DAMASK_EICMD/processing/pre/geom_euclideanDistance.py

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#!/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()