scripts deemed useless
This commit is contained in:
Martin Diehl
parent
f42c316aa2
commit
ac9a9cb6ac
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@ -1,61 +0,0 @@
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,string,h5py
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import numpy as np
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from optparse import OptionParser
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import damask
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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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('$Id$','\n','\\n')
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)
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parser.add_option('-f','--defgrad', dest='defgrad', \
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help='heading of columns containing deformation gradient [%default]')
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parser.add_option('-p','--stress', dest='stress', \
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help='heading of columns containing first Piola--Kirchhoff stress [%default]')
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parser.add_option('-o','--output', dest='output', \
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help='group containing requested data [%default]')
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parser.set_defaults(defgrad = 'f')
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parser.set_defaults(stress = 'p')
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parser.set_defaults(output = 'crystallite')
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(options,filenames) = parser.parse_args()
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if options.defgrad is None or options.stress is None or options.output is None:
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parser.error('missing data column...')
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# ------------------------------------------ setup file handles ---------------------------------------
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files = []
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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, 'file':h5py.File(name,"a")})
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# ------------------------------------------ loop over input files ------------------------------------
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for myFile in files:
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print(myFile['name'])
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# ------------------------------------------ loop over increments -------------------------------------
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for inc in myFile['file']['increments'].keys():
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print("Current Increment: "+inc)
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for instance in myFile['file']['increments/'+inc+'/'+options.output].keys():
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dsets = myFile['file']['increments/'+inc+'/'+options.output+'/'+instance].keys()
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if (options.defgrad in dsets and options.stress in dsets):
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defgrad = myFile['file']['increments/'+inc+'/'+options.output+'/'+instance+'/'+options.defgrad]
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stress = myFile['file']['increments/'+inc+'/'+options.output+'/'+instance+'/'+options.stress]
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cauchy=np.zeros(np.shape(stress),'f')
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for p in range(stress.shape[0]):
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cauchy[p,...] = 1.0/np.linalg.det(defgrad[p,...])*np.dot(stress[p,...],defgrad[p,...].T) # [Cauchy] = (1/det(F)) * [P].[F_transpose]
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cauchyFile = myFile['file']['increments/'+inc+'/'+options.output+'/'+instance].create_dataset('cauchy', data=cauchy)
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cauchyFile.attrs['units'] = 'Pa'
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,shutil
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import numpy as np
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import damask
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from optparse import OptionParser
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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# -----------------------------
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# MAIN FUNCTION STARTS HERE
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# -----------------------------
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# --- input parsing
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parser = OptionParser(usage='%prog [options] resultfile', description = """
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Create vtk files for the (deformed) geometry that belongs to a .t16 (MSC.Marc) results file.
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""", version = scriptID)
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parser.add_option('-d','--dir', dest='dir', \
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help='name of subdirectory to hold output [%default]')
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parser.add_option('-r','--range', dest='range', type='int', nargs=3, \
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help='range of positions (or increments) to output (start, end, step) [all]')
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parser.add_option('--increments', action='store_true', dest='getIncrements', \
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help='switch to increment range [%default]')
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parser.add_option('-t','--type', dest='type', type='choice', choices=['ipbased','nodebased'], \
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help='processed geometry type [ipbased and nodebased]')
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parser.set_defaults(dir = 'vtk')
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parser.set_defaults(getIncrements= False)
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(options, files) = parser.parse_args()
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# --- basic sanity checks
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if files == []:
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parser.print_help()
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parser.error('no file specified...')
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filename = os.path.splitext(files[0])[0]
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if not os.path.exists(filename+'.t16'):
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parser.print_help()
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parser.error('invalid file "%s" specified...'%filename+'.t16')
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if not options.type :
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options.type = ['nodebased', 'ipbased']
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else:
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options.type = [options.type]
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# --- more sanity checks
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sys.path.append(damask.solver.Marc().libraryPath('../../'))
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try:
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import py_post
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except:
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print('error: no valid Mentat release found')
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sys.exit(-1)
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# --------------------------- open results file and initialize mesh ----------
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p = py_post.post_open(filename+'.t16')
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p.moveto(0)
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Nnodes = p.nodes()
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Nincrements = p.increments() - 1 # t16 contains one "virtual" increment (at 0)
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if damask.core.mesh.mesh_init_postprocessing(filename+'.mesh') > 0:
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print('error: init not successful')
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sys.exit(-1)
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Ncellnodes = damask.core.mesh.mesh_get_Ncellnodes()
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unitlength = damask.core.mesh.mesh_get_unitlength()
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# --------------------------- create output dir --------------------------------
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dirname = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir))
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if not os.path.isdir(dirname):
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os.mkdir(dirname,0755)
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# --------------------------- get positions --------------------------------
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incAtPosition = {}
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positionOfInc = {}
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for position in range(Nincrements):
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p.moveto(position+1)
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incAtPosition[position] = p.increment # remember "real" increment at this position
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positionOfInc[p.increment] = position # remember position of "real" increment
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if not options.range:
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options.getIncrements = False
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locations = range(Nincrements) # process all positions
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else:
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options.range = list(options.range) # convert to list
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if options.getIncrements:
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locations = [positionOfInc[x] for x in range(options.range[0],options.range[1]+1,options.range[2])
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if x in positionOfInc]
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else:
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locations = range( max(0,options.range[0]),
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min(Nincrements,options.range[1]+1),
