Merge branch 'development' into consistent-naming
This commit is contained in:
Sharan Roongta
commit
05ca3c3d7f
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@ -3,6 +3,3 @@
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*.xdmf
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*.sta
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*.vt*
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*.geom
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*.seeds
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postProc
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@ -2,7 +2,6 @@ import copy
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import numpy as np
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from . import grid_filters
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from . import Config
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from . import Lattice
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from . import Rotation
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@ -26,7 +25,7 @@ class ConfigMaterial(Config):
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@staticmethod
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def from_table(table,coordinates=None,constituents={},**kwargs):
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def from_table(table,constituents={},**kwargs):
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"""
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Load from an ASCII table.
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@ -34,10 +33,6 @@ class ConfigMaterial(Config):
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----------
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table : damask.Table
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Table that contains material information.
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coordinates : str, optional
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Label of spatial coordiates. Used for sorting and performing a
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sanity check. Default to None, in which case no sorting or checking is
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peformed.
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constituents : dict, optional
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Entries for 'constituents'. The key is the name and the value specifies
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the label of the data column in the table
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@ -54,7 +49,7 @@ class ConfigMaterial(Config):
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pos pos pos qu qu qu qu phase homog
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0 0 0 0 0.19 0.8 0.24 -0.51 Aluminum SX
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1 1 0 0 0.8 0.19 0.24 -0.51 Steel SX
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>>> cm.from_table(t,'pos',{'O':'qu','phase':'phase'},homogenization='homog')
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>>> cm.from_table(t,{'O':'qu','phase':'phase'},homogenization='homog')
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material:
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- constituents:
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- O: [0.19, 0.8, 0.24, -0.51]
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@ -68,17 +63,12 @@ class ConfigMaterial(Config):
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homogenization: SX
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"""
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if coordinates is not None:
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t = table.sort_by([f'{i}_{coordinates}' for i in range(3,0,-1)])
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grid_filters.coord0_check(t.get(coordinates))
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else:
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t = table
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constituents_ = {k:t.get(v) for k,v in constituents.items()}
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kwargs_ = {k:t.get(v) for k,v in kwargs.items()}
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constituents_ = {k:table.get(v) for k,v in constituents.items()}
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kwargs_ = {k:table.get(v) for k,v in kwargs.items()}
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_,idx = np.unique(np.hstack(list({**constituents_,**kwargs_}.values())),return_index=True,axis=0)
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idx = np.sort(idx)
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constituents_ = {k:v[idx].squeeze() for k,v in constituents_.items()}
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kwargs_ = {k:v[idx].squeeze() for k,v in kwargs_.items()}
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@ -229,19 +219,18 @@ class ConfigMaterial(Config):
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Parameters
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----------
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constituents : dict
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Entries for 'constituents'. The key is the name and the value specifies
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the label of the data column in the table
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Entries for 'constituents' as key-value pair.
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**kwargs
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Keyword arguments where the key is the name and the value specifies
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the label of the data column in the table
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Key-value pairs.
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Examples
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--------
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>>> import damask
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>>> m = damask.ConfigMaterial()
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>>> O = damask.Rotation.from_random(3).as_quaternion()
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>>> phase = ['Aluminum','Steel','Aluminum']
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>>> m.material_add(constituents={'phase':phase,'O':O},homogenization='SX')
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>>> m = damask.ConfigMaterial().material_add(constituents={'phase':phase,'O':O},
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... homogenization='SX')
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>>> m
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material:
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- constituents:
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- O: [0.577764, -0.146299, -0.617669, 0.513010]
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@ -264,15 +253,14 @@ class ConfigMaterial(Config):
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for k,v in kwargs.items():
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if hasattr(v,'__len__') and not isinstance(v,str):
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if len(v) != len(c):
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raise ValueError('len mismatch 1')
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raise ValueError('Cannot add entries of different length')
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for i,vv in enumerate(v):
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c[i][k] = [w.item() for w in vv] if isinstance(vv,np.ndarray) else vv.item()
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else:
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for i in range(len(c)):
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c[i][k] = v
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dup = copy.deepcopy(self)
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if 'material' not in dup: dup['material'] = []
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dup['material'] +=c
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dup['material'] = dup['material'] + c if 'material' in dup else c
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return dup
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@ -288,7 +276,7 @@ class ConfigMaterial(Config):
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for k,v in kwargs.items():
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if hasattr(v,'__len__') and not isinstance(v,str):
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if len(v) != N_material:
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raise ValueError('len mismatch 2')
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raise ValueError('Cannot add entries of different length')
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for i,vv in enumerate(np.array(v)):
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m[i][0][k] = [w.item() for w in vv] if isinstance(vv,np.ndarray) else vv.item()
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else:
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@ -4,6 +4,7 @@ from functools import partial
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from os import path
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import numpy as np
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import pandas as pd
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import h5py
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from scipy import ndimage,spatial
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@ -254,21 +255,26 @@ class Geom:
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table : damask.Table
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Table that contains material information.
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coordinates : str
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Label of the column containing the spatial coordinates.
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Label of the column containing the vector of spatial coordinates.
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Need to be ordered (1./x fast, 3./z slow).
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labels : str or list of str
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Label(s) of the columns containing the material definition.
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Each unique combintation of values results in a material.
