypi_0 pypi jedi 0.19.1 pyhd8ed1ab_0 conda-forge joblib 1.4.2 pypi_0 pypi jsonschema 4.23.0 pyhd8ed1ab_0 conda-forge jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge jupyter_client 8.6.2 pyhd8ed1ab_0 conda-forge jupyter_core 5.7.2 py310hff52083_0 conda-forge keras 2.12.0 pypi_0 pypi keras-tuner 1.4.7 pypi_0 pypi keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.5 pypi_0 pypi krb5 1.21.3 h659f571_0 conda-forge kt-legacy 1.0.5 pypi_0 pypi lcms2 2.16 hb7c19ff_0 conda-forge ld_impl_linux-64 2.38 h1181459_1 lerc 4.0.0 h27087fc_0 conda-forge libclang 18.1.1 pypi_0 pypi libcublas 11.10.1.25 he442b6f_0 nvidia/label/cuda-11.7.0 libcublas-dev 11.10.1.25 h0c8ac2b_0 nvidia/label/cuda-11.7.0 libcufft 10.7.2.50 h80a1efe_0 nvidia/label/cuda-11.7.0 libcufft-dev 10.7.2.50 h59a5ac8_0 nvidia/label/cuda-11.7.0 libcufile 1.3.0.44 0 nvidia/label/cuda-11.7.0 libcufile-dev 1.3.0.44 0 nvidia/label/cuda-11.7.0 libcups 2.3.3 h4637d8d_4 conda-forge libcurand 10.2.10.50 heec50f7_0 nvidia/label/cuda-11.7.0 libcurand-dev 10.2.10.50 hd49a9cd_0 nvidia/label/cuda-11.7.0 libcusolver 11.3.5.50 hcab339c_0 nvidia/label/cuda-11.7.0 libcusolver-dev 11.3.5.50 hc6eba6f_0 nvidia/label/cuda-11.7.0 libcusparse 11.7.3.50 h6aaafad_0 nvidia/label/cuda-11.7.0 libcusparse-dev 11.7.3.50 hc644b96_0 nvidia/label/cuda-11.7.0 libdeflate 1.20 hd590300_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libexpat 2.6.2 h59595ed_0 conda-forge libffi 3.4.4 h6a678d5_1 libgcc-ng 14.1.0 h77fa898_0 conda-forge libglib 2.80.3 h8a4344b_1 conda-forge libgomp 14.1.0 h77fa898_0 conda-forge libiconv 1.17 hd590300_2 conda-forge libjpeg-turbo 3.0.0 hd590300_1 conda-forge libnpp 11.7.3.21 h3effbd9_0 nvidia/label/cuda-11.7.0 libnpp-dev 11.7.3.21 hb6476a9_0 nvidia/label/cuda-11.7.0 libnsl 2.0.1 hd590300_0 conda-forge libnvjpeg 11.7.2.34 hfe236c7_0 nvidia/label/cuda-11.7.0 libnvjpeg-dev 11.7.2.34 h2e48410_0 nvidia/label/cuda-11.7.0 libpng 1.6.43 h2797004_0 conda-forge librosa 0.9.2 pypi_0 pypi libsodium 1.0.18 h36c2ea0_1 conda-forge libsqlite 3.45.2 h2797004_0 conda-forge libstdcxx-ng 14.1.0 hc0a3c3a_0 conda-forge libtiff 4.6.0 h1dd3fc0_3 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libwebp-base 1.4.0 hd590300_0 conda-forge libxcb 1.16 hd590300_0 conda-forge libxcrypt 4.4.36 hd590300_1 conda-forge libzlib 1.3.1 h4ab18f5_1 conda-forge llvmlite 0.43.0 pypi_0 pypi markdown 3.6 pypi_0 pypi markupsafe 2.1.5 pypi_0 pypi matplotlib 3.9.1 pypi_0 pypi matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge ml-dtypes 0.4.0 pypi_0 pypi nbformat 5.10.4 pyhd8ed1ab_0 conda-forge ncurses 6.4 h6a678d5_0 nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge noisereduce 3.0.2 pypi_0 pypi nsight-compute 2022.2.0.13 0 nvidia/label/cuda-11.7.0 numba 0.60.0 pypi_0 pypi numpy 1.23.5 pypi_0 pypi nvidia-cublas-cu11 2022.4.8 pypi_0 pypi nvidia-cublas-cu117 11.10.1.25 pypi_0 pypi nvidia-cuda-cccl-cu11 11.8.89.post1 pypi_0 pypi nvidia-cuda-cupti-cu11 11.7.101 pypi_0 pypi nvidia-cuda-nvcc-cu11 11.7.99 pypi_0 pypi nvidia-cuda-nvrtc-cu11 11.7.99 pypi_0 pypi nvidia-cuda-runtime-cu11 2022.4.25 pypi_0 pypi nvidia-cuda-runtime-cu117 11.7.60 pypi_0 pypi nvidia-cuda-sanitizer-api-cu11 11.7.91 pypi_0 pypi nvidia-cudnn-cu11 8.6.0.163 pypi_0 pypi nvidia-cufft-cu11 2022.4.8 pypi_0 pypi nvidia-cufft-cu117 10.7.2.50 pypi_0 pypi nvidia-curand-cu11 2022.4.8 pypi_0 pypi nvidia-curand-cu117 10.2.10.50 pypi_0 pypi nvidia-cusolver-cu11 2022.4.8 pypi_0 pypi nvidia-cusolver-cu117 11.3.5.50 pypi_0 pypi nvidia-cusparse-cu11 11.7.4.91 pypi_0 pypi nvidia-npp-cu11 11.7.4.75 pypi_0 pypi nvidia-nvjpeg-cu11 11.8.0.2 pypi_0 pypi nvidia-nvml-dev-cu11 2022.4.8 pypi_0 pypi nvidia-nvml-dev-cu117 11.7.50 pypi_0 pypi nvidia-nvtx-cu11 11.7.91 pypi_0 pypi nvidia-pyindex 1.0.9 pypi_0 pypi oauthlib 3.2.2 pypi_0 pypi opencv-python 4.10.0.84 pypi_0 pypi openjdk 22.0.1 h8651b0f_1 conda-forge openssl 3.3.1 hb9d3cd8_3 conda-forge opt-einsum 3.3.0 pypi_0 pypi packaging 24.1 pyhd8ed1ab_0 conda-forge pandas 2.2.2 pypi_0 pypi parso 0.8.4 pyhd8ed1ab_0 conda-forge pcre2 10.44 h0f59acf_0 conda-forge pexpect 4.9.0 pyhd8ed1ab_0 conda-forge pickleshare 0.7.5 py_1003 conda-forge pillow 10.4.0 pypi_0 pypi pip 24.1.2 pypi_0 pypi pixman 0.43.2 h59595ed_0 conda-forge pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge platformdirs 4.2.2 pyhd8ed1ab_0 conda-forge plot-model 0.20 pypi_0 pypi plotly 5.23.0 pypi_0 pypi pooch 1.8.2 pypi_0 pypi prompt-toolkit 3.0.47 pyha770c72_0 conda-forge protobuf 4.25.3 pypi_0 pypi psutil 6.0.0 py310hc51659f_0 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge pure_eval 0.2.3 pyhd8ed1ab_0 conda-forge py4j 0.10.9.7 pypi_0 pypi pyarrow 6.0.1 pypi_0 pypi pyasn1 0.6.0 pypi_0 pypi pyasn1-modules 0.4.0 pypi_0 pypi pycparser 2.22 pypi_0 pypi pydicom 2.4.4 pypi_0 pypi pydot 3.0.1 pypi_0 pypi pydot-ng 2.0.0 pypi_0 pypi pygments 2.18.0 pyhd8ed1ab_0 conda-forge pyparsing 3.1.2 pypi_0 pypi pyspark 3.5.1 pypi_0 pypi python 3.10.13 hd12c33a_1_cpython conda-forge python-dateutil 2.9.0.post0 pypi_0 pypi python-fastjsonschema 2.20.0 pyhd8ed1ab_0 conda-forge python-graphviz 0.20.3 pypi_0 pypi python_abi 3.10 2_cp310 conda-forge pytz 2024.1 pypi_0 pypi pywavelets 1.6.0 pypi_0 pypi pyzmq 26.0.3 py310h6883aea_0 conda-forge readline 8.2 h5eee18b_0 referencing 0.35.1 pyhd8ed1ab_0 conda-forge requests 2.32.3 pypi_0 pypi requests-oauthlib 2.0.0 pypi_0 pypi resampy 0.4.3 pypi_0 pypi rpds-py 0.20.0 py310h42e942d_0 conda-forge rsa 4.9 pypi_0 pypi scikit-learn 1.5.1 pypi_0 pypi scipy 1.14.0 pypi_0 pypi seaborn 0.13.2 pypi_0 pypi setuptools 71.1.0 pypi_0 pypi six 1.16.0 pyh6c4a22f_0 conda-forge soundfile 0.12.1 pypi_0 pypi spark 0.2.1 pypi_0 pypi sqlite 3.45.2 h2c6b66d_0 conda-forge stack_data 0.6.2 pyhd8ed1ab_0 conda-forge tenacity 9.0.0 pypi_0 pypi tensorboard 2.12.3 pypi_0 pypi tensorboard-data-server 0.7.2 pypi_0 pypi tensorflow 2.12.0 pypi_0 pypi tensorflow-estimator 2.12.0 pypi_0 pypi tensorflow-io-gcs-filesystem 0.37.1 pypi_0 pypi termcolor 2.4.0 pypi_0 pypi threadpoolctl 3.5.0 pypi_0 pypi tk 8.6.13 noxft_h4845f30_101 conda-forge tornado 6.4.1 py310hc51659f_0 conda-forge tqdm 4.66.4 pypi_0 pypi traitlets 5.14.3 pyhd8ed1ab_0 conda-forge typing_extensions 4.12.2 pyha770c72_0 conda-forge tzdata 2024.1 pypi_0 pypi urllib3 2.2.2 pypi_0 pypi wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge werkzeug 3.0.3 pypi_0 pypi wheel 0.43.0 py310h06a4308_0 wrapt 1.14.1 pypi_0 pypi xorg-fixesproto 5.0 h7f98852_1002 conda-forge xorg-inputproto 2.3.2 h7f98852_1002 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.1.1 hd590300_0 conda-forge xorg-libsm 1.2.4 h7391055_0 conda-forge xorg-libx11 1.8.9 hb711507_1 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge xorg-libxi 1.7.10 h4bc722e_1 conda-forge xorg-libxrender 0.9.11 hd590300_0 conda-forge xorg-libxt 1.3.0 hd590300_1 conda-forge xorg-libxtst 1.2.4 h4bc722e_0 conda-forge xorg-recordproto 1.14.2 h7f98852_1002 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.4.6 h5eee18b_1 zeromq 4.3.5 h75354e8_4 conda-forge zipp 3.19.2 pyhd8ed1ab_0 conda-forge zlib 1.3.1 h4ab18f5_1 conda-forge zstd 1.5.6 ha6fb4c9_0 conda-forge
Librerías necesarias¶
Importamos las librerías asociadas a funciones del sistema.
In [4]:
# system libs
import os
import gc
import errno
import random
import time
import datetime
import humanize
from packaging import version
Importamos los paquetes relacionados con procesamiento de datos.
In [5]:
# data processing libs
import numpy as np
import pandas as pd
Importamos las librerías relacionadas con procesamiento de audio para la manipulación de muestras etiquetadas.
In [6]:
# audio processing libs
import librosa
import noisereduce as nr
from librosa.feature import melspectrogram
from librosa.decompose import hpss
from scipy.signal import lfilter, butter
from scipy.signal import spectrogram, stft
/opt/python/miniconda3/envs/python-ml-dl/lib/python3.10/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html from .autonotebook import tqdm as notebook_tqdm
Importamos librerías de procesamiento de imágenes y visión por computadora para la generación de imágenes desde datos de audio.
In [7]:
# image processing lib
import cv2 as cv
Importamos las librerías de visualización de datos para efectuar análisis exploratorio.
In [8]:
# data visualization libs
import IPython
import seaborn as sns
import matplotlib.pyplot as plt
from matplotlib.colors import hsv_to_rgb
from librosa.display import specshow
Importamos librerías de minería de datos para transformar arreglos de datos.
In [9]:
# data mining libs
from collections import Counter
from sklearn.model_selection import train_test_split, StratifiedShuffleSplit
from sklearn.preprocessing import LabelEncoder, OneHotEncoder
from sklearn.preprocessing import Normalizer, StandardScaler, MinMaxScaler, MaxAbsScaler
from sklearn.utils import resample
from imblearn.over_sampling import SMOTE
from tensorflow.keras.preprocessing.image import ImageDataGenerator
2024-09-18 19:30:27.926984: I tensorflow/core/util/port.cc:110] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`. 2024-09-18 19:30:35.970748: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations. To enable the following instructions: AVX2 AVX512F AVX512_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags. 2024-09-18 19:31:16.097266: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
Importamos ahora las librerías relacionadas con modelos de aprendizaje profundo.
In [10]:
# deep learning libs
from tensorflow.train import latest_checkpoint
from tensorflow.keras.callbacks import Callback, TensorBoard, ModelCheckpoint, EarlyStopping, ReduceLROnPlateau
from tensorflow.keras.models import Sequential, Model
from tensorflow.keras.layers import Input, Conv2D, MaxPool2D, MaxPooling2D, Dense, Dropout, Flatten
from tensorflow.keras.layers import BatchNormalization, Activation, Add, ZeroPadding2D, GlobalAveragePooling2D, \
AveragePooling2D
from tensorflow.keras.metrics import BinaryAccuracy, BinaryCrossentropy, CategoricalAccuracy, \
CategoricalCrossentropy
from tensorflow.keras.optimizers import SGD, RMSprop, Adam
from tensorflow.keras.regularizers import L1, L2
from tensorflow.keras.applications import ResNet50, VGG16, MobileNetV2
from tensorflow.keras.utils import set_random_seed, plot_model
from sklearn.metrics import r2_score, mean_squared_error, classification_report, confusion_matrix, roc_curve, \
roc_auc_score
Configuramos el estilo y el tamaño de la fuente para las visualizaciones.
In [11]:
# Set plot sizes to something larger than default
plt.rcParams['figure.figsize'] = (19, 8)
# Font plot properties
font = {'font.size': 16,
'font.family': 'serif',
'font.sans-serif': ['Times New Roman']}
plt.rcParams.update(font)
Definimos una función en Python que permita la conversión de una valor de tiempo en segundos a un formato de horas-minutos-segundos.
In [12]:
def s2hms(seconds):
hours = int(seconds / 60 / 60)
seconds -= hours * 60 * 60
minutes = int(seconds / 60)
seconds -= minutes * 60
return hours, minutes, seconds
Resumen de la base de datos¶
Primero que todo, cabe mencionar que las muestras son de diferentes tamaños y largos en la base de datos de BirdCLEF24 challenge.
In [13]:
%ls /data/fquiros/projects/birdCLEF24/datasets
20240910-200736_train.csv findsounds.tar.gz train_img_metadata.csv 20240910-200919_train_imgs.csv sample_submission.csv train_imgs/ birdclef-2024.zip test_audio/ train_metadata.csv eBird_Taxonomy_v2021.csv test_soundscapes/ findsounds/ train_audio/
train_audio/:el set de datos de entrenamiento consiste de grabaciones cortas de llamadas de pájaros individuales usuarios dexenocanto.org. Estos archivos han sido sub-muestreados a 32 KHz y convertidos a formato OGG. El set de datos de entrenamiento debería contener todos los archivos relevantes en los servidores dexenocanto.org.