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options.range[2] )
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increments = [incAtPosition[x] for x in locations] # build list of increments to process
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# --------------------------- loop over positions --------------------------------
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for incCount,position in enumerate(locations): # walk through locations
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p.moveto(position+1) # wind to correct position
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# --- get displacements
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node_displacement = [[0,0,0] for i in range(Nnodes)]
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for n in range(Nnodes):
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if p.node_displacements():
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node_displacement[n] = map(lambda x:x*unitlength,list(p.node_displacement(n)))
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c = damask.core.mesh.mesh_build_cellnodes(np.array(node_displacement).T,Ncellnodes)
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cellnode_displacement = [[c[i][n] for i in range(3)] for n in range(Ncellnodes)]
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# --- append displacements to corresponding files
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for geomtype in options.type:
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outFilename = eval('"'+eval("'%%s_%%s_inc%%0%ii.vtk'%(math.log10(max(increments+[1]))+1)")\
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+'"%(dirname + os.sep + os.path.split(filename)[1],geomtype,increments[incCount])')
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print outFilename
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shutil.copyfile('%s_%s.vtk'%(filename,geomtype),outFilename)
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with open(outFilename,'a') as myfile:
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myfile.write("POINT_DATA %i\n"%{'nodebased':Nnodes,'ipbased':Ncellnodes}[geomtype])
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myfile.write("VECTORS displacement double\n")
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coordinates = {'nodebased':node_displacement,'ipbased':cellnode_displacement}[geomtype]
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for n in range({'nodebased':Nnodes,'ipbased':Ncellnodes}[geomtype]):
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myfile.write("%.8e %.8e %.8e\n"%(coordinates[n][0],coordinates[n][1],coordinates[n][2]))
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# --------------------------- DONE --------------------------------
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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,time
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from optparse import OptionParser, OptionGroup
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import damask
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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# -----------------------------
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def ParseOutputFormat(filename,homogID,crystID,phaseID):
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"""parse .output* files in order to get a list of outputs"""
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myID = {'Homogenization': homogID,
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'Crystallite': crystID,
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'Constitutive': phaseID,
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}
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format = {}
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for what in ['Homogenization','Crystallite','Constitutive']:
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content = []
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format[what] = {'outputs':{},'specials':{'brothers':[]}}
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for prefix in ['']+map(str,range(1,17)):
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if os.path.exists(prefix+filename+'.output'+what):
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try:
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file = open(prefix+filename+'.output'+what)
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content = file.readlines()
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file.close()
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break
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except:
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pass
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if content == []: continue # nothing found...
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tag = ''
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tagID = 0
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for line in content:
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if re.match("\s*$",line) or re.match("#",line): # skip blank lines and comments
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continue
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m = re.match("\[(.+)\]",line) # look for block indicator
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if m: # next section
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tag = m.group(1)
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tagID += 1
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format[what]['specials']['brothers'].append(tag)
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if tag == myID[what] or (myID[what].isdigit() and tagID == int(myID[what])):
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format[what]['specials']['_id'] = tagID
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format[what]['outputs'] = []
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tag = myID[what]
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else: # data from section
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if tag == myID[what]:
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(output,length) = line.split()
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output.lower()
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if length.isdigit():
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length = int(length)
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if re.match("\((.+)\)",output): # special data, e.g. (Ngrains)
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format[what]['specials'][output] = length
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elif length > 0:
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format[what]['outputs'].append([output,length])
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if '_id' not in format[what]['specials']:
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print "\nsection '%s' not found in <%s>"%(myID[what], what)
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print '\n'.join(map(lambda x:' [%s]'%x, format[what]['specials']['brothers']))
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return format
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# -----------------------------
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def ParsePostfile(p,filename, outputFormat, legacyFormat):
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"""
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parse postfile in order to get position and labels of outputs
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needs "outputFormat" for mapping of output names to postfile output indices
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"""
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startVar = {True: 'GrainCount',
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False:'HomogenizationCount'}
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# --- build statistics
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stat = { \
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'IndexOfLabel': {}, \
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'Title': p.title(), \
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'Extrapolation': p.extrapolate, \
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'NumberOfIncrements': p.increments() - 1, \
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'NumberOfNodes': p.nodes(), \
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'NumberOfNodalScalars': p.node_scalars(), \
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'LabelOfNodalScalar': [None]*p.node_scalars() , \
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'NumberOfElements': p.elements(), \
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'NumberOfElementalScalars': p.element_scalars(), \
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'LabelOfElementalScalar': [None]*p.element_scalars() , \
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'NumberOfElementalTensors': p.element_tensors(), \
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'LabelOfElementalTensor': [None]*p.element_tensors(), \
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}
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# --- find labels
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for labelIndex in range(stat['NumberOfNodalScalars']):
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label = p.node_scalar_label(labelIndex)
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stat['IndexOfLabel'][label] = labelIndex
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stat['LabelOfNodalScalar'][labelIndex] = label
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for labelIndex in range(stat['NumberOfElementalScalars']):
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label = p.element_scalar_label(labelIndex)
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stat['IndexOfLabel'][label] = labelIndex
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stat['LabelOfElementalScalar'][labelIndex] = label
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for labelIndex in range(stat['NumberOfElementalTensors']):
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label = p.element_tensor_label(labelIndex)
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stat['IndexOfLabel'][label] = labelIndex
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stat['LabelOfElementalTensor'][labelIndex] = label
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if 'User Defined Variable 1' in stat['IndexOfLabel']: # output format without dedicated names?
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stat['IndexOfLabel'][startVar[legacyFormat]] = stat['IndexOfLabel']['User Defined Variable 1'] # adjust first named entry
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if startVar[legacyFormat] in stat['IndexOfLabel']: # does the result file contain relevant user defined output at all?
