diff --git a/processing/pre/geom_canvas.py b/processing/pre/geom_canvas.py index 5b76376c6..64f4741f2 100755 --- a/processing/pre/geom_canvas.py +++ b/processing/pre/geom_canvas.py @@ -4,10 +4,9 @@ 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 @@ -24,8 +23,9 @@ class extendedOption(Option): Option.take_action(self, action, dest, opt, value, values, parser) -# ----------------------- MAIN ------------------------------- - +#-------------------------------------------------------------------------------------------------- +# MAIN +#-------------------------------------------------------------------------------------------------- identifiers = { 'grid': ['a','b','c'], 'size': ['x','y','z'], @@ -38,7 +38,6 @@ mappings = { 'homogenization': lambda x: int(x), } - parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """ Changes the (three-dimensional) canvas of a spectral geometry description. """ + string.replace('$Id$','\n','\\n') @@ -60,7 +59,7 @@ parser.set_defaults(fill = 0) (options, filenames) = parser.parse_args() -# ------------------------------------------ setup file handles --------------------------------------- +#--- setup file handles -------------------------------------------------------------------------- files = [] if filenames == []: files.append({'name':'STDIN', @@ -77,13 +76,10 @@ else: 'croak':sys.stdout, }) -# ------------------------------------------ loop over input files --------------------------------------- - +#--- loop over input files ------------------------------------------------------------------------ for file in files: if file['name'] != 'STDIN': file['croak'].write(file['name']+'\n') - # 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: @@ -96,13 +92,20 @@ for file in files: content = file['input'].readlines() file['input'].close() +#--- interprete header ---------------------------------------------------------------------------- info = { - 'grid': numpy.array(options.grid), - 'size': numpy.array([0.0,0.0,0.0]), - 'origin': numpy.array([0.0,0.0,0.0]), + 'grid': numpy.zeros(3,'i'), + 'size': numpy.zeros(3,'d'), + 'origin': numpy.zeros(3,'d'), 'microstructures': 0, 'homogenization': 0, } + newInfo = { + 'grid': numpy.array(options.grid), + 'size': numpy.zeros(3,'d'), + 'origin': numpy.zeros(3,'d'), + 'microstructures': 0, + } new_header = [] for header in headers: @@ -117,15 +120,20 @@ for file in files: else: info[headitems[0]] = mappings[headitems[0]](headitems[1]) - if numpy.all(options.grid == 0): - options.grid = info['grid'] - if numpy.all(info['grid'] == 0): - file['croak'].write('no grid info found.\n') - continue - if numpy.all(info['size'] == 0.0): - file['croak'].write('no size info found.\n') - continue - + file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \ + 'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \ + 'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \ + 'homogenization: %i\n'%info['homogenization'] + \ + 'microstructures: %i\n'%info['microstructures']) + + if numpy.any(info['grid'] < 1): + file['croak'].write('invalid grid a b c.\n') + sys.exit() + if numpy.any(info['size'] <= 0.0): + file['croak'].write('invalid size x y z.\n') + sys.exit() + +#--- read data ------------------------------------------------------------------------------------ microstructure = numpy.zeros(info['grid'],'i') i = 0 for line in content: @@ -134,26 +142,9 @@ for file in files: (i/info['grid'][0])%info['grid'][1], i/info['grid'][0] /info['grid'][1]] = item i += 1 - - file['croak'].write('-- input --\n' + \ - 'grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \ - 'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \ - 'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \ - 'homogenization: %i\n'%info['homogenization'] + \ - 'microstructures: %i\n'%info['microstructures']) - - info['microstructures'] = microstructure.max() - - newSize = info['size']/info['grid']*options.grid - newOrigin = info['origin']+info['size']/info['grid']*options.offset - new_header.append("grid\ta %i\tb %i\tc %i\n"%(options.grid[0],options.grid[1],options.grid[2])) - new_header.append("size\tx %f\ty %f\tz %f\n"%(newSize[0],newSize[1],newSize[2])) - new_header.append("origin\tx %f\ty %f\tz %f\n"%(newOrigin[0],newOrigin[1],newOrigin[2])) - new_header.append("homogenization\t%i\n"%info['homogenization']) - new_header.append("microstructures\t%i\n"%info['microstructures']) - + microstructure_cropped = numpy.zeros(options.grid,'i') - microstructure_cropped.fill({True:options.fill,False:info['microstructures']+1}[options.fill>0]) + microstructure_cropped.fill({True:options.fill,False:microstructure.max()+1}[options.fill>0]) xindex = list(set(xrange(options.offset[0],options.offset[0]+options.grid[0])) & \ set(xrange(info['grid'][0]))) yindex = list(set(xrange(options.offset[1],options.offset[1]+options.grid[1])) & \ @@ -171,28 +162,49 @@ for file in files: min(zindex):(max(zindex)+1)] formatwidth = int(math.floor(math.log10(microstructure.max())+1)) - file['croak'].write('-- output --\n' +\ - 'grid a b c: %s\n'%(' x '.join(map(str,options.grid))) + \ - 'size x y z: %s\n'%(' x '.join(map(str,newSize))) + \ - 'origin x y z: %s\n'%(' x '.join(map(str,newOrigin))) + \ - 'microstructures: %i\n'%microstructure.max()) - -# ------------------------------------------ assemble header --------------------------------------- + if numpy.all(options.grid == 0): + newInfo['grid'] = info['grid'] + newInfo['microstructures'] = microstructure_cropped.max() + newInfo['size'] = info['size']/info['grid']*options.grid + newInfo['origin'] = info['origin']+info['size']/info['grid']*options.offset - output = '%i\theader\n'%(len(new_header)) - output += ''.join(new_header) -# ------------------------------------- regenerate texture information ---------------------------- +#--- report --------------------------------------------------------------------------------------- + if (any(newInfo['grid'] != info['grid'])): + file['croak'].write('--> grid a b c: %s\n'%(' x '.join(map(str,newInfo['grid'])))) + if (any(newInfo['size'] != info['size'])): + file['croak'].write('--> size x y z: %s\n'%(' x '.join(map(str,newInfo['size'])))) + if (any(newInfo['origin'] != info['origin'])): + file['croak'].write('--> origin x y z: %s\n'%(' : '.join(map(str,newInfo['size'])))) + if (newInfo['microstructures'] != info['microstructures']): + file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures']) + if numpy.any(newInfo['grid'] < 1): + file['croak'].write('invalid new grid a b c.\n') + sys.exit() + if numpy.any(newInfo['size'] <= 0.0): + file['croak'].write('invalid new size x y z.\n') + sys.exit() + +# --- assemble header ----------------------------------------------------------------------------- + new_header.append('$Id$\n') + new_header.append("grid\ta %i\tb %i\tc %i\n"%( + newInfo['grid'][0],newInfo['grid'][1],newInfo['grid'][2])) + new_header.append("size\tx %f\ty %f\tz %f\n"%( + newInfo['size'][0],newInfo['size'][1],newInfo['size'][2])) + new_header.append("origin\tx %f\ty %f\tz %f\n"%( + newInfo['origin'][0],newInfo['origin'][1],newInfo['origin'][2])) + new_header.append("homogenization\t%i\n"%info['homogenization']) + new_header.append("microstructures\t%i\n"%newInfo['microstructures']) + file['output'].write('%i\theader\n'%(len(new_header))+''.join(new_header)) + +# --- write microstructure information ------------------------------------------------------------ for z in xrange(options.grid[2]): for y in xrange(options.grid[1]): - output += {True:' ',False:'\n'}[options.twoD].join(map(lambda x: \ - ('%%%ii'%formatwidth)%x, microstructure_cropped[:,y,z])) + '\n' - -# ------------------------------------------ output result --------------------------------------- - - file['output'].write(output) + file['output'].write({True:' ',False:'\n'}[options.twoD].join(map(lambda x: \ + ('%%%ii'%formatwidth)%x, microstructure_cropped[:,y,z])) + '\n') +#--- output finalization -------------------------------------------------------------------------- if file['name'] != 'STDIN': file['output'].close() os.rename(file['name']+'_tmp',file['name']) diff --git a/processing/pre/geom_fromVoronoiTessellation.py b/processing/pre/geom_fromVoronoiTessellation.py index 539d246e4..6c11cf9bd 100755 --- a/processing/pre/geom_fromVoronoiTessellation.py +++ b/processing/pre/geom_fromVoronoiTessellation.py @@ -211,7 +211,6 @@ for file in files: False:'\n'}[options.twoD].