In [14]:
%ls /data/fquiros/projects/birdCLEF24/datasets/train_audio
asbfly/ brasta1/ copbar1/ grenig1/ integr/ marsan/ redspu1/ thbwar1/ ashdro1/ brcful1/ crbsun2/ grewar3/ isbduc1/ mawthr1/ rerswa1/ tibfly3/ ashpri1/ brfowl1/ cregos1/ grnsan/ jerbus2/ moipig1/ revbul/ tilwar1/ ashwoo2/ brnhao1/ crfbar1/ grnwar1/ junbab2/ negative/ rewbul/ vefnut1/ asikoe2/ brnshr/ crseag1/ grtdro1/ junmyn1/ nilfly2/ rewlap1/ vehpar1/ asiope1/ brodro1/ dafbab1/ gryfra/ junowl1/ niwpig1/ rocpig/ wbbfly1/ aspfly1/ brwjac1/ darter2/ grynig2/ kenplo1/ nutman/ rorpar/ wemhar1/ aspswi1/ brwowl1/ eaywag1/ grywag/ kerlau2/ orihob2/ rossta2/ whbbul2/ barfly1/ btbeat1/ emedov2/ gybpri1/ labcro1/ oripip1/ rufbab3/ whbsho3/ barswa/ bwfshr1/ eucdov/ gyhcaf1/ laudov1/ pabflo1/ ruftre2/ whbtre1/ bcnher/ categr/ eurbla2/ heswoo1/ lblwar1/ paisto1/ rufwoo2/ whbwag1/ bkcbul1/ chbeat1/ eurcoo/ hoopoe/ lesyel1/ piebus1/ rutfly6/ whbwat1/ bkrfla1/ cohcuc1/ forwag1/ houcro1/ lewduc1/ piekin1/ sbeowl1/ whbwoo2/ bkskit1/ comfla1/ gargan/ houspa/ lirplo/ placuc3/ scamin3/ whcbar1/ bkwsti/ comgre/ gloibi/ inbrob1/ litegr/ plaflo1/ shikra1/ whiter2/ bladro1/ comior1/ goflea1/ indpit1/ litgre1/ plapri1/ smamin1/ whrmun/ blaeag1/ comkin1/ graher1/ indrob1/ litspi1/ plhpar1/ sohmyn1/ whtkin2/ blakit1/ commoo3/ grbeat1/ indrol2/ litswi1/ pomgrp2/ spepic1/ woosan/ blhori1/ commyn/ grecou1/ indtit1/ lobsun2/ purher1/ spodov/ wynlau1/ blnmon1/ compea/ greegr/ ingori1/ maghor2/ pursun3/ spoowl1/ yebbab1/ blrwar1/ comros/ grefla1/ inpher1/ malpar1/ pursun4/ sqtbul1/ yebbul3/ bncwoo3/ comsan/ grehor1/ insbab1/ maltro1/ purswa3/ stbkin1/ zitcis1/ brakit1/ comtai1/ grejun2/ insowl1/ malwoo1/ putbab1/ sttwoo1/
- train_metadata.csv: Un rango amplio de metadata es facilitado por el set de entrenamiento. Los campos más relevantes son los siguientes:
* `primary_label` - un código para las especies de pájaros. Es posible revisar mayor información sobre los códigos de pájaros adjuntando el código a https://ebird.org/species/, como https://ebird.org/species/amecro para el Cuervo Americano.
* `latitude & longitude` - coordenadas donde la grabación fue tomada. Algunas especies pueden tener cantos locales llamados dialectos, por lo que explorar la diversidad geográfica también puede resultar de utilidad en el set de entrenamiento.
* `author` - el usuario que facilitó la grabación.
* `filename` - el nombre asociado al archivo de audio.Análisis exploratorio de los datos¶
Para el Exploratory Data Analysis (EDA), definimos parte de los argumentos de entrada para el procesamiento de los datos de audio.
In [15]:
# Define audio extension
audio_ext = 'ogg'
# Define dataset directory
data_dir = '/data/fquiros/projects/birdCLEF24/datasets'
# CSV file extension
file_ext = 'csv'
# Define operation mode
sys_mode = 'train'
Estructura de datos¶
Actualicemos el nombre del archivo de metada para los muestras de entrenamiento que se encuentran en el sistema de archivos.
In [16]:
# Define timestamp for training metadata
ts = datetime.datetime.now().strftime('%Y%m%d-%H%M%S')
# Define the input filepath
meta_file = os.path.join(data_dir, '{}_{}.{}'.format(ts, sys_mode, file_ext))
Definimos el directorio de entrada para los archivos de audio de entrenamiento.
In [17]:
# Init
train_fpaths = list()
# Define string related to train directory
train_dir = os.path.join(data_dir, 'train_audio/')
Declaremos un método para encontrar muestras con cierta extensión a través de un directorio de bases de datos.
In [18]:
def find_data_samples(data_dir, wrong_ch='--', ext='wav'):
files = list()
for root, _, filenames in os.walk(data_dir):
for i, filename in enumerate(filenames):
if filename.endswith('.{}'.format(ext)):
filepath = os.path.join(root, filename)
if wrong_ch in filename:
try:
new_filename = filename.replace(wrong_ch, '.')
new_filepath = os.path.join(root, new_filename)
os.rename(filepath, new_filepath)
print('[WARN] Renaming sample n:{}! {} -> {}'.format(i, filename,
new_filename))
filepath = new_filepath
except:
print('[ERROR] Permission denied during renaming!')
files.append(filepath)
print('[INFO] Total data samples -> {}:{}'.format(len(files), data_dir))
return files
Definimos una función que genera una lista de valores separados por comas (comma-separated values, CSV) relacionados con las muestras de audio etiquetadas.
In [19]:
def get_tagged_samples(datapaths, wrong_ch='--', shuffle=False):
items = []
for i, path in enumerate(datapaths):
dirs = path.split('/')
# label manipulation
label = dirs[7]
# filename manipulation
filename = dirs[-1]
if wrong_ch in filename:
print('[WARN] CSV line {}:{}:{} -> NA skipped!'.format(i, filename, label))
else:
item = ','.join([path, label])
items.append(item)
# random shuffling of CSV lines
if shuffle:
random.shuffle(items)
return items
Establecemos ahora un método para generar un archivo CSV relacionado con la transcripción del set de datos etiquetados.
In [20]:
def create_dataset_file(csv_name, dataset, headers=None):
with open(csv_name, 'w') as f:
# Verify input headers
if headers is not None:
f.write(','.join(headers) + '\n')
for item in dataset:
f.write(item + '\n')
print('[INFO] Length: {} samples -> CSV file created!'.format(len(dataset)))
Eliminamos cualquier otra transcripción existente en formato CSV dentro del directorio de los set de datos.
In [21]:
!rm -rf -v /data/fquiros/projects/birdCLEF24/datasets/2024*.csv
removed ‘/data/fquiros/projects/birdCLEF24/datasets/20240910-200736_train.csv’ removed ‘/data/fquiros/projects/birdCLEF24/datasets/20240910-200919_train_imgs.csv’
Obtenemos una lista de todos los archivos de audio contenido en el directorio de entrenamiento.
In [22]:
# Get the respective filepaths of the training samples using OGG extension
train_fpaths = find_data_samples(train_dir, ext=audio_ext)
# Include to current list of fpaths the training samples with WAV extension
train_fpaths.extend(find_data_samples(train_dir))
[INFO] Total data samples -> 24459:/data/fquiros/projects/birdCLEF24/datasets/train_audio/ [INFO] Total data samples -> 7412:/data/fquiros/projects/birdCLEF24/datasets/train_audio/
Generamos una lista de las muestras de audio etiquetadas sin mezclar aleatoriamente.
In [23]:
# Labeled items for dataset transcription
train_samples = get_tagged_samples(train_fpaths, ',', shuffle=False)
Creamos una transcripción personalizada como archivo CSV de la base de datos etiquetada que dispone la plataforma de BirdCLEF24.
In [24]:
# Run method to create CSV transcription of labeled database
create_dataset_file(meta_file, train_samples)
[INFO] Length: 31871 samples -> CSV file created!
Podemos generar y explorar la lista de especies o clases disponibles dentro del conjunto de datos recolectado.
In [25]:
species_list = sorted(os.listdir(train_dir))
print('[INFO] List of species:\n', species_list)
[INFO] List of species: ['asbfly', 'ashdro1', 'ashpri1', 'ashwoo2', 'asikoe2', 'asiope1', 'aspfly1', 'aspswi1', 'barfly1', 'barswa', 'bcnher', 'bkcbul1', 'bkrfla1', 'bkskit1', 'bkwsti', 'bladro1', 'blaeag1', 'blakit1', 'blhori1', 'blnmon1', 'blrwar1', 'bncwoo3', 'brakit1', 'brasta1', 'brcful1', 'brfowl1', 'brnhao1', 'brnshr', 'brodro1', 'brwjac1', 'brwowl1', 'btbeat1', 'bwfshr1', 'categr', 'chbeat1', 'cohcuc1', 'comfla1', 'comgre', 'comior1', 'comkin1', 'commoo3', 'commyn', 'compea', 'comros', 'comsan', 'comtai1', 'copbar1', 'crbsun2', 'cregos1', 'crfbar1', 'crseag1', 'dafbab1', 'darter2', 'eaywag1', 'emedov2', 'eucdov', 'eurbla2', 'eurcoo', 'forwag1', 'gargan', 'gloibi', 'goflea1', 'graher1', 'grbeat1', 'grecou1', 'greegr', 'grefla1', 'grehor1', 'grejun2', 'grenig1', 'grewar3', 'grnsan', 'grnwar1', 'grtdro1', 'gryfra', 'grynig2', 'grywag', 'gybpri1', 'gyhcaf1', 'heswoo1', 'hoopoe', 'houcro1', 'houspa', 'inbrob1', 'indpit1', 'indrob1', 'indrol2', 'indtit1', 'ingori1', 'inpher1', 'insbab1', 'insowl1', 'integr', 'isbduc1', 'jerbus2', 'junbab2', 'junmyn1', 'junowl1', 'kenplo1', 'kerlau2', 'labcro1', 'laudov1', 'lblwar1', 'lesyel1', 'lewduc1', 'lirplo', 'litegr', 'litgre1', 'litspi1', 'litswi1', 'lobsun2', 'maghor2', 'malpar1', 'maltro1', 'malwoo1', 'marsan', 'mawthr1', 'moipig1', 'negative', 'nilfly2', 'niwpig1', 'nutman', 'orihob2', 'oripip1', 'pabflo1', 'paisto1', 'piebus1', 'piekin1', 'placuc3', 'plaflo1', 'plapri1', 'plhpar1', 'pomgrp2', 'purher1', 'pursun3', 'pursun4', 'purswa3', 'putbab1', 'redspu1', 'rerswa1', 'revbul', 'rewbul', 'rewlap1', 'rocpig', 'rorpar', 'rossta2', 'rufbab3', 'ruftre2', 'rufwoo2', 'rutfly6', 'sbeowl1', 'scamin3', 'shikra1', 'smamin1', 'sohmyn1', 'spepic1', 'spodov', 'spoowl1', 'sqtbul1', 'stbkin1', 'sttwoo1', 'thbwar1', 'tibfly3', 'tilwar1', 'vefnut1', 'vehpar1', 'wbbfly1', 'wemhar1', 'whbbul2', 'whbsho3', 'whbtre1', 'whbwag1', 'whbwat1', 'whbwoo2', 'whcbar1', 'whiter2', 'whrmun', 'whtkin2', 'woosan', 'wynlau1', 'yebbab1', 'yebbul3', 'zitcis1']
Definimos una función que permite genear un marco de datos desde un archivo CSV de entrada.
In [26]:
def load_dataset_file(csv_file, n=25, headers=None, dbg=True):
# Load CSV transcription file
if headers is None:
df = pd.read_csv(csv_file)
else:
df = pd.read_csv(csv_file, names=headers)
# Debug info
if dbg:
print('[INFO] Dataset size: {} -> Display info of {} samples randomly selected...'.format(df.shape, n))
print(df.sample(n))
# Get dataframe of labels
df_labels = df.primary_label
print('[INFO] Display number of samples per class:\n{}'.format(df_labels.value_counts()))
# Display info about the target labels
print('[INFO] Number of unique names of birds: {}'.format(df_labels.nunique()))
# Debug info
if dbg:
target_labels = np.array(df_labels.unique())
print('[INFO] Target bird names: {}'.format(target_labels))
# Retrieve columns to drop from the dataframe of interest
df_cols = df.columns.tolist()
drop_cols = df_cols[1:-1]
df = df.drop(columns=drop_cols)
print('[INFO] Loading {} file as DF of {} shape...'.format(csv_file, df.shape))
bsize = df.memory_usage(deep=True).sum()
print('[INFO] Dataframe memory usage: {}'.format(humanize.naturalsize(bsize)))
return df
Cargamos el marco de datos de entrenamiento desde una transcripción personalizada de una base de datos etiquetada.
In [27]:
# Load CSV file to generate dataframe
df_in = load_dataset_file(meta_file, headers=['filename', 'primary_label'])
[INFO] Dataset size: (31871, 2) -> Display info of 25 samples randomly selected...
filename primary_label
16493 /data/fquiros/projects/birdCLEF24/datasets/tra... piekin1
5631 /data/fquiros/projects/birdCLEF24/datasets/tra... eaywag1
29290 /data/fquiros/projects/birdCLEF24/datasets/tra... negative
19921 /data/fquiros/projects/birdCLEF24/datasets/tra... gybpri1
21963 /data/fquiros/projects/birdCLEF24/datasets/tra... lirplo
30618 /data/fquiros/projects/birdCLEF24/datasets/tra... negative
14123 /data/fquiros/projects/birdCLEF24/datasets/tra... piebus1
1297 /data/fquiros/projects/birdCLEF24/datasets/tra... whbwat1
12608 /data/fquiros/projects/birdCLEF24/datasets/tra... comsan
4785 /data/fquiros/projects/birdCLEF24/datasets/tra... brodro1
335 /data/fquiros/projects/birdCLEF24/datasets/tra... eucdov
20191 /data/fquiros/projects/birdCLEF24/datasets/tra... eurcoo
10515 /data/fquiros/projects/birdCLEF24/datasets/tra... wemhar1
8964 /data/fquiros/projects/birdCLEF24/datasets/tra... plapri1
8838 /data/fquiros/projects/birdCLEF24/datasets/tra... plapri1
8674 /data/fquiros/projects/birdCLEF24/datasets/tra... blakit1
27218 /data/fquiros/projects/birdCLEF24/datasets/tra... negative
31018 /data/fquiros/projects/birdCLEF24/datasets/tra... negative
17518 /data/fquiros/projects/birdCLEF24/datasets/tra... zitcis1
9225 /data/fquiros/projects/birdCLEF24/datasets/tra... grywag
18694 /data/fquiros/projects/birdCLEF24/datasets/tra... greegr
28034 /data/fquiros/projects/birdCLEF24/datasets/tra... negative
7260 /data/fquiros/projects/birdCLEF24/datasets/tra... kenplo1
5165 /data/fquiros/projects/birdCLEF24/datasets/tra... labcro1
6568 /data/fquiros/projects/birdCLEF24/datasets/tra... litgre1
[INFO] Display number of samples per class:
primary_label
negative 7412
comros 500
comkin1 500
eaywag1 500
grnsan 500
...
wynlau1 6
blaeag1 6
asiope1 5
integr 5
niwpig1 5
Name: count, Length: 183, dtype: int64
[INFO] Number of unique names of birds: 183
[INFO] Target bird names: ['indtit1' 'whcbar1' 'rutfly6' 'revbul' 'whbsho3' 'grejun2' 'mawthr1'
'aspswi1' 'eucdov' 'ashwoo2' 'eurbla2' 'brnhao1' 'orihob2' 'goflea1'
'ashpri1' 'whbwat1' 'asiope1' 'crfbar1' 'asbfly' 'brnshr' 'litegr'
'rewbul' 'vefnut1' 'thbwar1' 'asikoe2' 'jerbus2' 'insowl1' 'sttwoo1'
'cregos1' 'rocpig' 'dafbab1' 'malwoo1' 'bkwsti' 'houspa' 'junbab2'
'rufwoo2' 'malpar1' 'crbsun2' 'purher1' 'plaflo1' 'ingori1' 'btbeat1'
'plhpar1' 'grenig1' 'purswa3' 'nutman' 'brodro1' 'ashdro1' 'labcro1'
'wynlau1' 'eaywag1' 'grbeat1' 'isbduc1' 'pomgrp2' 'grehor1' 'bwfshr1'
'sqtbul1' 'blhori1' 'brwowl1' 'litgre1' 'pursun4' 'whiter2' 'cohcuc1'
'kenplo1' 'brwjac1' 'lobsun2' 'bkrfla1' 'gargan' 'smamin1' 'grynig2'
'comtai1' 'inpher1' 'integr' 'gloibi' 'scamin3' 'putbab1' 'heswoo1'
'yebbab1' 'blnmon1' 'whbbul2' 'blakit1' 'forwag1' 'plapri1' 'rossta2'
'pursun3' 'grywag' 'tilwar1' 'whbwoo2' 'maltro1' 'redspu1' 'chbeat1'
'indpit1' 'grefla1' 'bncwoo3' 'lewduc1' 'blaeag1' 'nilfly2' 'litswi1'
'sohmyn1' 'pabflo1' 'wbbfly1' 'whtkin2' 'wemhar1' 'indrob1' 'insbab1'
'comior1' 'maghor2' 'brcful1' 'hoopoe' 'tibfly3' 'houcro1' 'bcnher'
'laudov1' 'marsan' 'junmyn1' 'comsan' 'comros' 'moipig1' 'paisto1'
'grewar3' 'brasta1' 'comfla1' 'piebus1' 'lesyel1' 'spodov' 'commyn'
'commoo3' 'sbeowl1' 'rewlap1' 'graher1' 'grecou1' 'niwpig1' 'indrol2'
'barfly1' 'vehpar1' 'brfowl1' 'barswa' 'piekin1' 'brakit1' 'comkin1'
'spepic1' 'zitcis1' 'litspi1' 'gryfra' 'whrmun' 'rufbab3' 'whbwag1'
'spoowl1' 'bkskit1' 'yebbul3' 'emedov2' 'stbkin1' 'greegr' 'rorpar'
'grnsan' 'whbtre1' 'ruftre2' 'gybpri1' 'junowl1' 'eurcoo' 'inbrob1'
'categr' 'shikra1' 'rerswa1' 'woosan' 'bladro1' 'crseag1' 'kerlau2'
'bkcbul1' 'lirplo' 'gyhcaf1' 'lblwar1' 'comgre' 'compea' 'copbar1'
'grnwar1' 'blrwar1' 'placuc3' 'aspfly1' 'grtdro1' 'darter2' 'oripip1'
'negative']
[INFO] Loading /data/fquiros/projects/birdCLEF24/datasets/20240918-193253_train.csv file as DF of (31871, 2) shape...