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startIndex = stat['IndexOfLabel'][startVar[legacyFormat]]
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stat['LabelOfElementalScalar'][startIndex] = startVar[legacyFormat]
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# We now have to find a mapping for each output label as defined in the .output* files to the output position in the post file
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# Since we know where the user defined outputs start ("startIndex"), we can simply assign increasing indices to the labels
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# given in the .output* file
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offset = 1
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if legacyFormat:
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stat['LabelOfElementalScalar'][startIndex + offset] = startVar[not legacyFormat] # add HomogenizationCount as second
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offset += 1
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for (name,N) in outputFormat['Homogenization']['outputs']:
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for i in range(N):
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label = {False: '%s'%( name),
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True:'%i_%s'%(i+1,name)}[N > 1]
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stat['IndexOfLabel'][label] = startIndex + offset
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stat['LabelOfElementalScalar'][startIndex + offset] = label
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offset += 1
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if not legacyFormat:
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stat['IndexOfLabel'][startVar[not legacyFormat]] = startIndex + offset
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stat['LabelOfElementalScalar'][startIndex + offset] = startVar[not legacyFormat] # add GrainCount
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offset += 1
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if '(ngrains)' in outputFormat['Homogenization']['specials']:
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for grain in range(outputFormat['Homogenization']['specials']['(ngrains)']):
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stat['IndexOfLabel']['%i_CrystalliteCount'%(grain+1)] = startIndex + offset # report crystallite count
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stat['LabelOfElementalScalar'][startIndex + offset] = '%i_CrystalliteCount'%(grain+1) # add GrainCount
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offset += 1
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for (name,N) in outputFormat['Crystallite']['outputs']: # add crystallite outputs
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for i in range(N):
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label = {False: '%i_%s'%(grain+1, name),
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True:'%i_%i_%s'%(grain+1,i+1,name)}[N > 1]
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stat['IndexOfLabel'][label] = startIndex + offset
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stat['LabelOfElementalScalar'][startIndex + offset] = label
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offset += 1
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stat['IndexOfLabel']['%i_ConstitutiveCount'%(grain+1)] = startIndex + offset # report constitutive count
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stat['LabelOfElementalScalar'][startIndex + offset] = '%i_ConstitutiveCount'%(grain+1) # add GrainCount
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offset += 1
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for (name,N) in outputFormat['Constitutive']['outputs']: # add constitutive outputs
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for i in range(N):
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label = {False: '%i_%s'%(grain+1, name),
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True:'%i_%i_%s'%(grain+1,i+1,name)}[N > 1]
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stat['IndexOfLabel'][label] = startIndex + offset
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try:
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stat['LabelOfElementalScalar'][startIndex + offset] = label
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except IndexError:
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print 'trying to assign %s at position %i+%i'%(label,startIndex,offset)
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sys.exit(1)
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offset += 1
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return stat
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# -----------------------------
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def GetIncrementLocations(p,Nincrements,options):
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"""get mapping between positions in postfile and increment number"""
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incAtPosition = {}
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positionOfInc = {}
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for position in range(Nincrements):
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p.moveto(position+1)
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incAtPosition[position] = p.increment # remember "real" increment at this position
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positionOfInc[p.increment] = position # remember position of "real" increment
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if not options.range:
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options.getIncrements = False
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locations = range(Nincrements) # process all positions
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else:
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options.range = list(options.range) # convert to list
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if options.getIncrements:
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locations = [positionOfInc[x] for x in range(options.range[0],options.range[1]+1,options.range[2])
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if x in positionOfInc]
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else:
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locations = range( max(0,options.range[0]),
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min(Nincrements,options.range[1]+1),
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options.range[2] )
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increments = [incAtPosition[x] for x in locations] # build list of increments to process
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return [increments,locations]
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# -----------------------------
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def SummarizePostfile(stat,where=sys.stdout):
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where.write('\n\n')
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where.write('title:\t%s'%stat['Title'] + '\n\n')
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where.write('extraplation:\t%s'%stat['Extrapolation'] + '\n\n')
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where.write('increments:\t%i'%(stat['NumberOfIncrements']) + '\n\n')
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where.write('nodes:\t%i'%stat['NumberOfNodes'] + '\n\n')
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where.write('elements:\t%i'%stat['NumberOfElements'] + '\n\n')
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where.write('nodal scalars:\t%i'%stat['NumberOfNodalScalars'] + '\n\n '\
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+'\n '.join(stat['LabelOfNodalScalar']) + '\n\n')
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where.write('elemental scalars:\t%i'%stat['NumberOfElementalScalars'] + '\n\n '\
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+ '\n '.join(stat['LabelOfElementalScalar']) + '\n\n')
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where.write('elemental tensors:\t%i'%stat['NumberOfElementalTensors'] + '\n\n '\
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+ '\n '.join(stat['LabelOfElementalTensor']) + '\n\n')
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return True
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# -----------------------------
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def SummarizeOutputfile(format,where=sys.stdout):
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where.write('\nUser Defined Outputs')
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for what in format.keys():
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where.write('\n\n %s:'%what)
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for output in format[what]['outputs']:
|
||||
where.write('\n %s'%output)
|
||||
|
||||
return True
|
||||
|
||||
|
||||
# -----------------------------
|
||||
def writeHeader(myfile,stat,geomtype):
|
||||
|
||||
myfile.write('2\theader\n')
|
||||
myfile.write(string.replace('$Id$','\n','\\n')+
|
||||
'\t' + ' '.join(sys.argv[1:]) + '\n')
|
||||
if geomtype == 'nodebased':
|
||||
myfile.write('node')
|
||||
for i in range(stat['NumberOfNodalScalars']):
|
||||
myfile.write('\t%s'%''.join(stat['LabelOfNodalScalar'][i].split()))
|
||||
|
||||
elif geomtype == 'ipbased':
|
||||
myfile.write('elem\tip')
|
||||
for i in range(stat['NumberOfElementalScalars']):
|
||||
myfile.write('\t%s'%''.join(stat['LabelOfElementalScalar'][i].split()))
|
||||
|
||||
myfile.write('\n')
|
||||
|
||||
return True
|
||||
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
Extract data from a .t16 (MSC.Marc) results file.
|
||||
|
||||
""", version = scriptID)
|
||||
|
||||
parser.add_option('-i','--info', action='store_true', dest='info', \
|
||||
help='list contents of resultfile [%default]')
|
||||
parser.add_option('-l','--legacy', action='store_true', dest='legacy', \
|
||||
help='legacy user result block (starts with GrainCount) [%default]')
|
||||
parser.add_option('-d','--dir', dest='dir', \
|
||||
help='name of subdirectory to hold output [%default]')
|
||||
parser.add_option('-r','--range', dest='range', type='int', nargs=3, \
|
||||
help='range of positions (or increments) to output (start, end, step) [all]')
|
||||
parser.add_option('--increments', action='store_true', dest='getIncrements', \
|
||||
help='switch to increment range [%default]')
|
||||
parser.add_option('-t','--type', dest='type', type='choice', choices=['ipbased','nodebased'], \
|
||||
help='processed geometry type [ipbased and nodebased]')
|
||||
|
||||
group_material = OptionGroup(parser,'Material identifier')
|
||||
|
||||
group_material.add_option('--homogenization', dest='homog', \
|
||||
help='homogenization identifier (as string or integer [%default])', metavar='<ID>')
|
||||
group_material.add_option('--crystallite', dest='cryst', \
|
||||
help='crystallite identifier (as string or integer [%default])', metavar='<ID>')
|
||||
group_material.add_option('--phase', dest='phase', \
|
||||
help='phase identifier (as string or integer [%default])', metavar='<ID>')
|
||||
|
||||
parser.add_option_group(group_material)
|
||||
|
||||
parser.set_defaults(info = False)
|
||||
parser.set_defaults(legacy = False)
|
||||
parser.set_defaults(dir = 'vtk')
|
||||
parser.set_defaults(getIncrements= False)
|
||||
parser.set_defaults(homog = '1')
|
||||
parser.set_defaults(cryst = '1')
|
||||
parser.set_defaults(phase = '1')
|
||||
|
||||
(options, files) = parser.parse_args()
|
||||
|
||||
|
||||
# --- sanity checks
|
||||
|
||||
if files == []:
|
||||
parser.print_help()
|
||||
parser.error('no file specified...')
|
||||
|
||||
filename = os.path.splitext(files[0])[0]
|
||||
if not os.path.exists(filename+'.t16'):
|
||||
parser.print_help()
|
||||
parser.error('invalid file "%s" specified...'%filename+'.t16')
|
||||
|
||||
sys.path.append(damask.solver.Marc().libraryPath('../../'))
|
||||
try:
|
||||
import py_post
|
||||
except:
|
||||
print('error: no valid Mentat release found')
|
||||
sys.exit(-1)
|
||||
|
||||
if not options.type :
|
||||
options.type = ['nodebased', 'ipbased']
|
||||
else:
|
||||
options.type = [options.type]
|
||||
|
||||
|
||||
# --- initialize mesh data
|
||||
|
||||
if damask.core.mesh.mesh_init_postprocessing(filename+'.mesh'):
|
||||
print('error: init not successful')
|
||||
sys.exit(-1)
|
||||
|
||||
|
||||
# --- check if ip data available for all elements; if not, then .t19 file is required
|
||||
|
||||
p = py_post.post_open(filename+'.t16')
|
||||
asciiFile = False
|
||||
p.moveto(1)
|
||||
for e in range(p.elements()):
|
||||
if not damask.core.mesh.mesh_get_nodeAtIP(str(p.element(e).type),1):
|
||||
if os.path.exists(filename+'.t19'):
|
||||
p.close()
|
||||
p = py_post.post_open(filename+'.t19')
|
||||
asciiFile = True
|
||||
break
|
||||
|
||||
|
||||
# --- parse *.output and *.t16 file
|
||||
|
||||
outputFormat = ParseOutputFormat(filename,options.homog,options.cryst,options.phase)
|
||||
p.moveto(1)
|
||||
p.extrapolation('translate')
|
||||
stat = ParsePostfile(p,filename,outputFormat,options.legacy)
|
||||
|
||||
|
||||
# --- output info
|
||||
|
||||
if options.info:
|
||||
print '\n\nMentat release %s'%damask.solver.Marc().version('../../')
|
||||
SummarizePostfile(stat)
|
||||
SummarizeOutputfile(outputFormat)
|
||||
sys.exit(0)
|
||||
|
||||
|
||||
# --- create output dir
|
||||
|
||||
dirname = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir))
|
||||
if not os.path.isdir(dirname):
|
||||
os.mkdir(dirname,0755)
|
||||
|
||||
|
||||
# --- get positions
|
||||
|
||||
[increments,locations] = GetIncrementLocations(p,stat['NumberOfIncrements'],options)
|
||||
|
||||
|
||||
# --- loop over positions
|
||||
|
||||
time_start = time.time()
|
||||
for incCount,position in enumerate(locations): # walk through locations
|
||||
p.moveto(position+1) # wind to correct position
|
||||
time_delta = (float(len(locations)) / float(incCount+1) - 1.0) * (time.time() - time_start)
|
||||
sys.stdout.write("\r(%02i:%02i:%02i) processing increment %i of %i..."\
|
||||
%(time_delta//3600,time_delta%3600//60,time_delta%60,incCount+1,len(locations)))
|
||||
sys.stdout.flush()
|
||||
|
||||
# --- write header
|
||||
|
||||
outFilename = {}
|
||||
for geomtype in options.type:
|
||||
outFilename[geomtype] = eval('"'+eval("'%%s_%%s_inc%%0%ii.txt'%(math.log10(max(increments+[1]))+1)")\
|
||||
