use new class
This commit is contained in:
Martin Diehl
parent
f20c8fcffd
commit
420abfa162
|
|
@ -1,7 +1,9 @@
|
|||
#!/usr/bin/env python3
|
||||
# -*- coding: UTF-8 no BOM -*-
|
||||
|
||||
import os,sys,math
|
||||
import os
|
||||
import sys
|
||||
import math
|
||||
import numpy as np
|
||||
from optparse import OptionParser
|
||||
import damask
|
||||
|
|
@ -71,60 +73,25 @@ parser.set_defaults(type = minimal_surfaces[0],
|
|||
if filenames == []: filenames = [None]
|
||||
|
||||
for name in filenames:
|
||||
try:
|
||||
table = damask.ASCIItable(outname = name,
|
||||
buffered = False, labeled = False)
|
||||
except: continue
|
||||
|
||||
damask.util.report(scriptName,name)
|
||||
|
||||
|
||||
# ------------------------------------------ make grid -------------------------------------
|
||||
|
||||
info = {
|
||||
'grid': np.array(options.grid),
|
||||
'size': np.array(options.size),
|
||||
'origin': np.zeros(3,'d'),
|
||||
'microstructures': max(options.microstructure),
|
||||
'homogenization': options.homogenization
|
||||
}
|
||||
|
||||
#--- report ---------------------------------------------------------------------------------------
|
||||
|
||||
damask.util.report_geom(info)
|
||||
|
||||
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
|
||||
|
||||
#--- write header ---------------------------------------------------------------------------------
|
||||
|
||||
table.labels_clear()
|
||||
table.info_clear()
|
||||
table.info_append([
|
||||
scriptID + ' ' + ' '.join(sys.argv[1:]),
|
||||
"grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=info['grid']),
|
||||
"size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=info['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=info['microstructures']),
|
||||
])
|
||||
table.head_write()
|
||||
|
||||
#--- write data -----------------------------------------------------------------------------------
|
||||
|
||||
X = options.periods*2.0*math.pi*(np.arange(options.grid[0])+0.5)/options.grid[0]
|
||||
Y = options.periods*2.0*math.pi*(np.arange(options.grid[1])+0.5)/options.grid[1]
|
||||
Z = options.periods*2.0*math.pi*(np.arange(options.grid[2])+0.5)/options.grid[2]
|
||||
|
||||
microstructure = np.empty(options.grid,dtype='int')
|
||||
for z in range(options.grid[2]):
|
||||
for y in range(options.grid[1]):
|
||||
table.data_clear()
|
||||
for x in range(options.grid[0]):
|
||||
table.data_append(options.microstructure[options.threshold < surface[options.type](X[x],Y[y],Z[z])])
|
||||
table.data_write()
|
||||
microstructure[x,y,z]=options.microstructure[options.threshold < surface[options.type](X[x],Y[y],Z[z])]
|
||||
|
||||
table.close()
|
||||
geom=damask.Geom(options.size,microstructure,options.homogenization,
|
||||
comments=[scriptID + ' ' + ' '.join(sys.argv[1:])])
|
||||
|
||||
damask.util.croak('\n'.join(geom.info()))
|
||||
|
||||
if name is None:
|
||||
sys.stdout.write(str(geom))
|
||||
else:
|
||||
geom.to_file(name)
|
||||
|
|
|
|||
|
|
@ -1,9 +1,11 @@
|
|||
#!/usr/bin/env python3
|
||||
# -*- coding: UTF-8 no BOM -*-
|
||||
|
||||
import os,sys,math
|
||||
import os
|
||||
import sys
|
||||
import numpy as np
|
||||
import damask
|
||||
from io import StringIO
|
||||
from scipy import ndimage
|
||||
from optparse import OptionParser
|
||||
|
||||
|
|
@ -42,15 +44,9 @@ parser.add_option('-q', '--quaternion',
|
|||
parser.add_option('-f', '--fill',
|
||||
dest = 'fill',
|
||||
type = 'int', metavar = 'int',
|
||||
help = 'background grain index. "0" selects maximum microstructure index + 1 [%default]')
|
||||
parser.add_option('--float',
|
||||
dest = 'float',
|
||||
action = 'store_true',
|
||||
help = 'use float input')
|
||||
help = 'background grain index, defaults to max + 1')
|
||||
|
||||
parser.set_defaults(degrees = False,
|
||||
fill = 0,
|
||||
float = False,
|
||||
)
|
||||
|
||||
(options, filenames) = parser.parse_args()
|
||||
|
|
@ -67,82 +63,38 @@ if options.matrix is not None:
|
|||
if options.eulers is not None:
|
||||
eulers = damask.Rotation.fromEulers(np.array(options.eulers),degrees=True).asEulers(degrees=True)
|
||||
|
||||
datatype = 'f' if options.float else 'i'
|
||||
|
||||
# --- loop over input files -------------------------------------------------------------------------
|
||||
|
||||
if filenames == []: filenames = [None]
|
||||
|
||||
for name in filenames:
|
||||
try:
|
||||
table = damask.ASCIItable(name = name,
|
||||
buffered = False,
|
||||
labeled = False)
|
||||
except: continue
|
||||
if name is None:
|
||||
virt_file = StringIO(''.join(sys.stdin.read()))
|
||||
geom = damask.Geom.from_file(virt_file)
|
||||
else:
|
||||
try: # really needed? Why not simply fail if file does not exists etc.
