#!/usr/bin/env python # -*- coding: UTF-8 no BOM -*- import os,sys,string,re,numpy,skfmm from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP from scipy import ndimage # ----------------------------- 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) 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) else: {\ 'File': outFile,\ 'Stdout': outStdout,\ }[dest](str(cmd),locals) return # +++++++++++++++++++++++++++++++++++++++++++++++++++ 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 $','\n','\\n'), 'ASCII', 'DATASET RECTILINEAR_GRID', 'DIMENSIONS %i %i %i'%(res[0]+1,res[1]+1,res[2]+1), 'X_COORDINATES %i float'%(res[0]+1), ' '.join(map(str,[i*dim[0]/res[0]+origin[0] for i in range(res[0]+1)])), 'Y_COORDINATES %i float'%(res[1]+1), ' '.join(map(str,[i*dim[1]/res[1]+origin[1] for i in range(res[1]+1)])), 'Z_COORDINATES %i float'%(res[2]+1), ' '.join(map(str,[i*dim[2]/res[2]+origin[2] for i in range(res[2]+1)])), 'CELL_DATA %i'%N, ] for datatype in data: for item in data[datatype]: cmds += [\ '%s %s float'%(datatype.upper()+{True:'',False:'S'}[datatype.lower().endswith('s')],item), 'LOOKUP_TABLE default', [[['\t'.join(map(str,data[datatype][item][:,j,k]))] for j in range(res[1])] for k in range(res[2])] ] return cmds # ----------------------- MAIN ------------------------------- identifiers = { 'resolution': ['a','b','c'], 'dimension': ['x','y','z'], 'origin': ['x','y','z'], } mappings = { 'resolution': lambda x: int(x), 'dimension': lambda x: float(x), 'origin': lambda x: float(x), } parser = OptionParser(option_class=extendedOption, usage='%prog [geomfile[s]]', description = """ Produce Euclidean distance map from geom description """ + string.replace('$Id: spectral_geomCheck.py 1575 2012-06-26 18:07:38Z MPIE\p.eisenlohr $','\n','\\n') ) (options, filenames) = parser.parse_args() # ------------------------------------------ setup file handles --------------------------------------- files = [] if filenames == []: files.append({'name':'STDIN', 'input':sys.stdin}) else: for name in filenames: if os.path.exists(name): files.append({'name':name, 'input':open(name)}) # ------------------------------------------ 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 = [file['input'].readline() for i in range(headerlines)] else: headerlines = 1 headers = firstline 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], } 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 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) 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']))) dx = info['dimension'][0]/info['resolution'][0] data = {'scalar':{'perimeter':numpy.zeros(info['resolution'],'i'), 'distance':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 i += 1 # data['scalar']['perimeter'] = numpy.where(ndimage.morphology.grey_dilation(data['scalar']['perimeter'],size=(3,3,3))-data['scalar']['perimeter']>0,0,1) 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) out = {} out['mesh'] = vtk_writeASCII_mesh(info['dimension'],info['resolution'],info['origin'],data) 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()