Let’s make sure we are using tensorflow v2+

Training and inference with colab

Google colab is a free server for running notebooks with GPU/TPU support - this is a great way to use DAS if you do not have a computer with a GPU.

This notebook demonstrates

  • how to setup DAS

  • how to load your own datasets

  • how to train a network and then use that network to label a new audio recording.

Open and edit this notebook in colab by clicking this badge:

Open In Colab

%tensorflow_version 2.x

Install DAS:

!pip install das
Collecting das
  Downloading das-0.22.1-py3-none-any.whl (77 kB)
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Building wheels for collected packages: defopt, asciitree
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Successfully built defopt asciitree
Installing collected packages: pockets, mypy-extensions, typing-inspect, sphinxcontrib-napoleon, numcodecs, fasteners, asciitree, zarr, peakutils, matplotlib-scalebar, flammkuchen, defopt, das
Successfully installed asciitree-0.3.3 das-0.22.1 defopt-6.1.0 fasteners-0.16.3 flammkuchen-0.9.2 matplotlib-scalebar-0.7.2 mypy-extensions-0.4.3 numcodecs-0.9.1 peakutils-1.3.3 pockets-0.9.1 sphinxcontrib-napoleon-0.7 typing-inspect-0.7.1 zarr-2.10.0

Import all the things:

import das.train, das.predict, das.utils, das.npy_dir
import matplotlib.pyplot as plt
import flammkuchen
import logging
logging.basicConfig(level=logging.INFO)

Mount your google drive so you can access your own datasets - this will ask for authentication.

from google.colab import drive
drive.mount('/content/drive')
Mounted at /content/drive

Train the model

Adjust the variable path_to_data to point to the dataset on your own google drive.

path_to_data = '/content/drive/MyDrive/Dmoj.wrigleyi.npy'

