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Merge branch 'geom-out-of-place' into 'development' 

Geom methods are now out-of-place, i.e. return an updated duplicate

See merge request damask/DAMASK!203
This commit is contained in:
Franz Roters 2020-08-31 12:39:01 +02:00
parent 3128297301 03b02ad641
commit 6986d20b32
40 changed files with 937 additions and 408 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
processing/pre/geom_grainGrowth.py
View File

@ -169,7 +169,7 @@ for name in filenames:
# undo any changes involving immutable microstructures
microstructure = np.where(immutable, microstructure_original,microstructure)
damask.util.croak(geom.update(microstructure[0:grid_original[0],0:grid_original[1],0:grid_original[2]]))
geom=geom.duplicate(microstructure[0:grid_original[0],0:grid_original[1],0:grid_original[2]])
geom.add_comments(scriptID + ' ' + ' '.join(sys.argv[1:]))
geom.to_file(sys.stdout if name is None else name,pack=False)

4
python/damask/_colormap.py
View File

@ -280,7 +280,7 @@ class Colormap(mpl.colors.ListedColormap):
colors+=[i]+c
out = [{
'Creator':util.version_date('Colormap'),
'Creator':util.execution_stamp('Colormap'),
'ColorSpace':'RGB',
'Name':colormap.name,
'DefaultMap':True,
@ -296,7 +296,7 @@ class Colormap(mpl.colors.ListedColormap):
def _export_ASCII(colormap,fhandle=None):
"""Write colormap to ASCII table."""
labels = {'RGBA':4} if colormap.colors.shape[1] == 4 else {'RGB': 3}
t = Table(colormap.colors,labels,f'Creator: {util.version_date("Colormap")}')
t = Table(colormap.colors,labels,f'Creator: {util.execution_stamp("Colormap")}')
if fhandle is None:
with open(colormap.name.replace(' ','_')+'.txt', 'w') as f:

239
python/damask/_geom.py
View File

@ -24,15 +24,15 @@ class Geom:
Parameters
----------
microstructure : numpy.ndarray
microstructure array (3D)
Microstructure array (3D)
size : list or numpy.ndarray
physical size of the microstructure in meter.
Physical size of the microstructure in meter.
origin : list or numpy.ndarray, optional
physical origin of the microstructure in meter.
Physical origin of the microstructure in meter.
homogenization : int, optional
homogenization index.
Homogenization index.
comments : list of str, optional
comments lines.
Comment lines.
"""
self.set_microstructure(microstructure)
@ -63,63 +63,73 @@ class Geom:
return self.__copy__()
def update(self,microstructure=None,size=None,origin=None,rescale=False):
def duplicate(self,microstructure=None,size=None,origin=None,comments=None,autosize=False):
"""
Update microstructure and size.
Create a duplicate having updated microstructure, size, and origin.
Parameters
----------
microstructure : numpy.ndarray, optional
microstructure array (3D).
Microstructure array (3D).
size : list or numpy.ndarray, optional
physical size of the microstructure in meter.
Physical size of the microstructure in meter.
origin : list or numpy.ndarray, optional
physical origin of the microstructure in meter.
rescale : bool, optional
ignore size parameter and rescale according to change of grid points.
Physical origin of the microstructure in meter.
comments : list of str, optional
Comment lines.
autosize : bool, optional
Ignore size parameter and rescale according to change of grid points.
"""
if size is not None and autosize:
raise ValueError('Auto-sizing conflicts with explicit size parameter.')
grid_old = self.get_grid()
size_old = self.get_size()
origin_old = self.get_origin()
unique_old = self.N_microstructure
max_old = np.nanmax(self.microstructure)
dup = self.copy()
dup.set_microstructure(microstructure)
dup.set_origin(origin)
if size is not None and rescale:
raise ValueError('Either set size explicitly or rescale automatically')
self.set_microstructure(microstructure)
self.set_origin(origin)
if comments is not None:
dup.set_comments(comments)
if size is not None:
self.set_size(size)
elif rescale:
self.set_size(self.get_grid()/grid_old*self.size)
dup.set_size(size)
elif autosize:
dup.set_size(dup.get_grid()/grid_old*self.get_size())
message = [f'grid a b c: {util.srepr(grid_old," x ")}']
if np.any(grid_old != self.get_grid()):
message[-1] = util.delete(message[-1])
return dup
def diff(self,other):
"""
Report property differences of self relative to other.
Parameters
----------
other : Geom
Geometry to compare self against.
"""
message = []
if np.any(other.get_grid() != self.get_grid()):
message.append(util.delete(f'grid a b c: {util.srepr(other.get_grid()," x ")}'))
message.append(util.emph( f'grid a b c: {util.srepr( self.get_grid()," x ")}'))
message.append(f'size x y z: {util.srepr(size_old," x ")}')
if np.any(size_old != self.get_size()):
message[-1] = util.delete(message[-1])
if np.any(other.get_size() != self.get_size()):
message.append(util.delete(f'size x y z: {util.srepr(other.get_size()," x ")}'))
message.append(util.emph( f'size x y z: {util.srepr( self.get_size()," x ")}'))
message.append(f'origin x y z: {util.srepr(origin_old," ")}')
if np.any(origin_old != self.get_origin()):
message[-1] = util.delete(message[-1])
if np.any(other.get_origin() != self.get_origin()):
message.append(util.delete(f'origin x y z: {util.srepr(other.get_origin()," ")}'))
message.append(util.emph( f'origin x y z: {util.srepr( self.get_origin()," ")}'))
message.append(f'# microstructures: {unique_old}')
if unique_old != self.N_microstructure:
message[-1] = util.delete(message[-1])
message.append(util.emph(f'# microstructures: {self.N_microstructure}'))
if other.N_microstructure != self.N_microstructure:
message.append(util.delete(f'# materialpoints: {other.N_microstructure}'))
message.append(util.emph( f'# materialpoints: { self.N_microstructure}'))
message.append(f'max microstructure: {max_old}')
if max_old != np.nanmax(self.microstructure):
message[-1] = util.delete(message[-1])
message.append(util.emph(f'max microstructure: {np.nanmax(self.microstructure)}'))
if np.nanmax(other.microstructure) != np.nanmax(self.microstructure):
message.append(util.delete(f'max materialpoint: {np.nanmax(other.microstructure)}'))
message.append(util.emph( f'max materialpoint: {np.nanmax( self.microstructure)}'))
return util.return_message(message)
@ -131,7 +141,7 @@ class Geom:
Parameters
----------
comments : list of str
new comments.
All comments.
"""
self.comments = []
@ -145,7 +155,7 @@ class Geom:
Parameters
----------
comments : list of str
new comments.
New comments.
"""
self.comments += [str(c) for c in comments] if isinstance(comments,list) else [str(comments)]
@ -172,6 +182,10 @@ class Geom:
else:
self.microstructure = np.copy(microstructure)
if self.microstructure.dtype in np.sctypes['float'] and \
np.all(self.microstructure == self.microstructure.astype(int).astype(float)):
self.microstructure = self.microstructure.astype(int)
if len(self.microstructure.shape) != 3:
raise ValueError(f'Invalid microstructure shape {microstructure.shape}')
elif self.microstructure.dtype not in np.sctypes['float'] + np.sctypes['int']:
@ -185,7 +199,7 @@ class Geom:
Parameters
----------
size : list or numpy.ndarray
physical size of the microstructure in meter.
Physical size of the microstructure in meter.
"""
if size is not None:
@ -202,7 +216,7 @@ class Geom:
Parameters
----------
origin : list or numpy.ndarray
physical origin of the microstructure in meter
Physical origin of the microstructure in meter.
"""
if origin is not None:
@ -219,12 +233,12 @@ class Geom:
Parameters
----------
homogenization : int
homogenization index
Homogenization index.
"""
if homogenization is not None:
if not isinstance(homogenization,int) or homogenization < 1:
raise TypeError(f'Invalid homogenization {homogenization}')
raise TypeError(f'Invalid homogenization {homogenization}.')
else:
self.homogenization = homogenization
@ -286,13 +300,16 @@ class Geom:
f = fname
f.seek(0)
try:
header_length,keyword = f.readline().split()[:2]
header_length = int(header_length)
content = f.readlines()
except ValueError:
header_length,keyword = (-1, 'invalid')
if not keyword.startswith('head') or header_length < 3:
raise TypeError('Header length information missing or invalid')
content = f.readlines()
comments = []
for i,line in enumerate(content[:header_length]):
items = line.split('#')[0].lower().strip().split()
@ -345,11 +362,12 @@ class Geom:
"""
v = VTK.from_file(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr')
grid = np.array(v.geom.GetDimensions())-1
bbox = np.array(v.geom.GetBounds()).reshape(3,2).T
comments = v.get_comments()
grid = np.array(v.vtk_data.GetDimensions())-1
bbox = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
size = bbox[1] - bbox[0]
return Geom(v.get('materialpoint').reshape(grid,order='F'),size,bbox[0])
return Geom(v.get('materialpoint').reshape(grid,order='F'),size,bbox[0],comments=comments)
@staticmethod
@ -398,8 +416,9 @@ class Geom:
else:
microstructure = microstructure.reshape(grid)
creator = util.version_date('Geom','from_Laguerre_tessellation')
return Geom(microstructure+1,size,homogenization=1,comments=creator)
return Geom(microstructure+1,size,homogenization=1,
comments=util.execution_stamp('Geom','from_Laguerre_tessellation'),
)
@staticmethod
@ -423,8 +442,9 @@ class Geom:
KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds)
devNull,microstructure = KDTree.query(coords)
creator = util.version_date('Geom','from_Voronoi_tessellation')
return Geom(microstructure.reshape(grid)+1,size,homogenization=1,comments=creator)
return Geom(microstructure.reshape(grid)+1,size,homogenization=1,
comments=util.execution_stamp('Geom','from_Voronoi_tessellation'),
)
def to_file(self,fname,pack=None):
@ -511,6 +531,7 @@ class Geom:
"""
v = VTK.from_rectilinearGrid(self.grid,self.size,self.origin)
v.add(self.microstructure.flatten(order='F'),'materialpoint')
v.add_comments(self.comments)
if fname:
v.write(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr')
@ -518,8 +539,8 @@ class Geom:
sys.stdout.write(v.__repr__())
def show(self):
"""Show raw content (as in file)."""
def as_ASCII(self):
"""Format geometry as human-readable ASCII."""
f = StringIO()
self.to_file(f)
f.seek(0)
@ -550,10 +571,10 @@ class Geom:
R : damask.Rotation, optional
Rotation of primitive. Defaults to no rotation.
inverse : Boolean, optional
Retain original microstructure within primitive and fill
outside. Defaults to False.
Retain original microstructure within primitive and fill outside.
Defaults to False.
periodic : Boolean, optional
Repeat primitive over boundaries. Defaults to False.
Repeat primitive over boundaries. Defaults to True.
"""
# normalized 'radius' and center
@ -563,11 +584,11 @@ class Geom:
(np.array(center) - self.origin)/self.size
coords = grid_filters.cell_coord0(self.grid,np.ones(3)) \
- (np.ones(3)*0.5 if periodic else c) # center if periodic
- ((np.ones(3)-(1./self.grid if np.array(center).dtype in np.sctypes['int'] else 0))*0.5 if periodic else c) # periodic center is always at CoG
coords_rot = R.broadcast_to(tuple(self.grid))@coords
with np.errstate(over='ignore',under='ignore'):
mask = np.where(np.sum(np.abs(coords_rot/r)**(2.0**exponent),axis=-1) < 1,True,False)
with np.errstate(all='ignore'):
mask = np.where(np.sum(np.power(coords_rot/r,2.0**exponent),axis=-1) > 1.0,True,False)
if periodic: # translate back to center
mask = np.roll(mask,((c-np.ones(3)*.5)*self.grid).astype(int),(0,1,2))
@ -575,8 +596,9 @@ class Geom:
fill_ = np.full_like(self.microstructure,np.nanmax(self.microstructure)+1 if fill is None else fill)
ms = np.ma.MaskedArray(fill_,np.logical_not(mask) if inverse else mask)
self.add_comments(util.version_date('Geom','add_primitive'))
return self.update(ms)
return self.duplicate(ms,
comments=self.get_comments()+[util.execution_stamp('Geom','add_primitive')],
)
def mirror(self,directions,reflect=False):
@ -589,10 +611,10 @@ class Geom:
Direction(s) along which the microstructure is mirrored.
Valid entries are 'x', 'y', 'z'.
reflect : bool, optional
Reflect (include) outermost layers.
Reflect (include) outermost layers. Defaults to False.
"""
valid = {'x','y','z'}
valid = ['x','y','z']
if not set(directions).issubset(valid):
raise ValueError(f'Invalid direction {set(directions).difference(valid)} specified.')
@ -606,8 +628,31 @@ class Geom:
if 'x' in directions:
ms = np.concatenate([ms,ms[limits[0]:limits[1]:-1,:,:]],0)
self.add_comments(util.version_date('Geom','mirror'))
return self.update(ms,rescale=True)
return self.duplicate(ms,
comments=self.get_comments()+[util.execution_stamp('Geom','mirror')],
autosize=True)
def flip(self,directions):
"""
Flip microstructure along given directions.
Parameters
----------
directions : iterable containing str
Direction(s) along which the microstructure is flipped.
Valid entries are 'x', 'y', 'z'.
"""
valid = ['x','y','z']
if not set(directions).issubset(valid):
raise ValueError(f'Invalid direction {set(directions).difference(valid)} specified.')
ms = np.flip(self.microstructure, (valid.index(d) for d in directions if d in valid))
return self.duplicate(ms,
comments=self.get_comments()+[util.execution_stamp('Geom','flip')],
)
def scale(self,grid,periodic=True):
@ -622,16 +667,15 @@ class Geom:
Assume geometry to be periodic. Defaults to True.
"""
self.add_comments(util.version_date('Geom','scale'))
return self.update(
ndimage.interpolation.zoom(
return self.duplicate(ndimage.interpolation.zoom(
self.microstructure,
grid/self.get_grid(),
output=self.microstructure.dtype,
order=0,
mode=('wrap' if periodic else 'nearest'),
prefilter=False
)
),
comments=self.get_comments()+[util.execution_stamp('Geom','scale')],
)
@ -657,14 +701,14 @@ class Geom:
else:
return me
self.add_comments(util.version_date('Geom','clean'))
return self.update(ndimage.filters.generic_filter(
return self.duplicate(ndimage.filters.generic_filter(
self.microstructure,
mostFrequent,
size=(stencil if selection is None else stencil//2*2+1,)*3,
mode=('wrap' if periodic else 'nearest'),
extra_keywords=dict(selection=selection),
).astype(self.microstructure.dtype)
).astype(self.microstructure.dtype),
comments=self.get_comments()+[util.execution_stamp('Geom','clean')],
)
@ -674,8 +718,9 @@ class Geom:
for i, oldID in enumerate(np.unique(self.microstructure)):
renumbered = np.where(self.microstructure == oldID, i+1, renumbered)
self.add_comments(util.version_date('Geom','renumber'))
return self.update(renumbered)
return self.duplicate(renumbered,
comments=self.get_comments()+[util.execution_stamp('Geom','renumber')],
)
def rotate(self,R,fill=None):
@ -709,8 +754,11 @@ class Geom:
origin = self.origin-(np.asarray(microstructure_in.shape)-self.grid)*.5 * self.size/self.grid
self.add_comments(util.version_date('Geom','rotate'))
return self.update(microstructure_in,origin=origin,rescale=True)
return self.duplicate(microstructure_in,
origin=origin,
comments=self.get_comments()+[util.execution_stamp('Geom','rotate')],
autosize=True,
)
def canvas(self,grid=None,offset=None,fill=None):
@ -724,16 +772,14 @@ class Geom:
offset : numpy.ndarray of shape (3)
Offset (measured in grid points) from old to new microstructure[0,0,0].
fill : int or float, optional
Microstructure index to fill the corners. Defaults to microstructure.max() + 1.
Microstructure index to fill the background. Defaults to microstructure.max() + 1.
"""
if fill is None: fill = np.nanmax(self.microstructure) + 1
if offset is None: offset = 0
dtype = float if int(fill) != fill or self.microstructure.dtype==np.float else int
if fill is None: fill = np.nanmax(self.microstructure) + 1
dtype = float if int(fill) != fill or self.microstructure.dtype in np.sctypes['float'] else int
canvas = np.full(self.grid if grid is None else grid,
np.nanmax(self.microstructure)+1 if fill is None else fill,
dtype)
canvas = np.full(self.grid if grid is None else grid,fill,dtype)
LL = np.clip( offset, 0,np.minimum(self.grid, grid+offset))
UR = np.clip( offset+grid, 0,np.minimum(self.grid, grid+offset))
@ -742,8 +788,11 @@ class Geom:
canvas[ll[0]:ur[0],ll[1]:ur[1],ll[2]:ur[2]] = self.microstructure[LL[0]:UR[0],LL[1]:UR[1],LL[2]:UR[2]]
self.add_comments(util.version_date('Geom','canvas'))
return self.update(canvas,origin=self.origin+offset*self.size/self.grid,rescale=True)
return self.duplicate(canvas,
origin=self.origin+offset*self.size/self.grid,
comments=self.get_comments()+[util.execution_stamp('Geom','canvas')],
autosize=True,
)
def substitute(self,from_microstructure,to_microstructure):
@ -762,8 +811,9 @@ class Geom:
for from_ms,to_ms in zip(from_microstructure,to_microstructure):
substituted[self.microstructure==from_ms] = to_ms
self.add_comments(util.version_date('Geom','substitute'))
return self.update(substituted)
return self.duplicate(substituted,
comments=self.get_comments()+[util.execution_stamp('Geom','substitute')],
)
def vicinity_offset(self,vicinity=1,offset=None,trigger=[],periodic=True):
@ -804,9 +854,10 @@ class Geom:
mask = ndimage.filters.generic_filter(self.microstructure,
tainted_neighborhood,
size=1+2*vicinity,
mode=('wrap' if periodic else 'nearest'),
mode='wrap' if periodic else 'nearest',
extra_keywords={'trigger':trigger})
microstructure = np.ma.MaskedArray(self.microstructure + offset_, np.logical_not(mask))
self.add_comments(util.version_date('Geom','vicinity_offset'))
return self.update(microstructure)
return self.duplicate(microstructure,
comments=self.get_comments()+[util.execution_stamp('Geom','vicinity_offset')],
)

