geom_check is now using vtk class, other scripts stop execution in case of invalid grid or size
This commit is contained in:
Martin Diehl
parent
9093cf2072
commit
0b4a5cfa9b
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@ -81,7 +81,11 @@ file = {'name':'STDIN',
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}
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if numpy.any(options.grid < 2):
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file['croak'].write('grid too low...\n')
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file['croak'].write('grid too small...\n')
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sys.exit()
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if numpy.any(options.size <= 0.0):
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file['croak'].write('size too small...\n')
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sys.exit()
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options.omega *= math.pi/180.0 # rescale ro radians
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@ -135,6 +139,13 @@ file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid'])))
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'homogenization: %i\n'%info['homogenization'])
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file['croak'].write("bounding box: %s\n"%(numpy.sqrt(numpy.sum(box*box,0))))
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if numpy.any(info['grid'] < 1):
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file['croak'].write('no valid grid info found.\n')
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sys.exit()
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if numpy.any(info['size'] <= 0.0):
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file['croak'].write('no valid size info found.\n')
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sys.exit()
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# -------------------------------------- switch according to task ----------------------------------
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formatwidth = 1+int(math.floor(math.log10(info['microstructures']-1)))
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if options.config:
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@ -1,12 +1,12 @@
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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
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import os,sys,string,re,numpy,vtk
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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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@ -23,74 +23,9 @@ class extendedOption(Option):
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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 $Id$','\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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#--------------------------------------------------------------------------------------------------
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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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@ -112,8 +47,7 @@ Produce VTK rectilinear mesh of structure data from geom description
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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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@ -128,13 +62,10 @@ 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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@ -147,11 +78,13 @@ for file in files:
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content = file['input'].readlines()
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file['input'].close()
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info = {'grid': [0,0,0],
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'size': [0.0,0.0,0.0],
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'origin': [0.0,0.0,0.0],
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'homogenization': 0,
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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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'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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for header in headers:
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@ -166,36 +99,56 @@ for file in files:
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else:
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info[headitems[0]] = mappings[headitems[0]](headitems[1])
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if numpy.all(info['grid'] == 0):
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file['croak'].write('no grid info found.\n')
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continue
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if numpy.all(info['size'] == 0.0):
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file['croak'].write('no size info found.\n')
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continue
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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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data = {'scalar':{'structure':numpy.zeros(info['grid'],'i')}}
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i = 0
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if numpy.all(any['grid'] < 1):
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file['croak'].write('no valid grid info found.\n')
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sys.exit()
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if numpy.any(info['size'] <= 0.0):
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file['croak'].write('no valid size info found.\n')
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sys.exit()
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#--- generate grid --------------------------------------------------------------------------------
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grid = vtk.vtkRectilinearGrid()
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grid.SetDimensions([x+1 for x in info['grid']])
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temp = vtk.vtkDoubleArray()
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for i in xrange(3):
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temp.SetNumberOfTuples(info['grid'][i]+1)
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for j in range(info['grid'][i]+1):
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temp.InsertTuple1(j,j*info['size'][i]/info['grid'][i]+info['origin'][i])
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if i == 0: grid.SetXCoordinates(temp)
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if i == 1: grid.SetYCoordinates(temp)
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if i == 2: grid.SetZCoordinates(temp)
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#--- read microstructure information --------------------------------------------------------------
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structure = vtk.vtkIntArray()
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structure.SetName('Microstructures')
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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']['structure'][i%info['grid'][0],(i/info['grid'][0])%info['grid'][1],i/info['grid'][0]/info['grid'][1]] = item
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i += 1
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structure.InsertNextValue(item)
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grid.GetCellData().AddArray(structure)
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out = {}
