polishing, unifying,simplifying
This commit is contained in:
Martin Diehl
parent
2acd737859
commit
9093cf2072
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@ -4,10 +4,9 @@
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import os,sys,string,math,numpy,time
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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# -----------------------------
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#------------------------------------------------------------------------------------------------
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class extendedOption(Option):
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# -----------------------------
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#------------------------------------------------------------------------------------------------
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# used for definition of new option parser action 'extend', which enables to take multiple option arguments
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# taken from online tutorial http://docs.python.org/library/optparse.html
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@ -24,10 +23,9 @@ class extendedOption(Option):
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Option.take_action(self, action, dest, opt, value, values, parser)
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# ----------------------- MAIN -------------------------------
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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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parser = OptionParser(option_class=extendedOption, usage='%prog', description = """
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Generate a geometry file of an osteon enclosing the Harvesian canal and separated by interstitial tissue.
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The osteon phase is lamellar with a twisted plywood structure.
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@ -75,8 +73,7 @@ parser.set_defaults(twoD = False)
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(options, args) = parser.parse_args()
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# ------------------------------------------ setup file handles ---------------------------------------
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#--- setup file handles ---------------------------------------------------------------------------
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file = {'name':'STDIN',
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'input':sys.stdin,
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'output':sys.stdout,
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@ -87,7 +84,7 @@ if numpy.any(options.grid < 2):
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file['croak'].write('grid too low...\n')
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sys.exit()
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options.omega *= math.pi/180.0 # rescale ro radians
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options.omega *= math.pi/180.0 # rescale ro radians
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rotation = numpy.array([[ math.cos(options.omega),math.sin(options.omega),],
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[-math.sin(options.omega),math.cos(options.omega),]],'d')
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@ -98,11 +95,10 @@ info = {
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'grid': numpy.ones(3,'i'),
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'size': numpy.ones(3,'d'),
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'origin': numpy.zeros(3,'d'),
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'microstructures': 0,
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'microstructures': 3,
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'homogenization': options.homogenization,
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}
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info['grid'][:2] = options.grid
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info['size'][:2] = options.size
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info['size'][2] = min(info['size'][0]/info['grid'][0],info['size'][1]/info['grid'][1])
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@ -113,8 +109,8 @@ X0 = info['size'][0]/info['grid'][0]*\
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Y0 = info['size'][1]/info['grid'][1]*\
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(numpy.tile(numpy.arange(info['grid'][1]),(info['grid'][0],1)).transpose() - info['grid'][1]/2 + 0.5)
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X = X0*rotation[0,0] + Y0*rotation[0,1] # rotate by omega
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Y = X0*rotation[1,0] + Y0*rotation[1,1] # rotate by omega
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X = X0*rotation[0,0] + Y0*rotation[0,1] # rotate by omega
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Y = X0*rotation[1,0] + Y0*rotation[1,1] # rotate by omega
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radius = numpy.sqrt(X*X + Y*Y/options.aspect/options.aspect)
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alpha = numpy.degrees(numpy.arctan2(Y/options.aspect,X))
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@ -122,7 +118,6 @@ beta = options.amplitude*numpy.sin(2.0*math.pi*(radius-options.canal)/options.pe
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microstructure = numpy.where(radius < float(options.canal),1,0) + numpy.where(radius > float(options.osteon),2,0)
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info['microstructures'] = 3
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alphaOfGrain = numpy.zeros(info['grid'][0]*info['grid'][1],'d')
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betaOfGrain = numpy.zeros(info['grid'][0]*info['grid'][1],'d')
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for y in xrange(info['grid'][1]):
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@ -165,15 +160,13 @@ if options.config:
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betaOfGrain[i]))
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else:
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file['output'].write("6 header\n" + \
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"$Id$\n" + \
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"grid\ta %i\tb %i\tc %i\n"%(info['grid'][0],info['grid'][1],info['grid'][2]) + \
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"size\tx %g\ty %g\tz %g\n"%(info['size'][0],info['size'][1],info['size'][2]) + \
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"origin\tx %g\ty %g\tz %g\n"%(info['origin'][0],info['origin'][1],info['origin'][2]) + \
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"microstructures\t%i\n"%(info['microstructures']) + \
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"homogenization\t%i\n"%(info['homogenization'])
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)
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header = ['$Id$\n']
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header.append("grid\ta %i\tb %i\tc %i\n"%(info['grid'][0],info['grid'][1],info['grid'][2],))
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header.append("size\tx %f\ty %f\tz %f\n"%(info['size'][0],info['size'][1],info['size'][2],))
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header.append("origin\tx %f\ty %f\tz %f\n"%(info['origin'][0],info['origin'][1],info['origin'][2],))
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header.append("microstructures\t%i\n"%info['microstructures'])
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header.append("homogenization\t%i\n"%info['homogenization'])
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file['output'].write('%i\theader\n'%(len(header))+''.join(header))
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for y in xrange(info['grid'][1]):
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for x in xrange(info['grid'][0]):
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@ -183,6 +176,5 @@ else:
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file['output'].write({True:'\n',False:''}[options.twoD])
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# ------------------------------------------ output finalization ---------------------------------------
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#--- output finalization --------------------------------------------------------------------------
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file['output'].close()
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@ -154,7 +154,8 @@ else:
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if os.path.exists(name):
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files.append({'name':name,