+'"%(dirname + os.sep + os.path.split(filename)[1],geomtype,increments[incCount])')
|
||||
with open(outFilename[geomtype],'w') as myfile:
|
||||
writeHeader(myfile,stat,geomtype)
|
||||
|
||||
# --- write node based data
|
||||
|
||||
if geomtype == 'nodebased':
|
||||
for n in range(stat['NumberOfNodes']):
|
||||
myfile.write(str(n))
|
||||
for l in range(stat['NumberOfNodalScalars']):
|
||||
myfile.write('\t'+str(p.node_scalar(n,l)))
|
||||
myfile.write('\n')
|
||||
|
||||
# --- write ip based data
|
||||
|
||||
elif geomtype == 'ipbased':
|
||||
for e in range(stat['NumberOfElements']):
|
||||
if asciiFile:
|
||||
print 'ascii postfile not yet supported'
|
||||
sys.exit(-1)
|
||||
else:
|
||||
ipData = [[]]
|
||||
for l in range(stat['NumberOfElementalScalars']):
|
||||
data = p.element_scalar(e,l)
|
||||
for i in range(len(data)): # at least as many nodes as ips
|
||||
node = damask.core.mesh.mesh_get_nodeAtIP(str(p.element(e).type),i+1) # fortran indexing starts at 1
|
||||
if not node: break # no more ips
|
||||
while i >= len(ipData): ipData.append([])
|
||||
ipData[i].extend([data[node-1].value]) # python indexing starts at 0
|
||||
for i in range(len(ipData)):
|
||||
myfile.write('\t'.join(map(str,[e,i]+ipData[i]))+'\n')
|
||||
|
||||
p.close()
|
||||
sys.stdout.write("\n")
|
||||
|
|
@ -1,135 +0,0 @@
|
|||
#!/usr/bin/env python
|
||||
# -*- coding: UTF-8 no BOM -*-
|
||||
|
||||
import os,sys,vtk
|
||||
import damask
|
||||
from collections import defaultdict
|
||||
from optparse import OptionParser
|
||||
|
||||
scriptName = os.path.splitext(os.path.basename(__file__))[0]
|
||||
scriptID = ' '.join([scriptName,damask.version])
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
Add scalar and RGB tuples from ASCIItable to existing VTK voxel cloud (.vtu/.vtk).
|
||||
|
||||
""", version = scriptID)
|
||||
|
||||
parser.add_option('-v', '--vtk', dest='vtk', \
|
||||
help = 'VTK file name')
|
||||
parser.add_option('-s', '--scalar', dest='scalar', action='extend', \
|
||||
help = 'scalar values')
|
||||
parser.add_option('-c', '--color', dest='color', action='extend', \
|
||||
help = 'RGB color tuples')
|
||||
|
||||
parser.set_defaults(scalar = [],
|
||||
color = [],
|
||||
render = False,
|
||||
)
|
||||
|
||||
(options, filenames) = parser.parse_args()
|
||||
|
||||
if options.vtk is None or not os.path.exists(options.vtk):
|
||||
parser.error('VTK file does not exist')
|
||||
|
||||
if os.path.splitext(options.vtk)[1] == '.vtu':
|
||||
reader = vtk.vtkXMLUnstructuredGridReader()
|
||||
reader.SetFileName(options.vtk)
|
||||
reader.Update()
|
||||
uGrid = reader.GetOutput()
|
||||
elif os.path.splitext(options.vtk)[1] == '.vtk':
|
||||
reader = vtk.vtkGenericDataObjectReader()
|
||||
reader.SetFileName(options.vtk)
|
||||
reader.Update()
|
||||
uGrid = reader.GetUnstructuredGridOutput()
|
||||
else:
|
||||
parser.error('unsupported VTK file type extension')
|
||||
|
||||
Npoints = uGrid.GetNumberOfPoints()
|
||||
Ncells = uGrid.GetNumberOfCells()
|
||||
|
||||
sys.stderr.write('{}: {} points and {} cells...\n'.format(damask.util.emph(options.vtk),Npoints,Ncells))
|
||||
|
||||
# --- loop over input files -------------------------------------------------------------------------
|
||||
|
||||
if filenames == []: filenames = [None]
|
||||
|
||||
for name in filenames:
|
||||
try:
|
||||
table = damask.ASCIItable(name = name,
|
||||
buffered = False, readonly = True)
|
||||
except: continue
|
||||
damask.util.croak(damask.util.emph(scriptName)+(': '+name if name else ''))
|
||||
|
||||
# --- interpret header ----------------------------------------------------------------------------
|
||||
|
||||
table.head_read()
|
||||
|
||||
remarks = []
|
||||
errors = []
|
||||
VTKarray = {}
|
||||
active = defaultdict(list)
|
||||
|
||||
for datatype,dimension,label in [['scalar',1,options.scalar],
|
||||
['color',3,options.color],
|
||||
]:
|
||||
for i,dim in enumerate(table.label_dimension(label)):
|
||||
me = label[i]
|
||||
if dim == -1: remarks.append('{} "{}" not found...'.format(datatype,me))
|
||||
elif dim > dimension: remarks.append('"{}" not of dimension{}...'.format(me,dimension))
|
||||
else:
|
||||
damask.util.croak('adding {} {}'.format(datatype,me))
|
||||
active[datatype].append(me)
|
||||
|
||||
if datatype in ['scalar']:
|
||||
VTKarray[me] = vtk.vtkDoubleArray()
|
||||
elif datatype == 'color':
|
||||
VTKarray[me] = vtk.vtkUnsignedCharArray()
|
||||
|
||||
VTKarray[me].SetNumberOfComponents(dimension)
|
||||
VTKarray[me].SetName(label[i])
|
||||
|
||||
if remarks != []: damask.util.croak(remarks)
|
||||
if errors != []:
|
||||
damask.util.croak(errors)
|
||||
table.close(dismiss=True)
|
||||
continue
|
||||
|
||||