|
||||
geom = damask.Geom.from_file(name)
|
||||
except: continue
|
||||
damask.util.report(scriptName,name)
|
||||
|
||||
# --- interpret header ----------------------------------------------------------------------------
|
||||
microstructure = geom.microstructure
|
||||
spacing = geom.get_size()/geom.get_grid()
|
||||
|
||||
table.head_read()
|
||||
info,extra_header = table.head_getGeom()
|
||||
damask.util.report_geom(info)
|
||||
newGrainID = options.fill if options.fill is not None else np.nanmax(microstructure)+1
|
||||
microstructure = ndimage.rotate(microstructure,eulers[2],(0,1),order=0,
|
||||
prefilter=False,output=microstructure.dtype,cval=newGrainID) # rotation around Z
|
||||
microstructure = ndimage.rotate(microstructure,eulers[1],(1,2),order=0,
|
||||
prefilter=False,output=microstructure.dtype,cval=newGrainID) # rotation around X
|
||||
microstructure = ndimage.rotate(microstructure,eulers[0],(0,1),order=0,
|
||||
prefilter=False,output=microstructure.dtype,cval=newGrainID) # rotation around Z
|
||||
|
||||
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
|
||||
geom.microstructure = microstructure
|
||||
geom.set_size(microstructure.shape*spacing)
|
||||
geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:]))
|
||||
|
||||
# --- read data ------------------------------------------------------------------------------------
|
||||
damask.util.croak('\n'.join(geom.info()))
|
||||
|
||||
microstructure = table.microstructure_read(info['grid'],datatype).reshape(info['grid'],order='F') # read microstructure
|
||||
|
||||
newGrainID = options.fill if options.fill != 0 else np.nanmax(microstructure)+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
|
||||
|
||||
# --- do work ------------------------------------------------------------------------------------
|
||||
|
||||
newInfo = {
|
||||
'size': microstructure.shape*info['size']/info['grid'],
|
||||
'grid': microstructure.shape,
|
||||
'microstructures': len(np.unique(microstructure)),
|
||||
}
|
||||
|
||||
# --- report ---------------------------------------------------------------------------------------
|
||||
|
||||
remarks = []
|
||||
if (any(newInfo['grid'] != info['grid'])):
|
||||
remarks.append('--> grid a b c: {}'.format(' x '.join(map(str,newInfo['grid']))))
|
||||
if (any(newInfo['size'] != info['size'])):
|
||||
remarks.append('--> size x y z: {}'.format(' x '.join(map(str,newInfo['size']))))
|
||||
if ( newInfo['microstructures'] != info['microstructures']):
|
||||
remarks.append('--> microstructures: {}'.format(newInfo['microstructures']))
|
||||
if remarks != []: damask.util.croak(remarks)
|
||||
|
||||
# --- write header ---------------------------------------------------------------------------------
|
||||
|
||||
table.labels_clear()
|
||||
table.info_clear()
|
||||
table.info_append(extra_header+[
|
||||
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 ------------------------------------------------------------
|
||||
|
||||
format = '%g' if options.float else '%{}i'.format(int(math.floor(math.log10(np.nanmax(microstructure))+1)))
|
||||
table.data = microstructure.reshape((newInfo['grid'][0],np.prod(newInfo['grid'][1:])),order='F').transpose()
|
||||
table.data_writeArray(format,delimiter=' ')
|
||||
|
||||
# --- output finalization --------------------------------------------------------------------------
|
||||
|
||||
table.close() # close ASCII table
|
||||
if name is None:
|
||||
sys.stdout.write(str(geom))
|
||||
else:
|
||||
geom.to_file(name)
|
||||
|
|
|
|||
|
|
@ -4,10 +4,9 @@ from io import StringIO
|
|||
import io
|
||||
|
||||
class Geom():
|
||||
"""Geometry definition for grid solvers"""
|
||||
|
||||
def __init__(self,size,microstructure,homogenization=1,comments=[]):
|
||||
"""Geometry definition for grid solvers"""
|
||||
|
||||
if len(size) != 3 or any(np.array(size)<=0):
|
||||
raise ValueError('invalid size')
|
||||
else:
|
||||
|
|
@ -29,6 +28,7 @@ class Geom():
|
|||
self.comments = [str(comment) for comment in comments]
|
||||
|
||||
def __repr__(self):
|
||||
"""Readable string"""
|
||||
f=StringIO()
|
||||
self.to_file(f)
|
||||
f.seek(0)
|
||||
|
|
|
|||
Loading…
Reference in New Issue