das.train.train(model_name='tcn',
                data_dir=path_to_data,
                save_dir='res',
                nb_hist=1024,
                kernel_size=32,
                nb_filters=32,
                ignore_boundaries=True,
                verbose=2,
                nb_conv=4,
                learning_rate=0.0005,
                use_separable=[True, True, False, False],
                nb_epoch=1000)
INFO:root:Loading data from /content/drive/MyDrive/Dmoj.wrigleyi.npy.
INFO:root:Version of the data:
INFO:root:   MD5 hash of /content/drive/MyDrive/Dmoj.wrigleyi.npy is
INFO:root:   5381c36663f3b7286b0a5c42c0e3e463
INFO:root:Parameters:
INFO:root:{'data_dir': '/content/drive/MyDrive/Dmoj.wrigleyi.npy', 'y_suffix': '', 'save_dir': 'res', 'save_prefix': '', 'model_name': 'tcn', 'nb_filters': 32, 'kernel_size': 32, 'nb_conv': 4, 'use_separable': [True, True, False, False], 'nb_hist': 1024, 'ignore_boundaries': True, 'batch_norm': True, 'nb_pre_conv': 0, 'pre_nb_dft': 64, 'pre_kernel_size': 3, 'pre_nb_filters': 16, 'pre_nb_conv': 2, 'nb_lstm_units': 0, 'verbose': 2, 'batch_size': 32, 'nb_epoch': 1000, 'learning_rate': 0.0005, 'reduce_lr': False, 'reduce_lr_patience': 5, 'fraction_data': None, 'seed': None, 'batch_level_subsampling': False, 'tensorboard': False, 'neptune_api_token': None, 'neptune_project': None, 'log_messages': False, 'nb_stacks': 2, 'with_y_hist': True, 'x_suffix': '', 'balance': False, 'version_data': True, 'sample_weight_mode': 'temporal', 'data_padding': 128, 'return_sequences': True, 'stride': 768, 'y_offset': 0, 'output_stride': 1, 'class_names': ['noise', 'pulse'], 'class_types': ['segment', 'event'], 'filename_endsample_test': [], 'filename_endsample_train': [], 'filename_endsample_val': [], 'filename_startsample_test': [], 'filename_startsample_train': [], 'filename_startsample_val': [], 'filename_train': [], 'filename_val': [], 'samplerate_x_Hz': 10000.0, 'samplerate_y_Hz': 10000.0, 'filename_test': [], 'data_hash': '5381c36663f3b7286b0a5c42c0e3e463', 'nb_freq': 16, 'nb_channels': 16, 'nb_classes': 2, 'first_sample_train': 0, 'last_sample_train': None, 'first_sample_val': 0, 'last_sample_val': None}
INFO:root:Preparing data
INFO:root:Training data:
INFO:root:   AudioSequence with 47 batches each with 32 items.
   Total of 1158000 samples with
   each x=(16,) and
   each y=(2,)
INFO:root:Validation data:
INFO:root:   AudioSequence with 15 batches each with 32 items.
   Total of 386000 samples with
   each x=(16,) and
   each y=(2,)
INFO:root:building network
/usr/local/lib/python3.7/dist-packages/keras/optimizer_v2/optimizer_v2.py:356: UserWarning: The `lr` argument is deprecated, use `learning_rate` instead.
  "The `lr` argument is deprecated, use `learning_rate` instead.")
INFO:root:None
INFO:root:Will save to res/20210925_132436.
INFO:root:start training
Model: "TCN"
__________________________________________________________________________________________________
Layer (type)                    Output Shape         Param #     Connected to                     
==================================================================================================
input_1 (InputLayer)            [(None, 1024, 16)]   0                                            
__________________________________________________________________________________________________
conv1d (Conv1D)                 (None, 1024, 32)     544         input_1[0][0]                    
__________________________________________________________________________________________________
separable_conv1d (SeparableConv (None, 1024, 32)     8224        conv1d[0][0]                     
__________________________________________________________________________________________________
activation (Activation)         (None, 1024, 32)     0           separable_conv1d[0][0]           
__________________________________________________________________________________________________
lambda (Lambda)                 (None, 1024, 32)     0           activation[0][0]                 
__________________________________________________________________________________________________
spatial_dropout1d (SpatialDropo (None, 1024, 32)     0           lambda[0][0]                     
__________________________________________________________________________________________________
conv1d_1 (Conv1D)               (None, 1024, 32)     1056        spatial_dropout1d[0][0]          
__________________________________________________________________________________________________
add (Add)                       (None, 1024, 32)     0           conv1d[0][0]                     
                                                                 conv1d_1[0][0]                   
__________________________________________________________________________________________________
separable_conv1d_1 (SeparableCo (None, 1024, 32)     8224        add[0][0]                        
__________________________________________________________________________________________________
activation_1 (Activation)       (None, 1024, 32)     0           separable_conv1d_1[0][0]         
__________________________________________________________________________________________________
lambda_1 (Lambda)               (None, 1024, 32)     0           activation_1[0][0]               
__________________________________________________________________________________________________
spatial_dropout1d_1 (SpatialDro (None, 1024, 32)     0           lambda_1[0][0]                   
__________________________________________________________________________________________________
conv1d_2 (Conv1D)               (None, 1024, 32)     1056        spatial_dropout1d_1[0][0]        
__________________________________________________________________________________________________
add_1 (Add)                     (None, 1024, 32)     0           add[0][0]                        
                                                                 conv1d_2[0][0]                   
__________________________________________________________________________________________________
separable_conv1d_2 (SeparableCo (None, 1024, 32)     8224        add_1[0][0]                      
__________________________________________________________________________________________________
activation_2 (Activation)       (None, 1024, 32)     0           separable_conv1d_2[0][0]         
__________________________________________________________________________________________________
lambda_2 (Lambda)               (None, 1024, 32)     0           activation_2[0][0]               
__________________________________________________________________________________________________
spatial_dropout1d_2 (SpatialDro (None, 1024, 32)     0           lambda_2[0][0]                   
__________________________________________________________________________________________________
conv1d_3 (Conv1D)               (None, 1024, 32)     1056        spatial_dropout1d_2[0][0]        
__________________________________________________________________________________________________
add_2 (Add)                     (None, 1024, 32)     0           add_1[0][0]                      
                                                                 conv1d_3[0][0]                   
__________________________________________________________________________________________________
separable_conv1d_3 (SeparableCo (None, 1024, 32)     8224        add_2[0][0]                      
__________________________________________________________________________________________________
activation_3 (Activation)       (None, 1024, 32)     0           separable_conv1d_3[0][0]         
__________________________________________________________________________________________________
lambda_3 (Lambda)               (None, 1024, 32)     0           activation_3[0][0]               
__________________________________________________________________________________________________
spatial_dropout1d_3 (SpatialDro (None, 1024, 32)     0           lambda_3[0][0]                   
