Merge branch 'development' into consistent-naming

This commit is contained in:
Sharan Roongta 2020-10-30 14:00:50 +01:00
commit 05ca3c3d7f
6 changed files with 71 additions and 46 deletions

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@ -1 +1 @@
v3.0.0-alpha-567-g21f095c9d
v3.0.0-alpha-594-g46e5023f8

3
examples/.gitignore vendored
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@ -3,6 +3,3 @@
*.xdmf
*.sta
*.vt*
*.geom
*.seeds
postProc

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@ -2,7 +2,6 @@ import copy
import numpy as np
from . import grid_filters
from . import Config
from . import Lattice
from . import Rotation
@ -26,7 +25,7 @@ class ConfigMaterial(Config):
@staticmethod
def from_table(table,coordinates=None,constituents={},**kwargs):
def from_table(table,constituents={},**kwargs):
"""
Load from an ASCII table.
@ -34,10 +33,6 @@ class ConfigMaterial(Config):
----------
table : damask.Table
Table that contains material information.
coordinates : str, optional
Label of spatial coordiates. Used for sorting and performing a
sanity check. Default to None, in which case no sorting or checking is
peformed.
constituents : dict, optional
Entries for 'constituents'. The key is the name and the value specifies
the label of the data column in the table
@ -54,7 +49,7 @@ class ConfigMaterial(Config):
pos pos pos qu qu qu qu phase homog
0 0 0 0 0.19 0.8 0.24 -0.51 Aluminum SX
1 1 0 0 0.8 0.19 0.24 -0.51 Steel SX
>>> cm.from_table(t,'pos',{'O':'qu','phase':'phase'},homogenization='homog')
>>> cm.from_table(t,{'O':'qu','phase':'phase'},homogenization='homog')
material:
- constituents:
- O: [0.19, 0.8, 0.24, -0.51]
@ -68,17 +63,12 @@ class ConfigMaterial(Config):
homogenization: SX
"""
if coordinates is not None:
t = table.sort_by([f'{i}_{coordinates}' for i in range(3,0,-1)])
grid_filters.coord0_check(t.get(coordinates))
else:
t = table
constituents_ = {k:t.get(v) for k,v in constituents.items()}
kwargs_ = {k:t.get(v) for k,v in kwargs.items()}
constituents_ = {k:table.get(v) for k,v in constituents.items()}
kwargs_ = {k:table.get(v) for k,v in kwargs.items()}
_,idx = np.unique(np.hstack(list({**constituents_,**kwargs_}.values())),return_index=True,axis=0)
idx = np.sort(idx)
constituents_ = {k:v[idx].squeeze() for k,v in constituents_.items()}
kwargs_ = {k:v[idx].squeeze() for k,v in kwargs_.items()}
@ -229,19 +219,18 @@ class ConfigMaterial(Config):
Parameters
----------
constituents : dict
Entries for 'constituents'. The key is the name and the value specifies
the label of the data column in the table
Entries for 'constituents' as key-value pair.
**kwargs
Keyword arguments where the key is the name and the value specifies
the label of the data column in the table
Key-value pairs.
Examples
--------
>>> import damask
>>> m = damask.ConfigMaterial()
>>> O = damask.Rotation.from_random(3).as_quaternion()
>>> phase = ['Aluminum','Steel','Aluminum']
>>> m.material_add(constituents={'phase':phase,'O':O},homogenization='SX')
>>> m = damask.ConfigMaterial().material_add(constituents={'phase':phase,'O':O},
... homogenization='SX')
>>> m
material:
- constituents:
- O: [0.577764, -0.146299, -0.617669, 0.513010]
@ -264,15 +253,14 @@ class ConfigMaterial(Config):
for k,v in kwargs.items():
if hasattr(v,'__len__') and not isinstance(v,str):
if len(v) != len(c):
raise ValueError('len mismatch 1')
raise ValueError('Cannot add entries of different length')
for i,vv in enumerate(v):
c[i][k] = [w.item() for w in vv] if isinstance(vv,np.ndarray) else vv.item()
else:
for i in range(len(c)):
c[i][k] = v
dup = copy.deepcopy(self)
if 'material' not in dup: dup['material'] = []
dup['material'] +=c
dup['material'] = dup['material'] + c if 'material' in dup else c
return dup
@ -288,7 +276,7 @@ class ConfigMaterial(Config):
for k,v in kwargs.items():
if hasattr(v,'__len__') and not isinstance(v,str):
if len(v) != N_material:
raise ValueError('len mismatch 2')
raise ValueError('Cannot add entries of different length')
for i,vv in enumerate(np.array(v)):
m[i][0][k] = [w.item() for w in vv] if isinstance(vv,np.ndarray) else vv.item()
else:

