DAMASK_EICMD/processing/pre/geom_rotate.py

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#!/usr/bin/env python3
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,math
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import numpy as np
import damask
from scipy import ndimage
from optparse import OptionParser
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
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#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
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Rotates spectral geometry description.
""", version=scriptID)
parser.add_option('-r', '--rotation',
dest='rotation',
type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
help = 'rotation given as angle and axis')
parser.add_option('-e', '--eulers',
dest = 'eulers',
type = 'float', nargs = 3, metavar = ' '.join(['float']*3),
help = 'rotation given as Euler angles')
parser.add_option('-d', '--degrees',
dest = 'degrees',
action = 'store_true',
help = 'Euler angles are given in degrees [%default]')
parser.add_option('-m', '--matrix',
dest = 'matrix',
type = 'float', nargs = 9, metavar = ' '.join(['float']*9),
help = 'rotation given as matrix')
parser.add_option('-q', '--quaternion',
dest = 'quaternion',
type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
help = 'rotation given as quaternion')
parser.add_option('-f', '--fill',
dest = 'fill',
type = 'int', metavar = 'int',
help = 'background grain index. "0" selects maximum microstructure index + 1 [%default]')
parser.set_defaults(degrees = False,
fill = 0)
(options, filenames) = parser.parse_args()
if sum(x is not None for x in [options.rotation,options.eulers,options.matrix,options.quaternion]) != 1:
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parser.error('not exactly one rotation specified...')
eulers = np.array(damask.orientation.Orientation(
quaternion = np.array(options.quaternion) if options.quaternion else None,
angleAxis = np.array(options.rotation) if options.rotation else None,
matrix = np.array(options.matrix) if options.matrix else None,
Eulers = np.array(options.eulers) if options.eulers else None,
degrees = options.degrees,
).asEulers(degrees=True))
damask.util.croak('{} {} {}'.format(*eulers))
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# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
buffered = False,
labeled = False)
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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: {}'.format(' x '.join(map(str,info['grid']))),
'size x y z: {}'.format(' x '.join(map(str,info['size']))),
'origin x y z: {}'.format(' : '.join(map(str,info['origin']))),
'homogenization: {}'.format(info['homogenization']),
'microstructures: {}'.format(info['microstructures']),
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])
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
newGrainID = options.fill if options.fill != 0 else microstructure.max()+1
microstructure = ndimage.rotate(microstructure,eulers[2],(0,1),order=0,prefilter=False,output=int,cval=newGrainID) # rotation around Z
microstructure = ndimage.rotate(microstructure,eulers[1],(1,2),order=0,prefilter=False,output=int,cval=newGrainID) # rotation around X
microstructure = ndimage.rotate(microstructure,eulers[0],(0,1),order=0,prefilter=False,output=int,cval=newGrainID) # rotation around Z
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# --- do work ------------------------------------------------------------------------------------
newInfo = {
'size': microstructure.shape*info['size']/info['grid'],
'grid': microstructure.shape,
'microstructures': microstructure.max(),
}
# --- report ---------------------------------------------------------------------------------------
remarks = []
if (any(newInfo['grid'] != info['grid'])):
remarks.append('--> grid a b c: %s'%(' x '.join(map(str,newInfo['grid']))))
if (any(newInfo['size'] != info['size'])):
remarks.append('--> size x y z: %s'%(' x '.join(map(str,newInfo['size']))))
if ( newInfo['microstructures'] != info['microstructures']):
remarks.append('--> microstructures: %i'%newInfo['microstructures'])
if remarks != []: damask.util.croak(remarks)
# --- write header ---------------------------------------------------------------------------------
table.labels_clear()
table.info_clear()
table.info_append(extra_header+[
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scriptID + ' ' + ' '.join(sys.argv[1:]),
"grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=newInfo['grid']),
"size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=newInfo['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=newInfo['microstructures']),
])
table.head_write()
# --- write microstructure information ------------------------------------------------------------
formatwidth = int(math.floor(math.log10(microstructure.max())+1))
table.data = microstructure.reshape((newInfo['grid'][0],np.prod(newInfo['grid'][1:])),order='F').transpose()
table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ')
# --- output finalization --------------------------------------------------------------------------
table.close() # close ASCII table