R clump within python with rpy2

Question

My specific issue is exactly the title. I have a large raster processing script in python and need to perform a clump function which I cannot find in gdal / python nor have I figured out how to 'write it' myself. I am becoming better with python all the time just still newish, but am learning R for this task. (installed R version 3.4.1 (2017-06-30))

I am able to get rpy2 installed within python after spending a little time learning R and through help on Stackoverflow I have been able to perform several 'tests' of rpy2. The most helpful info in getting rpy2 to respond was to establish where your R is within your python session or script. from another Stack answer. As below:

import os
os.environ['PYTHONHOME'] = r'C:\Python27\ArcGIS10.3\Scripts\new_ve_folder\Scripts'
os.environ['PYTHONPATH'] = r'C:\Python27\ArcGIS10.3\Scripts\new_ve_folder\Lib\site-packages'
os.environ['R_HOME'] = r'C:\Program Files\R\R-3.4.1'
os.environ['R_USER'] = r'C:\Python27\ArcGIS10.3\Scripts\new_ve_folder\Lib\site-packages\rpy2'

However, the main tests listed in the documentation http://rpy.sourceforge.net/rpy2/doc-2.1/html/overview.html I cannot get to work.

import rpy2.robjects.tests
import unittest

# the verbosity level can be increased if needed
tr = unittest.TextTestRunner(verbosity = 1)
suite = rpy2.robjects.tests.suite()

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  AttributeError: 'module' object has no attribute 'suite'

However:

import rpy2.robjects as robjects
pi = robjects.r['pi']
pi[0]

works just fine. as do a few other rpy2.robjects tests I have found. I can create string = ''' f <- functions ect ''' and call those from python.

If i use:

python -m 'rpy2.tests'

I get the following error. r\\Scripts>python -m 'rpy2.tests' r\\Scripts\\python.exe: No module named 'rpy2

Documentation states: On Python 2.6, this should return that all tests were successful. I am using Python 2.7 and I also tried this in Python 3.3.

My script for clump starts as below: I do not want to have to actually install the package names each time I run the script as they are already installed in my R Home. I would like to use my python variables if possible.

I need to figure out why rpy2 does not respond as the documentation indicates, or why I am getting errors. And then after that figure out the correct way to write my clump portion of my python script.

packageNames = ('raster', 'rgdal')
if all(rpackages.isinstalled(x) for x in packageNames):
    have_packages = True
else:
   have_packages = False
if not have_packages:
    utils = rpackages.importr('utils')
    utils.chooseCRANmirror(ind=1)
    packnames_to_install = [x for x in packageNames if not     rpackages.isinstalled(x)]
    if len(packnames_to_install) > 0:
        utils.install_packages(StrVector(packnames_to_install))

from rpy2.robjects.packages import importr
import rpy2.robjects as robjects

There are several ways I have found to call the raster and clump options from R, however, if I cannot get rpy2 to respond correctly, I am not going to get these to work at all But since several other tests work I am not positive.

raster = robjects.r['raster'] 
raster = importr('raster')   
clump = raster.clump
clump = robjects.r.clump
type(raster.clump)

tempDIR = r"C:\Users\script_out\temp"
slope_recode = os.path.join(tempDIR, "step2b_input.img")
outfile = os.path.join(tempDIR, "Rclumpfile.img")

raster.clump(slope_recode, filename=outfile, direction=4, gaps=True, format='HFA', overwrite=True)

Which results in a large amount of errors.

Traceback (most recent call last):
  File "C:/Python27/ArcGIS10.3/Scripts/new_ve_folder/Scripts/rpy2_practice.py", line 97, in <module>
      raster.clump(slope_recode, filename=outfile, direction=4, gaps=True, format='HFA', overwrite=True)
  File "C:\Python27\ArcGIS10.3\Scripts\new_ve_folder\lib\site-packages\rpy2\robjects\functions.py", line 178, in __call__
      return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)
  File "C:\Python27\ArcGIS10.3\Scripts\new_ve_folder\lib\site-packages\rpy2\robjects\functions.py", line 106, in __call__
      res = super(Function, self).__call__(*new_args, **new_kwargs)
rpy2.rinterface.RRuntimeError: Error in (function (classes, fdef, mtable)  : 
      unable to find an inherited method for function 'clump' for signature '"character"'

Issues: testing rpy2 in command line and script (both produce errors, but I am still able to use basic rpy2

importing the R packages so as not to install them each time

finally getting my clump script called correctly

If I have missed something basic, please point me in the right direction. Thanks all.

Answer 1

For your first problem, replace suite = rpy2.robjects.tests.suite() with suite = rpy2.tests.suite() .

For your third problem (getting clump to work correctly), you need to create a RasterLayer object in R using the image. I'm not familiar with the raster package, so I can't give you the exact steps.

I will point out the arcpy module is not "pythonic". Normally, strings of filenames are just strings in Python. arcpy is weird in using plain strings to represent objects like map layers.

In your example, slope_recode is just a string. That's why you got the error unable to find an inherited method for function 'clump' for signature '"character"' . It means slope_recode was passed to R as a character value (which it is), and the clump function expects a RasterLayer object. It doesn't know how to handle character values.

Answer 2

I got this all to work with the below code.

    import warnings
    os.environ['PATH'] =       os.path.join(scriptPath, 'path\\my_VE\\R\\R-3.4.2\\bin\\x64')
    os.environ['PYTHONHOME'] = os.path.join(scriptPath, 'path\\my_VE\\Scripts\\64bit')
    os.environ['PYTHONPATH'] = os.path.join(scriptPath, 'path\\my_VE\\Lib\\site-packages')
    os.environ['R_HOME'] =     os.path.join(scriptPath, 'path\\my_VE\\R\\R-3.4.2')
    os.environ['R_USER'] =     os.path.join(scriptPath, 'path\\my_VE\\Scripts\\new_ve_folder\\Scripts\\rpy2')
    #
    import platform
    z = platform.architecture()
    print(z)
    ## above will confirm you are working on 64 bit
    gc.collect()
    ## this code snippit will tell you which library is being Read
    command = 'Rscript'
    cmd = [command, '-e', ".libPaths()"]
    print(cmd)
    x = subprocess.Popen(cmd, shell=True)
    x.wait()

    import rpy2.robjects.packages as rpackages
    import rpy2.robjects as robjects
    from rpy2.robjects import r
    import rpy2.interactive.packages
    from rpy2.robjects import lib
    from rpy2.robjects.lib import grid
    # # grab r packages
    print("loading packages from R")
    ## fails at this point with the following error
    ##  Error: cannot allocate vector of size 232.6 Mb when working with large rasters
    rpy2.robjects.packages.importr('raster')
    rpy2.robjects.packages.importr('rgdal')
    rpy2.robjects.packages.importr('sp')
    rpy2.robjects.packages.importr('utils')
    # rpy2.robjects.packages.importr('memory')
    # rpy2.robjects.packages.importr('dplyr')
    rpy2.robjects.packages.importr('data.table')
    grid.activate()
    # set python variables for R code names
    raster = robjects.r['raster']
    writeRaster = robjects.r['writeRaster']
    # setwd = robjects.r['setwd']
    clump = robjects.r['clump']
    # head = robjects.r['head']
    crs = robjects.r['crs']
    dim = robjects.r['dim']
    projInfo = robjects.r['projInfo']
    slope_recode = os.path.join(tempDIR, "_lope_recode.img")
    outfile = os.path.join(tempDIR, "Rclumpfile.img")
    recode = raster(slope_recode)  # this is taking the image and                            reading it into R raster package
    ## https://stackoverflow.com/questions/47399682/clear-r-memory-using-rpy2
    gc.collect()  # No noticeable effect on memory usage
    time.sleep(2)
    gc.collect()  # Finally, memory usage drops
    R = robjects.r
    R('memory.limit()')
    R('memory.limit(size = 65535)')
    R('memory.limit()')

    print"starting Clump with rpy2"
    clump(recode, filename=outfile, direction=4, gaps="True", format="HFA")

    final = raster(outfile)
            final = crs("+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0,-0,-0,-0,0 +no_defs")

    print ("clump file created, CRS accurate, next step")