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DAMASK_EICMD
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cleaning

This commit is contained in:
Martin Diehl 2016-03-03 14:53:55 +01:00
parent 76a0a93c42
commit a51f2a29f6
4 changed files with 42 additions and 93 deletions
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5
processing/misc/ang_toTable.py
View File

@ -1,8 +1,7 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string,vtk
import numpy as np
import os
from optparse import OptionParser
import damask
@ -48,7 +47,7 @@ for name in filenames:
table.labels_append(['1_Euler','2_Euler','3_Euler',
'1_pos','2_pos',
'IQ','CI','PhaseID','Intensity','Fit',
], # labels according to OIM Analysis 7.2 Manual, p 403 (of 517)
], # OIM Analysis 7.2 Manual, p 403 (of 517)
reset = True)
# ------------------------------------------ assemble header ---------------------------------------

54
processing/misc/calculateAnisotropy.py
View File

@ -1,9 +1,9 @@
#!/usr/bin/python
# -*- coding: UTF-8 no BOM -*-
import threading,time,os,subprocess,shlex,string
import threading,os,string
import numpy as np
from optparse import OptionParser, OptionGroup
from optparse import OptionParser
from shutil import copy2
from re import split
import damask
@ -14,26 +14,10 @@ scriptID = ' '.join([scriptName,damask.version])
def list_split(option, opt, value, parser):
setattr(parser.values, option.dest, value.split(','))
def execute(cmd,streamIn=None,wd='./'):
'''
executes a command in given directory and returns stdout and stderr for optional stdin
'''
initialPath=os.getcwd()
os.chdir(wd)
process = subprocess.Popen(shlex.split(cmd),stdout=subprocess.PIPE,stderr = subprocess.PIPE,stdin=subprocess.PIPE)
if streamIn != None:
out,error = process.communicate(streamIn.read())
else:
out,error = process.communicate()
os.chdir(initialPath)
return out,error
#---------------------------------------------------------------------------------------------------
class myThread (threading.Thread):
#---------------------------------------------------------------------------------------------------
'''
Runner class
'''
"""Runner"""
def __init__(self, threadID):
threading.Thread.__init__(self)
self.threadID = threadID
@ -48,8 +32,6 @@ class myThread (threading.Thread):
s.release()
def doSim(delay,thread):
# s.acquire() and s.release() are couple
#
global dirCurrent
s.acquire()
delta_angle = offsetPhi()
@ -63,22 +45,22 @@ def doSim(delay,thread):
os.mkdir(dire,0755)
for file in [options.geometry+'.geom',options.load+'.load','numerics.config']:
copy2(dirCurrent+'/'+file, dire)
newMatConfig = newMaterialConfig(dirCurrent,delta_angle)
newMaterialConfig(dirCurrent,delta_angle)
os.chdir(dire)
if not os.path.isfile('%s_%s.spectralOut'%(options.geometry,options.load)):
print('starting uniaxial tension in direction of angle %s from %s'%(file_angle,thread))
s.release()
execute('DAMASK_spectral -g %s -l %s'%(options.geometry,options.load))
damask.util.execute('DAMASK_spectral -g %s -l %s'%(options.geometry,options.load))
else: s.release()
s.acquire()
if not os.path.isfile('./%s/%s_%s.txt'%('Rvalues',options.geometry,options.load)):
print('starting post processing for angle %s from %s'%(file_angle,thread))
s.release()
execute('postResults --cr f,p -d %s %s_%s.spectralOut'%('Rvalues',options.geometry,options.load))
execute('addCauchy ./%s/%s_%s.txt'%('Rvalues',options.geometry,options.load))
execute('addStrainTensors -l -v ./%s/%s_%s.txt'%('Rvalues',options.geometry,options.load))
damask.util.execute('postResults --cr f,p -d %s %s_%s.spectralOut'%('Rvalues',options.geometry,options.load))
damask.util.execute('addCauchy ./%s/%s_%s.txt'%('Rvalues',options.geometry,options.load))
damask.util.execute('addStrainTensors -l -v ./%s/%s_%s.txt'%('Rvalues',options.geometry,options.load))
print('post processing for angle %s from %s is finished'%(file_angle,thread))
else:
@ -122,7 +104,6 @@ def newMaterialConfig(dire,angle):
line2 = line
f.write(line2)
f.close()
return True
# --------------------------------------------------------------------
# MAIN
@ -135,15 +116,20 @@ strength anisotropic coefficients (normalized yield stress)
""", version=string.replace(scriptID,'\n','\\n')
)
parser.add_option('-l','--load' , dest='load', type='string',
parser.add_option('-l','--load' ,
dest='load', type='string',
help='name of the load file [%default]', metavar='string')
parser.add_option('-g','--geometry', dest='geometry', type='string',
parser.add_option('-g','--geometry',
dest='geometry', type='string',
help='name of the geometry file [%default]', metavar='string')
parser.add_option('-s', '--strain', dest='strain', type='string', action='callback', callback=list_split,
help='the threshold strains, using comma to seperate multiple strains [%default]', metavar='string')
parser.add_option('-t','--threads', dest='threads', type='int',
parser.add_option('-s', '--strain',
dest='strain', type='string', action='callback', callback=list_split,
help='threshold strains, using comma to seperate multiple strains [%default]', metavar='string')
parser.add_option('-t','--threads',
dest='threads', type='int',
help='number of parallel executions [%default]', metavar='int')
parser.add_option('-n','--number', dest='number', type='int',
parser.add_option('-n','--number',
dest='number', type='int',
help='Number of uni-axial tensile tests [%default]', metavar='int')
parser.set_defaults(geometry = '20grains16x16x16')

