#!/usr/bin/env python2.7 # -*- coding: UTF-8 no BOM -*- import os,sys,math import numpy as np from optparse import OptionParser import damask scriptName = os.path.splitext(os.path.basename(__file__))[0] scriptID = ' '.join([scriptName,damask.version]) #-------------------------------------------------------------------------------------------------- # MAIN #-------------------------------------------------------------------------------------------------- identifiers = { 'grid': ['a','b','c'], 'size': ['x','y','z'], 'origin': ['x','y','z'], } mappings = { 'grid': lambda x: int(x), 'size': lambda x: float(x), 'origin': lambda x: float(x), 'homogenization': lambda x: int(x), 'microstructures': lambda x: int(x), } parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [geomfile(s)]', description = """ Positions a geometric object within the (three-dimensional) canvas of a spectral geometry description. Depending on the sign of the dimension parameters, these objects can be boxes, cylinders, or ellipsoids. """, version = scriptID) parser.add_option('-c', '--center', dest='center', type='float', nargs = 3, metavar=' '.join(['float']*3), help='a,b,c origin of primitive %default') parser.add_option('-d', '--dimension', dest='dimension', type='float', nargs = 3, metavar=' '.join(['float']*3), help='a,b,c extension of hexahedral box; negative values are diameters') parser.add_option('-e', '--exponent', dest='exponent', type='float', nargs = 3, metavar=' '.join(['float']*3), help='i,j,k exponents for axes - 0 gives octahedron (|x|^(2^0) + |y|^(2^0) + |z|^(2^0) < 1), \ 1 gives a sphere (|x|^(2^1) + |y|^(2^1) + |z|^(2^1) < 1), \ large values produce boxes, negative turns concave.') parser.add_option('-f', '--fill', dest='fill', type='int', metavar = 'int', help='grain index to fill primitive. "0" selects maximum microstructure index + 1 [%default]') parser.add_option('-q', '--quaternion', dest='quaternion', type='float', nargs = 4, metavar=' '.join(['float']*4), help = 'rotation of primitive as quaternion') parser.add_option('-a', '--angleaxis', dest='angleaxis', nargs = 4, metavar=' '.join(['float']*4), help = 'angle,x,y,z clockwise rotation of primitive about axis by angle') parser.add_option( '--degrees', dest='degrees', action='store_true', help = 'angle is given in degrees [%default]') parser.add_option( '--nonperiodic', dest='periodic', action='store_false', help = 'wrap around edges [%default]') parser.add_option( '--realspace', dest='realspace', action='store_true', help = '-c and -d span [origin,origin+size] instead of [0,grid] coordinates') parser.set_defaults(center = (.0,.0,.0), fill = 0, degrees = False, exponent = (20,20,20), # box shape by default periodic = True, realspace = False, ) (options, filenames) = parser.parse_args() if options.dimension is None: parser.error('no dimension specified.') if options.angleaxis is not None: options.angleaxis = map(float,options.angleaxis) rotation = damask.Quaternion().fromAngleAxis(np.radians(options.angleaxis[0]) if options.degrees else options.angleaxis[0], options.angleaxis[1:4]) elif options.quaternion is not None: options.quaternion = map(float,options.quaternion) rotation = damask.Quaternion(options.quaternion) else: rotation = damask.Quaternion() options.center = np.array(options.center) options.dimension = np.array(options.dimension) # undo logarithmic sense of exponent and generate ellipsoids for negative dimensions (backward compatibility) options.exponent = np.where(np.array(options.dimension) > 0, np.power(2,options.exponent), 2) # --- loop over input files ------------------------------------------------------------------------- if filenames == []: filenames = [None] for name in filenames: try: table = damask.ASCIItable(name = name, buffered = False, labeled = False) except: continue damask.util.report(scriptName,name) # --- interpret header ---------------------------------------------------------------------------- table.head_read() info,extra_header = table.head_getGeom() 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'], ]) errors = [] if np.any(info['grid'] < 1): errors.append('invalid grid a b c.') if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.') if errors != []: damask.util.croak(errors) table.close(dismiss = True) continue #--- read data ------------------------------------------------------------------------------------ microstructure = table.microstructure_read(info['grid']) # read microstructure # --- do