use new class

This commit is contained in:
Martin Diehl 2019-05-24 22:31:34 +02:00
parent f20c8fcffd
commit 420abfa162
3 changed files with 48 additions and 129 deletions

View File

@ -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)

View File

@ -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)

View File

@ -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)