DAMASK_EICMD/processing/pre/geom_fromVoronoiTessellation.py

#!/usr/bin/env python3

import os
import sys
import multiprocessing
from io import StringIO
from functools import partial
from optparse import OptionParser,OptionGroup

import numpy as np
from scipy import spatial

import damask


scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID   = ' '.join([scriptName,damask.version])


def findClosestSeed(seeds, weights, point):
    return np.argmin(np.sum((np.broadcast_to(point,(len(seeds),3))-seeds)**2,axis=1) - weights)


def Laguerre_tessellation(grid, size, seeds, weights, origin = np.zeros(3), periodic = True, cpus = 2):

    if periodic:
        weights_p = np.tile(weights,27).flatten(order='F')                                          # Laguerre weights (1,2,3,1,2,3,...,1,2,3)
        seeds_p = np.vstack((seeds  -np.array([size[0],0.,0.]),seeds,  seeds  +np.array([size[0],0.,0.])))
        seeds_p = np.vstack((seeds_p-np.array([0.,size[1],0.]),seeds_p,seeds_p+np.array([0.,size[1],0.])))
        seeds_p = np.vstack((seeds_p-np.array([0.,0.,size[2]]),seeds_p,seeds_p+np.array([0.,0.,size[2]])))
        coords = damask.grid_filters.cell_coord0(grid*3,size*3,-origin-size).reshape(-1,3,order='F')
    else:
        weights_p = weights.flatten()
        seeds_p   = seeds
        coords = damask.grid_filters.cell_coord0(grid,size,-origin).reshape(-1,3,order='F')

    if cpus > 1:
        pool = multiprocessing.Pool(processes = cpus)
        result = pool.map_async(partial(findClosestSeed,seeds_p,weights_p), [coord for coord in coords])
        pool.close()
        pool.join()
        closest_seed = np.array(result.get())
    else:
        closest_seed= np.array([findClosestSeed(seeds_p,weights_p,coord) for coord in coords])

    if periodic:
        closest_seed = closest_seed.reshape(grid[2]*3,grid[1]*3,grid[0]*3)
        return closest_seed[grid[2]:grid[2]*2,grid[1]:grid[1]*2,grid[0]:grid[0]*2]%seeds.shape[0]
    else:
        return closest_seed


def Voronoi_tessellation(grid, size, seeds, origin = np.zeros(3), periodic = True):

    coords = damask.grid_filters.cell_coord0(grid,size,-origin).reshape(-1,3,order='F')
    KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds)
    devNull,closest_seed = KDTree.query(coords)

    return closest_seed


# --------------------------------------------------------------------
#                                MAIN
# --------------------------------------------------------------------

parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [seedfile(s)]', description = """
Generate geometry description and material configuration by tessellation of given seeds file.

""", version = scriptID)


group = OptionGroup(parser, "Tessellation","")

group.add_option('-l',
                 '--laguerre',
                 dest = 'laguerre',
                 action = 'store_true',
                 help = 'use Laguerre (weighted Voronoi) tessellation')
group.add_option('--cpus',
                 dest = 'cpus',
                 type = 'int', metavar = 'int',
                 help = 'number of parallel processes to use for Laguerre tessellation [%default]')
group.add_option('--nonperiodic',
                 dest = 'periodic',
                 action = 'store_false',
                 help = 'nonperiodic tessellation')

parser.add_option_group(group)

group = OptionGroup(parser, "Geometry","")

group.add_option('-g',
                 '--grid',
                 dest = 'grid',
                 type = 'int', nargs = 3, metavar = ' '.join(['int']*3),
                 help = 'a,b,c grid of hexahedral box')
group.add_option('-s',
                 '--size',
                 dest = 'size',
                 type = 'float', nargs = 3, metavar=' '.join(['float']*3),
                 help = 'x,y,z size of hexahedral box [1.0 1.0 1.0]')
group.add_option('-o',
                 '--origin',
                 dest = 'origin',
                 type = 'float', nargs = 3, metavar=' '.join(['float']*3),
                 help = 'origin of grid [0.0 0.0 0.0]')

parser.add_option_group(group)

group = OptionGroup(parser, "Seeds","")

