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DAMASK_EICMD
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polishing

This commit is contained in:
Martin Diehl 2014-12-18 19:26:52 +00:00
parent e4cb387571
commit 6604d0f8e8
46 changed files with 184 additions and 343 deletions
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2
processing/post/3Dvisualize.py
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@ -8,7 +8,7 @@ from vtk.util import numpy_support
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
# -----------------------------
class backgroundMessage(threading.Thread):

2
processing/post/addCalculation.py
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@ -7,7 +7,7 @@ from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
def unravel(item):
if hasattr(item,'__contains__'): return ' '.join(map(unravel,item))

2
processing/post/addCauchy.py
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@ -8,7 +8,7 @@ from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN

2
processing/post/addCompatibilityMismatch.py
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@ -7,7 +7,7 @@ from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN

2
processing/post/addCurl.py
View File

@ -8,7 +8,7 @@ from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN

2
processing/post/addDeformedConfiguration.py
View File

@ -8,7 +8,7 @@ from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN

2
processing/post/addDeterminant.py
View File

@ -7,7 +7,7 @@ from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
def determinant(m):
return +m[0]*m[4]*m[8] \

2
processing/post/addDeviator.py
View File

@ -7,7 +7,7 @@ from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
oneThird = 1.0/3.0

2
processing/post/addDivergence.py
View File

@ -8,7 +8,7 @@ from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN

2
processing/post/addEhkl.py
View File

@ -8,7 +8,7 @@ from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
def normalize(vec):
return vec/np.sqrt(np.inner(vec,vec))

2
processing/post/addEuclideanDistance.py
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@ -8,7 +8,7 @@ from scipy import ndimage
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
def periodic_3Dpad(array, rimdim=(1,1,1)):

2
processing/post/addMapped.py
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@ -6,7 +6,7 @@ from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN

2
processing/post/addMises.py
View File

@ -8,7 +8,7 @@ from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
def Mises(what,tensor):

2
processing/post/addNorm.py
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@ -7,7 +7,7 @@ from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
# definition of element-wise p-norms for matrices
def normAbs(object): # p = 1

2
processing/post/addOrientations.py
View File

@ -7,7 +7,7 @@ from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN

2
processing/post/addPK2.py
View File

@ -8,7 +8,7 @@ from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN

2
processing/post/addSchmidfactors.py
View File

@ -7,7 +7,7 @@ from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
slipnormal_temp = [
[0,0,0,1],

2
processing/post/addSpectralDecomposition.py
View File

@ -8,7 +8,7 @@ from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN

2
processing/post/addStrainTensors.py
View File

@ -8,7 +8,7 @@ from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
def operator(stretch,strain,eigenvalues):
return {

2
processing/post/averageDown.py
View File

@ -7,7 +7,7 @@ from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN

2
processing/post/binXY.py
View File

@ -7,7 +7,7 @@ from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN

2
processing/post/blowUp.py
View File

@ -7,7 +7,7 @@ from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN

2
processing/post/deleteColumn.py
View File

@ -6,7 +6,7 @@ from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN

2
processing/post/deleteInfo.py
View File

@ -6,7 +6,7 @@ from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN

2
processing/post/filterTable.py
View File

@ -6,7 +6,7 @@ from optparse import OptionParser
import damask
scriptID = '$Id$'
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN

7
processing/post/marc_deformedGeometry.py
View File

@ -5,7 +5,8 @@ import os, sys, math, string, numpy, shutil
import damask
from optparse import OptionParser
scriptID = '$Id$'
scriptName = os.path.splitext(scriptID.split()[1])[0]
# -----------------------------
# MAIN FUNCTION STARTS HERE
@ -15,8 +16,8 @@ from optparse import OptionParser
parser = OptionParser(usage='%prog [options] resultfile', description = """
Create vtk files for the (deformed) geometry that belongs to a .t16 (MSC.Marc) results file.
""" + string.replace('$Id$','\n','\\n')
)
""", version = scriptID)
parser.add_option('-d','--dir', dest='dir', \
help='name of subdirectory to hold output [%default]')