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"""
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t = table.sort_by([f'{i}_{coordinates}' for i in range(3,0,-1)])
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grid,size,origin = grid_filters.cell_coord0_gridSizeOrigin(t.get(coordinates))
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grid,size,origin = grid_filters.cell_coord0_gridSizeOrigin(table.get(coordinates))
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labels_ = [labels] if isinstance(labels,str) else labels
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_,unique_inverse = np.unique(np.hstack([t.get(l) for l in labels_]),return_inverse=True,axis=0)
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ma = unique_inverse.reshape(grid,order='F') + 1
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unique,unique_inverse = np.unique(np.hstack([table.get(l) for l in labels_]),return_inverse=True,axis=0)
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if len(unique) == grid.prod():
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ma = np.arange(grid.prod())
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else:
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from_ma = pd.unique(unique_inverse)
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sort_idx = np.argsort(from_ma)
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idx = np.searchsorted(from_ma,unique_inverse,sorter = sort_idx)
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ma = np.arange(from_ma.size)[sort_idx][idx]
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return Geom(ma,size,origin,util.execution_stamp('Geom','from_table'))
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return Geom(ma.reshape(grid,order='F'),size,origin,util.execution_stamp('Geom','from_table'))
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@staticmethod
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@ -417,7 +423,7 @@ class Geom:
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Number of periods per unit cell. Defaults to 1.
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materials : (int, int), optional
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Material IDs. Defaults to (1,2).
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Notes
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-----
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The following triply-periodic minimal surfaces are implemented:
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@ -687,12 +693,10 @@ class Geom:
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def renumber(self):
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"""Renumber sorted material indices to 1,...,N."""
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renumbered = np.empty(self.grid,dtype=self.material.dtype)
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for i, oldID in enumerate(np.unique(self.material)):
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renumbered = np.where(self.material == oldID, i+1, renumbered)
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"""Renumber sorted material indices to 0,...,N-1."""
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_,renumbered = np.unique(self.material,return_inverse=True)
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return Geom(material = renumbered,
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return Geom(material = renumbered.reshape(self.grid),
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size = self.size,
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origin = self.origin,
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comments = self.comments+[util.execution_stamp('Geom','renumber')],
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@ -783,11 +787,13 @@ class Geom:
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New material indices.
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"""
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substituted = self.material.copy()
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for from_ms,to_ms in zip(from_material,to_material):
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substituted[self.material==from_ms] = to_ms
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def mp(entry,mapper):
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return mapper[entry] if entry in mapper else entry
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mp = np.vectorize(mp)
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mapper = dict(zip(from_material,to_material))
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return Geom(material = substituted,
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return Geom(material = mp(self.material,mapper).reshape(self.grid),
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size = self.size,
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origin = self.origin,
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comments = self.comments+[util.execution_stamp('Geom','substitute')],
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@ -1,8 +1,10 @@
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import os
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import pytest
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import numpy as np
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from damask import ConfigMaterial
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from damask import Table
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@pytest.fixture
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def reference_dir(reference_dir_base):
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@ -74,3 +76,14 @@ class TestConfigMaterial:
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material_config = ConfigMaterial.load(reference_dir/'material.yaml')
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new = material_config.material_rename_homogenization({'Taylor':'isostrain'})
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assert not new.is_complete
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def test_from_table(self):
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N = np.random.randint(3,10)
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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
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t = Table(a,{'varying':2,'constant':2})
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c = ConfigMaterial.from_table(t,constituents={'a':'varying','b':'1_constant'},c='2_constant')
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assert len(c['material']) == N
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for i,m in enumerate(c['material']):
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c = m['constituents'][0]
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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
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from damask import VTK
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from damask import Geom
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from damask import Table
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from damask import Rotation
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from damask import util
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from damask import grid_filters
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def geom_equal(a,b):
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@ -176,6 +178,7 @@ class TestGeom:
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material = default.material.copy()
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for m in np.unique(material):
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material[material==m] = material.max() + np.random.randint(1,30)
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default.material -= 1
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modified = Geom(material,
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default.size,
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default.origin)
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@ -194,6 +197,13 @@ class TestGeom:
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modified.substitute(np.arange(default.material.max())+1+offset,
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np.arange(default.material.max())+1))
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def test_substitute_invariant(self,default):
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f = np.unique(default.material.flatten())[:np.random.randint(1,default.material.max())]
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t = np.random.permutation(f)
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modified = default.substitute(f,t)
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assert np.array_equiv(t,f) or (not geom_equal(modified,default))
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assert geom_equal(default, modified.substitute(t,f))
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@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]),
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np.array([1,0,0,175]),np.array([0,-1,0,178]),np.array([0,0,1,180])])
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@ -363,3 +373,14 @@ class TestGeom:
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grid = np.ones(3,dtype=int)*64
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geom = Geom.from_minimal_surface(grid,np.ones(3),surface,threshold)
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assert np.isclose(np.count_nonzero(geom.material==1)/np.prod(geom.grid),.5,rtol=1e-3)
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def test_from_table(self):
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grid = np.random.randint(60,100,3)
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size = np.ones(3)+np.random.rand(3)
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coords = grid_filters.cell_coord0(grid,size).reshape(-1,3,order='F')
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z=np.ones(grid.prod())
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z[grid[:2].prod()*int(grid[2]/2):]=0
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t = Table(np.column_stack((coords,z)),{'coords':3,'z':1})
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g = Geom.from_table(t,'coords',['1_coords','z'])
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assert g.N_materials == g.grid[0]*2 and (g.material[:,:,-1]-g.material[:,:,0] == grid[0]).all()
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