dtwParallel 0.1

Python implementation of Dynamic Time Warping (DTW), which allows computing the dtw distance between one-dimensional and multidimensional time series, with the possibility of visualisation (one-dimensional case) and parallelisation (multidimensional case).

Dynamic Time Warping

This package allows to measure the similarity between two time sequences, i.e., it finds the optimal alignment between two time-dependent sequences. It allows the calculation for univariate and multivariate time series. Any distance available in scipy.spatial.distance can be used. An extra functionality has been incorporated to transform the resulting DTW matrix into an exponential kernel.

Univariate Time Series:

• It incorporates the possibility of visualising the cost matrix, as well as the path to reach the DTW distance value. This will allow it to be used in a didactic way, providing a better understanding of the method used.
• It allows the calculation for regular and irregular univariate time series.

Multivariate Time Series:

• The calculation of dependent DTW and independent DTW is available.
• The calculation can be parallelised.
• The computation can be CPU parallelised by selecting the number of threads.
• The distance matrix obtained can be transformed to a kernel.

Package structure

Installation

dtwParallel can be installed using pip, a tool for installing Python packages. To do it, run the following command:

pip3 install -i https://test.pypi.org/simple/ dtwParallel

Requirements

• Python >= 3.6.1

Note that you should have also the following packages installed in your system:

• numpy
• pandas
• matplotlib
• seaborn
• gower
• setuptools
• scipy
• joblib

Usage

Based on the previous scheme, this package can be used in three different contexts:

1) Calculation of the DTW distance with input from the terminal.

The generic example is shown below:

  dtwParallel -x <floats> -y <floats> -d <str> -ce <bool> -of <bool>

Note that only the x and y values need to be set. The rest of the values, if not indicated, will be selected from the file containing the default values, configuration.ini.

Next, different uses are shown by modifying the parameters of the function:

a) Example 1. Setting only the mandatory values.

dtwParallel -x 1 2 3 -y 1 1 1

[out]: 3.0

b) Example 2. Setting all values.

dtwParallel -x 1 2 3 -y 1 1 1 -d euclidean -ce True

[out]: 3.0

c) Example 3. By setting all values, modifying the distance used.

dtwParallel -x 1.5 2 3.7 -y 1.4 1 1.05 -d gower -ce True

[out]: 3.0000000596046448

Remarks: The calculation of the DTW distance from the command line is limited to simple examples that allow a quick understanding, due to the complexity of the terminal handling:

• Univariate time series.
• Dependent DTW.
• To carry out the visualization of the cost matrix and the routing it will be necessary to make use of an integrated development environment.

2) Calculation of the DTW distance with input from a file, haciendo uso de terminal.

The generic example of univariate time series entered by means of csv files is shown below:

dtwParallel <file_X> -d <str> -ce <bool> -of <bool>

In case you want to modify any of the possible values, it is necessary to carry out the modification in the configuration.ini file. The possible values are those shown in Configuration.

a) Example 1. Calculation of univariate time series taking as input a csv file containing x and y.

dtwParallel exampleData/example_1.csv

[out]: 40.6

dtwParallel exampleData/example_1.csv -d "gower"

[out]: 10.000000178813934

The generic example of multivariate time series entered by means of csv files is shown below:

dtwParallel <file_X> -d <str> -t <str> -ce <bool> -of <bool> -n <int> -k <bool> -s <float>

b) Example 2. Multivariate time series computation using a csv file containing x and y as input.

dtwParallel exampleData/example_2.csv

[out]: 81.99196512684249

dtwParallel exampleData/example_2.csv -d gower -t i 

[out]: 9.666666567325592

The generic example for npy files is shown below:

dtwParallel <file_X> <file_Y> -d <str> -t <str> -ce <bool> -of <bool> -n <int> -k <bool> -s <float>

c) Example 3. It computes the distance to itself.

dtwParallel exampleData/X_train.npy 

[out]: [[0.00000000e+00 6.36756028e+17 2.94977907e+16 9.96457616e+17]
       [6.36756028e+17 0.00000000e+00 6.07258237e+17 1.63321364e+18]
       [2.94977907e+16 6.07258237e+17 0.00000000e+00 1.02595541e+18]
       [9.96457616e+17 1.63321364e+18 1.02595541e+18 0.00000000e+00]]

d) Example 4. Compute the distance between X and Y.

