updated to state-of-the art file handling etc

This commit is contained in:
Martin Diehl 2014-08-04 20:07:20 +00:00
parent 0874ebe096
commit a0f9865133
1 changed files with 132 additions and 110 deletions

View File

@ -1,11 +1,16 @@
#!/usr/bin/env python
# -*- coding: UTF-8 no BOM -*-
import os,re,sys,math
import os,re,sys,math,string
import numpy as np
from collections import defaultdict
from optparse import OptionParser
import damask
CoverA=1.587
slipnormal_temp = [ # This is the real slip system information for hex aka titanium for now.
scriptID = '$Id$'
scriptName = scriptID.split()[1]
slipnormal_temp = [
[0,0,0,1],
[0,0,0,1],
[0,0,0,1],
@ -198,15 +203,21 @@ slipdirection = { \
],
}
# --------------------------------------------------------------------
def applyEulers(phi1,Phi,phi2,x):
""" transform x given in crystal coordinates to xbar returned in lab coordinates for Euler angles phi1,Phi,phi2 """
eulerRot = [[ math.cos(phi1)*math.cos(phi2) - math.cos(Phi)*math.sin(phi1)*math.sin(phi2), - math.cos(phi1)*math.sin(phi2) - math.cos(Phi)*math.cos(phi2)*math.sin(phi1), math.sin(Phi)*math.sin(phi1)], \
[ math.cos(phi2)*math.sin(phi1) + math.cos(Phi)*math.cos(phi1)*math.sin(phi2), math.cos(Phi)*math.cos(phi1)*math.cos(phi2) - math.sin(phi1)*math.sin(phi2), -math.sin(Phi)*math.cos(phi1)], \
[ math.sin(Phi)*math.sin(phi2), math.sin(Phi)*math.cos(phi2), math.cos(Phi)]]
eulerRot = [[ math.cos(phi1)*math.cos(phi2) - math.cos(Phi)*math.sin(phi1)*math.sin(phi2),
-math.cos(phi1)*math.sin(phi2) - math.cos(Phi)*math.cos(phi2)*math.sin(phi1),
math.sin(Phi)*math.sin(phi1)
],
[ math.cos(phi2)*math.sin(phi1) + math.cos(Phi)*math.cos(phi1)*math.sin(phi2),
math.cos(Phi)*math.cos(phi1)*math.cos(phi2) - math.sin(phi1)*math.sin(phi2),
-math.sin(Phi)*math.cos(phi1)
],
[ math.sin(Phi)*math.sin(phi2),
math.sin(Phi)*math.cos(phi2),
math.cos(Phi)
]]
xbar = [0,0,0]
if len(x) == 3:
@ -214,16 +225,12 @@ def applyEulers(phi1,Phi,phi2,x):
xbar[i] = sum([eulerRot[i][j]*x[j] for j in range(3)])
return xbar
# --------------------------------------------------------------------
def normalize(x):
norm = math.sqrt(sum([x[i]*x[i] for i in range(len(x))]))
return [x[i]/norm for i in range(len(x))]
# --------------------------------------------------------------------
def crossproduct(x,y):
return [
@ -232,37 +239,42 @@ def crossproduct(x,y):
x[0]*y[1]-y[0]*x[1],
]
# --------------------------------------------------------------------
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(usage='%prog [options] [file]', description = """
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Add columns listing Schmid factors (and optional trace vector of selected system) for given Euler angles.
Column headings need to have names 'phi1', 'Phi', 'phi2'.
