From 0e93d51fed46a8a010ed5f21729fb32e388192f7 Mon Sep 17 00:00:00 2001 From: Pratheek Shanthraj Date: Fri, 18 Jan 2013 11:42:27 +0000 Subject: [PATCH] adopted same algorithm as in addEuclideanDistance --- processing/pre/geom_euclideanDistance.py | 340 ++++++++++++++--------- 1 file changed, 215 insertions(+), 125 deletions(-) diff --git a/processing/pre/geom_euclideanDistance.py b/processing/pre/geom_euclideanDistance.py index 0fed81883..f8250f235 100755 --- a/processing/pre/geom_euclideanDistance.py +++ b/processing/pre/geom_euclideanDistance.py @@ -1,96 +1,52 @@ #!/usr/bin/env python -# -*- coding: UTF-8 no BOM -*- -import os,sys,string,re,numpy,skfmm -from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP +import os,re,sys,math,numpy,string,damask from scipy import ndimage +from optparse import OptionParser, Option # ----------------------------- -class extendedOption(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",) + + 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) - - - -def outStdout(cmd,locals): - if cmd[0:3] == '(!)': - exec(cmd[3:]) - elif cmd[0:3] == '(?)': - cmd = eval(cmd[3:]) - print cmd - else: - print cmd - return - -def outFile(cmd,locals): - if cmd[0:3] == '(!)': - exec(cmd[3:]) - elif cmd[0:3] == '(?)': - cmd = eval(cmd[3:]) - locals['filepointer'].write(cmd+'\n') - else: - locals['filepointer'].write(cmd+'\n') - return - - -def output(cmds,locals,dest): - for cmd in cmds: - if isinstance(cmd,list): - output(cmd,locals,dest) + def take_action(self, action, dest, opt, value, values, parser): + if action == "extend": + lvalue = value.split(",") + values.ensure_value(dest, []).extend(lvalue) else: - {\ - 'File': outFile,\ - 'Stdout': outStdout,\ - }[dest](str(cmd),locals) - return + Option.take_action(self, action, dest, opt, value, values, parser) -# +++++++++++++++++++++++++++++++++++++++++++++++++++ -def vtk_writeASCII_mesh(dim,res,origin,data): -# +++++++++++++++++++++++++++++++++++++++++++++++++++ - """ function writes data array defined on a rectilinear grid """ - N = res[0]*res[1]*res[2] - - cmds = [\ - '# vtk DataFile Version 3.1', - string.replace('powered by $Id: spectral_geomCheck.py 1575 2012-06-26 18:07:38Z MPIE\p.eisenlohr $','\n','\\n'), - 'ASCII', - 'DATASET RECTILINEAR_GRID', - 'DIMENSIONS %i %i %i'%(res[0]+1,res[1]+1,res[2]+1), - 'X_COORDINATES %i float'%(res[0]+1), - ' '.join(map(str,[i*dim[0]/res[0]+origin[0] for i in range(res[0]+1)])), - 'Y_COORDINATES %i float'%(res[1]+1), - ' '.join(map(str,[i*dim[1]/res[1]+origin[1] for i in range(res[1]+1)])), - 'Z_COORDINATES %i float'%(res[2]+1), - ' '.join(map(str,[i*dim[2]/res[2]+origin[2] for i in range(res[2]+1)])), - 'CELL_DATA %i'%N, - ] - - for datatype in data: - for item in data[datatype]: - cmds += [\ - '%s %s float'%(datatype.upper()+{True:'',False:'S'}[datatype.lower().endswith('s')],item), - 'LOOKUP_TABLE default', - [[['\t'.join(map(str,data[datatype][item][:,j,k]))] for j in range(res[1])] for k in range(res[2])] - ] +def periodic_3Dpad(array, rimdim=(1,1,1)): - return cmds + rimdim = numpy.array(rimdim,'i') + size = numpy.array(array.shape,'i') + padded = numpy.empty(size+2*rimdim,array.dtype) + padded[rimdim[0]:rimdim[0]+size[0], + rimdim[1]:rimdim[1]+size[1], + rimdim[2]:rimdim[2]+size[2]] = array + p = numpy.zeros(3,'i') + for side in xrange(3): + for p[(side+2)%3] in