Merge branch '238-tail_repack-behavior-and-use' into 'development'

simplifications of Python code

Closes #238

See merge request damask/DAMASK!684
This commit is contained in:
Philip Eisenlohr 2022-12-13 18:32:19 +00:00
commit 5d2d611898
17 changed files with 78 additions and 139 deletions

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@ -399,7 +399,7 @@ class Colormap(mpl.colors.ListedColormap):
"""
labels = {'RGBA':4} if self.colors.shape[1] == 4 else {'RGB': 3}
t = Table(labels,self.colors,f'Creator: {util.execution_stamp("Colormap")}')
t = Table(labels,self.colors,[f'Creator: {util.execution_stamp("Colormap")}'])
t.save(self._get_file_handle(fname,'.txt'))

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@ -4,7 +4,7 @@ import warnings
import multiprocessing as mp
from functools import partial
import typing
from typing import Optional, Union, TextIO, List, Sequence, Dict
from typing import Optional, Union, TextIO, Sequence, Dict
from pathlib import Path
import numpy as np
@ -18,7 +18,7 @@ from . import grid_filters
from . import Rotation
from . import Table
from . import Colormap
from ._typehints import FloatSequence, IntSequence, IntCollection, NumpyRngSeed
from ._typehints import FloatSequence, IntSequence, NumpyRngSeed
try:
import numba as nb # type: ignore
except ImportError:
@ -66,8 +66,9 @@ class Grid:
self.size = size # type: ignore
self.origin = origin # type: ignore
self.initial_conditions = {} if initial_conditions is None else initial_conditions
comments_ = [comments] if isinstance(comments,str) else comments
self.comments = [] if comments_ is None else [str(c) for c in comments_]
self.comments = [] if comments is None else \
[comments] if isinstance(comments,str) else \
[str(c) for c in comments]
def __repr__(self) -> str:
"""
@ -183,17 +184,6 @@ class Grid:
self._ic = ic
@property
def comments(self) -> List[str]:
"""Comments, e.g. history of operations."""
return self._comments
@comments.setter
def comments(self,
comments: Union[str, Sequence[str]]):
self._comments = [str(c) for c in comments] if isinstance(comments,Sequence) else [str(comments)]
@property
def cells(self) -> np.ndarray:
"""Number of cells in x,y,z direction."""
@ -226,14 +216,13 @@ class Grid:
v = VTK.load(fname if str(fname).endswith('.vti') else str(fname)+'.vti')
cells = np.array(v.vtk_data.GetDimensions())-1
bbox = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
comments = v.comments
ic = {label:v.get(label).reshape(cells,order='F') for label in set(v.labels['Cell Data']) - {'material'}}
return Grid(material = v.get('material').reshape(cells,order='F'),
size = bbox[1] - bbox[0],
origin = bbox[0],
initial_conditions = ic,
comments = comments,
comments = v.comments,
)
@ -1103,7 +1092,7 @@ class Grid:
def clean(self,
distance: float = np.sqrt(3),
selection: Optional[IntCollection] = None,
selection: Optional[IntSequence] = None,
invert_selection: bool = False,
periodic: bool = True,
rng_seed: Optional[NumpyRngSeed] = None) -> 'Grid':
@ -1115,7 +1104,7 @@ class Grid:
distance : float, optional
Voxel distance checked for presence of other materials.
Defaults to sqrt(3).
selection : (collection of) int, optional
selection : (sequence of) int, optional
Material IDs to consider. Defaults to all.
invert_selection : bool, optional
Consider all material IDs except those in selection. Defaults to False.
@ -1136,7 +1125,7 @@ class Grid:
"""
def most_frequent(stencil: np.ndarray,
selection: Union[None,set],
selection: Union[None,np.ndarray],
rng: np.random.Generator):
me = stencil[stencil.size//2]
if selection is None or me in selection:
@ -1152,8 +1141,8 @@ class Grid:
xx,yy,zz = np.meshgrid(ext,ext,ext)
footprint = xx**2+yy**2+zz**2 <= distance**2+distance*1e-8
selection_ = None if selection is None else \
set(self.material.flatten()) - set(util.aslist(selection)) if invert_selection else \
set(self.material.flatten()) & set(util.aslist(selection))
np.setdiff1d(self.material,selection) if invert_selection else \
np.intersect1d(self.material,selection)
material = ndimage.generic_filter(
self.material,
most_frequent,
@ -1265,7 +1254,7 @@ class Grid:
def vicinity_offset(self,
distance: float = np.sqrt(3),
offset: Optional[int] = None,
selection: Optional[IntCollection] = None,
selection: Optional[IntSequence] = None,
invert_selection: bool = False,
periodic: bool = True) -> 'Grid':
"""
@ -1282,7 +1271,7 @@ class Grid:
offset : int, optional
Offset (positive or negative) to tag material IDs.
Defaults to material.max()+1.
selection : (collection of) int, optional
selection : (sequence of) int, optional
Material IDs that trigger an offset.
Defaults to any other than own material ID.
invert_selection : bool, optional
@ -1315,8 +1304,8 @@ class Grid:
footprint = xx**2+yy**2+zz**2 <= distance**2+distance*1e-8
offset_ = np.nanmax(self.material)+1 if offset is None else offset
selection_ = None if selection is None else \
np.array(list(set(self.material.flatten()) - set(util.aslist(selection)))) if invert_selection else \
np.array(list(set(self.material.flatten()) & set(util.aslist(selection))))
np.setdiff1d(self.material,selection) if invert_selection else \
np.intersect1d(self.material,selection)
mask = ndimage.generic_filter(self.material,
tainted_neighborhood,