__________________________________________________________________________________________________
conv1d_4 (Conv1D)               (None, 1024, 32)     1056        spatial_dropout1d_3[0][0]        
__________________________________________________________________________________________________
add_3 (Add)                     (None, 1024, 32)     0           add_2[0][0]                      
                                                                 conv1d_4[0][0]                   
__________________________________________________________________________________________________
separable_conv1d_4 (SeparableCo (None, 1024, 32)     8224        add_3[0][0]                      
__________________________________________________________________________________________________
activation_4 (Activation)       (None, 1024, 32)     0           separable_conv1d_4[0][0]         
__________________________________________________________________________________________________
lambda_4 (Lambda)               (None, 1024, 32)     0           activation_4[0][0]               
__________________________________________________________________________________________________
spatial_dropout1d_4 (SpatialDro (None, 1024, 32)     0           lambda_4[0][0]                   
__________________________________________________________________________________________________
conv1d_5 (Conv1D)               (None, 1024, 32)     1056        spatial_dropout1d_4[0][0]        
__________________________________________________________________________________________________
add_4 (Add)                     (None, 1024, 32)     0           add_3[0][0]                      
                                                                 conv1d_5[0][0]                   
__________________________________________________________________________________________________
separable_conv1d_5 (SeparableCo (None, 1024, 32)     8224        add_4[0][0]                      
__________________________________________________________________________________________________
activation_5 (Activation)       (None, 1024, 32)     0           separable_conv1d_5[0][0]         
__________________________________________________________________________________________________
lambda_5 (Lambda)               (None, 1024, 32)     0           activation_5[0][0]               
__________________________________________________________________________________________________
spatial_dropout1d_5 (SpatialDro (None, 1024, 32)     0           lambda_5[0][0]                   
__________________________________________________________________________________________________
conv1d_6 (Conv1D)               (None, 1024, 32)     1056        spatial_dropout1d_5[0][0]        
__________________________________________________________________________________________________
add_5 (Add)                     (None, 1024, 32)     0           add_4[0][0]                      
                                                                 conv1d_6[0][0]                   
__________________________________________________________________________________________________
separable_conv1d_6 (SeparableCo (None, 1024, 32)     8224        add_5[0][0]                      
__________________________________________________________________________________________________
activation_6 (Activation)       (None, 1024, 32)     0           separable_conv1d_6[0][0]         
__________________________________________________________________________________________________
lambda_6 (Lambda)               (None, 1024, 32)     0           activation_6[0][0]               
__________________________________________________________________________________________________
spatial_dropout1d_6 (SpatialDro (None, 1024, 32)     0           lambda_6[0][0]                   
__________________________________________________________________________________________________
conv1d_7 (Conv1D)               (None, 1024, 32)     1056        spatial_dropout1d_6[0][0]        
__________________________________________________________________________________________________
add_6 (Add)                     (None, 1024, 32)     0           add_5[0][0]                      
                                                                 conv1d_7[0][0]                   
__________________________________________________________________________________________________
separable_conv1d_7 (SeparableCo (None, 1024, 32)     8224        add_6[0][0]                      
__________________________________________________________________________________________________
activation_7 (Activation)       (None, 1024, 32)     0           separable_conv1d_7[0][0]         
__________________________________________________________________________________________________
lambda_7 (Lambda)               (None, 1024, 32)     0           activation_7[0][0]               
__________________________________________________________________________________________________
spatial_dropout1d_7 (SpatialDro (None, 1024, 32)     0           lambda_7[0][0]                   
__________________________________________________________________________________________________
conv1d_8 (Conv1D)               (None, 1024, 32)     1056        spatial_dropout1d_7[0][0]        
__________________________________________________________________________________________________
add_7 (Add)                     (None, 1024, 32)     0           add_6[0][0]                      
                                                                 conv1d_8[0][0]                   
__________________________________________________________________________________________________
separable_conv1d_8 (SeparableCo (None, 1024, 32)     8224        add_7[0][0]                      
__________________________________________________________________________________________________
activation_8 (Activation)       (None, 1024, 32)     0           separable_conv1d_8[0][0]         
__________________________________________________________________________________________________
lambda_8 (Lambda)               (None, 1024, 32)     0           activation_8[0][0]               
__________________________________________________________________________________________________
spatial_dropout1d_8 (SpatialDro (None, 1024, 32)     0           lambda_8[0][0]                   
__________________________________________________________________________________________________
conv1d_9 (Conv1D)               (None, 1024, 32)     1056        spatial_dropout1d_8[0][0]        
__________________________________________________________________________________________________
add_8 (Add)                     (None, 1024, 32)     0           add_7[0][0]                      
                                                                 conv1d_9[0][0]                   
__________________________________________________________________________________________________
separable_conv1d_9 (SeparableCo (None, 1024, 32)     8224        add_8[0][0]                      
__________________________________________________________________________________________________
activation_9 (Activation)       (None, 1024, 32)     0           separable_conv1d_9[0][0]         
__________________________________________________________________________________________________
lambda_9 (Lambda)               (None, 1024, 32)     0           activation_9[0][0]               
__________________________________________________________________________________________________
spatial_dropout1d_9 (SpatialDro (None, 1024, 32)     0           lambda_9[0][0]                   
__________________________________________________________________________________________________
conv1d_10 (Conv1D)              (None, 1024, 32)     1056        spatial_dropout1d_9[0][0]        
__________________________________________________________________________________________________
add_9 (Add)                     (None, 1024, 32)     0           add_8[0][0]                      
                                                                 conv1d_10[0][0]                  
