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DAMASK_EICMD
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This commit is contained in:
Martin Diehl 2019-05-25 10:14:53 +02:00
parent 17eb0d1b20
commit 875643c363
8 changed files with 82 additions and 181 deletions
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6
processing/pre/geom_fromMinimalSurface.py
View File

@ -73,7 +73,6 @@ parser.set_defaults(type = minimal_surfaces[0],
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
X = options.periods*2.0*math.pi*(np.arange(options.grid[0])+0.5)/options.grid[0]
@ -89,9 +88,8 @@ for name in filenames:
geom=damask.Geom(options.size,microstructure,options.homogenization,
comments=[scriptID + ' ' + ' '.join(sys.argv[1:])])
damask.util.croak('\n'.join(geom.info()))
damask.util.croak(geom)
if name is None:
sys.stdout.write(str(geom))
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)

3
processing/pre/geom_mirror.py
View File

@ -4,8 +4,9 @@
import os
import sys
import numpy as np
import damask
from optparse import OptionParser
from io import StringIO
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])

78
processing/pre/geom_renumber.py
View File

@ -1,10 +1,12 @@
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
import os
import sys
import numpy as np
import damask
from optparse import OptionParser
from io import StringIO
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
@ -25,36 +27,14 @@ renumber sorted microstructure indices to 1,...,N.
if filenames == []: filenames = [None]
for name in filenames:
try: table = damask.ASCIItable(name = name,
buffered = False,
labeled = False)
except: continue
damask.util.report(scriptName,name)
# --- interpret header ---------------------------------------------------------------------------
table.head_read()
info,extra_header = table.head_getGeom()
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
# --- read data ----------------------------------------------------------------------------------
microstructure = table.microstructure_read(info['grid']) # read microstructure
# --- do work ------------------------------------------------------------------------------------
newInfo = {
'origin': np.zeros(3,'d'),
'microstructures': 0,
}
if name is None:
virt_file = StringIO(''.join(sys.stdin.read()))
geom = damask.Geom.from_file(virt_file)
else:
geom = damask.Geom.from_file(name)
microstructure = geom.microstructure
grainIDs = np.unique(microstructure)
renumbered = np.copy(microstructure)
@ -62,35 +42,11 @@ for name in filenames:
for i, oldID in enumerate(grainIDs):
renumbered = np.where(microstructure == oldID, i+1, renumbered)
newInfo['microstructures'] = len(grainIDs)
geom.microstructure = renumbered
geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:]))
# --- report -------------------------------------------------------------------------------------
remarks = []
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+[
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=newInfo['microstructures']),
])
table.head_write()
# --- write microstructure information -----------------------------------------------------------
format = '%{}i'.format(int(math.floor(math.log10(np.nanmax(renumbered))+1)))
table.data = renumbered.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
table.data_writeArray(format,delimiter = ' ')
# --- output finalization ------------------------------------------------------------------------
table.close() # close ASCII table
damask.util.croak(geom)
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)

15
processing/pre/geom_rotate.py
View File

@ -57,26 +57,26 @@ if sum(x is not None for x in [options.rotation,options.eulers,options.matrix,op
if options.quaternion is not None:
eulers = damask.Rotation.fromQuaternion(np.array(options.quaternion)).asEulers(degrees=True)
if options.rotation is not None:
eulers = damask.Rotation.fromAxisAngle(np.array(options.rotation,degrees=True)).asEulers(degrees=True)
eulers = damask.Rotation.fromAxisAngle(np.array(options.rotation,degrees=options.degrees)).asEulers(degrees=True)
if options.matrix is not None:
eulers = damask.Rotation.fromMatrix(np.array(options.Matrix)).asEulers(degrees=True)
if options.eulers is not None:
eulers = damask.Rotation.fromEulers(np.array(options.eulers),degrees=True).asEulers(degrees=True)
eulers = damask.Rotation.fromEulers(np.array(options.eulers),degrees=options.degrees).asEulers(degrees=True)
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
if name is None:
virt_file = StringIO(''.join(sys.stdin.read()))
geom = damask.Geom.from_file(virt_file)
else:
geom = damask.Geom.from_file(name)
damask.util.report(scriptName,name)
microstructure = geom.microstructure
spacing = geom.get_size()/geom.get_grid()
newGrainID = options.fill if options.fill is not None else np.nanmax(microstructure)+1
@ -91,9 +91,8 @@ for name in filenames:
geom.set_size(microstructure.shape*spacing)
geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:]))
damask.util.croak('\n'.join(geom.info()))
damask.util.croak(geom)
if name is None:
sys.stdout.write(str(geom))
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)

