polished scripts (option parser, numpy)
This commit is contained in:
Martin Diehl
parent
fd2164b391
commit
f72a87f94b
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@ -1,33 +1,14 @@
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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# This script is used for the post processing of the results achieved by the spectral method.
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# As it reads in the data coming from "materialpoint_results", it can be adopted to the data
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# computed using the FEM solvers. Its capable to handle elements with one IP in a regular order
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import os,sys,threading,re,numpy,time,string,fnmatch,vtk
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import os,sys,threading,re,time,string,fnmatch,vtk
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import numpy as np
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from optparse import OptionParser
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from vtk.util import numpy_support
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import damask
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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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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scriptID = '$Id$'
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scriptName = scriptID.split()[1]
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# -----------------------------
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class backgroundMessage(threading.Thread):
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@ -130,7 +111,7 @@ def vtk_writeASCII_mesh(mesh,data,res,sep):
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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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string.replace('powered by %s'%scriptID,'\n','\\n'),
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'ASCII',
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'DATASET UNSTRUCTURED_GRID',
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'POINTS %i double'%N1,
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@ -247,7 +228,7 @@ def vtk_writeASCII_points(coordinates,data,res,sep):
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cmds = [\
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'# vtk DataFile Version 3.1',
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'powered by $Id$',
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string.replace('powered by %s'%scriptID,'\n','\\n'),
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'ASCII',
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'DATASET UNSTRUCTURED_GRID',
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'POINTS %i float'%N,
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@ -275,28 +256,30 @@ def vtk_writeASCII_points(coordinates,data,res,sep):
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# ----------------------- MAIN -------------------------------
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parser = OptionParser(option_class=extendedOption, usage='%prog [options] datafile[s]', description = """
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog [options] datafile[s]', description = """
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Produce VTK file from data field. Coordinates are taken from (consecutive) x, y, and z columns.
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""" + string.replace('$Id$','\n','\\n')
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""",version = string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-s', '--scalar', action='extend', dest='scalar', type='string', \
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help='list of scalars to visualize')
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help='list of single scalars to visualize', metavar = '<string LIST>')
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parser.add_option( '--double', action='extend', dest='double', type='string', \
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help='list of scalars to visualize')
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help='list of two scalars to visualize', metavar = '<string LIST>')
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parser.add_option( '--triple', action='extend', dest='triple', type='string', \
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help='list of scalars to visualize')
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help='list of three scalars to visualize', metavar = '<string LIST>')
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parser.add_option( '--quadruple', action='extend', dest='quadruple', type='string', \
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help='list of scalars to visualize')
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help='list of four scalars to visualize', metavar = '<string LIST>')
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parser.add_option('-v', '--vector', action='extend', dest='vector', type='string', \
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help='list of vectors to visualize')
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help='list of vectors to visualize', metavar = '<string LIST>')
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parser.add_option('-t', '--tensor', action='extend', dest='tensor', type='string', \
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help='list of tensors to visualize', metavar = '<string LIST>')
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parser.add_option('-d', '--deformation', dest='defgrad', type='string', \
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help='heading of deformation gradient columns [%default]')
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help='heading of deformation gradient columns [%default]', metavar = 'string')
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parser.add_option('--reference', dest='undeformed', action='store_true',\
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help='map results to reference (undeformed) configuration')
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help='map results to reference (undeformed) configuration [%default]')
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parser.add_option('-c','--cell', dest='cell', action='store_true',\
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help='data is cell-centered')
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help='data is cell-centered [%default]')
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parser.add_option('-p','--vertex', dest='cell', action='store_false',\
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help='data is vertex-centered')
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parser.add_option('--mesh', dest='output_mesh', action='store_true', \
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@ -308,15 +291,15 @@ parser.add_option('--points', dest='output_points', action='store_true', \
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parser.add_option('--nopoints', dest='output_points', action='store_false', \
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help='omit VTK points file')
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parser.add_option('--separator', dest='separator', type='string', \
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help='data separator [t(ab), n(ewline), s(pace)]')
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help='data separator (t(ab), n(ewline), s(pace)) [%default]', metavar = 'string')
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parser.add_option('--scaling', dest='scaling', action='extend', type='string', \