40
processing/post/marc_extractData.py
View File

@ -2,30 +2,11 @@
# -*- coding: UTF-8 no BOM -*-
import os, sys, math, string, re, time
from optparse import OptionParser, OptionGroup
import damask
from optparse import OptionParser, OptionGroup, Option
# -----------------------------
class MyOption(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)
scriptID = string.replace('$Id$','\n','\\n')
scriptName = os.path.splitext(scriptID.split()[1])[0]
# -----------------------------
def ParseOutputFormat(filename,homogID,crystID,phaseID):
@ -278,17 +259,14 @@ def writeHeader(myfile,stat,geomtype):
return True
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
# -----------------------------
# MAIN FUNCTION STARTS HERE
# -----------------------------
# --- input parsing
parser = OptionParser(option_class=MyOption, usage='%prog [options] resultfile', description = """
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Extract data from a .t16 (MSC.Marc) results file.
""" + string.replace('$Id$','\n','\\n')
)
""", version = scriptID)
parser.add_option('-i','--info', action='store_true', dest='info', \
help='list contents of resultfile [%default]')

9
processing/post/mentat_colorMap.py
View File

@ -1,10 +1,12 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import sys, string
import os, sys, string
import damask
from optparse import OptionParser
scriptID = string.replace('$Id$','\n','\\n')
scriptName = os.path.splitext(scriptID.split()[1])[0]
# -----------------------------
def outMentat(cmd,locals):
@ -57,13 +59,12 @@ def colorMap(colors,baseIdx=32):
# MAIN FUNCTION STARTS HERE
# -----------------------------
parser = OptionParser(usage="%prog [options] predefinedScheme | (lower_h,s,l upper_h,s,l)", description = """
parser = OptionParser(option_class=damask.extendableOption, usage="%prog [options] predefinedScheme | (lower_h,s,l upper_h,s,l)", description = """
Changes the color map in MSC.Mentat.
Interpolates colors between "lower_hsl" and "upper_hsl".
""" + string.replace('$Id$','\n','\\n')
)
""", version = scriptID)
parser.add_option("-i","--inverse", action = "store_true",
dest = "inverse", \

30
processing/post/perceptualUniformColorMap.py
View File

@ -2,38 +2,20 @@
# -*- coding: UTF-8 no BOM -*-
import math, string, sys, os
from damask import Color,Colormap
from optparse import OptionParser, Option
# -----------------------------
class extendableOption(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)
import damask
from optparse import OptionParser
scriptID = string.replace('$Id$','\n','\\n')
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Produces perceptually linear diverging and sequential colormaps in formats suitable for visualization software or simply as a list of interpolated colors.
""" + string.replace('$Id$','\n','\\n')
)
""", version = scriptID)
parser.add_option('-l','--left', dest='left', type='float', nargs=3, \
help='left color %default')

2
processing/post/permuteData.py
View File

@ -7,7 +7,7 @@ from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN

8
processing/post/postResults.py
View File

@ -5,6 +5,9 @@ import pdb, os, sys, gc, math, re, threading, time, struct, string
import damask
from optparse import OptionParser, OptionGroup
scriptID = string.replace('$Id$','\n','\\n')
scriptName = os.path.splitext(scriptID.split()[1])[0]
fileExtensions = { \
'marc': ['.t16',],
@ -623,7 +626,7 @@ def SummarizePostfile(stat,where=sys.stdout,format='marc'):
# --- input parsing
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [options] resultfile', description = """
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Extract data from a .t16 (MSC.Marc) or .spectralOut results file.
List of output variables is given by options '--ns','--es','--et','--ho','--cr','--co'.
@ -640,8 +643,7 @@ User mappings need to be formulated in an incremental fashion for each new data
and may use the current (incremental) result, b(ase), as well as the number, n(umber),
of already processed data points for evaluation.
""", version = string.replace('$Id$','\n','\\n')
)
""", version = scriptID)
parser.add_option('-i','--info', action='store_true', dest='info', \
help='list contents of resultfile [%default]')