[INFO] Dataframe memory usage: 6.4 MB
Por otro lado, declaramos un método que convierte valores de etiquetas a números de color para efectos de visualización de categorías.
In [28]:
def label2color(label,
num_colors,
norm=True,
to_hex=False,
s=1.0, v=1.0,
rgb_max=255, color_size=3):
# Generate hue values equally spaced in HSV color space
h = label/num_colors
# Color space conversion (CSC): HSV to RGB (norm)
hsv_color = (h, s, v)
# Normalized RGB components
r, g, b = hsv_to_rgb(hsv_color)
# RGB color tuple
color = (r, g, b)
# RGB denormalization
if not norm:
# White color: RBG format
wcolor = (rgb_max,)*color_size
# Map color value to [0, 255]
color = tuple(int(a * b) for a, b in zip(color, wcolor))
# RGB values to HEX
if to_hex:
# Retrieve color channels
r, g, b = color
# Update color value
color = '#{:02x}{:02x}{:02x}'.format(r, g, b)
# Return the color value
return color
Definimos una función para graficar la distribución de las muestras etiquetadas en la base de datos de interés.
In [29]:
def data_distribution_chart(df, data_dir=None, tag=None):
# init
c_list = list()
# dataframe of labels
df_labels = df.primary_label
# target tags
target_labels = np.array(df_labels.unique())
print('[INFO] Target bird labels: {}'.format(target_labels))
# number of classes
n_classes = df_labels.nunique()
# info about the target labels
print('[INFO] Number of unique names of birds: {}'.format(n_classes))
# encode target categories
target_classes = LabelEncoder().fit_transform(target_labels)
print('[INFO] Target bird classes: {}'.format(target_classes))
# generate color list
for _, clabel in enumerate(target_classes):
color = label2color(clabel + 1, n_classes, norm=False, to_hex=True)
c_list.append(color)
# dataframe distribution
df_dist = df_labels.value_counts()
# define chart storage location
if tag is None:
tag = datetime.datetime.now().strftime('%Y%m%d-%H%M%S')
fname = '{}_dist_chart.pdf'.format(tag)
# start figure
fig = plt.figure()
# bar countplot
sns.countplot(data=df, x='primary_label', hue='primary_label',
order=df_dist.index, palette=sns.color_palette(c_list, n_classes))
plt.xticks(rotation=45)
plt.title('Distribution of Bird Species')
plt.xlabel('Bird Species')
plt.ylabel('Count')
if data_dir is None:
# show chart file
plt.show()
else:
chart_path = os.path.join(data_dir, fname)
# save chart file
fig.savefig(chart_path)
print('[INFO] Saving data distribution chart file: {}'.format(chart_path))
plt.close(fig)
# delete figure object
del fig
# run garbage collector
gc.collect()
Ejecutamos un paso de EDA empleando un método para graficar la distribución de las muestras en un marco de datos de entrada.
In [30]:
# Plot data distribution chart
data_distribution_chart(df_in)
[INFO] Target bird labels: ['indtit1' 'whcbar1' 'rutfly6' 'revbul' 'whbsho3' 'grejun2' 'mawthr1' 'aspswi1' 'eucdov' 'ashwoo2' 'eurbla2' 'brnhao1' 'orihob2' 'goflea1' 'ashpri1' 'whbwat1' 'asiope1' 'crfbar1' 'asbfly' 'brnshr' 'litegr' 'rewbul' 'vefnut1' 'thbwar1' 'asikoe2' 'jerbus2' 'insowl1' 'sttwoo1' 'cregos1' 'rocpig' 'dafbab1' 'malwoo1' 'bkwsti' 'houspa' 'junbab2' 'rufwoo2' 'malpar1' 'crbsun2' 'purher1' 'plaflo1' 'ingori1' 'btbeat1' 'plhpar1' 'grenig1' 'purswa3' 'nutman' 'brodro1' 'ashdro1' 'labcro1' 'wynlau1' 'eaywag1' 'grbeat1' 'isbduc1' 'pomgrp2' 'grehor1' 'bwfshr1' 'sqtbul1' 'blhori1' 'brwowl1' 'litgre1' 'pursun4' 'whiter2' 'cohcuc1' 'kenplo1' 'brwjac1' 'lobsun2' 'bkrfla1' 'gargan' 'smamin1' 'grynig2' 'comtai1' 'inpher1' 'integr' 'gloibi' 'scamin3' 'putbab1' 'heswoo1' 'yebbab1' 'blnmon1' 'whbbul2' 'blakit1' 'forwag1' 'plapri1' 'rossta2' 'pursun3' 'grywag' 'tilwar1' 'whbwoo2' 'maltro1' 'redspu1' 'chbeat1' 'indpit1' 'grefla1' 'bncwoo3' 'lewduc1' 'blaeag1' 'nilfly2' 'litswi1' 'sohmyn1' 'pabflo1' 'wbbfly1' 'whtkin2' 'wemhar1' 'indrob1' 'insbab1' 'comior1' 'maghor2' 'brcful1' 'hoopoe' 'tibfly3' 'houcro1' 'bcnher' 'laudov1' 'marsan' 'junmyn1' 'comsan' 'comros' 'moipig1' 'paisto1' 'grewar3' 'brasta1' 'comfla1' 'piebus1' 'lesyel1' 'spodov' 'commyn' 'commoo3' 'sbeowl1' 'rewlap1' 'graher1' 'grecou1' 'niwpig1' 'indrol2' 'barfly1' 'vehpar1' 'brfowl1' 'barswa' 'piekin1' 'brakit1' 'comkin1' 'spepic1' 'zitcis1' 'litspi1' 'gryfra' 'whrmun' 'rufbab3' 'whbwag1' 'spoowl1' 'bkskit1' 'yebbul3' 'emedov2' 'stbkin1' 'greegr' 'rorpar' 'grnsan' 'whbtre1' 'ruftre2' 'gybpri1' 'junowl1' 'eurcoo' 'inbrob1' 'categr' 'shikra1' 'rerswa1' 'woosan' 'bladro1' 'crseag1' 'kerlau2' 'bkcbul1' 'lirplo' 'gyhcaf1' 'lblwar1' 'comgre' 'compea' 'copbar1' 'grnwar1' 'blrwar1' 'placuc3' 'aspfly1' 'grtdro1' 'darter2' 'oripip1' 'negative'] [INFO] Number of unique names of birds: 183 [INFO] Target bird classes: [ 87 174 149 140 169 68 116 7 55 3 56 26 122 61 2 172 5 49 0 27 106 141 164 161 4 94 91 160 48 143 51 114 14 82 95 148 112 47 133 129 88 31 131 69 136 121 28 1 100 179 53 63 93 132 67 32 158 18 30 107 135 175 35 98 29 110 12 59 153 75 45 89 92 60 151 137 79 180 19 168 17 58 130 145 134 76 163 173 113 138 34 84 66 21 104 16 119 109 154 124 166 177 167 85 90 38 111 24 80 162 81 10 101 115 96 44 43 117 125 70 23 36 126 103 156 41 40 150 142 62 64 120 86 8 165 25 9 127 22 39 155 182 108 74 176 146 171 157 13 181 54 159 65 144 71 170 147 77 97 57 83 33 152 139 178 15 50 99 11 105 78 102 37 42 46 72 20 128 6 73 52 123 118]
Verifiquemos ahora la existencia del archivo de metadata de la base de datos de BirdCLEF24.
In [31]:
# Define the input filepath (optional)
meta_file = os.path.join(data_dir, '{}_metadata.{}'.format(sys_mode, file_ext))
# Insepct whether the file exits
os.path.exists(meta_file)
Out[31]:
True
Definimos un método para cargar un marco de datos del archivo de entrenamiento para la base de datos BirdCLEF24.
In [32]:
def load_train_dataset(data_dir, file_name):
# Load metadata dataframe from CSV file
meta_file = os.path.join(data_dir, file_name)
meta_df = pd.read_csv(meta_file)
# Retrieve columns to drop from the dataframe of interest
df_cols = meta_df.columns.tolist()
drop_cols = df_cols[1:-1]
df = meta_df.drop(columns=drop_cols)
print('[INFO] Loading {} file as DF of {} shape...'.format(meta_file, df.shape))
bsize = df.memory_usage(deep=True).sum()
print('[INFO] Dataframe memory usage: {}'.format(humanize.naturalsize(bsize)))
# Delete metadata dataframe object
del meta_df
# Run garbage collection
gc.collect()
return df
Creamos un nuevo marco de datos de entrada para su procesamiento y exploración.
In [33]:
# Generate the complete dataframe for the 182-birds species
df_in = load_train_dataset(data_dir, meta_file)
[INFO] Loading /data/fquiros/projects/birdCLEF24/datasets/train_metadata.csv file as DF of (24459, 2) shape... [INFO] Dataframe memory usage: 3.4 MB
Grafiquemos la distribución de los datos en la estructura de entrada.
In [34]:
# Store data distribution chart
data_distribution_chart(df_in)
[INFO] Target bird labels: ['asbfly' 'ashdro1' 'ashpri1' 'ashwoo2' 'asikoe2' 'asiope1' 'aspfly1' 'aspswi1' 'barfly1' 'barswa' 'bcnher' 'bkcbul1' 'bkrfla1' 'bkskit1' 'bkwsti' 'bladro1' 'blaeag1' 'blakit1' 'blhori1' 'blnmon1' 'blrwar1' 'bncwoo3' 'brakit1' 'brasta1' 'brcful1' 'brfowl1' 'brnhao1' 'brnshr' 'brodro1' 'brwjac1' 'brwowl1' 'btbeat1' 'bwfshr1' 'categr' 'chbeat1' 'cohcuc1' 'comfla1' 'comgre' 'comior1' 'comkin1' 'commoo3' 'commyn' 'compea' 'comros' 'comsan' 'comtai1' 'copbar1' 'crbsun2' 'cregos1' 'crfbar1' 'crseag1' 'dafbab1' 'darter2' 'eaywag1' 'emedov2' 'eucdov' 'eurbla2' 'eurcoo' 'forwag1' 'gargan' 'gloibi' 'goflea1' 'graher1' 'grbeat1' 'grecou1' 'greegr' 'grefla1' 'grehor1' 'grejun2' 'grenig1' 'grewar3' 'grnsan' 'grnwar1' 'grtdro1' 'gryfra' 'grynig2' 'grywag' 'gybpri1' 'gyhcaf1' 'heswoo1' 'hoopoe' 'houcro1' 'houspa' 'inbrob1' 'indpit1' 'indrob1' 'indrol2' 'indtit1' 'ingori1' 'inpher1' 'insbab1' 'insowl1' 'integr' 'isbduc1' 'jerbus2' 'junbab2' 'junmyn1' 'junowl1' 'kenplo1' 'kerlau2' 'labcro1' 'laudov1' 'lblwar1' 'lesyel1' 'lewduc1' 'lirplo' 'litegr' 'litgre1' 'litspi1' 'litswi1' 'lobsun2' 'maghor2' 'malpar1' 'maltro1' 'malwoo1' 'marsan' 'mawthr1' 'moipig1' 'nilfly2' 'niwpig1' 'nutman' 'orihob2' 'oripip1' 'pabflo1' 'paisto1' 'piebus1' 'piekin1' 'placuc3' 'plaflo1' 'plapri1' 'plhpar1' 'pomgrp2' 'purher1' 'pursun3' 'pursun4' 'purswa3' 'putbab1' 'redspu1' 'rerswa1' 'revbul' 'rewbul' 'rewlap1' 'rocpig' 'rorpar' 'rossta2' 'rufbab3' 'ruftre2' 'rufwoo2' 'rutfly6' 'sbeowl1' 'scamin3' 'shikra1' 'smamin1' 'sohmyn1' 'spepic1' 'spodov' 'spoowl1' 'sqtbul1' 'stbkin1' 'sttwoo1' 'thbwar1' 'tibfly3' 'tilwar1' 'vefnut1' 'vehpar1' 'wbbfly1' 'wemhar1' 'whbbul2' 'whbsho3' 'whbtre1' 'whbwag1' 'whbwat1' 'whbwoo2' 'whcbar1' 'whiter2' 'whrmun' 'whtkin2' 'woosan' 'wynlau1' 'yebbab1' 'yebbul3' 'zitcis1'] [INFO] Number of unique names of birds: 182 [INFO] Target bird classes: [ 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181]
Con el fin de balancear las clases rápidamente en el conjunto de datos, instanciamos un método que retorne una estructura de datos que maneje las clases y las muestras correspondientes al conteo máximo en el set.
In [35]:
def get_df_classes_max_count(df):
# Define an empty dataframe
df_tmp = pd.DataFrame()
# Create dataframe of classes from train dataframe
df_classes = df.primary_label
# Obtain distribution of the categories dataframe
df_dist = df_classes.value_counts()
# Get the data distribution with max. number of samples
max_dist = df_dist[df_dist == df_dist.max()]
# Retrieve the corresponding indexes (i.e., labels)
max_index = max_dist.index
# Convert to list and sort it
idx_list = max_index.tolist()
idx_list.sort()
# Iterate through list of labels
for i in idx_list:
df_in = df[df_classes == i]
df_tmp = pd.concat([df_tmp, df_in], ignore_index=True)
# Create a dataframe with samples associated with max. categories
df_out = df_tmp
print('[INFO] Create the dataframe of interest with {} dimensions'.format(df_out.shape))
# Display dataframe memory usage
bsize = df_out.memory_usage(deep=True).sum()
print('[INFO] Dataframe memory usage: {}'.format(humanize.naturalsize(bsize)))
# Delete dataframes objects
del df, df_tmp
# Run garbage collector
gc.collect()
# Return the output dataframe
return df_out
Obtenemos el dataframe de las vocalizaciones de especies con más repiticiones dentro del set de datos de la competición BirdCLEF 2024.
In [36]:
# Retrieve an input dataframe that considers classes with most samples
df_in = get_df_classes_max_count(df_in)
[INFO] Create the dataframe of interest with (11000, 2) dimensions [INFO] Dataframe memory usage: 1.5 MB
Ejecutamos la visualización EDA con el fin de estudiar el balanceo de datos.
In [37]:
# Plot the data distribution chart using the maximum count dataframe
data_distribution_chart(df_in)
[INFO] Target bird labels: ['barswa' 'bcnher' 'bkwsti' 'blrwar1' 'comgre' 'comkin1' 'commoo3' 'comros' 'comsan' 'eaywag1' 'eucdov' 'eurcoo' 'graher1' 'grewar3' 'grnsan' 'grywag' 'hoopoe' 'houspa' 'lirplo' 'litgre1' 'woosan' 'zitcis1'] [INFO] Number of unique names of birds: 22 [INFO] Target bird classes: [ 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21]
Obtenemos ahora la lista de las rutas de los archivos de audio y sus respetivas etiquetadas para la extración de características de estas señales.
In [38]:
# Get dataframe of labels
df_labels = df_in.primary_label
# List of target labels
labels = df_labels.values.tolist()
# Get the filenames of WAV samples
filenames = df_in.filename.values.tolist()
Procesamiento de audio¶
Declaramos un método genérico para cargar las tramas de audio desde un archivo.
In [39]:
def load_audio_data(filename, sr=None, mono=True, dtype='float32', silent=False):
# Load audio data and retrieve sampling rate
s, fs = librosa.load(filename,
sr=sr,
mono=mono,
dtype=dtype)
Ts = 1 / float(fs)
N = len(s)
T = N * Ts
if not silent:
print('[INFO] Audio data loaded: {}, sampling rate: {}, duration: {} s'.format(filename, fs, T))
return s, fs, T
Definimos una función para efectuar sub-muestreo y sobre-muestreo.