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help='scaling of fluctuation')
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help='scaling of fluctuation', metavar = '<float LIST>')
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parser.add_option('-u', '--unitlength', dest='unitlength', type='float', \
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help='set unit length for 2D model [%default]')
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help='set unit length for 2D model [%default]', metavar = 'float')
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parser.add_option('--filenodalcoords', dest='filenodalcoords', type='string', \
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help='ASCII table containing nodal coords')
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parser.add_option('--labelnodalcoords', dest='nodalcoords', type='string', nargs=3, \
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help='labels of nodal coords in ASCII table')
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help='ASCII table containing nodal coords', metavar = 'string')
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parser.add_option('--labelnodalcoords', dest='labelnodalcoords', type='string', nargs=3, \
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help='labels of nodal coords in ASCII table %default', metavar = 'string string string')
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parser.add_option('-l', '--linear', dest='linearreconstruction', action='store_true',\
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help='use linear reconstruction of geometry [%default]')
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@ -345,8 +328,8 @@ sep = {'n': '\n', 't': '\t', 's': ' '}
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options.scaling += [1.0 for i in xrange(max(0,3-len(options.scaling)))]
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options.scaling = map(float, options.scaling)
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if numpy.any(options.scaling != 1.0) and options.linearreconstruction: print 'cannot scale for linear reconstruction'
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if numpy.any(options.scaling != 1.0) and options.filenodalcoords != '': print 'cannot scale when reading coordinate from file'
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if np.any(options.scaling != 1.0) and options.linearreconstruction: print 'cannot scale for linear reconstruction'
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if np.any(options.scaling != 1.0) and options.filenodalcoords != '': print 'cannot scale when reading coordinate from file'
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options.separator = options.separator.lower()
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for filename in args:
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@ -419,7 +402,7 @@ for filename in args:
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matches[what][needle] += [head]
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values = numpy.array(sorted([map(transliterateToFloat,line.split()[:maxcol]) for line in content[headrow+1:]],
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values = np.array(sorted([map(transliterateToFloat,line.split()[:maxcol]) for line in content[headrow+1:]],
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key=lambda x:(x[locol+0],x[locol+1],x[locol+2])),'d') # sort with z as fastest and x as slowest index
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N = len(values)
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@ -429,11 +412,11 @@ for filename in args:
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for i in xrange(N):
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tempGrid[j][str(values[i,locol+j])] = True
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grid = numpy.array([len(tempGrid[0]),\
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grid = np.array([len(tempGrid[0]),\
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len(tempGrid[1]),\
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len(tempGrid[2]),],'i')
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dim = numpy.ones(3)
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dim = np.ones(3)
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for i,r in enumerate(grid):
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if r > 1:
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@ -445,14 +428,14 @@ for filename in args:
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dim[2] = options.unitlength
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print dim
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if options.undeformed:
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Favg = numpy.eye(3)
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Favg = np.eye(3)
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else:
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Favg = damask.core.math.tensorAvg(
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numpy.reshape(numpy.transpose(values[:,column['tensor'][options.defgrad]:
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np.reshape(np.transpose(values[:,column['tensor'][options.defgrad]:
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column['tensor'][options.defgrad]+9]),
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(3,3,grid[0],grid[1],grid[2])))
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if not options.filenodalcoords:
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F = numpy.reshape(numpy.transpose(values[:,column['tensor'][options.defgrad]:
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F = np.reshape(np.transpose(values[:,column['tensor'][options.defgrad]:
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column['tensor'][options.defgrad]+9]),
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(3,3,grid[0],grid[1],grid[2]))
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if options.linearreconstruction:
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@ -462,7 +445,7 @@ for filename in args:
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nodes = damask.core.mesh.nodesAroundCentres(dim,Favg,centroids)
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else:
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nodes = numpy.zeros(((3,grid[0]+1)*(grid[1]+1)*(grid[2]+1)),'d')
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nodes = np.zeros(((3,grid[0]+1)*(grid[1]+1)*(grid[2]+1)),'d')
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filenodalcoords = open(options.filenodalcoords)
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tablenodalcoords = damask.ASCIItable(filenodalcoords)
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@ -555,7 +538,7 @@ for filename in args:
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col = column[datatype][label]
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if col != -1:
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print label,
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fields[datatype][label] = numpy.reshape(values[:,col:col+length[datatype]],[grid[0],grid[1],grid[2]]+reshape[datatype])
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fields[datatype][label] = np.reshape(values[:,col:col+length[datatype]],[grid[0],grid[1],grid[2]]+reshape[datatype])
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fields[datatype]['_order_'] += [label]
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print '\n'
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@ -19,17 +19,16 @@ def unravel(item):
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Add column(s) with derived values according to user defined arithmetic operation between column(s).