2
processing/post/rotateData.py
View File

@ -8,7 +8,7 @@ from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN

2
processing/post/scaleData.py
View File

@ -8,7 +8,7 @@ from optparse import OptionParser
import damask
scriptID = '$Id$'
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN

2
processing/post/shiftData.py
View File

@ -8,7 +8,7 @@ from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN

2
processing/post/showTable.py
View File

@ -6,7 +6,7 @@ from optparse import OptionParser
import damask
scriptID = '$Id$'
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN

2
processing/post/sortTable.py
View File

@ -7,7 +7,7 @@ from optparse import OptionParser
import damask
scriptID = string.replace('$Id$','\n','\\n')
scriptName = scriptID.split()[1][:-3]
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN

83
processing/post/stddevDown.py
View File

@ -1,52 +1,23 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,re,sys,math,string,numpy,damask,time
from optparse import OptionParser, Option
# -----------------------------
class extendableOption(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)
def location(idx,res):
return numpy.array([ idx % res[0], \
(idx // res[0]) % res[1], \
(idx // res[0] // res[1]) % res[2] ])
def index(location,res):
return ( location[0] % res[0] + \
(location[1] % res[1]) * res[0] + \
(location[2] % res[2]) * res[0] * res[1] )
import os,re,sys,math,string,time
import numpy as np
import damask
from optparse import OptionParser
scriptID = string.replace('$Id$','\n','\\n')
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=extendableOption, usage='%prog [options] [file[s]]', description = """
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [options] datafile[s]', description = """
Calculates the standard deviation of data in blocks of size 'packing' thus reducing the former resolution
to resolution/packing. (Requires numpy.)
to resolution/packing. (Requires np.)
""" + string.replace('$Id$','\n','\\n')
)
""", version = scriptID)
parser.add_option('-c','--coordinates', dest='coords', type='string',\
help='column heading for coordinates [%default]')
@ -71,11 +42,11 @@ if len(options.packing) < 3:
if len(options.shift) < 3:
parser.error('shift needs three parameters...')
options.packing = numpy.array(options.packing)
options.shift = numpy.array(options.shift)
options.packing = np.array(options.packing)
options.shift = np.array(options.shift)
prefix = 'stddevDown%ix%ix%i_'%(options.packing[0],options.packing[1],options.packing[2])
if numpy.any(options.shift != 0):
if np.any(options.shift != 0):
prefix += 'shift%+i%+i%+i_'%(options.shift[0],options.shift[1],options.shift[2])
# ------------------------------------------ setup file handles ---------------------------------------
@ -114,27 +85,27 @@ for file in files:
while table.data_read(): # read next data line of ASCII table
for j in xrange(3):
grid[j][str(table.data[locationCol+j])] = True # remember coordinate along x,y,z
resolution = numpy.array([len(grid[0]),\
resolution = np.array([len(grid[0]),\
len(grid[1]),\
len(grid[2]),],'i') # resolution is number of distinct coordinates found
dimension = resolution/numpy.maximum(numpy.ones(3,'d'),resolution-1.0)* \
numpy.array([max(map(float,grid[0].keys()))-min(map(float,grid[0].keys())),\
dimension = resolution/np.maximum(np.ones(3,'d'),resolution-1.0)* \
np.array([max(map(float,grid[0].keys()))-min(map(float,grid[0].keys())),\
max(map(float,grid[1].keys()))-min(map(float,grid[1].keys())),\
max(map(float,grid[2].keys()))-min(map(float,grid[2].keys())),\
],'d') # dimension from bounding box, corrected for cell-centeredness
else:
resolution = numpy.array(options.resolution,'i')
dimension = numpy.array(options.dimension,'d')
resolution = np.array(options.resolution,'i')
dimension = np.array(options.dimension,'d')
if resolution[2] == 1:
options.packing[2] = 1
options.shift[2] = 0
dimension[2] = min(dimension[:2]/resolution[:2]) # z spacing equal to smaller of x or y spacing
packing = numpy.array(options.packing,'i')
shift = numpy.array(options.shift,'i')
downSized = numpy.maximum(numpy.ones(3,'i'),resolution//packing)
outSize = numpy.ceil(numpy.array(resolution,'d')/numpy.array(packing,'d'))
packing = np.array(options.packing,'i')
shift = np.array(options.shift,'i')
downSized = np.maximum(np.ones(3,'i'),resolution//packing)
outSize = np.ceil(np.array(resolution,'d')/np.array(packing,'d'))
print '\t%s @ %s --> %s'%(dimension,resolution,downSized)
@ -144,9 +115,9 @@ for file in files:
# ------------------------------------------ process data ---------------------------------------
dataavg = numpy.zeros(outSize.tolist()+[len(table.labels)])
datavar = numpy.zeros(outSize.tolist()+[len(table.labels)])
p = numpy.zeros(3,'i')
dataavg = np.zeros(outSize.tolist()+[len(table.labels)])
datavar = np.zeros(outSize.tolist()+[len(table.labels)])
p = np.zeros(3,'i')
table.data_rewind()
for p[2] in xrange(resolution[2]):
@ -154,7 +125,7 @@ for file in files:
for p[0] in xrange(resolution[0]):
d = ((p-shift)%resolution)//packing
table.data_read()
dataavg[d[0],d[1],d[2],:] += numpy.array(table.data_asFloat(),'d') # convert to numpy array
dataavg[d[0],d[1],d[2],:] += np.array(table.data_asFloat(),'d') # convert to np array
dataavg /= packing.prod()
@ -164,9 +135,9 @@ for file in files:
for p[0] in xrange(resolution[0]):
d = ((p-shift)%resolution)//packing
table.data_read()
datavar[d[0],d[1],d[2],:] += (numpy.array(table.data_asFloat(),'d') - dataavg[d[0],d[1],d[2],:])**2
datavar[d[0],d[1],d[2],:] += (np.array(table.data_asFloat(),'d') - dataavg[d[0],d[1],d[2],:])**2
datavar = numpy.sqrt(datavar/packing.prod())
datavar = np.sqrt(datavar/packing.prod())
posOffset = (shift+[0.5,0.5,0.5])*dimension/resolution
elementSize = dimension/resolution*packing