In [40]:
def resampling(signal, src_fs, dst_fs=None, dtype='float32', silent=False):
# update source sampling rate
fs = src_fs
# adjust data type
audio = signal.astype(dtype)
# if: check the resampling enable
if dst_fs is not None:
# compare current fs and eventual fs
if dst_fs < src_fs:
# downsampling
if not silent:
print('[INFO] Downsampling ({}->{}) audio track'.format(src_fs, dst_fs))
audio_down = librosa.resample(y=audio, orig_sr=src_fs, target_sr=dst_fs)
audio = audio_down.astype(dtype)
fs = dst_fs
elif dst_fs > src_fs:
# upsampling
if not silent:
print('[INFO] Upsampling ({}->{}) audio track'.format(src_fs, dst_fs))
audio_up = librosa.resample(y=audio, orig_sr=src_fs, target_sr=dst_fs)
audio = audio_up.astype(dtype)
fs = dst_fs
else:
# no resampling
if not silent:
print('[INFO] No resampling ({}->{}) audio track'.format(src_fs, dst_fs))
return audio, fs
# else: no resampling
return audio, fs
Establecemos un método para graficar el archivo de audio en el dominio del tiempo.
In [41]:
def plot_audio_signal(s, fs, tag, path=None, markers=np.array([])):
fig = plt.figure()
Ts = 1 / float(fs)
N = len(s)
T = N * Ts
t = np.arange(N) * Ts
if markers.size != 0:
# Normalize signal for marked plots
s = s / np.amax(s)
print('[INFO] Amount of signal markers: {}'.format(len(markers)))
plt.vlines(markers, s.min(), s.max(), color='orange')
plt.ylim(s.min(), s.max())
plt.plot(t, s)
plt.xlim(0, T)
plt.title('Audio signal plot'.format(tag))
plt.grid(True)
plt.xlabel('Time [s]')
plt.ylabel('Gain')
if path is None:
plt.show()
else:
imgpath = os.path.join(path, '{}_signal.pdf'.format(tag))
fig.savefig(imgpath)
print('[INFO] Saving plot file of audio signal: {}'.format(imgpath))
plt.close(fig)
del fig
gc.collect()
Definimos un índice de forma aleatoria para obtener una muestra de audio de la lista de archivos de audio.
In [42]:
# define a random index of audio files
rand_value = random.sample(range(len(df_in)), 1)
index = int(rand_value[0])
audio_file = os.path.join(train_dir, filenames[index])
label_file = labels[index]
audio_file, label_file
Out[42]:
('/data/fquiros/projects/birdCLEF24/datasets/train_audio/eucdov/XC760696.ogg',
'eucdov')
Cargamos el archivo de audio determinado de forma aleatoria de la lista de nombres de archivos de audio.
In [43]:
# perform waveform extraction
waveform, sampling_rate, duration = load_audio_data(audio_file, silent=False)
[INFO] Audio data loaded: /data/fquiros/projects/birdCLEF24/datasets/train_audio/eucdov/XC760696.ogg, sampling rate: 32000, duration: 5.3020000000000005 s
Desplegamos una representación en el dominio del tiempo de la señal de audio, así como un reproductor del archivo de audio, para analizar auditivamente la muestra en cuestión.
In [44]:
sample_tag = '{}:{}:{}'.format(index, audio_file, label_file)
plot_audio_signal(waveform, sampling_rate, sample_tag)
# Enable Python player
IPython.display.Audio(audio_file)
Out[44]:
Extracción de características¶
Establecemos distintos métodos que conforman la secuencias de pasos que conforma la extracción de características (feature extraction, FE), donde transformas las muestras de audio en representaciones de audio que se adecuan a modelos de aprendizaje profundo.
Primero, definimos la función de un filtrado pasa-altas para remover ruido de baja frecuencia.
In [45]:
def high_pass_filter(s, fs, f_ord, f_hpf):
nyq = fs*0.5
f_cut = f_hpf/nyq
b, a = butter(f_ord, f_cut, 'hp')
x = lfilter(b, a, s)
return b, a, x
Instanciamos un método para efectuar la separación fuentes sonoras harmónicas usando la magnitud del espectrograma de audio.
In [46]:
def harmonic_source_separation(S_mag,
hfilt_width=5,
pfilt_width=27,
hmask_margin=7,
pmask_margin=1):
# Harmonic filter size and margin
kernel_size = (hfilt_width, pfilt_width)
margin = (hmask_margin, pmask_margin)
# HPSS stage
H_mag, _ = hpss(S=S_mag, kernel_size=kernel_size, margin=margin)
# Return harmonic spectrum magnitude
return H_mag
Declaramos ahora funciones y rutinas útiles para ejecutar la conversión de una representación en 1D a otra en 2D, así como su respecitva visualización. Para este caso, nos enfocamos principalmente en los espectrogramas en escala de Mel.
In [47]:
def stft_magnitude(s, sr, n_fft, hop_length, win='hann'):
# hann window by default: periodic window for spectral analysis
f, t, S_mag = stft(x=s,
fs=sr,
window=win,
nperseg=n_fft,
noverlap=hop_length,
nfft=n_fft,
scaling='spectrum')
return t, f, S_mag
Instanciamos un método alternativo para generar la magnitud espectral utilizando transformadas sucesivas de Fourier empleando la librería scipy.
In [48]:
def spectral_magnitude(s, sr, n_fft, hop_length, win='hann'):
# hann window by default: periodic window for spectral analysis
f, t, S_mag = spectrogram(x=s,
fs=sr,
window=win,
nperseg=n_fft,
noverlap=hop_length,
nfft=n_fft,
scaling='spectrum',
mode='magnitude')
return t, f, S_mag
Define a method to generate a Mel-spectrogram.
In [49]:
def mel_spectrogram(s, sr, n_fft, hop_length, n_mels, win='hann'):
# compute mel-spectrogram
S = librosa.feature.melspectrogram(y=s, sr=sr,
n_fft=n_fft,
hop_length=hop_length,
window=win,
n_mels=n_mels)
# mel-spectrogram magnitude
S_mag = np.abs(S)
# time and frequency coefficients
t = librosa.frames_to_time(np.arange(S_mag.shape[1]), sr=sr, hop_length=hop_length)
f = librosa.fft_frequencies(sr=sr, n_fft=n_fft)
return t, f, S_mag
Declaramos un método para graficar el espectrograma de entrada en dB.
In [50]:
def plot_spectrogram(S_dB, t, f, title):
plt.pcolormesh(t, f, S_dB)
plt.ylabel('Frequency [Hz]')
plt.xlabel('Time [s]')
plt.colorbar(format='%+2.0f dB')
plt.title('Power spectrogram in dB - {}'.format(title))
plt.show()
Define a function to plot Mel-spectrogram.
In [51]:
def plot_mel_spectrogram(S_dB, sr, hop_length, title, y_axis='hz'):
specshow(S_dB, sr=sr, hop_length=hop_length, x_axis='time', y_axis=y_axis)
plt.colorbar(format='%+2.0f dB')
plt.title('Mel-spectrogram in dB - {}'.format(title))
plt.show()
Establish the input arguments of the feature extraction to get a spectral representation of labeled audio samples.
In [52]:
# mel-spectrogram parameters
n_fft = 2046
mel_bands = 104
fft_overlap = 0.5
hop_length = int(n_fft * (1 - fft_overlap))
Calculamos la magnitud spectral en escala de Mel como representación de características de la señal de entrada.
In [53]:
_, _, S_mag = mel_spectrogram(s=waveform,
sr=sampling_rate,
n_fft=n_fft,
hop_length=hop_length,
n_mels=mel_bands)
Generamos el espectrogram mediante la conversión de la magnitud en escala Mel a dB y lo graficamos.
In [54]:
S_dB = librosa.amplitude_to_db(S_mag, ref=np.max)
print('[INFO] MFCC: Mel-spectrogram array - dtype: {}, (freq. bin x time frames): {}, dtype: {}'.format(S_dB.dtype, S_dB.shape, S_dB.dtype))
plot_mel_spectrogram(S_dB=S_dB, sr=sampling_rate, hop_length=hop_length, title=sample_tag)
[INFO] MFCC: Mel-spectrogram array - dtype: float32, (freq. bin x time frames): (104, 166), dtype: float32
Filtramos la señal de entrada para remover el sonido de baja frecuencia (orden 4, corte$@2kHz$). Graficamos la señal en el dominio del tiempo.
In [55]:
# filtered the input waveform
_, _, waveform = high_pass_filter(waveform,
sampling_rate,
f_ord=4,
f_hpf=2000)
plot_audio_signal(waveform, sampling_rate, sample_tag)
Calculamos y graficamos el espectrograma en escala de Mel de la señal filtrada.
In [56]:
_, _, S_mag = mel_spectrogram(s=waveform,
sr=sampling_rate,
n_fft=n_fft,
hop_length=hop_length,
n_mels=mel_bands)
S_dB = librosa.amplitude_to_db(S_mag, ref=np.max)
print('[INFO] MFCC: Mel-spectrogram array - dtype: {}, (freq. bin x time frames): {}, dtype: {}'.format(S_dB.dtype, S_dB.shape, S_dB.dtype))
plot_mel_spectrogram(S_dB=S_dB, sr=sampling_rate, hop_length=hop_length, title=sample_tag)
[INFO] MFCC: Mel-spectrogram array - dtype: float64, (freq. bin x time frames): (104, 166), dtype: float64
Normalizamos la señal filtrada.
In [57]:
# normalized the filtered signal
waveform = waveform / np.amax(waveform)
Aplicamos el algoritmo de reducción de ruido basado en spectral gating para suprimir el ruido de fondo.
In [58]:
waveform = nr.reduce_noise(y=waveform,
sr=sampling_rate,
n_fft=n_fft,
hop_length=hop_length)
Graficamos la señal normalizada sin ruido.
In [59]:
plot_audio_signal(waveform, sampling_rate, sample_tag)
Calculamos y desplegamos el espectrograma en escala de Mel de la señal sin ruido junto con la separación de fuentes harmónicas.
In [60]:
_, _, S_mag = mel_spectrogram(s=waveform,
sr=sampling_rate,
n_fft=n_fft,
hop_length=hop_length,
n_mels=mel_bands)
# perform harmonic source separation
S_mag = harmonic_source_separation(S_mag)
# convert amplitude to dB
S_dB = librosa.amplitude_to_db(S_mag, ref=np.max)
plot_mel_spectrogram(S_dB=S_dB, sr=sampling_rate, hop_length=hop_length, title=sample_tag)
Despleguemos una muestra espectral en dB como un arreglo de datos.
In [61]:
print('[INFO] Plot Mel-spectrogram magnitude as image array: {}'.format(S_dB.shape))
plt.imshow(S_dB)
[INFO] Plot Mel-spectrogram magnitude as image array: (104, 166)
Out[61]:
<matplotlib.image.AxesImage at 0x7f5c3e053460>
Define image processing constants.
In [62]:
# define pixel values
img_depth, img_val = 3, 255.0
# define dimensions of the resizing method
img_height, img_width = 256, 256
img_dims = (img_height, img_width)
# define interpolation method for resizing
intpol = cv.INTER_AREA
Perform spectrogram normalization for image processing.
In [63]:
# spectrogram normalization
S_dB -= S_dB.min()
# update normalized spectrogram in dB
S_dB /= (S_dB.max()- S_dB.min())
Execute image shrinking and flipping to the input spectrogram.
In [64]:
# shrink the image
S_img = cv.resize(S_dB,
img_dims,
interpolation=intpol)
# flip image
S_img = cv.flip(S_img, 0)
print('[INFO] Spectral image resized and flipped: {}'.format(S_img.shape))
[INFO] Spectral image resized and flipped: (256, 256)
Ejecutamos una conversión de espacio de color a RGB o escala de grises.
In [65]:
# color space conversion
S_img = (S_img * img_val).astype(np.uint8)
# apply JET color map as BGR format
S_img = cv.applyColorMap(S_img, cv.COLORMAP_JET)
if img_depth == 1:
# BGR2GRAY grayscale images
S_img = cv.cvtColor(S_img, cv.COLOR_BGR2GRAY)
plt.imshow(S_img, cmap='gray')
else:
# BGR2RGB color images
S_img = cv.cvtColor(S_img, cv.COLOR_BGR2RGB)
plt.imshow(S_img, cmap='jet')
Verifiquemos la escritura de imágenes en el sistema de archivos utilizando este ejemplo.
In [66]:
# Define the image file extension
img_ext = 'jpeg'
# Define the image input directory
img_dir = '{}/{}_imgs'.format(data_dir, sys_mode)
# Get audio tag
sample_tag = audio_file.split('/')[-2:][1].split('.')[0]
# Retrieve image filepath
img_sample = [sample_tag, img_ext]
img_sample = '.'.join(img_sample)
img_sample = '{}/{}'.format(label_file, img_sample)
img_path = os.path.join(img_dir, img_sample)
print(img_path)
# Store spectrogram as an image
#plt.imsave(img_path, S_img)
cv.imwrite(img_path, S_img)
# Set env variable with image filepath
/data/fquiros/projects/birdCLEF24/datasets/train_imgs/eucdov/XC760696.jpeg
Out[66]:
True
Desde el sistema de archivos, revisemos desde la consola del sistema la creación de la imagen correspondiente en formato JPEG
In [67]:
!ls -lha /data/fquiros/projects/birdCLEF24/datasets/train_imgs/eucdov/XC760696.jpeg
-rw-r--r-- 1 fquiros cluster 9.9K Sep 18 19:40 /data/fquiros/projects/birdCLEF24/datasets/train_imgs/eucdov/XC760696.jpeg
Carguemos los datos de la imagen JPEG previamente creada y mostremos su contenido usando matplotlib.
In [68]:
# get image without changes
image = cv.imread(img_path)
plt.imshow(image)
Out[68]:
<matplotlib.image.AxesImage at 0x7f5c9e15efe0>
Define a function to create a pipeline to pre-process and convert 1D-signal to 2D-images.
In [69]:
def gen_mel_spectral_image(filename,
n_fft,
hop_length,
mel_bands,
img_val,
img_depth,
img_dims,
train_dir=None,
dst_sr=None,
den=False,
f_ord=4,
f_hpf=2000,
int_pol=cv.INTER_AREA):
# define filepath to load audio sample
if train_dir == None:
filepath = filename
else:
filepath = os.path.join(train_dir, filename)
# perform waveform loading
wav_data, sampling_rate, duration = load_audio_data(filename=filepath, silent=True)
# resampling waveform
wav_data, sampling_rate = resampling(wav_data, sampling_rate, dst_fs=dst_sr, silent=True)
# denoising routine
if den:
# high-pass filtering
_, _, wav_data = high_pass_filter(wav_data,
sampling_rate,
f_ord=f_ord,
f_hpf=f_hpf)
# normalize audio signal
wav_data = wav_data / np.amax(wav_data)
# apply noise reduction
wav_data = nr.reduce_noise(y=wav_data,
sr=sampling_rate,
n_fft=n_fft,
hop_length=hop_length)
# compute mel-spectrogram in dB
_, _, S_mag = mel_spectrogram(s=wav_data,
sr=sampling_rate,
n_fft=n_fft,
hop_length=hop_length,
n_mels=mel_bands)
# final denoising step
if den:
# perform harmonic source separation
S_mag = harmonic_source_separation(S_mag)
# convert to dB
S_dB = librosa.amplitude_to_db(S_mag, ref=np.max)
# spectrogram normalization
S_dB -= S_dB.min()
# update normalized spectrogram in dB
S_dB /= (S_dB.max()- S_dB.min())
# shrink the image
S_img = cv.resize(S_dB,
img_dims,
interpolation=intpol)
# flip image
S_img = cv.flip(S_img, 0)
# color space conversion
S_img = (S_img * img_val).astype(np.uint8)
# apply JET color map as BGR format
S_img = cv.applyColorMap(S_img, cv.COLORMAP_JET)
# check number of channels
if img_depth == 1:
# BGR2GRAY grayscale images
S_img = cv.cvtColor(S_img, cv.COLOR_BGR2GRAY)
else:
# BGR2RGB color images
S_img = cv.cvtColor(S_img, cv.COLOR_BGR2RGB)
# Delete intermediate outputs
del wav_data, S_mag, S_dB
# Run garbage collector
gc.collect()
# return spectral image
return S_img
Define a method to extract spectral images by iterating through the train directory and applying audio processing to the data for spectral image generation.
