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DAMASK_EICMD
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Merge branch 'development' into even-more-HDF5-postprocessing

This commit is contained in:
Martin Diehl 2019-06-04 22:39:10 +02:00
parent 9612dd1d82 038aed1f6e
commit 1186bd16f5
41 changed files with 1238 additions and 1916 deletions
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2
PRIVATE

@ -1 +1 @@
Subproject commit d31da38cf25734a91e994a3d5d33bb048eb2f44f
Subproject commit 64cda1c010d500f662cd9a298c7b7ad10ab91c3c

2
VERSION
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@ -1 +1 @@
v2.0.3-367-g70428155
v2.0.3-369-g951134d1

2
processing/post/addGradient.py
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@ -52,7 +52,7 @@ def gradFFT(geomdim,field):
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog option [ASCIItable(s)]', description = """
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Add column(s) containing gradient of requested column(s).
Operates on periodic ordered three-dimensional data sets
of vector and scalar fields.

2
processing/post/vtk_pointCloud.py
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@ -98,6 +98,6 @@ for name in filenames:
writer.Write()
if name is None: sys.stdout.write(writer.GetOutputString()[:writer.GetOutputStringLength()]) # limiting of outputString is fix for vtk <7.0
if name is None: sys.stdout.write(writer.GetOutputString())
table.close()

2
processing/post/vtk_rectilinearGrid.py
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@ -129,6 +129,6 @@ for name in filenames:
writer.Write()
if name is None: sys.stdout.write(writer.GetOutputString()[:writer.GetOutputStringLength()]) # limiting of outputString is fix for vtk <7.0
if name is None: sys.stdout.write(writer.GetOutputString())
table.close()

255
processing/pre/geom_addPrimitive.py
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@ -1,85 +1,88 @@
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
import numpy as np
import os
import sys
from io import StringIO
from optparse import OptionParser
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
identifiers = {
'grid': ['a','b','c'],
'size': ['x','y','z'],
'origin': ['x','y','z'],
}
mappings = {
'grid': lambda x: int(x),
'size': lambda x: float(x),
'origin': lambda x: float(x),
'homogenization': lambda x: int(x),
'microstructures': lambda x: int(x),
}
parser = OptionParser(option_class=damask.extendableOption, usage='%prog option [geomfile(s)]', description = """
Positions a geometric object within the (three-dimensional) canvas of a spectral geometry description.
Depending on the sign of the dimension parameters, these objects can be boxes, cylinders, or ellipsoids.
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
Inserts a primitive geometric object at a given position.
These objects can be boxes, cylinders, or ellipsoids.
""", version = scriptID)
parser.add_option('-c', '--center', dest='center',
parser.add_option('-c', '--center',
dest='center',
type='float', nargs = 3, metavar=' '.join(['float']*3),
help='a,b,c origin of primitive %default')
parser.add_option('-d', '--dimension', dest='dimension',
parser.add_option('-d', '--dimension',
dest='dimension',
type='float', nargs = 3, metavar=' '.join(['float']*3),
help='a,b,c extension of hexahedral box; negative values are diameters')
parser.add_option('-e', '--exponent', dest='exponent',
help='a,b,c extension of hexahedral box')
parser.add_option('-e', '--exponent',
dest='exponent',
type='float', nargs = 3, metavar=' '.join(['float']*3),
help='i,j,k exponents for axes - 0 gives octahedron (|x|^(2^0) + |y|^(2^0) + |z|^(2^0) < 1), \
1 gives a sphere (|x|^(2^1) + |y|^(2^1) + |z|^(2^1) < 1), \
large values produce boxes, negative turns concave.')
parser.add_option('-f', '--fill', dest='fill',
type='float', metavar = 'float',
help='grain index to fill primitive. "0" selects maximum microstructure index + 1 [%default]')
parser.add_option('-q', '--quaternion', dest='quaternion',
help='i,j,k exponents for axes: '+
'0 gives octahedron (|x|^(2^0) + |y|^(2^0) + |z|^(2^0) < 1), '+
'1 gives a sphere (|x|^(2^1) + |y|^(2^1) + |z|^(2^1) < 1), '+
'large values produce boxes, negative turn concave.')
parser.add_option('-f', '--fill',
dest='fill',
type='float', metavar = 'int',
help='microstructure index to fill primitive, defaults to max microstructure index + 1')
parser.add_option('-q', '--quaternion',
dest='quaternion',
type='float', nargs = 4, metavar=' '.join(['float']*4),
help = 'rotation of primitive as quaternion')
parser.add_option('-a', '--angleaxis', dest='angleaxis', type=float,
nargs = 4, metavar=' '.join(['float']*4),
parser.add_option('-a', '--angleaxis',
dest='angleaxis',
type=float, nargs = 4, metavar=' '.join(['float']*4),
help = 'axis and angle to rotate primitive')
parser.add_option( '--degrees', dest='degrees',
parser.add_option( '--degrees',
dest='degrees',
action='store_true',
help = 'angle is given in degrees [%default]')
parser.add_option( '--nonperiodic', dest='periodic',
help = 'angle is given in degrees')
parser.add_option( '--nonperiodic',
dest='periodic',
action='store_false',
help = 'wrap around edges [%default]')
parser.add_option( '--realspace', dest='realspace',
help = 'wrap around edges')
parser.add_option( '--realspace',
dest='realspace',
action='store_true',
help = '-c and -d span [origin,origin+size] instead of [0,grid] coordinates')
parser.add_option( '--invert', dest='inside',
parser.add_option( '--invert',
dest='inside',
action='store_false',
help = 'invert the volume filled by the primitive (inside/outside)')
parser.add_option('--float', dest = 'float',
action = 'store_true',
help = 'use float input')
parser.set_defaults(center = (.0,.0,.0),
fill = 0.0,
degrees = False,
exponent = (20,20,20), # box shape by default
periodic = True,
realspace = False,
inside = True,
float = False,
)
(options, filenames) = parser.parse_args()
if options.dimension is None:
parser.error('no dimension specified.')
if [options.angleaxis,options.quaternion].count(None) == 0:
parser.error('more than one rotation specified.')
if options.angleaxis is not None:
rotation = damask.Rotation.fromAxisAngle(np.array(options.angleaxis),options.degrees,normalise=True)
elif options.quaternion is not None:
@ -87,157 +90,49 @@ elif options.quaternion is not None:
else:
rotation = damask.Rotation()
datatype = 'f' if options.float else 'i'
options.center = np.array(options.center)
options.dimension = np.array(options.dimension)
# undo logarithmic sense of exponent and generate ellipsoids for negative dimensions (backward compatibility)
options.exponent = np.where(np.array(options.dimension) > 0, np.power(2,options.exponent), 2)
# --- 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 ----------------------------------------------------------------------------
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
grid = geom.get_grid()
size = geom.get_size()
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'],datatype) # read microstructure
# --- do work ------------------------------------------------------------------------------------
newInfo = {
'microstructures': 0,
}
options.fill = np.nanmax(microstructure)+1 if options.fill == 0 else options.fill
microstructure = microstructure.reshape(info['grid'],order='F')
# coordinates given in real space (default) vs voxel space
# scale to box of size [1.0,1.0,1.0]
if options.realspace:
options.center -= info['origin']
options.center *= np.array(info['grid']) / np.array(info['size'])
options.dimension *= np.array(info['grid']) / np.array(info['size'])
center = (np.array(options.center) - geom.get_origin())/size
r = np.array(options.dimension)/size/2.0
else:
center = (np.array(options.center) + 0.5)/grid
r = np.array(options.dimension)/grid/2.0
grid = microstructure.shape
if np.any(center<0.0) or np.any(center>=1.0): print('error')
# change to coordinate space where the primitive is the unit sphere/cube/etc
if options.periodic: # use padding to achieve periodicity
(X, Y, Z) = np.meshgrid(np.arange(-grid[0]/2, (3*grid[0])/2, dtype=np.float32), # 50% padding on each side
np.arange(-grid[1]/2, (3*grid[1])/2, dtype=np.float32),
np.arange(-grid[2]/2, (3*grid[2])/2, dtype=np.float32),
indexing='ij')
# Padding handling
X = np.roll(np.roll(np.roll(X,
-grid[0]//2, axis=0),
-grid[1]//2, axis=1),
-grid[2]//2, axis=2)
Y = np.roll(np.roll(np.roll(Y,
-grid[0]//2, axis=0),
-grid[1]//2, axis=1),
-grid[2]//2, axis=2)
Z = np.roll(np.roll(np.roll(Z,
-grid[0]//2, axis=0),
-grid[1]//2, axis=1),
-grid[2]//2, axis=2)
else: # nonperiodic, much lighter on resources
# change to coordinate space where the primitive is the unit sphere/cube/etc
(X, Y, Z) = np.meshgrid(np.arange(0, grid[0], dtype=np.float32),
np.arange(0, grid[1], dtype=np.float32),
np.arange(0, grid[2], dtype=np.float32),
indexing='ij')
# first by translating the center onto 0, 0.5 shifts the voxel origin onto the center of the voxel
X -= options.center[0] - 0.5
Y -= options.center[1] - 0.5
Z -= options.center[2] - 0.5
# and then by applying the rotation
(X, Y, Z) = rotation * (X, Y, Z)
# and finally by scaling (we don't worry about options.dimension being negative, np.abs occurs on the microstructure = np.where... line)
X /= options.dimension[0] * 0.5
Y /= options.dimension[1] * 0.5
Z /= options.dimension[2] * 0.5
# High exponents can cause underflow & overflow - loss of precision is okay here, we just compare it to 1, so +infinity and 0 are fine
old_settings = np.seterr()
offset = np.ones(3)*0.5 if options.periodic else center
mask = np.full(grid,False)
# High exponents can cause underflow & overflow - okay here, just compare to 1, so +infinity and 0 are fine
np.seterr(over='ignore', under='ignore')
if options.periodic: # use padding to achieve periodicity
inside = np.zeros(grid, dtype=bool)
for i in range(2):
for j in range(2):
for k in range(2):
inside = inside | ( # Most of this is handling the padding
np.abs(X[grid[0] * i : grid[0] * (i+1),
grid[1] * j : grid[1] * (j+1),
grid[2] * k : grid[2] * (k+1)])**options.exponent[0] +
np.abs(Y[grid[0] * i : grid[0] * (i+1),
grid[1] * j : grid[1] * (j+1),
grid[2] * k : grid[2] * (k+1)])**options.exponent[1] +
np.abs(Z[grid[0] * i : grid[0] * (i+1),
grid[1] * j : grid[1] * (j+1),
grid[2] * k : grid[2] * (k+1)])**options.exponent[2] <= 1.0)
e = 2.0**np.array(options.exponent)
for x in range(grid[0]):
for y in range(grid[1]):
for z in range(grid[2]):
coords = np.array([x+0.5,y+0.5,z+0.5])/grid
mask[x,y,z] = np.sum(np.abs((rotation*(coords-offset))/r)**e) < 1
microstructure = np.where(inside,
options.fill if options.inside else microstructure,
microstructure if options.inside else options.fill)
if options.periodic:
shift = ((offset-center)*grid).astype(int)
mask = np.roll(mask,shift,(0,1,2))
else: # nonperiodic, much lighter on resources
microstructure = np.where(np.abs(X)**options.exponent[0] +
np.abs(Y)**options.exponent[1] +
np.abs(Z)**options.exponent[2] <= 1.0,
options.fill if options.inside else microstructure,
microstructure if options.inside else options.fill)
if options.inside: mask = np.logical_not(mask)
fill = np.nanmax(geom.microstructure)+1 if options.fill is None else options.fill
np.seterr(**old_settings) # Reset warnings to old state
newInfo['microstructures'] = len(np.unique(microstructure))
damask.util.croak(geom.update(np.where(mask,geom.microstructure,fill)))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
# --- report ---------------------------------------------------------------------------------------
if (newInfo['microstructures'] != info['microstructures']):
damask.util.croak('--> microstructures: {}'.format(newInfo['microstructures']))
#--- write header ---------------------------------------------------------------------------------
table.info_clear()
table.info_append(extra_header+[
scriptID + ' ' + ' '.join(sys.argv[1:]),
"grid\ta {}\tb {}\tc {}".format(*info['grid']),
"size\tx {}\ty {}\tz {}".format(*info['size']),
"origin\tx {}\ty {}\tz {}".format(*info['origin']),
"homogenization\t{}".format(info['homogenization']),
"microstructures\t{}".format(newInfo['microstructures']),
])
table.labels_clear()
table.head_write()
table.output_flush()
# --- write microstructure information ------------------------------------------------------------
format = '%g' if options.float else '%{}i'.format(int(math.floor(math.log10(np.nanmax(microstructure))+1)))
table.data = microstructure.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
table.data_writeArray(format,delimiter = ' ')
#--- output finalization --------------------------------------------------------------------------
table.close()
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)

