geom_rotate: rotates a geometry
This commit is contained in:
Martin Diehl
parent
900b072781
commit
4ca566efa8
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@ -0,0 +1,146 @@
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#!/usr/bin/env python
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# -*- coding: UTF-8 no BOM -*-
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import os,sys,string,math
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import numpy as np
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import damask
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from scipy import ndimage
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from optparse import OptionParser
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scriptID = string.replace('$Id$','\n','\\n')
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scriptName = os.path.splitext(scriptID.split()[1])[0]
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#--------------------------------------------------------------------------------------------------
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# MAIN
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#--------------------------------------------------------------------------------------------------
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parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
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Rotates spectral geometry description.
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""", version=scriptID)
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parser.add_option('-r', '--rotation',
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dest='rotation',
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type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
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help = 'rotation given as angle and axis')
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parser.add_option('-e', '--eulers',
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dest = 'eulers',
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type = 'float', nargs = 3, metavar = ' '.join(['float']*3),
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help = 'rotation given as Euler angles')
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parser.add_option('-d', '--degrees',
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dest = 'degrees',
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action = 'store_true',
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help = 'Euler angles are given in degrees [%default]')
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parser.add_option('-m', '--matrix',
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dest = 'matrix',
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type = 'float', nargs = 9, metavar = ' '.join(['float']*9),
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help = 'rotation given as matrix')
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parser.add_option('-q', '--quaternion',
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dest = 'quaternion',
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type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
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help = 'rotation given as quaternion')
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parser.add_option('-f', '--fill',
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dest = 'fill',
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type = 'int', metavar = 'int',
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help = 'background grain index. "0" selects maximum microstructure index + 1 [%default]')
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parser.set_defaults(degrees = False,
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fill = 0)
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(options, filenames) = parser.parse_args()
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if sum(x != None for x in [options.rotation,options.eulers,options.matrix,options.quaternion]) !=1:
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parser.error('not exactly one rotation specified...')
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toRadian = math.pi/180. if options.degrees else 1.0
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eulers = np.array(damask.orientation.Orientation(
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quaternion=np.array(options.quaternion) if options.quaternion else None,
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angleAxis =np.array(options.rotation) if options.rotation else None,
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matrix =np.array(options.matrix) if options.matrix else None,
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Eulers =np.array(options.eulers)*toRadian if options.eulers else None
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).asEulers()) *180./math.pi
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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for name in filenames:
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try:
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table = damask.ASCIItable(name = name,
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buffered = False, labeled = False)
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except: continue
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damask.util.report(scriptName,name)
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# --- interpret header ----------------------------------------------------------------------------
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table.head_read()
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info,extra_header = table.head_getGeom()
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damask.util.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))),
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'size x y z: %s'%(' x '.join(map(str,info['size']))),
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'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
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'homogenization: %i'%info['homogenization'],
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'microstructures: %i'%info['microstructures'],
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])
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errors = []
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if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
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if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.')
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if errors != []:
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damask.util.croak(errors)
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table.close(dismiss = True)
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continue
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# --- read data ------------------------------------------------------------------------------------
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microstructure = table.microstructure_read(info['grid']).reshape(info['grid'],order='F') # read microstructure
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newGrainID = options.fill if options.fill > 0 else microstructure.max()+1
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microstructure = ndimage.rotate(microstructure,eulers[2],(0,1),order=0,output=np.dtype(int),cval=newGrainID) # rotation around Z
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microstructure = ndimage.rotate(microstructure,eulers[1],(1,2),order=0,output=np.dtype(int),cval=newGrainID) # rotation around X
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microstructure = ndimage.rotate(microstructure,eulers[0],(0,1),order=0,output=np.dtype(int),cval=newGrainID) # rotation around Z
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# --- do work ------------------------------------------------------------------------------------
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newInfo = {
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'size': microstructure.shape*info['size']/info['grid'],
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'grid': microstructure.shape,
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'microstructures': microstructure.max(),
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}
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# --- report ---------------------------------------------------------------------------------------
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remarks = []
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if (any(newInfo['grid'] != info['grid'])):
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remarks.append('--> grid a b c: %s'%(' x '.join(map(str,newInfo['grid']))))
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if (any(newInfo['size'] != info['size'])):
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remarks.append('--> size x y z: %s'%(' x '.join(map(str,newInfo['size']))))
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if ( newInfo['microstructures'] != info['microstructures']):
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remarks.append('--> microstructures: %i'%newInfo['microstructures'])
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if remarks != []: damask.util.croak(remarks)
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# --- write header ---------------------------------------------------------------------------------
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table.labels_clear()
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table.info_clear()
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table.info_append([
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scriptID + ' ' + ' '.join(sys.argv[1:]),
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"grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=newInfo['grid']),
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"size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=newInfo['size']),
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"origin\tx {origin[0]}\ty {origin[1]}\tz {origin[2]}".format(origin=info['origin']),
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"homogenization\t{homog}".format(homog=info['homogenization']),
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"microstructures\t{microstructures}".format(microstructures=newInfo['microstructures']),
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extra_header
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])
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table.head_write()
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# --- write microstructure information ------------------------------------------------------------
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formatwidth = int(math.floor(math.log10(microstructure.max())+1))
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table.data = microstructure.reshape((newInfo['grid'][0],np.prod(newInfo['grid'][1:])),order='F').transpose()
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table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ')
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# --- output finalization --------------------------------------------------------------------------
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table.close() # close ASCII table
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