#!/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 #% keywords: 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: output #% type: string #% gisprompt: new,cell,raster #% key_desc: name #% description: Name of output raster map #% 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 #% 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 # import library import os, sys, re import grass.script as grass # main function def main(): # set the home path home=os.path.expanduser('~') # check if GISBASE is set if "GISBASE" not in os.environ: # return an error advice print "You must be in GRASS GIS to run this program." sys.exit(1) # input raster map map_in = options['input'] # output raster map map_out = options['output'] # 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) print alpha_value # check if ~/.r.li path exists if not os.path.exists(home + '/.r.li'): # create ~/.r.li os.mkdir(home + '/.r.li') # create ~/.r.li/history os.mkdir(home + '/.r.li/history') else: if not os.path.exists(home + '/.r.li/history'): # create ~/.r.li/history os.mkdir(home + '/.r.li/history') # set overwrite if grass.overwrite(): env['GRASS_OVERWRITE'] = '1' # if method and exclude option are not null return an error if methods != '' and excludes != '': print "You can use method or exclude option not both" sys.exit(1) # if method and exclude option are null calculate all module elif methods == '' and excludes == '': # check if alpha_value is set, else return an error if alpha_value == '': print "Please you must set alpha value for Renyi entropy" sys.exit(1) calculateAll(home, map_in, map_out, resolution, alpha_value) # calculate method elif methods != '': methods = methods.split(',') checkAlpha(methods,alpha_value) calculateM(home, map_in, map_out, resolution, alpha_value,methods) # calculate not excluded index elif excludes != '': excludes = excludes.split(',') checkAlpha(excludes,alpha_value,True) calculateE(home, map_in, map_out, resolution, alpha_value,excludes) # remove configuration files removeConfFile(resolution,home) print 'All works are terminated' # calculate all index def calculateAll(home, map_in, map_out, res, alpha): # for each resolution create the config file and calculate all index for r in res: createConfFile(r,map_in,home) r = str(r) grass.run_command('r.li.simpson', map = map_in, out = map_out + '_simpson_size_' + r, conf = 'conf_diversity_' + r) grass.run_command('r.li.shannon', map = map_in, out = map_out + '_shannon_size_' + r, conf = 'conf_diversity_' + r) grass.run_command('r.li.pielou', map = map_in, out = map_out + '_pielou_size_' + r, conf = 'conf_diversity_' + r) for alp in alpha: grass.run_command('r.li.renyi', map = map_in, out = map_out+ '_renyi_size_' + r + '_alpha_'+ str(alp), conf = 'conf_diversity_' + r, alpha = alp) # calculate only method included in method option def calculateM(home, map_in, map_out, res, alpha, method): # 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', map = map_in, out = map_out + '_renyi_size_' + r + '_alpha_' + str(alp), conf = 'conf_diversity_' + r, alpha = alp) else: grass.run_command('r.li.' + i, map = map_in, out = map_out + '_' + i + '_size_' + r, conf = 'conf_diversity_' + r) # calculate only method excluded with exclude option def calculateE(home, map_in, map_out, res, alpha, method): # 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', map = map_in, out = map_out + '_renyi_size_' + r + '_alpha_' + str(alp), conf = 'conf_diversity_' + r, alpha = alp) else: grass.run_command('r.li.' + i, map = map_in, out = map_out + '_' + i+ '_size_' + r, conf = 'conf_diversity_' + r) # 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 == '': print "Please you must set alpha value for Renyi entropy" sys.exit(1) # it's used when we check the method option else: if method.count('renyi') == 1 and alpha == '': print "Please you must set alpha value for Renyi entropy" sys.exit(1) #create configuration file instead using r.li.setup def createConfFile(res,inpumap,home): # set the name of conf file confilename = home + '/.r.li/history/conf_diversity_' + str(res) # 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,'w') # 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] # trasforn 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 reso[i] % 2 == 0: # return the error advice print "Your size option could not contain odd number" sys.exit(1) # create a range if typ == 'range': if alpha: print "Range for alpha values it isn't supported" sys.exit(1) else: reso = range(reso[0],reso[1]+1,2) return reso def removeConfFile(res,home): for r in res: confilename = home + '/.r.li/history/conf_diversity_' + str(r) os.remove(confilename) if __name__ == "__main__": options, flags = grass.parser() sys.exit(main())