xrange(padded.shape[(side+2)%3]): + for p[(side+1)%3] in xrange(padded.shape[(side+1)%3]): + for p[side%3] in xrange(rimdim[side%3]): + spot = (p-rimdim)%size + padded[p[0],p[1],p[2]] = array[spot[0],spot[1],spot[2]] + for p[side%3] in xrange(rimdim[side%3]+size[side%3],size[side%3]+2*rimdim[side%3]): + spot = (p-rimdim)%size + padded[p[0],p[1],p[2]] = array[spot[0],spot[1],spot[2]] + return padded -# ----------------------- MAIN ------------------------------- +# -------------------------------------------------------------------- +# MAIN +# -------------------------------------------------------------------- identifiers = { 'resolution': ['a','b','c'], @@ -103,28 +59,108 @@ mappings = { 'origin': lambda x: float(x), } -parser = OptionParser(option_class=extendedOption, usage='%prog [geomfile[s]]', description = """ -Produce Euclidean distance map from geom description +features = [ \ + {'aliens': 1, 'names': ['boundary','biplane'],}, + {'aliens': 2, 'names': ['tripleline',],}, + {'aliens': 3, 'names': ['quadruplepoint',],} + ] -""" + string.replace('$Id: spectral_geomCheck.py 1575 2012-06-26 18:07:38Z MPIE\p.eisenlohr $','\n','\\n') +neighborhoods = { + 'neumann':numpy.array([ + [-1, 0, 0], + [ 1, 0, 0], + [ 0,-1, 0], + [ 0, 1, 0], + [ 0, 0,-1], + [ 0, 0, 1], + ]), + 'moore':numpy.array([ + [-1,-1,-1], + [ 0,-1,-1], + [ 1,-1,-1], + [-1, 0,-1], + [ 0, 0,-1], + [ 1, 0,-1], + [-1, 1,-1], + [ 0, 1,-1], + [ 1, 1,-1], + [-1,-1, 0], + [ 0,-1, 0], + [ 1,-1, 0], + [-1, 0, 0], +# + [ 1, 0, 0], + [-1, 1, 0], + [ 0, 1, 0], + [ 1, 1, 0], + [-1,-1, 1], + [ 0,-1, 1], + [ 1,-1, 1], + [-1, 0, 1], + [ 0, 0, 1], + [ 1, 0, 1], + [-1, 1, 1], + [ 0, 1, 1], + [ 1, 1, 1], + ]) + } + +parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """ +Produce geom files containing Euclidean distance to grain structural features: +boundaries, triple lines, and quadruple points. + +""" + string.replace('$Id: addEuclideanDistance.py 2039 2012-12-19 14:50:45Z MPIE\p.shanthraj $','\n','\\n') ) -(options, filenames) = parser.parse_args() +parser.add_option('-t','--type', dest='type', action='extend', type='string', \ + help='feature type (%s)'%(', '.join(map(lambda x:', '.join(x['names']),features)))) +parser.add_option('-n','--neighborhood', dest='neigborhood', action='store', type='string', \ + help='type of neighborhood (%s)'%(', '.join(neighborhoods.keys())), \ + metavar='') +parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \ + help='output geom file with two-dimensional data arrangement') +parser.set_defaults(type = []) +parser.set_defaults(neighborhood = 'neumann') +parser.set_defaults(twoD = False) + +(options,filenames) = parser.parse_args() + +options.neighborhood = options.neighborhood.lower() +if options.neighborhood not in neighborhoods: + parser.error('unknown neighborhood %s!'%options.neighborhood) + +feature_list = [] +for i,feature in enumerate(features): + for name in feature['names']: + for type in options.type: + if name.startswith(type): + feature_list.append(i) # remember valid features + break + +print feature_list # ------------------------------------------ setup file handles --------------------------------------- files = [] if filenames == []: - files.append({'name':'STDIN', 'input':sys.stdin}) + files.append({'name':'STDIN', + 'input':sys.stdin, + 'output':sys.stdout, + 'croak':sys.stderr, + }) else: for name in filenames: if os.path.exists(name): - files.append({'name':name, 'input':open(name)}) + files.append({'name':name, + 'input':open(name), + 'output':[open(features[feature]['names'][0]+'_'+name,'w') for feature in feature_list], + 'croak':sys.stdout, + }) # ------------------------------------------ loop over input files --------------------------------------- for file in files: - if file['name'] != 'STDIN': print file['name'] + 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 @@ -132,7 +168,7 @@ for file in files: m = re.search('(\d+)\s*head', firstline.lower()) if m: headerlines = int(m.group(1)) - headers = [file['input'].readline() for i in range(headerlines)] + headers = [firstline]+[file['input'].readline() for i in range(headerlines)] else: headerlines = 1 headers = firstline @@ -140,56 +176,110 @@ for file in files: content = file['input'].readlines() file['input'].close() - info = {'resolution': [0,0,0], - 'dimension': [0.0,0.0,0.0], - 'origin': [0.0,0.0,0.0], + info = {'resolution': numpy.array([0,0,0]), + 'dimension': numpy.array([0.0,0.0,0.0]), + 'origin': numpy.array([0.0,0.0,0.0]), + 'homogenization': 1, } + + new_header = [] for header in headers: headitems = map(str.lower,header.split()) - if headitems[0] in identifiers.keys(): - for i in xrange(len(identifiers[headitems[0]])): - info[headitems[0]][i] = mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1]) + if headitems[0] in mappings.keys(): + if headitems[0] in identifiers.keys(): + for i in xrange(len(identifiers[headitems[0]])): + info[headitems[0]][i] = \ + mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1]) + else: + info[headitems[0]] = mappings[headitems[0]](headitems[1]) - if info['resolution'] == [0,0,0]: - print 'no resolution info found.' - sys.exit(1) - if info['dimension'] == [0.0,0.0,0.0]: - print 'no dimension info found.' - sys.exit(1) + if numpy.all(info['resolution'] == 0): + file['croak'].write('no resolution info found.\n') + continue + if numpy.all(info['dimension'] == 0.0): + file['croak'].write('no dimension info found.\n') + continue - print 'resolution: %s'%(' x '.join(map(str,info['resolution']))) - print 'dimension: %s'%(' x '.join(map(str,info['dimension']))) - print 'origin: %s'%(' : '.join(map(str,info['origin']))) + file['croak'].write('resolution: %s\n'%(' x '.join(map(str,info['resolution']))) + \ + 'dimension: %s\n'%(' x '.join(map(str,info['dimension']))) + \ + 'origin: %s\n'%(' : '.join(map(str,info['origin']))) + \ + 'homogenization: %i\n'%info['homogenization']) - dx = info['dimension'][0]/info['resolution'][0] - - data = {'scalar':{'perimeter':numpy.zeros(info['resolution'],'i'), - 'distance':numpy.zeros(info['resolution'],'i')}} + new_header.append("resolution\ta %i\tb %i\tc %i\n"%( + info['resolution'][0], + info['resolution'][1], + info['resolution'][2],)) + new_header.append("dimension\tx %f\ty %f\tz %f\n"%( + info['dimension'][0], + info['dimension'][1], + info['dimension'][2],)) + new_header.append("origin\tx %f\ty %f\tz %f\n"%( + info['origin'][0], + info['origin'][1], + info['origin'][2],)) + new_header.append("homogenization\t%i\n"%info['homogenization']) + + structure = numpy.zeros(info['resolution'],'i') i = 0 for line in content: for item in