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out['mesh'] = vtk_writeASCII_mesh(info['size'],info['grid'],info['origin'],data)
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for what in out.keys():
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#--- write data -----------------------------------------------------------------------------------
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if file['name'] == 'STDIN':
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output(out[what],{},'Stdout')
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outWriter = vtk.vtkRectilinearGridWriter()
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outWriter.WriteToOutputStringOn()
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outWriter.SetFileTypeToASCII()
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outWriter.SetHeader('# powered by $Id$')
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outWriter.SetInput(grid)
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outWriter.Write()
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sys.stdout.write(outWriter.GetOutputString()[0:outWriter.GetOutputStringLength()])
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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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outWriter = vtk.vtkXMLRectilinearGridWriter()
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outWriter.SetDataModeToBinary()
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outWriter.SetCompressorTypeToZLib()
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outWriter.SetFileName(os.path.join(head,'mesh_'+os.path.splitext(tail)[0]
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+'.'+outWriter.GetDefaultFileExtension()))
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outWriter.SetInput(grid)
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outWriter.Write()
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@ -202,19 +202,19 @@ for file in files:
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else:
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new_header.append(header)
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if numpy.all(info['grid'] == 0):
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file['croak'].write('no grid info found.\n')
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continue
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if numpy.all(info['size'] == 0.0):
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file['croak'].write('no size info found.\n')
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continue
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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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if numpy.any(info['grid'] < 1):
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file['croak'].write('no valid grid info found.\n')
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sys.exit()
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if numpy.any(info['size'] <= 0.0):
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file['croak'].write('no valid size info found.\n')
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sys.exit()
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new_header.append('$Id$\n')
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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'][2],))
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@ -79,7 +79,7 @@ for file in files:
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info = {
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'grid': numpy.array([0,0,1]),
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'size': numpy.array([0.0,0.0,0.0]),
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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': options.homogenization
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@ -126,6 +126,13 @@ for file in files:
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'homogenization: %i\n'%info['homogenization'] + \
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'microstructures: %i\n\n'%info['microstructures'])
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if numpy.any(info['grid'] < 1):
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file['croak'].write('no valid grid info found.\n')
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sys.exit()
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if numpy.any(info['size'] <= 0.0):
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file['croak'].write('no valid size info found.\n')
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sys.exit()
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#--- write data -----------------------------------------------------------------------------------
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if options.config:
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file['output'].write('\n'.join(microstructure) + \
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@ -74,15 +74,7 @@ file = {'name':'STDIN',
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'output':sys.stdout,
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'croak':sys.stderr,
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}
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if numpy.any(options.grid < 1):
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file['croak'].write('invalid grid...\n')
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sys.exit()
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if numpy.any(options.size < 0.0):
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file['croak'].write('invalid size...\n')
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sys.exit()
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info = {
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info = {
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'grid': numpy.array(options.grid),
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'size': numpy.array(options.size),
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'origin': numpy.zeros(3,'d'),
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@ -97,6 +89,13 @@ file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid'])))
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'homogenization: %i\n'%info['homogenization'] + \
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'microstructures: %i\n\n'%info['microstructures'])
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if numpy.any(info['grid'] < 1):
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file['croak'].write('no valid grid info found.\n')
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sys.exit()
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if numpy.any(info['size'] <= 0.0):
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file['croak'].write('no valid size info found.\n')
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sys.exit()
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#--- write header ---------------------------------------------------------------------------------
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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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@ -77,8 +77,8 @@ for file in files:
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if file['name'] != 'STDIN': file['croak'].write(file['name']+'\n')
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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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'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': options.homogenization
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@ -116,6 +116,13 @@ for file in files:
