diff --git a/processing/pre/seeds_fromPokes.py b/processing/pre/seeds_fromPokes.py index 08e600ffe..4a6edc94d 100755 --- a/processing/pre/seeds_fromPokes.py +++ b/processing/pre/seeds_fromPokes.py @@ -1,11 +1,13 @@ #!/usr/bin/env python3 -# -*- coding: UTF-8 no BOM -*- -import os,math,sys -import numpy as np -import damask +import os +import sys from optparse import OptionParser +import numpy as np + +import damask + scriptName = os.path.splitext(os.path.basename(__file__))[0] scriptID = ' '.join([scriptName,damask.version]) @@ -35,109 +37,73 @@ parser.add_option('-y', action = 'store_true', dest = 'y', help = 'poke 45 deg along y') -parser.add_option('-p','--position', - dest = 'position', - type = 'string', metavar = 'string', - help = 'column label for coordinates [%default]') parser.set_defaults(x = False, y = False, box = [0.0,1.0,0.0,1.0,0.0,1.0], N = 16, - position = 'pos', ) (options,filenames) = parser.parse_args() +if filenames == []: filenames = [None] options.box = np.array(options.box).reshape(3,2) -# --- loop over output files ------------------------------------------------------------------------- - -if filenames == []: filenames = [None] - for name in filenames: - try: - table = damask.ASCIItable(name = name, - outname = os.path.splitext(name)[-2]+'_poked_{}.seeds'.format(options.N) if name else name, - buffered = False, labeled = False) - except: continue + table = damask.ASCIItable(name = name, + outname = os.path.splitext(name)[-2]+'_poked_{}.seeds'.format(options.N) if name else name, + buffered = False, labeled = False) 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']).reshape(info['grid'],order='F') # read microstructure - -# --- do work ------------------------------------------------------------------------------------ - newInfo = { - 'microstructures': 0, - } - offset = (np.amin(options.box, axis=1)*info['grid']/info['size']).astype(int) - box = np.amax(options.box, axis=1) - np.amin(options.box, axis=1) + grid = info['grid'] + size = info['size'] - Nx = int(options.N/math.sqrt(options.N*info['size'][1]*box[1]/info['size'][0]/box[0])) - Ny = int(options.N/math.sqrt(options.N*info['size'][0]*box[0]/info['size'][1]/box[1])) - Nz = int(box[2]*info['grid'][2]) + microstructure = table.microstructure_read(grid).reshape(grid) # read microstructure + + offset =(np.amin(options.box, axis=1)*grid/size).astype(int) + box = np.amax(options.box, axis=1) \ + - np.amin(options.box, axis=1) + + Nx = int(options.N/np.sqrt(options.N*size[1]*box[1]/size[0]/box[0])) + Ny = int(options.N/np.sqrt(options.N*size[0]*box[0]/size[1]/box[1])) + Nz = int(box[2]*grid[2]) damask.util.croak('poking {} x {} x {} in box {} {} {}...'.format(Nx,Ny,Nz,*box)) seeds = np.zeros((Nx*Ny*Nz,4),'d') - grid = np.zeros(3,'i') + g = np.zeros(3,'i') n = 0 for i in range(Nx): for j in range(Ny): - grid[0] = round((i+0.5)*box[0]*info['grid'][0]/Nx-0.5)+offset[0] - grid[1] = round((j+0.5)*box[1]*info['grid'][1]/Ny-0.5)+offset[1] + g[0] = round((i+0.5)*box[0]*grid[0]/Nx-0.5)+offset[0] + g[1] = round((j+0.5)*box[1]*grid[1]/Ny-0.5)+offset[1] for k in range(Nz): - grid[2] = k + offset[2] - grid %= info['grid'] - seeds[n,0:3] = (0.5+grid)/info['grid'] # normalize coordinates to box - seeds[n, 3] = microstructure[grid[0],grid[1],grid[2]] - if options.x: grid[0] += 1 - if options.y: grid[1] += 1 + g[2] = k + offset[2] + g %= grid + seeds[n,0:3] = (g+0.5)/grid # normalize coordinates to box + seeds[n, 3] = microstructure[g[2],g[1],g[0]] + if options.x: g[0] += 1 + if options.y: g[1] += 1 n += 1 - newInfo['microstructures'] = len(np.unique(seeds[:,3])) - -# --- report --------------------------------------------------------------------------------------- - if (newInfo['microstructures'] != info['microstructures']): - damask.util.croak('--> microstructures: %i'%newInfo['microstructures']) - # ------------------------------------------ assemble header --------------------------------------- table.info_clear() table.info_append(extra_header+[ scriptID + ' ' + ' '.join(sys.argv[1:]), "poking\ta {}\tb {}\tc {}".format(Nx,Ny,Nz), - "grid\ta {}\tb {}\tc {}".format(*info['grid']), - "size\tx {}\ty {}\tz {}".format(*info['size']), + "grid\ta {}\tb {}\tc {}".format(*grid), + "size\tx {}\ty {}\tz {}".format(*size), "origin\tx {}\ty {}\tz {}".format(*info['origin']), "homogenization\t{}".format(info['homogenization']), - "microstructures\t{}".format(newInfo['microstructures']), ]) table.labels_clear() - table.labels_append(['{dim}_{label}'.format(dim = 1+i,label = options.position) for i in range(3)]+['microstructure']) + table.labels_append(['{dim}_{label}'.format(dim = 1+i,label = 'pos') for i in range(3)]+['microstructure']) table.head_write() table.output_flush()