101
processing/pre/geom_translate.py
View File

@ -1,10 +1,12 @@
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
import os
import sys
import numpy as np
import damask
from optparse import OptionParser
from io import StringIO
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
@ -30,98 +32,47 @@ parser.add_option('-s', '--substitute',
dest = 'substitute',
action = 'extend', metavar = '<string LIST>',
help = 'substitutions of microstructure indices from,to,from,to,...')
parser.add_option('--float',
dest = 'float',
action = 'store_true',
help = 'use float input')
parser.set_defaults(origin = (0.0,0.0,0.0),
microstructure = 0,
substitute = [],
float = False,
substitute = []
)
(options, filenames) = parser.parse_args()
datatype = 'f' if options.float else 'i'
sub = {}
for i in range(len(options.substitute)//2): # split substitution list into "from" -> "to"
sub[int(options.substitute[i*2])] = int(options.substitute[i*2+1])
# --- loop over input files ----------------------------------------------------------------------
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try: table = damask.ASCIItable(name = name,
buffered = False,
labeled = False)
except: continue
damask.util.report(scriptName,name)
# --- interpret header ---------------------------------------------------------------------------
if name is None:
virt_file = StringIO(''.join(sys.stdin.read()))
geom = damask.Geom.from_file(virt_file)
else:
geom = damask.Geom.from_file(name)
microstructure = geom.microstructure
table.head_read()
info,extra_header = table.head_getGeom()
damask.util.report_geom(info)
for k, v in sub.items(): microstructure[geom.microstructure==k] = v # substitute microstructure indices
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
microstructure += options.microstructure # shift microstructure indices
# --- read data ----------------------------------------------------------------------------------
for i,line in enumerate(geom.comments):
if line.lower().strip().startswith('origin'):
origin= np.array([float(line.split()[j]) for j in [2,4,6]]) # assume correct order (x,y,z)
origin += np.array(origin)
geom.comments[i] = 'origin x {} y {} z {}'.format(*origin)
microstructure = table.microstructure_read(info['grid'],datatype) # read microstructure
geom.microstructure = microstructure
geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:]))
# --- do work ------------------------------------------------------------------------------------
newInfo = {
'origin': np.zeros(3,'d'),
'microstructures': 0,
}
substituted = np.copy(microstructure)
for k, v in sub.items(): substituted[microstructure==k] = v # substitute microstructure indices
substituted += options.microstructure # shift microstructure indices
newInfo['origin'] = info['origin'] + options.origin
newInfo['microstructures'] = len(np.unique(substituted))
# --- report -------------------------------------------------------------------------------------
remarks = []
if (any(newInfo['origin'] != info['origin'])):
remarks.append('--> origin x y z: {}'.format(' : '.join(map(str,newInfo['origin']))))
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=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=newInfo['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(substituted))+1)))
table.data = substituted.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
table.data_writeArray(format,delimiter = ' ')
# --- output finalization ------------------------------------------------------------------------
table.close() # close ASCII table
damask.util.croak(geom)
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)

12
processing/pre/geom_unpack.py
View File

@ -3,9 +3,8 @@
import os
import sys
import math
import numpy as np
from optparse import OptionParser
from io import StringIO
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
@ -35,19 +34,18 @@ parser.set_defaults(oneD = False,
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
if name is None:
virt_file = StringIO(''.join(sys.stdin.read()))
geom = damask.Geom.from_file(virt_file)
else:
geom = damask.Geom.from_file(name)
damask.util.report(scriptName,name)
geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:]))
damask.util.croak('\n'.join(geom.info()))
damask.util.croak(geom)
if name is None:
sys.stdout.write(str(geom))
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)

10
processing/pre/geom_vicinityOffset.py
View File

@ -65,14 +65,13 @@ options.trigger = np.array(options.trigger, dtype=int)
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
if name is None:
virt_file = StringIO(''.join(sys.stdin.read()))
geom = damask.Geom.from_file(virt_file)
else:
geom = damask.Geom.from_file(name)
damask.util.report(scriptName,name)
microstructure = geom.microstructure
if options.offset == 0: options.offset = microstructure.max()
@ -87,9 +86,8 @@ for name in filenames:
geom.microstructure = microstructure
geom.add_comment(scriptID + ' ' + ' '.join(sys.argv[1:]))
damask.util.croak('\n'.join(geom.info()))
damask.util.croak(geom)
if name is None:
sys.stdout.write(str(geom))
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)

24
python/damask/geom.py
View File

@ -6,6 +6,7 @@ class Geom():
"""Geometry definition for grid solvers"""
def __init__(self,size,microstructure,homogenization=1,comments=[]):
"""New geometry definition from array of microstructures and size"""
if len(size) != 3 or any(np.array(size)<=0):
raise ValueError('invalid size')
else:
@ -27,11 +28,12 @@ class Geom():
self.comments = [str(comment) for comment in comments]
def __repr__(self):
"""Readable string"""
f=StringIO()
self.to_file(f)
f.seek(0)
return ''.join(f.readlines())
"""Basic information on geometry definition"""
return 'grid a b c: {}\n'.format(' x '.join(map(str,self.get_grid()))) + \
'size x y z: {}\n'.format(' x '.join(map(str,self.get_size()))) + \
'homogenization: {}\n'.format(self.get_homogenization()) + \
'# microstructures: {}\n'.format(len(np.unique(self.microstructure))) + \
'max microstructures: {}\n'.format(np.max(self.microstructure))
def add_comment(self,comment):
if not isinstance(comment,list):
@ -119,10 +121,8 @@ class Geom():
np.savetxt(fname, self.microstructure.reshape([grid[0],np.prod(grid[1:])],order='F').T,
header='\n'.join(header), fmt=format_string, comments='')
def info(self):
return ['grid a b c: {}'.format(' x '.join(map(str,self.get_grid()))),
'size x y z: {}'.format(' x '.join(map(str,self.get_size()))),
'homogenization: {}'.format(self.get_homogenization()),
'# microstructures: {}'.format(len(np.unique(self.microstructure))),
'max microstructures: {}'.format(np.max(self.microstructure)),
]
def show(self):
f=StringIO()
self.to_file(f)
f.seek(0)
return ''.join(f.readlines())