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'homogenization: %i\n'%info['homogenization'] + \
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'microstructures: %i\n\n'%info['microstructures'])
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if numpy.any(info['grid'] < 1):
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file['croak'].write('no valid grid info found.\n')
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sys.exit()
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if numpy.any(info['size'] <= 0.0):
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file['croak'].write('no valid size info found.\n')
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sys.exit()
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#--- write data -----------------------------------------------------------------------------------
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if options.config:
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file['output'].write('\n'.join(microstructure) + \
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@ -119,19 +119,19 @@ for file in files:
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else:
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new_header.append(header)
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if numpy.all(info['grid'] == 0):
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file['croak'].write('no grid info found.\n')
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continue
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if numpy.all(info['size'] == 0.0):
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file['croak'].write('no size info found.\n')
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continue
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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\n'%info['microstructures'])
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if numpy.any(info['grid'] < 1):
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file['croak'].write('no valid grid info found.\n')
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sys.exit()
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if numpy.any(info['size'] <= 0.0):
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file['croak'].write('no valid size info found.\n')
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sys.exit()
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if numpy.all(info['grid'] == 0):
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newInfo['grid'] = info['grid']
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if numpy.all(info['size'] == 0.0)::
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@ -156,6 +156,13 @@ for file in files:
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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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if numpy.any(newInfo['grid'] < 1):
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file['croak'].write('no valid new grid info found.\n')
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sys.exit()
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if numpy.any(newInfo['size'] <= 0.0):
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file['croak'].write('no valid new size info found.\n')
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sys.exit()
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#--- assemble header ------------------------------------------------------------------------------
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new_header.append('$Id$\n')
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new_header.append("grid\ta %i\tb %i\tc %i\n"%(newInfo['grid'][0],newInfo['grid'][1],newInfo['grid'][2]))
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@ -167,12 +174,12 @@ for file in files:
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output += ''.join(new_header)
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#--- scale microstructure -------------------------------------------------------------------------
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for c in xrange(options.grid[2]):
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z = int(info['grid'][2]*(c+0.5)/options.grid[2])%info['grid'][2]
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for b in xrange(options.grid[1]):
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y = int(info['grid'][1]*(b+0.5)/options.grid[1])%info['grid'][1]
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for a in xrange(options.grid[0]):
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x = int(info['grid'][0]*(a+0.5)/options.grid[0])%info['grid'][0]
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for c in xrange(newInfo['grid'][2]):
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z = int(info['grid'][2]*(c+0.5)/newInfo['grid'][2])%info['grid'][2]
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for b in xrange(newInfo['grid'][1]):
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y = int(info['grid'][1]*(b+0.5)/newInfo['grid'][1])%info['grid'][1]
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for a in xrange(newInfo['grid'][0]):
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x = int(info['grid'][0]*(a+0.5)/newInfo['grid'][0])%info['grid'][0]
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output += str(microstructure[x,y,z]).rjust(formatwidth) + {True:' ',False:'\n'}[options.twoD]
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output += {True:'\n',False:''}[options.twoD]
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||||
file['output'].write(output)
|
||||
|
|
|
|||
|
|
@ -122,12 +122,6 @@ for file in files:
|
|||
else:
|
||||
new_header.append(header)
|
||||
|
||||
if numpy.all(info['grid'] == 0):
|
||||
file['croak'].write('no grid info found.\n')
|
||||
continue
|
||||
if numpy.all(info['size'] == 0.0):
|
||||
file['croak'].write('no size info found.\n')
|
||||
continue
|
||||
|
||||
file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
|
||||
'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
|
||||
|
|
@ -135,6 +129,13 @@ for file in files:
|
|||
'homogenization: %i\n'%info['homogenization'] + \
|
||||
'microstructures: %i\n\n'%info['microstructures'])
|
||||
|
||||
if numpy.any(info['grid'] < 1):
|
||||
file['croak'].write('no valid grid info found.\n')
|
||||
sys.exit()
|
||||
if numpy.any(info['size'] <= 0.0):
|
||||
file['croak'].write('no valid size info found.\n')
|
||||
sys.exit()
|
||||
|
||||
#--- process input --------------------------------------------------------------------------------
|
||||
N = info['grid'][0]*info['grid'][1]*info['grid'][2]
|
||||
microstructure = numpy.zeros(N,'i')
|
||||
|
|
|
|||
|
|
@ -119,19 +119,19 @@ for file in files:
|
|||
else:
|
||||
new_header.append(header)
|
||||
|
||||
if numpy.all(info['grid'] == 0):
|
||||
file['croak'].write('no grid info found.\n')
|
||||
continue
|
||||
if numpy.all(info['size'] == 0.0):
|
||||
file['croak'].write('no dimension info found.\n')
|
||||
continue
|
||||
|
||||
file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
|
||||
'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
|
||||
'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \
|
||||
'homogenization: %i\n'%info['homogenization'] + \
|
||||
'microstructures: %i\n'%info['microstructures'])
|
||||
|
||||
if numpy.any(info['grid'] < 1):
|
||||
file['croak'].write('no valid grid info found.\n')
|
||||
sys.exit()
|
||||
if numpy.any(info['size'] <= 0.0):
|
||||
file['croak'].write('no valid size info found.\n')
|
||||
sys.exit()
|
||||
|
||||
#--- read data ------------------------------------------------------------------------------------
|
||||
microstructure = numpy.zeros(info['grid'],'i')
|
||||
i = 0
|
||||
|
|
|
|||
Loading…
Reference in New Issue