rpy2 dtw missing argument window.size

问题

I'm using the R DTW package with rpy2. I would like to be able specify a window type and size for running the DTW analysis.

I have run the following code:

import numpy as np
import rpy2.robjects as robjects
import rpy2.robjects.numpy2ri
rpy2.robjects.numpy2ri.activate()

r = robjects.r
r('library("dtw")')

query = np.array([0.0,1.0,2.0,3.0])
reference = np.array([0.0,1.9,2.4,3.0])

# Attempt 1:
kwargs = {'step':r("asymmetric"),'window_type':r("sakoeChibaWindow"),'window_size':r("as.integer(\"3\")")}
alig = r.dtw(query, reference, **kwargs)

# Attempt 2:
alig = r.dtw(query, reference, keep=r('TRUE'), step=r('asymmetric'),window_type=r('sakoeChibaWindow'),window_size="as.integer(\"3\")")

# Attempt 3:
alig = r.dtw(query, reference, keep=r('TRUE'), step=r('asymmetric'),window_type=r('sakoeChibaWindow'),window_size=3)

# Note: The line of code below works correctly.
# alig = r.dtw(query, reference, keep=r('TRUE'), step=r('asymmetric'))

robjects.globalenv["alignment"] =  alig
print r('alignment$distance')

I get the following error message:

Error in abs(jw - iw) <= window.size : 'window.size' is missing
Traceback (most recent call last):
  File "testrdtw.py", line 19, in <module>
    alig = r.dtw(query, reference, **kwargs)
  File "/Users/jsmith/Dropbox/IW/env/lib/python2.7/site-packages/rpy2/robjects/functions.py", line 86, in __call__
    return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)
  File "/Users/jsmith/Dropbox/IW/env/lib/python2.7/site-packages/rpy2/robjects/functions.py", line 35, in __call__
    res = super(Function, self).__call__(*new_args, **new_kwargs)
rpy2.rinterface.RRuntimeError: Error in abs(jw - iw) <= window.size : 'window.size' is missing

How do I properly specify the window.size argument such that it is passed correctly?

I'm quite new to R and rpy so I could very well be using these libraries incorrectly. Any suggestions,hints, or help greatly appreciated.

-- js

回答1:

Use importr():

from rpy2.robjects.packages import importr
dtw = importr('dtw')
alig = dtw.dtw(query, reference, keep=True,
               step='asymmetric',
               window_type='sakoeChibaWindow',
               window_size=3)

回答2:

This works for me:

import numpy as np
import rpy2.robjects.numpy2ri
from rpy2.robjects.packages import importr

rpy2.robjects.numpy2ri.activate()
R = rpy2.robjects.r
DTW = importr('dtw')

x = np.array([0.0, 1.0, 2.0, 3.0])
y = np.array([0.0, 1.9, 2.4, 3.0])

alignment1 = R.dtw(x, y, keep=True,  dist_method="Euclidean",step_pattern=DTW.asymmetric,type="sakoechiba")
alignment2 = R.dtw(x, y, keep=True, dist_method="Euclidean",step_pattern=DTW.symmetric1,type="itakura")
alignment3 = R.dtw(x, y, keep=True, dist_method="Euclidean", step_pattern=DTW.symmetric2, type=DTW.sakoeChibaWindow, window_size=2)
dist1 = alignment1.rx('distance')[0][0]
dist2 = alignment2.rx('distance')[0][0]
dist3= alignment3.rx('distance')[0][0]
print(dist1)
#1.0
print(dist2)
#1.3
print(dist3)
#1.3

The documentation states:"window.type can also be an user-defined windowing function. See dtwWindowingFunctions for all available windowing functions" There u can fix the window.size.

Hope it helps

来源：https://stackoverflow.com/questions/23089501/rpy2-dtw-missing-argument-window-size

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python

rpy2