31
processing/post/tagLabel.py
View File

@ -1,38 +1,21 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,re,sys,math,string,damask
from optparse import OptionParser, Option
# -----------------------------
class extendableOption(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)
import os,re,sys,math,string
import damask
from optparse import OptionParser
scriptID = string.replace('$Id$','\n','\\n')
scriptName = os.path.splitext(scriptID.split()[1])[0]
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=extendableOption, usage='%prog options [file[s]]', description = """
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [options] dfile[s]', description = """
Tag scalar, vectorial, and/or tensorial data header labels by specified suffix.
""" + string.replace('$Id$','\n','\\n')
)
""", version = scriptID)
parser.add_option('-l','--tag', dest='tag', \
help='tag to use as suffix for labels')

41
processing/post/vtk2ang.py
View File

@ -1,11 +1,13 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,numpy,string,math,sys
from optparse import OptionParser, Option
import os,string,math,sys
import numpy as np
from optparse import OptionParser
from vtk import *
scriptID = string.replace('$Id$','\n','\\n')
scriptName = os.path.splitext(scriptID.split()[1])[0]
# -----------------------------
def getHeader(filename,sizeFastIndex,sizeSlowIndex,stepsize):
@ -79,8 +81,7 @@ def getDataLine(angles,x,y,validData=True):
parser = OptionParser(usage='%prog options [file[s]]', description = """
Builds a ang files from a vtk file.
""" + string.replace('$Id$','\n','\\n')
)
""", version = scriptID)
parser.add_option('--disp','--displacement',dest='dispLabel', \
@ -137,7 +138,7 @@ for filename in filenames:
# check for othogonality of normal and up vector
if numpy.dot(numpy.array(options.normal),numpy.array(options.up)) > 1e-3:
if np.dot(np.array(options.normal),np.array(options.up)) > 1e-3:
parser.error('normal vector and up vector have to be orthogonal')
@ -221,12 +222,12 @@ for filename in filenames:
# "R" rotates coordinates from the mesh system into the TSL system
if options.verbose: sys.stdout.write("\nGETTING COORDINATE SYSTEM FOR ANG FILES\n")
z = numpy.array(options.normal,dtype='float')
z = z / numpy.linalg.norm(z)
x = numpy.array(options.up,dtype='float')
x = x / numpy.linalg.norm(x)
y = numpy.cross(z,x)
R = numpy.array([x,y,z])
z = np.array(options.normal,dtype='float')
z = z / np.linalg.norm(z)
x = np.array(options.up,dtype='float')
x = x / np.linalg.norm(x)
y = np.cross(z,x)
R = np.array([x,y,z])
if options.verbose:
sys.stdout.write(" axis (x: up direction, z: slice normal)\n")