__________________________________________________________________________________________________
conv1d_11 (Conv1D)              (None, 1024, 32)     32800       add_9[0][0]                      
__________________________________________________________________________________________________
activation_10 (Activation)      (None, 1024, 32)     0           conv1d_11[0][0]                  
__________________________________________________________________________________________________
lambda_10 (Lambda)              (None, 1024, 32)     0           activation_10[0][0]              
__________________________________________________________________________________________________
spatial_dropout1d_10 (SpatialDr (None, 1024, 32)     0           lambda_10[0][0]                  
__________________________________________________________________________________________________
conv1d_12 (Conv1D)              (None, 1024, 32)     1056        spatial_dropout1d_10[0][0]       
__________________________________________________________________________________________________
add_10 (Add)                    (None, 1024, 32)     0           add_9[0][0]                      
                                                                 conv1d_12[0][0]                  
__________________________________________________________________________________________________
conv1d_13 (Conv1D)              (None, 1024, 32)     32800       add_10[0][0]                     
__________________________________________________________________________________________________
activation_11 (Activation)      (None, 1024, 32)     0           conv1d_13[0][0]                  
__________________________________________________________________________________________________
lambda_11 (Lambda)              (None, 1024, 32)     0           activation_11[0][0]              
__________________________________________________________________________________________________
spatial_dropout1d_11 (SpatialDr (None, 1024, 32)     0           lambda_11[0][0]                  
__________________________________________________________________________________________________
conv1d_14 (Conv1D)              (None, 1024, 32)     1056        spatial_dropout1d_11[0][0]       
__________________________________________________________________________________________________
add_11 (Add)                    (None, 1024, 32)     0           add_10[0][0]                     
                                                                 conv1d_14[0][0]                  
__________________________________________________________________________________________________
conv1d_15 (Conv1D)              (None, 1024, 32)     32800       add_11[0][0]                     
__________________________________________________________________________________________________
activation_12 (Activation)      (None, 1024, 32)     0           conv1d_15[0][0]                  
__________________________________________________________________________________________________
lambda_12 (Lambda)              (None, 1024, 32)     0           activation_12[0][0]              
__________________________________________________________________________________________________
spatial_dropout1d_12 (SpatialDr (None, 1024, 32)     0           lambda_12[0][0]                  
__________________________________________________________________________________________________
conv1d_16 (Conv1D)              (None, 1024, 32)     1056        spatial_dropout1d_12[0][0]       
__________________________________________________________________________________________________
add_12 (Add)                    (None, 1024, 32)     0           add_11[0][0]                     
                                                                 conv1d_16[0][0]                  
__________________________________________________________________________________________________
conv1d_17 (Conv1D)              (None, 1024, 32)     32800       add_12[0][0]                     
__________________________________________________________________________________________________
activation_13 (Activation)      (None, 1024, 32)     0           conv1d_17[0][0]                  
__________________________________________________________________________________________________
lambda_13 (Lambda)              (None, 1024, 32)     0           activation_13[0][0]              
__________________________________________________________________________________________________
spatial_dropout1d_13 (SpatialDr (None, 1024, 32)     0           lambda_13[0][0]                  
__________________________________________________________________________________________________
conv1d_18 (Conv1D)              (None, 1024, 32)     1056        spatial_dropout1d_13[0][0]       
__________________________________________________________________________________________________
add_13 (Add)                    (None, 1024, 32)     0           add_12[0][0]                     
                                                                 conv1d_18[0][0]                  
__________________________________________________________________________________________________
conv1d_19 (Conv1D)              (None, 1024, 32)     32800       add_13[0][0]                     
__________________________________________________________________________________________________
activation_14 (Activation)      (None, 1024, 32)     0           conv1d_19[0][0]                  
__________________________________________________________________________________________________
lambda_14 (Lambda)              (None, 1024, 32)     0           activation_14[0][0]              
__________________________________________________________________________________________________
spatial_dropout1d_14 (SpatialDr (None, 1024, 32)     0           lambda_14[0][0]                  
__________________________________________________________________________________________________
conv1d_20 (Conv1D)              (None, 1024, 32)     1056        spatial_dropout1d_14[0][0]       
__________________________________________________________________________________________________
add_14 (Add)                    (None, 1024, 32)     0           add_13[0][0]                     
                                                                 conv1d_20[0][0]                  
__________________________________________________________________________________________________
conv1d_21 (Conv1D)              (None, 1024, 32)     32800       add_14[0][0]                     
__________________________________________________________________________________________________
activation_15 (Activation)      (None, 1024, 32)     0           conv1d_21[0][0]                  
__________________________________________________________________________________________________
lambda_15 (Lambda)              (None, 1024, 32)     0           activation_15[0][0]              
__________________________________________________________________________________________________
spatial_dropout1d_15 (SpatialDr (None, 1024, 32)     0           lambda_15[0][0]                  
__________________________________________________________________________________________________
conv1d_22 (Conv1D)              (None, 1024, 32)     1056        spatial_dropout1d_15[0][0]       
__________________________________________________________________________________________________
add_15 (Add)                    (None, 1024, 32)     0           add_14[0][0]                     
                                                                 conv1d_22[0][0]                  
__________________________________________________________________________________________________
conv1d_23 (Conv1D)              (None, 1024, 32)     32800       add_15[0][0]                     
__________________________________________________________________________________________________
activation_16 (Activation)      (None, 1024, 32)     0           conv1d_23[0][0]                  
