rpy2 dtw缺少参数window.size答案

【问题标题】：rpy2 dtw missing argument window.sizerpy2 dtw缺少参数window.size
【发布时间】：2014-04-15 16:31:30
【问题描述】：

我正在使用带有 rpy2 的 R DTW 包。我希望能够指定用于运行 DTW 分析的窗口类型和大小。

我已经运行了以下代码：

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')

我收到以下错误消息：

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

如何正确指定 window.size 参数以便正确传递？

我对 R 和 rpy 还很陌生，所以我很可能会错误地使用这些库。非常感谢任何建议、提示或帮助。

--js

【问题讨论】：

标签： python r rpy2

【解决方案1】：

使用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)

【讨论】：

这不起作用。我从 rpy 收到以下错误： RuntimeError: Error in .canonicalizeWindowFunction(window.type) : Ambiguous or unsupported char argument for window.type
@Koffiman 你能让它工作吗？当我尝试将步骤更改为“不对称”时出现一些错误

【解决方案2】：

这对我有用：

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

documentation 声明：“window.type 也可以是用户定义的窗口函数。请参阅 dtwWindowingFunctions 了解所有可用的窗口函数” 在那里你可以修复window.size。

希望对你有帮助

【讨论】：