dtw-python: Dynamic Time Warping in Python

The dtw-python module is a faithful Python equivalent of the R package; it provides the same algorithms and options.

Installation

To install the stable version of the package, issue the following command:

pip install dtw-python

Getting started

Begin from the installed documentation:

> from dtw import *
> ?dtw
> help(DTW)

Online documentation

The package documentation can also be browsed online.

Quickstart

import numpy as np

## A noisy sine wave as query
idx = np.linspace(0,6.28,num=100)
query = np.sin(idx) + np.random.uniform(size=100)/10.0

## A cosine is for template; sin and cos are offset by 25 samples
template = np.cos(idx)

## Find the best match with the canonical recursion formula
from dtw import *
alignment = dtw(query, template, keep_internals=True)

## Display the warping curve, i.e. the alignment curve
alignment.plot(type="threeway")

## Align and plot with the Rabiner-Juang type VI-c unsmoothed recursion
dtw(query, template, keep_internals=True, 
    step_pattern=rabinerJuangStepPattern(6, "c"))\
    .plot(type="twoway",offset=-2)

## See the recursion relation, as formula and diagram
print(rabinerJuangStepPattern(6,"c"))
rabinerJuangStepPattern(6,"c").plot()

## And much more!

 

Try online!

Differences with R

Indices are 0-based

R uses 1-based indexing, whereas Python uses 0-based arrays. Wherever indices are returned (most importantly in the .index1, .index2, .index1s and .index2s attributes of alignments), these must be assumed to be 0-based in Python. Hence, indices can be used as subscripts in both environments as natural.

Object-oriented methods

Python OO method calls use the postfix "dot" notation. This mostly affects the plot() methods. Note that non-overloaded functional style such as dtwPlotThreeWay are unaffected. Hence:

## In R
plot(alignment, type="threeway")

## In Python
alignment.plot(type="threeway")
## or
dtwPlotThreeWay(alignment)

The alignment class

The class name of alignment objects in DTW (all capitals) in Python. Its attributes are accessed with the usual "dot" notation (R uses $ as for lists).

Dots vs underscores

R commonly uses the dot (.) separator for function argument names, while Python uses the underscore (_) for the same purpose. The function prototypes reflect this difference. Also, Python does not accept abbreviated argument names. Therefore:

## In R
alignment = dtw(query, template, keep.int=TRUE)

## In Python
alignment = dtw(query, template, keep_internals=True)

Plots

The graphing functions have been re-implemented within the matplotlib framework. They return axes objects, which can be used to customize the plot appearance.

Installation notes

Pre-installing the scipy and numpy packages (e.g. with conda) will speed up installation.

The errors undefined symbol: alloca (at runtime), or about C99 mode (if compiling from source), are likely due to old system or compiler. If using conda, the following may help:

conda install gcc_linux-64
pip install dtw-python

Note that you may have to delete cached .whl files.