diff --git a/processing/pre/geom_canvas.py b/processing/pre/geom_canvas.py index 8ed1f5ab2..c20871371 100755 --- a/processing/pre/geom_canvas.py +++ b/processing/pre/geom_canvas.py @@ -47,7 +47,7 @@ for name in filenames: table = damask.ASCIItable(name = name, buffered = False, labeled = False) except: continue - table.croak('\033[1m'+scriptName+'\033[0m'+(': '+name if name else '')) + table.croak(damask.util.emph(scriptName)+(': '+name if name else '')) # --- interpret header ---------------------------------------------------------------------------- diff --git a/processing/pre/geom_fromAng.py b/processing/pre/geom_fromAng.py index 0261f94f1..04d5499b4 100755 --- a/processing/pre/geom_fromAng.py +++ b/processing/pre/geom_fromAng.py @@ -13,103 +13,107 @@ scriptName = os.path.splitext(scriptID.split()[1])[0] # MAIN #-------------------------------------------------------------------------------------------------- parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """ -Generate geometry description and material configuration from input files used by R.A. Lebensohn. + +Generate geometry description and material configuration from EBSD data in given square-gridded 'ang' file. +Two phases can be discriminated based on threshold value in a given data column. """, version = scriptID) -parser.add_option('--column', dest='column', type='int', metavar = 'int', +parser.add_option('--column', dest='column', type='int', metavar = 'int', help='data column to discriminate between both phases [%default]') parser.add_option('-t','--threshold', dest='threshold', type='float', metavar = 'float', help='threshold value for phase discrimination [%default]') -parser.add_option('--homogenization', dest='homogenization', type='int', metavar = 'int', +parser.add_option('--homogenization', dest='homogenization', type='int', metavar = 'int', help='homogenization index for configuration [%default]') -parser.add_option('--phase', dest='phase', type='int', nargs = 2, metavar = 'int int', +parser.add_option('--phase', dest='phase', type='int', nargs = 2, metavar = 'int int', help='phase indices for configuration %default') -parser.add_option('--crystallite', dest='crystallite', type='int', metavar = 'int', +parser.add_option('--crystallite', dest='crystallite', type='int', metavar = 'int', help='crystallite index for configuration [%default]') parser.add_option('-c', '--configuration', dest='config', action='store_true', help='output material configuration [%default]') parser.add_option('--compress', dest='compress', action='store_true', help='lump identical microstructure and texture information [%default]') +parser.add_option('-a', '--axes', dest='axes', nargs = 3, metavar = 'string string string', + help='Euler angle coordinate system for configuration x,y,z = %default') parser.add_option('-p', '--precision', dest='precision', choices=['0','1','2','3'], metavar = 'int', help = 'euler angles decimal places for output format and compressing (0,1,2,3) [2]') - -parser.set_defaults(column = 7) -parser.set_defaults(threshold = 1.0) + +parser.set_defaults(column = 11) +parser.set_defaults(threshold = 0.5) parser.set_defaults(homogenization = 1) parser.set_defaults(phase = [1,2]) parser.set_defaults(crystallite = 1) parser.set_defaults(config = False) parser.set_defaults(compress = False) +parser.set_defaults(axes = ['y','x','-z']) parser.set_defaults(precision = '2') - (options,filenames) = parser.parse_args() -#--- 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.stdout, - }) +for i in options.axes: + if i.lower() not in ['x','+x','-x','y','+y','-y','z','+z','-z']: + parser.error('invalid axes %s %s %s' %(options.axes[0],options.axes[1],options.axes[2])) -#--- loop over input files ------------------------------------------------------------------------ -for file in files: - file['croak'].write('\033[1m' + scriptName + '\033[0m: ' + (file['name'] if