work ------------------------------------------------------------------------------------ newInfo = { 'microstructures': 0, } options.fill = microstructure.max()+1 if options.fill == 0 else options.fill microstructure = microstructure.reshape(info['grid'],order='F') # coordinates given in real space (default) vs voxel space if options.realspace: options.center -= info['origin'] options.center *= np.array(info['grid']) / np.array(info['size']) options.dimension *= np.array(info['grid']) / np.array(info['size']) grid = microstructure.shape # change to coordinate space where the primitive is the unit sphere/cube/etc if options.periodic: # use padding to achieve periodicity (X, Y, Z) = np.meshgrid(np.arange(-grid[0]/2, (3*grid[0])/2, dtype=np.float32), # 50% padding on each side np.arange(-grid[1]/2, (3*grid[1])/2, dtype=np.float32), np.arange(-grid[2]/2, (3*grid[2])/2, dtype=np.float32), indexing='ij') # Padding handling X = np.roll(np.roll(np.roll(X, -grid[0]/2, axis=0), -grid[1]/2, axis=1), -grid[2]/2, axis=2) Y = np.roll(np.roll(np.roll(Y, -grid[0]/2, axis=0), -grid[1]/2, axis=1), -grid[2]/2, axis=2) Z = np.roll(np.roll(np.roll(Z, -grid[0]/2, axis=0), -grid[1]/2, axis=1), -grid[2]/2, axis=2) else: # nonperiodic, much lighter on resources # change to coordinate space where the primitive is the unit sphere/cube/etc (X, Y, Z) = np.meshgrid(np.arange(0, grid[0], dtype=np.float32), np.arange(0, grid[1], dtype=np.float32), np.arange(0, grid[2], dtype=np.float32), indexing='ij') # first by translating the center onto 0, 0.5 shifts the voxel origin onto the center of the voxel X -= options.center[0] - 0.5 Y -= options.center[1] - 0.5 Z -= options.center[2] - 0.5 # and then by applying the quaternion # this should be rotation.conjugate() * (X,Y,Z), but it is this way for backwards compatibility with the older version of this script (X, Y, Z) = rotation * (X, Y, Z) # and finally by scaling (we don't worry about options.dimension being negative, np.abs occurs on the microstructure = np.where... line) X /= options.dimension[0] * 0.5 Y /= options.dimension[1] * 0.5 Z /= options.dimension[2] * 0.5 # High exponents can cause underflow & overflow - loss of precision is okay here, we just compare it to 1, so +infinity and 0 are fine old_settings = np.seterr() np.seterr(over='ignore', under='ignore') if options.periodic: # use padding to achieve periodicity inside = np.zeros(grid, dtype=bool) for i in range(2): for j in range(2): for k in range(2): inside = inside | ( # Most of this is handling the padding np.abs(X[grid[0] * i : grid[0] * (i+1), grid[1] * j : grid[1] * (j+1), grid[2] * k : grid[2] * (k+1)])**options.exponent[0] + np.abs(Y[grid[0] * i : grid[0] * (i+1), grid[1] * j : grid[1] * (j+1), grid[2] * k : grid[2] * (k+1)])**options.exponent[1] + np.abs(Z[grid[0] * i : grid[0] * (i+1), grid[1] * j : grid[1] * (j+1), grid[2] * k : grid[2] * (k+1)])**options.exponent[2] <= 1.0) microstructure = np.where(inside, options.fill, microstructure) else: # nonperiodic, much lighter on resources microstructure = np.where(np.abs(X)**options.exponent[0] + np.abs(Y)**options.exponent[1] + np.abs(Z)**options.exponent[2] <= 1.0, options.fill, microstructure) np.seterr(**old_settings) # Reset warnings to old state newInfo['microstructures'] = microstructure.max() # --- report --------------------------------------------------------------------------------------- if (newInfo['microstructures'] != info['microstructures']): damask.util.croak('--> microstructures: %i'%newInfo['microstructures']) #--- write header --------------------------------------------------------------------------------- table.info_clear() table.info_append(extra_header+[ scriptID + ' ' + ' '.join(sys.argv[1:]), "grid\ta {}\tb {}\tc {}".format(*info['grid']), "size\tx {}\ty {}\tz {}".format(*info['size']), "origin\tx {}\ty {}\tz {}".format(*info['origin']), "homogenization\t{}".format(info['homogenization']), "microstructures\t{}".format(newInfo['microstructures']), ]) table.labels_clear() table.head_write() table.output_flush() # --- write microstructure information ------------------------------------------------------------ formatwidth = int(math.floor(math.log10(microstructure.max())+1)) table.data = microstructure.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose() table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ') #--- output finalization -------------------------------------------------------------------------- table.close()