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'input':open(name),
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'output':[open(features[feature]['names'][0]+'_'+name,'w') for feature in feature_list],
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'output':[open(features[feature]['names'][0]+'_'+name,'w')
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for string.split(feature,sep=',')[0] in feature_list],
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'croak':sys.stdout,
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})
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@ -174,15 +175,14 @@ for file in files:
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content = file['input'].readlines()
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file['input'].close()
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#--- interpretate header --------------------------------------------------------------------------
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#--- interprete header ----------------------------------------------------------------------------
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info = {
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'grid': numpy.array([0,0,0]),
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'size': numpy.array([0.0,0.0,0.0]),
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'origin': numpy.array([0.0,0.0,0.0]),
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'microstructures': 0,
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'homogenization': 0
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'grid': numpy.zeros(3,'i'),
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'size': numpy.zeros(3,'d'),
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'origin': numpy.zeros(3,'d'),
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'microstructures': 0,
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'homogenization': 0
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}
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newInfo = {
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'microstructures': 0,
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}
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@ -264,8 +264,7 @@ for file in files:
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formatwidth = int(math.floor(math.log10(distance[i,:,:,:].max())+1))
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#--- assemble header and report changes -----------------------------------------------------------
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output = '%i\theader\n'%(len(new_header)+1)
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output += ''.join(new_header)
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output = '%i\theader\n'%(len(new_header)+1)+''.join(new_header)
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output += "microstructures\t%i\n"%newInfo['microstructures']
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file['croak'].write('\n'+features[i]['names'][0]+'\n')
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if (newInfo['microstructures'] != info['microstructures']):
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@ -87,9 +87,9 @@ for file in files:
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microstructure = ['<microstructure>']
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texture = ['<texture>']
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point = 0
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step = [0,0]
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point = 0
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for line in file['input']:
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words = line.split()
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if words[0] == '#': # process initial comments block
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@ -137,7 +137,7 @@ for file in files:
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header.append("origin\tx %f\ty %f\tz %f\n"%(info['origin'][0],info['origin'][1],info['origin'][2],))
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header.append("microstructures\t%i\n"%info['microstructures'])
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header.append("homogenization\t%i\n"%info['homogenization'])
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file['output'].write('%i\theader\n'%(len(new_header))+''.join(new_header))
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file['output'].write('%i\theader\n'%(len(header))+''.join(header))
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file['output'].write("1 to %i\n"%(info['microstructures']))
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#--- output finalization --------------------------------------------------------------------------
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@ -54,7 +54,7 @@ parser.set_defaults(config = False)
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(options,filenames) = parser.parse_args()
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#--- setup file handles --------------------------------------------------------------------------
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#--- setup file handles ---------------------------------------------------------------------------
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files = []
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if filenames == []:
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files.append({'name':'STDIN',
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@ -127,7 +127,7 @@ for file in files:
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header.append("origin\tx %f\ty %f\tz %f\n"%(info['origin'][0],info['origin'][1],info['origin'][2],))
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header.append("microstructures\t%i\n"%info['microstructures'])
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header.append("homogenization\t%i\n"%info['homogenization'])
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file['output'].write('%i\theader\n'%(len(new_header))+''.join(new_header))
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file['output'].write('%i\theader\n'%(len(header))+''.join(header))
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file['output'].write("1 to %i\n"%(info['microstructures']))
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#--- output finalization --------------------------------------------------------------------------
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@ -4,10 +4,9 @@
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import os,sys,string,re,math,numpy
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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# -----------------------------
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#--------------------------------------------------------------------------------------------------
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class extendedOption(Option):
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# -----------------------------
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#--------------------------------------------------------------------------------------------------
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# used for definition of new option parser action 'extend', which enables to take multiple option arguments
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# taken from online tutorial http://docs.python.org/library/optparse.html
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@ -24,8 +23,9 @@ class extendedOption(Option):
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Option.take_action(self, action, dest, opt, value, values, parser)
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# ----------------------- MAIN -------------------------------
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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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identifiers = {
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'grid': ['a','b','c'],
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'size': ['x','y','z'],
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@ -39,7 +39,6 @@ mappings = {
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'microstructures': lambda x: int(x),
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}
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parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
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Offset microstructure index for points which see a microstructure different from themselves within a given (cubic) vicinity,
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i.e. within the region close to a grain/phase boundary.
