From 361b7ad398415eaecce1458a1fbe0b5e4c364c54 Mon Sep 17 00:00:00 2001 From: Philip Eisenlohr Date: Mon, 7 May 2012 19:09:11 +0000 Subject: [PATCH] new script to generate a twoD probability density map from ASCIItable data --- processing/post/binXY.py | 117 +++++++++++++++++++++++++++ processing/setup/setup_processing.py | 1 + 2 files changed, 118 insertions(+) create mode 100755 processing/post/binXY.py diff --git a/processing/post/binXY.py b/processing/post/binXY.py new file mode 100755 index 000000000..91cd5fdda --- /dev/null +++ b/processing/post/binXY.py @@ -0,0 +1,117 @@ +#!/usr/bin/env python + +import os,sys,string,numpy +from optparse import OptionParser, Option + +# ----------------------------- +class extendableOption(Option): +# ----------------------------- +# used for definition of new option parser action 'extend', which enables to take multiple option arguments +# taken from online tutorial http://docs.python.org/library/optparse.html + + ACTIONS = Option.ACTIONS + ("extend",) + STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",) + TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",) + ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",) + + def take_action(self, action, dest, opt, value, values, parser): + if action == "extend": + lvalue = value.split(",") + values.ensure_value(dest, []).extend(lvalue) + else: + Option.take_action(self, action, dest, opt, value, values, parser) + + + +# -------------------------------------------------------------------- +# MAIN +# -------------------------------------------------------------------- + +parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """ +Produces a binned grid of two columns from an ASCIItable, i.e. a two-dimensional probability density map. +""" + string.replace('$Id: addCalculation.py 1355 2012-02-23 13:53:12Z MPIE\p.eisenlohr $','\n','\\n') +) + + +parser.add_option('-d','--data', dest='data', nargs=2, type='int', \ + help='columns containing x and y') +parser.add_option('-b','--bins', dest='bins', nargs=2, type='int', \ + help='number of bins in x and y direction') +parser.add_option('-t','--type', dest='type', nargs=3, type='string', \ + help='type of x, y, and z axis [linear]') +parser.add_option('-x','--xrange', dest='xrange', nargs=2, type='float', \ + help='value range in x direction [auto]') +parser.add_option('-y','--yrange', dest='yrange', nargs=2, type='float', \ + help='value range in y direction [auto]') +parser.add_option('-z','--zrange', dest='zrange', nargs=2, type='float', \ + help='value range in z direction [auto]') + +parser.set_defaults(data = [1,2]) +parser.set_defaults(bins = [10,10]) +parser.set_defaults(type = ['linear','linear','linear']) +parser.set_defaults(xrange = [0.0,0.0]) +parser.set_defaults(yrange = [0.0,0.0]) +parser.set_defaults(zrange = [0.0,0.0]) + +(options,filenames) = parser.parse_args() + +range = numpy.array([numpy.array(options.xrange), + numpy.array(options.yrange), + numpy.array(options.zrange)]) +grid = numpy.zeros(options.bins,'i') +result = numpy.zeros((options.bins[0]*options.bins[1],3),'f') +# ------------------------------------------ setup file handles --------------------------------------- + +files = [] +if filenames == []: + files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout}) +else: + for name in filenames: + if os.path.exists(name): + files.append({'name':name, 'input':open(name), 'output':open(os.path.splitext(name)[0]+'_binned'+os.path.splitext(name)[1],'w')}) + +# ------------------------------------------ loop over input files --------------------------------------- + +for file in files: + if file['name'] != 'STDIN': print file['name'] + + skip = int(file['input'].readline().split()[0]) + print skip + for i in xrange(skip): headers = file['input'].readline().split() + print headers + data = numpy.loadtxt(file['input'],usecols=numpy.array(options.data)-1) + file['input'].close() # close input ASCII table + + for i in (0,1): + if (range[i] == 0.0).all(): range[i] = [data[:,i].min(),data[:,i].max()] + if options.type[i].lower() == 'log': + data[:,i] = numpy.log(data[:,i]) + range[i] = numpy.log(range[i]) + + delta = range[:,1]-range[:,0] + + for i in xrange(len(data)): + x = int(options.bins[0]*(data[i,0]-range[0,0])/delta[0]) + y = int(options.bins[1]*(data[i,1]-range[1,0])/delta[1]) + if x >=0 and x < options.bins[0] and y >= 0 and y < options.bins[1]: grid[x,y] += 1 + + if (range[2] == 0.0).all(): range[2] = [grid.min(),grid.max()] + if options.type[2].lower() == 'log': + grid = numpy.log(grid) + range[2] = numpy.log(range[2]) + delta[2] = range[2,1]-range[2,0] + + i = 0 + for x in xrange(options.bins[0]): + for y in xrange(options.bins[1]): + result[i,:] = [range[0,0]+delta[0]/options.bins[0]*(x+0.5),\ + range[1,0]+delta[1]/options.bins[1]*(y+0.5),\ + min(1.0,max(0.0,(grid[x,y]-range[2,0])/delta[2]))] + if options.type[0].lower() == 'log': result[i,0] = numpy.exp(result[i,0]) + if options.type[1].lower() == 'log': result[i,1] = numpy.exp(result[i,1]) + i += 1 + + file['output'].write('1\thead\n') + file['output'].write('bin_%s\tbin_%s\tz\n'%(headers[options.data[0]-1],headers[options.data[1]-1])) + numpy.savetxt(file['output'],result) + file['output'].close() # close output ASCII table diff --git a/processing/setup/setup_processing.py b/processing/setup/setup_processing.py index b3a2b3330..6f89afc1a 100755 --- a/processing/setup/setup_processing.py +++ b/processing/setup/setup_processing.py @@ -105,6 +105,7 @@ bin_link = { \ 'addCompatibilityMismatch.py', 'addDeformedConfiguration.py', 'averageDown.py', + 'binXY.py', 'deleteColumn.py', 'deleteInfo.py', 'filterTable.py',