From 1336c8d0e6b944c034c363e2dfc098d2a271ffb6 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Mon, 16 Nov 2015 09:54:39 +0000 Subject: [PATCH] now using default 2D output for geometry --- processing/pre/geom_fromOsteonGeometry.py | 176 ++++++++++------------ 1 file changed, 80 insertions(+), 96 deletions(-) diff --git a/processing/pre/geom_fromOsteonGeometry.py b/processing/pre/geom_fromOsteonGeometry.py index 351038aff..660058c33 100755 --- a/processing/pre/geom_fromOsteonGeometry.py +++ b/processing/pre/geom_fromOsteonGeometry.py @@ -21,63 +21,57 @@ Its fiber orientation is oscillating by +/- amplitude within one period. """, version = scriptID) -parser.add_option('-g', '--grid', dest='grid', type='int', nargs=2, metavar = 'int int', \ - help='a,b grid of hexahedral box %default') -parser.add_option('-s', '--size', dest='size', type='float', nargs=2, metavar = 'float float', \ - help='x,y size of hexahedral box %default') -parser.add_option('-c', '--canal', dest='canal', type='float', metavar = 'float', \ +parser.add_option('-g', '--grid', dest='grid', type='int', nargs=2, metavar = 'int int', + help='a,b grid of hexahedral box [%default]') +parser.add_option('-s', '--size', dest='size', type='float', nargs=2, metavar = 'float float', + help='x,y size of hexahedral box [%default]') +parser.add_option('-c', '--canal', dest='canal', type='float', metavar = 'float', help='Haversian canal radius [%default]') -parser.add_option('-o', '--osteon', dest='osteon', type='float', metavar = 'float', \ - help='osteon radius (horizontal) [%default]') -parser.add_option('-l', '--lamella', dest='period', type='float', metavar = 'float', \ +parser.add_option('-o', '--osteon', dest='osteon', type='float', metavar = 'float', + help='horizontal osteon radius [%default]') +parser.add_option('-l', '--lamella', dest='period', type='float', metavar = 'float', help='lamella width [%default]') -parser.add_option('-a', '--amplitude', dest='amplitude', type='float', metavar = 'float', \ +parser.add_option('-a', '--amplitude', dest='amplitude', type='float', metavar = 'float', help='amplitude of twisted plywood wiggle in deg [%default]') -parser.add_option( '--aspect', dest='aspect', type='float', metavar = 'float', \ - help='osteon aspect ratio (vert/horiz) [%default]') -parser.add_option('-w', '--omega', dest='omega', type='float', metavar = 'float', \ - help='rotation angle (around normal) of osteon [%default]') -parser.add_option('--homogenization', dest='homogenization', type='int', metavar = 'int', \ +parser.add_option( '--aspect', dest='aspect', type='float', metavar = 'float', + help='vertical/horizontal osteon aspect ratio [%default]') +parser.add_option('-w', '--omega', dest='omega', type='float', metavar = 'float', + help='rotation angle around normal of osteon [%default]') +parser.add_option('--homogenization', dest='homogenization', type='int', metavar = 'int', help='homogenization index to be used [%default]') -parser.add_option('--crystallite', dest='crystallite', type='int', metavar = 'int', \ +parser.add_option('--crystallite', dest='crystallite', type='int', metavar = 'int', help='crystallite index to be used [%default]') -parser.add_option('--configuration', dest='config', action='store_true', \ - help='output material configuration [%default]') -parser.add_option('-2', '--twodimensional', dest='twoD', action='store_true', \ - help='use two-dimensional geom data arrangement [%default]') -parser.set_defaults(canal = 25e-6) -parser.set_defaults(osteon = 100e-6) -parser.set_defaults(aspect = 1.0) -parser.set_defaults(omega = 0.0) -parser.set_defaults(period = 5e-6) -parser.set_defaults(amplitude = 60) -parser.set_defaults(size = np.array([300e-6,300e-6],'d')) -parser.set_defaults(grid = np.array([512,512],'i')) -parser.set_defaults(homogenization = 1) -parser.set_defaults(crystallite = 1) -parser.set_defaults(config = False) -parser.set_defaults(twoD = False) +parser.set_defaults(canal = 25e-6, + osteon = 100e-6, + aspect = 1.0, + omega = 0.0, + period = 5e-6, + amplitude = 60, + size = (300e-6,300e-6), + grid = (512,512), + homogenization = 1, + crystallite = 1) (options,filename) = parser.parse_args() -# ------------------------------------------ setup file handle ------------------------------------- -if filename == []: - file = {'output':sys.stdout, 'croak':sys.stderr} -else: - file = {'output':open(filename[0],'w'), 'croak':sys.stderr} - if np.any(options.grid < 2): - file['croak'].write('grid too small...\n') - sys.exit() - + parser('invalid grid a b c.') if np.any(options.size <= 0.0): - file['croak'].write('size too small...\n') - sys.exit() + parser('invalid size x y z.') + +# --- open input files ---------------------------------------------------------------------------- + +if filename == []: filename = [None] + +table = damask.ASCIItable(outname = filename[0], + buffered = False) + +damask.util.report(scriptName,filename[0]) options.omega *= math.pi/180.0 # rescale ro radians rotation = np.