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@ -59,8 +58,7 @@ parser.set_defaults(twoD = False)
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(options, filenames) = parser.parse_args()
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# ------------------------------------------ setup file handles ---------------------------------------
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#--- setup file handles --------------------------------------------------------------------------
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files = []
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if filenames == []:
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files.append({'name':'STDIN',
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@ -77,14 +75,10 @@ else:
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'croak':sys.stdout,
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})
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# ------------------------------------------ loop over input files ---------------------------------------
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#--- loop over input files ------------------------------------------------------------------------
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for file in files:
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if file['name'] != 'STDIN': file['croak'].write(file['name']+'\n')
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# get labels by either read the first row, or - if keyword header is present - the last line of the header
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firstline = file['input'].readline()
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m = re.search('(\d+)\s*head', firstline.lower())
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if m:
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@ -97,6 +91,7 @@ for file in files:
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content = file['input'].readlines()
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file['input'].close()
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#--- interprete header ----------------------------------------------------------------------------
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info = {
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'grid': numpy.zeros(3,'i'),
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'size': numpy.zeros(3,'d'),
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@ -104,6 +99,9 @@ for file in files:
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'microstructures': 0,
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'homogenization': 0
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}
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newInfo = {
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'microstructures': 0,
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}
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new_header = []
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new_header.append('$Id$\n')
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@ -128,13 +126,13 @@ for file in files:
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file['croak'].write('no dimension info found.\n')
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continue
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file['croak'].write('-- input --\n' +\
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'grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
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file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
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'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
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'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \
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'homogenization: %i\n'%info['homogenization'] + \
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'microstructures: %i\n'%info['microstructures'])
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#--- read data ------------------------------------------------------------------------------------
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microstructure = numpy.zeros(info['grid'],'i')
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i = 0
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for line in content:
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@ -149,6 +147,7 @@ for file in files:
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options.offset = microstructure.max()
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formatwidth = 1+int(math.floor(math.log10(abs(microstructure.max()+options.offset))))
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#--- search ---------------------------------------------------------------------------------------
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for x in xrange(info['grid'][0]):
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for y in xrange(info['grid'][1]):
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for z in xrange(info['grid'][2]):
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@ -161,8 +160,8 @@ for file in files:
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for dz in xrange(-options.vicinity,options.vicinity+1):
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they = microstructure[(x+dx)%info['grid'][0],(y+dy)%info['grid'][1],(z+dz)%info['grid'][2]]
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if they != me and they != me+options.offset: # located alien microstructure in vicinity
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microstructure[x,y,z] += options.offset # tag myself as close to aliens!
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if they != me and they != me+options.offset: # located alien microstructure in vicinity
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microstructure[x,y,z] += options.offset # tag myself as close to aliens!
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breaker = True
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break
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@ -170,33 +169,27 @@ for file in files:
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if breaker: break
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info['microstructures'] = microstructure.max()
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file['croak'].write('-- output --\n' +\
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'microstructures: %i\n'%info['microstructures'])
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newInfo['microstructures'] = microstructure.max()
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if (newInfo['microstructures'] != info['microstructures']):
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file['croak'].write('--> microstructures: %i\n'%newInfo['microstructures'])
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# ------------------------------------------ assemble header ---------------------------------------
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# --- assemble header -----------------------------------------------------------------------------
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new_header.append("grid\ta %i\tb %i\tc %i\n"%(info['grid'][0],info['grid'][1],info['grid'][2]))
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new_header.append("size\tx %f\ty %f\tz %f\n"%(info['size'][0],info['size'][1],info['size'][0]))
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new_header.append("origin\tx %f\ty %f\tz %f\n"%(info['origin'][0],info['origin'][1],info['origin'][2]))
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new_header.append("microstructures\t%i\n"%info['microstructures'])
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new_header.append("microstructures\t%i\n"%newInfo['microstructures'])
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new_header.append("homogenization\t%i\n"%info['homogenization'])
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file['output'].write('%i\theader\n'%(len(new_header))+''.join(new_header))
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output = '%i\theader\n'%(len(new_header))
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output += ''.join(new_header)
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# ------------------------------------- regenerate texture information ----------------------------------
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# --- write microstructure information ------------------------------------------------------------
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for z in xrange(info['grid'][2]):
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for y in xrange(info['grid'][1]):
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output += {True:' ',False:'\n'}[options.twoD].join(map(lambda x: str(x).rjust(formatwidth), microstructure[:,y,z])) + '\n'
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output += '\n'
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# ------------------------------------------ output result ---------------------------------------
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file['output'].write(output)
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#--- output finalization --------------------------------------------------------------------------
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if file['name'] != 'STDIN':
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file['output'].close
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file['output'].close()
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os.rename(file['name']+'_tmp',file['name'])
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