30
processing/misc/gwyddion_filter.py
View File

@ -1,33 +1,15 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string,re,numpy,scipy.ndimage,scipy.signal,vtk
import os,string,scipy
import numpy as np
import damask
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
from optparse import OptionParser
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
class extendedOption(Option):
#--------------------------------------------------------------------------------------------------
# used for definition of new option parser action 'extend', which enables to take multiple option arguments
# taken from online tutorial http://docs.python.org/library/optparse.html
ACTIONS = Option.ACTIONS + ("extend",)
STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
def take_action(self, action, dest, opt, value, values, parser):
if action == "extend":
lvalue = value.split(",")
values.ensure_value(dest, []).extend(lvalue)
else:
Option.take_action(self, action, dest, opt, value, values, parser)
parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Apply filter(s) to Gwyddion data.
""" + string.replace(scriptID,'\n','\\n')
)
@ -59,7 +41,7 @@ for file in filenames:
if pieces[1] == 'Height:': height = float(pieces[2])
header.append(line.lstrip('#').strip())
elevation = numpy.loadtxt(file)#*1e6
elevation = np.loadtxt(file)#*1e6
if options.opening > 0:
elevation = scipy.ndimage.morphology.grey_opening(elevation,options.opening)
@ -80,5 +62,5 @@ for file in filenames:
elevation = scipy.ndimage.filters.median_filter(elevation,options.median)
filters += '_median%i'%options.median
numpy.savetxt(os.path.splitext(file)[0]+filters+os.path.splitext(file)[1],elevation,header='\n'.join(header))
np.savetxt(os.path.splitext(file)[0]+filters+os.path.splitext(file)[1],elevation,header='\n'.join(header))

36
processing/misc/vtk_fromGwyddion.py
View File

@ -1,9 +1,10 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string,re,numpy,scipy.ndimage,scipy.signal,vtk
import os,string,vtk
import numpy as np
import damask
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
from optparse import OptionParser
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
@ -26,26 +27,7 @@ scalingFactor = { \
},
}
#--------------------------------------------------------------------------------------------------
class extendedOption(Option):
#--------------------------------------------------------------------------------------------------
# used for definition of new option parser action 'extend', which enables to take multiple option arguments
# taken from online tutorial http://docs.python.org/library/optparse.html
ACTIONS = Option.ACTIONS + ("extend",)
STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
def take_action(self, action, dest, opt, value, values, parser):
if action == "extend":
lvalue = value.split(",")
values.ensure_value(dest, []).extend(lvalue)
else:
Option.take_action(self, action, dest, opt, value, values, parser)
parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Produce VTK rectilinear grid from Gwyddion dataset exported as text.
""" + string.replace(scriptID,'\n','\\n')
)
@ -78,16 +60,16 @@ for file in filenames:
if options.scaling == 0.0:
options.scaling = scalingFactor[lateralunit][elevationunit]
elevation = numpy.loadtxt(file)*options.scaling
elevation = np.loadtxt(file)*options.scaling
grid = vtk.vtkRectilinearGrid()
grid.SetDimensions(elevation.shape[1],elevation.shape[0],1)
xCoords = vtk.vtkDoubleArray()
for x in numpy.arange(0.0,width,width/elevation.shape[1],'d'):
for x in np.arange(0.0,width,width/elevation.shape[1],'d'):
xCoords.InsertNextValue(x)
yCoords = vtk.vtkDoubleArray()
for y in numpy.arange(0.0,height,height/elevation.shape[0],'d'):
for y in np.arange(0.0,height,height/elevation.shape[0],'d'):
yCoords.InsertNextValue(y)
zCoords = vtk.vtkDoubleArray()
zCoords.InsertNextValue(0.0)
@ -99,8 +81,8 @@ for file in filenames:
vector = vtk.vtkFloatArray()
vector.SetName("elevation");
vector.SetNumberOfComponents(3);
vector.SetNumberOfTuples(numpy.prod(elevation.shape));
for i,z in enumerate(numpy.ravel(elevation)):
vector.SetNumberOfTuples(np.prod(elevation.shape));
for i,z in enumerate(np.ravel(elevation)):
vector.SetTuple3(i,0,0,z)
grid.GetPointData().AddArray(vector)