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DAMASK_EICMD
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centralize functionality

This commit is contained in:
Martin Diehl 2020-05-24 09:06:42 +02:00
parent a26cba1457
commit 3231a49107
5 changed files with 92 additions and 81 deletions
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27
processing/pre/geom_canvas.py
View File

@ -40,35 +40,22 @@ parser.add_option('-f','--fill',
parser.set_defaults(offset = (0,0,0))
(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)
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))
grid = 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(geom.grid,options.grid)],dtype=int))
else:
grid = np.array(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)) # noqa
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))
damask.util.croak(geom.canvas(grid,np.asarray(options.offset),options.fill))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
geom.to_file(sys.stdout if name is None else name,pack=False)

12
processing/pre/geom_renumber.py
View File

@ -22,14 +22,12 @@ Renumber sorted microstructure indices to 1,...,N.
""", version=scriptID)
(options, filenames) = parser.parse_args()
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
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.renumber())
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
geom.to_file(sys.stdout if name is None else name,pack=False)
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
damask.util.croak(geom.renumber())
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
geom.to_file(sys.stdout if name is None else name,pack=False)

60
processing/pre/geom_rotate.py
View File

@ -52,47 +52,27 @@ parser.add_option('-f', '--fill',
parser.set_defaults(degrees = False)
(options, filenames) = parser.parse_args()
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:
rot = damask.Rotation.from_quaternion(np.array(options.quaternion)) # we might need P=+1 here, too...
if options.rotation is not None:
rot = damask.Rotation.from_axis_angle(np.array(options.rotation),degrees=options.degrees,normalise=True,P=+1)
if options.matrix is not None:
rot = damask.Rotation.from_matrix(np.array(options.Matrix))
if options.eulers is not None:
rot = damask.Rotation.from_Eulers(np.array(options.eulers),degrees=options.degrees)
eulers = rot.as_Eulers(degrees=True)
if filenames == []: filenames = [None]
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:
rot = damask.Rotation.from_quaternion(np.array(options.quaternion)) # we might need P=+1 here, too...
if options.rotation is not None:
rot = damask.Rotation.from_axis_angle(np.array(options.rotation),degrees=options.degrees,normalise=True,P=+1)
if options.matrix is not None:
rot = damask.Rotation.from_matrix(np.array(options.Matrix))
if options.eulers is not None:
rot = damask.Rotation.from_Eulers(np.array(options.eulers),degrees=options.degrees)
for name in filenames:
damask.util.report(scriptName,name)
damask.util.report(scriptName,name)
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
# 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
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:]))
geom.to_file(sys.stdout if name is None else name,pack=False)
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
damask.util.croak(geom.rotate(rot,options.fill))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
geom.to_file(sys.stdout if name is None else name,pack=False)

22
processing/pre/geom_translate.py
View File

@ -40,22 +40,16 @@ parser.set_defaults(origin = (0.0,0.0,0.0),
)
(options, filenames) = parser.parse_args()
if filenames == []: filenames = [None]
sub = list(map(int,options.substitute))
if filenames == []: filenames = [None]
for name in filenames:
damask.util.report(scriptName,name)
damask.util.report(scriptName,name)
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
substituted = geom.get_microstructure()
for old,new in zip(sub[0::2],sub[1::2]): substituted[geom.microstructure==old] = new # substitute microstructure indices
substituted += options.microstructure # constant shift
damask.util.croak(geom.update(substituted,origin=geom.get_origin()+options.origin))
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
geom.to_file(sys.stdout if name is None else name,pack=False)
geom = damask.Geom.from_file(StringIO(''.join(sys.stdin.read())) if name is None else name)
geom.renumber(sub[0::2],sub[1::2],origin=geom.origin+options.origin)
geom.microstructure+= option.microstructure
damask.util.croak(geom)
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
geom.to_file(sys.stdout if name is None else name,pack=False)

52
python/damask/_geom.py
View File

@ -10,6 +10,7 @@ from . import VTK
from . import util
from . import Environment
from . import grid_filters
from . import Rotation
class Geom:
@ -581,3 +582,54 @@ class Geom:
#self.add_comments('geom.py:renumber v{}'.format(version)
return self.update(renumbered)
def rotate(self,R,fill=None):
"""Rotate microstructure (pad if required)."""
if fill is None: fill = np.nanmax(self.microstructure) + 1
dtype = float if np.isnan(fill) or int(fill) != fill or self.microstructure.dtype==np.float else int
Eulers = R.as_Eulers(degrees=True)
# 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(self.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
origin = self.origin-(np.asarray(microstructure.shape)-self.grid)//2 * self.size/self.grid
#self.add_comments('geom.py:renumber v{}'.format(version)
return self.update(microstructure,origin=origin,rescale=True)
def canvas(self,grid=None,offset=None,fill=None):
"""Rotate microstructure (pad if required)."""
if fill is None: fill = np.nanmax(self.microstructure) + 1
dtype = float if np.isnan(fill) or int(fill) != fill or self.microstructure.dtype==np.float else int
canvas = np.full(self.grid if grid is None else grid,
fill if fill is not None else np.nanmax(self.microstructure)+1,
self.microstructure.dtype)
if offset is None: offset = 0
l = np.clip( offset, 0,np.minimum(self.grid +offset,grid)) # noqa
r = np.clip( offset+self.grid,0,np.minimum(self.grid*2+offset,grid))
L = np.clip(-offset, 0,np.minimum(grid -offset,self.grid))
R = np.clip(-offset+grid, 0,np.minimum(grid*2 -offset,self.grid))
canvas[l[0]:r[0],l[1]:r[1],l[2]:r[2]] = self.microstructure[L[0]:R[0],L[1]:R[1],L[2]:R[2]]
#self.add_comments('geom.py:renumber v{}'.format(version)
return self.update(canvas,origin=self.origin+offset*self.size/self.grid,rescale=True)
def substitute(self,from_microstructure,to_microstructure):
"""Substitude microstructure indices."""
substituted = self.get_microstructure()
for from_ms,to_ms in zip(from_microstructure,to_microstructure):
substituted[self.microstructure==from_ms] = to_ms
return self.update(substituted)