map(int,line.split()): - data['scalar']['perimeter'][i%info['resolution'][0],(i/info['resolution'][0])%info['resolution'][1],i/info['resolution'][0]/info['resolution'][1]] = item + structure[i%info['resolution'][0], + (i/info['resolution'][0])%info['resolution'][1], + i/info['resolution'][0] /info['resolution'][1]] = item i += 1 + + neighborhood = neighborhoods[options.neighborhood] + convoluted = numpy.empty([len(neighborhood)]+list(info['resolution']+2),'i') + microstructure = periodic_3Dpad(structure) + + for i,p in enumerate(neighborhood): + stencil = numpy.zeros((3,3,3),'i') + stencil[1,1,1] = -1 + stencil[p[0]+1, + p[1]+1, + p[2]+1] = 1 -# data['scalar']['perimeter'] = numpy.where(ndimage.morphology.grey_dilation(data['scalar']['perimeter'],size=(3,3,3))-data['scalar']['perimeter']>0,0,1) + convoluted[i,:,:,:] = ndimage.convolve(microstructure,stencil) - FDstencil_x = numpy.zeros([3,3,3]) - FDstencil_x[:,1,1] = [-1,0,1] - FDstencil_y = numpy.zeros([3,3,3]) - FDstencil_y[1,:,1] = [-1,0,1] - FDstencil_z = numpy.zeros([3,3,3]) - FDstencil_z[1,1,:] = [-1,0,1] - data['scalar']['perimeter'] = numpy.where(numpy.abs(ndimage.convolve(data['scalar']['perimeter'], FDstencil_x)) + numpy.abs(ndimage.convolve(data['scalar']['perimeter'], FDstencil_y)) + numpy.abs(ndimage.convolve(data['scalar']['perimeter'], FDstencil_z))>0,0,1) - data['scalar']['distance'] = skfmm.distance(data['scalar']['perimeter'], dx=dx) + distance = numpy.ones((len(feature_list),info['resolution'][0],info['resolution'][1],info['resolution'][2]),'d') - out = {} - out['mesh'] = vtk_writeASCII_mesh(info['dimension'],info['resolution'],info['origin'],data) + convoluted = numpy.sort(convoluted,axis=0) + uniques = numpy.zeros(info['resolution']) + check = numpy.empty(info['resolution']) + check[:,:,:] = numpy.nan + for i in xrange(len(neighborhood)): + uniques += numpy.where(convoluted[i,1:-1,1:-1,1:-1] == check,0,1) + check = convoluted[i,1:-1,1:-1,1:-1] + for i,feature_id in enumerate(feature_list): + distance[i,:,:,:] = numpy.where(uniques > features[feature_id]['aliens'],0.0,1.0) - for what in out.keys(): - if file['name'] == 'STDIN': - output(out[what],{},'Stdout') - else: - (head,tail) = os.path.split(file['name']) - vtk = open(os.path.join(head,what+'_'+os.path.splitext(tail)[0]+'.vtk'), 'w') - output(out[what],{'filepointer':vtk},'File') - vtk.close() + for i in xrange(len(feature_list)): + distance[i,:,:,:] = ndimage.morphology.distance_transform_edt(distance[i,:,:,:])*[max(info['dimension']/info['resolution'])]*3 + + + for i,feature in enumerate(feature_list): + formatwidth = int(math.floor(math.log10(distance[i,:,:,:].max())+1)) + +# ------------------------------------------ assemble header --------------------------------------- + + output = '%i\theader\n'%(len(new_header)) + output += ''.join(new_header) + +# ------------------------------------- regenerate texture information ---------------------------------- + + for z in xrange(info['resolution'][2]): + for y in xrange(info['resolution'][1]): + output += {True:' ',False:'\n'}[options.twoD].join(map(lambda x: ('%%%ii'%formatwidth)%(round(x)), distance[i,:,y,z])) + '\n' + + +# ------------------------------------------ output result --------------------------------------- + + file['output'][i].write(output) + + if file['name'] != 'STDIN': + file['output'][i].close() + + if file['name'] != 'STDIN': + file['input'].close() # close input geom file + +