use new class
This commit is contained in:
Martin Diehl
parent
f20c8fcffd
commit
420abfa162
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@ -1,7 +1,9 @@
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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 os
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import sys
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import math
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import numpy as np
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from optparse import OptionParser
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import damask
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@ -71,60 +73,25 @@ parser.set_defaults(type = minimal_surfaces[0],
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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(outname = 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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# ------------------------------------------ make grid -------------------------------------
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info = {
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'grid': np.array(options.grid),
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'size': np.array(options.size),
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'origin': np.zeros(3,'d'),
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'microstructures': max(options.microstructure),
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'homogenization': options.homogenization
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}
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#--- report ---------------------------------------------------------------------------------------
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damask.util.report_geom(info)
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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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#--- 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=info['grid']),
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"size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=info['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=info['microstructures']),
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])
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table.head_write()
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#--- write data -----------------------------------------------------------------------------------
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X = options.periods*2.0*math.pi*(np.arange(options.grid[0])+0.5)/options.grid[0]
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Y = options.periods*2.0*math.pi*(np.arange(options.grid[1])+0.5)/options.grid[1]
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Z = options.periods*2.0*math.pi*(np.arange(options.grid[2])+0.5)/options.grid[2]
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microstructure = np.empty(options.grid,dtype='int')
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for z in range(options.grid[2]):
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for y in range(options.grid[1]):
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table.data_clear()
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for x in range(options.grid[0]):
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table.data_append(options.microstructure[options.threshold < surface[options.type](X[x],Y[y],Z[z])])
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table.data_write()
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microstructure[x,y,z]=options.microstructure[options.threshold < surface[options.type](X[x],Y[y],Z[z])]
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table.close()
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geom=damask.Geom(options.size,microstructure,options.homogenization,
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comments=[scriptID + ' ' + ' '.join(sys.argv[1:])])
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damask.util.croak('\n'.join(geom.info()))
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if name is None:
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sys.stdout.write(str(geom))
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else:
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geom.to_file(name)
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@ -1,9 +1,11 @@
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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 os
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import sys
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import numpy as np
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import damask
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from io import StringIO
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from scipy import ndimage
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from optparse import OptionParser
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@ -42,15 +44,9 @@ parser.add_option('-q', '--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.add_option('--float',
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dest = 'float',
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action = 'store_true',
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help = 'use float input')
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help = 'background grain index, defaults to max + 1')
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parser.set_defaults(degrees = False,
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fill = 0,
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float = False,
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)
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(options, filenames) = parser.parse_args()
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@ -67,82 +63,38 @@ if options.matrix is not None:
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if options.eulers is not None:
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eulers = damask.Rotation.fromEulers(np.array(options.eulers),degrees=True).asEulers(degrees=True)
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datatype = 'f' if options.float else 'i'
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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,
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labeled = False)
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if name is None:
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virt_file = StringIO(''.join(sys.stdin.read()))
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geom = damask.Geom.from_file(virt_file)
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else:
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try: # really needed? Why not simply fail if file does not exists etc.
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geom = damask.Geom.from_file(name)
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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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microstructure = geom.microstructure
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spacing = geom.get_size()/geom.get_grid()
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table.head_read()
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info,extra_header = table.head_getGeom()
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damask.util.report_geom(info)
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newGrainID = options.fill if options.fill is not None else np.nanmax(microstructure)+1
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microstructure = ndimage.rotate(microstructure,eulers[2],(0,1),order=0,
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prefilter=False,output=microstructure.dtype,cval=newGrainID) # rotation around Z
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microstructure = ndimage.rotate(microstructure,eulers[1],(1,2),order=0,
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prefilter=False,output=microstructure.dtype,cval=newGrainID) # rotation around X
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microstructure = ndimage.rotate(microstructure,eulers[0],(0,1),order=0,
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prefilter=False,output=microstructure.dtype,cval=newGrainID) # rotation around Z
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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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geom.microstructure = microstructure
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geom.set_size(microstructure.shape*spacing)
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geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:]))
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# --- read data ------------------------------------------------------------------------------------
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damask.util.croak('\n'.join(geom.info()))
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microstructure = table.microstructure_read(info['grid'],datatype).reshape(info['grid'],order='F') # read microstructure
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newGrainID = options.fill if options.fill != 0 else np.nanmax(microstructure)+1
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microstructure = ndimage.rotate(microstructure,eulers[2],(0,1),order=0,prefilter=False,output=int,cval=newGrainID) # rotation around Z
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microstructure = ndimage.rotate(microstructure,eulers[1],(1,2),order=0,prefilter=False,output=int,cval=newGrainID) # rotation around X
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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 ------------------------------------------------------------------------------------
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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': len(np.unique(microstructure)),
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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: {}'.format(' 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: {}'.format(' x '.join(map(str,newInfo['size']))))
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if ( newInfo['microstructures'] != info['microstructures']):
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remarks.append('--> microstructures: {}'.format(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(extra_header+[
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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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])
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table.head_write()
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# --- write microstructure information ------------------------------------------------------------
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format = '%g' if options.float else '%{}i'.format(int(math.floor(math.log10(np.nanmax(microstructure))+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(format,delimiter=' ')
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# --- output finalization --------------------------------------------------------------------------
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table.close() # close ASCII table
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if name is None:
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sys.stdout.write(str(geom))
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else:
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geom.to_file(name)
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@ -4,10 +4,9 @@ from io import StringIO
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import io
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class Geom():
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def __init__(self,size,microstructure,homogenization=1,comments=[]):
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"""Geometry definition for grid solvers"""
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def __init__(self,size,microstructure,homogenization=1,comments=[]):
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if len(size) != 3 or any(np.array(size)<=0):
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raise ValueError('invalid size')
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else:
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@ -29,6 +28,7 @@ class Geom():
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self.comments = [str(comment) for comment in comments]
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def __repr__(self):
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"""Readable string"""
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f=StringIO()
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self.to_file(f)
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f.seek(0)
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