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@ -1874,7 +1874,7 @@ class Result:
if self.version_minor >= 13:
creator = f.attrs['creator'] if h5py3 else f.attrs['creator'].decode()
created = f.attrs['created'] if h5py3 else f.attrs['created'].decode()
v.comments += f'{creator} ({created})'
v.comments += [f'{creator} ({created})']
for inc in util.show_progress(self.visible['increments']):

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@ -29,8 +29,9 @@ class Table:
Additional, human-readable information.
"""
comments_ = [comments] if isinstance(comments,str) else comments
self.comments = [] if comments_ is None else [str(c) for c in comments_]
self.comments = [] if comments is None else \
[comments] if isinstance(comments,str) else \
[str(c) for c in comments]
self.shapes = { k:(v,) if isinstance(v,(np.int64,np.int32,int)) else v for k,v in shapes.items() }
self.data = pd.DataFrame(data=data)
self._relabel('uniform')
@ -185,16 +186,6 @@ class Table:
self.data.columns = self._label(self.shapes,how) # type: ignore
def _add_comment(self,
label: str,
shape: Tuple[int, ...],
info: Optional[str] = None):
if info is not None:
specific = f'{label}{" "+str(shape) if np.prod(shape,dtype=np.int64) > 1 else ""}: {info}'
general = util.execution_stamp('Table')
self.comments.append(f'{specific} / {general}')
def isclose(self,
other: 'Table',
rtol: float = 1e-5,
@ -402,13 +393,15 @@ class Table:
Updated table.
"""
dup = self.copy()
dup._add_comment(label, data.shape[1:], info)
def add_comment(label: str, shape: Tuple[int, ...],info: str) -> List[str]:
specific = f'{label}{" "+str(shape) if np.prod(shape,dtype=np.int64) > 1 else ""}: {info}'
general = util.execution_stamp('Table')
return [f'{specific} / {general}']
if m := re.match(r'(.*)\[((\d+,)*(\d+))\]',label):
key = m.group(1)
else:
key = label
dup = self.copy()
if info is not None: self.comments += add_comment(label,data.shape[1:],info)
key = m.group(1) if (m := re.match(r'(.*)\[((\d+,)*(\d+))\]',label)) else label
if key in dup.shapes:

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@ -1,6 +1,6 @@
"""Functionality for typehints."""
from typing import Sequence, Union, Literal, TextIO, Collection
from typing import Sequence, Union, Literal, TextIO
from pathlib import Path
import numpy as np
@ -8,7 +8,6 @@ import numpy as np
FloatSequence = Union[np.ndarray,Sequence[float]]
IntSequence = Union[np.ndarray,Sequence[int]]
IntCollection = Union[np.ndarray,Collection[int]]
FileHandle = Union[TextIO, str, Path]
CrystalFamily = Union[None,Literal['triclinic', 'monoclinic', 'orthorhombic', 'tetragonal', 'hexagonal', 'cubic']]
CrystalLattice = Union[None,Literal['aP', 'mP', 'mS', 'oP', 'oS', 'oI', 'oF', 'tP', 'tI', 'hP', 'cP', 'cI', 'cF']]