__________________________________________________________________________________________________
lambda_16 (Lambda)              (None, 1024, 32)     0           activation_16[0][0]              
__________________________________________________________________________________________________
spatial_dropout1d_16 (SpatialDr (None, 1024, 32)     0           lambda_16[0][0]                  
__________________________________________________________________________________________________
conv1d_24 (Conv1D)              (None, 1024, 32)     1056        spatial_dropout1d_16[0][0]       
__________________________________________________________________________________________________
add_16 (Add)                    (None, 1024, 32)     0           add_15[0][0]                     
                                                                 conv1d_24[0][0]                  
__________________________________________________________________________________________________
conv1d_25 (Conv1D)              (None, 1024, 32)     32800       add_16[0][0]                     
__________________________________________________________________________________________________
activation_17 (Activation)      (None, 1024, 32)     0           conv1d_25[0][0]                  
__________________________________________________________________________________________________
lambda_17 (Lambda)              (None, 1024, 32)     0           activation_17[0][0]              
__________________________________________________________________________________________________
spatial_dropout1d_17 (SpatialDr (None, 1024, 32)     0           lambda_17[0][0]                  
__________________________________________________________________________________________________
conv1d_26 (Conv1D)              (None, 1024, 32)     1056        spatial_dropout1d_17[0][0]       
__________________________________________________________________________________________________
add_17 (Add)                    (None, 1024, 32)     0           add_16[0][0]                     
                                                                 conv1d_26[0][0]                  
__________________________________________________________________________________________________
conv1d_27 (Conv1D)              (None, 1024, 32)     32800       add_17[0][0]                     
__________________________________________________________________________________________________
activation_18 (Activation)      (None, 1024, 32)     0           conv1d_27[0][0]                  
__________________________________________________________________________________________________
lambda_18 (Lambda)              (None, 1024, 32)     0           activation_18[0][0]              
__________________________________________________________________________________________________
spatial_dropout1d_18 (SpatialDr (None, 1024, 32)     0           lambda_18[0][0]                  
__________________________________________________________________________________________________
conv1d_28 (Conv1D)              (None, 1024, 32)     1056        spatial_dropout1d_18[0][0]       
__________________________________________________________________________________________________
add_18 (Add)                    (None, 1024, 32)     0           add_17[0][0]                     
                                                                 conv1d_28[0][0]                  
__________________________________________________________________________________________________
conv1d_29 (Conv1D)              (None, 1024, 32)     32800       add_18[0][0]                     
__________________________________________________________________________________________________
activation_19 (Activation)      (None, 1024, 32)     0           conv1d_29[0][0]                  
__________________________________________________________________________________________________
lambda_19 (Lambda)              (None, 1024, 32)     0           activation_19[0][0]              
__________________________________________________________________________________________________
spatial_dropout1d_19 (SpatialDr (None, 1024, 32)     0           lambda_19[0][0]                  
__________________________________________________________________________________________________
conv1d_30 (Conv1D)              (None, 1024, 32)     1056        spatial_dropout1d_19[0][0]       
__________________________________________________________________________________________________
add_20 (Add)                    (None, 1024, 32)     0           conv1d_1[0][0]                   
                                                                 conv1d_2[0][0]                   
                                                                 conv1d_3[0][0]                   
                                                                 conv1d_4[0][0]                   
                                                                 conv1d_5[0][0]                   
                                                                 conv1d_6[0][0]                   
                                                                 conv1d_7[0][0]                   
                                                                 conv1d_8[0][0]                   
                                                                 conv1d_9[0][0]                   
                                                                 conv1d_10[0][0]                  
                                                                 conv1d_12[0][0]                  
                                                                 conv1d_14[0][0]                  
                                                                 conv1d_16[0][0]                  
                                                                 conv1d_18[0][0]                  
                                                                 conv1d_20[0][0]                  
                                                                 conv1d_22[0][0]                  
                                                                 conv1d_24[0][0]                  
                                                                 conv1d_26[0][0]                  
                                                                 conv1d_28[0][0]                  
                                                                 conv1d_30[0][0]                  
__________________________________________________________________________________________________
activation_20 (Activation)      (None, 1024, 32)     0           add_20[0][0]                     
__________________________________________________________________________________________________
dense (Dense)                   (None, 1024, 2)      66          activation_20[0][0]              
__________________________________________________________________________________________________
activation_21 (Activation)      (None, 1024, 2)      0           dense[0][0]                      
==================================================================================================
Total params: 431,970
Trainable params: 431,970
Non-trainable params: 0
__________________________________________________________________________________________________
Epoch 1/1000
/usr/local/lib/python3.7/dist-packages/keras/engine/training.py:2470: UserWarning: `Model.state_updates` will be removed in a future version. This property should not be used in TensorFlow 2.0, as `updates` are applied automatically.
  warnings.warn('`Model.state_updates` will be removed in a future version. '
Epoch 00001: val_loss improved from inf to 0.04569, saving model to res/20210925_132436_model.h5
/usr/local/lib/python3.7/dist-packages/keras/utils/generic_utils.py:497: CustomMaskWarning: Custom mask layers require a config and must override get_config. When loading, the custom mask layer must be passed to the custom_objects argument.
  category=CustomMaskWarning)
47/47 - 68s - loss: 0.0796 - val_loss: 0.0457
Epoch 2/1000