In [70]:
def get_mel_spectral_data(filenames,
in_dir,
n_fft,
fft_overlap,
mel_bands,
img_val,
img_depth,
img_dims,
dir_tag='train',
labels=None,
dst_sr=None,
img_ext=None):
# Objects initialization
spec_imgs, spec_labels, spec_samples = list(), list(), list() # List of spectral images and its label
# Define hop length for spectrogram
hop_length = int(n_fft * (1 - fft_overlap))
# Iterate throught a list of filenames
for i, fn in enumerate(filenames):
# Define training directory: input
data_dir = '{}/{}_audio'.format(in_dir, dir_tag)
# Get the corresponding file
filename = fn
# Define the label value according the input
if labels is None:
# Invalid value
wav_label = np.NaN
else:
# Valid bird category
wav_label = labels[i]
# Create spectral image for a list of training files
S_img = gen_mel_spectral_image(filename,
n_fft,
hop_length,
mel_bands,
img_val,
img_depth,
img_dims,
data_dir,
dst_sr,
den=True)
# increase sample count
img_cnt = i + 1
# Verify whether image is invalid or not
nan_img = np.isnan(S_img).any()
# verification
if nan_img:
print('[WARN] Audio-FE {}/{} [{}]: Invalid spectral image [{}]'.format(img_cnt,
len(filenames),
filename,
wav_label))
else:
# Check whether the image storage is enabled or not
if img_ext is None:
# Update spectral images list
spec_imgs.append(S_img)
# Update labels list
spec_labels.append(wav_label)
else:
# Update training directory as images
data_dir = '{}/{}_imgs'.format(in_dir, dir_tag)
# Try to create a new directory for the incoming spectral images
try:
os.makedirs(data_dir)
print('[INFO] Create a directory for spectral images: {}'.format(data_dir))
# skip directory generation
except OSError as oe:
# Raise OSError when the directory exists
if oe.errno != errno.EEXIST:
raise
# Check if label is invalid
if pd.isnull(wav_label):
# define JPEG path
img_dir = data_dir
else:
# define JPEG path
img_dir = os.path.join(data_dir, wav_label)
# create the corresponding directory if it does not exist
try:
os.makedirs(img_dir)
print('[INFO] Create images directory for a target class: {}'.format(img_dir))
# skip directory generation
except OSError as oe:
# raise OSError when the directory exists
if oe.errno != errno.EEXIST:
raise
# Store images as JPEG files
spec_file = store_spectral_image(S_img, wav_label, filename, img_ext, img_dir)
# Append image observation to list
spec_samples.append(spec_file)
# Display basic sample info
print('[INFO] Audio-FE {}/{} [{}]: Spectral image [{}] - dtype = {}, dims = {}'.format(img_cnt,
len(filenames),
filename,
wav_label,
S_img.dtype,
S_img.shape))
# delete spectral image object
del S_img
# run garbage collector
gc.collect()
if img_ext is None:
# convert the list of spectral images into an array
data = np.stack(spec_imgs, axis=0)
# get array of classes
classes = np.array(spec_labels)
# delete list of spectral images
del spec_imgs, spec_labels
# run garbage collector
gc.collect()
# data array dimensions with its labels
print('[INFO] {} data array of type {} with {} labels'.format(data.shape, data.dtype, classes.shape))
return data, classes
else:
# define transcription filename
meta_file = os.path.join(in_dir, '{}_img_metadata.{}'.format(dir_tag, 'csv'))
# create a transcription file of the labeled dataset
create_dataset_file(meta_file, spec_samples)
# delete object functions
del spec_samples
# run garbage collector
gc.collect()
Exercise the FE method to get a data array with Mel-spectrogram of WAV samples from multi-species of birds. Perform time measurement of this module.
In [ ]:
# feature extraction - Mel-spectrogram images
t0 = time.process_time() # time measurement
# execute FE method
data, classes = get_mel_spectral_data(filenames,
data_dir,
n_fft,
fft_overlap,
mel_bands,
img_val,
img_depth,
img_dims,
dir_tag='train',
labels=labels,
dst_sr=sampling_rate)
# run garbage collector
gc.collect()
# GPU seconds elapsed (FE)
t1 = time.process_time() - t0
print('[INFO] Data features extraction - duration = {:.3f}s'.format(float(t1)))
# GPU seconds to hours-minutes-seconds format
th, tm, ts = s2hms(t1)
print('[INFO] Data features extraction - duration = ({:.3f} h, {:.3f} min, {:.3f} s)'.format(float(th),
float(tm),
float(ts)))
Estructura de datos¶
Dentro de nuestro dataset personalizado, contamos con imágenes pre-generadas, puesto que la extracción de características desde archivos de audio resulta ser más extensivo en comparación a tener las imágenes espectrales listas.
In [71]:
%ls /data/fquiros/projects/birdCLEF24/datasets
20240918-193253_train.csv findsounds.tar.gz train_audio/ birdclef-2024.zip sample_submission.csv train_img_metadata.csv eBird_Taxonomy_v2021.csv test_audio/ train_imgs/ findsounds/ test_soundscapes/ train_metadata.csv
In [72]:
%ls /data/fquiros/projects/birdCLEF24/datasets/train_imgs
barswa/ blrwar1/ commoo3/ eaywag1/ graher1/ grywag/ lirplo/ zitcis1/ bcnher/ comgre/ comros/ eucdov/ grewar3/ hoopoe/ litgre1/ bkwsti/ comkin1/ comsan/ eurcoo/ grnsan/ houspa/ woosan/
Actualizamos argumentos de entrada a la etapa de procesamiento de imágenes.
In [73]:
# Define image extension
img_ext = 'png'
# Update training directory
train_dir = '{}/{}_imgs'.format(data_dir, sys_mode)
# Define timestamp for training metadata
ts = datetime.datetime.now().strftime('%Y%m%d-%H%M%S')
# Define the input filepath
meta_file = os.path.join(data_dir, '{}_{}_imgs.{}'.format(ts, sys_mode, file_ext))
train_dir, meta_file
Out[73]:
('/data/fquiros/projects/birdCLEF24/datasets/train_imgs',
'/data/fquiros/projects/birdCLEF24/datasets/20240918-194057_train_imgs.csv')
Obtenemos una lista de todas las imágenes contenidas contenido en el directorio de entrenamiento.
In [74]:
# Init
train_fpaths = list()
# Get the respective filepaths of the training samples using JPEG extension
train_fpaths = find_data_samples(train_dir, ext=img_ext)
[INFO] Total data samples -> 11000:/data/fquiros/projects/birdCLEF24/datasets/train_imgs
Generamos una lista de las imágenes etiquetadas sin mezclar aleatoriamente.
In [75]:
# Labeled items for dataset transcription
train_samples = get_tagged_samples(train_fpaths, ',', shuffle=False)
Creamos una transcripción personalizada como archivo CSV de el set imágenes etiquetadas, generadas a partir de archivos de audio de la base de datos de BirdCLEF24.
In [76]:
# Run method to create CSV transcription of labeled database
create_dataset_file(meta_file, train_samples)
[INFO] Length: 11000 samples -> CSV file created!
Creamos un nuevo marco de datos de entrada para su procesamiento y exploración.
In [77]:
# Load CSV file to generate dataframe
df_in = load_dataset_file(meta_file, headers=['filename', 'primary_label'])
[INFO] Dataset size: (11000, 2) -> Display info of 25 samples randomly selected...
filename primary_label
1691 /data/fquiros/projects/birdCLEF24/datasets/tra... grewar3
2102 /data/fquiros/projects/birdCLEF24/datasets/tra... eucdov
1353 /data/fquiros/projects/birdCLEF24/datasets/tra... graher1
3547 /data/fquiros/projects/birdCLEF24/datasets/tra... comkin1
10772 /data/fquiros/projects/birdCLEF24/datasets/tra... grnsan
5031 /data/fquiros/projects/birdCLEF24/datasets/tra... barswa
3594 /data/fquiros/projects/birdCLEF24/datasets/tra... comkin1
1129 /data/fquiros/projects/birdCLEF24/datasets/tra... graher1
10665 /data/fquiros/projects/birdCLEF24/datasets/tra... grnsan
8270 /data/fquiros/projects/birdCLEF24/datasets/tra... lirplo
319 /data/fquiros/projects/birdCLEF24/datasets/tra... bkwsti
195 /data/fquiros/projects/birdCLEF24/datasets/tra... bkwsti
8567 /data/fquiros/projects/birdCLEF24/datasets/tra... eaywag1
2750 /data/fquiros/projects/birdCLEF24/datasets/tra... commoo3
3587 /data/fquiros/projects/birdCLEF24/datasets/tra... comkin1
4762 /data/fquiros/projects/birdCLEF24/datasets/tra... blrwar1
8062 /data/fquiros/projects/birdCLEF24/datasets/tra... lirplo
6307 /data/fquiros/projects/birdCLEF24/datasets/tra... comros
1947 /data/fquiros/projects/birdCLEF24/datasets/tra... grewar3
7300 /data/fquiros/projects/birdCLEF24/datasets/tra... bcnher
1223 /data/fquiros/projects/birdCLEF24/datasets/tra... graher1
8739 /data/fquiros/projects/birdCLEF24/datasets/tra... eaywag1
4395 /data/fquiros/projects/birdCLEF24/datasets/tra... zitcis1
8055 /data/fquiros/projects/birdCLEF24/datasets/tra... lirplo
3914 /data/fquiros/projects/birdCLEF24/datasets/tra... comkin1
[INFO] Display number of samples per class:
primary_label
bkwsti 500
houspa 500
woosan 500
eurcoo 500
comgre 500
eaywag1 500
lirplo 500
litgre1 500
bcnher 500
hoopoe 500
comros 500
comsan 500
barswa 500
blrwar1 500
zitcis1 500
comkin1 500
grywag 500
commoo3 500
eucdov 500
grewar3 500
graher1 500
grnsan 500
Name: count, dtype: int64
[INFO] Number of unique names of birds: 22
[INFO] Target bird names: ['bkwsti' 'houspa' 'graher1' 'grewar3' 'eucdov' 'commoo3' 'grywag'
'comkin1' 'zitcis1' 'blrwar1' 'barswa' 'comsan' 'comros' 'hoopoe'
'bcnher' 'litgre1' 'lirplo' 'eaywag1' 'comgre' 'eurcoo' 'woosan' 'grnsan']
[INFO] Loading /data/fquiros/projects/birdCLEF24/datasets/20240918-194057_train_imgs.csv file as DF of (11000, 2) shape...
[INFO] Dataframe memory usage: 2.1 MB
Grafiquemos la distribución de los datos en la estructura de entrada, producto de la transcripción.
In [78]:
# Store data distribution chart
data_distribution_chart(df_in)
[INFO] Target bird labels: ['bkwsti' 'houspa' 'graher1' 'grewar3' 'eucdov' 'commoo3' 'grywag' 'comkin1' 'zitcis1' 'blrwar1' 'barswa' 'comsan' 'comros' 'hoopoe' 'bcnher' 'litgre1' 'lirplo' 'eaywag1' 'comgre' 'eurcoo' 'woosan' 'grnsan'] [INFO] Number of unique names of birds: 22 [INFO] Target bird classes: [ 2 17 12 13 10 6 15 5 21 3 0 8 7 16 1 19 18 9 4 11 20 14]
Obtenemos el dataframe de las vocalizaciones de especies con más repiticiones dentro del set de datos de la competición BirdCLEF 2024.
In [79]:
# Retrieve an input dataframe that considers classes with most samples
df_in = get_df_classes_max_count(df_in)
[INFO] Create the dataframe of interest with (11000, 2) dimensions [INFO] Dataframe memory usage: 2.1 MB
Ejecutamos la visualización EDA con el fin de estudiar el balanceo de datos.
In [80]:
# Plot the data distribution chart using the maximum count dataframe
data_distribution_chart(df_in)
[INFO] Target bird labels: ['barswa' 'bcnher' 'bkwsti' 'blrwar1' 'comgre' 'comkin1' 'commoo3' 'comros' 'comsan' 'eaywag1' 'eucdov' 'eurcoo' 'graher1' 'grewar3' 'grnsan' 'grywag' 'hoopoe' 'houspa' 'lirplo' 'litgre1' 'woosan' 'zitcis1'] [INFO] Number of unique names of birds: 22 [INFO] Target bird classes: [ 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21]
Actualizamos la lista de las rutas de las imágenes y sus respetivas etiquetadas para la extración de características de estas señales.
In [81]:
# Get dataframe of labels
df_labels = df_in.primary_label
# List of target labels
labels = df_labels.values.tolist()
# Get the filenames of WAV samples
filenames = df_in.filename.values.tolist()
Procesamiento de imágenes¶
Definimos un índice de forma aleatoria para obtener una imagen de la lista correspondiente.
In [85]:
# define a random index of audio files
rand_value = random.sample(range(len(df_in)), 1)
index = int(rand_value[0])
img_file = os.path.join(train_dir, filenames[index])
label_file = labels[index]
img_file, label_file
Out[85]:
('/data/fquiros/projects/birdCLEF24/datasets/train_imgs/grnsan/XC754737.png',
'grnsan')
Cargamos y desplegamos la imagen determinada de forma aleatoria de la lista de imágenes.
In [86]:
# get image data without changes
img = cv.imread(img_file, cv.IMREAD_UNCHANGED)
print('[INFO] Loading spectral image {}/{} - filename={}, class={}, image size={}'.format(index,
len(df_in),
filenames[index],
labels[index],
img.shape))
# plot the respective image data
plt.imshow(img)
[INFO] Loading spectral image 7376/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/grnsan/XC754737.png, class=grnsan, image size=(256, 256, 3)
Out[86]:
<matplotlib.image.AxesImage at 0x7f5c9e1eb130>
Definimos un método que nos permita crear un arreglo de datos con las imágenes espectrales y sus correspondientes etiquetas a partir de la transcripción del set de datos.
In [87]:
def load_spectral_images(filename):
# desired output parameters
list_imgs, list_labels = list(), list()
# Retrive filenames and labels from input data transcription
df_in = load_dataset_file(filename, headers=['filename', 'primary_label'], dbg=False)
# Get dataframe of labels
df_labels = df_in.primary_label
# List of target labels
labels = df_labels.values.tolist()
# Iterate through the filenames of WAV samples
filenames = df_in.filename.values.tolist()
# number of samples
n_imgs = len(filenames)
# main loop
for i, fn in enumerate(filenames):
# update filename
filename = fn
# get image without changes
image = cv.imread(filename, cv.IMREAD_UNCHANGED)
# get image label
label = labels[i]
print('[INFO] Loading spectral image {}/{} - filename={}, class={}, image size={}'.format(i + 1,
n_imgs,
filename,
label,
image.shape))
# append image name to list
list_imgs.append(image)
# append label image to list
list_labels.append(label)
# how many spectral images did we get?
print('[INFO] {} images'.format(len(list_imgs)))
# a list of many time-frequency spectrograms is made into 1 big array
data = np.array(list_imgs)
# data array dimensions
print('[INFO] {} image data array - dtype: {}'.format(data.shape, data.dtype))
classes = np.array(list_labels)
print('[INFO] {} labels array - dtype: {}'.format(classes.shape, classes.dtype))
# delete function objects
del labels, filenames, list_imgs, list_labels
# run garbage collector
gc.collect()
# return data array
return data, classes
Generamos los arreglos de datos y etiquetas que utilizaremos para la minería de datos.
