Error in running a Python code from R with the package rPithon

Question

I would like to run this Python code from R:

>>> import nlmpy 
>>> nlm = nlmpy.mpd(nRow=50, nCol=50, h=0.75) 
>>> nlmpy.exportASCIIGrid("raster.asc", nlm)

Nlmpy is a Python package to build neutral landscape models. The example comes from the website

To run this Python code from R, I 'm trying to use the package rPithon. However, I obtain this error message:

if (pithon.available()) 
{ 
  nRow <- 50 
  nCol <- 50 
  h <- 0.75 

  # this file contains the definition of function concat 
  pithon.load("C:/Users/Anaconda2/Lib/site-packages/nlmpy/nlmpy.py") 
  pithon.call( "mpd", nRow, nCol, h) 

} else { 
  print("Unable to execute python") 
} 

Error in pithon.get("_r_call_return", instance.name = instname) : 
Couldn't retrieve variable: Traceback (most recent call last): 
File "C:/Users/Documents/R/win-library/3.3/rPithon/pythonwrapperscript.py", line 110, in <module> 
reallyReallyLongAndUnnecessaryPrefix.data = json.dumps([eval(reallyReallyLongAndUnnecessaryPrefix.argData)]) 
File "C:\Users\ANACON~1\lib\json\__init__.py", line 244, in dumps 
return _default_encoder.encode(obj) 
File "C:\Users\ANACON~1\lib\json\encoder.py", line 207, in encode 
chunks = self.iterencode(o, _one_shot=True) 
File "C:\Users\ANACON~1\lib\json\encoder.py", line 270, in iterencode 
return _iterencode(o, 0) 
File "C:\Users\ANACON~1\lib\json\encoder.py", line 184, in default 
raise TypeError(repr(o) + " is not JSON serializable") 
TypeError: array([[ 0.36534654,  0.31962481,  0.44229946, ...,  0.11513079, 
0.07156331,  0.00286971], [ 0.41534291,  0.41333479,  0.48118995, ...,  0.19203674, 
0.04192771,  0.03679473], [ 0.5188

Is this error caused by a syntax issue in my code ? I work with the Anaconda 4.2.0 platform for Windows which uses the Python 2.7 version.

The mpd function in python returns a 2D array which is not supported by the JSONEncoder by default. In python, do import json help(json.encoder) to see more information. Also, this post appears to be related stackoverflow.com/questions/22281059/… — jmuhlenkamp
– jmuhlenkamp, Commented Nov 22, 2016 at 20:09
How determined are you to use the rPithon package? Are you open to use some other approaches which calls Python functions from R? — Ronak Shah
– Ronak Shah, Commented Nov 23, 2016 at 6:07
Why not call Python script at command line with args using R's system()? — Parfait
– Parfait, Commented Nov 24, 2016 at 0:44
Thanks a lot for your answers. I don't know system() or other approaches to call Python functions from R. — Nell
– Nell, Commented Nov 24, 2016 at 16:13

Ronak Shah · Accepted Answer · 2016-11-24 05:37:08Z

3

+50

I haven't used the nlmpy package hence, I am not sure what would be your expected output. However, this code successfully communicates between R and Python.

There are two files,

nlmpyInR.R

command ="python"
path2script="path_to_your_pythoncode/nlmpyInPython.py"

nRow <-50 
nCol <-50 
h <- 0.75

# Build up args in a vector
args = c(nRow, nCol, h)

# Add path to script as first arg
allArgs = c(path2script, args)

Routput = system2(command, args=allArgs, stdout=TRUE)
#The command would be python nlmpyInPython.py 50 50 0.75

print(paste("The Output is:\n", Routput))

nlmpyInPython.py

import sys
import nlmpy 
#Getting the arguments from the command line call
nRow = sys.argv[1]
nCol = sys.argv[2]
h = sys.argv[3]

nlm = nlmpy.mpd(nRow, nCol, h) 
pyhtonOutput = nlmpy.exportASCIIGrid("raster.asc", nlm)
#Whatever you print will get stored in the R's output variable. 
print pyhtonOutput

answered Nov 24, 2016 at 5:37

Ronak Shah

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9 Comments

Nell Over a year ago

Thanks a lot for your response ! I have a error message when I run the code from R (The code in "nlmpylnPython.py" works in Python):

running command '"python" C:/nlmpyInPython.py 50 50 0.75' had status [1] "Traceback (most recent call last):"                                                                      [2] "  File \"C:/nlmpyInPython.py\", line 14, in <module>" [3] "    nlm = nlmpy.mpd(nRow, nCol, h) "                                                                  [4] "  File \"C:\\Users\\ANACON~1\\lib\\site-packages\\nlmpy\\nlmpy.py\", line 523, in mpd"

Nell Over a year ago

The rest of the error message is

[5] "    mask = np.ones((nRow, nCol))  "                                                                      [6] "  File \"C:\\Users\\ANACON~1\\lib\\site-packages\\numpy\\core\\numeric.py\", line 190, in ones"  [7] "    a = empty(shape, dtype, order)"                                                                      [8] "TypeError: an integer is required"                                                                       attr(,"status") [1] 1

Ronak Shah Over a year ago

@Nell I had ran on my windows system and it was working fine. The python call seems a bit doubtful. why it is '"python" C:/nlmpyInPython.py 50 50 0.75'?Rather shouldn't it be python C:/nlmpyInPython.py 50 50 0.75 ? Looks like the numbers 50 50 0.75 are going as string.

Nell Over a year ago

I have checked that nRow, nCol and h are numbers by using class(nRow) in R. All these arguments are numeric. I've also tested the Python path by running command="C:/Users/Anaconda2/python.exe" instead of command="python". I have again the same error message.

Ronak Shah Over a year ago

Can you run python C:/nlmpyInPython.py 50 50 0.75 from command line and check if it is running properly?

|

brm · Accepted Answer · 2017-04-30 16:02:47Z

The cause of the error that you're getting is hinted at by the "is not JSON serializable" line. Your R code calls the mpd function with certain arguments, and that function itself will execute correctly. The rPithon library will then try to send the return value of the function back to R, and to do this it will try to create a JSON object that describes the return value.

This works well for integers, floating point values, arrays, etc, but not every kind of Python object can be converted to such a JSON representation. And because rPithon can't convert the return value of mpd this way, an error is generated.

You can still use rPithon to call the mpd function though. The following code creates a new Python function that performs two steps: first it calls the mpd function with the specified parameters, and then it exports the result to a file, of which the filename is also an argument. Using rPithon, the new function is then called from R. Because myFunction doesn't return anything, representing the return value in JSON format will not be a problem.

library("rPithon")

pythonCode = paste("import nlmpy.nlmpy as nlmpy",
                   "",
                   "def myFunction(nRow, nCol, h, fileName):",
                   "    nlm = nlmpy.mpd(nRow, nCol, h)",
                   "    nlmpy.exportASCIIGrid(fileName, nlm)", 
                   sep = "\n")
pithon.exec(pythonCode)

nRow <- 50 
nCol <- 50 
h <- 0.75 

pithon.call("myFunction", nRow, nCol, h, "outputraster.asc")

Here, the Python code defined as an R string, and executed using pithon.exec. You could also put that Python code in a separate file and use pithon.load to process the code so that the myFunction function is known.

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