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@ -4,6 +4,7 @@ from functools import partial
from os import path
import numpy as np
import pandas as pd
import h5py
from scipy import ndimage,spatial
@ -254,21 +255,26 @@ class Geom:
table : damask.Table
Table that contains material information.
coordinates : str
Label of the column containing the spatial coordinates.
Label of the column containing the vector of spatial coordinates.
Need to be ordered (1./x fast, 3./z slow).
labels : str or list of str
Label(s) of the columns containing the material definition.
Each unique combintation of values results in a material.
"""
t = table.sort_by([f'{i}_{coordinates}' for i in range(3,0,-1)])
grid,size,origin = grid_filters.cell_coord0_gridSizeOrigin(t.get(coordinates))
grid,size,origin = grid_filters.cell_coord0_gridSizeOrigin(table.get(coordinates))
labels_ = [labels] if isinstance(labels,str) else labels
_,unique_inverse = np.unique(np.hstack([t.get(l) for l in labels_]),return_inverse=True,axis=0)
ma = unique_inverse.reshape(grid,order='F') + 1
unique,unique_inverse = np.unique(np.hstack([table.get(l) for l in labels_]),return_inverse=True,axis=0)
if len(unique) == grid.prod():
ma = np.arange(grid.prod())
else:
from_ma = pd.unique(unique_inverse)
sort_idx = np.argsort(from_ma)
idx = np.searchsorted(from_ma,unique_inverse,sorter = sort_idx)
ma = np.arange(from_ma.size)[sort_idx][idx]
return Geom(ma,size,origin,util.execution_stamp('Geom','from_table'))
return Geom(ma.reshape(grid,order='F'),size,origin,util.execution_stamp('Geom','from_table'))
@staticmethod
@ -687,12 +693,10 @@ class Geom:
def renumber(self):
"""Renumber sorted material indices to 1,...,N."""
renumbered = np.empty(self.grid,dtype=self.material.dtype)
for i, oldID in enumerate(np.unique(self.material)):
renumbered = np.where(self.material == oldID, i+1, renumbered)
"""Renumber sorted material indices to 0,...,N-1."""
_,renumbered = np.unique(self.material,return_inverse=True)
return Geom(material = renumbered,
return Geom(material = renumbered.reshape(self.grid),
size = self.size,
origin = self.origin,
comments = self.comments+[util.execution_stamp('Geom','renumber')],
@ -783,11 +787,13 @@ class Geom:
New material indices.
"""
substituted = self.material.copy()
for from_ms,to_ms in zip(from_material,to_material):
substituted[self.material==from_ms] = to_ms
def mp(entry,mapper):
return mapper[entry] if entry in mapper else entry
return Geom(material = substituted,
mp = np.vectorize(mp)
mapper = dict(zip(from_material,to_material))
return Geom(material = mp(self.material,mapper).reshape(self.grid),
size = self.size,
origin = self.origin,
comments = self.comments+[util.execution_stamp('Geom','substitute')],

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@ -1,8 +1,10 @@
import os
import pytest
import numpy as np
from damask import ConfigMaterial
from damask import Table
@pytest.fixture
def reference_dir(reference_dir_base):
@ -74,3 +76,14 @@ class TestConfigMaterial:
material_config = ConfigMaterial.load(reference_dir/'material.yaml')
new = material_config.material_rename_homogenization({'Taylor':'isostrain'})
assert not new.is_complete
def test_from_table(self):
N = np.random.randint(3,10)
a = np.vstack((np.hstack((np.arange(N),np.arange(N)[::-1])),np.ones(N*2),np.zeros(N*2),np.ones(N*2))).T
t = Table(a,{'varying':2,'constant':2})
c = ConfigMaterial.from_table(t,constituents={'a':'varying','b':'1_constant'},c='2_constant')
assert len(c['material']) == N
for i,m in enumerate(c['material']):
c = m['constituents'][0]
assert m['c'] == 1 and c['b'] == 0 and c['a'] == [i,1]

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@ -3,8 +3,10 @@ import numpy as np
from damask import VTK
from damask import Geom
from damask import Table
from damask import Rotation
from damask import util
from damask import grid_filters
def geom_equal(a,b):
@ -176,6 +178,7 @@ class TestGeom:
material = default.material.copy()
for m in np.unique(material):
material[material==m] = material.max() + np.random.randint(1,30)
default.material -= 1
modified = Geom(material,
default.size,
default.origin)
@ -194,6 +197,13 @@ class TestGeom:
modified.substitute(np.arange(default.material.max())+1+offset,
np.arange(default.material.max())+1))
def test_substitute_invariant(self,default):
f = np.unique(default.material.flatten())[:np.random.randint(1,default.material.max())]
t = np.random.permutation(f)
modified = default.substitute(f,t)
assert np.array_equiv(t,f) or (not geom_equal(modified,default))
assert geom_equal(default, modified.substitute(t,f))
@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])])
@ -363,3 +373,14 @@ class TestGeom:
grid = np.ones(3,dtype=int)*64
geom = Geom.from_minimal_surface(grid,np.ones(3),surface,threshold)
assert np.isclose(np.count_nonzero(geom.material==1)/np.prod(geom.grid),.5,rtol=1e-3)
def test_from_table(self):
grid = np.random.randint(60,100,3)
size = np.ones(3)+np.random.rand(3)
coords = grid_filters.cell_coord0(grid,size).reshape(-1,3,order='F')
z=np.ones(grid.prod())
z[grid[:2].prod()*int(grid[2]/2):]=0
t = Table(np.column_stack((coords,z)),{'coords':3,'z':1})
g = Geom.from_table(t,'coords',['1_coords','z'])
assert g.N_materials == g.grid[0]*2 and (g.material[:,:,-1]-g.material[:,:,0] == grid[0]).all()