RcppCNPy: Rcpp bindings for NumPy files
About
This package uses the cnpy library
written by Carl Rogers to provide read and write facilities for files created
with (or for) the NumPy extension for Python. Vectors and matrices of
numeric types can be read or written to and from files as well as compressed
files. Support for integer files is available if the package has been built
with -std=c++11 which is the default starting with release 0.2.3 following
the release of R 3.1.0, and available on all platforms following the release
of R 3.3.0 with the updated 'Rtools'.
Example
The following Python code
>>> import numpy as np
>>> fm = np.arange(12).reshape(3,4) * 1.1
>>> fm
array([[ 0. , 1.1, 2.2, 3.3],
[ 4.4, 5.5, 6.6, 7.7],
[ 8.8, 9.9, 11. , 12.1]])
>>> np.save("fmat.npy", fm)
>>>
>>> im = np.arange(12).reshape(3,4)
>>> im
array([[ 0, 1, 2, 3],
[ 4, 5, 6, 7],
[ 8, 9, 10, 11]])
>>> np.save("imat.npy", im)
>>>
saves two matrices in floating-point and integer representation.
With this R code we can read and assign the files:
R> library(RcppCNPy)
R> fmat <- npyLoad("fmat.npy")
R> fmat
[,1] [,2] [,3] [,4]
[1,] 0.0 1.1 2.2 3.3
[2,] 4.4 5.5 6.6 7.7
[3,] 8.8 9.9 11.0 12.1
R>
R> imat <- npyLoad("imat.npy", "integer")
R> imat
[,1] [,2] [,3] [,4]
[1,] 0 1 2 3
[2,] 4 5 6 7
[3,] 8 9 10 11
R>
Going the opposite way by saving in R and reading in Python works equally well. An extension not present in CNPy allows reading and writing of gzip-compressed files.
The package has been tested and used on several architecture, and copes correctly with little-vs-big endian switches.
More details are available in the package vignette.
Installation
The package is on CRAN and can be installed per:
R> install.packages("RcppCNPy")
Status
On CRAN, stable and mostly feature-complete.
Alternative: reticulate
The reticulate package can also provide easy and comprehensive access to NumPy data; see the additional vignette in RcppCNPy for examples and more details.
Feedback
Contributions are welcome, please use the GitHub issue tracker for bug reports, feature requests or general discussions before sending pull requests.
Author
Dirk Eddelbuettel and Wush Wu
License
GPL (>= 2)