192
processing/pre/geom_canvas.py
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@ -1,181 +1,77 @@
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
import numpy as np
import os
import sys
from io import StringIO
from optparse import OptionParser
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [geomfile(s)]', description = """
Changes the (three-dimensional) canvas of a spectral geometry description.
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
Increases or decreases the (three-dimensional) canvas.
Grid can be given as absolute or relative values, e.g. 16 16 16 or 2x 0.5x 32.
""", version = scriptID)
parser.add_option('-g',
'--grid',
parser.add_option('-g','--grid',
dest = 'grid',
type = 'string', nargs = 3, metavar = ' '.join(['string']*3),
help = 'a,b,c grid of hexahedral box. [auto]')
parser.add_option('-o',
'--offset',
help = 'a,b,c grid of hexahedral box')
parser.add_option('-o','--offset',
dest = 'offset',
type = 'int', nargs = 3, metavar = ' '.join(['int']*3),
help = 'a,b,c offset from old to new origin of grid [%default]')
parser.add_option('-f',
'--fill',
parser.add_option('-f','--fill',
dest = 'fill',
type = 'float', metavar = 'float',
help = '(background) canvas grain index. "0" selects maximum microstructure index + 1 [%default]')
parser.add_option('--float',
dest = 'float',
action = 'store_true',
help = 'use float input')
parser.add_option('--blank',
dest = 'blank',
action = 'store_true',
help = 'blank out (optional) input canvas content')
type = 'float', metavar = 'int',
help = 'background microstructure index, defaults to max microstructure index + 1')
parser.set_defaults(grid = ['0','0','0'],
offset = (0,0,0),
fill = 0.0,
float = False,
)
parser.set_defaults(offset = (0,0,0))
(options, filenames) = parser.parse_args()
datatype = 'f' if options.float else 'i'
options.grid = ['1','1','1'] if options.blank and options.grid == ['0','0','0'] else options.grid
options.fill = 1 if options.blank and options.fill == 0 else options.fill
# --- 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)
if options.blank:
extra_header = []
info = {}
info['grid'] = np.zeros(3,dtype=int)
info['size'] = np.zeros(3,dtype=float)
info['origin'] = np.zeros(3,dtype=float)
info['microstructures'] = 0
info['homogenization'] = 1
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
origin = geom.get_origin()
size = geom.get_size()
old = new = geom.get_grid()
offset = np.asarray(options.offset)
if options.grid is not None:
new = np.maximum(1,
np.array([int(o*float(n.lower().replace('x',''))) if n.lower().endswith('x') \
else int(n) for o,n in zip(old,options.grid)],dtype=int))
canvas = np.full(new,options.fill if options.fill is not None
else np.nanmax(geom.microstructure)+1,geom.microstructure.dtype)
l = np.clip( offset, 0,np.minimum(old +offset,new))
r = np.clip( offset+old,0,np.minimum(old*2+offset,new))
L = np.clip(-offset, 0,np.minimum(new -offset,old))
R = np.clip(-offset+new,0,np.minimum(new*2-offset,old))
canvas[l[0]:r[0],l[1]:r[1],l[2]:r[2]] = geom.microstructure[L[0]:R[0],L[1]:R[1],L[2]:R[2]]
damask.util.croak(geom.update(canvas,origin=origin+offset*size/old,rescale=True))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
if name is None:
sys.stdout.write(str(geom.show()))
else:
# --- 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'],datatype).reshape(info['grid'],order='F') # read microstructure
# --- do work ------------------------------------------------------------------------------------
newInfo = {
'grid': np.zeros(3,'i'),
'origin': np.zeros(3,'d'),
'microstructures': 0,
}
newInfo['grid'] = np.array([int(o*float(n.translate(None,'xX'))) if n[-1].lower() == 'x'\
else int(n) for o,n in zip(info['grid'],options.grid)],'i')
newInfo['grid'] = np.where(newInfo['grid'] > 0, newInfo['grid'],info['grid'])
microstructure_cropped = np.zeros(newInfo['grid'],datatype)
microstructure_cropped.fill(options.fill if options.float or options.fill > 0 else np.nanmax(microstructure)+1)
if not options.blank:
xindex = np.arange(max(options.offset[0],0),min(options.offset[0]+newInfo['grid'][0],info['grid'][0]))
yindex = np.arange(max(options.offset[1],0),min(options.offset[1]+newInfo['grid'][1],info['grid'][1]))
zindex = np.arange(max(options.offset[2],0),min(options.offset[2]+newInfo['grid'][2],info['grid'][2]))
translate_x = [i - options.offset[0] for i in xindex]
translate_y = [i - options.offset[1] for i in yindex]
translate_z = [i - options.offset[2] for i in zindex]
if 0 in map(len,[xindex,yindex,zindex,translate_x,translate_y,translate_z]):
damask.util.croak('invaldid combination of grid and offset.')
table.close(dismiss = True)
continue
microstructure_cropped[min(translate_x):max(translate_x)+1,
min(translate_y):max(translate_y)+1,
min(translate_z):max(translate_z)+1] \
= microstructure[min(xindex):max(xindex)+1,
min(yindex):max(yindex)+1,
min(zindex):max(zindex)+1]
newInfo['size'] = info['size']/info['grid']*newInfo['grid'] if np.all(info['grid'] > 0) else newInfo['grid']
newInfo['origin'] = info['origin']+(info['size']/info['grid'] if np.all(info['grid'] > 0) \
else newInfo['size']/newInfo['grid'])*options.offset
newInfo['microstructures'] = len(np.unique(microstructure_cropped))
# --- report ---------------------------------------------------------------------------------------
remarks = []
errors = []
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 (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 np.any(newInfo['grid'] < 1): errors.append('invalid new grid a b c.')
if np.any(newInfo['size'] <= 0.0): errors.append('invalid new size x y z.')
if remarks != []: damask.util.croak(remarks)
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
# --- write header ---------------------------------------------------------------------------------
table.info_clear()
table.info_append(extra_header+[
scriptID + ' ' + ' '.join(sys.argv[1:]),
"grid\ta {}\tb {}\tc {}".format(*newInfo['grid']),
"size\tx {}\ty {}\tz {}".format(*newInfo['size']),
"origin\tx {}\ty {}\tz {}".format(*newInfo['origin']),
"homogenization\t{}".format(info['homogenization']),
"microstructures\t{}".format(newInfo['microstructures']),
])
table.labels_clear()
table.head_write()
table.output_flush()
# --- write microstructure information ------------------------------------------------------------
format = '%g' if options.float else '%{}i'.format(int(math.floor(math.log10(np.nanmax(microstructure_cropped))+1)))
table.data = microstructure_cropped.reshape((newInfo['grid'][0],newInfo['grid'][1]*newInfo['grid'][2]),order='F').transpose()
table.data_writeArray(format,delimiter=' ')
# --- output finalization --------------------------------------------------------------------------
table.close() # close ASCII table
geom.to_file(name)

39
processing/pre/geom_check.py Executable file
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@ -0,0 +1,39 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [geomfile(s)]', description = """
Writes vtk file for visualization.
""", version = scriptID)
(options, filenames) = parser.parse_args()
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
damask.util.croak(geom)
if name is None:
sys.stdout.write(geom.to_vtk())
else:
geom.to_vtk(os.path.splitext(name)[0])

25
processing/pre/geom_check.sh
View File

@ -1,25 +0,0 @@
#!/usr/bin/env bash
if [[ "$1" == "-f" || "$1" == "--float" ]]; then
shift
arg='--float'
else
arg=''
fi
for geom in "$@"
do
geom_toTable $arg \
< $geom \
| \
vtk_rectilinearGrid > ${geom%.*}.vtk
geom_toTable $arg \
< $geom \
| \
vtk_addRectilinearGridData \
--vtk ${geom%.*}.vtk \
--data microstructure \
rm ${geom%.*}.vtk
done

83
processing/pre/geom_clean.py
View File

@ -1,17 +1,23 @@
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
import numpy as np
import damask
from scipy import ndimage
import os
import sys
from io import StringIO
from optparse import OptionParser
from scipy import ndimage
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
def mostFrequent(arr):
return np.argmax(np.bincount(arr.astype('int')))
unique, inverse = np.unique(arr, return_inverse=True)
return unique[np.argmax(np.bincount(inverse))]
#--------------------------------------------------------------------------------------------------
@ -19,76 +25,33 @@ def mostFrequent(arr):
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
Smooth geometry by selecting most frequent microstructure index within given stencil at each location.
Smooth microstructure by selecting most frequent index within given stencil at each location.
""", version=scriptID)
parser.add_option('-s','--stencil',
dest = 'stencil',
type = 'int', metavar = 'int',
help = 'size of smoothing stencil [%default]')
parser.set_defaults(stencil = 3,
)
parser.set_defaults(stencil = 3)
(options, filenames) = parser.parse_args()
# --- 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 ----------------------------------------------------------------------------
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
table.head_read()
info,extra_header = table.head_getGeom()
damask.util.report_geom(info)
damask.util.croak(geom.update(ndimage.filters.generic_filter(
geom.microstructure,mostFrequent,
size=(options.stencil,)*3).astype(geom.microstructure.dtype)))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
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']).reshape(info['grid'],order='F') # read microstructure
# --- do work ------------------------------------------------------------------------------------
microstructure = ndimage.filters.generic_filter(microstructure,mostFrequent,size=(options.stencil,)*3).astype('int_')
newInfo = {'microstructures': len(np.unique(microstructure))}
# --- report ---------------------------------------------------------------------------------------
if ( newInfo['microstructures'] != info['microstructures']):
damask.util.croak('--> microstructures: %i'%newInfo['microstructures'])
info['microstructures'] == newInfo['microstructures']
# --- write header ---------------------------------------------------------------------------------
table.info_clear()
table.info_append([scriptID + ' ' + ' '.join(sys.argv[1:]),])
table.head_putGeom(info)
table.info_append([extra_header])
table.labels_clear()
table.head_write()
# --- write microstructure information ------------------------------------------------------------
formatwidth = int(math.floor(math.log10(np.nanmax(microstructure))+1))
table.data = microstructure.reshape((info['grid'][0],np.prod(info['grid'][1:])),order='F').transpose()
table.data_writeArray('%{}i'.format(formatwidth),delimiter = ' ')
# --- output finalization --------------------------------------------------------------------------
table.close() # close ASCII table
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)

142
processing/pre/geom_fromDREAM3D.py
View File

@ -1,11 +1,15 @@
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys,h5py
import numpy as np
import os
import sys
from optparse import OptionParser
import h5py
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
@ -14,40 +18,50 @@ scriptID = ' '.join([scriptName,damask.version])
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [dream3dfile[s]]', description = """
Convert DREAM3D file to geometry file. This can be done from cell data (direct pointwise takeover) or
from grain data (individual grains are segmented). Requires orientation data as quaternion.
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [DREAM.3Dfile(s)]', description = """
Converts DREAM.3D file. Input can be cell data (direct pointwise takeover) or grain data (individual
grains are segmented). Requires orientation data as quaternion.
""", version = scriptID)
parser.add_option('-b','--basegroup',
dest = 'basegroup', metavar = 'string',
dest = 'basegroup',
metavar = 'string',
help = 'name of the group in "DataContainers" containing the pointwise (and, if applicable grain average) data')
parser.add_option('-p','--pointwise',
dest = 'pointwise', metavar = 'string',
dest = 'pointwise',
metavar = 'string',
help = 'name of the group in "DataContainers/<basegroup>" containing pointwise data [%default]')
parser.add_option('-a','--average',
dest = 'average', metavar = 'string',
dest = 'average',
metavar = 'string',
help = 'name of the group in "DataContainers</basegroup>" containing grain average data. '\
+ 'Leave empty for pointwise data')
parser.add_option('--phase',
dest = 'phase',
type = 'string', metavar = 'string',
type = 'string',
metavar = 'string',
help = 'name of the dataset containing pointwise/average phase IDs [%default]')
parser.add_option('--microstructure',
dest = 'microstructure',
type = 'string', metavar = 'string',
type = 'string',
metavar = 'string',
help = 'name of the dataset connecting pointwise and average data [%default]')
parser.add_option('-q', '--quaternion',
dest = 'quaternion',
type = 'string', metavar='string',
type = 'string',
metavar='string',
help = 'name of the dataset containing pointwise/average orientation as quaternion [%default]')
parser.add_option('--homogenization',
dest = 'homogenization',
type = 'int', metavar = 'int',
help = 'homogenization index to be used [%default]')
parser.set_defaults(pointwise = 'CellData',
quaternion = 'Quats',
phase = 'Phases',
microstructure = 'FeatureIds',
crystallite = 1,
homogenization = 1,
)
(options, filenames) = parser.parse_args()
@ -57,59 +71,51 @@ if options.basegroup is None:
rootDir ='DataContainers'
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: parser.error('no input file specified.')
for name in filenames:
try:
table = damask.ASCIItable(outname = os.path.splitext(name)[0]+'.geom',
buffered = False, labeled=False,
)
except: continue
damask.util.report(scriptName,name)
errors = []
info = {}
ori = []
inFile = h5py.File(name, 'r')
group_geom = os.path.join(rootDir,options.basegroup,'_SIMPL_GEOMETRY')
try:
info['size'] = inFile[os.path.join(group_geom,'DIMENSIONS')][...] \
size = inFile[os.path.join(group_geom,'DIMENSIONS')][...] \
* inFile[os.path.join(group_geom,'SPACING')][...]
info['grid'] = inFile[os.path.join(group_geom,'DIMENSIONS')][...]
info['origin'] = inFile[os.path.join(group_geom,'ORIGIN')][...]
grid = inFile[os.path.join(group_geom,'DIMENSIONS')][...]
origin = inFile[os.path.join(group_geom,'ORIGIN')][...]
except:
errors.append('Geometry data ({}) not found'.format(group_geom))
group_pointwise = os.path.join(rootDir,options.basegroup,options.pointwise)
if options.average is None:
label = 'point'
N_microstructure = np.product(info['grid'])
label = 'Point'
dataset = os.path.join(group_pointwise,options.quaternion)
try:
quats = np.reshape(inFile[dataset][...],(N_microstructure,4))
texture = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in quats]
quats = np.reshape(inFile[dataset][...],(np.product(grid),4))
rot = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in quats]
except:
errors.append('Pointwise orientation (quaternion) data ({}) not readable'.format(dataset))
dataset = os.path.join(group_pointwise,options.phase)
try:
phase = np.reshape(inFile[dataset][...],(N_microstructure))
phase = np.reshape(inFile[dataset][...],(np.product(grid)))
except:
errors.append('Pointwise phase data ({}) not readable'.format(dataset))
microstructure = np.arange(1,np.product(grid)+1,dtype=int).reshape(grid,order='F')
else:
label = 'grain'
label = 'Grain'
dataset = os.path.join(group_pointwise,options.microstructure)
try:
microstructure = np.reshape(inFile[dataset][...],(np.product(info['grid'])))
N_microstructure = np.max(microstructure)
microstructure = np.transpose(inFile[dataset][...].reshape(grid[::-1]),(2,1,0)) # convert from C ordering
except:
errors.append('Link between pointwise and grain average data ({}) not readable'.format(dataset))
@ -117,7 +123,7 @@ for name in filenames:
dataset = os.path.join(group_average,options.quaternion)
try:
texture = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in inFile[dataset][...][1:]] # skip first entry (unindexed)
rot = [damask.Rotation.fromQuaternion(q,True,P=+1) for q in inFile[dataset][...][1:]] # skip first entry (unindexed)
except:
errors.append('Average orientation data ({}) not readable'.format(dataset))
@ -129,60 +135,24 @@ for name in filenames:
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
config_header = ['<texture>']
for i in range(np.nanmax(microstructure)):
config_header += ['[{}{}]'.format(label,i+1),
'(gauss)\tphi1 {:.2f}\tPhi {:.2f}\tphi2 {:.2f}'.format(*rot[i].asEulers(degrees = True)),
]
config_header += ['<microstructure>']
for i in range(np.nanmax(microstructure)):
config_header += ['[{}{}]'.format(label,i+1),
'crystallite 1',
'(constituent)\tphase {}\ttexture {}\tfraction 1.0'.format(phase[i],i+1),
]
mat = damask.Material()
mat.verbose = False
header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
+ config_header
geom = damask.Geom(microstructure,size,origin,
homogenization=options.homogenization,comments=header)
damask.util.croak(geom)
# dummy <homogenization>
h = damask.config.material.Homogenization()
mat.add_section('Homogenization','none',h)
info['homogenization'] = 1
# <crystallite> placeholder (same for all microstructures at the moment)
c = damask.config.material.Crystallite()
mat.add_section('Crystallite','tbd',c)
# <phase> placeholders
for i in range(np.max(phase)):
p = damask.config.material.Phase()
mat.add_section('phase','phase{}-tbd'.format(i+1),p)
# <texture>
for i,o in enumerate(texture):
t = damask.config.material.Texture()
t.add_component('gauss',{'eulers':o.asEulers(degrees=True)})
mat.add_section(part='texture', section='{}{}'.format(label,i+1),initialData=t)
# <microstructure>
for i in range(N_microstructure):
m = damask.config.material.Microstructure()
mat.add_section('microstructure','{}{}'.format(label,i+1),m)
mat.add_microstructure('{}{}'.format(label,i+1),
{'phase': 'phase{}-tbd'.format(phase[i]),
'texture':'{}{}'.format(label,i+1),
'crystallite':'tbd',
'fraction':1
})
table.info_append([
scriptID + ' ' + ' '.join(sys.argv[1:]),
"grid\ta {}\tb {}\tc {}".format(*info['grid']),
"size\tx {}\ty {}\tz {}".format(*info['size']),
"origin\tx {}\ty {}\tz {}".format(*info['origin']),
"homogenization\t{}".format(info['homogenization']),
str(mat).split('\n')
])
table.head_write()
if options.average is None:
table.data = [1, 'to', format(N_microstructure)]
table.data_write()
else:
table.data = microstructure.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
table.data_writeArray()
table.close()
geom.to_file(os.path.splitext(name)[0]+'.geom')