Epoch 00002: val_loss improved from 0.04569 to 0.04298, saving model to res/20210925_132436_model.h5
47/47 - 21s - loss: 0.0333 - val_loss: 0.0430
Epoch 3/1000

Epoch 00003: val_loss improved from 0.04298 to 0.04224, saving model to res/20210925_132436_model.h5
47/47 - 21s - loss: 0.0325 - val_loss: 0.0422
Epoch 4/1000

Epoch 00004: val_loss improved from 0.04224 to 0.04108, saving model to res/20210925_132436_model.h5
47/47 - 21s - loss: 0.0317 - val_loss: 0.0411
Epoch 5/1000

Epoch 00005: val_loss did not improve from 0.04108
47/47 - 21s - loss: 0.0328 - val_loss: 0.0416
Epoch 6/1000

Epoch 00006: val_loss improved from 0.04108 to 0.04089, saving model to res/20210925_132436_model.h5
47/47 - 21s - loss: 0.0301 - val_loss: 0.0409
Epoch 7/1000

Epoch 00007: val_loss did not improve from 0.04089
47/47 - 21s - loss: 0.0303 - val_loss: 0.0410
Epoch 8/1000

Epoch 00008: val_loss did not improve from 0.04089
47/47 - 21s - loss: 0.0289 - val_loss: 0.0410
Epoch 9/1000

Epoch 00009: val_loss did not improve from 0.04089
47/47 - 21s - loss: 0.0302 - val_loss: 0.0413
Epoch 10/1000

Epoch 00010: val_loss improved from 0.04089 to 0.04059, saving model to res/20210925_132436_model.h5
47/47 - 21s - loss: 0.0283 - val_loss: 0.0406
Epoch 11/1000

Epoch 00011: val_loss did not improve from 0.04059
47/47 - 21s - loss: 0.0269 - val_loss: 0.0409
Epoch 12/1000

Epoch 00012: val_loss did not improve from 0.04059
47/47 - 21s - loss: 0.0279 - val_loss: 0.0410
Epoch 13/1000

Epoch 00013: val_loss did not improve from 0.04059
47/47 - 21s - loss: 0.0278 - val_loss: 0.0410
Epoch 14/1000

Epoch 00014: val_loss did not improve from 0.04059
47/47 - 21s - loss: 0.0267 - val_loss: 0.0417
Epoch 15/1000

Epoch 00015: val_loss did not improve from 0.04059
47/47 - 21s - loss: 0.0267 - val_loss: 0.0409
Epoch 16/1000

Epoch 00016: val_loss did not improve from 0.04059
47/47 - 21s - loss: 0.0265 - val_loss: 0.0408
Epoch 17/1000