35
python/damask/_result.py
View File

@ -1,6 +1,5 @@
import multiprocessing as mp
import re
import inspect
import glob
import os
import datetime
@ -537,7 +536,7 @@ class Result:
'meta': {
'Unit': x['meta']['Unit'],
'Description': f"Absolute value of {x['label']} ({x['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_absolute'
}
}
def add_absolute(self,x):
@ -565,7 +564,7 @@ class Result:
'meta': {
'Unit': kwargs['unit'],
'Description': f"{kwargs['description']} (formula: {kwargs['formula']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_calculation'
}
}
def add_calculation(self,label,formula,unit='n/a',description=None):
@ -599,7 +598,7 @@ class Result:
'Description': "Cauchy stress calculated "
f"from {P['label']} ({P['meta']['Description']})"
f" and {F['label']} ({F['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_Cauchy'
}
}
def add_Cauchy(self,P='P',F='F'):
@ -625,7 +624,7 @@ class Result:
'meta': {
'Unit': T['meta']['Unit'],
'Description': f"Determinant of tensor {T['label']} ({T['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_determinant'
}
}
def add_determinant(self,T):
@ -649,7 +648,7 @@ class Result:
'meta': {
'Unit': T['meta']['Unit'],
'Description': f"Deviator of tensor {T['label']} ({T['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_deviator'
}
}
def add_deviator(self,T):
@ -680,7 +679,7 @@ class Result:
'meta' : {
'Unit': T_sym['meta']['Unit'],
'Description': f"{label} eigenvalue of {T_sym['label']} ({T_sym['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_eigenvalue'
}
}
def add_eigenvalue(self,T_sym,eigenvalue='max'):
@ -713,7 +712,7 @@ class Result:
'Unit': '1',
'Description': f"Eigenvector corresponding to {label} eigenvalue"
f" of {T_sym['label']} ({T_sym['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_eigenvector'
}
}
def add_eigenvector(self,T_sym,eigenvalue='max'):
@ -746,7 +745,7 @@ class Result:
'Unit': '8-bit RGB',
'Lattice': q['meta']['Lattice'],
'Description': 'Inverse Pole Figure (IPF) colors along sample direction [{} {} {}]'.format(*m),
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_IPF_color'
}
}
def add_IPF_color(self,q,l):
@ -772,7 +771,7 @@ class Result:
'meta': {
'Unit': T_sym['meta']['Unit'],
'Description': f"Maximum shear component of {T_sym['label']} ({T_sym['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_maximum_shear'
}
}
def add_maximum_shear(self,T_sym):
@ -799,7 +798,7 @@ class Result:
'meta': {
'Unit': T_sym['meta']['Unit'],
'Description': f"Mises equivalent {t} of {T_sym['label']} ({T_sym['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_Mises'
}
}
def add_Mises(self,T_sym):
@ -835,7 +834,7 @@ class Result:
'meta': {
'Unit': x['meta']['Unit'],
'Description': f"{o}-norm of {t} {x['label']} ({x['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_norm'
}
}
def add_norm(self,x,ord=None):
@ -863,7 +862,7 @@ class Result:
'Description': "2. Piola-Kirchhoff stress calculated "
f"from {P['label']} ({P['meta']['Description']})"
f" and {F['label']} ({F['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_PK2'
}
}
def add_PK2(self,P='P',F='F'):
@ -899,7 +898,7 @@ class Result:
'Unit': '1',
'Description': '{} coordinates of stereographic projection of pole (direction/plane) in crystal frame'\
.format('Polar' if polar else 'Cartesian'),
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_pole'
}
}
def add_pole(self,q,p,polar=False):
@ -927,7 +926,7 @@ class Result:
'meta': {
'Unit': F['meta']['Unit'],
'Description': f"Rotational part of {F['label']} ({F['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_rotational_part'
}
}
def add_rotational_part(self,F):
@ -951,7 +950,7 @@ class Result:
'meta': {
'Unit': T['meta']['Unit'],
'Description': f"Spherical component of tensor {T['label']} ({T['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_spherical'
}
}
def add_spherical(self,T):
@ -975,7 +974,7 @@ class Result:
'meta': {
'Unit': F['meta']['Unit'],
'Description': f"Strain tensor of {F['label']} ({F['meta']['Description']})",
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_strain_tensor'
}
}
def add_strain_tensor(self,F='F',t='V',m=0.0):
@ -1007,7 +1006,7 @@ class Result:
'Unit': F['meta']['Unit'],
'Description': '{} stretch tensor of {} ({})'.format('Left' if t.upper() == 'V' else 'Right',
F['label'],F['meta']['Description']),
'Creator': inspect.stack()[0][3][1:]
'Creator': 'add_stretch_tensor'
}
}
def add_stretch_tensor(self,F='F',t='V'):

4
python/damask/_table.py
View File

@ -49,7 +49,7 @@ class Table:
def _add_comment(self,label,shape,info):
if info is not None:
specific = f'{label}{" "+str(shape) if np.prod(shape,dtype=int) > 1 else ""}: {info}'
general = util.version_date('Table')
general = util.execution_stamp('Table')
self.comments.append(f'{specific} / {general}')
@ -136,7 +136,7 @@ class Table:
content = f.readlines()
comments = [util.version_date('Table','from_ang')]
comments = [util.execution_stamp('Table','from_ang')]
for line in content:
if line.startswith('#'):
comments.append(line.strip())

103
python/damask/_vtk.py
View File

@ -20,18 +20,19 @@ class VTK:
High-level interface to VTK.
"""
def __init__(self,geom):
def __init__(self,vtk_data):
"""
Set geometry and topology.
Initialize from vtk dataset.
Parameters
----------
geom : subclass of vtk.vtkDataSet
Description of geometry and topology. Valid types are vtk.vtkRectilinearGrid,
vtk.vtkUnstructuredGrid, or vtk.vtkPolyData.
vtk_data : subclass of vtk.vtkDataSet
Description of geometry and topology, optionally with attached data.
Valid types are vtk.vtkRectilinearGrid, vtk.vtkUnstructuredGrid,
or vtk.vtkPolyData.
"""
self.geom = geom
self.vtk_data = vtk_data
@staticmethod
@ -51,15 +52,15 @@ class VTK:
Spatial origin.
"""
geom = vtk.vtkRectilinearGrid()
geom.SetDimensions(*(grid+1))
vtk_data = vtk.vtkRectilinearGrid()
vtk_data.SetDimensions(*(grid+1))
coord = [np_to_vtk(np.linspace(origin[i],origin[i]+size[i],grid[i]+1),deep=True) for i in [0,1,2]]
[coord[i].SetName(n) for i,n in enumerate(['x','y','z'])]
geom.SetXCoordinates(coord[0])
geom.SetYCoordinates(coord[1])
geom.SetZCoordinates(coord[2])
vtk_data.SetXCoordinates(coord[0])
vtk_data.SetYCoordinates(coord[1])
vtk_data.SetZCoordinates(coord[2])
return VTK(geom)
return VTK(vtk_data)
@staticmethod
@ -87,11 +88,11 @@ class VTK:
connectivity),axis=1).ravel()
cells.SetCells(connectivity.shape[0],np_to_vtkIdTypeArray(T,deep=True))
geom = vtk.vtkUnstructuredGrid()
geom.SetPoints(vtk_nodes)
geom.SetCells(eval(f'vtk.VTK_{cell_type.split("_",1)[-1].upper()}'),cells)
vtk_data = vtk.vtkUnstructuredGrid()
vtk_data.SetPoints(vtk_nodes)
vtk_data.SetCells(eval(f'vtk.VTK_{cell_type.split("_",1)[-1].upper()}'),cells)
return VTK(geom)
return VTK(vtk_data)
@staticmethod
@ -110,10 +111,10 @@ class VTK:
vtk_points = vtk.vtkPoints()
vtk_points.SetData(np_to_vtk(points))
geom = vtk.vtkPolyData()
geom.SetPoints(vtk_points)
vtk_data = vtk.vtkPolyData()
vtk_data.SetPoints(vtk_points)
return VTK(geom)
return VTK(vtk_data)
@staticmethod
@ -131,18 +132,20 @@ class VTK:
"""
ext = Path(fname).suffix
if ext == '.vtk' or dataset_type:
if ext == '.vtk' or dataset_type is not None:
reader = vtk.vtkGenericDataObjectReader()
reader.SetFileName(str(fname))
reader.Update()
if dataset_type is None:
raise TypeError('Dataset type for *.vtk file not given.')
elif dataset_type.lower().endswith('rectilineargrid'):
geom = reader.GetRectilinearGridOutput()
reader.Update()
vtk_data = reader.GetRectilinearGridOutput()
elif dataset_type.lower().endswith('unstructuredgrid'):
geom = reader.GetUnstructuredGridOutput()
reader.Update()
vtk_data = reader.GetUnstructuredGridOutput()
elif dataset_type.lower().endswith('polydata'):
geom = reader.GetPolyDataOutput()
reader.Update()
vtk_data = reader.GetPolyDataOutput()
else:
raise TypeError(f'Unknown dataset type {dataset_type} for vtk file')
else:
@ -157,9 +160,9 @@ class VTK:
reader.SetFileName(str(fname))
reader.Update()
geom = reader.GetOutput()
vtk_data = reader.GetOutput()
return VTK(geom)
return VTK(vtk_data)
@staticmethod
def _write(writer):
@ -177,11 +180,11 @@ class VTK:
Write data in parallel background process. Defaults to True.
"""
if isinstance(self.geom,vtk.vtkRectilinearGrid):
if isinstance(self.vtk_data,vtk.vtkRectilinearGrid):
writer = vtk.vtkXMLRectilinearGridWriter()
elif isinstance(self.geom,vtk.vtkUnstructuredGrid):
elif isinstance(self.vtk_data,vtk.vtkUnstructuredGrid):
writer = vtk.vtkXMLUnstructuredGridWriter()
elif isinstance(self.geom,vtk.vtkPolyData):
elif isinstance(self.vtk_data,vtk.vtkPolyData):
writer = vtk.vtkXMLPolyDataWriter()
default_ext = writer.GetDefaultFileExtension()
@ -191,7 +194,7 @@ class VTK:
writer.SetFileName(str(Path(fname).with_suffix('.'+default_ext)))
writer.SetCompressorTypeToZLib()
writer.SetDataModeToBinary()
writer.SetInputData(self.geom)
writer.SetInputData(self.vtk_data)
if parallel:
try:
@ -218,8 +221,8 @@ class VTK:
Data label.
"""
N_points = self.geom.GetNumberOfPoints()
N_cells = self.geom.GetNumberOfCells()
N_points = self.vtk_data.GetNumberOfPoints()
N_cells = self.vtk_data.GetNumberOfCells()
if isinstance(data,np.ndarray):
if label is None:
@ -232,9 +235,9 @@ class VTK:
d.SetName(label)
if data.shape[0] == N_cells:
self.geom.GetCellData().AddArray(d)
self.vtk_data.GetCellData().AddArray(d)
elif data.shape[0] == N_points:
self.geom.GetPointData().AddArray(d)
self.vtk_data.GetPointData().AddArray(d)
else:
raise ValueError(f'Invalid shape {data.shape[0]}')
elif isinstance(data,pd.DataFrame):
@ -259,22 +262,22 @@ class VTK:
Data label.
"""
celldata = self.geom.GetCellData()
for a in range(celldata.GetNumberOfArrays()):
if celldata.GetArrayName(a) == label:
return vtk_to_np(celldata.GetArray(a))
cell_data = self.vtk_data.GetCellData()
for a in range(cell_data.GetNumberOfArrays()):
if cell_data.GetArrayName(a) == label:
return vtk_to_np(cell_data.GetArray(a))
pointdata = self.geom.GetPointData()
for a in range(celldata.GetNumberOfArrays()):
if pointdata.GetArrayName(a) == label:
return vtk_to_np(pointdata.GetArray(a))
point_data = self.vtk_data.GetPointData()
for a in range(point_data.GetNumberOfArrays()):
if point_data.GetArrayName(a) == label:
return vtk_to_np(point_data.GetArray(a))
raise ValueError(f'array "{label}" not found')
def get_comments(self):
"""Return the comments."""
fielddata = self.geom.GetFieldData()
fielddata = self.vtk_data.GetFieldData()
for a in range(fielddata.GetNumberOfArrays()):
if fielddata.GetArrayName(a) == 'comments':
comments = fielddata.GetAbstractArray(a)
@ -284,7 +287,7 @@ class VTK:
def set_comments(self,comments):
"""
Set Comments.
Set comments.
Parameters
----------
@ -296,12 +299,12 @@ class VTK:
s.SetName('comments')
for c in [comments] if isinstance(comments,str) else comments:
s.InsertNextValue(c)
self.geom.GetFieldData().AddArray(s)
self.vtk_data.GetFieldData().AddArray(s)
def add_comments(self,comments):
"""
Add Comments.
Add comments.
Parameters
----------
@ -309,15 +312,15 @@ class VTK:
Comments to add.
"""
self.set_comments(self.get_comments + ([comments] if isinstance(comments,str) else comments))
self.set_comments(self.get_comments() + ([comments] if isinstance(comments,str) else comments))
def __repr__(self):
"""ASCII representation of the VTK data."""
writer = vtk.vtkDataSetWriter()
writer.SetHeader(f'# {util.version_date("VTK")}')
writer.SetHeader(f'# {util.execution_stamp("VTK")}')
writer.WriteToOutputStringOn()
writer.SetInputData(self.geom)
writer.SetInputData(self.vtk_data)
writer.Write()
return writer.GetOutputString()
@ -329,7 +332,7 @@ class VTK:
See http://compilatrix.com/article/vtk-1 for further ideas.
"""
mapper = vtk.vtkDataSetMapper()
mapper.SetInputData(self.geom)
mapper.SetInputData(self.vtk_data)
actor = vtk.vtkActor()
actor.SetMapper(mapper)

8
python/damask/util.py
View File

@ -22,7 +22,7 @@ __all__=[
'scale_to_coprime',
'return_message',
'extendableOption',
'version_date'
'execution_stamp'
]
####################################################################################################
@ -178,10 +178,10 @@ def scale_to_coprime(v):
return m
def version_date(class_name,function_name=None):
"""tbd."""
_function_name = '' if function_name is None else f'.{function_name}'
def execution_stamp(class_name,function_name=None):
"""Timestamp the execution of a (function within a) class."""
now = datetime.datetime.now().astimezone().strftime('%Y-%m-%d %H:%M:%S%z')
_function_name = '' if function_name is None else f'.{function_name}'
return f'damask.{class_name}{_function_name} v{version} ({now})'

8
python/tests/conftest.py
View File

@ -26,13 +26,13 @@ def patch_datetime_now(monkeypatch):
monkeypatch.setattr(datetime, 'datetime', mydatetime)
@pytest.fixture
def version_date(monkeypatch):
"""Set damask.util.version_date for reproducible tests results."""
def version_date(class_name,function_name=None):
def execution_stamp(monkeypatch):
"""Set damask.util.execution_stamp for reproducible tests results."""
def execution_stamp(class_name,function_name=None):
_function_name = '' if function_name is None else f'.{function_name}'
return f'damask.{class_name}{_function_name} v{patched_version} ({patched_date})'
monkeypatch.setattr(damask.util, 'version_date', version_date)
monkeypatch.setattr(damask.util, 'execution_stamp', execution_stamp)
def pytest_addoption(parser):

25
python/tests/reference/Geom/clean.vtr
View File

@ -1,25 +0,0 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 20 0 18 0 8">
<Piece Extent="0 20 0 18 0 8">
<PointData>
</PointData>
<CellData>
<DataArray type="Int32" Name="materialpoint" format="binary" RangeMin="1" RangeMax="2">
AQAAAACAAAAALQAANQAAAA==eF7t1CECACAMxLBj/380fhYwIyK2spWkmnWgt6b3AF65/avfegAAAAAAAAAAAMy0AfYtC2k=
</DataArray>
</CellData>
<Coordinates>
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="1">
AQAAAACAAACoAAAAVQAAAA==eF5jYICAWTNBYKU9hN5pb2IMAoeh/JP2EFUXoOKX7dPTQOAaVP6m/dkzIHAHqu4BVPwhVP1jqPwTqL5nUHUvoOpeQtW9hqp7A1X3Dqrugz0ASSZF3Q==
</DataArray>
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="1">
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</DataArray>
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="1">
AQAAAACAAABIAAAAIgAAAA==eF5jYEAGB+wh9AUofQNKP4DST6D0Cyj9Bkp/sAcAAU8I6Q==
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</Coordinates>
</Piece>
</RectilinearGrid>
</VTKFile>

25
python/tests/reference/Geom/clean_1_1+2+3_False.vtr Normal file
View File

@ -0,0 +1,25 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
<Piece Extent="0 8 0 5 0 4">
<PointData>
</PointData>
<CellData>
<DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
AQAAAACAAAAABQAAYwAAAA==eF7t0scBgkAAAEHBgBEwgDmBsf8GfTANCN/bzzSwUa8pCrYyZp8DDjliwjEnnHLGORdMmTHnkiuuuWHBklvuuOeBR5545oVX3nhnxZoPPvnimx9+GQc7GT5sqvjvhz+ZtAcJ
</DataArray>
</CellData>
<Coordinates>
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
AQAAAACAAABIAAAAOgAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2D3IeNxx9YfV6DiN+22x9tFGsbchco/sAMA/fQl6g==
</DataArray>
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
AQAAAACAAAAwAAAAKwAAAA==eF5jYICAvrdbF3w/tsEOQh+wC30iUFisdRLKv2D3MeNxx9YfV+wAD5wZgw==
</DataArray>
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
AQAAAACAAAAoAAAAIwAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2AHAFVBE/w=
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</Coordinates>
</Piece>
</RectilinearGrid>
</VTKFile>

25
python/tests/reference/Geom/clean_1_1+2+3_True.vtr Normal file
View File

@ -0,0 +1,25 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
<Piece Extent="0 8 0 5 0 4">
<PointData>
</PointData>
<CellData>
<DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
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</DataArray>
</CellData>
<Coordinates>
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
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</DataArray>
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
AQAAAACAAAAwAAAAKwAAAA==eF5jYICAvrdbF3w/tsEOQh+wC30iUFisdRLKv2D3MeNxx9YfV+wAD5wZgw==
</DataArray>
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
AQAAAACAAAAoAAAAIwAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2AHAFVBE/w=
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</Coordinates>
</Piece>
</RectilinearGrid>
</VTKFile>

25
python/tests/reference/Geom/clean_1_1_False.vtr Normal file
View File

@ -0,0 +1,25 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
<Piece Extent="0 8 0 5 0 4">
<PointData>
</PointData>
<CellData>
<DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
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</CellData>
<Coordinates>
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</VTKFile>

25
python/tests/reference/Geom/clean_1_1_True.vtr Normal file
View File

@ -0,0 +1,25 @@
<?xml version="1.0"?>
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<RectilinearGrid WholeExtent="0 8 0 5 0 4">
<Piece Extent="0 8 0 5 0 4">
<PointData>
</PointData>
<CellData>
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</CellData>
<Coordinates>
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25
python/tests/reference/Geom/clean_1_None_False.vtr Normal file
View File

@ -0,0 +1,25 @@
<?xml version="1.0"?>
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<RectilinearGrid WholeExtent="0 8 0 5 0 4">
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25
python/tests/reference/Geom/clean_1_None_True.vtr Normal file
View File

@ -0,0 +1,25 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
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<PointData>
</PointData>
<CellData>
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</CellData>
<Coordinates>
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</DataArray>
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
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<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
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</Coordinates>
</Piece>
</RectilinearGrid>
</VTKFile>

25
python/tests/reference/Geom/clean_2_1+2+3_False.vtr Normal file
View File

@ -0,0 +1,25 @@
<?xml version="1.0"?>
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32 31 30 29 28 27 26 25
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16 15 14 13 12 11 10 9
8 7 6 5 4 3 2 1
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
41 40 39 38 37 36 35 34
33 32 31 30 29 28 27 26
25 24 23 22 21 20 19 18
17 16 15 14 13 12 11 10
9 8 7 6 5 4 3 2
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1

25
python/tests/reference/Geom/flip_directions=x.geom Normal file
View File

@ -0,0 +1,25 @@
4 header
grid a 8 b 5 c 4
size x 8e-06 y 5e-06 z 4e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
9 8 7 6 5 4 3 2
17 16 15 14 13 12 11 10
25 24 23 22 21 20 19 18
33 32 31 30 29 28 27 26
41 40 39 38 37 36 35 34
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
8 7 6 5 4 3 2 1
16 15 14 13 12 11 10 9
24 23 22 21 20 19 18 17
32 31 30 29 28 27 26 25
40 39 38 37 36 35 34 33

25
python/tests/reference/Geom/flip_directions=y-z.geom Normal file
View File

@ -0,0 +1,25 @@
4 header
grid a 8 b 5 c 4
size x 8e-06 y 5e-06 z 4e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
33 34 35 36 37 38 39 40
25 26 27 28 29 30 31 32
17 18 19 20 21 22 23 24
9 10 11 12 13 14 15 16
1 2 3 4 5 6 7 8
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
34 35 36 37 38 39 40 41
26 27 28 29 30 31 32 33
18 19 20 21 22 23 24 25
10 11 12 13 14 15 16 17
2 3 4 5 6 7 8 9
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1

25
python/tests/reference/Geom/flip_directions=z-x-y.geom Normal file
View File

@ -0,0 +1,25 @@
4 header
grid a 8 b 5 c 4
size x 8e-06 y 5e-06 z 4e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
40 39 38 37 36 35 34 33
32 31 30 29 28 27 26 25
24 23 22 21 20 19 18 17
16 15 14 13 12 11 10 9
8 7 6 5 4 3 2 1
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
41 40 39 38 37 36 35 34
33 32 31 30 29 28 27 26
25 24 23 22 21 20 19 18
17 16 15 14 13 12 11 10
9 8 7 6 5 4 3 2
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1

4
python/tests/test_Colormap.py
View File

@ -17,8 +17,8 @@ def reference_dir(reference_dir_base):
class TestColormap:
@pytest.fixture(autouse=True)
def _version_date(self, version_date):
print('patched damask.util.version_date')
def _execution_stamp(self, execution_stamp):
print('patched damask.util.execution_stamp')
def test_conversion(self):
specials = np.array([[0.,0.,0.],

177
python/tests/test_Geom.py
View File

@ -13,7 +13,8 @@ from damask import util
def geom_equal(a,b):
return np.all(a.get_microstructure() == b.get_microstructure()) and \
np.all(a.get_grid() == b.get_grid()) and \
np.allclose(a.get_size(), b.get_size())
np.allclose(a.get_size(), b.get_size()) and \
str(a.diff(b)) == str(b.diff(a))
@pytest.fixture
def default():
@ -32,15 +33,26 @@ def reference_dir(reference_dir_base):
class TestGeom:
def test_update(self,default):
modified = default.copy()
modified.update(
@pytest.mark.parametrize('flavor',['plain','explicit'])
def test_duplicate(self,default,flavor):
if flavor == 'plain':
modified = default.duplicate()
elif flavor == 'explicit':
modified = default.duplicate(
default.get_microstructure(),
default.get_size(),
default.get_origin()
)
print(modified)
assert geom_equal(modified,default)
assert geom_equal(default,modified)
def test_diff_equal(self,default):
assert str(default.diff(default)) == ''
def test_diff_not_equal(self,default):
new = Geom(default.microstructure[1:,1:,1:]+1,default.size*.9,np.ones(3)-default.origin,comments=['modified'])
assert str(default.diff(new)) != ''
@pytest.mark.parametrize('masked',[True,False])
def test_set_microstructure(self,default,masked):
@ -53,24 +65,25 @@ class TestGeom:
def test_write_read_str(self,default,tmpdir):
default.to_file(str(tmpdir/'default.geom'))
new = Geom.from_file(str(tmpdir/'default.geom'))
assert geom_equal(new,default)
assert geom_equal(default,new)
def test_write_read_file(self,default,tmpdir):
with open(tmpdir/'default.geom','w') as f:
default.to_file(f)
default.to_file(f,pack=True)
with open(tmpdir/'default.geom') as f:
new = Geom.from_file(f)
assert geom_equal(new,default)
assert geom_equal(default,new)
def test_write_show(self,default,tmpdir):
def test_write_as_ASCII(self,default,tmpdir):
with open(tmpdir/'str.geom','w') as f:
f.write(default.show())
f.write(default.as_ASCII())
with open(tmpdir/'str.geom') as f:
new = Geom.from_file(f)
assert geom_equal(new,default)
assert geom_equal(default,new)
def test_read_write_vtr(self,default,tmpdir):
default.to_vtr(tmpdir/'default')
print(default.to_vtr())
for _ in range(10):
time.sleep(.2)
if os.path.exists(tmpdir/'default.vtr'): break
@ -78,6 +91,13 @@ class TestGeom:
new = Geom.from_vtr(tmpdir/'default.vtr')
assert geom_equal(new,default)
def test_invalid_geom(self,tmpdir):
with open('invalid_file','w') as f:
f.write('this is not a valid header')
with open('invalid_file','r') as f:
with pytest.raises(TypeError):
Geom.from_file(f)
def test_invalid_vtr(self,tmpdir):
v = VTK.from_rectilinearGrid(np.random.randint(5,10,3)*2,np.random.random(3) + 1.0)
v.write(tmpdir/'no_materialpoint.vtr')
@ -96,25 +116,25 @@ class TestGeom:
def test_invalid_combination(self,default):
with pytest.raises(ValueError):
default.update(default.microstructure[1:,1:,1:],size=np.ones(3), rescale=True)
default.duplicate(default.microstructure[1:,1:,1:],size=np.ones(3), autosize=True)
def test_invalid_size(self,default):
with pytest.raises(ValueError):
default.update(default.microstructure[1:,1:,1:],size=np.ones(2))
default.duplicate(default.microstructure[1:,1:,1:],size=np.ones(2))
def test_invalid_origin(self,default):
with pytest.raises(ValueError):
default.update(default.microstructure[1:,1:,1:],origin=np.ones(4))
default.duplicate(default.microstructure[1:,1:,1:],origin=np.ones(4))
def test_invalid_microstructure_size(self,default):
microstructure = np.ones((3,3))
with pytest.raises(ValueError):
default.update(microstructure)
default.duplicate(microstructure)
def test_invalid_microstructure_type(self,default):
microstructure = np.random.randint(1,300,(3,4,5))==1
with pytest.raises(TypeError):
default.update(microstructure)
default.duplicate(microstructure)
def test_invalid_homogenization(self,default):
with pytest.raises(TypeError):
@ -128,31 +148,61 @@ class TestGeom:
]
)
def test_mirror(self,default,update,reference_dir,directions,reflect):
modified = default.copy()
modified.mirror(directions,reflect)
modified = default.mirror(directions,reflect)
tag = f'directions={"-".join(directions)}_reflect={reflect}'
reference = reference_dir/f'mirror_{tag}.geom'
if update: modified.to_file(reference)
assert geom_equal(modified,Geom.from_file(reference))
assert geom_equal(Geom.from_file(reference),
modified)
@pytest.mark.parametrize('directions',[(1,2,'y'),('a','b','x'),[1]])
def test_mirror_invalid(self,default,directions):
with pytest.raises(ValueError):
default.mirror(directions)
@pytest.mark.parametrize('directions',[
['x'],
['x','y','z'],
['z','x','y'],
['y','z'],
]
)
def test_flip(self,default,update,reference_dir,directions):
modified = default.flip(directions)
tag = f'directions={"-".join(directions)}'
reference = reference_dir/f'flip_{tag}.geom'
if update: modified.to_file(reference)
assert geom_equal(Geom.from_file(reference),
modified)
def test_flip_invariant(self,default):
assert geom_equal(default,default.flip([]))
@pytest.mark.parametrize('direction',[['x'],['x','y']])
def test_flip_double(self,default,direction):
assert geom_equal(default,default.flip(direction).flip(direction))
@pytest.mark.parametrize('directions',[(1,2,'y'),('a','b','x'),[1]])
def test_flip_invalid(self,default,directions):
with pytest.raises(ValueError):
default.flip(directions)
@pytest.mark.parametrize('stencil',[1,2,3,4])
@pytest.mark.parametrize('selection',[None,1,2])
@pytest.mark.parametrize('selection',[None,[1],[1,2,3]])
@pytest.mark.parametrize('periodic',[True,False])
def test_clean(self,update,reference_dir,stencil,selection,periodic):
current = Geom.from_vtr((reference_dir/'clean').with_suffix('.vtr'))
current.clean(stencil,None if selection is None else [selection],periodic)
reference = reference_dir/f'clean_{stencil}_{selection}_{periodic}'
if update and stencil !=1:
def test_clean(self,default,update,reference_dir,stencil,selection,periodic):
current = default.clean(stencil,selection,periodic)
reference = reference_dir/f'clean_{stencil}_{"+".join(map(str,[None] if selection is None else selection))}_{periodic}'
if update and stencil > 1:
current.to_vtr(reference)
for _ in range(10):
time.sleep(.2)
if os.path.exists(reference.with_suffix('.vtr')): break
assert geom_equal(current,Geom.from_vtr(reference if stencil !=1 else reference_dir/'clean'))
assert geom_equal(Geom.from_vtr(reference) if stencil > 1 else default,
current
)
@pytest.mark.parametrize('grid',[
(10,11,10),
@ -164,33 +214,29 @@ class TestGeom:
]
)
def test_scale(self,default,update,reference_dir,grid):
modified = default.copy()
modified.scale(grid)
modified = default.scale(grid)
tag = f'grid={util.srepr(grid,"-")}'
reference = reference_dir/f'scale_{tag}.geom'
if update: modified.to_file(reference)
assert geom_equal(modified,Geom.from_file(reference))
assert geom_equal(Geom.from_file(reference),
modified)
def test_renumber(self,default):
modified = default.copy()
microstructure = modified.get_microstructure()
microstructure = default.get_microstructure()
for m in np.unique(microstructure):
microstructure[microstructure==m] = microstructure.max() + np.random.randint(1,30)
modified.update(microstructure)
modified = default.duplicate(microstructure)
assert not geom_equal(modified,default)
modified.renumber()
assert geom_equal(modified,default)
assert geom_equal(default,
modified.renumber())
def test_substitute(self,default):
modified = default.copy()
microstructure = modified.get_microstructure()
offset = np.random.randint(1,500)
microstructure += offset
modified.update(microstructure)
modified = default.duplicate(default.get_microstructure() + offset)
assert not geom_equal(modified,default)
assert geom_equal(default,
modified.substitute(np.arange(default.microstructure.max())+1+offset,
np.arange(default.microstructure.max())+1)
assert geom_equal(modified,default)
np.arange(default.microstructure.max())+1))
@pytest.mark.parametrize('axis_angle',[np.array([1,0,0,86.7]), np.array([0,1,0,90.4]), np.array([0,0,1,90]),
np.array([1,0,0,175]),np.array([0,-1,0,178]),np.array([0,0,1,180])])
@ -198,40 +244,58 @@ class TestGeom:
modified = default.copy()
for i in range(np.rint(360/axis_angle[3]).astype(int)):
modified.rotate(Rotation.from_axis_angle(axis_angle,degrees=True))
assert geom_equal(modified,default)
assert geom_equal(default,modified)
@pytest.mark.parametrize('Eulers',[[32.0,68.0,21.0],
[0.0,32.0,240.0]])
def test_rotate(self,default,update,reference_dir,Eulers):
modified = default.copy()
modified.rotate(Rotation.from_Eulers(Eulers,degrees=True))
modified = default.rotate(Rotation.from_Eulers(Eulers,degrees=True))
tag = f'Eulers={util.srepr(Eulers,"-")}'
reference = reference_dir/f'rotate_{tag}.geom'
if update: modified.to_file(reference)
assert geom_equal(modified,Geom.from_file(reference))
assert geom_equal(Geom.from_file(reference),
modified)
def test_canvas(self,default):
grid = default.grid
grid_add = np.random.randint(0,30,(3))
modified = default.copy()
modified.canvas(modified.grid + grid_add)
e = default.grid
assert np.all(modified.microstructure[:e[0],:e[1],:e[2]] == default.microstructure)
modified = default.canvas(grid + grid_add)
assert np.all(modified.microstructure[:grid[0],:grid[1],:grid[2]] == default.microstructure)
@pytest.mark.parametrize('center1,center2',[(np.random.random(3)*.5,np.random.random(3)),
@pytest.mark.parametrize('center1,center2',[(np.random.random(3)*.5,np.random.random()*8),
(np.random.randint(4,8,(3)),np.random.randint(9,12,(3)))])
@pytest.mark.parametrize('diameter',[np.random.random(3)*.5,
np.random.randint(4,10,(3))])
def test_add_primitive(self,diameter,center1,center2):
np.random.randint(4,10,(3)),
np.random.rand(),
np.random.randint(30)])
@pytest.mark.parametrize('exponent',[np.random.random(3)*.5,
np.random.randint(4,10,(3)),
np.random.rand()*4,
np.random.randint(20)])
def test_add_primitive_shift(self,center1,center2,diameter,exponent):
"""Same volume fraction for periodic microstructures and different center."""
o = np.random.random(3)-.5
g = np.random.randint(8,32,(3))
s = np.random.random(3)+.5
G_1 = Geom(np.ones(g,'i'),s,o)
G_2 = Geom(np.ones(g,'i'),s,o)
G_1.add_primitive(diameter,center1,1)
G_2.add_primitive(diameter,center2,1)
G_1 = Geom(np.ones(g,'i'),s,o).add_primitive(diameter,center1,exponent)
G_2 = Geom(np.ones(g,'i'),s,o).add_primitive(diameter,center2,exponent)
assert np.count_nonzero(G_1.microstructure!=2) == np.count_nonzero(G_2.microstructure!=2)
@pytest.mark.parametrize('center',[np.random.randint(4,10,(3)),
np.random.randint(2,10),
np.random.rand()*4,
np.random.rand(3)*10])
@pytest.mark.parametrize('inverse',[True,False])
@pytest.mark.parametrize('periodic',[True,False])
def test_add_primitive_rotation(self,center,inverse,periodic):
"""Rotation should not change result for sphere (except for discretization errors)."""
g = np.array([32,32,32])
fill = np.random.randint(10)+2
eu=np.array([np.random.randint(4),np.random.randint(2),np.random.randint(4)])*.5*np.pi
G_1 = Geom(np.ones(g,'i'),[1.,1.,1.]).add_primitive(.3,center,1,fill,inverse=inverse,periodic=periodic)
G_2 = Geom(np.ones(g,'i'),[1.,1.,1.]).add_primitive(.3,center,1,fill,Rotation.from_Eulers(eu),inverse,periodic=periodic)
assert geom_equal(G_1,G_2)
@pytest.mark.parametrize('trigger',[[1],[]])
def test_vicinity_offset(self,trigger):
offset = np.random.randint(2,4)
@ -248,8 +312,7 @@ class TestGeom:
if len(trigger) > 0:
m2[m==1] = 1
geom = Geom(m,np.random.rand(3))
geom.vicinity_offset(vicinity,offset,trigger=trigger)
geom = Geom(m,np.random.rand(3)).vicinity_offset(vicinity,offset,trigger=trigger)
assert np.all(m2==geom.microstructure)

48
python/tests/test_VTK.py
View File

@ -13,8 +13,19 @@ def reference_dir(reference_dir_base):
"""Directory containing reference results."""
return reference_dir_base/'VTK'
@pytest.fixture
def default():
"""Simple VTK."""
grid = np.array([5,6,7],int)
size = np.array([.6,1.,.5])
return VTK.from_rectilinearGrid(grid,size)
class TestVTK:
@pytest.fixture(autouse=True)
def _execution_stamp(self, execution_stamp):
print('patched damask.util.execution_stamp')
def test_rectilinearGrid(self,tmp_path):
grid = np.random.randint(5,10,3)*2
size = np.random.random(3) + 1.0
@ -77,10 +88,36 @@ class TestVTK:
@pytest.mark.parametrize('name,dataset_type',[('this_file_does_not_exist.vtk', None),
('this_file_does_not_exist.vtk','vtk'),
('this_file_does_not_exist.vtx', None)])
def test_invalid_dataset_type(self,dataset_type,name):
def test_invalid_dataset_type(self,name,dataset_type):
with pytest.raises(TypeError):
VTK.from_file('this_file_does_not_exist.vtk',dataset_type)
VTK.from_file(name,dataset_type)
def test_invalid_extension_write(self,default):
with pytest.raises(ValueError):
default.write('default.txt')
def test_invalid_get(self,default):
with pytest.raises(ValueError):
default.get('does_not_exist')
def test_invalid_add_shape(self,default):
with pytest.raises(ValueError):
default.add(np.ones(3),'valid')
def test_invalid_add_missing_label(self,default):
data = np.random.randint(9,size=np.prod(np.array(default.vtk_data.GetDimensions())-1))
with pytest.raises(ValueError):
default.add(data)
def test_invalid_add_type(self,default):
with pytest.raises(TypeError):
default.add('invalid_type','valid')
def test_comments(self,tmp_path,default):
default.add_comments(['this is a comment'])
default.write(tmp_path/'with_comments',parallel=False)
new = VTK.from_file(tmp_path/'with_comments.vtr')
assert new.get_comments() == ['this is a comment']
def test_compare_reference_polyData(self,update,reference_dir,tmp_path):
points=np.dstack((np.linspace(0.,1.,10),np.linspace(0.,2.,10),np.linspace(-1.,1.,10))).squeeze()
@ -90,7 +127,8 @@ class TestVTK:
polyData.write(reference_dir/'polyData')
else:
reference = VTK.from_file(reference_dir/'polyData.vtp')
assert polyData.__repr__() == reference.__repr__()
assert polyData.__repr__() == reference.__repr__() and \
np.allclose(polyData.get('coordinates'),points)
def test_compare_reference_rectilinearGrid(self,update,reference_dir,tmp_path):
grid = np.array([5,6,7],int)
@ -104,5 +142,5 @@ class TestVTK:
rectilinearGrid.write(reference_dir/'rectilinearGrid')
else:
reference = VTK.from_file(reference_dir/'rectilinearGrid.vtr')
assert rectilinearGrid.__repr__() == reference.__repr__()
assert rectilinearGrid.__repr__() == reference.__repr__() and \
np.allclose(rectilinearGrid.get('cell'),c)