105
processing/pre/geom_fromMinimalSurface.py
View File

@ -1,28 +1,33 @@
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
import numpy as np
import os
import sys
from optparse import OptionParser
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
minimal_surfaces = ['primitive','gyroid','diamond']
surface = {
'primitive': lambda x,y,z: np.cos(x)+np.cos(y)+np.cos(z),
'gyroid': lambda x,y,z: np.sin(x)*np.cos(y)+np.sin(y)*np.cos(z)+np.cos(x)*np.sin(z),
'diamond': lambda x,y,z: np.cos(x-y)*np.cos(z)+np.sin(x+y)*np.sin(z),
}
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
minimal_surfaces = ['primitive','gyroid','diamond',]
surface = {
'primitive': lambda x,y,z: math.cos(x)+math.cos(y)+math.cos(z),
'gyroid': lambda x,y,z: math.sin(x)*math.cos(y)+math.sin(y)*math.cos(z)+math.cos(x)*math.sin(z),
'diamond': lambda x,y,z: math.cos(x-y)*math.cos(z)+math.sin(x+y)*math.sin(z),
}
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [option(s)] [geomfile]', description = """
Generate a geometry file of a bicontinuous structure of given type.
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile]', description = """
Generate a bicontinuous structure of given type.
""", version = scriptID)
@ -55,6 +60,7 @@ parser.add_option('--m',
dest = 'microstructure',
type = 'int', nargs = 2, metavar = 'int int',
help = 'two microstructure indices to be used [%default]')
parser.set_defaults(type = minimal_surfaces[0],
threshold = 0.0,
periods = 1,
@ -64,67 +70,26 @@ parser.set_defaults(type = minimal_surfaces[0],
microstructure = (1,2),
)
(options,filenames) = parser.parse_args()
(options,filename) = parser.parse_args()
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(outname = name,
buffered = False, labeled = False)
except: continue
name = None if filename == [] else filename[0]
damask.util.report(scriptName,name)
x,y,z = np.meshgrid(options.periods*2.0*np.pi*(np.arange(options.grid[0])+0.5)/options.grid[0],
options.periods*2.0*np.pi*(np.arange(options.grid[1])+0.5)/options.grid[1],
options.periods*2.0*np.pi*(np.arange(options.grid[2])+0.5)/options.grid[2],
indexing='xy',sparse=True)
# ------------------------------------------ make grid -------------------------------------
microstructure = np.where(options.threshold < surface[options.type](x,y,z),
options.microstructure[1],options.microstructure[0])
info = {
'grid': np.array(options.grid),
'size': np.array(options.size),
'origin': np.zeros(3,'d'),
'microstructures': max(options.microstructure),
'homogenization': options.homogenization
}
geom=damask.Geom(microstructure,options.size,
homogenization=options.homogenization,
comments=[scriptID + ' ' + ' '.join(sys.argv[1:])])
damask.util.croak(geom)
#--- 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]
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()
table.close()
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)

195
processing/pre/geom_fromOsteonGeometry.py
View File

@ -1,46 +1,66 @@
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
import numpy as np
import os
import sys
from optparse import OptionParser
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [option(s)] [geomfile]', description = """
Generate a geometry file of an osteon enclosing the Harvesian canal and separated by interstitial tissue.
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile]', description = """
Generate description of an osteon enclosing the Harvesian canal and separated by interstitial tissue.
The osteon phase is lamellar with a twisted plywood structure.
Its fiber orientation is oscillating by +/- amplitude within one period.
""", version = scriptID)
parser.add_option('-g', '--grid', dest='grid', type='int', nargs=2, metavar = 'int int',
parser.add_option('-g', '--grid',
dest='grid', type='int',
nargs=2, metavar = 'int int',
help='a,b grid of hexahedral box [%default]')
parser.add_option('-s', '--size', dest='size', type='float', nargs=2, metavar = 'float float',
parser.add_option('-s', '--size',
dest='size',
type='float', nargs=2, metavar = 'float float',
help='x,y size of hexahedral box [%default]')
parser.add_option('-c', '--canal', dest='canal', type='float', metavar = 'float',
parser.add_option('-c', '--canal',
dest='canal',
type='float', metavar = 'float',
help='Haversian canal radius [%default]')
parser.add_option('-o', '--osteon', dest='osteon', type='float', metavar = 'float',
parser.add_option('-o', '--osteon',
dest='osteon',
type='float', metavar = 'float',
help='horizontal osteon radius [%default]')
parser.add_option('-l', '--lamella', dest='period', type='float', metavar = 'float',
parser.add_option('-l', '--lamella',
dest='period',
type='float', metavar = 'float',
help='lamella width [%default]')
parser.add_option('-a', '--amplitude', dest='amplitude', type='float', metavar = 'float',
parser.add_option('-a', '--amplitude',
dest='amplitude',
type='float', metavar = 'float',
help='amplitude of twisted plywood wiggle in deg [%default]')
parser.add_option( '--aspect', dest='aspect', type='float', metavar = 'float',
parser.add_option( '--aspect',
dest='aspect',
type='float', metavar = 'float',
help='vertical/horizontal osteon aspect ratio [%default]')
parser.add_option('-w', '--omega', dest='omega', type='float', metavar = 'float',
parser.add_option('-w', '--omega',
dest='omega',
type='float', metavar = 'float',
help='rotation angle around normal of osteon [%default]')
parser.add_option('--homogenization', dest='homogenization', type='int', metavar = 'int',
parser.add_option( '--homogenization',
dest='homogenization',
type='int', metavar = 'int',
help='homogenization index to be used [%default]')
parser.add_option('--crystallite', dest='crystallite', type='int', metavar = 'int',
help='crystallite index to be used [%default]')
parser.set_defaults(canal = 25e-6,
osteon = 100e-6,
@ -50,107 +70,82 @@ parser.set_defaults(canal = 25e-6,
amplitude = 60,
size = (300e-6,300e-6),
grid = (512,512),
homogenization = 1,
crystallite = 1)
homogenization = 1)
(options,filename) = parser.parse_args()
if np.any(np.array(options.grid) < 2):
parser('invalid grid a b c.')
if np.any(np.array(options.size) <= 0.0):
parser('invalid size x y z.')
# --- open input files ----------------------------------------------------------------------------
name = None if filename == [] else filename[0]
damask.util.report(scriptName,name)
if filename == []: filename = [None]
omega = np.deg2rad(options.omega)
rotation = np.array([[ np.cos(omega),np.sin(omega),],
[-np.sin(omega),np.cos(omega),]])
table = damask.ASCIItable(outname = filename[0],
buffered = False, labeled=False)
grid = np.array(options.grid,'i')
size = np.array(options.size,'d')
damask.util.report(scriptName,filename[0])
options.omega *= math.pi/180.0 # rescale ro radians
rotation = np.array([[ math.cos(options.omega),math.sin(options.omega),],
[-math.sin(options.omega),math.cos(options.omega),]],'d')
box = np.dot(np.array([[options.canal,0.],[0.,options.aspect*options.canal]]).transpose(),rotation)
info = {
'grid': np.ones(3,'i'),
'size': np.ones(3,'d'),
'origin': np.zeros(3,'d'),
'microstructures': 3,
'homogenization': options.homogenization,
}
info['grid'][:2] = np.array(options.grid,'i')
info['size'][:2] = np.array(options.size,'d')
info['size'][2] = min(info['size'][0]/info['grid'][0],info['size'][1]/info['grid'][1])
info['origin'] = -info['size']/2.0
X0 = info['size'][0]/info['grid'][0]*\
(np.tile(np.arange(info['grid'][0]),(info['grid'][1],1)) - info['grid'][0]/2 + 0.5)
Y0 = info['size'][1]/info['grid'][1]*\
(np.tile(np.arange(info['grid'][1]),(info['grid'][0],1)).transpose() - info['grid'][1]/2 + 0.5)
X0,Y0 = np.meshgrid(size[0]/grid[0] * (np.arange(grid[0]) - grid[0]/2 + 0.5),
size[1]/grid[0] * (np.arange(grid[1]) - grid[1]/2 + 0.5), indexing='ij')
X = X0*rotation[0,0] + Y0*rotation[0,1] # rotate by omega
Y = X0*rotation[1,0] + Y0*rotation[1,1] # rotate by omega
radius = np.sqrt(X*X + Y*Y/options.aspect/options.aspect)
radius = np.sqrt(X*X + Y*Y/options.aspect**2.0)
alpha = np.degrees(np.arctan2(Y/options.aspect,X))
beta = options.amplitude*np.sin(2.0*math.pi*(radius-options.canal)/options.period)
beta = options.amplitude*np.sin(2.0*np.pi*(radius-options.canal)/options.period)
microstructure = np.where(radius < float(options.canal),1,0) + np.where(radius > float(options.osteon),2,0)
microstructure = np.where(radius < float(options.canal), 1,0) \
+ np.where(radius > float(options.osteon),2,0)
alphaOfGrain = np.zeros(info['grid'][0]*info['grid'][1],'d')
betaOfGrain = np.zeros(info['grid'][0]*info['grid'][1],'d')
for y in range(info['grid'][1]):
for x in range(info['grid'][0]):
if microstructure[y,x] == 0:
microstructure[y,x] = info['microstructures']
alphaOfGrain[info['microstructures']] = alpha[y,x]
betaOfGrain[ info['microstructures']] = beta[y,x]
info['microstructures'] += 1
# extend to 3D
size = np.append(size,np.min(size/grid))
grid = np.append(grid,1)
microstructure = microstructure.reshape(microstructure.shape+(1,))
#--- report ---------------------------------------------------------------------------------------
damask.util.report_geom(info,['grid','size','origin','homogenization','microstructures'])
Alpha = np.zeros(grid[0]*grid[1],'d')
Beta = np.zeros(grid[0]*grid[1],'d')
formatwidth = 1+int(math.floor(math.log10(info['microstructures']-1)))
header = [scriptID + ' ' + ' '.join(sys.argv[1:])]
header.append('<microstructure>')
header.append('[canal]')
header.append('crystallite %i'%options.crystallite)
header.append('(constituent)\tphase 1\ttexture 1\tfraction 1.0')
header.append('[interstitial]')
header.append('crystallite %i'%options.crystallite)
header.append('(constituent)\tphase 2\ttexture 2\tfraction 1.0')
for i in range(3,info['microstructures']):
header.append('[Grain%s]'%(str(i).zfill(formatwidth)))
header.append('crystallite %i'%options.crystallite)
header.append('(constituent)\tphase 3\ttexture %s\tfraction 1.0'%(str(i).rjust(formatwidth)))
i = 3
for y in range(grid[1]):
for x in range(grid[0]):
if microstructure[x,y] == 0:
microstructure[x,y] = i
Alpha[i] = alpha[x,y]
Beta [i] = beta [x,y]
i+=1
header.append('<texture>')
header.append('[canal]')
header.append('[interstitial]')
for i in range(3,info['microstructures']):
header.append('[Grain%s]'%(str(i).zfill(formatwidth)))
header.append('(gauss)\tphi1 %g\tPhi %g\tphi2 0\tscatter 0.0\tfraction 1.0'\
%(alphaOfGrain[i],betaOfGrain[i]))
header.append([
"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'])])
config_header = ['<texture>',
'[canal]',
'[interstitial]'
]
for i in range(3,np.max(microstructure)):
config_header += ['[Point{}]'.format(i-2),
'(gauss)\tphi1 {:.2f}\tPhi {:.2f}\tphi2 0'.format(Alpha[i],Beta[i])
]
table.info_append(header)
table.head_write()
config_header = ['<microstructure>',
'[canal]',
'crystallite 1',
'(constituent)\tphase 1\ttexture 1\tfraction 1.0',
'[interstitial]',
'crystallite 1',
'(constituent)\tphase 2\ttexture 2\tfraction 1.0'
]
for i in range(3,np.max(microstructure)):
config_header += ['[Point{}]'.format(i-2),
'crystallite 1',
'(constituent)\tphase 3\ttexture {}\tfraction 1.0'.format(i)
]
# --- write microstructure information ------------------------------------------------------------
header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
+ config_header
geom = damask.Geom(microstructure.reshape(grid),
size,-size/2,
homogenization=options.homogenization,comments=header)
damask.util.croak(geom)
table.data = microstructure.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
table.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
#--- output finalization --------------------------------------------------------------------------
table.close()
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)