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 = np.dot(np.array([[options.canal,0.],[0.,options.aspect*options.canal]]).transpose(),rotation) @@ -90,8 +84,8 @@ info = { 'homogenization': options.homogenization, } -info['grid'][:2] = options.grid -info['size'][:2] = options.size +info['grid'][:2] = np.array(options.grid,'i') +info['size'][:2] = np.array(options.size,'d') info['size'][2] = min(info['size'][0]/info['grid'][0],info['size'][1]/info['grid'][1]) info['origin'] = -info['size']/2.0 @@ -118,59 +112,49 @@ for y in xrange(info['grid'][1]): alphaOfGrain[info['microstructures']] = alpha[y,x] betaOfGrain[ info['microstructures']] = beta[y,x] info['microstructures'] += 1 + #--- report --------------------------------------------------------------------------------------- -else: file['croak'].write('\033[1m'+scriptName+'\033[0m\n') -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"%(np.sqrt(np.sum(box*box,0)))) - -if np.any(info['grid'] < 1): - file['croak'].write('invalid grid a b c.\n') - sys.exit() -if np.any(info['size'] <= 0.0): - file['croak'].write('invalid size x y z.\n') - sys.exit() - +damask.util.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))), + 'size x y z: %s'%(' x '.join(map(str,info['size']))), + 'origin x y z: %s'%(' : '.join(map(str,info['origin']))), + 'homogenization: %i'%info['homogenization'], + 'microstructures: %i'%info['microstructures']]) # -------------------------------------- switch according to task ---------------------------------- formatwidth = 1+int(math.floor(math.log10(info['microstructures']-1))) -if options.config: - file['output'].write('\n') - file['output'].write('\n[canal]\n' + \ - 'crystallite %i\n'%options.crystallite + \ - '(constituent)\tphase 1\ttexture 1\tfraction 1.0\n') - file['output'].write('\n[interstitial]\n' + \ - 'crystallite %i\n'%options.crystallite + \ - '(constituent)\tphase 2\ttexture 2\tfraction 1.0\n') - for i in xrange(3,info['microstructures']): - file['output'].write('\n[Grain%s]\n'%(str(i).zfill(formatwidth)) + \ - 'crystallite %i\n'%options.crystallite + \ - '(constituent)\tphase 3\ttexture %s\tfraction 1.0\n'%(str(i).rjust(formatwidth))) +header = [scriptID + ' ' + ' '.join(sys.argv[1:])] +header.append('') +header.append('[canal]') +header.append('crystallite %i'%options.crystallite) +header.append('(constituent)\tphase 1\ttexture 1\tfraction 1.0') +header.append('[interstitial]') +header.append('crystallite %i'%options.crystallite) +header.append('(constituent)\tphase 2\ttexture 2\tfraction 1.0') +for i in xrange(3,info['microstructures']): + header.append('[Grain%s]'%(str(i).zfill(formatwidth))) + header.append('crystallite %i'%options.crystallite) + header.append('(constituent)\tphase 3\ttexture %s\tfraction 1.0'%(str(i).rjust(formatwidth))) - file['output'].write('\n\n') - file['output'].write('\n[canal]\n') - file['output'].write('\n[interstitial]\n') - for i in xrange(3,info['microstructures']): - file['output'].write('\n[Grain%s]\n'%(str(i).zfill(formatwidth)) + \ - '(gauss)\tphi1 %g\tPhi %g\tphi2 0\tscatter 0.0\tfraction 1.0\n'%(\ - alphaOfGrain[i],\ - betaOfGrain[i])) +header.append('') +header.append('[canal]') +header.append('[interstitial]') +for i in xrange(3,info['microstructures']): + header.append('[Grain%s]'%(str(i).zfill(formatwidth))) + header.append('(gauss)\tphi1 %g\tPhi %g\tphi2 0\tscatter 0.0\tfraction 1.0'\ + %(alphaOfGrain[i],betaOfGrain[i])) +header.append([ + "grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=info['grid']), + "size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=info['size']), + "origin\tx {origin[0]}\ty {origin[1]}\tz {origin[2]}".format(origin=info['origin']), + "homogenization\t{homog}".format(homog=info['homogenization']), + "microstructures\t{microstructures}".format(microstructures=info['microstructures'])]) -else: - header = [scriptID + ' ' + ' '.join(sys.argv[1:])+'\n'] - header.append("grid\ta %i\tb %i\tc %i\n"%(info['grid'][0],info['grid'][1],info['grid'][2],)) - header.append("size\tx %f\ty %f\tz %f\n"%(info['size'][0],info['size'][1],info['size'][2],)) - header.append("origin\tx %f\ty %f\tz %f\n"%(info['origin'][0],info['origin'][1],info['origin'][2],)) - header.append("microstructures\t%i\n"%info['microstructures']) - header.append("homogenization\t%i\n"%info['homogenization']) - file['output'].write('%i\theader\n'%(len(header))+''.join(header)) - - for y in xrange(info['grid'][1]): - for x in xrange(info['grid'][0]): - file['output'].write(\ - str(microstructure[y,x]).rjust(formatwidth) + \ - {True:' ',False:'\n'}[options.twoD] ) - file['output'].write({True:'\n',False:''}[options.twoD]) - +table.info_append(header) +table.head_write() + +# --- write microstructure information ------------------------------------------------------------ + +table.data = microstructure.reshape(info['grid'][1]*info['grid'][2],info['grid'][0]) +table.data_writeArray('%%%ii'%(formatwidth),delimiter=' ') + +#--- output finalization -------------------------------------------------------------------------- +table.close()