cleaning
This commit is contained in:
Martin Diehl
parent
76a0a93c42
commit
a51f2a29f6
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@ -1,8 +1,7 @@
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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,vtk
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import numpy as np
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import os
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from optparse import OptionParser
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import damask
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@ -48,7 +47,7 @@ for name in filenames:
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table.labels_append(['1_Euler','2_Euler','3_Euler',
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'1_pos','2_pos',
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'IQ','CI','PhaseID','Intensity','Fit',
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], # labels according to OIM Analysis 7.2 Manual, p 403 (of 517)
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], # OIM Analysis 7.2 Manual, p 403 (of 517)
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reset = True)
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# ------------------------------------------ assemble header ---------------------------------------
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@ -1,9 +1,9 @@
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#!/usr/bin/python
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# -*- coding: UTF-8 no BOM -*-
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import threading,time,os,subprocess,shlex,string
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import threading,os,string
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import numpy as np
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from optparse import OptionParser, OptionGroup
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from optparse import OptionParser
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from shutil import copy2
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from re import split
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import damask
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@ -14,26 +14,10 @@ scriptID = ' '.join([scriptName,damask.version])
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def list_split(option, opt, value, parser):
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setattr(parser.values, option.dest, value.split(','))
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def execute(cmd,streamIn=None,wd='./'):
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'''
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executes a command in given directory and returns stdout and stderr for optional stdin
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'''
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initialPath=os.getcwd()
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os.chdir(wd)
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process = subprocess.Popen(shlex.split(cmd),stdout=subprocess.PIPE,stderr = subprocess.PIPE,stdin=subprocess.PIPE)
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if streamIn != None:
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out,error = process.communicate(streamIn.read())
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else:
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out,error = process.communicate()
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os.chdir(initialPath)
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return out,error
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#---------------------------------------------------------------------------------------------------
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class myThread (threading.Thread):
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#---------------------------------------------------------------------------------------------------
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'''
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Runner class
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'''
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"""Runner"""
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def __init__(self, threadID):
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threading.Thread.__init__(self)
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self.threadID = threadID
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@ -48,8 +32,6 @@ class myThread (threading.Thread):
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s.release()
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def doSim(delay,thread):
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# s.acquire() and s.release() are couple
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#
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global dirCurrent
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s.acquire()
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delta_angle = offsetPhi()
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@ -63,22 +45,22 @@ def doSim(delay,thread):
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os.mkdir(dire,0755)
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for file in [options.geometry+'.geom',options.load+'.load','numerics.config']:
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copy2(dirCurrent+'/'+file, dire)
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newMatConfig = newMaterialConfig(dirCurrent,delta_angle)
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newMaterialConfig(dirCurrent,delta_angle)
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os.chdir(dire)
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if not os.path.isfile('%s_%s.spectralOut'%(options.geometry,options.load)):
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print('starting uniaxial tension in direction of angle %s from %s'%(file_angle,thread))
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s.release()
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execute('DAMASK_spectral -g %s -l %s'%(options.geometry,options.load))
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damask.util.execute('DAMASK_spectral -g %s -l %s'%(options.geometry,options.load))
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else: s.release()
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s.acquire()
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if not os.path.isfile('./%s/%s_%s.txt'%('Rvalues',options.geometry,options.load)):
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print('starting post processing for angle %s from %s'%(file_angle,thread))
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s.release()
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execute('postResults --cr f,p -d %s %s_%s.spectralOut'%('Rvalues',options.geometry,options.load))
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execute('addCauchy ./%s/%s_%s.txt'%('Rvalues',options.geometry,options.load))
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execute('addStrainTensors -l -v ./%s/%s_%s.txt'%('Rvalues',options.geometry,options.load))
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damask.util.execute('postResults --cr f,p -d %s %s_%s.spectralOut'%('Rvalues',options.geometry,options.load))
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damask.util.execute('addCauchy ./%s/%s_%s.txt'%('Rvalues',options.geometry,options.load))
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damask.util.execute('addStrainTensors -l -v ./%s/%s_%s.txt'%('Rvalues',options.geometry,options.load))
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print('post processing for angle %s from %s is finished'%(file_angle,thread))
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else:
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@ -122,7 +104,6 @@ def newMaterialConfig(dire,angle):
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line2 = line
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f.write(line2)
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f.close()
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return True
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# --------------------------------------------------------------------
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# MAIN
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@ -135,16 +116,21 @@ strength anisotropic coefficients (normalized yield stress)
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""", version=string.replace(scriptID,'\n','\\n')
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)
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parser.add_option('-l','--load' , dest='load', type='string',
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help='name of the load file [%default]', metavar='string')
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parser.add_option('-g','--geometry', dest='geometry', type='string',
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help='name of the geometry file [%default]', metavar='string')