69
processing/pre/geom_fromScratch.py Executable file
View File

@ -0,0 +1,69 @@
#!/usr/bin/env python3
import os
import sys
from optparse import OptionParser
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
Generate homogeneous geometry.
""", version = scriptID)
parser.add_option('-g','--grid',
dest = 'grid',
type = 'int', nargs = 3, metavar = ' '.join(['int']*3),
help = 'a,b,c grid of hexahedral box %default')
parser.add_option('-s', '--size',
dest = 'size',
type = 'float', nargs = 3, metavar = ' '.join(['float']*3),
help = 'x,y,z of geometry size')
parser.add_option('-o','--origin',
dest = 'origin',
type = 'float', nargs = 3, metavar = ' '.join(['float']*3),
help = 'x,y,z of geometry origin %default')
parser.add_option('--homogenization',
dest = 'homogenization',
type = 'int', metavar = 'int',
help = 'homogenization index [%default]')
parser.add_option('-f','--fill',
dest = 'fill',
type = 'float', metavar = 'int',
help = 'microstructure index [%default]')
parser.set_defaults(grid = (16,16,16),
origin = (0.,0.,0.),
homogenization = 1,
fill = 1,
)
(options, filename) = parser.parse_args()
name = None if filename == [] else filename[0]
damask.util.report(scriptName,name)
dtype = float if np.isnan(options.fill) or int(options.fill) != options.fill else int
geom = damask.Geom(microstructure=np.full(options.grid,options.fill,dtype=dtype),
size=options.size,
origin=options.origin,
homogenization=options.homogenization,
comments=scriptID + ' ' + ' '.join(sys.argv[1:]))
damask.util.croak(geom)
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)

170
processing/pre/geom_fromTable.py
View File

@ -1,22 +1,25 @@
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
import numpy as np
import os
import sys
from optparse import OptionParser
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [ASCIItable(s)]', description = """
Generate geometry description and material configuration from position, phase, and orientation (or microstructure) data.
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [ASCIItable(s)]', description = """
Converts ASCII table. Input can be microstructure or orientation (as quaternion). For the latter,
phase information can be given additionally.
""", version = scriptID)
@ -40,19 +43,13 @@ parser.add_option('--axes',
dest = 'axes',
type = 'string', nargs = 3, metavar = ' '.join(['string']*3),
help = 'orientation coordinate frame in terms of position coordinate frame [+x +y +z]')
parser.add_option('--homogenization',
dest = 'homogenization',
type = 'int', metavar = 'int',
help = 'homogenization index to be used [%default]')
parser.add_option('--crystallite',
dest = 'crystallite',
type = 'int', metavar = 'int',
help = 'crystallite index to be used [%default]')
parser.set_defaults(homogenization = 1,
crystallite = 1,
pos = 'pos',
)
@ -63,7 +60,9 @@ input = [ options.quaternion is not None,
]
if np.sum(input) != 1:
parser.error('need either microstructure label or exactly one orientation input format.')
parser.error('need either microstructure or quaternion (and optionally phase) as input.')
if options.microstructure is not None and options.phase is not None:
parser.error('need either microstructure or phase (and mandatory quaternion) as input.')
if options.axes is not None and not set(options.axes).issubset(set(['x','+x','-x','y','+y','-y','z','+z','-z'])):
parser.error('invalid axes {} {} {}.'.format(*options.axes))
@ -71,20 +70,12 @@ if options.axes is not None and not set(options.axes).issubset(set(['x','+x','-x
(options.microstructure,1,'microstructure'),
][np.where(input)[0][0]] # select input label that was requested
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
outname = os.path.splitext(name)[-2]+'.geom' if name else name,
buffered = False)
except: continue
damask.util.report(scriptName,name)
# ------------------------------------------ read head ---------------------------------------
table = damask.ASCIItable(name = name,readonly=True)
table.head_read() # read ASCII header info
# ------------------------------------------ sanity checks ---------------------------------------
@ -101,7 +92,6 @@ for name in filenames:
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
table.data_readArray([options.pos] \
@ -113,120 +103,56 @@ for name in filenames:
if options.phase is None:
table.data = np.column_stack((table.data,np.ones(len(table.data)))) # add single phase if no phase column given
# --------------- figure out size and grid ---------------------------------------------------------
grid,size = damask.util.coordGridAndSize(table.data[:,0:3])
coords = [np.unique(table.data[:,i]) for i in range(3)]
mincorner = np.array(list(map(min,coords)))
maxcorner = np.array(list(map(max,coords)))
grid = np.array(list(map(len,coords)),'i')
size = grid/np.maximum(np.ones(3,'d'), grid-1.0) * (maxcorner-mincorner) # size from edge to edge = dim * n/(n-1)
size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 set to smallest among other spacings
delta = size/np.maximum(np.ones(3,'d'), grid)
origin = mincorner - 0.5*delta # shift from cell center to corner
origin = mincorner - 0.5*size/grid # shift from cell center to corner
N = grid.prod()
if N != len(table.data):
errors.append('data count {} does not match grid {}.'.format(len(table.data),' x '.join(map(repr,grid))))
if np.any(np.abs(np.log10((coords[0][1:]-coords[0][:-1])/delta[0])) > 0.01) \
or np.any(np.abs(np.log10((coords[1][1:]-coords[1][:-1])/delta[1])) > 0.01) \
or np.any(np.abs(np.log10((coords[2][1:]-coords[2][:-1])/delta[2])) > 0.01):
errors.append('regular grid spacing {} violated.'.format(' x '.join(map(repr,delta))))
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
# ------------------------------------------ process data ------------------------------------------
colOri = table.label_index(label)+(3-coordDim) # column(s) of orientation data followed by 3 coordinates
indices = np.lexsort((table.data[:,0],table.data[:,1],table.data[:,2])) # indices of position when sorting x fast, z slow
microstructure = np.empty(grid,dtype = int) # initialize empty microstructure
i = 0
if inputtype == 'microstructure':
for z in range(grid[2]):
for y in range(grid[1]):
for x in range(grid[0]):
microstructure[x,y,z] = table.data[indices[i],3]
i+=1
grain = table.data[:,colOri]
nGrains = len(np.unique(grain))
config_header = []
elif inputtype == 'quaternion':
colPhase = -1 # column of phase data comes last
index = np.lexsort((table.data[:,0],table.data[:,1],table.data[:,2])) # index of position when sorting x fast, z slow
grain = -np.ones(N,dtype = 'int32') # initialize empty microstructure
orientations = [] # orientations
multiplicity = [] # orientation multiplicity (number of group members)
phases = [] # phase info
nGrains = 0 # counter for detected grains
existingGrains = np.arange(nGrains)
myPos = 0 # position (in list) of current grid point
unique,unique_inverse = np.unique(table.data[:,3:8],return_inverse=True,axis=0)
for z in range(grid[2]):
for y in range(grid[1]):
for x in range(grid[0]):
microstructure[x,y,z] = unique_inverse[indices[i]]+1
i+=1
config_header = ['<texture>']
for i,data in enumerate(unique):
ori = damask.Rotation(data[0:4])
config_header += ['[Grain{}]'.format(i+1),
'(gauss)\tphi1 {:.2f}\tPhi {:.2f}\tphi2 {:.2f}'.format(*ori.asEulers(degrees = True)),
]
if options.axes is not None: config_header += ['axes\t{} {} {}'.format(*options.axes)]
myData = table.data[index[myPos]] # read data for current grid point
myPhase = int(myData[colPhase])
config_header += ['<microstructure>']
for i,data in enumerate(unique):
config_header += ['[Grain{}]'.format(i+1),
'crystallite 1',
'(constituent)\tphase {}\ttexture {}\tfraction 1.0'.format(int(data[4]),i+1),
]
o = damask.Rotation(myData[colOri:colOri+4])
header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
+ config_header
geom = damask.Geom(microstructure,size,origin,
homogenization=options.homogenization,comments=header)
damask.util.croak(geom)
grain[myPos] = nGrains # assign new grain to me ...
nGrains += 1 # ... and update counter
orientations.append(o) # store new orientation for future comparison
multiplicity.append(1) # having single occurrence so far
phases.append(myPhase) # store phase info for future reporting
existingGrains = np.arange(nGrains) # update list of existing grains
myPos += 1
grain += 1 # offset from starting index 0 to 1
# --- generate header ----------------------------------------------------------------------------
info = {
'grid': grid,
'size': size,
'origin': origin,
'microstructures': nGrains,
'homogenization': options.homogenization,
}
damask.util.report_geom(info)
# --- write header ---------------------------------------------------------------------------------
formatwidth = 1+int(math.log10(info['microstructures']))
if inputtype == 'microstructure':
config_header = []
if name is None:
sys.stdout.write(str(geom.show()))
else:
config_header = ['<microstructure>']
for i,phase in enumerate(phases):
config_header += ['[Grain%s]'%(str(i+1).zfill(formatwidth)),
'crystallite %i'%options.crystallite,
'(constituent)\tphase %i\ttexture %s\tfraction 1.0'%(phase,str(i+1).rjust(formatwidth)),
]
config_header += ['<texture>']
for i,orientation in enumerate(orientations):
config_header += ['[Grain%s]'%(str(i+1).zfill(formatwidth)),
'axes\t%s %s %s'%tuple(options.axes) if options.axes is not None else '',
'(gauss)\tphi1 %g\tPhi %g\tphi2 %g\tscatter 0.0\tfraction 1.0'%tuple(orientation.asEulers(degrees = True)),
]
table.labels_clear()
table.info_clear()
table.info_append([scriptID + ' ' + ' '.join(sys.argv[1:])])
table.head_putGeom(info)
table.info_append(config_header)
table.head_write()
# --- write microstructure information ------------------------------------------------------------
table.data = grain.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
table.data_writeArray('%{}i'.format(formatwidth),delimiter=' ')
#--- output finalization --------------------------------------------------------------------------
table.close()
geom.to_file(os.path.splitext(name)[0]+'.geom')

120
processing/pre/geom_fromVoronoiTessellation.py
View File

@ -1,33 +1,21 @@
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
import numpy as np
import os
import sys
import multiprocessing
from optparse import OptionParser,OptionGroup
import numpy as np
from scipy import spatial
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
def meshgrid2(*arrs):
"""Code inspired by http://stackoverflow.com/questions/1827489/numpy-meshgrid-in-3d"""
arrs = tuple(reversed(arrs))
lens = np.array(list(map(len, arrs)))
dim = len(arrs)
ans = []
for i, arr in enumerate(arrs):
slc = np.ones(dim,'i')
slc[i] = lens[i]
arr2 = np.asarray(arr).reshape(slc)
for j, sz in enumerate(lens):
if j != i:
arr2 = arr2.repeat(sz, axis=j)
ans.insert(0,arr2)
return tuple(ans)
def laguerreTessellation(undeformed, coords, weights, grains, periodic = True, cpus = 2):
def findClosestSeed(fargs):
point, seeds, myWeights = fargs
@ -35,9 +23,6 @@ def findClosestSeed(fargs):
dist = np.sum((tmp - seeds)**2,axis=1) -myWeights
return np.argmin(dist) # seed point closest to point
def laguerreTessellation(undeformed, coords, weights, grains, periodic = True, cpus = 2):
copies = \
np.array([
[ -1,-1,-1 ],
@ -98,6 +83,7 @@ def laguerreTessellation(undeformed, coords, weights, grains, periodic = True, c
# closestSeed is modulo number of original seed points (i.e. excluding periodic copies)
return grains[closestSeeds%coords.shape[0]]
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
@ -189,10 +175,6 @@ group.add_option('--homogenization',
dest = 'homogenization',
type = 'int', metavar = 'int',
help = 'homogenization index to be used [%default]')
group.add_option('--crystallite',
dest = 'crystallite',
type = 'int', metavar = 'int',
help = 'crystallite index to be used [%default]')
group.add_option('--phase',
dest = 'phase',
type = 'int', metavar = 'int',
@ -205,7 +187,6 @@ parser.set_defaults(pos = 'pos',
microstructure = 'microstructure',
eulers = 'euler',
homogenization = 1,
crystallite = 1,
phase = 1,
cpus = 2,
laguerre = False,
@ -213,19 +194,18 @@ parser.set_defaults(pos = 'pos',
normalized = True,
config = True,
)
(options,filenames) = parser.parse_args()
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try: table = damask.ASCIItable(name = name,
outname = os.path.splitext(name)[0]+'.geom' if name else name,
buffered = False)
except: continue
damask.util.report(scriptName,name)
table = damask.ASCIItable(name = name, readonly = True)
# --- read header ----------------------------------------------------------------------------
table.head_read()
@ -245,10 +225,6 @@ for name in filenames:
hasEulers = table.label_dimension(options.eulers) == 3
hasWeights = table.label_dimension(options.weight) == 1 and options.laguerre
if np.any(np.array(info['grid']) < 1): errors.append('invalid grid a b c.')
if np.any(np.array(info['size']) <= 0.0) \
and np.all(np.array(info['grid']) < 1): errors.append('invalid size x y z.')
else:
for i in range(3):
if info['size'][i] <= 0.0: # any invalid size?
info['size'][i] = float(info['grid'][i])/max(info['grid']) # normalize to grid
@ -281,7 +257,7 @@ for name in filenames:
else table.data[:,table.label_indexrange(options.pos)] - info['origin']
eulers = table.data[:,table.label_indexrange(options.eulers)] if hasEulers \
else np.zeros(3*len(coords))
grains = table.data[:,table.label_indexrange(options.microstructure)].astype('i') if hasGrains \
grains = table.data[:,table.label_indexrange(options.microstructure)].astype(int) if hasGrains \
else 1+np.arange(len(coords))
weights = table.data[:,table.label_indexrange(options.weight)] if hasWeights \
else np.zeros(len(coords))
@ -293,62 +269,40 @@ for name in filenames:
x = (np.arange(info['grid'][0])+0.5)*info['size'][0]/info['grid'][0]
y = (np.arange(info['grid'][1])+0.5)*info['size'][1]/info['grid'][1]
z = (np.arange(info['grid'][2])+0.5)*info['size'][2]/info['grid'][2]
X,Y,Z = np.meshgrid(x, y, z,indexing='ij')
grid = np.stack((X,Y,Z),axis=-1).reshape((np.prod(info['grid']),3),order='F')
damask.util.croak('tessellating...')
grid = np.vstack(meshgrid2(x, y, z)).reshape(3,-1).T
indices = laguerreTessellation(grid, coords, weights, grains, options.periodic, options.cpus)
# --- write header ------------------------------------------------------------------------
usedGrainIDs = np.intersect1d(grainIDs,indices)
info['microstructures'] = len(usedGrainIDs)
if info['homogenization'] == 0: info['homogenization'] = options.homogenization
damask.util.report_geom(info,['grid','size','origin','homogenization',])
damask.util.croak(['microstructures: {}{}'.format(info['microstructures'],
(' out of {}'.format(NgrainIDs) if NgrainIDs != info['microstructures'] else '')),
])
config_header = []
formatwidth = 1+int(math.log10(NgrainIDs))
if options.config:
config_header += ['<microstructure>']
for i,ID in enumerate(grainIDs):
config_header += ['[Grain{}]'.format(str(ID).zfill(formatwidth)),
'crystallite {}'.format(options.crystallite),
'(constituent)\tphase {}\ttexture {}\tfraction 1.0'.format(options.phase,str(ID).rjust(formatwidth)),
]
if hasEulers:
config_header += ['<texture>']
theAxes = [] if options.axes is None else ['axes\t{} {} {}'.format(*options.axes)]
for ID in grainIDs:
eulerID = np.nonzero(grains == ID)[0][0] # find first occurrence of this grain id
config_header += ['[Grain{}]'.format(str(ID).zfill(formatwidth)),
'(gauss)\tphi1 {:g}\tPhi {:g}\tphi2 {:g}\tscatter 0.0\tfraction 1.0'.format(*eulers[eulerID])
] + theAxes
config_header += ['[Grain{}]'.format(ID),
'(gauss)\tphi1 {:.2f}\tPhi {:.2f}\tphi2 {:.2f}'.format(*eulers[eulerID])
]
if options.axes is not None: config_header += ['axes\t{} {} {}'.format(*options.axes)]
config_header += ['<microstructure>']
for ID in grainIDs:
config_header += ['[Grain{}]'.format(ID),
'crystallite 1',
'(constituent)\tphase {}\ttexture {}\tfraction 1.0'.format(options.phase,ID)
]
config_header += ['<!skip>']
table.labels_clear()
table.info_clear()
table.info_append([
scriptID + ' ' + ' '.join(sys.argv[1:]),
"grid\ta {}\tb {}\tc {}".format(*info['grid']),
"size\tx {}\ty {}\tz {}".format(*info['size']),
"origin\tx {}\ty {}\tz {}".format(*info['origin']),
"homogenization\t{}".format(info['homogenization']),
"microstructures\t{}".format(info['microstructures']),
config_header,
])
table.head_write()
header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
+ config_header
geom = damask.Geom(indices.reshape(info['grid'],order='F'),info['size'],info['origin'],
homogenization=options.homogenization,comments=header)
damask.util.croak(geom)
# --- write microstructure information ------------------------------------------------------------
table.data = indices.reshape(info['grid'][1]*info['grid'][2],info['grid'][0])
table.data_writeArray('%%%ii'%(formatwidth),delimiter=' ')
#--- output finalization --------------------------------------------------------------------------
table.close()
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(os.path.splitext(name)[0]+'.geom')

104
processing/pre/geom_grainGrowth.py
View File

@ -1,21 +1,30 @@
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
import numpy as np
import os
import sys
from io import StringIO
from optparse import OptionParser
import numpy as np
from scipy import ndimage
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
getInterfaceEnergy = lambda A,B: np.float32((A*B != 0)*(A != B)*1.0) # 1.0 if A & B are distinct & nonzero, 0.0 otherwise
struc = ndimage.generate_binary_structure(3,1) # 3D von Neumann neighborhood
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [option(s)] [geomfile(s)]', description = """
Smoothens out interface roughness by simulated curvature flow.
parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [geomfile(s)]', description = """
Smoothen interface roughness by simulated curvature flow.
This is achieved by the diffusion of each initially sharply bounded grain volume within the periodic domain
up to a given distance 'd' voxels.
The final geometry is assembled by selecting at each voxel that grain index for which the concentration remains largest.
@ -33,9 +42,6 @@ parser.add_option('-N', '--iterations',
parser.add_option('-i', '--immutable',
action = 'extend', dest = 'immutable', metavar = '<int LIST>',
help = 'list of immutable microstructure indices')
parser.add_option('-r', '--renumber',
dest = 'renumber', action='store_true',
help = 'output consecutive microstructure indices')
parser.add_option('--ndimage',
dest = 'ndimage', action='store_true',
help = 'use ndimage.gaussian_filter in lieu of explicit FFT')
@ -43,7 +49,6 @@ parser.add_option('--ndimage',
parser.set_defaults(d = 1,
N = 1,
immutable = [],
renumber = False,
ndimage = False,
)
@ -51,37 +56,17 @@ parser.set_defaults(d = 1,
options.immutable = list(map(int,options.immutable))
getInterfaceEnergy = lambda A,B: np.float32((A*B != 0)*(A != B)*1.0) # 1.0 if A & B are distinct & nonzero, 0.0 otherwise
struc = ndimage.generate_binary_structure(3,1) # 3D von Neumann neighborhood
# --- 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 ----------------------------------------------------------------------------
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
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 = np.tile(table.microstructure_read(info['grid']).reshape(info['grid'],order='F'),
np.where(info['grid'] == 1, 2,1)) # make one copy along dimensions with grid == 1
grid_original = geom.get_grid()
damask.util.croak(geom)
microstructure = np.tile(geom.microstructure,np.where(grid_original == 1, 2,1)) # make one copy along dimensions with grid == 1
grid = np.array(microstructure.shape)
# --- initialize support data ---------------------------------------------------------------------
@ -94,7 +79,7 @@ for name in filenames:
# Calculates gaussian weights for simulating 3d diffusion
gauss = np.exp(-(X*X + Y*Y + Z*Z)/(2.0*options.d*options.d),dtype=np.float32) \
/np.power(2.0*np.pi*options.d*options.d,(3.0 - np.count_nonzero(info['grid'] == 1))/2.,dtype=np.float32)
/np.power(2.0*np.pi*options.d*options.d,(3.0 - np.count_nonzero(grid_original == 1))/2.,dtype=np.float32)
gauss[:,:,:grid[2]//2:-1] = gauss[:,:,1:(grid[2]+1)//2] # trying to cope with uneven (odd) grid size
gauss[:,:grid[1]//2:-1,:] = gauss[:,1:(grid[1]+1)//2,:]
@ -184,49 +169,10 @@ for name in filenames:
# undo any changes involving immutable microstructures
microstructure = np.where(immutable, microstructure_original,microstructure)
# --- renumber to sequence 1...Ngrains if requested -----------------------------------------------
# http://stackoverflow.com/questions/10741346/np-frequency-counts-for-unique-values-in-an-array
if options.renumber:
newID = 0
for microstructureID,count in enumerate(np.bincount(microstructure.flatten())):
if count != 0:
newID += 1
microstructure = np.where(microstructure == microstructureID, newID, microstructure)
newInfo = {'microstructures': len(np.unique(microstructure)),}
# --- report --------------------------------------------------------------------------------------
remarks = []
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=info['origin']),
"homogenization\t{homog}".format(homog=info['homogenization']),
"microstructures\t{microstructures}".format(microstructures=newInfo['microstructures']),
])
table.head_write()
# --- write microstructure information ------------------------------------------------------------
formatwidth = int(math.floor(math.log10(np.nanmax(microstructure))+1))
table.data = microstructure[::1 if info['grid'][0]>1 else 2,
::1 if info['grid'][1]>1 else 2,
::1 if info['grid'][2]>1 else 2,].\
reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
table.data_writeArray('%{}i'.format(formatwidth),delimiter = ' ')
# --- output finalization --------------------------------------------------------------------------
table.close()
damask.util.croak(geom.update(microstructure[0:grid_original[0],0:grid_original[1],0:grid_original[2]]))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)

108
processing/pre/geom_mirror.py
View File

@ -1,120 +1,72 @@
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
import numpy as np
import damask
import os
import sys
from io import StringIO
from optparse import OptionParser
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
validDirections = ['x','y','z']
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
Mirrors spectral geometry description along given directions.
Mirror along given directions.
""", version=scriptID)
validDirections = ['x','y','z']
parser.add_option('-d','--direction',
dest = 'directions',
action = 'extend', metavar = '<string LIST>',
help = "directions in which to mirror {'x','y','z'}")
parser.add_option('--float',
dest = 'float',
help = "directions in which to mirror {{{}}}".format(','.join(validDirections)))
parser.add_option( '--reflect',
dest = 'reflect',
action = 'store_true',
help = 'use float input')
help = 'reflect (include) outermost layers')
parser.set_defaults(float = False,
)
parser.set_defaults(reflect = False)
(options, filenames) = parser.parse_args()
if options.directions is None:
parser.error('no direction given.')
if not set(options.directions).issubset(validDirections):
invalidDirections = [str(e) for e in set(options.directions).difference(validDirections)]
parser.error('invalid directions {}. '.format(*invalidDirections))
datatype = 'f' if options.float else 'i'
limits = [None,None] if options.reflect else [-2,0]
# --- 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 ----------------------------------------------------------------------------
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'],datatype).reshape(info['grid'],order='F') # read microstructure
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
microstructure = geom.get_microstructure()
if 'z' in options.directions:
microstructure = np.concatenate([microstructure,microstructure[:,:,::-1]],2)
microstructure = np.concatenate([microstructure,microstructure[:,:,limits[0]:limits[1]:-1]],2)
if 'y' in options.directions:
microstructure = np.concatenate([microstructure,microstructure[:,::-1,:]],1)
microstructure = np.concatenate([microstructure,microstructure[:,limits[0]:limits[1]:-1,:]],1)
if 'x' in options.directions:
microstructure = np.concatenate([microstructure,microstructure[::-1,:,:]],0)
microstructure = np.concatenate([microstructure,microstructure[limits[0]:limits[1]:-1,:,:]],0)
# --- do work ------------------------------------------------------------------------------------
damask.util.croak(geom.update(microstructure,rescale=True))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
newInfo = {
'size': microstructure.shape*info['size']/info['grid'],
'grid': microstructure.shape,
}
# --- report ---------------------------------------------------------------------------------------
remarks = []
if (any(newInfo['grid'] != info['grid'])):
remarks.append('--> grid a b c: %s'%(' x '.join(map(str,newInfo['grid']))))
if (any(newInfo['size'] != info['size'])):
remarks.append('--> size x y z: %s'%(' x '.join(map(str,newInfo['size']))))
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=info['microstructures']),
])
table.head_write()
# --- write microstructure information ------------------------------------------------------------
formatwidth = 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('%{}i'.format(formatwidth),delimiter = ' ')
# --- output finalization --------------------------------------------------------------------------
table.close() # close ASCII table
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)

92
processing/pre/geom_pack.py
View File

@ -1,80 +1,49 @@
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys
import numpy as np
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [geomfile(s)]', description = """
compress geometry files with ranges "a to b" and/or multiples "n of x".
Pack ranges to "a to b" and/or multiples to "n of x".
""", version = scriptID)
(options, filenames) = parser.parse_args()
# --- 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 ----------------------------------------------------------------------------
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
table.head_read()
info,extra_header = table.head_getGeom()
damask.util.report_geom(info)
damask.util.croak(geom)
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
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(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=info['microstructures']),
])
table.head_write()
# --- write packed microstructure information -----------------------------------------------------
compressType = ''
compressType = None
former = start = -1
reps = 0
outputAlive = True
while outputAlive and table.data_read(): # read next data line of ASCII table
items = table.data
if len(items) > 2:
if items[1].lower() == 'of': items = [int(items[2])]*int(items[0])
elif items[1].lower() == 'to': items = range(int(items[0]),1+int(items[2]))
else: items = map(int,items)
else: items = map(int,items)
if name is None:
f = sys.stdout
else:
f= open(name,'w')
for current in items:
for current in geom.microstructure.flatten('F'):
if abs(current - former) == 1 and (start - current) == reps*(former - current):
compressType = 'to'
reps += 1
@ -82,16 +51,14 @@ for name in filenames:
compressType = 'of'
reps += 1
else:
if compressType == '':
table.data = []
if compressType is None:
f.write('\n'.join(geom.get_header())+'\n')
elif compressType == '.':
table.data = [former]
f.write('{}\n'.format(former))
elif compressType == 'to':
table.data = [start,'to',former]
f.write('{} to {}\n'.format(start,former))
elif compressType == 'of':
table.data = [reps,'of',former]
outputAlive = table.data_write(delimiter = ' ') # output processed line
f.write('{} of {}\n'.format(reps,former))
compressType = '.'
start = current
@ -99,14 +66,9 @@ for name in filenames:
former = current
table.data = {
'.' : [former],
'to': [start,'to',former],
'of': [reps,'of',former],
}[compressType]
outputAlive = table.data_write(delimiter = ' ') # output processed line
# --- output finalization --------------------------------------------------------------------------
table.close() # close ASCII table
if compressType == '.':
f.write('{}\n'.format(former))
elif compressType == 'to':
f.write('{} to {}\n'.format(start,former))
elif compressType == 'of':
f.write('{} of {}\n'.format(reps,former))

92
processing/pre/geom_renumber.py
View File

@ -1,96 +1,46 @@
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
import numpy as np
import damask
import os
import sys
from io import StringIO
from optparse import OptionParser
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [file[s]]', description = """
renumber sorted microstructure indices to 1,...,N.
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [geomfile(s)]', description = """
Renumber sorted microstructure indices to 1,...,N.
""", version=scriptID)
(options, filenames) = parser.parse_args()
# --- 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 ---------------------------------------------------------------------------
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
table.head_read()
info,extra_header = table.head_getGeom()
damask.util.report_geom(info)
renumbered = np.empty(geom.get_grid(),dtype=geom.microstructure.dtype)
for i, oldID in enumerate(np.unique(geom.microstructure)):
renumbered = np.where(geom.microstructure == oldID, i+1, renumbered)
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
damask.util.croak(geom.update(renumbered))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
# --- read data ----------------------------------------------------------------------------------
microstructure = table.microstructure_read(info['grid']) # read microstructure
# --- do work ------------------------------------------------------------------------------------
newInfo = {
'origin': np.zeros(3,'d'),
'microstructures': 0,
}
grainIDs = np.unique(microstructure)
renumbered = np.copy(microstructure)
for i, oldID in enumerate(grainIDs):
renumbered = np.where(microstructure == oldID, i+1, renumbered)
newInfo['microstructures'] = len(grainIDs)
# --- 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
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)

161
processing/pre/geom_rescale.py
View File

@ -1,20 +1,26 @@
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
import os
import sys
import numpy as np
from io import StringIO
from optparse import OptionParser
from scipy import ndimage
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
Scales a geometry description independently in x, y, and z direction in terms of grid and/or size.
Scales independently in x, y, and z direction in terms of grid and/or size.
Either absolute values or relative factors (like "0.25x") can be used.
""", version = scriptID)
@ -22,142 +28,47 @@ Either absolute values or relative factors (like "0.25x") can be used.
parser.add_option('-g', '--grid',
dest = 'grid',
type = 'string', nargs = 3, metavar = 'string string string',
help = 'a,b,c grid of hexahedral box [unchanged]')
help = 'a,b,c grid of hexahedral box')
parser.add_option('-s', '--size',
dest = 'size',
type = 'string', nargs = 3, metavar = 'string string string',
help = 'x,y,z size of hexahedral box [unchanged]')
parser.add_option('-r', '--renumber',
dest = 'renumber',
action = 'store_true',
help = 'renumber microstructure indices from 1..N [%default]')
parser.add_option('--float',
dest = 'float',
action = 'store_true',
help = 'use float input')
parser.set_defaults(renumber = False,
grid = ['0','0','0'],
size = ['0.0','0.0','0.0'],
float = False,
)
help = 'x,y,z size of hexahedral box')
(options, filenames) = parser.parse_args()
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
damask.util.report(scriptName,name)
# --- interpret header ----------------------------------------------------------------------------
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
table.head_read()
info,extra_header = table.head_getGeom()
damask.util.report_geom(info)
grid = geom.get_grid()
size = geom.get_size()
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
new_grid = grid if options.grid is None else \
np.array([int(o*float(n.lower().replace('x',''))) if n.lower().endswith('x') \
else int(n) for o,n in zip(grid,options.grid)],dtype=int)
# --- read data ------------------------------------------------------------------------------------
new_size = size if options.size is None else \
np.array([o*float(n.lower().replace('x','')) if n.lower().endswith('x') \
else float(n) for o,n in zip(size,options.size)],dtype=float)
microstructure = table.microstructure_read(info['grid'],datatype) # read microstructure
damask.util.croak(geom.update(microstructure =
ndimage.interpolation.zoom(
geom.microstructure,
new_grid/grid,
output=geom.microstructure.dtype,
order=0,
mode='nearest',
prefilter=False,
) if np.any(new_grid != grid) \
else None,
size = new_size))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
# --- do work ------------------------------------------------------------------------------------
newInfo = {
'grid': np.zeros(3,'i'),
'origin': np.zeros(3,'d'),
'microstructures': 0,
}
newInfo['grid'] = np.array([{True: round(o*float(n.lower().replace('x',''))),
False: round(float(n.lower().replace('x','')))}[n[-1].lower() == 'x']
for o,n in zip(info['grid'],options.grid)],'i')
newInfo['size'] = np.array([{True: o*float(n.lower().replace('x','')),
False: float(n.lower().replace('x',''))}[n[-1].lower() == 'x']
for o,n in zip(info['size'],options.size)],'d')
newInfo['grid'] = np.where(newInfo['grid'] <= 0 , info['grid'],newInfo['grid'])
newInfo['size'] = np.where(newInfo['size'] <= 0.0, info['size'],newInfo['size'])
multiplicity = []
for j in range(3):
multiplicity.append([])
last = 0
for i in range(info['grid'][j]):
this = int((i+1)*float(newInfo['grid'][j])/info['grid'][j])
multiplicity[j].append(this-last)
last = this
microstructure = microstructure.reshape(info['grid'],order='F')
microstructure = np.repeat(np.repeat(np.repeat(microstructure,
multiplicity[0], axis=0),multiplicity[1], axis=1),multiplicity[2], axis=2)
# --- renumber to sequence 1...Ngrains if requested ------------------------------------------------
# http://stackoverflow.com/questions/10741346/np-frequency-counts-for-unique-values-in-an-array
if options.renumber:
newID = 0
for microstructureID,count in enumerate(np.bincount(microstructure.reshape(newInfo['grid'].prod()))):
if count != 0:
newID += 1
microstructure = np.where(microstructure == microstructureID, newID,microstructure).reshape(microstructure.shape)
newInfo['microstructures'] = len(np.unique(microstructure))
# --- report ---------------------------------------------------------------------------------------
remarks = []
errors = []
if (any(newInfo['grid'] != info['grid'])):
remarks.append('--> grid a b c: %s'%(' x '.join(map(str,newInfo['grid']))))
if (any(newInfo['size'] != info['size'])):
remarks.append('--> size x y z: %s'%(' x '.join(map(str,newInfo['size']))))
if ( newInfo['microstructures'] != info['microstructures']):
remarks.append('--> microstructures: %i'%newInfo['microstructures'])
if np.any(newInfo['grid'] < 1): errors.append('invalid new grid a b c.')
if np.any(newInfo['size'] <= 0.0): errors.append('invalid new size x y z.')
if remarks != []: damask.util.croak(remarks)
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
# --- write header ---------------------------------------------------------------------------------
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.labels_clear()
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],newInfo['grid'][1]*newInfo['grid'][2]),order='F').transpose()
table.data_writeArray(format,delimiter=' ')
# --- output finalization --------------------------------------------------------------------------
table.close() # close ASCII table
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)

139
processing/pre/geom_rotate.py
View File

@ -1,28 +1,33 @@
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
import numpy as np
import damask
from scipy import ndimage
import os
import sys
from io import StringIO
from optparse import OptionParser
from scipy import ndimage
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
Rotates spectral geometry description.
Rotates original microstructure and embeddeds it into buffer material.
""", version=scriptID)
parser.add_option('-r', '--rotation',
dest='rotation',
type = 'float', nargs = 4, metavar = ' '.join(['float']*4),
help = 'rotation given as angle and axis')
help = 'rotation given as axis and angle')
parser.add_option('-e', '--eulers',
dest = 'eulers',
type = 'float', nargs = 3, metavar = ' '.join(['float']*3),
@ -30,7 +35,7 @@ parser.add_option('-e', '--eulers',
parser.add_option('-d', '--degrees',
dest = 'degrees',
action = 'store_true',
help = 'Euler angles are given in degrees [%default]')
help = 'Euler angles/axis angle are given in degrees')
parser.add_option('-m', '--matrix',
dest = 'matrix',
type = 'float', nargs = 9, metavar = ' '.join(['float']*9),
@ -41,108 +46,56 @@ parser.add_option('-q', '--quaternion',
help = 'rotation given as 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')
type = 'float', metavar = 'int',
help = 'background microstructure index, defaults to max microstructure index + 1')
parser.set_defaults(degrees = False,
fill = 0,
float = False,
)
parser.set_defaults(degrees = False)
(options, filenames) = parser.parse_args()
if sum(x is not None for x in [options.rotation,options.eulers,options.matrix,options.quaternion]) != 1:
parser.error('not exactly one rotation specified...')
if [options.rotation,options.eulers,options.matrix,options.quaternion].count(None) < 3:
parser.error('more than one rotation specified.')
if [options.rotation,options.eulers,options.matrix,options.quaternion].count(None) > 3:
parser.error('no rotation specified.')
if options.quaternion is not None:
eulers = damask.Rotation.fromQuaternion(np.array(options.quaternion)).asEulers(degrees=True)
rot = damask.Rotation.fromQuaternion(np.array(options.quaternion)) # we might need P=+1 here, too...
if options.rotation is not None:
eulers = damask.Rotation.fromAxisAngle(np.array(options.rotation,degrees=True)).asEulers(degrees=True)
rot = damask.Rotation.fromAxisAngle(np.array(options.rotation),degrees=options.degrees,normalise=True,P=+1)
if options.matrix is not None:
eulers = damask.Rotation.fromMatrix(np.array(options.Matrix)).asEulers(degrees=True)
rot = damask.Rotation.fromMatrix(np.array(options.Matrix))
if options.eulers is not None:
eulers = damask.Rotation.fromEulers(np.array(options.eulers),degrees=True).asEulers(degrees=True)
rot = damask.Rotation.fromEulers(np.array(options.eulers),degrees=options.degrees)
datatype = 'f' if options.float else 'i'
eulers = rot.asEulers(degrees=True)
# --- 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 ----------------------------------------------------------------------------
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
size = geom.get_size()
grid = geom.get_grid()
origin = geom.get_origin()
microstructure = geom.get_microstructure()
fill = np.nanmax(microstructure)+1 if options.fill is None else options.fill
dtype = float if np.isnan(fill) or int(fill) != fill or microstructure.dtype==np.float else int
table.head_read()
info,extra_header = table.head_getGeom()
damask.util.report_geom(info)
# These rotations are always applied in the reference coordinate system, i.e. (z,x,z) not (z,x',z'')
# this seems to be ok, see https://www.cs.utexas.edu/~theshark/courses/cs354/lectures/cs354-14.pdf
microstructure = ndimage.rotate(microstructure,eulers[2],(0,1),order=0,
prefilter=False,output=dtype,cval=fill) # rotation around z
microstructure = ndimage.rotate(microstructure,eulers[1],(1,2),order=0,
prefilter=False,output=dtype,cval=fill) # rotation around x
microstructure = ndimage.rotate(microstructure,eulers[0],(0,1),order=0,
prefilter=False,output=dtype,cval=fill) # 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
damask.util.croak(geom.update(microstructure,origin=origin-(np.asarray(microstructure.shape)-grid)/2*size/grid,rescale=True))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
# --- read data ------------------------------------------------------------------------------------
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.show()))
else:
geom.to_file(name)

81
processing/pre/geom_toTable.py
View File

@ -1,11 +1,15 @@
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys
import numpy as np
import os
import sys
from optparse import OptionParser
from io import StringIO
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
@ -19,70 +23,39 @@ Translate geom description into ASCIItable containing position and microstructur
""", version = scriptID)
parser.add_option('--float',
dest = 'float',
action = 'store_true',
help = 'use float input')
parser.set_defaults(float = False,
)
(options, filenames) = parser.parse_args()
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,
outname = os.path.splitext(name)[0]+'.txt' if name else name,
buffered = False,
labeled = False,
)
except: continue
damask.util.report(scriptName,name)
# --- interpret header ----------------------------------------------------------------------------
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
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'],datatype)
# ------------------------------------------ assemble header ---------------------------------------
table.info_clear()
table.info_append(extra_header + [scriptID + '\t' + ' '.join(sys.argv[1:])])
table.labels_clear()
table.labels_append(['{}_{}'.format(1+i,'pos') for i in range(3)]+['microstructure'])
table.head_write()
table.output_flush()
damask.util.croak(geom)
# --- generate grid --------------------------------------------------------------------------------
x = (0.5 + np.arange(info['grid'][0],dtype=float))/info['grid'][0]*info['size'][0]+info['origin'][0]
y = (0.5 + np.arange(info['grid'][1],dtype=float))/info['grid'][1]*info['size'][1]+info['origin'][1]
z = (0.5 + np.arange(info['grid'][2],dtype=float))/info['grid'][2]*info['size'][2]+info['origin'][2]
grid = geom.get_grid()
size = geom.get_size()
origin = geom.get_origin()
xx = np.tile( x, info['grid'][1]* info['grid'][2])
yy = np.tile(np.repeat(y,info['grid'][0] ),info['grid'][2])
zz = np.repeat(z,info['grid'][0]*info['grid'][1])
x = (0.5 + np.arange(grid[0],dtype=float))/grid[0]*size[0]+origin[0]
y = (0.5 + np.arange(grid[1],dtype=float))/grid[1]*size[1]+origin[1]
z = (0.5 + np.arange(grid[2],dtype=float))/grid[2]*size[2]+origin[2]
table.data = np.squeeze(np.dstack((xx,yy,zz,microstructure)),axis=0)
xx = np.tile( x, grid[1]* grid[2])
yy = np.tile(np.repeat(y,grid[0] ),grid[2])
zz = np.repeat(z,grid[0]*grid[1])
# --- create ASCII table --------------------------------------------------------------------------
table = damask.ASCIItable(outname = os.path.splitext(name)[0]+'.txt' if name else name)
table.info_append(geom.get_comments() + [scriptID + '\t' + ' '.join(sys.argv[1:])])
table.labels_append(['{}_{}'.format(1+i,'pos') for i in range(3)]+['microstructure'])
table.head_write()
table.output_flush()
table.data = np.squeeze(np.dstack((xx,yy,zz,geom.microstructure.flatten('F'))),axis=0)
table.data_writeArray()
# ------------------------------------------ finalize output ---------------------------------------
table.close()

107
processing/pre/geom_translate.py
View File

@ -1,20 +1,23 @@
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
import numpy as np
import damask
import os
import sys
from optparse import OptionParser
from io import StringIO
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
translate microstructure indices (shift or substitute) and/or geometry origin.
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
Translate microstructure indices (shift or substitute) and/or geometry origin.
""", version=scriptID)
@ -25,103 +28,37 @@ parser.add_option('-o', '--origin',
parser.add_option('-m', '--microstructure',
dest = 'microstructure',
type = 'int', metavar = 'int',
help = 'offset from old to new microstructure indices')
help = 'offset from old to new microstructure indices (after substitution)')
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 = list(map(int,options.substitute))
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 ----------------------------------------------------------------------
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 ---------------------------------------------------------------------------
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
table.head_read()
info,extra_header = table.head_getGeom()
damask.util.report_geom(info)
substituted = geom.get_microstructure()
for old,new in zip(sub[0::2],sub[1::2]): substituted[substituted==old] = new # substitute microstructure indices
substituted += options.microstructure # constant shift
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
damask.util.croak(geom.update(substituted,origin=geom.get_origin()+options.origin))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
# --- read data ----------------------------------------------------------------------------------
microstructure = table.microstructure_read(info['grid'],datatype) # read microstructure
# --- 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
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)

70
processing/pre/geom_unpack.py
View File

@ -1,80 +1,40 @@
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
import numpy as np
import os
import sys
from optparse import OptionParser
from io import StringIO
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Unpack geometry files containing ranges "a to b" and/or "n of x" multiples (exclusively in one line).
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [geomfile(s)]', description = """
Unpack ranges "a to b" and/or "n of x" multiples (exclusively in one line).
""", version = scriptID)
parser.add_option('-1', '--onedimensional',
dest = 'oneD',
action = 'store_true',
help = 'output geom file with one-dimensional data arrangement')
parser.set_defaults(oneD = False,
)
(options, filenames) = parser.parse_args()
# --- 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 ----------------------------------------------------------------------------
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
table.head_read()
info,extra_header = table.head_getGeom()
damask.util.report_geom(info)
damask.util.croak(geom)
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
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(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=info['microstructures']),
])
table.head_write()
# --- write microstructure information ------------------------------------------------------------
microstructure = table.microstructure_read(info['grid']) # read microstructure
formatwidth = int(math.floor(math.log10(microstructure.max())+1)) # efficient number printing format
table.data = microstructure if options.oneD else \
microstructure.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ')
#--- output finalization --------------------------------------------------------------------------
table.close() # close ASCII table
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)

98
processing/pre/geom_vicinityOffset.py
View File

@ -1,15 +1,20 @@
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
import numpy as np
from scipy import ndimage
import os
import sys
from io import StringIO
from optparse import OptionParser
from scipy import ndimage
import numpy as np
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
def taintedNeighborhood(stencil,trigger=[],size=1):
me = stencil[stencil.shape[0]//2]
@ -21,11 +26,12 @@ def taintedNeighborhood(stencil,trigger=[],size=1):
trigger = list(trigger)
return np.any(np.in1d(stencil,np.array(trigger)))
#--------------------------------------------------------------------------------------------------
# MAIN
#--------------------------------------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
Offset microstructure index for points which see a microstructure different from themselves
(or listed as triggers) within a given (cubic) vicinity, i.e. within the region close to a grain/phase boundary.
@ -35,13 +41,13 @@ parser.add_option('-v', '--vicinity',
dest = 'vicinity',
type = 'int', metavar = 'int',
help = 'voxel distance checked for presence of other microstructure [%default]')
parser.add_option('-m', '--microstructureoffset',
parser.add_option('-o', '--offset',
dest='offset',
type = 'int', metavar = 'int',
help = 'offset (positive or negative) for tagged microstructure indices. '+
'"0" selects maximum microstructure index [%default]')
help='offset (positive or negative) to tag microstructure indices, defaults to max microstructure index')
parser.add_option('-t', '--trigger',
action = 'extend', dest = 'trigger', metavar = '<int LIST>',
dest = 'trigger',
action = 'extend', metavar = '<int LIST>',
help = 'list of microstructure indices triggering a change')
parser.add_option('-n', '--nonperiodic',
dest = 'mode',
@ -49,86 +55,34 @@ parser.add_option('-n', '--nonperiodic',
help = 'assume geometry to be non-periodic')
parser.set_defaults(vicinity = 1,
offset = 0,
trigger = [],
mode = 'wrap',
)
(options, filenames) = parser.parse_args()
options.trigger = np.array(options.trigger, dtype=int)
# --- 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 ----------------------------------------------------------------------------
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
table.head_read()
info,extra_header = table.head_getGeom()
damask.util.report_geom(info)
offset = np.nanmax(geom.microstructure) if options.offset is None else options.offset
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']).reshape(info['grid'],order='F') # read microstructure
# --- do work ------------------------------------------------------------------------------------
newInfo = {
'microstructures': 0,
}
if options.offset == 0: options.offset = microstructure.max()
microstructure = np.where(ndimage.filters.generic_filter(microstructure,
damask.util.croak(geom.update(np.where(ndimage.filters.generic_filter(
geom.microstructure,
taintedNeighborhood,
size=1+2*options.vicinity,mode=options.mode,
extra_arguments=(),
extra_keywords={"trigger":options.trigger,"size":1+2*options.vicinity}),
microstructure + options.offset,microstructure)
geom.microstructure + offset,geom.microstructure)))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
newInfo['microstructures'] = len(np.unique(microstructure))
# --- report ---------------------------------------------------------------------------------------
if (newInfo['microstructures'] != info['microstructures']):
damask.util.croak('--> microstructures: %i'%newInfo['microstructures'])
# --- 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 ------------------------------------------------------------
formatwidth = int(math.floor(math.log10(np.nanmax(microstructure))+1))
table.data = microstructure.reshape((info['grid'][0],info['grid'][1]*info['grid'][2]),order='F').transpose()
table.data_writeArray('%{}i'.format(formatwidth),delimiter = ' ')
# --- output finalization --------------------------------------------------------------------------
table.close() # close ASCII table
if name is None:
sys.stdout.write(str(geom.show()))
else:
geom.to_file(name)

2
python/damask/Lambert.py
View File

@ -1,5 +1,3 @@
# -*- coding: UTF-8 no BOM -*-
####################################################################################################
# Code below available according to the followin conditions on https://github.com/MarDiehl/3Drotations
####################################################################################################

3
python/damask/__init__.py
View File

@ -17,8 +17,7 @@ from .orientation import Symmetry, Lattice, Rotation, Orientation # noqa
from .dadf5 import DADF5 # noqa
#from .block import Block # only one class
from .result import Result # noqa
from .geometry import Geometry # noqa
from .geom import Geom # noqa
from .solver import Solver # noqa
from .test import Test # noqa
from .util import extendableOption # noqa

34
python/damask/asciitable.py
View File

@ -1,6 +1,9 @@
# -*- coding: UTF-8 no BOM -*-
import os
import sys
import re
import shlex
from collections import Iterable
import os, sys
import numpy as np
# ------------------------------------------------------------------
@ -80,8 +83,6 @@ class ASCIItable():
def _quote(self,
what):
"""Quote empty or white space-containing output"""
import re
return '{quote}{content}{quote}'.format(
quote = ('"' if str(what)=='' or re.search(r"\s",str(what)) else ''),
content = what)
@ -147,8 +148,6 @@ class ASCIItable():
by either reading the first row or,
if keyword "head[*]" is present, the last line of the header
"""
import re,shlex
try:
self.__IO__['in'].seek(0)
except IOError:
@ -244,17 +243,6 @@ class ASCIItable():
return info,extra_header
# ------------------------------------------------------------------
def head_putGeom(self,info):
"""Translate geometry description to header"""
self.info_append([
"grid\ta {}\tb {}\tc {}".format(*info['grid']),
"size\tx {}\ty {}\tz {}".format(*info['size']),
"origin\tx {}\ty {}\tz {}".format(*info['origin']),
"homogenization\t{}".format(info['homogenization']),
"microstructures\t{}".format(info['microstructures']),
])
# ------------------------------------------------------------------
def labels_append(self,
what,
@ -287,8 +275,6 @@ class ASCIItable():
"x" for "1_x","2_x",... unless raw output is requested.
operates on object tags or given list.
"""
from collections import Iterable
if tags is None: tags = self.tags
if isinstance(tags, Iterable) and not raw: # check whether list of tags is requested
@ -324,8 +310,6 @@ class ASCIItable():
return numpy array if asked for list of labels.
transparently deals with label positions implicitly given as numbers or their headings given as strings.
"""
from collections import Iterable
if isinstance(labels, Iterable) and not isinstance(labels, str): # check whether list of labels is requested
idx = []
for label in labels:
@ -365,8 +349,6 @@ class ASCIItable():
return numpy array if asked for list of labels.
transparently deals with label positions implicitly given as numbers or their headings given as strings.
"""
from collections import Iterable
listOfLabels = isinstance(labels, Iterable) and not isinstance(labels, str) # check whether list of labels is requested
if not listOfLabels: labels = [labels]
@ -400,8 +382,6 @@ class ASCIItable():
return numpy array if asked for list of labels.
transparently deals with label positions implicitly given as numbers or their headings given as strings.
"""
from collections import Iterable
start = self.label_index(labels)
dim = self.label_dimension(labels)
@ -447,8 +427,6 @@ class ASCIItable():
advance = True,
respectLabels = True):
"""Read next line (possibly buffered) and parse it into data array"""
import shlex
self.line = self.__IO__['readBuffer'].pop(0) if len(self.__IO__['readBuffer']) > 0 \
else self.__IO__['in'].readline().strip() # take buffered content or get next data row from file
@ -469,8 +447,6 @@ class ASCIItable():
def data_readArray(self,
labels = []):
"""Read whole data of all (given) labels as numpy array"""
from collections import Iterable
try: self.data_rewind() # try to wind back to start of data
except: pass # assume/hope we are at data start already...

6
python/damask/colormaps.py
View File

@ -1,8 +1,6 @@
# -*- coding: UTF-8 no BOM -*-
import math
import math,numpy as np
### --- COLOR CLASS --------------------------------------------------
import numpy as np
class Color():
"""

5
python/damask/environment.py
View File

@ -1,6 +1,5 @@
# -*- coding: UTF-8 no BOM -*-
import os,re
import os
import re
class Environment():
__slots__ = [ \