In [88]:
# Load spectral images data and its labels from the metadata file
data, classes = load_spectral_images(meta_file)
[INFO] Display number of samples per class: primary_label bkwsti 500 houspa 500 woosan 500 eurcoo 500 comgre 500 eaywag1 500 lirplo 500 litgre1 500 bcnher 500 hoopoe 500 comros 500 comsan 500 barswa 500 blrwar1 500 zitcis1 500 comkin1 500 grywag 500 commoo3 500 eucdov 500 grewar3 500 graher1 500 grnsan 500 Name: count, dtype: int64 [INFO] Number of unique names of birds: 22 [INFO] Loading /data/fquiros/projects/birdCLEF24/datasets/20240918-194057_train_imgs.csv file as DF of (11000, 2) shape... [INFO] Dataframe memory usage: 2.1 MB [INFO] Loading spectral image 1/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/bkwsti/XC413271.png, class=bkwsti, image size=(256, 256, 3) [INFO] Loading spectral image 2/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/bkwsti/XC721370.png, class=bkwsti, image size=(256, 256, 3) [INFO] Loading spectral image 3/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/bkwsti/XC436974.png, class=bkwsti, image size=(256, 256, 3) [INFO] Loading spectral image 4/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/bkwsti/XC194511.png, class=bkwsti, image size=(256, 256, 3) [INFO] Loading spectral image 5/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/bkwsti/XC284629.png, class=bkwsti, image size=(256, 256, 3) [INFO] Loading spectral image 6/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/bkwsti/XC658287.png, class=bkwsti, image size=(256, 256, 3) [INFO] Loading spectral image 7/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/bkwsti/XC503215.png, class=bkwsti, image size=(256, 256, 3) [INFO] Loading spectral image 8/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/bkwsti/XC185109.png, class=bkwsti, image size=(256, 256, 3) [INFO] Loading spectral image 9/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/bkwsti/XC786975.png, class=bkwsti, image size=(256, 256, 3) [INFO] Loading spectral image 10/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/bkwsti/XC361994.png, class=bkwsti, image size=(256, 256, 3) [INFO] Loading spectral image 11/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/bkwsti/XC175409.png, class=bkwsti, image size=(256, 256, 3) [INFO] Loading spectral image 12/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/bkwsti/XC419885.png, class=bkwsti, image size=(256, 256, 3) [INFO] Loading spectral image 13/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/bkwsti/XC649285.png, class=bkwsti, image size=(256, 256, 3) [INFO] Loading spectral image 14/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/bkwsti/XC690160.png, class=bkwsti, image size=(256, 256, 3) [INFO] Loading spectral image 15/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/bkwsti/XC277296.png, class=bkwsti, image size=(256, 256, 3) [INFO] Loading spectral image 16/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/bkwsti/XC795870.png, class=bkwsti, image size=(256, 256, 3) [INFO] Loading spectral image 17/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/bkwsti/XC269609.png, class=bkwsti, image size=(256, 256, 3) [INFO] Loading spectral image 18/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/bkwsti/XC573631.png, class=bkwsti, image size=(256, 256, 3) [INFO] Loading spectral image 19/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/bkwsti/XC184425.png, class=bkwsti, image size=(256, 256, 3) [INFO] Loading spectral image 20/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/bkwsti/XC236580.png, class=bkwsti, image size=(256, 256, 3) [INFO] Loading spectral image 21/11000 - 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filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/grnsan/XC579538.png, class=grnsan, image size=(256, 256, 3) [INFO] Loading spectral image 10900/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/grnsan/XC497064.png, class=grnsan, image size=(256, 256, 3) [INFO] Loading spectral image 10901/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/grnsan/XC615244.png, class=grnsan, image size=(256, 256, 3) [INFO] Loading spectral image 10902/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/grnsan/XC580688.png, class=grnsan, image size=(256, 256, 3) [INFO] Loading spectral image 10903/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/grnsan/XC209221.png, class=grnsan, image size=(256, 256, 3) [INFO] Loading spectral image 10904/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/grnsan/XC697918.png, class=grnsan, image size=(256, 256, 3) [INFO] Loading spectral image 10905/11000 - 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filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/grnsan/XC549266.png, class=grnsan, image size=(256, 256, 3) [INFO] Loading spectral image 10978/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/grnsan/XC579133.png, class=grnsan, image size=(256, 256, 3) [INFO] Loading spectral image 10979/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/grnsan/XC597777.png, class=grnsan, image size=(256, 256, 3) [INFO] Loading spectral image 10980/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/grnsan/XC838660.png, class=grnsan, image size=(256, 256, 3) [INFO] Loading spectral image 10981/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/grnsan/XC642159.png, class=grnsan, image size=(256, 256, 3) [INFO] Loading spectral image 10982/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/grnsan/XC751085.png, class=grnsan, image size=(256, 256, 3) [INFO] Loading spectral image 10983/11000 - 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filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/grnsan/XC211882.png, class=grnsan, image size=(256, 256, 3) [INFO] Loading spectral image 10990/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/grnsan/XC658875.png, class=grnsan, image size=(256, 256, 3) [INFO] Loading spectral image 10991/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/grnsan/XC140653.png, class=grnsan, image size=(256, 256, 3) [INFO] Loading spectral image 10992/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/grnsan/XC586152.png, class=grnsan, image size=(256, 256, 3) [INFO] Loading spectral image 10993/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/grnsan/XC840089.png, class=grnsan, image size=(256, 256, 3) [INFO] Loading spectral image 10994/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/grnsan/XC283867.png, class=grnsan, image size=(256, 256, 3) [INFO] Loading spectral image 10995/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/grnsan/XC656836.png, class=grnsan, image size=(256, 256, 3) [INFO] Loading spectral image 10996/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/grnsan/XC326538.png, class=grnsan, image size=(256, 256, 3) [INFO] Loading spectral image 10997/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/grnsan/XC828569.png, class=grnsan, image size=(256, 256, 3) [INFO] Loading spectral image 10998/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/grnsan/XC584394.png, class=grnsan, image size=(256, 256, 3) [INFO] Loading spectral image 10999/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/grnsan/XC488380.png, class=grnsan, image size=(256, 256, 3) [INFO] Loading spectral image 11000/11000 - filename=/data/fquiros/projects/birdCLEF24/datasets/train_imgs/grnsan/XC367641.png, class=grnsan, image size=(256, 256, 3) [INFO] 11000 images [INFO] (11000, 256, 256, 3) image data array - dtype: uint8 [INFO] (11000,) labels array - dtype: <U7
Minería de datos¶
Definimos un método que nos permite vectorizar el arreglo de datos de entrada.
In [89]:
def data_vectorization(data):
# depth: grayscale
zdim = 1
# vectorize
dims = data.shape
# image data
if len(dims) == 4:
# dims: N (samples), ydim (height), xdim (width), zdim (depth)
N, ydim, xdim, zdim = dims
# time-series data
else:
# dims: N (samples), ydim (features), xdim (timesteps)
N, ydim, xdim = dims
# reshape input array
data = data.reshape(N, xdim * ydim * zdim)
print('[INFO] Vector data size: {}, dtype: {}'.format(data.shape, data.dtype))
# return data vector
return data, xdim, ydim, zdim
Ejecutamos la rutina de vectorización para cada una de las entradas del arreglo de datos.
In [90]:
# Data mining: vectorization
data, width, height, depth = data_vectorization(data)
[INFO] Vector data size: (11000, 196608), dtype: uint8
Escalamiento de datos¶
Instanciamos un método que estandariza un vector de datos.
In [91]:
def data_standardization(data):
# standardize
scaler = StandardScaler(copy=False)
data = scaler.fit_transform(data)
del scaler
gc.collect()
print('[INFO] Standardized vector size: {}, dtype: {}'.format(data[0:1].shape, data.dtype))
return data
Definimos también una función que normaliza un vector de datos.
In [92]:
def data_normalization(data, norm='l2'):
# normalization scaling
scaler = Normalizer(norm=norm, copy=False)
data = scaler.fit_transform(data)
del scaler
gc.collect()
print('[INFO] Normalized (norm={}) data size: {}, dtype: {}'.format(norm, data[0:1].shape, data.dtype))
return data
Declaramos un método que efectúa la normalización min-max al vector de datos.
In [93]:
def data_min_max_scaling(data, min_max):
# min-max scaling
scaler = MinMaxScaler(feature_range=min_max, copy=False)
data = scaler.fit_transform(data)
del scaler
gc.collect()
print('[INFO] Min-Max Scaled data size: {}, dtype: {}'.format(data[0:1].shape, data.dtype))
return data
Instanciamos una función para aplicar el escalamiento máximo-absoluto a un vector de datos.
In [94]:
def data_max_abs_scaling(data):
# max-abs scaling
scaler = MaxAbsScaler(copy=False)
data = scaler.fit_transform(data)
del scaler
gc.collect()
print('[INFO] Max-Abs Scaled data size: {}, dtype: {}'.format(data[0:1].shape, data.dtype))
return data
Establecemos el método principal que implementa los métodos de escalamiento de datos.
In [95]:
def data_scaling(data, dtype, scaler=None, min_max=(-1, 1)):
# Execute data scaling
if scaler == 'min_max':
# Minimum-maximum normalization
data = data_min_max_scaling(data, min_max=min_max)
elif scaler == 'max_abs':
# Maximum-absolute normalization
data = data_max_abs_scaling(data)
elif scaler == 'norm_max':
# Maximum normalization
data = data_normalization(data, norm='max')
elif scaler == 'norm_l1':
# L1 normalization
data = data_normalization(data, norm='l1')
elif scaler == 'norm_l2':
# L2 normalization
data = data_normalization(data, norm='l2')
elif scaler == 'norm':
# Default normalization
data = data_normalization(data)
elif scaler == 'std':
# Standardization
data = data_standardization(data)
else:
print('[INFO] Unscaled vector size: {}, dtype: {}'.format(data[0:1].shape, data.dtype))
# Set output data type
data = data.astype(dtype)
# Return data array
return data
Execute scaling method to the data vector.
In [96]:
# 'min_max': NO
# 'max_abs': YES
# 'norm_max': YES
# 'norm_l1': NO
# 'norm' & 'norm_l2': NO
# 'std': YES
# Default: 'std'
data_type = 'float32' # vector data type
dscaler = None # data scaler option
# Data mining: scaling
data = data_scaling(data, data_type, dscaler)
[INFO] Unscaled vector size: (1, 196608), dtype: uint8
Declare a function to plot samples from a large data vector with its corresponding class label.
In [97]:
def data_plotting(data,
y_dim, x_dim, n_ch,
path=None,
tag=None,
classes=None,
grid_rows=3, grid_cols=3, color_map='jet'):
# Init
fig = plt.figure()
# Generate random sample indexes
len_data = len(data)
samples_range = range(len_data)
# Grid dimensions: 3x3 by default
n_samples = grid_rows * grid_cols
# Adjust number of samples with the data length
if len_data < n_samples:
n_samples = len_data
# Create data grid
rand_index = random.sample(samples_range, n_samples)
for i in range(0, n_samples):
sample_id = rand_index[i]
sample = data[sample_id]
plt.subplot(grid_rows, grid_cols, i + 1)
if isinstance(sample, tuple):
# Batch data tuple
spec, sample_label = sample
# Take one spectrogram from the batch
spec = spec[0]
sample_label = sample_label[0]
else:
# Single data sample
spec = sample
if classes is not None:
sample_label = classes[sample_id]
else:
sample_label = sample_id
# Spectral image
spectrogram = np.reshape(spec, (y_dim, x_dim, n_ch))
# Avoid 3-dimension for plotting
img = spectrogram[:, :, 0]
# Set a title for image batch title
plt.title('Sample: {}, Label: {}'.format(sample_id + 1, sample_label))
# Plot using colormap
if n_ch == 1:
plt.imshow(img, cmap=plt.get_cmap('gray'))
else:
plt.imshow(img, cmap=plt.get_cmap(color_map))
# Keep spacing between subplots
fig.tight_layout()
# Show or store the corresponding figure
if path is None:
# Show data batch image
plt.show()
else:
if tag is None:
# Set timestamp tag
tag = datetime.datetime.now().strftime('%Y%m%d-%H%M%S')
# Create filename of the plot
f_name = '{}_img_batch.pdf'.format(tag)
# Datafile path
img_path = os.path.join(path, f_name)
# Save plot file
fig.savefig(img_path)
print('[INFO] Saving data batch plot file: {}'.format(img_path))
plt.close(fig)
# Delete function objects
del fig, img, spectrogram, spec, sample
# Run garbage collector
gc.collect()
Finalmente, producimos una visualización con imágenes y clases selecionadas de forma aleatoria.
In [99]:
# EDA: random sample of data vector
data_plotting(data=data, y_dim=height, x_dim=width, n_ch=depth, classes=classes)
Codificación de datos¶
Definimos ahora un método para codificar las classes en un arreglo de etiquetas numéricas.
In [100]:
def label_encoding(labels, data_type, to_col=False):
# label encoding
encoder = LabelEncoder()
encoder.fit(labels)
# we keep (and print) the number of classes
target_classes = list(encoder.classes_)
print('[INFO] {} classes - {}'.format(len(target_classes), target_classes))
enc_labels = encoder.transform(labels)
if to_col:
# make a row vector a column vector
classes_num = enc_labels.reshape(-1, 1)
else:
classes_num = enc_labels
# update labels data type
classes_num = classes_num.astype(data_type)
print('[INFO] Ordinal scheme size: {}, dtype={}'.format(classes_num.shape, classes_num.dtype))
# delete encoding object
del encoder
# run garbage collector
gc.collect()
return classes_num, target_classes
Instanciamos el método de codificación One-Hot para la transformación de etiquetas numéricas a un esquema de codificación binaria.
In [101]:
def one_hot_encoding(classes_num, data_type):
# make a row vector to a column vector, as needed by OneHotEncoder, using reshape(-1,1)
target = classes_num.reshape(-1, 1)
# one-hot encoding
encoder = OneHotEncoder(sparse_output=False)
encoder.fit(target)
classes_num_1hot = encoder.transform(target)
# update data type
classes_num_1hot = classes_num_1hot.astype(data_type)
print('[INFO] One-Hot scheme size: ({}, {}), dtype={}'.format(classes_num_1hot.shape[0],
classes_num_1hot.shape[1],
classes_num_1hot.dtype))
# delete encoding object
del encoder
# run garbage collector
gc.collect()
return classes_num_1hot
Ejecutamos la rutina de codificación de etiquetas usando el esquema One-Hot.
In [102]:
# Data mining: encoding
one_hot = True
if one_hot:
# Run One-Hot scheme
classes_num, target_labels = label_encoding(classes, data_type)
classes_num = one_hot_encoding(classes_num, data_type)
else:
# Ordinal scheme
classes_num, target_labels = label_encoding(classes, data_type, to_col=True)
print('[INFO] BIRDs classes array: dtype={}, shape={}, nan={}'.format(classes_num.dtype, classes_num.shape,
np.isnan(classes_num).any()))
[INFO] 22 classes - ['barswa', 'bcnher', 'bkwsti', 'blrwar1', 'comgre', 'comkin1', 'commoo3', 'comros', 'comsan', 'eaywag1', 'eucdov', 'eurcoo', 'graher1', 'grewar3', 'grnsan', 'grywag', 'hoopoe', 'houspa', 'lirplo', 'litgre1', 'woosan', 'zitcis1'] [INFO] Ordinal scheme size: (11000,), dtype=float32 [INFO] One-Hot scheme size: (11000, 22), dtype=float32 [INFO] BIRDs classes array: dtype=float32, shape=(11000, 22), nan=False
Establecemos un método que nos permite generar información sobre el balance de clases.
In [103]:
def get_data_balance(classes_num, dtag='DATA'):
# verify one-hot encoding
one_hot = (classes_num.shape[1] != 1)
# get row vectors of ground truth and prediction column vectors
if one_hot:
# decode one-hot scheme
cnt_classes = np.argmax(classes_num, axis=1)
else:
# decode ordinal scheme
cnt_classes = classes_num.reshape(1, -1)[0]
# verify amount of samples per class in data SPLIT
cnt_classes = cnt_classes.tolist()
# create counter object
cnt_obj = Counter(cnt_classes)
print('[INFO] Number of samples for each category in {} set:'.format(dtag))
for k in sorted(cnt_obj.keys()):
print('[INFO] {}:{}'.format(int(k), cnt_obj[k]))
return cnt_obj, cnt_classes
Obtenemos el balanceo de clases actual que manejamos en nuestro arreglo de etiquetas.
In [104]:
_, _ = get_data_balance(classes_num)
[INFO] Number of samples for each category in DATA set: [INFO] 0:500 [INFO] 1:500 [INFO] 2:500 [INFO] 3:500 [INFO] 4:500 [INFO] 5:500 [INFO] 6:500 [INFO] 7:500 [INFO] 8:500 [INFO] 9:500 [INFO] 10:500 [INFO] 11:500 [INFO] 12:500 [INFO] 13:500 [INFO] 14:500 [INFO] 15:500 [INFO] 16:500 [INFO] 17:500 [INFO] 18:500 [INFO] 19:500 [INFO] 20:500 [INFO] 21:500
Partición de datos¶
Instanciamos un método que nos permita generar los porciones de datos etiquetados para entrenamiento, validación y pruebas.
In [105]:
def prepare_datasets(data,
classes_num,
y_dim,
x_dim,
n_channels,
test_size,
random_split,
n_splits=1):
# Init: train-val-test splits
X_train, X_val, X_test, y_train, y_val, y_test = [], [], [], [], [], []
# Dataset splits:
# 1. training data
# 2. testing (evaluation) data
# 3. validation data
if random_split:
# perform random split: train-test
X_train, X_test, y_train, y_test = train_test_split(data,
classes_num,
test_size=test_size,
random_state=0,
stratify=classes_num)
# delete input data-labels array
del data, classes_num
# run garbage collector
gc.collect()
# perform random split: train-val
X_train, X_val, y_train, y_val = train_test_split(X_train,
y_train,
test_size=test_size,
random_state=42,
stratify=y_train)
print('[INFO] Random split - Training: {}'.format(len(X_train)))
print('[INFO] Random split - Testing: {}'.format(len(X_test)))
print('[INFO] Random split - Validation: {}'.format(len(X_val)))
else:
# perform stratified split: train-test
splitter = StratifiedShuffleSplit(n_splits=n_splits, test_size=test_size, random_state=0)
splits = splitter.split(data, classes_num)
for train_index, test_index in splits:
print('[INFO] Train-test stratified split - Training: {}'.format(len(train_index)))
print('[INFO] Train-test stratified split - Testing: {}'.format(len(test_index)))
X_train, X_test = data[train_index], data[test_index]
y_train, y_test = classes_num[train_index], classes_num[test_index]
# perform stratified split: train-val
splits = splitter.split(X_train, y_train)
for train_index, val_index in splits:
print('[INFO] Train-val stratified split - Training: {}'.format(len(train_index)))
print('[INFO] Train-val stratified split - Validation: {}'.format(len(val_index)))
X_train, X_val = data[train_index], data[val_index]
y_train, y_val = classes_num[train_index], classes_num[val_index]
# delete splitter object
del splitter, data, classes_num
# run garbage collector
gc.collect()
# 2D-array reshaping for TRAIN split
print('[INFO] Reshape TRAIN input data {} back to matrix form...'.format(X_train.shape))
X_train = X_train.reshape(X_train.shape[0], x_dim, y_dim, n_channels)
print('[INFO] Done! TRAIN input data: shape={}, dtype={}'.format(X_train.shape, X_train.dtype))
# 2D-array reshaping for TEST split
print('[INFO] Reshape TEST input data {} back to matrix form...'.format(X_test.shape))
X_test = X_test.reshape(X_test.shape[0], x_dim, y_dim, n_channels)
print('[INFO] Done! TEST input data: shape={}, dtype={}'.format(X_test.shape, X_test.dtype))
# 2D-array reshaping for VAL split
print('[INFO] Reshape VAL input data {} back to matrix form...'.format(X_val.shape))
X_val = X_val.reshape(X_val.shape[0], x_dim, y_dim, n_channels)
print('[INFO] Done! VAL input data: shape={}, dtype={}'.format(X_val.shape, X_val.dtype))
# Return data and label splits: train, test, and val
return X_train, X_test, X_val, y_train, y_test, y_val
Ejecutamos la particiación del vector de datos etiquetados para el entrenamiento del modelo, su validación y la evaluación del mismo.