sys.stdout.write(" x (% .8f % .8f % .8f)\n"%tuple(x))
@ -237,12 +238,12 @@ for filename in filenames:
# Get bounding box in rotated system (x,y,z)
if options.verbose: sys.stdout.write("\nGETTING BOUNDING BOX IN ROTATED SYSTEM\n")
rotatedbox = [[numpy.inf,-numpy.inf] for i in range(3)] # bounding box in rotated TSL system
rotatedbox = [[np.inf,-np.inf] for i in range(3)] # bounding box in rotated TSL system
for n in range(8): # loop over eight vertices of mesh bounding box
vert = numpy.array([box[0+(n/1)%2],
vert = np.array([box[0+(n/1)%2],
box[2+(n/2)%2],
box[4+(n/4)%2]]) # vertex in mesh system
rotatedvert = numpy.dot(R,vert) # vertex in rotated system
rotatedvert = np.dot(R,vert) # vertex in rotated system
for i in range(3):
rotatedbox[i][0] = min(rotatedbox[i][0],rotatedvert[i])
rotatedbox[i][1] = max(rotatedbox[i][1],rotatedvert[i])
@ -292,10 +293,10 @@ for filename in filenames:
for k in xrange(Npoints[2]):
for j in xrange(Npoints[0]):
for i in xrange(Npoints[1]): # y is fastest index
rotatedpoint = numpy.array([rotatedbox[0][0] + (float(j) + 0.5) * options.resolution,
rotatedpoint = np.array([rotatedbox[0][0] + (float(j) + 0.5) * options.resolution,
rotatedbox[1][0] + (float(i) + 0.5) * options.resolution,
rotatedbox[2][0] + (float(k) + 0.5) * options.distance ]) # point in rotated system
point = numpy.dot(R.T,rotatedpoint) # point in mesh system
point = np.dot(R.T,rotatedpoint) # point in mesh system
points.InsertNextPoint(list(point))
if options.verbose:
sys.stdout.write("\rGENERATING POINTS FOR POINT GRID %d%%" %(100*(Npoints[1]*(k*Npoints[0]+j)+i+1)/totalNpoints))
@ -363,7 +364,7 @@ for filename in filenames:
if options.verbose:
sys.stdout.write("\nWRITING OUT ANG FILES\n")
sys.stdout.write(" scaling all length with %f\n"%options.scale)
x0,y0,z0 = numpy.dot(R,pointgrid.GetPoint(0)) # first point on slice defines origin
x0,y0,z0 = np.dot(R,pointgrid.GetPoint(0)) # first point on slice defines origin
for sliceN in range(Npoints[2]):
# Open file and write header
@ -396,7 +397,7 @@ for filename in filenames:
# write data to ang file
x,y,z = numpy.dot(R,pointgrid.GetPoint(i)) # point in rotated TSL system
x,y,z = np.dot(R,pointgrid.GetPoint(i)) # point in rotated TSL system
x -= x0 # first point on slice defines origin
y -= y0 # first point on slice defines origin
x *= options.scale
@ -423,7 +424,7 @@ for filename in filenames:
P = [rotatedbox[0][(n/1)%2],
rotatedbox[1][(n/2)%2],
rotatedbox[2][(n/4)%2]]
boxpoints.InsertNextPoint(list(numpy.dot(R.T,numpy.array(P))))
boxpoints.InsertNextPoint(list(np.dot(R.T,np.array(P))))
box = vtkHexahedron()
for n,i in enumerate([0,1,3,2,4,5,7,6]):
box.GetPointIds().SetId(n,i)

