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.
The (pip) package name is
dtw-python; the import
statement is just
To install the stable version of the package, issue the following command:
pip install dtw-python
Begin from the installed documentation:
> from dtw import * > ?dtw > help(DTW)
Note: the documentation for the Python module is auto-generated from the R version. It may contain minor inconsistencies.
The package documentation can also be browsed online.
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!
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
.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.
Python OO method calls use the postfix "dot" notation. This mostly
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
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)
The graphing functions have been re-implemented within the
matplotlib framework. They return
axes objects, which can be used
to customize the plot appearance.
numpy packages (e.g. with
will speed up installation.
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