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parser.add_option('-s', '--strain', dest='strain', type='string', action='callback', callback=list_split,
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help='the threshold strains, using comma to seperate multiple strains [%default]', metavar='string')
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parser.add_option('-t','--threads', dest='threads', type='int',
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help='number of parallel executions [%default]', metavar='int')
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parser.add_option('-n','--number', dest='number', type='int',
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help='Number of uni-axial tensile tests [%default]', metavar='int')
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parser.add_option('-l','--load' ,
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dest='load', type='string',
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help='name of the load file [%default]', metavar='string')
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parser.add_option('-g','--geometry',
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dest='geometry', type='string',
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help='name of the geometry file [%default]', metavar='string')
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parser.add_option('-s', '--strain',
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dest='strain', type='string', action='callback', callback=list_split,
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help='threshold strains, using comma to seperate multiple strains [%default]', metavar='string')
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parser.add_option('-t','--threads',
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dest='threads', type='int',
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help='number of parallel executions [%default]', metavar='int')
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parser.add_option('-n','--number',
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dest='number', type='int',
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help='Number of uni-axial tensile tests [%default]', metavar='int')
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parser.set_defaults(geometry = '20grains16x16x16')
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parser.set_defaults(load = 'tensionX')
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@ -248,4 +234,4 @@ for i in xrange(2):
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aniso_list_ang_strain.append('none')
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writeformat = writeformat+'%-12s'
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f.write('%-10s'%file_angle + writeformat%(tuple(aniso_list_ang_strain))+'\n')
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f.close()
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f.close()
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@ -1,33 +1,15 @@
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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,scipy.ndimage,scipy.signal,vtk
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import os,string,scipy
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import numpy as np
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import damask
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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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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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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parser = OptionParser(option_class=extendedOption, 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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Apply filter(s) to Gwyddion data.
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""" + string.replace(scriptID,'\n','\\n')
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)
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@ -59,7 +41,7 @@ for file in filenames:
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if pieces[1] == 'Height:': height = float(pieces[2])
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header.append(line.lstrip('#').strip())
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elevation = numpy.loadtxt(file)#*1e6
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elevation = np.loadtxt(file)#*1e6
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if options.opening > 0:
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elevation = scipy.ndimage.morphology.grey_opening(elevation,options.opening)
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elevation = scipy.ndimage.filters.median_filter(elevation,options.median)
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filters += '_median%i'%options.median
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numpy.savetxt(os.path.splitext(file)[0]+filters+os.path.splitext(file)[1],elevation,header='\n'.join(header))
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np.savetxt(os.path.splitext(file)[0]+filters+os.path.splitext(file)[1],elevation,header='\n'.join(header))
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@ -1,9 +1,10 @@
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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,scipy.ndimage,scipy.signal,vtk
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import os,string,vtk
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import numpy as np
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import damask
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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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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@ -26,26 +27,7 @@ scalingFactor = { \
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},
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}
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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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parser = OptionParser(option_class=extendedOption, 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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Produce VTK rectilinear grid from Gwyddion dataset exported as text.
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""" + string.replace(scriptID,'\n','\\n')
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)
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@ -78,16 +60,16 @@ for file in filenames:
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if options.scaling == 0.0:
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options.scaling = scalingFactor[lateralunit][elevationunit]
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elevation = numpy.loadtxt(file)*options.scaling
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elevation = np.loadtxt(file)*options.scaling
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grid = vtk.vtkRectilinearGrid()
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grid.SetDimensions(elevation.shape[1],elevation.shape[0],1)
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xCoords = vtk.vtkDoubleArray()
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for x in numpy.arange(0.0,width,width/elevation.shape[1],'d'):
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for x in np.arange(0.0,width,width/elevation.shape[1],'d'):
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xCoords.InsertNextValue(x)
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yCoords = vtk.vtkDoubleArray()
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for y in numpy.arange(0.0,height,height/elevation.shape[0],'d'):
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for y in np.arange(0.0,height,height/elevation.shape[0],'d'):
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yCoords.InsertNextValue(y)
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zCoords = vtk.vtkDoubleArray()
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zCoords.InsertNextValue(0.0)
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@ -99,8 +81,8 @@ for file in filenames:
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vector = vtk.vtkFloatArray()
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vector.SetName("elevation");
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vector.SetNumberOfComponents(3);
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vector.SetNumberOfTuples(numpy.prod(elevation.shape));
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for i,z in enumerate(numpy.ravel(elevation)):
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vector.SetNumberOfTuples(np.prod(elevation.shape));
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for i,z in enumerate(np.ravel(elevation)):
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vector.SetTuple3(i,0,0,z)
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grid.GetPointData().AddArray(vector)
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