# ------------------------------------------ process data ---------------------------------------
|
||||
|
||||
while table.data_read(): # read next data line of ASCII table
|
||||
|
||||
for datatype,labels in active.items(): # loop over scalar,color
|
||||
for me in labels: # loop over all requested items
|
||||
theData = [table.data[i] for i in table.label_indexrange(me)] # read strings
|
||||
if datatype == 'color':
|
||||
VTKarray[me].InsertNextTuple3(*map(lambda x: int(255.*float(x)),theData))
|
||||
elif datatype == 'scalar':
|
||||
VTKarray[me].InsertNextValue(float(theData[0]))
|
||||
|
||||
# ------------------------------------------ add data ---------------------------------------
|
||||
|
||||
for datatype,labels in active.items(): # loop over scalar,color
|
||||
if datatype == 'color':
|
||||
uGrid.GetCellData().SetScalars(VTKarray[active['color'][0]])
|
||||
for label in labels: # loop over all requested items
|
||||
uGrid.GetCellData().AddArray(VTKarray[me])
|
||||
|
||||
uGrid.Modified()
|
||||
if vtk.VTK_MAJOR_VERSION <= 5:
|
||||
uGrid.Update()
|
||||
|
||||
# ------------------------------------------ output result ---------------------------------------
|
||||
|
||||
writer = vtk.vtkXMLUnstructuredGridWriter()
|
||||
writer.SetDataModeToBinary()
|
||||
writer.SetCompressorTypeToZLib()
|
||||
writer.SetFileName(os.path.splitext(options.vtk)[0]+'_added.vtu')
|
||||
if vtk.VTK_MAJOR_VERSION <= 5:
|
||||
writer.SetInput(uGrid)
|
||||
else:
|
||||
writer.SetInputData(uGrid)
|
||||
writer.Write()
|
||||
|
|
@ -1,122 +0,0 @@
|
|||
#!/usr/bin/env python
|
||||
# -*- coding: UTF-8 no BOM -*-
|
||||
|
||||
import os,sys,shutil
|
||||
import damask
|
||||
from optparse import OptionParser
|
||||
import vtk
|
||||
|
||||
scriptName = os.path.splitext(os.path.basename(__file__))[0]
|
||||
scriptID = ' '.join([scriptName,damask.version])
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
|
||||
""", version = scriptID)
|
||||
|
||||
parser.add_option('-v','--vector', nargs=3, dest='vector', \
|
||||
help='suffices indicating vector components [%default]')
|
||||
parser.add_option('-s','--separator', dest='separator', \
|
||||
help='separator between label and suffix [%default]')
|
||||
|
||||
parser.set_defaults(vector = ['x','y','z'])
|
||||
parser.set_defaults(separator = '.')
|
||||
|
||||
(options, filenames) = parser.parse_args()
|
||||
|
||||
|
||||
# --- sanity checks
|
||||
|
||||
if filenames == []:
|
||||
parser.print_help()
|
||||
parser.error('no file specified...')
|
||||
|
||||
for filename in filenames:
|
||||
if not os.path.isfile(filename):
|
||||
parser.print_help()
|
||||
parser.error('invalid file "%s" specified...'%filename)
|
||||
|
||||
|
||||
# --- ITERATE OVER FILES AND PROCESS THEM
|
||||
|
||||
for filename in filenames:
|
||||
|
||||
sys.stdout.write('read file "%s" ...'%filename)
|
||||
sys.stdout.flush()
|
||||
suffix = os.path.splitext(filename)[1]
|
||||
if suffix == '.vtk':
|
||||
reader = vtk.vtkUnstructuredGridReader()
|
||||
reader.ReadAllScalarsOn()
|
||||
reader.ReadAllVectorsOn()
|
||||
reader.ReadAllTensorsOn()
|
||||
elif suffix == '.vtu':
|
||||
reader = vtk.vtkXMLUnstructuredGridReader()
|
||||
else:
|
||||
parser.error('filetype "%s" not supported'%suffix)
|
||||
reader.SetFileName(filename)
|
||||
reader.Update()
|
||||
uGrid = reader.GetOutput()
|
||||
sys.stdout.write(' done\n')
|
||||
sys.stdout.flush()
|
||||
|
||||
|
||||
# Read the scalar data
|
||||
|
||||
scalarData = {}
|
||||
scalarsToBeRemoved = []
|
||||
Nscalars = uGrid.GetCellData().GetNumberOfArrays()
|
||||
for i in range(Nscalars):
|
||||
sys.stdout.write("\rread scalar data %d%%" %(100*i/Nscalars))
|
||||
sys.stdout.flush()
|
||||
scalarName = uGrid.GetCellData().GetArrayName(i)
|
||||
if scalarName.split(options.separator)[-1] in options.vector:
|
||||
label,suffix = scalarName.split(options.separator)
|
||||
if label not in scalarData:
|
||||
scalarData[label] = [[],[],[]]
|
||||
uGrid.GetCellData().SetActiveScalars(scalarName)
|
||||
scalarData[label][options.vector.index(suffix)] = uGrid.GetCellData().GetScalars(scalarName)
|
||||
scalarsToBeRemoved.append(scalarName)
|
||||
for scalarName in scalarsToBeRemoved:
|
||||
uGrid.GetCellData().RemoveArray(scalarName)
|
||||
sys.stdout.write('\rread scalar data done\n')
|
||||
sys.stdout.flush()
|
||||
|
||||
|
||||
# Convert the scalar data to vector data
|
||||
|
||||
NscalarData = len(scalarData)
|
||||
for n,label in enumerate(scalarData):
|
||||
sys.stdout.write("\rconvert to vector data %d%%" %(100*n/NscalarData))
|
||||
sys.stdout.flush()
|
||||
Nvalues = scalarData[label][0].GetNumberOfTuples()
|
||||
vectorData = vtk.vtkDoubleArray()
|
||||
vectorData.SetName(label)
|
||||
vectorData.SetNumberOfComponents(3) # set this before NumberOfTuples !!!
