diff --git a/processing/pre/spectral_geomCrop.py b/processing/pre/spectral_geomCrop.py deleted file mode 100755 index d719e007b..000000000 --- a/processing/pre/spectral_geomCrop.py +++ /dev/null @@ -1,151 +0,0 @@ -#!/usr/bin/env python -# -*- coding: UTF-8 no BOM -*- - -import os,sys,string,re,math,numpy -from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP - - -# ----------------------------- -class extendedOption(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 ------------------------------- - -identifiers = { - 'resolution': ['a','b','c'], - 'dimension': ['x','y','z'], - } -mappings = { - 'resolution': lambda x: int(x), - 'dimension': lambda x: float(x), - } - - -parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """ -Crops a spectral geometry description at given offset and by given points. -""" + string.replace('$Id$','\n','\\n') -) - -parser.add_option('-r', '--resolution', dest='resolution', type='int', nargs = 3, \ - help='a,b,c resolution of cropped box') -parser.add_option('-o', '--offset', dest='offset', type='int', nargs = 3, \ - help='a,b,c offset of cropped box') -parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \ - help='output geom file with two-dimensional data arrangement') - -parser.set_defaults(resolution = [0,0,0]) -parser.set_defaults(offset = [0,0,0]) -parser.set_defaults(twoD = False) - -(options, filenames) = parser.parse_args() - -# ------------------------------------------ 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(name+'_tmp','w')}) - -# ------------------------------------------ loop over input files --------------------------------------- - -for file in files: - if file['name'] != 'STDIN': print file['name'] - - # get labels by either read the first row, or - if keyword header is present - the last line of the header - - firstline = file['input'].readline() - m = re.search('(\d+)\s*head', firstline.lower()) - if m: - headerlines = int(m.group(1)) - headers = [firstline]+[file['input'].readline() for i in range(headerlines)] - else: - headerlines = 1 - headers = firstline - - content = file['input'].readlines() - file['input'].close() - if 0 in options.resolution: - for header in headers: - headitems = header.split() - if headitems[0] == 'resolution': # located resolution entry - for i in xrange(3): - options.resolution[i] = mappings['resolution'](headitems[headitems.index(identifiers['resolution'][i])+1]) - - resolution = [0,0,0] - dimension = [0.0,0.0,0.0] - new_header = [] - for header in headers: - headitems = header.split() - if headitems[0] == 'resolution': # located resolution entry - for i in xrange(3): - resolution[i] = mappings['resolution'](headitems[headitems.index(identifiers['resolution'][i])+1]) - header = "resolution\ta %i\tb %i\tc %i\n"%(options.resolution[0],options.resolution[1],options.resolution[2],) - if headitems[0] == 'dimension': # located dimension entry - for i in xrange(3): - dimension[i] = mappings['dimension'](headitems[headitems.index(identifiers['dimension'][i])+1]) - header = "dimension\tx %f\ty %f\tz %f\n"%(dimension[0]/resolution[0]*options.resolution[0], - dimension[1]/resolution[1]*options.resolution[1], - dimension[2]/resolution[2]*options.resolution[2],) - - new_header.append(header) - - if resolution == [0,0,0]: - print 'no resolution info found.' - sys.exit(1) - if dimension == [0.0,0.0,0.0]: - print 'no dimension info found.' - sys.exit(1) - - if file['name'] != 'STDIN': - print 'resolution: %s'%(' x '.join(map(str,resolution))) - print 'dimension: %s'%(' x '.join(map(str,dimension))) - - microstructure = numpy.zeros(resolution,'i') - i = 0 - for line in content: - for item in map(int,line.split()): - microstructure[i%resolution[0],(i/resolution[0])%resolution[1],i/resolution[0]/resolution[1]] = item - i += 1 - - formatwidth = int(math.floor(math.log10(microstructure.max()))) - - - -# ------------------------------------------ assemble header --------------------------------------- - - output = ''.join(new_header) - -# ------------------------------------- regenerate texture information ---------------------------------- - - for z in xrange(options.offset[2],options.offset[2]+options.resolution[2]): - for y in xrange(options.offset[1],options.offset[1]+options.resolution[1]): - output += {True:' ',False:'\n'}[options.twoD].join(map(lambda x: ('%%%ii'%formatwidth)%x, microstructure[options.offset[0]:options.offset[0]+options.resolution[0],y,z])) + '\n' - - #output += '\n' - -# ------------------------------------------ output result --------------------------------------- - - file['output'].write(output) - - if file['name'] != 'STDIN': - file['output'].close - os.rename(file['name']+'_tmp',file['name']) - \ No newline at end of file