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DAMASK_EICMD
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added options to specify the columns for the grain IDs and segments 

improved error handling
This commit is contained in:
Christoph Kords 2014-03-12 14:26:44 +00:00
parent 3aea8b39e9
commit f19955c84a
1 changed files with 40 additions and 14 deletions
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54
processing/pre/patchFromReconstructedBoundaries.py
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@ -78,24 +78,31 @@ def output(cmds,locals,dest):
return
def rcbOrientationParser(content):
def rcbOrientationParser(content,idcolumn):
grains = []
myOrientation = [0.0,0.0,0.0]
for line in content:
m = re.match(r'\s*(#|$)',line)
if m: continue # skip comments and blank lines
if m: continue # skip comments and blank lines
for grain in range(2):
myID = int(line.split()[12+grain]) # get grain id
myID = int(line.split()[idcolumn+grain]) # get grain id
myOrientation = map(float,line.split())[3*grain:3+3*grain] # get orientation
if len(grains) < myID:
for i in range(myID-len(grains)): # extend list to necessary length
for i in range(myID-len(grains)): # extend list to necessary length
grains.append([0.0,0.0,0.0])
grains[myID-1] = myOrientation # store Euler angles
try:
grains[myID-1] = myOrientation # store Euler angles
except IndexError:
message = 'You might not have chosen the correct column for the grain IDs! Please check the "--id" option.'
print '\033[1;31m'+message+'\033[0m\n'
raise
except:
raise
return grains
def rcbParser(content,M,size,tolerance): # parser for TSL-OIM reconstructed boundary files
def rcbParser(content,M,size,tolerance,idcolumn,segmentcolumn): # parser for TSL-OIM reconstructed boundary files
# find bounding box
@ -106,7 +113,14 @@ def rcbParser(content,M,size,tolerance): # parser for TSL-O
for line in content:
m = re.match(r'\s*(#|$)',line)
if m: continue # skip comments and blank lines
(x[0],y[0],x[1],y[1]) = map(float,line.split())[8:12] # get start and end coordinates of each segment.
try:
(x[0],y[0],x[1],y[1]) = map(float,line.split())[segmentcolumn:segmentcolumn+4] # get start and end coordinates of each segment.
except IndexError:
message = 'You might not have chosen the correct column for the segment end points! Please check the "--segment" option.'
print '\033[1;31m'+message+'\033[0m\n'
raise
except:
raise
(x[0],y[0]) = (M[0]*x[0]+M[1]*y[0],M[2]*x[0]+M[3]*y[0]) # apply transformation to coordinates
(x[1],y[1]) = (M[0]*x[1]+M[1]*y[1],M[2]*x[1]+M[3]*y[1]) # to get rcb --> Euler system
boxX[0] = min(boxX[0],x[0],x[1])
@ -130,7 +144,7 @@ def rcbParser(content,M,size,tolerance): # parser for TSL-O
for line in content:
m = re.match(r'\s*(#|$)',line)
if m: continue # skip comments and blank lines
(x[0],y[0],x[1],y[1]) = map(float,line.split())[8:12] # get start and end coordinates of each segment
(x[0],y[0],x[1],y[1]) = map(float,line.split())[segmentcolumn:segmentcolumn+4] # get start and end coordinates of each segment.
(x[0],y[0]) = (M[0]*x[0]+M[1]*y[0],M[2]*x[0]+M[3]*y[0]) # apply transformation to coordinates
(x[1],y[1]) = (M[0]*x[1]+M[1]*y[1],M[2]*x[1]+M[3]*y[1]) # to get rcb --> Euler system
@ -138,7 +152,7 @@ def rcbParser(content,M,size,tolerance): # parser for TSL-O
x[1] -= boxX[0]
y[0] -= boxY[0]
y[1] -= boxY[0]
grainNeighbors.append(map(int,line.split()[12:14])) # remember right and left grain per segment
grainNeighbors.append(map(int,line.split()[idcolumn:idcolumn+2])) # remember right and left grain per segment
for i in range(2): # store segment to both points
match = False # check whether point is already known (within a small range)
for posX in connectivityXY.keys():
@ -844,6 +858,12 @@ parser.add_option("-M", "--coordtransformation", type="float", nargs=4, \
parser.add_option("--scatter", type="float",\
dest="scatter",\
help="orientation scatter %default")
parser.add_option("--id", type="int",\
dest="idcolumn",\
help="column holding the right hand grain ID in the rcb file %default")
parser.add_option("--segment", type="int",\
dest="segmentcolumn",\
help="column holding the first entry for the segment end points in the rcb file %default")
parser.set_defaults(output = [])
parser.set_defaults(size = 1.0)
@ -861,6 +881,8 @@ parser.set_defaults(strainrate = 1.0e-3)
parser.set_defaults(increments = 200)
parser.set_defaults(mesh = 'dt_planar_trimesh')
parser.set_defaults(twoD = False)
parser.set_defaults(idcolumn = 13)
parser.set_defaults(segmentcolumn = 9)
(options, args) = parser.parse_args()
@ -874,15 +896,17 @@ try:
boundaryFile.close()
except:
print 'unable to read boundary file "%s"'%args[0]
sys.exit(-1)
raise
options.output = [s.lower() for s in options.output] # lower case
options.idcolumn -= 1 # python indexing starts with 0
options.segmentcolumn -= 1 # python indexing starts with 0
myName = os.path.splitext(args[0])[0]
print "%s\n"%myName
orientationData = rcbOrientationParser(boundarySegments)
rcData = rcbParser(boundarySegments,options.M,options.size,options.tolerance)
orientationData = rcbOrientationParser(boundarySegments,options.idcolumn)
rcData = rcbParser(boundarySegments,options.M,options.size,options.tolerance,options.idcolumn,options.segmentcolumn)
# ----- write image -----
@ -943,8 +967,10 @@ if 'mentat' in options.output:
outputLocals = {'log':[]}
if (options.port != None):
py_connect('',options.port)
output(cmds,outputLocals,'Mentat')
py_disconnect()
try:
output(cmds,outputLocals,'Mentat')
finally:
py_disconnect()
if 'procedure' in options.output:
output(outputLocals['log'],outputLocals,'Stdout')
else: