223031012
/
DAMASK_EICMD
mirror of https://github.com/achalhp/DAMASK_EICMD.git
1
0
Fork 0
Code Issues Projects Releases Wiki Activity

added ID information of creator script to header, changed keywords (resolution->grid, dimension->size)

This commit is contained in:
Martin Diehl 2013-04-12 12:48:39 +00:00
parent 4314ab236e
commit 7bcf1d6072
2 changed files with 92 additions and 73 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

107
processing/pre/geom_Osteon.py
View File

@ -35,30 +35,30 @@ Its fiber orientation is oscillating by +/- amplitude within one period.
""" + string.replace('$Id$','\n','\\n') """ + string.replace('$Id$','\n','\\n')
) )
parser.add_option('-r', '--resolution', dest='resolution', type='int', nargs=2, \ parser.add_option('-g', '--grid', dest='grid', type='int', nargs=2, \
help='resolution (a,b) of grid') help='a,b grid of hexahedral box %default')
parser.add_option('-d', '--dimension', dest='dimension', type='float', nargs=2, \ parser.add_option('-s', '--size', dest='size', type='float', nargs=2, \
help='physical dimension (x,y) of periodic patch') help='x,y size of hexahedral box %default')
parser.add_option('-c', '--canal', dest='canal', type='float', \ parser.add_option('-c', '--canal', dest='canal', type='float', \
help='Haversian canal radius') help='Haversian canal radius [%default]')
parser.add_option('-o', '--osteon', dest='osteon', type='float', \ parser.add_option('-o', '--osteon', dest='osteon', type='float', \
help='osteon radius (horizontal)') help='osteon radius (horizontal) [%default]')
parser.add_option('-l', '--lamella', dest='period', type='float', \ parser.add_option('-l', '--lamella', dest='period', type='float', \
help='lamella width') help='lamella width [%default]')
parser.add_option('-a', '--amplitude', dest='amplitude', type='float', \ parser.add_option('-a', '--amplitude', dest='amplitude', type='float', \
help='amplitude of twisted plywood wiggle in deg') help='amplitude of twisted plywood wiggle in deg [%default]')
parser.add_option( '--aspect', dest='aspect', type='float', \ parser.add_option( '--aspect', dest='aspect', type='float', \
help='osteon aspect ratio (vert/horiz)') help='osteon aspect ratio (vert/horiz) [%default]')
parser.add_option('-w', '--omega', dest='omega', type='float', \ parser.add_option('-w', '--omega', dest='omega', type='float', \
help='rotation angle (around normal) of osteon') help='rotation angle (around normal) of osteon [%default]')
parser.add_option('--homogenization', dest='homogenization', type='int', \ parser.add_option('--homogenization', dest='homogenization', type='int', \
help='homogenization index to be used') help='homogenization index to be used [%default]')
parser.add_option('--crystallite', dest='crystallite', type='int', \ parser.add_option('--crystallite', dest='crystallite', type='int', \
help='crystallite index to be used') help='crystallite index to be used [%default]')
parser.add_option('--configuration', dest='config', action='store_true', \ parser.add_option('--configuration', dest='config', action='store_true', \
help='output material configuration') help='output material configuration [%default]')
parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \ parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \
help='use two-dimensional geom data arrangement') help='use two-dimensional geom data arrangement [%default]')
parser.set_defaults(canal = 25e-6) parser.set_defaults(canal = 25e-6)
parser.set_defaults(osteon = 100e-6) parser.set_defaults(osteon = 100e-6)
@ -66,8 +66,8 @@ parser.set_defaults(aspect = 1.0)
parser.set_defaults(omega = 0.0) parser.set_defaults(omega = 0.0)
parser.set_defaults(period = 5e-6) parser.set_defaults(period = 5e-6)
parser.set_defaults(amplitude = 60) parser.set_defaults(amplitude = 60)
parser.set_defaults(dimension = numpy.array([300e-6,300e-6],'d')) parser.set_defaults(size = numpy.array([300e-6,300e-6],'d'))
parser.set_defaults(resolution = numpy.array([512,512],'i')) parser.set_defaults(grid = numpy.array([512,512],'i'))
parser.set_defaults(homogenization = 1) parser.set_defaults(homogenization = 1)
parser.set_defaults(crystallite = 1) parser.set_defaults(crystallite = 1)
parser.set_defaults(config = False) parser.set_defaults(config = False)
@ -83,8 +83,8 @@ file = {'name':'STDIN',
'croak':sys.stderr, 'croak':sys.stderr,
} }
if numpy.any(options.resolution < 2): if numpy.any(options.grid < 2):
file['croak'].write('resolution too low...\n') file['croak'].write('grid too low...\n')
sys.exit() sys.exit()
options.omega *= math.pi/180.0 # rescale ro radians options.omega *= math.pi/180.0 # rescale ro radians
@ -92,25 +92,26 @@ rotation = numpy.array([[ math.cos(options.omega),math.sin(options.omega),],
[-math.sin(options.omega),math.cos(options.omega),]],'d') [-math.sin(options.omega),math.cos(options.omega),]],'d')
box = numpy.dot(numpy.array([[options.canal,0.],[0.,options.aspect*options.canal]]).transpose(),rotation) box = numpy.dot(numpy.array([[options.canal,0.],[0.,options.aspect*options.canal]]).transpose(),rotation)
sys.stderr.write("bounding box: %s\n"%(numpy.sqrt(numpy.sum(box*box,0))))
info = {'grains': 0,
'resolution': numpy.ones(3,'i'), info = {
'dimension': numpy.ones(3,'d'), 'grid': numpy.ones(3,'i'),
'origin': numpy.zeros(3,'d'), 'size': numpy.ones(3,'d'),
'homogenization': options.homogenization, 'origin': numpy.zeros(3,'d'),
'microstructures': 0,
'homogenization': options.homogenization,
} }
info['resolution'][:2] = options.resolution info['grid'][:2] = options.grid
info['dimension'][:2] = options.dimension info['size'][:2] = options.size
info['dimension'][2] = min(info['dimension'][0]/info['resolution'][0],info['dimension'][1]/info['resolution'][1]) info['size'][2] = min(info['size'][0]/info['grid'][0],info['size'][1]/info['grid'][1])
info['origin'] = -info['dimension']/2.0 info['origin'] = -info['size']/2.0
X0 = info['dimension'][0]/info['resolution'][0]*\ X0 = info['size'][0]/info['grid'][0]*\
(numpy.tile(numpy.arange(info['resolution'][0]),(info['resolution'][1],1)) - info['resolution'][0]/2 + 0.5) (numpy.tile(numpy.arange(info['grid'][0]),(info['grid'][1],1)) - info['grid'][0]/2 + 0.5)
Y0 = info['dimension'][1]/info['resolution'][1]*\ Y0 = info['size'][1]/info['grid'][1]*\
(numpy.tile(numpy.arange(info['resolution'][1]),(info['resolution'][0],1)).transpose() - info['resolution'][1]/2 + 0.5) (numpy.tile(numpy.arange(info['grid'][1]),(info['grid'][0],1)).transpose() - info['grid'][1]/2 + 0.5)
X = X0*rotation[0,0] + Y0*rotation[0,1] # rotate by omega X = X0*rotation[0,0] + Y0*rotation[0,1] # rotate by omega
Y = X0*rotation[1,0] + Y0*rotation[1,1] # rotate by omega Y = X0*rotation[1,0] + Y0*rotation[1,1] # rotate by omega
@ -121,22 +122,26 @@ beta = options.amplitude*numpy.sin(2.0*math.pi*(radius-options.canal)/options.pe
microstructure = numpy.where(radius < float(options.canal),1,0) + numpy.where(radius > float(options.osteon),2,0) microstructure = numpy.where(radius < float(options.canal),1,0) + numpy.where(radius > float(options.osteon),2,0)
info['grains'] = 3 info['microstructures'] = 3
alphaOfGrain = numpy.zeros(info['resolution'][0]*info['resolution'][1],'d') alphaOfGrain = numpy.zeros(info['grid'][0]*info['grid'][1],'d')
betaOfGrain = numpy.zeros(info['resolution'][0]*info['resolution'][1],'d') betaOfGrain = numpy.zeros(info['grid'][0]*info['grid'][1],'d')
for y in xrange(info['resolution'][1]): for y in xrange(info['grid'][1]):
for x in xrange(info['resolution'][0]): for x in xrange(info['grid'][0]):
if microstructure[y,x] == 0: if microstructure[y,x] == 0:
microstructure[y,x] = info['grains'] microstructure[y,x] = info['microstructures']
alphaOfGrain[info['grains']] = alpha[y,x] alphaOfGrain[info['microstructures']] = alpha[y,x]
betaOfGrain[ info['grains']] = beta[y,x] betaOfGrain[ info['microstructures']] = beta[y,x]
info['grains'] += 1 info['microstructures'] += 1
file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \
'microstructures: %i\n'%info['microstructures'] + \
'homogenization: %i\n'%info['homogenization'])
file['croak'].write("bounding box: %s\n"%(numpy.sqrt(numpy.sum(box*box,0))))
# -------------------------------------- switch according to task ---------------------------------- # -------------------------------------- switch according to task ----------------------------------
formatwidth = 1+int(math.floor(math.log10(info['microstructures']-1)))
formatwidth = 1+int(math.floor(math.log10(info['grains']-1)))
if options.config: if options.config:
file['output'].write('<microstructure>\n') file['output'].write('<microstructure>\n')
file['output'].write('\n[canal]\n' + \ file['output'].write('\n[canal]\n' + \
@ -161,15 +166,17 @@ if options.config:
else: else:
file['output'].write("4 header\n" + \ file['output'].write("6 header\n" + \
"resolution\ta %i\tb %i\tc %i\n"%(info['resolution'][0],info['resolution'][1],info['resolution'][2]) + \ "$Id$\n" + \
"dimension\tx %g\ty %g\tz %g\n"%(info['dimension'][0],info['dimension'][1],info['dimension'][2]) + \ "grid\ta %i\tb %i\tc %i\n"%(info['grid'][0],info['grid'][1],info['grid'][2]) + \
"size\tx %g\ty %g\tz %g\n"%(info['size'][0],info['size'][1],info['size'][2]) + \
"origin\tx %g\ty %g\tz %g\n"%(info['origin'][0],info['origin'][1],info['origin'][2]) + \ "origin\tx %g\ty %g\tz %g\n"%(info['origin'][0],info['origin'][1],info['origin'][2]) + \
"homogenization 1\n" "microstructures\t%i\n"%(info['microstructures']) + \
"homogenization\t%i\n"%(info['homogenization'])
) )
for y in xrange(info['resolution'][1]): for y in xrange(info['grid'][1]):
for x in xrange(info['resolution'][0]): for x in xrange(info['grid'][0]):
file['output'].write(\ file['output'].write(\
str(microstructure[y,x]).rjust(formatwidth) + \ str(microstructure[y,x]).rjust(formatwidth) + \
{True:' ',False:'\n'}[options.twoD] ) {True:' ',False:'\n'}[options.twoD] )

58
processing/pre/geom_check.py
View File

@ -92,14 +92,16 @@ def vtk_writeASCII_mesh(dim,res,origin,data):
# ----------------------- MAIN ------------------------------- # ----------------------- MAIN -------------------------------
identifiers = { identifiers = {
'resolution': ['a','b','c'], 'grid': ['a','b','c'],
'dimension': ['x','y','z'], 'size': ['x','y','z'],
'origin': ['x','y','z'], 'origin': ['x','y','z'],
} }
mappings = { mappings = {
'resolution': lambda x: int(x), 'grid': lambda x: int(x),
'dimension': lambda x: float(x), 'size': lambda x: float(x),
'origin': lambda x: float(x), 'origin': lambda x: float(x),
'homogenization': lambda x: int(x),
'microstructures': lambda x: int(x),
} }
parser = OptionParser(option_class=extendedOption, usage='%prog [geomfile[s]]', description = """ parser = OptionParser(option_class=extendedOption, usage='%prog [geomfile[s]]', description = """
@ -145,39 +147,49 @@ for file in files:
content = file['input'].readlines() content = file['input'].readlines()
file['input'].close() file['input'].close()
info = {'resolution': [0,0,0], info = {'grid': [0,0,0],
'dimension': [0.0,0.0,0.0], 'size': [0.0,0.0,0.0],
'origin': [0.0,0.0,0.0], 'origin': [0.0,0.0,0.0],
'homogenization': 1,
'microstructures': 0,
} }
for header in headers: for header in headers:
headitems = map(str.lower,header.split()) headitems = map(str.lower,header.split())
if headitems[0] in identifiers.keys(): if headitems[0] == 'resolution': headitems[0] = 'grid'
for i in xrange(len(identifiers[headitems[0]])): if headitems[0] == 'dimension': headitems[0] = 'size'
info[headitems[0]][i] = mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1]) if headitems[0] in mappings.keys():
if headitems[0] in identifiers.keys():
for i in xrange(len(identifiers[headitems[0]])):
info[headitems[0]][i] = \
mappings[headitems[0]](headitems[headitems.index(identifiers[headitems[0]][i])+1])
else:
info[headitems[0]] = mappings[headitems[0]](headitems[1])
if numpy.all(info['resolution'] == 0): if numpy.all(info['grid'] == 0):
file['croak'].write('no resolution info found.\n') file['croak'].write('no grid info found.\n')
continue continue
if numpy.all(info['dimension'] == 0.0): if numpy.all(info['size'] == 0.0):
file['croak'].write('no dimension info found.\n') file['croak'].write('no size info found.\n')
continue continue
file['croak'].write('resolution: %s\n'%(' x '.join(map(str,info['resolution']))) + \ file['croak'].write('grid a b c: %s\n'%(' x '.join(map(str,info['grid']))) + \
'dimension: %s\n'%(' x '.join(map(str,info['dimension']))) + \ 'size x y z: %s\n'%(' x '.join(map(str,info['size']))) + \
'origin: %s\n'%(' : '.join(map(str,info['origin']))) 'origin x y z: %s\n'%(' : '.join(map(str,info['origin']))) + \
) 'homogenization: %i\n'%info['homogenization'] + \
'microstructures: %i\n'%info['microstructures'])
data = {'scalar':{'structure':numpy.zeros(info['resolution'],'i')}} data = {'scalar':{'structure':numpy.zeros(info['grid'],'i')}}
i = 0 i = 0
for line in content: for line in content:
for item in map(int,line.split()): for item in map(int,line.split()):
data['scalar']['structure'][i%info['resolution'][0],(i/info['resolution'][0])%info['resolution'][1],i/info['resolution'][0]/info['resolution'][1]] = item data['scalar']['structure'][i%info['grid'][0],(i/info['grid'][0])%info['grid'][1],i/info['grid'][0]/info['grid'][1]] = item
i += 1 i += 1
out = {} out = {}
out['mesh'] = vtk_writeASCII_mesh(info['dimension'],info['resolution'],info['origin'],data) out['mesh'] = vtk_writeASCII_mesh(info['size'],info['grid'],info['origin'],data)
for what in out.keys(): for what in out.keys():
if file['name'] == 'STDIN': if file['name'] == 'STDIN':