#!/usr/bin/env python # -*- coding: utf-8 -*- ############################################################################ # # MODULE: r.diversity # AUTHOR(S): Luca Delucchi # PURPOSE: It calculates the mostly used indices of diversity based on # information theory # # COPYRIGHT: (C) 2010-2012 by Luca Delucchi # # This program is free software under the GNU General Public # License (>=v2). Read the file COPYING that comes with GRASS # for details. # ############################################################################# #%module #% description: Calculate diversity indices based on a moving window using r.li packages #% keyword: raster #%end #%option #% key: input #% type: string #% gisprompt: old,cell,raster #% key_desc: name #% description: Name of input raster map #% required: yes #%end #%option #% key: prefix #% type: string #% gisprompt: new,cell,raster #% key_desc: name #% description: Prefix for output raster map(s) #% required: yes #%end #%option #% key: alpha #% type: double #% key_desc: alpha value for Renyi entropy #% description: Order of generalized entropy (> 0.0; undefined for 1.0) #% multiple: yes #% required: no #%end #%option #% key: size #% type: integer #% key_desc: moving window #% multiple: yes #% description: Size of processing window (odd number only) #% answer: 3 #% required: no #%end #%option #% key: method #% type: string #% key_desc: method #% options: simpson,shannon,pielou,renyi #% multiple: yes #% description: Name of methods to use #% answer: simpson,shannon,pielou,renyi #% required: no #%end #%option #% key: exclude #% type: string #% key_desc: exclude method #% options: simpson,shannon,pielou,renyi #% multiple: yes #% description: Exclude methods #% required: no #%end #%flag #% key: t #% description: Preserve configuration files #%end # import library import os import sys import grass.script as grass # main function def main(): # set the home path grass_env_file = None # see check_shell() if sys.platform == 'win32': grass_config_dirname = "GRASS7" grass_config_dir = os.path.join(os.getenv('APPDATA'), grass_config_dirname) else: grass_config_dirname = ".grass7" grass_config_dir = os.path.join(os.getenv('HOME'), grass_config_dirname) # configuration directory rlidir = os.path.join(grass_config_dir, 'r.li') # check if GISBASE is set if "GISBASE" not in os.environ: # return an error advice grass.fatal(_("You must be in GRASS GIS to run this program.")) # input raster map map_in = options['input'] # output raster map map_out = options['prefix'] # resolution of moving windows res = options['size'] # alpha value for r.renyi alpha = options['alpha'] # method to use methods = options['method'] # excluded method excludes = options['exclude'] resolution = checkValues(res) if alpha != '': alpha_value = checkValues(alpha, True) else: alpha_value = '' # check if ~/.r.li path exists if not os.path.exists(rlidir): # create ~/.grass7/r.li os.mkdir(rlidir) # set overwrite overwrite = grass.overwrite() quiet = True if grass.verbosity() > 2: quiet = False # if method and exclude option are not null return an error if methods != 'simpson,shannon,pielou,renyi' and excludes != '': grass.fatal(_("You can either use 'method' or 'exclude' option but not both")) # calculate not excluded index elif excludes != '': excludes = excludes.split(',') checkAlpha(excludes, alpha_value, True) calculateE(rlidir, map_in, map_out, resolution, alpha_value, excludes, quiet, overwrite) # calculate method elif methods != '': methods = methods.split(',') checkAlpha(methods, alpha_value) calculateM(rlidir, map_in, map_out, resolution, alpha_value, methods, quiet, overwrite) # remove configuration files if not flags['t']: removeConfFile(resolution, rlidir) grass.message(_("Done.")) # calculate only method included in method option def calculateM(home, map_in, map_out, res, alpha, method, quiet, overw): # for each resolution create the config file for r in res: createConfFile(r, map_in, home) r = str(r) # for each method in method option calculate index for i in method: if i == 'renyi': for alp in alpha: grass.run_command('r.li.renyi', input=map_in, output=map_out + '_renyi_size_' + r + \ '_alpha_' + str(alp), alpha=alp, conf='conf_diversity_' + r, overwrite=overw) else: grass.run_command('r.li.' + i, input=map_in, output=map_out + '_' + i + '_size_' + r, conf='conf_diversity_' + r, overwrite=overw) # calculate only method excluded with exclude option def calculateE(home, map_in, map_out, res, alpha, method, quiet, overw): # set a tuple with all index methods = ('simpson', 'shannon', 'pielou', 'renyi') # for each resolution create the config file for r in res: createConfFile(r, map_in, home) r = str(r) # for each method for i in methods: # if method it isn't in exclude option it is possible to calculate if method.count(i) == 0: if i == 'renyi': for alp in alpha: grass.run_command('r.li.renyi', input=map_in, output=map_out + '_renyi_size_' + r \ + '_alpha_' + str(alp), alpha=alp, conf='conf_diversity_' + r, overwrite=overw) else: grass.run_command('r.li.' + i, input=map_in, output=map_out \ + '_' + i + '_size_' + r, conf='conf_diversity_' + r, overwrite=overw) # check if alpha value it's set when renyi entropy must be calculate def checkAlpha(method, alpha_val, negative=False): for alpha in alpha_val: # it's used when we check the exclude option if negative: if method.count('renyi') != 1 and alpha == '': grass.fatal(_("You must set alpha value for Renyi entropy")) # it's used when we check the method option else: if method.count('renyi') == 1 and alpha == '': grass.fatal(_("You must set alpha value for Renyi entropy")) #create configuration file instead using r.li.setup def createConfFile(res, inpumap, home): # set the name of conf file name = 'conf_diversity_' + str(res) confilename = os.path.join(home, name) # start the text for the conf file outputLine = ['SAMPLINGFRAME 0|0|1|1\n'] # return r.info about input file rinfo = grass.raster_info(inpumap) # calculate number of lines rows = (rinfo["north"] - rinfo["south"]) / rinfo['nsres'] # calculate number of columns columns = (rinfo['east'] - rinfo['west']) / rinfo['ewres'] # value for row rV = int(res) / rows # value for column cV = int(res) / columns # append the text for the conf file outputLine.append('SAMPLEAREA -1|-1|' + str(rV) + '|' + str(cV) + '\n') outputLine.append('MOVINGWINDOW\n') # open configuration file fileConf = open(confilename, 'wb') # write file fileConf.writelines(outputLine) # close file fileConf.close() # return a list of resolution def checkValues(res, alpha=False): # check if more values are passed if res.count(',') == 1: typ = 'values' reso = res.split(',') # check if a range of values are passed elif res.count('-') == 1: typ = 'range' reso = res.split('-') # else only a value is passed else: typ = 'value' reso = [res] # transform string to int and check if is a odd number for i in range(len(reso)): # check if is a odd number reso[i] = float(reso[i]) if alpha else int(reso[i]) if not alpha and reso[i] % 2 == 0: # return the error advice grass.fatal(_("The size setting must be an odd number " \ "(found %d)" % reso[i])) # create a range if typ == 'range': if alpha: grass.fatal(_("Range for alpha values is not supported")) else: reso = range(reso[0], reso[1] + 1, 2) return reso def removeConfFile(res, home): for r in res: confilename = os.path.join(home, 'conf_diversity_' + str(r)) os.remove(confilename) if __name__ == "__main__": options, flags = grass.parser() sys.exit(main())