269
python/damask/geom.py Normal file
View File

@ -0,0 +1,269 @@
import os
from io import StringIO
import numpy as np
import vtk
from vtk.util import numpy_support
from . import util
from . import version
class Geom():
"""Geometry definition for grid solvers"""
def __init__(self,microstructure,size,origin=[0.0,0.0,0.0],homogenization=1,comments=[]):
"""New geometry definition from array of microstructures and size"""
self.set_microstructure(microstructure)
self.set_size(size)
self.set_origin(origin)
self.set_homogenization(homogenization)
self.set_comments(comments)
def __repr__(self):
"""Basic information on geometry definition"""
return util.srepr([
'grid a b c: {}'.format(' x '.join(map(str,self.get_grid ()))),
'size x y z: {}'.format(' x '.join(map(str,self.get_size ()))),
'origin x y z: {}'.format(' '.join(map(str,self.get_origin()))),
'homogenization: {}'.format(self.get_homogenization()),
'# microstructures: {}'.format(len(np.unique(self.microstructure))),
'max microstructure: {}'.format(np.nanmax(self.microstructure)),
])
def update(self,microstructure=None,size=None,origin=None,rescale=False):
"""Updates microstructure and size"""
grid_old = self.get_grid()
size_old = self.get_size()
origin_old = self.get_origin()
unique_old = len(np.unique(self.microstructure))
max_old = np.nanmax(self.microstructure)
if size is not None and rescale:
raise ValueError('Either set size explicitly or rescale automatically')
self.set_microstructure(microstructure)
self.set_size(self.get_grid()/grid_old*self.size if rescale else size)
self.set_origin(origin)
message = ['grid a b c: {}'.format(' x '.join(map(str,grid_old)))]
if np.any(grid_old != self.get_grid()):
message[-1] = util.delete(message[-1])
message.append('grid a b c: {}'.format(' x '.join(map(str,self.get_grid()))))
message.append('size x y z: {}'.format(' x '.join(map(str,size_old))))
if np.any(size_old != self.get_size()):
message[-1] = util.delete(message[-1])
message.append('size x y z: {}'.format(' x '.join(map(str,self.get_size()))))
message.append('origin x y z: {}'.format(' '.join(map(str,origin_old))))
if np.any(origin_old != self.get_origin()):
message[-1] = util.delete(message[-1])
message.append('origin x y z: {}'.format(' '.join(map(str,self.get_origin()))))
message.append('homogenization: {}'.format(self.get_homogenization()))
message.append('# microstructures: {}'.format(unique_old))
if unique_old != len(np.unique(self.microstructure)):
message[-1] = util.delete(message[-1])
message.append('# microstructures: {}'.format(len(np.unique(self.microstructure))))
message.append('max microstructure: {}'.format(max_old))
if max_old != np.nanmax(self.microstructure):
message[-1] = util.delete(message[-1])
message.append('max microstructure: {}'.format(np.nanmax(self.microstructure)))
return util.return_message(message)
def set_comments(self,comments):
self.comments = []
self.add_comments(comments)
def add_comments(self,comments):
self.comments += [str(c) for c in comments] if isinstance(comments,list) else [str(comments)]
def set_microstructure(self,microstructure):
if microstructure is not None:
if len(microstructure.shape) != 3:
raise ValueError('Invalid microstructure shape {}'.format(*microstructure.shape))
elif microstructure.dtype not in np.sctypes['float'] + np.sctypes['int']:
raise TypeError('Invalid data type {} for microstructure'.format(microstructure.dtype))
else:
self.microstructure = np.copy(microstructure)
def set_size(self,size):
if size is None:
grid = np.asarray(self.microstructure.shape)
self.size = grid/np.max(grid)
else:
if len(size) != 3 or any(np.array(size)<=0):
raise ValueError('Invalid size {}'.format(*size))
else:
self.size = np.array(size)
def set_origin(self,origin):
if origin is not None:
if len(origin) != 3:
raise ValueError('Invalid origin {}'.format(*origin))
else:
self.origin = np.array(origin)
def set_homogenization(self,homogenization):
if homogenization is not None:
if not isinstance(homogenization,int) or homogenization < 1:
raise TypeError('Invalid homogenization {}'.format(homogenization))
else:
self.homogenization = homogenization
def get_microstructure(self):
return np.copy(self.microstructure)
def get_size(self):
return np.copy(self.size)
def get_origin(self):
return np.copy(self.origin)
def get_grid(self):
return np.array(self.microstructure.shape)
def get_homogenization(self):
return self.homogenization
def get_comments(self):
return self.comments[:]
def get_header(self):
header = ['{} header'.format(len(self.comments)+4)] + self.comments
header.append('grid a {} b {} c {}'.format(*self.get_grid()))
header.append('size x {} y {} z {}'.format(*self.get_size()))
header.append('origin x {} y {} z {}'.format(*self.get_origin()))
header.append('homogenization {}'.format(self.get_homogenization()))
return header
@classmethod
def from_file(cls,fname):
"""Reads a geom file"""
with (open(fname) if isinstance(fname,str) else fname) as f:
f.seek(0)
header_length,keyword = f.readline().split()[:2]
header_length = int(header_length)
content = f.readlines()
if not keyword.startswith('head') or header_length < 3:
raise TypeError('Header length information missing or invalid')
comments = []
for i,line in enumerate(content[:header_length]):
items = line.lower().strip().split()
key = items[0] if len(items) > 0 else ''
if key == 'grid':
grid = np.array([ int(dict(zip(items[1::2],items[2::2]))[i]) for i in ['a','b','c']])
elif key == 'size':
size = np.array([float(dict(zip(items[1::2],items[2::2]))[i]) for i in ['x','y','z']])
elif key == 'origin':
origin = np.array([float(dict(zip(items[1::2],items[2::2]))[i]) for i in ['x','y','z']])
elif key == 'homogenization':
homogenization = int(items[1])
else:
comments.append(line.strip())
microstructure = np.empty(grid.prod()) # initialize as flat array
i = 0
for line in content[header_length:]:
items = line.split()
if len(items) == 3:
if items[1].lower() == 'of':
items = np.ones(int(items[0]))*float(items[2])
elif items[1].lower() == 'to':
items = np.linspace(int(items[0]),int(items[2]),
abs(int(items[2])-int(items[0]))+1,dtype=float)
else: items = list(map(float,items))
else: items = list(map(float,items))
microstructure[i:i+len(items)] = items
i += len(items)
if i != grid.prod():
raise TypeError('Invalid file: expected {} entries,found {}'.format(grid.prod(),i))
microstructure = microstructure.reshape(grid,order='F')
if not np.any(np.mod(microstructure.flatten(),1) != 0.0): # no float present
microstructure = microstructure.astype('int')
return cls(microstructure.reshape(grid),size,origin,homogenization,comments)
def to_file(self,fname):
"""Writes to file"""
header = self.get_header()
grid = self.get_grid()
format_string = '%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.microstructure))))) if self.microstructure.dtype == int \
else '%g'
np.savetxt(fname,
self.microstructure.reshape([grid[0],np.prod(grid[1:])],order='F').T,
header='\n'.join(header), fmt=format_string, comments='')
def to_vtk(self,fname=None):
"""Generates vtk file. If file name is given, stored in file otherwise returned as string"""
grid = self.get_grid() + np.ones(3,dtype=int)
size = self.get_size()
origin = self.get_origin()
coords = [
np.linspace(0,size[0],grid[0]) + origin[0],
np.linspace(0,size[1],grid[1]) + origin[1],
np.linspace(0,size[2],grid[2]) + origin[2]
]
rGrid = vtk.vtkRectilinearGrid()
coordArray = [vtk.vtkDoubleArray(),vtk.vtkDoubleArray(),vtk.vtkDoubleArray()]
rGrid.SetDimensions(*grid)
for d,coord in enumerate(coords):
for c in coord:
coordArray[d].InsertNextValue(c)
rGrid.SetXCoordinates(coordArray[0])
rGrid.SetYCoordinates(coordArray[1])
rGrid.SetZCoordinates(coordArray[2])
ms = numpy_support.numpy_to_vtk(num_array=self.microstructure.flatten(order='F'),
array_type=vtk.VTK_INT if self.microstructure.dtype == int else vtk.VTK_FLOAT)
ms.SetName('microstructure')
rGrid.GetCellData().AddArray(ms)
if fname is None:
writer = vtk.vtkDataSetWriter()
writer.SetHeader('damask.Geom '+version)
writer.WriteToOutputStringOn()
else:
writer = vtk.vtkXMLRectilinearGridWriter()
writer.SetCompressorTypeToZLib()
writer.SetDataModeToBinary()
ext = os.path.splitext(fname)[1]
if ext == '':
name = fname + '.' + writer.GetDefaultFileExtension()
elif ext == writer.GetDefaultFileExtension():
name = fname
else:
raise ValueError("unknown extension {}".format(ext))
writer.SetFileName(name)
writer.SetInputData(rGrid)
writer.Write()
if fname is None: return writer.GetOutputString()
def show(self):
"""Show raw content (as in file)"""
f=StringIO()
self.to_file(f)
f.seek(0)
return ''.join(f.readlines())

7
python/damask/geometry/__init__.py
View File

@ -1,7 +0,0 @@
# -*- coding: UTF-8 no BOM -*-
"""Aggregator for geometry handling"""
from .geometry import Geometry # noqa
from .spectral import Spectral # noqa
from .marc import Marc # noqa

21
python/damask/geometry/geometry.py
View File

@ -1,21 +0,0 @@
# -*- coding: UTF-8 no BOM -*-
import damask.geometry
class Geometry():
"""
General class for geometry parsing.
Sub-classed by the individual solvers.
"""
def __init__(self,solver=''):
solverClass = {
'spectral': damask.geometry.Spectral,
'marc': damask.geometry.Marc,
}
if solver.lower() in list(solverClass.keys()):
self.__class__=solverClass[solver.lower()]
self.__init__()

9
python/damask/geometry/marc.py
View File

@ -1,9 +0,0 @@
# -*- coding: UTF-8 no BOM -*-
from .geometry import Geometry
class Marc(Geometry):
def __init__(self):
self.solver='Marc'

9
python/damask/geometry/spectral.py
View File

@ -1,9 +0,0 @@
# -*- coding: UTF-8 no BOM -*-
from .geometry import Geometry
class Spectral(Geometry):
def __init__(self):
self.solver='Spectral'

4
python/damask/orientation.py
View File

@ -1,7 +1,7 @@
# -*- coding: UTF-8 no BOM -*-
import math
import numpy as np
from . import Lambert
from .quaternion import Quaternion
from .quaternion import P

2
python/damask/quaternion.py
View File

@ -1,5 +1,3 @@
# -*- coding: UTF-8 no BOM -*-
import numpy as np
P = -1 # convention (see DOI:10.1088/0965-0393/23/8/083501)

41
python/damask/result.py
View File

@ -1,41 +0,0 @@
# -*- coding: UTF-8 no BOM -*-
import numpy as np
try:
import h5py
except (ImportError) as e:
pass # sys.stderr.write('\nREMARK: h5py module not available \n\n')
class Result():
"""
General class for result parsing.
Needs h5py to be installed
"""
def __init__(self,resultsFile):
self.data=h5py.File(resultsFile,"r")
self.Npoints=self.data.attrs['Number of Materialpoints']
print("Opened {} with {} points".format(resultsFile,self.Npoints))
def getCrystallite(self,labels,inc,constituent=1,points=None):
if points is None: points = np.array(np.array(range(self.Npoints)))
results = {}
mapping=self.data['mapping/crystallite']
for instance in self.data['increments/%s/crystallite/'%inc]:
dsets = list(self.data['increments/%s/crystallite/%s'%(inc,instance)].keys())
for label in labels:
if label in dsets and label not in results:
shape = np.shape(self.data['increments/%s/crystallite/%s/%s'%(inc,instance,label)])[1:]
results[label] = np.nan*np.ones(np.array((self.Npoints,)+shape))
for myPoint in range(len(points)):
matPoint = points[myPoint]
pos = mapping[matPoint,constituent-1]
if pos[0] != 0:
try:
for label in labels:
results[label][matPoint,...] = self.data['increments/%s/crystallite/%s/%s'%(inc,pos[0],label)][pos[1],...]
except:
pass
return results

44
python/damask/util.py
View File

@ -1,11 +1,15 @@
# -*- coding: UTF-8 no BOM -*-
import sys,time,os,subprocess,shlex
import numpy as np
import sys
import time
import os
import subprocess
import shlex
from optparse import Option
from queue import Queue
from threading import Thread
import numpy as np
class bcolors:
"""
ASCII Colors (Blender code)
@ -23,6 +27,7 @@ class bcolors:
BOLD = '\033[1m'
DIM = '\033[2m'
UNDERLINE = '\033[4m'
CROSSOUT = '\033[9m'
def disable(self):
self.HEADER = ''
@ -33,6 +38,7 @@ class bcolors:
self.ENDC = ''
self.BOLD = ''
self.UNDERLINE = ''
self.CROSSOUT = ''
# -----------------------------
@ -47,6 +53,7 @@ def srepr(arg,glue = '\n'):
# -----------------------------
def croak(what, newline = True):
"""Writes formated to stderr"""
if what is not None:
sys.stderr.write(srepr(what,glue = '\n') + ('\n' if newline else ''))
sys.stderr.flush()
@ -54,7 +61,7 @@ def croak(what, newline = True):
def report(who = None,
what = None):
"""Reports script and file name"""
croak( (emph(who)+': ' if who is not None else '') + (what if what is not None else '') )
croak( (emph(who)+': ' if who is not None else '') + (what if what is not None else '') + '\n' )
# -----------------------------
@ -85,6 +92,11 @@ def delete(what):
"""Dims string"""
return bcolors.DIM+srepr(what)+bcolors.ENDC
# -----------------------------
def strikeout(what):
"""Dims string"""
return bcolors.CROSSOUT+srepr(what)+bcolors.ENDC
# -----------------------------
def execute(cmd,
streamIn = None,
@ -113,6 +125,19 @@ def coordGridAndSize(coordinates):
grid = np.array(list(map(len,coords)),'i')
size = grid/np.maximum(np.ones(dim,'d'), grid-1.0) * (maxcorner-mincorner) # size from edge to edge = dim * n/(n-1)
size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 equal to smallest among other ones
delta = size/grid
N = grid.prod()
if N != len(coordinates):
raise ValueError('Data count {} does not match grid {}.'.format(len(coordinates),' x '.join(map(repr,grid))))
if np.any(np.abs(np.log10((coords[0][1:]-coords[0][:-1])/delta[0])) > 0.01) \
or np.any(np.abs(np.log10((coords[1][1:]-coords[1][:-1])/delta[1])) > 0.01):
raise ValueError('regular grid spacing {} violated.'.format(' x '.join(map(repr,delta))))
if dim==3 and np.any(np.abs(np.log10((coords[2][1:]-coords[2][:-1])/delta[2])) > 0.01):
raise ValueError('regular grid spacing {} violated.'.format(' x '.join(map(repr,delta))))
return grid,size
# -----------------------------
@ -173,6 +198,17 @@ def progressBar(iteration, total, prefix='', bar_length=50):
sys.stderr.flush()
class return_message():
"""Object with formatted return message"""
def __init__(self,message):
self.message = message
def __repr__(self):
"""Return message suitable for interactive shells"""
return srepr(self.message)
def leastsqBound(func, x0, args=(), bounds=None, Dfun=None, full_output=0,
col_deriv=0, ftol=1.49012e-8, xtol=1.49012e-8,
gtol=0.0, maxfev=0, epsfcn=None, factor=100, diag=None):

11
src/lattice.f90
View File

@ -491,7 +491,7 @@ module lattice
end enum
integer(kind(LATTICE_undefined_ID)), dimension(:), allocatable, public, protected :: &
lattice_structure, trans_lattice_structure
lattice_structure
interface lattice_forestProjection ! DEPRECATED, use lattice_forestProjection_edge
@ -557,7 +557,6 @@ subroutine lattice_init
Nphases = size(config_phase)
allocate(lattice_structure(Nphases),source = LATTICE_undefined_ID)
allocate(trans_lattice_structure(Nphases),source = LATTICE_undefined_ID)
allocate(lattice_C66(6,6,Nphases), source=0.0_pReal)
allocate(lattice_C3333(3,3,3,3,Nphases), source=0.0_pReal)
@ -595,14 +594,6 @@ subroutine lattice_init
lattice_structure(p) = LATTICE_ort_ID
end select
tag = 'undefined'
tag = config_phase(p)%getString('trans_lattice_structure',defaultVal=tag)
select case(trim(tag))
case('bcc')
trans_lattice_structure(p) = LATTICE_bcc_ID
case('hex','hexagonal')
trans_lattice_structure(p) = LATTICE_hex_ID
end select
lattice_C66(1,1,p) = config_phase(p)%getFloat('c11',defaultVal=0.0_pReal)
lattice_C66(1,2,p) = config_phase(p)%getFloat('c12',defaultVal=0.0_pReal)