$Id$
""")
""", version = string.replace(scriptID,'\n','\\n')
)
parser.add_option('-l','--lattice', dest='lattice', choices=('fcc','bcc','hex'), \
help='key for lattice type [%default]')
parser.add_option('-d','--forcedirection', dest='forcedirection', type='int', nargs=3, \
help='force direction in lab coordinates [%default]')
parser.add_option('-n','--stressnormal', dest='stressnormal', type='int', nargs=3, \
help='stress plane normal in lab coordinates [%default]')
parser.add_option('-t','--trace', dest='traceplane', type='int', nargs=3, \
help="normal (in lab coordinates) of plane on which the plane trace of the Schmid factor(s) is reported [%default]")
parser.add_option('-r','--rank', dest='rank', type='int', \
parser.add_option('-l','--lattice', dest='lattice', action='store', type='choice',
choices=('fcc','bcc','hex'), metavar='string',
help="type of neighborhood ('fcc','bcc','hex') [%default]")
parser.add_option('--direction', dest='forcedirection', action='store', type='int', nargs=3, metavar='int int int',
help='force direction in lab coordinates %default')
parser.add_option('-n','--normal', dest='stressnormal', action='store', type='int', nargs=3, metavar='int int int',
help='stress plane normal in lab coordinates ')
parser.add_option('--trace', dest='traceplane', action='store', type='int', nargs=3, metavar='int int int',
help='normal (in lab coordinates) of plane on which the plane trace of the Schmid factor(s) is reported')
parser.add_option('--covera', dest='CoverA', action='store', type='float', metavar='float',
help='C over A ratio for hexagonal systems')
parser.add_option('-r','--rank', dest='rank', action='store', type='int', nargs=3, metavar='int int int',
help="report trace of r'th highest Schmid factor [%default]")
parser.add_option('-e', '--eulers', dest='eulers', action='store', type='string', metavar='string',
help='Euler angles label')
parser.add_option('-d', '--degrees', dest='degrees', action='store_true',
help = 'Euler angles are given in degrees [%default]')
parser.set_defaults(lattice = 'fcc')
parser.set_defaults(forcedirection = [0, 0, 1])
parser.set_defaults(stressnormal = None)
parser.set_defaults(traceplane = None)
parser.set_defaults(rank = 0)
parser.set_defaults(CoverA = 1.587)
parser.set_defaults(eulers = 'eulerangles')
(options,filename) = parser.parse_args()
(options,filenames) = parser.parse_args()
options.forcedirection = normalize(options.forcedirection)
if options.stressnormal:
@ -276,52 +288,64 @@ if options.traceplane:
options.traceplane = normalize(options.traceplane)
options.rank = min(options.rank,Nslipsystems[options.lattice])
# read from standard input unless input file specified
if filename == []:
file = sys.stdin
elif os.path.exists(filename[0]):
file = open(filename[0])
datainfo = { # list of requested labels per datatype
'vector': {'len':3,
'label':[]},
}
# read data
content = file.readlines()
file.close()
datainfo['vector']['label'] += [options.eulers]
# get labels by either read the first row, or - if keyword header is present - the last line of the header
headerlines = 1
m = re.search('(\d+)\s*head', content[0].lower())
if m:
headerlines = int(m.group(1))+1
labels = content[headerlines-1].split()
data = content[headerlines:]
toRadians = math.pi/180.0 if options.degrees else 1.0 # rescale degrees to radians
# Convert 4 Miller indices notation of hex to orthogonal 3 Miller indices notation
if options.lattice=="hex":
if options.lattice=='hex': # Convert 4 Miller indices notation of hex to orthogonal 3 Miller indices notation
for i in range(Nslipsystems[options.lattice]):
slipnormal[options.lattice][i][0]=slipnormal_temp[i][0]
slipnormal[options.lattice][i][1]=(slipnormal_temp[i][0]+2.0*slipnormal_temp[i][1])/math.sqrt(3.0)
slipnormal[options.lattice][i][2]=slipnormal_temp[i][3]/CoverA
slipnormal[options.lattice][i][2]=slipnormal_temp[i][3]/options.CoverA
slipdirection[options.lattice][i][0]=slipdirection_temp[i][0]*1.5 # direction [uvtw]->[3u/2 (u+2v)*sqrt(3)/2 w*(c/a)] ,
slipdirection[options.lattice][i][1]=(slipdirection_temp[i][0]+2.0*slipdirection_temp[i][1])*(0.5*math.sqrt(3.0))
slipdirection[options.lattice][i][2]=slipdirection_temp[i][3]*CoverA
slipdirection[options.lattice][i][2]=slipdirection_temp[i][3]*options.CoverA
for i in range(Nslipsystems[options.lattice]):
slipnormal[options.lattice][i]=normalize(slipnormal[options.lattice][i])
slipdirection[options.lattice][i]=normalize(slipdirection[options.lattice][i])
for c in range(len(labels)):
m = re.search('.*([Pp]hi\d*).*', labels[c])
if m:
if m.group(1).lower() == "phi1":
phi1Column = c
elif m.group(1).lower() == "phi":
PhiColumn = c
elif m.group(1).lower() == "phi2":
phi2Column = c
# ------------------------------------------ setup file handles ---------------------------------------
files = []
if filenames == []:
files.append({'name':'STDIN', 'input':sys.stdin, 'output':sys.stdout, 'croak':sys.stderr})