In [159]:
# Data mining: split data vector
test_size = 0.2
rand_split = True
print('[INFO] Split the dataset - Train set split: {}%, Test set split: {}%'.format((1-test_size)*100,
test_size*100))
train_set, test_set, val_set, \
train_classes, test_classes, val_classes = prepare_datasets(data=data,
classes_num=classes_num,
y_dim=height,
x_dim=width,
n_channels=depth,
test_size=test_size,
random_split=rand_split)
[INFO] Split the dataset - Train set split: 80.0%, Test set split: 20.0%
--------------------------------------------------------------------------- MemoryError Traceback (most recent call last) Cell In[159], line 7 3 rand_split = True 4 print('[INFO] Split the dataset - Train set split: {}%, Test set split: {}%'.format((1-test_size)*100, 5 test_size*100)) 6 train_set, test_set, val_set, \ ----> 7 train_classes, test_classes, val_classes = prepare_datasets(data=data, 8 classes_num=classes_num, 9 y_dim=height, 10 x_dim=width, 11 n_channels=depth, 12 test_size=test_size, 13 random_split=rand_split) Cell In[105], line 27, in prepare_datasets(***failed resolving arguments***) 25 gc.collect() 26 # perform random split: train-val ---> 27 X_train, X_val, y_train, y_val = train_test_split(X_train, 28 y_train, 29 test_size=test_size, 30 random_state=42, 31 stratify=y_train) 32 print('[INFO] Random split - Training: {}'.format(len(X_train))) 33 print('[INFO] Random split - Testing: {}'.format(len(X_test))) File /opt/python/miniconda3/envs/python-ml-dl/lib/python3.10/site-packages/sklearn/utils/_param_validation.py:213, in validate_params.<locals>.decorator.<locals>.wrapper(*args, **kwargs) 207 try: 208 with config_context( 209 skip_parameter_validation=( 210 prefer_skip_nested_validation or global_skip_validation 211 ) 212 ): --> 213 return func(*args, **kwargs) 214 except InvalidParameterError as e: 215 # When the function is just a wrapper around an estimator, we allow 216 # the function to delegate validation to the estimator, but we replace 217 # the name of the estimator by the name of the function in the error 218 # message to avoid confusion. 219 msg = re.sub( 220 r"parameter of \w+ must be", 221 f"parameter of {func.__qualname__} must be", 222 str(e), 223 ) File /opt/python/miniconda3/envs/python-ml-dl/lib/python3.10/site-packages/sklearn/model_selection/_split.py:2805, in train_test_split(test_size, train_size, random_state, shuffle, stratify, *arrays) 2801 train, test = next(cv.split(X=arrays[0], y=stratify)) 2803 train, test = ensure_common_namespace_device(arrays[0], train, test) -> 2805 return list( 2806 chain.from_iterable( 2807 (_safe_indexing(a, train), _safe_indexing(a, test)) for a in arrays 2808 ) 2809 ) File /opt/python/miniconda3/envs/python-ml-dl/lib/python3.10/site-packages/sklearn/model_selection/_split.py:2807, in <genexpr>(.0) 2801 train, test = next(cv.split(X=arrays[0], y=stratify)) 2803 train, test = ensure_common_namespace_device(arrays[0], train, test) 2805 return list( 2806 chain.from_iterable( -> 2807 (_safe_indexing(a, train), _safe_indexing(a, test)) for a in arrays 2808 ) 2809 ) File /opt/python/miniconda3/envs/python-ml-dl/lib/python3.10/site-packages/sklearn/utils/_indexing.py:267, in _safe_indexing(X, indices, axis) 265 return _polars_indexing(X, indices, indices_dtype, axis=axis) 266 elif hasattr(X, "shape"): --> 267 return _array_indexing(X, indices, indices_dtype, axis=axis) 268 else: 269 return _list_indexing(X, indices, indices_dtype) File /opt/python/miniconda3/envs/python-ml-dl/lib/python3.10/site-packages/sklearn/utils/_indexing.py:33, in _array_indexing(array, key, key_dtype, axis) 31 if isinstance(key, tuple): 32 key = list(key) ---> 33 return array[key, ...] if axis == 0 else array[:, key] MemoryError: Unable to allocate 1.29 GiB for an array with shape (1760, 196608) and data type float32
Realizamos un EDA de las particiones de los datos que hemos generado. Primero, el arreglo de entrenamiento:
In [ ]:
print('[INFO] Training Data Splits - X: {}, dtype: {}, y: {}, dtype: {}'.format(train_set.shape,
train_set.dtype,
train_classes.shape,
train_classes.dtype))
_ = get_data_balance(train_classes, dtag='TRAIN')
# Plot raw data samples from the training split
data_plotting(data=train_set,
y_dim=height, x_dim=width, n_ch=depth,
tag='img_TRAIN', classes=train_classes)
Ahora, procedemos con el EDA para la partición de datos relacionada con la evaluación del modelo.
In [ ]:
print('[INFO] Testing Data Splits - X: {}, dtype: {}, y: {}, dtype: {}'.format(test_set.shape,
test_set.dtype,
test_classes.shape,
test_classes.dtype))
_ = get_data_balance(test_classes, dtag='TEST')
# Plot raw data samples from the testing split
data_plotting(data=test_set,
y_dim=height, x_dim=width, n_ch=depth,
tag='img_TEST', classes=test_classes)
Realizamos finalmente el EDA para la partición de datos para la validación.
In [ ]:
print('[INFO] Validation Data Splits - X: {}, dtype: {}, y: {}, dtype: {}'.format(val_set.shape,
val_set.dtype,
val_classes.shape,
val_classes.dtype))
_ = get_data_balance(val_classes, dtag='VAL')
# Plot raw data samples from the validation split
data_plotting(data=val_set,
y_dim=height, x_dim=width, n_ch=depth,
tag='img_VAL', classes=val_classes)
Aumentación de datos¶
Definimos un método que emplea la técnica de bootstrapping para generar muestras etiquetadas sintéticas.
In [158]:
def generate_synthetic_data(data, dtype, dtag, classes_num, n_samples=5000):
# Init random state for resampling
random_state = 42
# Verify one-hot encoding
one_hot = (classes_num.shape[1] != 1)
# Inspect data balancing and get classes counter
classes_cnt, tmp_list = get_data_balance(classes_num, dtag=dtag)
# Update target labels
classes_num = np.array(tmp_list)
# Get associated classes
classes = list(classes_cnt.keys())
# Init - data arrays
X_in, y_in = np.copy(data), np.copy(classes_num)
# Main loop
for cl in sorted(classes):
# Get count value per class 'cl'
count_val = classes_cnt[cl]
# Determine the location by index of the data corresponding to certain class
data_idx = np.where(classes_num == cl)[0].tolist()
# Get data and labels per class from the input data
X_class, y_class = data[data_idx], classes_num[data_idx]
# Generate synthetic data using data-labels arrays
n_resamp = abs(n_samples - count_val)
# Verify the count of samples according to the expected samples to balance the dataset
if count_val < n_samples:
# Perform data upsampling
X_tmp, y_tmp = resample(X_class, y_class, n_samples=n_resamp, random_state=random_state)
# Increase random state value
random_state += 1
else:
# Perform data downsampling
X_tmp, y_tmp = X_class[:n_samples], y_class[:n_samples]
in_idx = np.where(y_in == cl)[0].tolist()
X_in, y_in = np.delete(X_in, in_idx, axis=0), np.delete(y_in, in_idx, axis=0)
# Update synthetic data-labels
X_in, y_in = np.concatenate((X_in, X_tmp)), np.concatenate((y_in, y_tmp))
# Verify current state
if random_state == 43:
# Update random state
random_state = 122
# Data-labels output
X_out, y_out = np.stack(X_in, axis=0).astype(dtype), np.stack(y_in, axis=0).astype(dtype)
# restore label encoding for synthetic data
if one_hot:
y_out = self.one_hot_encoding(y_out, dtype)
else:
# update data type
y_out = y_out.reshape(-1, 1).astype(dtype)
# Display synthetic data balance
_, _ = self.get_data_balance(y_out, dtag=dtag)
# Final messages
print('[INFO] Synth-WAV data output - X: {}, dtype: {}, NaNs: {}'.format(X_out.shape, X_out.dtype,
np.isnan(X_out).any()))
print('[INFO] Synth-labels output - y: {}, dtype: {}, NaNs {}'.format(y_out.shape, y_out.dtype,
np.isnan(y_out).any()))
# Return: synthetic data-labels pairs
return X_out, y_out
Establecemos los argumentos de entrada para la etapa de balanceo de datos mediante generación de datos sintéticos.
In [156]:
# Number of synthentic samples
syn_samples = 500
# Define number of classes
n_classes = len(target_labels)
# Define number of samples per class
n_samples = syn_samples*n_classes
# Number of samples per class for training
train_samples = n_samples * (1 - test_size)
# Number of samples per class for testing
test_samples = int(n_samples * test_size)
# Number of samples per class for validation
val_samples = int(train_samples * test_size)
# Update training samples
train_samples = int(train_samples * (1 - test_size))
print('[INFO] Number of samples per class in splits - TRAIN:{}, VAL:{}, TEST:{}'.format(train_samples,
val_samples,
test_samples))
[INFO] Number of samples per class in splits - TRAIN:7040, VAL:1760, TEST:2200
Generamos un nuevo split de entrenamiento con datos etiquetados sintéticos.
In [157]:
# Generate synthetic data to balance the labeled TRAIN split
train_set, train_classes = generate_synthetic_data(train_set, data_type, 'TRAIN',
train_classes,
n_samples=train_samples)
# Plot raw and synthetic data samples from the training split
data_plotting(data=train_set,
y_dim=height, x_dim=width, n_ch=depth,
tag='img_synth_TRAIN', classes=train_classes)
[INFO] Number of samples for each category in TRAIN set: [INFO] 0:320 [INFO] 1:320 [INFO] 2:320 [INFO] 3:320 [INFO] 4:320 [INFO] 5:320 [INFO] 6:320 [INFO] 7:320 [INFO] 8:320 [INFO] 9:320 [INFO] 10:320 [INFO] 11:320 [INFO] 12:320 [INFO] 13:320 [INFO] 14:320 [INFO] 15:320 [INFO] 16:320 [INFO] 17:320 [INFO] 18:320 [INFO] 19:320 [INFO] 20:320 [INFO] 21:320
--------------------------------------------------------------------------- MemoryError Traceback (most recent call last) Cell In[157], line 2 1 # Generate synthetic data to balance the labeled TRAIN split ----> 2 train_set, train_classes = generate_synthetic_data(train_set, data_type, 'TRAIN', 3 train_classes, 4 n_samples=train_samples) 5 # Plot raw and synthetic data samples from the training split 6 data_plotting(data=train_set, 7 y_dim=height, x_dim=width, n_ch=depth, 8 tag='img_synth_TRAIN', classes=train_classes) Cell In[150], line 27, in generate_synthetic_data(data, dtype, dtag, classes_num, n_samples) 24 # Verify the count of samples according to the expected samples to balance the dataset 25 if count_val < n_samples: 26 # Perform data upsampling ---> 27 X_tmp, y_tmp = resample(X_class, y_class, n_samples=n_resamp, random_state=random_state) 28 # Increase random state value 29 random_state += 1 File /opt/python/miniconda3/envs/python-ml-dl/lib/python3.10/site-packages/sklearn/utils/_param_validation.py:213, in validate_params.<locals>.decorator.<locals>.wrapper(*args, **kwargs) 207 try: 208 with config_context( 209 skip_parameter_validation=( 210 prefer_skip_nested_validation or global_skip_validation 211 ) 212 ): --> 213 return func(*args, **kwargs) 214 except InvalidParameterError as e: 215 # When the function is just a wrapper around an estimator, we allow 216 # the function to delegate validation to the estimator, but we replace 217 # the name of the estimator by the name of the function in the error 218 # message to avoid confusion. 219 msg = re.sub( 220 r"parameter of \w+ must be", 221 f"parameter of {func.__qualname__} must be", 222 str(e), 223 ) File /opt/python/miniconda3/envs/python-ml-dl/lib/python3.10/site-packages/sklearn/utils/_indexing.py:559, in resample(replace, n_samples, random_state, stratify, *arrays) 557 # convert sparse matrices to CSR for row-based indexing 558 arrays = [a.tocsr() if issparse(a) else a for a in arrays] --> 559 resampled_arrays = [_safe_indexing(a, indices) for a in arrays] 560 if len(resampled_arrays) == 1: 561 # syntactic sugar for the unit argument case 562 return resampled_arrays[0] File /opt/python/miniconda3/envs/python-ml-dl/lib/python3.10/site-packages/sklearn/utils/_indexing.py:559, in <listcomp>(.0) 557 # convert sparse matrices to CSR for row-based indexing 558 arrays = [a.tocsr() if issparse(a) else a for a in arrays] --> 559 resampled_arrays = [_safe_indexing(a, indices) for a in arrays] 560 if len(resampled_arrays) == 1: 561 # syntactic sugar for the unit argument case 562 return resampled_arrays[0] File /opt/python/miniconda3/envs/python-ml-dl/lib/python3.10/site-packages/sklearn/utils/_indexing.py:267, in _safe_indexing(X, indices, axis) 265 return _polars_indexing(X, indices, indices_dtype, axis=axis) 266 elif hasattr(X, "shape"): --> 267 return _array_indexing(X, indices, indices_dtype, axis=axis) 268 else: 269 return _list_indexing(X, indices, indices_dtype) File /opt/python/miniconda3/envs/python-ml-dl/lib/python3.10/site-packages/sklearn/utils/_indexing.py:33, in _array_indexing(array, key, key_dtype, axis) 31 if isinstance(key, tuple): 32 key = list(key) ---> 33 return array[key, ...] if axis == 0 else array[:, key] MemoryError: Unable to allocate 4.92 GiB for an array with shape (6720, 256, 256, 3) and data type float32
Producimos un nuevo split de evaluación con datos etiquetados sintéticos.
In [ ]:
# Generate synthetic data to balance the labeled TEST split
test_set, test_classes = generate_synthetic_data(test_set, data_type, 'TEST',
test_classes,
n_samples=test_samples)
# Plot raw data samples from the testing split
data_plotting(data=test_set,
y_dim=height, x_dim=width, n_ch=depth,
tag='img_synth_TEST', classes=test_classes)
Generamos un nuevo split de validación con datos etiquetados sintéticos.