dtwParallel exampleData/X_train.npy exampleData/X_test.npy

[out]: [[2.47396197e+16 9.07388652e+17 2.23522660e+17 1.68210525e+18]
       [6.12016408e+17 1.54414468e+18 8.60278687e+17 2.31886127e+18]
       [4.75817098e+15 9.36886443e+17 2.53020450e+17 1.71160304e+18]
       [1.02119724e+18 8.90689643e+16 7.72934957e+17 6.85647630e+17]]

e) Example 5. Compute the gower distance between X and Y.

dtwParallel exampleData/X_train.npy exampleData/X_test.npy -d "gower"

[out]: [[1.7200027  2.16000016 1.92000033 2.53999992]
       [1.59999973 1.79999978 1.83999987 2.27999987]
       [0.5399895  1.52000002 1.04000024 1.66      ]
       [0.70000006 1.57999993 1.10000018 1.69999999]]

f) Example 6. Compute the gower distance between X and Y and we vary the number of threads.

dtwParallel exampleData/X_train.npy exampleData/X_test.npy -d "gower" -n 12

[out]: [[1.7200027  2.16000016 1.92000033 2.53999992]
       [1.59999973 1.79999978 1.83999987 2.27999987]
       [0.5399895  1.52000002 1.04000024 1.66      ]
       [0.70000006 1.57999993 1.10000018 1.69999999]]

g) Example 7. Compute the gower distance between X and Y and we obtain the output per file.

dtwParallel exampleData/X_train.npy exampleData/X_test.npy -d "gower" -n 12 -of True

[out]: output.csv

h) Example 8. We calculate the distance between X and Y and transform to Gaussian kernel with sigma=0.5.

dtwParallel exampleData/X_train.npy -k True -s 1000000000

[out]: [[1.         0.7273278  0.98535934 0.60760589]
       [0.7273278  1.         0.73813458 0.44192866]
       [0.98535934 0.73813458 1.         0.59871014]
       [0.60760589 0.44192866 0.59871014 1.        ]]

Remarks:

• You can run from any repository, but be careful! The .npy file must be found.

3) Making use of the API

The generic example is shown below:

from dtwParallel import dtw_functions
 
# For Univariate Time Series
dtw_functions.dtw(x,y,type_dtw, distance, MTS, get_visualization, check_errors)

# For Multivariate Time Series
dtw_functions.dtw_tensor(X_1, X_2, type_dtw, dist, n_threads, check_erros, dtw_to_kernel, sigma)

The examples shown below are executed in jupyter-notebook. These examples can be executed in any Integrated Development Environment.

Example 1. For univariate time series.

from dtwParallel import dtw_functions
from scipy.spatial import distance as d

# For Univariate Time Series
x = [1,2,3]
y = [0,0,1]

distance = d.euclidean
dtw_functions.dtw(x,y,distance)

[out]: 5.0

Example 2. For univariate time series with visualization.

from dtwParallel import dtw_functions
from scipy.spatial import distance as d

# For Univariate Time Series
x = [4,2,8,4,5]
y = [0,1,0,8,9]

distance = d.euclidean
visualization=True
dtw_functions.dtw(x,y,distance, get_visualization=visualization)

[out]: 15.0

Example 3. For multivariate time series.

from dtwParallel import dtw_functions
from scipy.spatial import distance as d
import numpy as np

x = np.array([[3,5,8], 
             [5, 1,9]])

y = np.array([[2, 0,8],
             [4, 3,8]])
            
dtw_functions.dtw(x,y,"d", d.euclidean, MTS=True)

[out]: 7.548509256375962

Example 4. For a tensor formed by N x T x F, where N is the number of observations, T the time instants and F the characteristics.

from dtwParallel import dtw_functions
import numpy as np

x = np.load('X_train.npy')
y = np.load('X_test.npy')

dtw_functions.dtw_tensor_3d(x, y, "gower")

[out]: 
array([[2.47396197e+16, 6.12016408e+17, 4.75817098e+15, 1.02119724e+18],
    [9.07388652e+17, 1.54414468e+18, 9.36886443e+17, 8.90689643e+16],
    [2.23522660e+17, 8.60278687e+17, 2.53020450e+17, 7.72934957e+17],
    [1.68210525e+18, 2.31886127e+18, 1.71160304e+18, 6.85647630e+17]])

Configuration

For any modification of the default parameters, the configuration.ini file can be edited.

The default values are:

[DEFAULT]
check_errors = False
distance = euclidean
type_dtw = d
mts = False
n_threads = -1
visualization = False
output_file = False
dtw_to_kernel = False
sigma = 1

Examples with public data

Reference

If you use dtwParallel in your research papers, please refer to ...

[To be done]

License

Licensed under the BSD 2-Clause License.