file['name'] != 'STDIN' else '') + '\n') +# --- loop over input files ------------------------------------------------------------------------- + +if filenames == []: filenames = [None] + +for name in filenames: + try: + table = damask.ASCIItable(name = name, outname = os.path.splitext(name)[0] +'%s'%('_material.config' if options.config else '.geom'), + buffered = False, labeled = False, readonly=True) + except: continue + table.croak(damask.util.emph(scriptName)+(': '+name if name else '')) info = { - 'grid': np.zeros(3,'i'), + 'grid': np.ones(3,'i'), 'size': np.zeros(3,'d'), 'origin': np.zeros(3,'d'), 'microstructures': 0, 'homogenization': options.homogenization } - coords = [{},{},{}] - pos = {'min':[ float("inf"), float("inf"), float("inf")], - 'max':[-float("inf"),-float("inf"),-float("inf")]} + coords = [{},{},{1:True}] + pos = {'min':[ float("inf"), float("inf")], + 'max':[-float("inf"),-float("inf")]} phase = [] eulerangles = [] + # --------------- read data ----------------------------------------------------------------------- - for line in file['input']: - if line.strip(): - words = line.split() - currPos = words[3:6] - for i in xrange(3): + while table.data_read(): + words = table.data + if words[0] == '#': # process initial comments/header block + if len(words) > 2: + if words[2].lower() == 'hexgrid': + table.croak('The file has HexGrid format. Please first convert to SquareGrid...\n') + break + else: + currPos = words[3:5] + for i in xrange(2): coords[i][currPos[i]] = True currPos = map(float,currPos) - for i in xrange(3): + for i in xrange(2): pos['min'][i] = min(pos['min'][i],currPos[i]) pos['max'][i] = max(pos['max'][i],currPos[i]) eulerangles.append(map(math.degrees,map(float,words[:3]))) phase.append(options.phase[int(float(words[options.column-1]) > options.threshold)]) - + # --------------- determine size and grid --------------------------------------------------------- info['grid'] = np.array(map(len,coords),'i') - info['size'] = info['grid']/np.maximum(np.ones(3,'d'),info['grid']-1.0)* \ - np.array([pos['max'][0]-pos['min'][0], - pos['max'][1]-pos['min'][1], - pos['max'][2]-pos['min'][2]],'d') + info['size'][0:2] = info['grid'][0:2]/(info['grid'][0:2]-1.0)* \ + np.array([pos['max'][0]-pos['min'][0], + pos['max'][1]-pos['min'][1]],'d') + info['size'][2]=info['size'][0]/info['grid'][0] eulerangles = np.array(eulerangles,dtype='f').reshape(info['grid'].prod(),3) phase = np.array(phase,dtype='i').reshape(info['grid'].prod()) limits = [360,180,360] if any([np.any(eulerangles[:,i]>=limits[i]) for i in [0,1,2]]): - file['croak'].write('Error: euler angles out of bound. Ang file might contain unidexed poins.\n') + table.croak('Error: euler angles out of bound. Ang file might contain unidexed poins.\n') for i,angle in enumerate(['phi1','PHI','phi2']): for n in np.nditer(np.where(eulerangles[:,i]>=limits[i]),['zerosize_ok']): - file['croak'].write('%s in line %i (%4.2f %4.2f %4.2f)\n' + table.croak('%s in line %i (%4.2f %4.2f %4.2f)\n' %(angle,n,eulerangles[n,0],eulerangles[n,1],eulerangles[n,2])) continue eulerangles=np.around(eulerangles,int(options.precision)) # round to desired precision @@ -121,7 +125,7 @@ for file in files: euleranglesRadInt = (eulerangles*10**int(options.precision)).astype('int') # scale by desired precision and convert to int eulerKeys = np.array([int(''.join(map(formatString.format,euleranglesRadInt[i,:]))) \ for i in xrange(info['grid'].prod())]) # create unique integer key from three euler angles by concatenating the string representation with leading zeros and store as integer - devNull, texture, eulerKeys_idx = np.unique(eulerKeys, return_index = True, return_inverse=True)# search unique euler angle keys. Texture IDs are the indices of the first occurence, the inverse is used to construct the microstructure + devNull, texture, eulerKeys_idx = np.unique(eulerKeys, return_index = True, return_inverse=True)# search unique euler angle keys. Texture IDs are the indices of the first occurrence, the inverse is used to construct the microstructure msFull = np.array([[eulerKeys_idx[i],phase[i]] for i in xrange(info['grid'].prod())],'i8') # create a microstructure (texture/phase pair) for each point using unique texture IDs. Use longInt (64bit, i8) because the keys might be long devNull,msUnique,matPoints = np.unique(msFull.view('c16'),True,True) matPoints+=1 @@ -136,6 +140,7 @@ for file in files: outStringAngles='(gauss) phi1 '+eulerFormatOut+' Phi '+eulerFormatOut+' phi2 '+eulerFormatOut+' scatter 0.0 fraction 1.0\n' for i in xrange(len(texture)): textureOut += ['[Texture%s]\n'%str(i+1).zfill(formatOut) + + 'axes %s %s %s\n'%(options.axes[0],options.axes[1],options.axes[2]) + outStringAngles%tuple(eulerangles[texture[i],...]) ] formatOut = 1+int(math.log10(len(microstructure))) @@ -149,41 +154,41 @@ for file in files: info['microstructures'] = len(microstructure) #--- report --------------------------------------------------------------------------------------- - 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']))) + - 'homogenization: %i\n'%info['homogenization'] + - 'microstructures: %i\n\n'%info['microstructures']) + table.croak('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']))) + + 'homogenization: %i\n'%info['homogenization'] + + 'microstructures: %i\n\n'%info['microstructures']) if np.any(info['grid'] < 1): - file['croak'].write('invalid grid a b c.\n') + table.croak('invalid grid a b c.\n') continue if np.any(info['size'] <= 0.0): - file['croak'].write('invalid size x y z.\n') + table.croak('invalid size x y z.\n') continue -#--- write data ----------------------------------------------------------------------------------- +#--- write data/header -------------------------------------------------------------------------------- + table.info_clear() if options.config: - file['output'].write('\n'.join(microstructureOut+ textureOut) + '\n') + table.output_write(line for line in microstructureOut+ textureOut) else: - header = [' '.join([scriptID] + sys.argv[1:]), - "grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],), - "size\tx %f\ty %f\tz %f"%(info['size'][0],info['size'][1],info['size'][2],), - "origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2],), - "microstructures\t%i"%info['microstructures'], - "homogenization\t%i"%info['homogenization'], - ] - file['output'].write('\n'.join(['%i\theader'%(len(header))] + header) + '\n') + table.info_append([' '.join([scriptID] + sys.argv[1:]), + "grid\ta %i\tb %i\tc %i"%(info['grid'][0],info['grid'][1],info['grid'][2],), + "size\tx %f\ty %f\tz %f"%(info['size'][0],info['size'][1],info['size'][2],), + "origin\tx %f\ty %f\tz %f"%(info['origin'][0],info['origin'][1],info['origin'][2],), + "microstructures\t%i"%info['microstructures'], + "homogenization\t%i"%info['homogenization'], + ]) + table.head_write() if options.compress: - matPoints = matPoints.reshape([info['grid'][1]*info['grid'][2],info['grid'][0]]) - np.savetxt(file['output'],matPoints,fmt='%0'+str(1+int(math.log10(np.amax(matPoints))))+'d') + matPoints = matPoints.reshape((info['grid'][1],info['grid'][0])) + table.data = matPoints + table.data_writeArray('%%%ii'%(1+int(math.log10(np.amax(matPoints)))),delimiter=' ') else: - file['output'].write("1 to %i\n"%(info['microstructures'])) - -#--- output finalization -------------------------------------------------------------------------- - if file['name'] != 'STDIN': - file['output'].close() - os.rename(file['name']+'_tmp', - os.path.splitext(file['name'])[0] +'%s'%('_material.config' if options.config else '.geom')) + table.output_write("1 to %i\n"%(info['microstructures'])) + table.output_flush() +# --- output finalization -------------------------------------------------------------------------- + + table.close()