group.add_option('-p',
                 '--pos', '--seedposition',
                  dest = 'pos',
                  type = 'string', metavar = 'string',
                  help = 'label of coordinates [%default]')
group.add_option('-w',
                 '--weight',
                 dest = 'weight',
                 type = 'string', metavar = 'string',
                 help = 'label of weights [%default]')
group.add_option('-m',
                 '--microstructure',
                 dest = 'microstructure',
                 type = 'string', metavar = 'string',
                 help = 'label of microstructures [%default]')
group.add_option('-e',
                 '--eulers',
                 dest = 'eulers',
                 type = 'string', metavar = 'string',
                 help = 'label of Euler angles [%default]')
group.add_option('--axes',
                 dest = 'axes',
                 type = 'string', nargs = 3, metavar = ' '.join(['string']*3),
                 help = 'orientation coordinate frame in terms of position coordinate frame')

parser.add_option_group(group)

group = OptionGroup(parser, "Configuration","")

group.add_option('--without-config',
                 dest = 'config',
                 action = 'store_false',
                 help = 'omit material configuration header')
group.add_option('--homogenization',
                 dest = 'homogenization',
                 type = 'int', metavar = 'int',
                 help = 'homogenization index to be used [%default]')
group.add_option('--phase',
                 dest = 'phase',
                 type = 'int', metavar = 'int',
                 help = 'phase index to be used [%default]')

parser.add_option_group(group)

parser.set_defaults(pos            = 'pos',
                    weight         = 'weight',
                    microstructure = 'microstructure',
                    eulers         = 'euler',
                    homogenization = 1,
                    phase          = 1,
                    cpus           = 2,
                    laguerre       = False,
                    periodic       = True,
                    config         = True,
                  )

(options,filenames) = parser.parse_args()
if filenames == []: filenames = [None]

for name in filenames:
    damask.util.report(scriptName,name)

    table = damask.Table.from_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)

    size   = np.ones(3)
    origin = np.zeros(3)
    for line in table.comments:
        items = line.lower().strip().split()
        key = items[0] if items else ''
        if   key == 'grid':
            grid   = np.array([  int(dict(zip(items[1::2],items[2::2]))[i]) for i in ['a','b','c']])
        elif key == 'size':
            size   = np.array([float(dict(zip(items[1::2],items[2::2]))[i]) for i in ['x','y','z']])
        elif key == 'origin':
            origin = np.array([float(dict(zip(items[1::2],items[2::2]))[i]) for i in ['x','y','z']])
    if options.grid:   grid   = np.array(options.grid)
    if options.size:   size   = np.array(options.size)
    if options.origin: origin = np.array(options.origin)

    seeds  = table.get(options.pos)

    grains = table.get(options.microstructure) if options.microstructure in table.labels else np.arange(len(seeds))+1
    grainIDs  = np.unique(grains).astype('i')
    NgrainIDs = len(grainIDs)

    if options.eulers in table.labels:
        eulers = table.get(options.eulers)

    if options.laguerre:
        indices = grains[Laguerre_tessellation(grid,size,seeds,table.get(options.weight),origin,
                                               options.periodic,options.cpus)]
    else:
        indices = grains[Voronoi_tessellation (grid,size,seeds,origin,options.periodic)]

    config_header = []
    if options.config:

        if options.eulers in table.labels:
            config_header += ['<texture>']
            for ID in grainIDs:
                eulerID = np.nonzero(grains == ID)[0][0]                                            # find first occurrence of this grain id
                config_header += ['[Grain{}]'.format(ID),
                                  '(gauss)\tphi1 {:.2f}\tPhi {:.2f}\tphi2 {:.2f}'.format(*eulers[eulerID])
                                 ]
                if options.axes: config_header += ['axes\t{} {} {}'.format(*options.axes)]

        config_header += ['<microstructure>']
        for ID in grainIDs:
            config_header += ['[Grain{}]'.format(ID),
                              '(constituent)\tphase {}\ttexture {}\tfraction 1.0'.format(options.phase,ID)
                             ]

        config_header += ['<!skip>']

    header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
           + config_header
    geom = damask.Geom(indices.reshape(grid),size,origin,
                       homogenization=options.homogenization,comments=header)
    damask.util.croak(geom)

    geom.to_file(sys.stdout if name is None else os.path.splitext(name)[0]+'.geom',pack=False)