call python with system() in R to run a python script emulating the python console

Question

I want to pass a chunk of Python code to Python in R with something like system(\'python ...\'), and I\'m wondering if there is an easy way to emulate the pytho

Answer 1

The system command has an option called intern = FALSE. Make this TRUE and Whatever output was just visible before, will be stored in a variable.

Now run your system command with this option and you should get your output directly in your variable. Like this

tmp <- system("python -c 'print \"hello world\"'",intern=T)

Answer 2

Do you mean something like this?

export NUM=10
R -q -e "rnorm($NUM)"

You might also like to check out littler - http://dirk.eddelbuettel.com/code/littler.html

UPDATED

Following your comment below, I think I am beginning to understand your question better. You are asking about running python inside the R shell.

So here's an example:-

# code in a file named myfirstpythonfile.py

a = 1 
b = 19
c = 3 
mylist = [a, b, c]
for item in mylist:
    print item

In your R shell, therefore, do this:

> system('python myfirstpythonfile.py')
1
19
3

Essentially, you can simply call python /path/to/your/python/file.py to execute a block of python code.

In my case, I can simply call python myfirstpythonfile.py assuming that I launched my R shell in the same directory (path) my python file resides.

FURTHER UPDATED

And if you really want to print out the source code, here's a brute force method that might be possible. In your R shell:-

> system('python -c "import sys; sys.stdout.write(file(\'myfirstpythonfile.py\', \'r\').read());"; python myfirstpythonfile.py')
a = 1
b = 19
c = 3
mylist = [a, b, c]
for item in mylist:
    print item
1
19
3

AND FURTHER FURTHER UPDATED :-)

So if the purpose is to print the python code before the execution of a code, we can use the python trace module (reference: http://docs.python.org/library/trace.html). In command line, we use the -m option to call a python module and we specify the options for that python module following it.

So for my example above, it would be:-

$ python -m trace --trace myfirstpythonfile.py
 --- modulename: myfirstpythonfile, funcname: <module>
myfirstpythonfile.py(1): a = 1
myfirstpythonfile.py(2): b = 19
myfirstpythonfile.py(3): c = 3
myfirstpythonfile.py(4): mylist = [a, b, c]
myfirstpythonfile.py(5): for item in mylist:
myfirstpythonfile.py(6):     print item
1
myfirstpythonfile.py(5): for item in mylist:
myfirstpythonfile.py(6):     print item
19
myfirstpythonfile.py(5): for item in mylist:
myfirstpythonfile.py(6):     print item
3
myfirstpythonfile.py(5): for item in mylist:
 --- modulename: trace, funcname: _unsettrace
trace.py(80):         sys.settrace(None)

Which as we can see, traces the exact line of python code, executes the result immediately after and outputs it into stdout.

Answer 3

My work around for this problem is defining my own functions that paste in parameters, write out a temporary .py file, and them execute the python file via a system call. Here is an example that calls ArcGIS's Euclidean Distance function:

py.EucDistance = function(poly_path,poly_name,snap_raster,out_raster_path_name,maximum_distance,mask){

    py_path = 'G:/Faculty/Mann/EucDistance_temp.py'
    poly_path_name = paste(poly_path,poly_name, sep='')

    fileConn<-file(paste(py_path))
    writeLines(c(
        paste('import arcpy'),
        paste('from arcpy import env'),
        paste('from arcpy.sa import *'),
        paste('arcpy.CheckOutExtension("spatial")'),

        paste('out_raster_path_name = "',out_raster_path_name,'"',sep=""),
        paste('snap_raster = "',snap_raster,'"',sep=""),
        paste('cellsize =arcpy.GetRasterProperties_management(snap_raster,"CELLSIZEX")'),
        paste('mask = "',mask,'"',sep=""),
        paste('maximum_distance = "',maximum_distance,'"',sep=""),
        paste('sr = arcpy.Describe(snap_raster).spatialReference'),

        paste('arcpy.env.overwriteOutput = True'),
        paste('arcpy.env.snapRaster = "',snap_raster,'"',sep=""),
        paste('arcpy.env.mask = mask'),
        paste('arcpy.env.scratchWorkspace ="G:/Faculty/Mann/Historic_BCM/Aggregated1080/Scratch.gdb"'),
        paste('arcpy.env.outputCoordinateSystem = sr'),


        # get spatial reference for raster and force output to that
        paste('sr = arcpy.Describe(snap_raster).spatialReference'),
        paste('py_projection = sr.exportToString()'),     
        paste('arcpy.env.extent = snap_raster'),
        paste('poly_name = "',poly_name,'"',sep=""),
        paste('poly_path_name = "',poly_path_name,'"',sep=""),

        paste('holder = EucDistance(poly_path_name, maximum_distance, cellsize, "")'),
        paste('holder = SetNull(holder < -9999, holder)'),
        paste('holder.save(out_raster_path_name) ')

    ), fileConn, sep = "\n")
    close(fileConn)

    system(paste('C:\\Python27\\ArcGIS10.1\\python.exe', py_path))
}