7
processing/post/vtk_addData.py
View File

@ -5,7 +5,8 @@ import os, sys, string, glob, re
import damask
from optparse import OptionParser
scriptID = string.replace('$Id$','\n','\\n')
scriptName = os.path.splitext(scriptID.split()[1])[0]
# -----------------------------
def findTag(filename,tag):
@ -27,8 +28,8 @@ def findTag(filename,tag):
parser = OptionParser(usage='%prog [options] directory', description = """
Add data from an ASCII table to a VTK geometry file.
""" + string.replace('$Id$','\n','\\n')
)
""", version = scriptID)
parser.add_option('-s','--sub', action='store_true', dest='subdir', \
help='include files in subdirectories [%default]')

35
processing/post/vtk_addPointcloudData.py
View File

@ -1,36 +1,21 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string,re,numpy,vtk
import os,sys,string,re,vtk
import damask
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
from optparse import OptionParser
scriptID = '$Id$'
scriptName = scriptID.split()[1]
scriptID = string.replace('$Id$','\n','\\n')
scriptName = os.path.splitext(scriptID.split()[1])[0]
#--------------------------------------------------------------------------------------------------
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",)
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
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 = """
Add scalar and RGB tuples from ASCIItable to existing VTK point cloud (.vtp).
""" + string.replace(scriptID,'\n','\\n')
)
""", version = scriptID)
parser.add_option('-v', '--vtk', dest='vtk', \
help = 'VTK file name')

35
processing/post/vtk_addVoxelcloudData.py
View File

@ -1,36 +1,21 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string,re,numpy,vtk
import os,sys,string,re,vtk
import damask
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
from optparse import OptionParser
scriptID = '$Id$'
scriptName = scriptID.split()[1]
scriptID = string.replace('$Id$','\n','\\n')
scriptName = os.path.splitext(scriptID.split()[1])[0]
#--------------------------------------------------------------------------------------------------
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",)
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
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 = """
Add scalar and RGB tuples from ASCIItable to existing VTK voxel cloud (.vtu).
""" + string.replace(scriptID,'\n','\\n')
)
""", version = scriptID)
parser.add_option('-v', '--vtk', dest='vtk', \
help = 'VTK file name')

33
processing/post/vtk_addVoxelgridData.py
View File

@ -1,37 +1,22 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string,re,numpy,vtk
import os,sys,string,re,vtk
import damask
from collections import defaultdict
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
from optparse import OptionParser
scriptID = '$Id: vtk_addVoxelgridData.py 3064 2014-04-03 01:00:00Z p.eisenlohr $'
scriptID = string.replace('$Id: addCalculation.py 3465 2014-09-12 14:14:55Z MPIE\m.diehl $','\n','\\n')
scriptName = os.path.splitext(scriptID.split()[1])[0]
#--------------------------------------------------------------------------------------------------
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",)
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
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 = """
Add scalar and RGB tuples from ASCIItable to existing VTK voxel grid (.vtr).
""" + string.replace(scriptID,'\n','\\n')
)
""", version = scriptID)
parser.add_option('-v', '--vtk', dest='vtk', type='string',
help = 'VTK file name')