Epoch 00017: val_loss did not improve from 0.04059
47/47 - 21s - loss: 0.0266 - val_loss: 0.0415
Epoch 18/1000

Epoch 00018: val_loss did not improve from 0.04059
47/47 - 21s - loss: 0.0271 - val_loss: 0.0424
Epoch 19/1000

Epoch 00019: val_loss did not improve from 0.04059
47/47 - 21s - loss: 0.0287 - val_loss: 0.0429
Epoch 20/1000

Epoch 00020: val_loss did not improve from 0.04059
47/47 - 21s - loss: 0.0268 - val_loss: 0.0412
Epoch 21/1000

Epoch 00021: val_loss did not improve from 0.04059
47/47 - 21s - loss: 0.0272 - val_loss: 0.0423
Epoch 22/1000

Epoch 00022: val_loss did not improve from 0.04059
47/47 - 21s - loss: 0.0276 - val_loss: 0.0417
Epoch 23/1000

Epoch 00023: val_loss did not improve from 0.04059
47/47 - 21s - loss: 0.0268 - val_loss: 0.0417
Epoch 24/1000

Epoch 00024: val_loss did not improve from 0.04059
47/47 - 21s - loss: 0.0271 - val_loss: 0.0418
Epoch 25/1000

Epoch 00025: val_loss did not improve from 0.04059
47/47 - 21s - loss: 0.0269 - val_loss: 0.0421
Epoch 26/1000

Epoch 00026: val_loss did not improve from 0.04059
47/47 - 21s - loss: 0.0258 - val_loss: 0.0420
Epoch 27/1000

Epoch 00027: val_loss did not improve from 0.04059
47/47 - 21s - loss: 0.0259 - val_loss: 0.0421
Epoch 28/1000

Epoch 00028: val_loss did not improve from 0.04059
47/47 - 21s - loss: 0.0256 - val_loss: 0.0424
Epoch 29/1000

Epoch 00029: val_loss did not improve from 0.04059
47/47 - 21s - loss: 0.0281 - val_loss: 0.0438
Epoch 30/1000

Epoch 00030: val_loss did not improve from 0.04059
47/47 - 21s - loss: 0.0269 - val_loss: 0.0424
INFO:root:re-loading last best model
INFO:root:predicting
INFO:root:evaluating
INFO:root:[[354461   1856]
 [  1718  10605]]
INFO:root:{'noise': {'precision': 0.9951765825610157, 'recall': 0.9947911550669769, 'f1-score': 0.9949838314881768, 'support': 356317}, 'pulse': {'precision': 0.8510552925126394, 'recall': 0.8605858962914875, 'f1-score': 0.8557940606843125, 'support': 12323}, 'accuracy': 0.9903049045138889, 'macro avg': {'precision': 0.9231159375368276, 'recall': 0.9276885256792322, 'f1-score': 0.9253889460862447, 'support': 368640}, 'weighted avg': {'precision': 0.9903588561686921, 'recall': 0.9903049045138889, 'f1-score': 0.9903309572867444, 'support': 368640}}
INFO:root:saving to res/20210925_132436_results.h5.
/usr/local/lib/python3.7/dist-packages/tables/path.py:112: NaturalNameWarning: object name is not a valid Python identifier: 'f1-score'; it does not match the pattern ``^[a-zA-Z_][a-zA-Z0-9_]*$``; you will not be able to use natural naming to access this object; using ``getattr()`` will still work, though
  NaturalNameWarning)
/usr/local/lib/python3.7/dist-packages/tables/path.py:112: NaturalNameWarning: object name is not a valid Python identifier: 'macro avg'; it does not match the pattern ``^[a-zA-Z_][a-zA-Z0-9_]*$``; you will not be able to use natural naming to access this object; using ``getattr()`` will still work, though
  NaturalNameWarning)
/usr/local/lib/python3.7/dist-packages/tables/path.py:112: NaturalNameWarning: object name is not a valid Python identifier: 'weighted avg'; it does not match the pattern ``^[a-zA-Z_][a-zA-Z0-9_]*$``; you will not be able to use natural naming to access this object; using ``getattr()`` will still work, though
  NaturalNameWarning)
INFO:root:DONE.
(<keras.engine.functional.Functional at 0x7f269f6ed290>,
 {'balance': False,
  'batch_level_subsampling': False,
  'batch_norm': True,
  'batch_size': 32,
  'class_names': ['noise', 'pulse'],
  'class_types': ['segment', 'event'],
  'class_weights': None,
  'data_dir': '/content/drive/MyDrive/Dmoj.wrigleyi.npy',
  'data_hash': '5381c36663f3b7286b0a5c42c0e3e463',
  'data_padding': 128,
  'filename_endsample_test': [],
  'filename_endsample_train': [],
  'filename_endsample_val': [],
  'filename_startsample_test': [],
  'filename_startsample_train': [],
  'filename_startsample_val': [],
  'filename_test': [],
  'filename_train': [],
  'filename_val': [],
  'first_sample_train': 0,
  'first_sample_val': 0,
  'fraction_data': None,
  'ignore_boundaries': True,
  'kernel_size': 32,
  'last_sample_train': None,
  'last_sample_val': None,
  'learning_rate': 0.0005,
  'log_messages': False,
  'model_name': 'tcn',
  'nb_channels': 16,
  'nb_classes': 2,
  'nb_conv': 4,
  'nb_epoch': 1000,
  'nb_filters': 32,
  'nb_freq': 16,
  'nb_hist': 1024,
  'nb_lstm_units': 0,
  'nb_pre_conv': 0,
  'nb_stacks': 2,
  'neptune_project': None,
  'output_stride': 1,
  'pre_kernel_size': 3,
  'pre_nb_conv': 2,
  'pre_nb_dft': 64,
  'pre_nb_filters': 16,
  'reduce_lr': False,
  'reduce_lr_patience': 5,
  'return_sequences': True,
  'sample_weight_mode': 'temporal',
  'samplerate_x_Hz': 10000.0,
  'samplerate_y_Hz': 10000.0,
  'save_dir': 'res',
  'save_prefix': '',
  'seed': None,
  'stride': 768,
  'tensorboard': False,
  'use_separable': [True, True, False, False],
  'verbose': 2,
  'version_data': True,
  'with_y_hist': True,
  'x_suffix': '',
  'y_offset': 0,
  'y_suffix': ''})