else:
for name in filenames:
if os.path.exists(name):
files.append({'name':name, 'input':open(name), 'output':open(name+'_tmp','w'), 'croak':sys.stderr})
output = '1\theader\n' + \
'\t'.join(map(str,labels)) + \
'\t' + \
'\t'.join(['(%i)S(%i %i %i)[%i %i %i]'%(i+1,
# ------------------------------------------ loop over input files ---------------------------------------
for file in files:
if file['name'] != 'STDIN': file['croak'].write('\033[1m'+scriptName+'\033[0m: '+file['name']+'\n')
else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n')
table = damask.ASCIItable(file['input'],file['output'],False) # make unbuffered ASCII_table
table.head_read() # read ASCII header info
table.info_append(string.replace(scriptID,'\n','\\n') + '\t' + ' '.join(sys.argv[1:]))
active = defaultdict(list)
column = defaultdict(dict)
for datatype,info in datainfo.items():
for label in info['label']:
foundIt = False
for key in ['1_'+label,label]:
if key in table.labels:
foundIt = True
active[datatype].append(label)
column[datatype][label] = table.labels.index(key) # remember columns of requested data
if not foundIt:
file['croak'].write('column %s not found...\n'%label)
break
# ------------------------------------------ assemble header ---------------------------------------
table.labels_append(['(%i)S(%i %i %i)[%i %i %i]'%(i+1,
slipnormal[options.lattice][i][0],
slipnormal[options.lattice][i][1],
slipnormal[options.lattice][i][2],
@ -329,42 +353,40 @@ output = '1\theader\n' + \
slipdirection[options.lattice][i][1],
slipdirection[options.lattice][i][2],
) for i in range(Nslipsystems[options.lattice])])
if options.traceplane:
if options.rank > 0:
output += '\ttrace_x\ttrace_y\ttrace_z\tsystem'
else:
output += '\t' + '\t'.join(['(%i)tx\tty\ttz'%(i+1) for i in range(Nslipsystems[options.lattice])])
output += '\n'
for line in data:
items = line.split()[:len(labels)]
if items == []:
continue
phi1 = math.radians(float(items[phi1Column]))
Phi = math.radians(float(items[PhiColumn]))
phi2 = math.radians(float(items[phi2Column]))
S = [ sum( [applyEulers(phi1,Phi,phi2,normalize( slipnormal[options.lattice][slipsystem]))[i]*options.stressnormal[i] for i in range(3)] ) * \
sum( [applyEulers(phi1,Phi,phi2,normalize(slipdirection[options.lattice][slipsystem]))[i]*options.forcedirection[i] for i in range(3)] ) \
if options.traceplane:
if options.rank > 0:
table.labels_append('trace_x trace_y trace_z system')
else:
table.labels_append(['(%i)tx\tty\ttz'%(i+1) for i in range(Nslipsystems[options.lattice])])
table.head_write()
# ------------------------------------------ process data ----------------------------------------
outputAlive = True
while outputAlive and table.data_read(): # read next data line of ASCII table
[phi1,Phi,phi2] = Eulers=toRadians*np.array(map(\
float,table.data[column['vector'][options.eulers]:\
column['vector'][options.eulers]+datainfo['vector']['len']]))
S = [ sum( [applyEulers(phi1,Phi,phi2,normalize( \
slipnormal[options.lattice][slipsystem]))[i]*options.stressnormal[i] for i in range(3)] ) * \
sum( [applyEulers(phi1,Phi,phi2,normalize( \
slipdirection[options.lattice][slipsystem]))[i]*options.forcedirection[i] for i in range(3)] ) \
for slipsystem in range(Nslipsystems[options.lattice]) ]
output += '\t'.join(items + map(str,S))
table.data_append(S)
if options.traceplane:
trace = [crossproduct(options.traceplane,applyEulers(phi1,Phi,phi2,normalize(slipnormal[options.lattice][slipsystem]))) \
for slipsystem in range(Nslipsystems[options.lattice]) ]
if options.rank == 0:
output += '\t' + '\t'.join(map(lambda x:'%f\t%f\t%f'%(x[0],x[1],x[2]),trace))
table.data_append('\t'.join(map(lambda x:'%f\t%f\t%f'%(x[0],x[1],x[2]),trace)))
elif options.rank > 0:
SabsSorted = sorted([(abs(S[i]),i) for i in range(len(S))])
output += '\t' + '\t'.join(map(str,trace[SabsSorted[-options.rank][1]])) + '\t%i'%(1+SabsSorted[-options.rank][1])
# for t in [normalize(crossproduct(options.traceplane,applyEulers(phi1,Phi,phi2,normalize(slipnormal[options.lattice][i])))) for i in range(12,24)]:
# print '\t'.join(map(str,t))
# print '\t'.join(map(lambda x: str(-x),t))
# print '\t'.join(['0','0','0'])
# print
output += '\n'
table.data_append('\t'.join(map(str,trace[SabsSorted[-options.rank][1]])) + '\t%i'%(1+SabsSorted[-options.rank][1]))
outputAlive = table.data_write() # output processed line
if filename == []:
print output
else:
file = open(filename[0],'w')
file.write(output)
file.close()
# ------------------------------------------ output result ---------------------------------------
outputAlive and table.output_flush() # just in case of buffered ASCII table
file['input'].close() # close input ASCII table (works for stdin)
file['output'].close() # close output ASCII table (works for stdout)
if file['name'] != 'STDIN':
os.rename(file['name']+'_tmp',file['name']) # overwrite old one with tmp new