\ join(map(lambda x: str(x).rjust(formatwidth),\ indices[n*info['grid'][0]:(n+1)*info['grid'][0]]))+'\n') - #--- output finalization -------------------------------------------------------------------------- if file['name'] != 'STDIN': diff --git a/processing/pre/geom_rescale.py b/processing/pre/geom_rescale.py index fcb5a0f02..b1321973e 100755 --- a/processing/pre/geom_rescale.py +++ b/processing/pre/geom_rescale.py @@ -126,15 +126,15 @@ for file in files: 'microstructures: %i\n\n'%info['microstructures']) if numpy.any(info['grid'] < 1): - file['croak'].write('no valid grid info found.\n') + file['croak'].write('invalid grid a b c.\n') sys.exit() if numpy.any(info['size'] <= 0.0): - file['croak'].write('no valid size info found.\n') + file['croak'].write('invalid size x y z.\n') sys.exit() if numpy.all(info['grid'] == 0): newInfo['grid'] = info['grid'] - if numpy.all(info['size'] == 0.0):: + if numpy.all(info['size'] == 0.0): newInfo['size'] = info['size'] #--- read data ------------------------------------------------------------------------------------ @@ -157,10 +157,10 @@ for file in files: file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures']) if numpy.any(newInfo['grid'] < 1): - file['croak'].write('no valid new grid info found.\n') + file['croak'].write('invalid new grid a b c.\n') sys.exit() if numpy.any(newInfo['size'] <= 0.0): - file['croak'].write('no valid new size info found.\n') + file['croak'].write('invalid new size x y z.\n') sys.exit() #--- assemble header ------------------------------------------------------------------------------ @@ -170,8 +170,7 @@ for file in files: new_header.append("origin\tx %f\ty %f\tz %f\n"%(info['origin'][0],info['origin'][1],info['origin'][2])) new_header.append("microstructures\t%i\n"%newInfo['microstructures']) new_header.append("homogenization\t%i\n"%info['homogenization']) - output = '%i\theader\n'%(len(new_header)) - output += ''.join(new_header) + file['output'].write('%i\theader\n'%(len(new_header))+''.join(new_header)) #--- scale microstructure ------------------------------------------------------------------------- for c in xrange(newInfo['grid'][2]): @@ -180,9 +179,9 @@ for file in files: y = int(info['grid'][1]*(b+0.5)/newInfo['grid'][1])%info['grid'][1] for a in xrange(newInfo['grid'][0]): x = int(info['grid'][0]*(a+0.5)/newInfo['grid'][0])%info['grid'][0] - output += str(microstructure[x,y,z]).rjust(formatwidth) + {True:' ',False:'\n'}[options.twoD] - output += {True:'\n',False:''}[options.twoD] - file['output'].write(output) + file['output'].write(str(microstructure[x,y,z]).rjust(formatwidth) + {True:' ',False:'\n'} + [options.twoD]) + file['output'].write({True:'\n',False:''}[options.twoD]) #--- output finalization -------------------------------------------------------------------------- if file['name'] != 'STDIN': diff --git a/processing/pre/geom_translate.py b/processing/pre/geom_translate.py index 29f615cb6..0e1568694 100755 --- a/processing/pre/geom_translate.py +++ b/processing/pre/geom_translate.py @@ -130,14 +130,14 @@ for file in files: 'microstructures: %i\n\n'%info['microstructures']) if numpy.any(info['grid'] < 1): - file['croak'].write('no valid grid info found.\n') + file['croak'].write('invalid grid a b c.\n') sys.exit() if numpy.any(info['size'] <= 0.0): - file['croak'].write('no valid size info found.\n') + file['croak'].write('invalid size x y z.\n') sys.exit() #--- process input -------------------------------------------------------------------------------- - N = info['grid'][0]*info['grid'][1]*info['grid'][2] + N = info['grid'].prod() microstructure = numpy.zeros(N,'i') i = 0