Adjust the name to point to the results:

res_name = '/content/res/20210925_132436'
res = flammkuchen.load(f'{res_name}_results.h5')

Inspect the history of the training and validation loss

plt.plot(res['fit_hist']['loss'], label='train')
plt.plot(res['fit_hist']['val_loss'], label='val')
plt.xlabel('Epoch')
plt.ylabel('Loss')
plt.legend()
plt.show()
../_images/colab_14_0.png

Plot the test results:

# t0, t1 = 1_020_000, 1_040_000  # dmel tutorial dataset
t0, t1 = 40_000, 60_000

plt.figure(figsize=(40, 8))
plt.subplot(311)
plt.plot(res['x_test'][t0:t1], 'k')
plt.ylabel('Audio')

plt.subplot(312)
plt.plot(res['y_test'][t0:t1, 1:])
plt.ylabel('Prediction targets')

plt.subplot(313)
plt.plot(res['y_pred'][t0:t1, 1:])
plt.ylabel('Predictions')

plt.show()
../_images/colab_16_0.png

You can download the model results via the file tab on the left, from /contest/res

Predict on new data

Load a new recording for prediction

model, params = das.utils.load_model_and_params(res_name)  # load the model and runtime parameters
ds = das.npy_dir.load('/content/drive/MyDrive/Dmoj.wrigleyi.npy', memmap_dirs=['train','val'])  # load the new data
print(ds)
x = ds['test']['x']
Data:
   test:
      x: (386000, 16)
      y: (386000, 2)
   val:
      y: (386000, 2)
      x: (386000, 16)
   train:
      y: (1158000, 2)
      x: (1158000, 16)

Attributes:
    class_names: ['noise', 'pulse']
    class_types: ['segment', 'event']
    filename_endsample_test: []
    filename_endsample_train: []
    filename_endsample_val: []
    filename_startsample_test: []
    filename_startsample_train: []
    filename_startsample_val: []
    filename_train: []
    filename_val: []
    samplerate_x_Hz: 10000.0
    samplerate_y_Hz: 10000.0
    filename_test: []

Run inference - this will calculate the confidence score and extract segment boundaries and event times.

events, segments, class_probabilities, _ = das.predict.predict(x, model=model, params=params, verbose=1)
/usr/local/lib/python3.7/dist-packages/keras/engine/training.py:2470: UserWarning: `Model.state_updates` will be removed in a future version. This property should not be used in TensorFlow 2.0, as `updates` are applied automatically.
  warnings.warn('`Model.state_updates` will be removed in a future version. '
t0, t1 = 42_000, 48_000
plt.figure(figsize=(20, 8))
plt.plot(x[t0:t1, 0], alpha=0.25, c='k', label='Audio')
plt.plot(class_probabilities[t0:t1, 1:], label='Prediction')
plt.xlim(0, t1-t0)
plt.legend(['Audio', 'Prediction'])
plt.show()
../_images/colab_22_0.png