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Columns can be specified either by label or index. Use ';' for ',' in functions.
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Columns can be specified either by label or index. Use ';' for ',' in functions. Numpy is available as np
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Example: distance to IP coordinates -- "math.sqrt( #ip.x#**2 + #ip.y#**2 + round(#ip.z#;3)**2 )"
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""" + string.replace(scriptID,'\n','\\n')
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""", version = string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-l','--label', dest='labels', action='extend', type='string', \
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help='(list of) new column labels', metavar='<LIST>')
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help='(list of) new column labels', metavar='<string LIST>')
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parser.add_option('-f','--formula', dest='formulas', action='extend', type='string', \
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help='(list of) formulas corresponding to labels', metavar='<LIST>')
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help='(list of) formulas corresponding to labels', metavar='<string LIST>')
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parser.set_defaults(labels= [])
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parser.set_defaults(formulas= [])
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@ -42,7 +41,6 @@ for i in xrange(len(options.formulas)):
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options.formulas[i]=options.formulas[i].replace(';',',')
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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, 'output':sys.stdout, 'croak':sys.stderr})
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@ -52,7 +50,6 @@ else:
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files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
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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('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
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else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
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@ -63,8 +60,7 @@ for file in files:
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table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
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table.head_read() # read ASCII header info
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table.info_append(string.replace(scriptID,'\n','\\n') + \
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'\t' + ' '.join(sys.argv[1:]))
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table.info_append(string.replace(scriptID,'\n','\\n') + '\t' + ' '.join(sys.argv[1:]))
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evaluator = {}
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brokenFormula = {}
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@ -110,7 +106,6 @@ for file in files:
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table.head_write()
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# ------------------------------------------ process data ---------------------------------------
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outputAlive = True
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table.data_rewind()
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@ -121,7 +116,6 @@ for file in files:
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outputAlive = table.data_write() # output processed line
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# ------------------------------------------ output result ---------------------------------------
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outputAlive and table.output_flush() # just in case of buffered ASCII table
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file['input'].close() # close input ASCII table
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@ -1,45 +1,25 @@
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,re,sys,math,numpy,string,damask
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import os,re,sys,math,numpy,string
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from collections import defaultdict
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from optparse import OptionParser, Option
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from optparse import OptionParser
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import damask
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scriptID = '$Id$'
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scriptName = scriptID.split()[1]
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# -----------------------------
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class extendableOption(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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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Add column(s) containing Cauchy stress based on given column(s) of
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deformation gradient and first Piola--Kirchhoff stress.
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""" + string.replace(scriptID,'\n','\\n')
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""", version = string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-f','--defgrad', dest='defgrad', type='string', metavar='string', \
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help='heading of columns containing deformation gradient [%default]')
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parser.add_option('-p','--stress', dest='stress', type='string', metavar='string', \
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@ -68,7 +48,6 @@ datainfo['stress']['label'].append(options.stress)
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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, 'output':sys.stdout, 'croak':sys.stderr})
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@ -78,7 +57,6 @@ else:
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files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
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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('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
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else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
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@ -109,11 +87,9 @@ for file in files:
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for i in xrange(datainfo['stress']['len'])]) # extend ASCII header with new labels
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# ------------------------------------------ assemble header ---------------------------------------
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table.head_write()
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# ------------------------------------------ process data ---------------------------------------
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outputAlive = True
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while outputAlive and table.data_read(): # read next data line of ASCII table
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@ -126,10 +102,9 @@ for file in files:
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outputAlive = table.data_write() # output processed line
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# ------------------------------------------ output result ---------------------------------------
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table.output_flush() # just in case of buffered ASCII table
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file['input'].close() # close input ASCII table
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if file['name'] != 'STDIN':
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file['output'].close # close output ASCII table
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file['output'].close() # close output ASCII table
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os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new
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