|
||||
vectorData.SetNumberOfTuples(Nvalues)
|
||||
for i in range(Nvalues):
|
||||
for j in range(3):
|
||||
vectorData.SetComponent(i,j,scalarData[label][j].GetValue(i))
|
||||
uGrid.GetCellData().AddArray(vectorData)
|
||||
sys.stdout.write('\rconvert to vector data done\n')
|
||||
|
||||
|
||||
# Write to new vtk file
|
||||
|
||||
outfilename = os.path.splitext(filename)[0]+'.vtu'
|
||||
sys.stdout.write('write to file "%s" ...'%outfilename)
|
||||
sys.stdout.flush()
|
||||
writer = vtk.vtkXMLUnstructuredGridWriter()
|
||||
writer.SetFileName(outfilename+'_tmp')
|
||||
writer.SetDataModeToAscii()
|
||||
writer.SetInput(uGrid)
|
||||
writer.Write()
|
||||
sys.stdout.write(' done\n')
|
||||
sys.stdout.flush()
|
||||
shutil.move(outfilename+'_tmp',outfilename)
|
||||
|
||||
|
||||
|
||||
# --------------------------- DONE --------------------------------
|
||||
|
|
@ -1,118 +0,0 @@
|
|||
#!/usr/bin/env python
|
||||
# -*- coding: UTF-8 no BOM -*-
|
||||
|
||||
import os,sys,vtk
|
||||
import numpy as np
|
||||
from optparse import OptionParser
|
||||
import damask
|
||||
|
||||
scriptName = os.path.splitext(os.path.basename(__file__))[0]
|
||||
scriptID = ' '.join([scriptName,damask.version])
|
||||
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# MAIN
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
Create hexahedral voxels around points in an ASCIItable.
|
||||
|
||||
""", version = scriptID)
|
||||
|
||||
parser.add_option('-d', '--deformed',
|
||||
dest = 'deformed',
|
||||
type = 'string', metavar = 'string',
|
||||
help = 'deformed coordinate label [%default]')
|
||||
parser.add_option('-c','--coordinates',
|
||||
dest = 'coords',
|
||||
type = 'string', metavar='string',
|
||||
help = 'undeformed coordinates label [%default]')
|
||||
parser.set_defaults(deformed = 'ipdeformedcoord',
|
||||
coords = 'ipinitialcoord',
|
||||
)
|
||||
|
||||
(options, filenames) = parser.parse_args()
|
||||
|
||||
|
||||
# --- loop over input files -------------------------------------------------------------------------
|
||||
|
||||
if filenames == []: filenames = [None]
|
||||
|
||||
for name in filenames:
|
||||
try:
|
||||
table = damask.ASCIItable(name = name,
|
||||
buffered = False, readonly = True)
|
||||
except: continue
|
||||
damask.util.report(scriptName,name)
|
||||
|
||||
# --------------- interprete header -----------------------------------------------------------------
|
||||
table.head_read()
|
||||
errors=[]
|
||||
if table.label_dimension(options.deformed) != 3:
|
||||
errors.append('columns "{}" have dimension {}'.format(options.deformed,table.label_dimension(options.deformed)))
|
||||
if table.label_dimension(options.coords) != 3:
|
||||
errors.append('coordinates {} are not a vector.'.format(options.coords))
|
||||
|
||||
table.data_readArray([options.coords,options.deformed])
|
||||
|
||||
# --------------- figure out size and grid ---------------------------------------------------------
|
||||
coords = [{},{},{}]
|
||||
for i in xrange(len(table.data)):
|
||||
for j in xrange(3):
|
||||
coords[j][str(table.data[i,table.label_index(options.coords)+j])] = True
|
||||
grid = np.array(map(len,coords),'i')
|
||||
size = grid/np.maximum(np.ones(3,'d'),grid-1.0)* \
|
||||
np.array([max(map(float,coords[0].keys()))-min(map(float,coords[0].keys())),\
|
||||
max(map(float,coords[1].keys()))-min(map(float,coords[1].keys())),\
|
||||
max(map(float,coords[2].keys()))-min(map(float,coords[2].keys())),\
|
||||
],'d') # size from bounding box, corrected for cell-centeredness
|
||||
|
||||
size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 set to smallest among other spacings
|
||||
|
||||
# ------------------------------------------ process data ---------------------------------------
|
||||
hexPoints = np.array([[-1,-1,-1],
|
||||
[ 1,-1,-1],
|
||||
[ 1, 1,-1],
|
||||
[-1, 1,-1],
|
||||
[-1,-1, 1],
|
||||
[ 1,-1, 1],
|
||||
[ 1, 1, 1],
|
||||
[-1, 1, 1],
|
||||
])
|
||||
|
||||
halfDelta = 0.5*size/grid
|
||||
|
||||
Points = vtk.vtkPoints()
|
||||
Hex = vtk.vtkHexahedron()
|
||||
uGrid = vtk.vtkUnstructuredGrid()
|
||||
|
||||
for p in table.data:
|
||||
for i,h in enumerate(hexPoints):
|
||||
pointID = Points.InsertNextPoint(p[table.label_index(options.deformed):table.label_index(options.deformed)+3]+h*halfDelta)
|
||||
Hex.GetPointIds().SetId(i,pointID)
|
||||
|
||||
uGrid.InsertNextCell(Hex.GetCellType(), Hex.GetPointIds())
|
||||
|
||||
uGrid.SetPoints(Points)
|
||||
|
||||
# ------------------------------------------ output result ---------------------------------------
|
||||
|
||||
if name:
|
||||
writer = vtk.vtkXMLUnstructuredGridWriter()
|
||||
(directory,filename) = os.path.split(name)
|
||||
writer.SetDataModeToBinary()
|
||||
writer.SetCompressorTypeToZLib()
|
||||
writer.SetFileName(os.path.join(directory,os.path.splitext(filename)[0]\
|
||||
+'.'+writer.GetDefaultFileExtension()))
|
||||
else:
|
||||
writer = vtk.vtkDataSetWriter()
|
||||