35
processing/post/vtk_pointcloud.py
View File

@ -1,36 +1,21 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string,re,numpy,vtk
import os,sys,string,re,vtk
import damask
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
from optparse import OptionParser
scriptID = '$Id$'
scriptName = scriptID.split()[1]
scriptID = string.replace('$Id$','\n','\\n')
scriptName = os.path.splitext(scriptID.split()[1])[0]
#--------------------------------------------------------------------------------------------------
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",)
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
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 = """
Add grain index based on similitude of crystal lattice orientation.
""" + string.replace(scriptID,'\n','\\n')
)
""", version = scriptID)
parser.add_option('-p', '--positions', dest='pos', \
help = 'coordinate label')

15
processing/post/vtk_scalars2vectors.py
View File

@ -2,19 +2,20 @@
# -*- coding: UTF-8 no BOM -*-
import os, sys, string, re, shutil
import damask
from optparse import OptionParser
from vtk import *
scriptID = string.replace('$Id$','\n','\\n')
scriptName = os.path.splitext(scriptID.split()[1])[0]
# -----------------------------
# MAIN FUNCTION STARTS HERE
# -----------------------------
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
# --- input parsing
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
parser = OptionParser(usage='%prog [options] vtkfile', description = """
""" + string.replace('$Id$','\n','\\n')
)
""", version = scriptID)
parser.add_option('-v','--vector', nargs=3, dest='vector', \
help='suffices indicating vector components [%default]')

56
processing/post/vtk_voxelcloud.py
View File

@ -1,35 +1,14 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,sys,string,re,numpy,vtk
import os,sys,string,re,vtk
import numpy as np
from optparse import OptionParser
import damask
from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
scriptID = '$Id$'
scriptName = os.path.splitext(scriptID.split()[1])[0]
#--------------------------------------------------------------------------------------------------
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)
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
synonyms = {
'grid': ['resolution'],
'size': ['dimension'],
@ -46,11 +25,14 @@ mappings = {
'microstructures': lambda x: int(x),
}
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=extendedOption, usage='%prog options [file[s]]', description = """
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Create hexahedral voxels around points in an ASCIItable.
""" + string.replace(scriptID,'\n','\\n')
)
""", version = scriptID)
parser.add_option('-p', '--positions', dest='pos', type='string',
help = 'coordinate label')
@ -91,12 +73,11 @@ for file in files:
table = damask.ASCIItable(file['input'],file['croak'],False) # make unbuffered ASCII_table
table.head_read() # read ASCII header info
#--- interpret header ----------------------------------------------------------------------------
info = {
'grid': numpy.zeros(3,'i'),
'size': numpy.zeros(3,'d'),
'origin': numpy.zeros(3,'d'),
'grid': np.zeros(3,'i'),
'size': np.zeros(3,'d'),
'origin': np.zeros(3,'d'),
'homogenization': 0,
'microstructures': 0,
}
@ -121,18 +102,17 @@ for file in files:
'homogenization: %i\n'%info['homogenization'] + \
'microstructures: %i\n'%info['microstructures'])
if numpy.any(info['grid'] < 1):
if np.any(info['grid'] < 1):
file['croak'].write('invalid grid a b c.\n')
continue
if numpy.any(info['size'] <= 0.0):
if np.any(info['size'] <= 0.0):
file['croak'].write('invalid size x y z.\n')
continue
else:
info['size'] = numpy.ones(3)
info['size'] = np.ones(3)
info['grid'] = info['size'] / options.size
info['origin'] = options.origin
# --------------- figure out columns to process
active = {}
@ -156,7 +136,7 @@ for file in files:
# ------------------------------------------ process data ---------------------------------------
hexPoints = numpy.array([[-1,-1,-1],
hexPoints = np.array([[-1,-1,-1],
[ 1,-1,-1],
[ 1, 1,-1],
[-1, 1,-1],
@ -175,9 +155,9 @@ for file in files:
table.data[:,0:3] *= info['size']
table.data[:,0:3] += info['origin']
# minD = numpy.array(options.size,dtype=float)
# minD = np.array(options.size,dtype=float)
# for i in xrange(3):
# coords = numpy.unique(table.data[:,i])
# coords = np.unique(table.data[:,i])
# minD[i] = coords[-1]-coords[0]
# for j in xrange(len(coords)-1):
# d = coords[j+1]-coords[j]