script to calculate the euclidean distance map (shortest distance to a grain boundary) of a given geom description using fast marching method (O(N logN) ops). grain boundary extracted using FD stencil.
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Pratheek Shanthraj
parent
62ddbf26df
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f63bb747c1
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,string,re,numpy,skfmm
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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from scipy import ndimage
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# -----------------------------
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class extendedOption(Option):
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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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ACTIONS = Option.ACTIONS + ("extend",)
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STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
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TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
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ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
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def take_action(self, action, dest, opt, value, values, parser):
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if action == "extend":
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lvalue = value.split(",")
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values.ensure_value(dest, []).extend(lvalue)
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else:
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Option.take_action(self, action, dest, opt, value, values, parser)
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def outStdout(cmd,locals):
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if cmd[0:3] == '(!)':
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exec(cmd[3:])
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elif cmd[0:3] == '(?)':
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cmd = eval(cmd[3:])
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print cmd
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else:
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print cmd
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return
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def outFile(cmd,locals):
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if cmd[0:3] == '(!)':
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exec(cmd[3:])
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elif cmd[0:3] == '(?)':
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cmd = eval(cmd[3:])
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locals['filepointer'].write(cmd+'\n')
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else:
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locals['filepointer'].write(cmd+'\n')
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return
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def output(cmds,locals,dest):
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for cmd in cmds:
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if isinstance(cmd,list):
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output(cmd,locals,dest)
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else:
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{\
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'File': outFile,\
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'Stdout': outStdout,\
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}[dest](str(cmd),locals)
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return
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# +++++++++++++++++++++++++++++++++++++++++++++++++++
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def vtk_writeASCII_mesh(dim,res,origin,data):
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# +++++++++++++++++++++++++++++++++++++++++++++++++++
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""" function writes data array defined on a rectilinear grid """
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N = res[0]*res[1]*res[2]
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cmds = [\
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'# vtk DataFile Version 3.1',
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string.replace('powered by $Id: spectral_geomCheck.py 1575 2012-06-26 18:07:38Z MPIE\p.eisenlohr $','\n','\\n'),
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'ASCII',
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'DATASET RECTILINEAR_GRID',
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'DIMENSIONS %i %i %i'%(res[0]+1,res[1]+1,res[2]+1),
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'X_COORDINATES %i float'%(res[0]+1),
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' '.join(map(str,[i*dim[0]/res[0]+origin[0] for i in range(res[0]+1)])),
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'Y_COORDINATES %i float'%(res[1]+1),
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' '.join(map(str,[i*dim[1]/res[1]+origin[1] for i in range(res[1]+1)])),
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'Z_COORDINATES %i float'%(res[2]+1),
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' '.join(map(str,[i*dim[2]/res[2]+origin[2] for i in range(res[2]+1)])),
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'CELL_DATA %i'%N,
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]
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for datatype in data:
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for item in data[datatype]:
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cmds += [\
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'%s %s float'%(datatype.upper()+{True:'',False:'S'}[datatype.lower().endswith('s')],item),
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'LOOKUP_TABLE default',
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[[['\t'.join(map(str,data[datatype][item][:,j,k]))] for j in range(res[1])] for k in range(res[2])]
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]
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return cmds
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# ----------------------- MAIN -------------------------------
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identifiers = {
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'resolution': ['a','b','c'],
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'dimension': ['x','y','z'],
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'origin': ['x','y','z'],
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}
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mappings = {
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'resolution': lambda x: int(x),
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'dimension': lambda x: float(x),
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'origin': lambda x: float(x),
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}
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parser = OptionParser(option_class=extendedOption, usage='%prog [geomfile[s]]', description = """
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Produce Euclidean distance map from geom description
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""" + string.replace('$Id: spectral_geomCheck.py 1575 2012-06-26 18:07:38Z MPIE\p.eisenlohr $','\n','\\n')
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)
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(options, filenames) = parser.parse_args()
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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', 'input':sys.stdin})
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else:
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for name in filenames:
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if os.path.exists(name):
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files.append({'name':name, 'input':open(name)})
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# ------------------------------------------ loop over input files ---------------------------------------
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for file in files:
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if file['name'] != 'STDIN': print file['name']
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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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headerlines = int(m.group(1))
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headers = [file['input'].readline() for i in range(headerlines)]
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else:
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headerlines = 1
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headers = firstline
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content = file['input'].readlines()
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file['input'].close()
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info = {'resolution': [0,0,0],
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'dimension': [0.0,0.0,0.0],
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'origin': [0.0,0.0,0.0],
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}
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for header in headers:
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headitems = map(str.lower,header.split())
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if headitems[0] in identifiers.keys():
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for i in xrange(len(identifiers[headitems[0]])):
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info[headitems[0]][i] = mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1])
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if info['resolution'] == [0,0,0]:
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print 'no resolution info found.'
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sys.exit(1)
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if info['dimension'] == [0.0,0.0,0.0]:
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print 'no dimension info found.'
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sys.exit(1)
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print 'resolution: %s'%(' x '.join(map(str,info['resolution'])))
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print 'dimension: %s'%(' x '.join(map(str,info['dimension'])))
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print 'origin: %s'%(' : '.join(map(str,info['origin'])))
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dx = info['dimension'][0]/info['resolution'][0]
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data = {'scalar':{'perimeter':numpy.zeros(info['resolution'],'i'),
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'distance':numpy.zeros(info['resolution'],'i')}}
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i = 0
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for line in content:
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for item in map(int,line.split()):
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data['scalar']['perimeter'][i%info['resolution'][0],(i/info['resolution'][0])%info['resolution'][1],i/info['resolution'][0]/info['resolution'][1]] = item
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i += 1
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# data['scalar']['perimeter'] = numpy.where(ndimage.morphology.grey_dilation(data['scalar']['perimeter'],size=(3,3,3))-data['scalar']['perimeter']>0,0,1)
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FDstencil_x = numpy.zeros([3,3,3])
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FDstencil_x[:,1,1] = [-1,0,1]
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FDstencil_y = numpy.zeros([3,3,3])
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FDstencil_y[1,:,1] = [-1,0,1]
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FDstencil_z = numpy.zeros([3,3,3])
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FDstencil_z[1,1,:] = [-1,0,1]
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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)
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data['scalar']['distance'] = skfmm.distance(data['scalar']['perimeter'], dx=dx)
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out = {}
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out['mesh'] = vtk_writeASCII_mesh(info['dimension'],info['resolution'],info['origin'],data)
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for what in out.keys():
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if file['name'] == 'STDIN':
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output(out[what],{},'Stdout')
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else:
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(head,tail) = os.path.split(file['name'])
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vtk = open(os.path.join(head,what+'_'+os.path.splitext(tail)[0]+'.vtk'), 'w')
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output(out[what],{'filepointer':vtk},'File')
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vtk.close()
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