In [ ]:
# Generate synthetic data to balance the labeled VAL split
val_set, val_classes = generate_synthetic_data(val_set, data_type, 'VAL',
val_classes,
n_samples=val_samples)
# Plot raw data samples from the validation split
data_plotting(data=val_set,
y_dim=height, x_dim=width, n_ch=depth,
tag='img_synth_VAL', classes=val_classes)
Modelos de clasificación¶
La presente sección corresponde a la implementación del multi-clasificador de especies de pájaros, empleando distintos modelos de redes neuronales profundas. Definimos un método para construir una DNN personalizada con FCLs:
In [ ]:
def dnn_model(model,
dtype,
input_shape,
output_size,
layers,
units,
dropout,
regularization=L2(0.0001),
hidden_activation='relu',
output_activation='softmax'):
# Init
layer_index = 1
# Adding Input layer
model.add(Input(shape=input_shape, dtype=dtype))
# Adding a FCL layer
model.add(Dense(units,
activation=hidden_activation,
kernel_regularizer=regularization,
bias_regularizer=regularization))
print('[INFO] FCL layer: {}, FCL depth: {}, FCL activation: {}'.format(layer_index,
units,
hidden_activation))
# Add FC n-layers
for i in range(layer_index + 1, layers + 1):
# Update layer index
layer_index = i
# Adding a FCL layer
model.add(Dense(units,
activation=hidden_activation,
kernel_regularizer=regularization,
bias_regularizer=regularization))
print('[INFO] FCL layer: {}, FCL depth: {}, FCL activation: {}'.format(layer_index,
units,
hidden_activation))
# Adding a Flatten layer
model.add(Flatten())
# Dropout layer (generalization)
model.add(Dropout(dropout))
# Output layer
model.add(Dense(output_size,
activation=output_activation,
kernel_regularizer=regularization,
bias_regularizer=regularization))
# Return custom DNN
return model
Instanciamos una función que permite la construcción de una CNN.
In [ ]:
def cnn_2d_model(model,
dtype,
input_shape,
output_size,
layers,
units,
filters,
kernel_size,
dropout,
regularization=L2(0.0001),
hidden_activation='relu',
output_activation='softmax'):
# Init
layer_index = 1
# Adding Input layer
model.add(Input(shape=input_shape, dtype=dtype))
# Adding a Convolution Layer
model.add(Conv2D(filters=filters,
kernel_size=kernel_size,
padding='same',
activation=hidden_activation,
kernel_regularizer=regularization,
bias_regularizer=regularization))
# Adding an Max-Pooling Layer
model.add(MaxPool2D(pool_size=2, strides=2))
print('[INFO] CNN layer: {}, CNN depth: {}, CNN kernel size: {}'.format(layer_index,
filters,
(kernel_size, kernel_size)))
# Add n-convolutional layers
for i in range(layer_index + 1, layers + 1):
# Update layer index
layer_index = i
# Update filters value
filters *= 2
# Update kernel size value
kernel_size += 2
# Adding a Convolution Layer
model.add(Conv2D(filters=filters,
kernel_size=kernel_size,
padding='same',
activation=hidden_activation,
kernel_regularizer=regularization,
bias_regularizer=regularization))
# Adding an Max-Pooling Layer
model.add(MaxPool2D(pool_size=2, strides=2))
print('[INFO] CNN layer: {}, CNN depth: {}, CNN kernel size: {}'.format(layer_index,
filters,
(kernel_size, kernel_size)))
# Global pooling instead of flatten()
model.add(Flatten())
# FCL layer
model.add(Dense(units,
kernel_regularizer=regularization,
bias_regularizer=regularization))
# Dropout the layer (generalization)
model.add(Dropout(dropout))
# Output layer
model.add(Dense(output_size,
activation=output_activation,
kernel_regularizer=regularization,
bias_regularizer=regularization))
# Return custom CNN
return model
Construcción del modelo¶
Establecemos una rutina que permita ensamblar diferentes arquitecturas de modelos de red neuronal.
In [ ]:
def create_model(model_type,
data_type,
input_shape,
num_classes,
num_layers,
num_units,
dropout,
num_filters=None,
kernel_size=None,
seed=1001):
# make results repeatable
set_random_seed(seed)
# input layer - sequential model
model = Sequential()
# check model type
if model_type == 'dnn':
# Create custom ANN model
model = dnn_model(model,
data_type,
input_shape,
num_classes,
num_layers,
num_units,
dropout)
elif model_type == 'cnn2d':
# Create custom CNN-2D model
model = cnn_2d_model(model,
data_type,
input_shape,
num_classes,
num_layers,
num_units,
num_filters,
kernel_size,
dropout)
# else: transfer learning
# return DL model
return model
Definimos ahora el tamaño de la entrada del modelo y el de su salida.
In [ ]:
# Define mode input shape for image processing analysis: (height x width x depth)}
input_shape = (train_set.shape[1], train_set.shape[2], train_set.shape[3])
# Define model output size
output_size = train_classes.shape[1]
input_shape, output_size
Establecemos hiper-parámetros para la construcción del modelo de redes neuronales.
In [ ]:
# Define DL model type
model_type = 'cnn2d'
# Define layers hyper-parameter as input argument
layers = 7
# Define neurons hyper-parameter as input argument
units = 32
# Define generalization magnitude
dropout = 0.4
Ejecutamos la creación de la arquitectura de redes neuronales.
In [ ]:
# Init
model = None
# Create a DNN architecture
model = create_model(model_type,
data_type,
input_shape,
output_size,
layers,
units,
dropout)
Compilación del modelo¶
Instanciamos un método que nos permite realizar la compilación del modelo construido.
In [140]:
def compile_model(model, opt, lr, loss, metrics, dtype, mm=0.0):
# Init loss: cross-entropy (classification problems)
cross_entropy = loss
# Init metrics: accuracy (multiple classification)
accuracy = metrics
# Init optimizer
optimizer = opt
# Update loss function to categorical crossentropy
if cross_entropy == 'binary_crossentropy':
loss = BinaryCrossentropy(name=cross_entropy, from_logits=False)
# Update loss function to categorical crossentropy
if cross_entropy == 'categorical_crossentropy':
loss = CategoricalCrossentropy(name=cross_entropy, from_logits=False)
# Update metrics function to categorical accuracy
if accuracy == 'binary_accuracy':
metrics = BinaryAccuracy(name=accuracy, dtype=dtype)
# Update metrics function to categorical accuracy
if accuracy == 'categorical_accuracy':
metrics = CategoricalAccuracy(name=accuracy, dtype=dtype)
# Update optimizer to SGD
if opt == 'sgd':
optimizer = SGD(learning_rate=lr, momentum=mm)
# Update optimizer to RMSprop
if opt == 'rms':
optimizer = RMSprop(learning_rate=lr, momentum=mm)
# Update optimizer to Adam
if opt == 'adam':
optimizer = Adam(learning_rate=lr)
# Compiling model
model.compile(loss=loss, optimizer=optimizer, metrics=[metrics])
# Return compiled model
return model
Establecemos hiper-parámetros ahora para la compilación del modelo de redes neuronales.
In [141]:
# Define optimizer function
optimizer = 'adam' # used for multi-classification
# Define learning rate
learning_rate = 1e-5
# Define momentum magnitude
momentum = 0.55
# Define loss function
loss = 'categorical_crossentropy'
# Define metrics function
metrics = 'categorical_accuracy'
Ejecutamos la compilación del modelo construido.
In [142]:
# Compile model: DNN network
model = compile_model(model,
optimizer,
learning_rate,
loss,
metrics,
dtype=data_type,
mm=momentum)
Desplegamos un resumen del modelo construido.
In [143]:
# Display model info summary
model.summary()
Model: "sequential_3"
_________________________________________________________________
Layer (type) Output Shape Param #
=================================================================
dense_20 (Dense) (None, 256, 256, 32) 128
dense_21 (Dense) (None, 256, 256, 32) 1056
dense_22 (Dense) (None, 256, 256, 32) 1056
dense_23 (Dense) (None, 256, 256, 32) 1056
dense_24 (Dense) (None, 256, 256, 32) 1056
dense_25 (Dense) (None, 256, 256, 32) 1056
dense_26 (Dense) (None, 256, 256, 32) 1056
flatten_3 (Flatten) (None, 2097152) 0
dropout_3 (Dropout) (None, 2097152) 0
dense_27 (Dense) (None, 22) 46137366
=================================================================
Total params: 46,143,830
Trainable params: 46,143,830
Non-trainable params: 0
_________________________________________________________________
Entrenamiento del modelo¶
Instanciamos un método genérico que nos permite obtener y visualizar las métricas durante el entrenamiento y la evaluación de nuestro modelo.
In [122]:
def save_model_metrics(history, metric, file_dir=None, tag=None, history_ft=None, ext='pdf'):
# init metrics plot
fig = plt.figure()
# compute latest epoch
latest_epoch = history.epoch[-1] + 1
# create vectors for train and val metrics
train_metric = history.history[metric]
val_metric = history.history['val_{}'.format(metric)]
# add fine-tune history
if history_ft is not None:
train_metric += history_ft.history[metric]
val_metric += history_ft.history['val_{}'.format(metric)]
# create plot labels for both functions
train_label = 'train {}'.format(metric)
val_label = 'val {}'.format(metric)
# create metric plot
plt.plot(train_metric, label=train_label)
plt.plot(val_metric, label=val_label)
# plot where the fine tune starts
if history_ft is not None:
plt.plot([latest_epoch, latest_epoch],
plt.ylim([0, 1.0]), label='fine-tuning start')
plt.xlabel('epoch')
plt.ylabel('{}'.format(metric))
if metric == 'loss':
plt.legend(loc='upper right')
else:
plt.legend(loc='lower right')
plt.title('Train-val: {}'.format(tag))
# enable grid
plt.grid(True)
# check filedir
if file_dir is None:
# show data batch image
plt.show()
else:
# metrics timestamp
ts = datetime.datetime.now().strftime('%Y%m%d-%H%M%S')
# set tag as the metric string
if tag is None:
tag = metric
# define filepath
file_path = os.path.join(file_dir, '{}_{}.{}'.format(ts, tag, ext))
# store accuracy plot
fig.savefig(file_path)
print('[INFO] Saving {} plot file: {}'.format(metric, file_path))
plt.close(fig)
# Free memory space
del fig
gc.collect()
Definimos los hiper-parámetros del entrenamiento del modelo de redes neuronales.
In [144]:
# Init
cbs = None
# Define a validation split ratio during fit
val_split = 0.0
# Define the number of sables per gradient update
batch_size = 64
# Define the number of training iterations
epochs = 50
# Define arguments for early stopping callback
patience, min_delta = 5, 0.0001
Declaramos de igual forma las llamadas que implementamos durante el entrenamiento.
In [145]:
# callbacks
cbs = list()
# early stopping callback
es_callback = EarlyStopping(monitor='val_{}'.format(loss),
min_delta=min_delta,
patience=patience)
# append to list
cbs.append(es_callback)
# learning rate reduction on-plateau
lr_callback = ReduceLROnPlateau(monitor='val_{}'.format(loss),
min_delta=min_delta,
patience=patience)
# append to list
cbs.append(lr_callback)
Ejecutamos la función relacionada con el entrenamiento del modelo construido y compilado.
In [146]:
# create validation set tuple
val_data = (val_set, val_classes)
# for training, we need the "1 hot encoded" numeric classes of the ground truth
History = model.fit(x=train_set,
y=train_classes,
batch_size=batch_size,
epochs=epochs,
verbose=1,
callbacks=cbs,
validation_split=val_split,
validation_data=val_data)
Epoch 1/50
2024-09-18 19:57:50.096030: I tensorflow/compiler/xla/service/service.cc:169] XLA service 0x7f589fbf7f10 initialized for platform CUDA (this does not guarantee that XLA will be used). Devices: 2024-09-18 19:57:50.096105: I tensorflow/compiler/xla/service/service.cc:177] StreamExecutor device (0): Tesla V100-PCIE-32GB, Compute Capability 7.0 2024-09-18 19:57:51.032753: I tensorflow/compiler/mlir/tensorflow/utils/dump_mlir_util.cc:269] disabling MLIR crash reproducer, set env var `MLIR_CRASH_REPRODUCER_DIRECTORY` to enable. 2024-09-18 19:57:53.065058: I tensorflow/compiler/xla/stream_executor/cuda/cuda_dnn.cc:424] Loaded cuDNN version 8700 2024-09-18 19:57:59.121610: I ./tensorflow/compiler/jit/device_compiler.h:180] Compiled cluster using XLA! This line is logged at most once for the lifetime of the process.
110/110 [==============================] - 41s 132ms/step - loss: 22.6440 - categorical_accuracy: 0.0496 - categorical_crossentropy: 21.0954 - val_loss: 14.3518 - val_categorical_accuracy: 0.0460 - val_categorical_crossentropy: 14.2867 - lr: 1.0000e-05 Epoch 2/50 110/110 [==============================] - 12s 105ms/step - loss: 15.5813 - categorical_accuracy: 0.0422 - categorical_crossentropy: 13.8537 - val_loss: 8.9131 - val_categorical_accuracy: 0.0466 - val_categorical_crossentropy: 8.8619 - lr: 1.0000e-05 Epoch 3/50 110/110 [==============================] - 12s 107ms/step - loss: 9.3869 - categorical_accuracy: 0.0432 - categorical_crossentropy: 8.1884 - val_loss: 5.2934 - val_categorical_accuracy: 0.0466 - val_categorical_crossentropy: 5.2588 - lr: 1.0000e-05 Epoch 4/50 110/110 [==============================] - 12s 105ms/step - loss: 5.5377 - categorical_accuracy: 0.0482 - categorical_crossentropy: 4.8814 - val_loss: 3.6641 - val_categorical_accuracy: 0.0460 - val_categorical_crossentropy: 3.6389 - lr: 1.0000e-05 Epoch 5/50 110/110 [==============================] - 12s 107ms/step - loss: 3.7123 - categorical_accuracy: 0.0453 - categorical_crossentropy: 3.5243 - val_loss: 3.2152 - val_categorical_accuracy: 0.0460 - val_categorical_crossentropy: 3.1935 - lr: 1.0000e-05 Epoch 6/50 110/110 [==============================] - 12s 107ms/step - loss: 3.2383 - categorical_accuracy: 0.0456 - categorical_crossentropy: 3.1732 - val_loss: 3.1269 - val_categorical_accuracy: 0.0460 - val_categorical_crossentropy: 3.1070 - lr: 1.0000e-05 Epoch 7/50 110/110 [==============================] - 12s 109ms/step - loss: 3.1320 - categorical_accuracy: 0.0419 - categorical_crossentropy: 3.1037 - val_loss: 3.1121 - val_categorical_accuracy: 0.0460 - val_categorical_crossentropy: 3.0932 - lr: 1.0000e-05 Epoch 8/50 110/110 [==============================] - 12s 106ms/step - loss: 3.1137 - categorical_accuracy: 0.0447 - categorical_crossentropy: 3.0932 - val_loss: 3.1097 - val_categorical_accuracy: 0.0455 - val_categorical_crossentropy: 3.0913 - lr: 1.0000e-05 Epoch 9/50 110/110 [==============================] - 11s 101ms/step - loss: 3.1099 - categorical_accuracy: 0.0470 - categorical_crossentropy: 3.0914 - val_loss: 3.1091 - val_categorical_accuracy: 0.0455 - val_categorical_crossentropy: 3.0911 - lr: 1.0000e-05 Epoch 10/50 110/110 [==============================] - 12s 105ms/step - loss: 3.1090 - categorical_accuracy: 0.0429 - categorical_crossentropy: 3.0911 - val_loss: 3.1088 - val_categorical_accuracy: 0.0455 - val_categorical_crossentropy: 3.0910 - lr: 1.0000e-05 Epoch 11/50 110/110 [==============================] - 11s 102ms/step - loss: 3.1087 - categorical_accuracy: 0.0463 - categorical_crossentropy: 3.0910 - val_loss: 3.1086 - val_categorical_accuracy: 0.0455 - val_categorical_crossentropy: 3.0910 - lr: 1.0000e-05 Epoch 12/50 110/110 [==============================] - 12s 107ms/step - loss: 3.1086 - categorical_accuracy: 0.0445 - categorical_crossentropy: 3.0911 - val_loss: 3.1084 - val_categorical_accuracy: 0.0455 - val_categorical_crossentropy: 3.0910 - lr: 1.0000e-05 Epoch 13/50 110/110 [==============================] - 11s 101ms/step - loss: 3.1084 - categorical_accuracy: 0.0456 - categorical_crossentropy: 3.0910 - val_loss: 3.1083 - val_categorical_accuracy: 0.0455 - val_categorical_crossentropy: 3.0910 - lr: 1.0000e-05 Epoch 14/50 110/110 [==============================] - 11s 105ms/step - loss: 3.1082 - categorical_accuracy: 0.0452 - categorical_crossentropy: 3.0910 - val_loss: 3.1081 - val_categorical_accuracy: 0.0455 - val_categorical_crossentropy: 3.0910 - lr: 1.0000e-05
Revisemos los resultados de nuestro entrenamiento y su validación.
In [148]:
# get validation accuracy scores per epoch as a data aray
val_acc_per_epoch = History.history['val_{}'.format(metrics)]
# get max accuracy score during epochs
max_val_acc = max(val_acc_per_epoch)
# get the number of epoch related to the max validation accuracy
best_epoch = val_acc_per_epoch.index(max_val_acc) + 1
print('[INFO] Training/Validation done! - best epoch: {}/{}, best validation score: {}'.format(best_epoch,
epochs,
max_val_acc))
[INFO] Training/Validation done! - best epoch: 2/50, best validation score: 0.046590909361839294