writer.WriteToOutputStringOn()
|
||||
writer.SetHeader('# powered by '+scriptID)
|
||||
|
||||
if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(uGrid)
|
||||
else: writer.SetInputData(uGrid)
|
||||
writer.Write()
|
||||
if name is None: sys.stdout.write(writer.GetOutputString()[0:writer.GetOutputStringLength()])
|
||||
|
||||
table.close() # close input ASCII table
|
||||
|
||||
|
|
@ -1,110 +0,0 @@
|
|||
#!/usr/bin/env python
|
||||
# -*- coding: UTF-8 no BOM -*-
|
||||
|
||||
import os,sys,math
|
||||
import numpy as np
|
||||
from optparse import OptionParser
|
||||
from PIL import Image
|
||||
import damask
|
||||
|
||||
scriptName = os.path.splitext(os.path.basename(__file__))[0]
|
||||
scriptID = ' '.join([scriptName,damask.version])
|
||||
|
||||
#--------------------------------------------------------------------------------------------------
|
||||
# MAIN
|
||||
#--------------------------------------------------------------------------------------------------
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
|
||||
|
||||
Generate geometry description from (multilayer) images.
|
||||
Microstructure index is based on gray scale value (1..256).
|
||||
|
||||
""", version = scriptID)
|
||||
|
||||
parser.add_option('--homogenization',
|
||||
dest = 'homogenization',
|
||||
type = 'int', metavar = 'int',
|
||||
help = 'homogenization index [%default]')
|
||||
|
||||
parser.set_defaults(homogenization = 1,
|
||||
)
|
||||
|
||||
(options,filenames) = parser.parse_args()
|
||||
|
||||
# --- loop over input files -------------------------------------------------------------------------
|
||||
|
||||
if filenames == []: filenames = [None]
|
||||
|
||||
for name in filenames:
|
||||
try:
|
||||
table = damask.ASCIItable(name = name,
|
||||
outname = os.path.splitext(name)[0]+'.geom' if name else name,
|
||||
buffered = False, labeled = False)
|
||||
except: continue
|
||||
table.croak('\033[1m'+scriptName+'\033[0m'+(': '+name if name else ''))
|
||||
|
||||
# --- read image ------------------------------------------------------------------------------------
|
||||
|
||||
img = Image.open(name).convert(mode = 'L') # open and convert to grayscale 8bit
|
||||
|
||||
slice = 0
|
||||
while True:
|
||||
try:
|
||||
img.seek(slice) # advance to slice
|
||||
layer = np.expand_dims(1+np.array(img,dtype = 'uint16'),axis = 0) # read image layer
|
||||
microstructure = layer if slice == 0 else np.vstack((microstructure,layer)) # noqa
|
||||
slice += 1 # advance to next slice
|
||||
except EOFError:
|
||||
break
|
||||
|
||||
# http://docs.scipy.org/doc/scipy/reference/ndimage.html
|
||||
# http://scipy-lectures.github.io/advanced/image_processing/
|
||||
|
||||
info = {
|
||||
'grid': np.array(microstructure.shape,'i')[::-1],
|
||||
'size': np.array(microstructure.shape,'d')[::-1],
|
||||
'origin': np.zeros(3,'d'),
|
||||
'microstructures': len(np.unique(microstructure)),
|
||||
'homogenization': options.homogenization,
|
||||
}
|
||||
|
||||
# --- report ---------------------------------------------------------------------------------------
|
||||
|
||||
table.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))),
|
||||
'size x y z: %s'%(' x '.join(map(str,info['size']))),
|
||||
'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
|
||||
'homogenization: %i'%info['homogenization'],
|
||||
'microstructures: %i'%info['microstructures'],
|
||||
])
|
||||
|
||||
errors = []
|
||||
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
|
||||
if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.')
|
||||
if errors != []:
|
||||
table.croak(errors)
|
||||
table.close(dismiss = True)
|
||||
continue
|
||||
|
||||
# --- write header ---------------------------------------------------------------------------------
|
||||
|
||||
table.info_clear()
|
||||
table.info_append([
|
||||
scriptID + ' ' + ' '.join(sys.argv[1:]),
|
||||
"grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=info['grid']),
|
||||
"size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=info['size']),
|
||||
"origin\tx {origin[0]}\ty {origin[1]}\tz {origin[2]}".format(origin=info['origin']),
|
||||
"homogenization\t{homog}".format(homog=info['homogenization']),
|
||||
"microstructures\t{microstructures}".format(microstructures=info['microstructures']),
|
||||
])
|
||||
table.labels_clear()
|
||||
table.head_write()
|
||||
table.output_flush()
|
||||
|
||||
# --- write microstructure information ------------------------------------------------------------
|
||||
|
||||
formatwidth = int(math.floor(math.log10(microstructure.max())+1))
|
||||
table.data = microstructure.reshape((info['grid'][1]*info['grid'][2],info['grid'][0]),order='C')
|
||||
table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ')
|
||||
|
||||
# --- output finalization --------------------------------------------------------------------------
|
||||
|
||||
table.close() # close ASCII table
|
||||
Loading…
Reference in New Issue