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@ -104,22 +104,19 @@ class VTK:
@comments.setter
def comments(self,
comments: Union[str, Sequence[str]]):
comments: Sequence[str]):
"""
Set comments.
Parameters
----------
comments : (sequence of) str
comments : sequence of str
Comments.
"""
s = vtk.vtkStringArray()
s.SetName('comments')
comments_ = util.tail_repack(comments,self.comments) if comments[:len(self.comments)] == self.comments else \
[comments] if isinstance(comments,str) else \
comments
for c in comments_:
for c in comments:
s.InsertNextValue(c)
self.vtk_data.GetFieldData().AddArray(s)
@ -478,13 +475,13 @@ class VTK:
_add_array(dup.vtk_data,
label,
np.where(data.mask,data.fill_value,data) if isinstance(data,np.ma.MaskedArray) else data)
if info is not None: dup.comments += f'{label}: {info}'
if info is not None: dup.comments += [f'{label}: {info}']
else:
raise ValueError('no label defined for data')
elif isinstance(table,Table):
for l in table.labels:
_add_array(dup.vtk_data,l,table.get(l))
if info is not None: dup.comments += f'{l}: {info}'
if info is not None: dup.comments += [f'{l}: {info}']
else:
raise TypeError

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@ -6,7 +6,7 @@ from scipy import spatial as _spatial
import numpy as _np
from ._typehints import FloatSequence as _FloatSequence, IntSequence as _IntSequence, \
NumpyRngSeed as _NumpyRngSeed, IntCollection as _IntCollection
NumpyRngSeed as _NumpyRngSeed
from . import util as _util
from . import grid_filters as _grid_filters
@ -106,7 +106,7 @@ def from_Poisson_disc(size: _FloatSequence,
def from_grid(grid,
selection: _Optional[_IntCollection] = None,
selection: _Optional[_IntSequence] = None,
invert_selection: bool = False,
average: bool = False,
periodic: bool = True) -> _Tuple[_np.ndarray, _np.ndarray]:
@ -117,7 +117,7 @@ def from_grid(grid,
----------
grid : damask.Grid
Grid from which the material IDs are used as seeds.
selection : (collection of) int, optional
selection : (sequence of) int, optional
Material IDs to consider.
invert_selection : bool, optional
Consider all material IDs except those in selection. Defaults to False.
@ -134,7 +134,7 @@ def from_grid(grid,
"""
material = grid.material.reshape((-1,1),order='F')
mask = _np.full(grid.cells.prod(),True,dtype=bool) if selection is None else \
_np.isin(material,_util.aslist(selection),invert=invert_selection).flatten()
_np.isin(material,selection,invert=invert_selection).flatten()
coords = _grid_filters.coordinates0_point(grid.cells,grid.size).reshape(-1,3,order='F')
if not average:

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@ -11,16 +11,15 @@ import fractions as _fractions
from collections import abc as _abc
from functools import reduce as _reduce, partial as _partial
from typing import Optional as _Optional, Callable as _Callable, Union as _Union, Iterable as _Iterable, \
Sequence as _Sequence, Dict as _Dict, List as _List, Tuple as _Tuple, Literal as _Literal, \
Any as _Any, Collection as _Collection, TextIO as _TextIO
Dict as _Dict, List as _List, Tuple as _Tuple, Literal as _Literal, \
Any as _Any, TextIO as _TextIO
from pathlib import Path as _Path
import numpy as _np
import h5py as _h5py
from . import version as _version
from ._typehints import FloatSequence as _FloatSequence, NumpyRngSeed as _NumpyRngSeed, IntCollection as _IntCollection, \
FileHandle as _FileHandle
from ._typehints import FloatSequence as _FloatSequence, NumpyRngSeed as _NumpyRngSeed, FileHandle as _FileHandle
# https://svn.blender.org/svnroot/bf-blender/trunk/blender/build_files/scons/tools/bcolors.py
# https://stackoverflow.com/questions/287871
@ -786,54 +785,6 @@ def dict_flatten(d: _Dict) -> _Dict:
return new
def tail_repack(extended: _Union[str, _Sequence[str]],
existing: _List[str] = []) -> _List[str]:
"""
Repack tailing characters into single string if all are new.
Parameters
----------
extended : (sequence of) str
Extended string list with potentially autosplitted tailing string relative to `existing`.
existing : list of str
Base string list.
Returns
-------
repacked : list of str
Repacked version of `extended`.
Examples
--------
>>> tail_repack(['a','new','e','n','t','r','y'],['a','new'])
['a','new','entry']
>>> tail_repack(['a','new','shiny','e','n','t','r','y'],['a','new'])
['a','new','shiny','e','n','t','r','y']
"""
new = extended[len(existing):]
return [extended] if isinstance(extended,str) else \
existing + list([''.join(new)] if _np.prod([len(i) for i in new]) == 1 else new)
def aslist(arg: _Union[_IntCollection, int, None]) -> _List:
"""
Transform argument to list.
Parameters
----------
arg : (collection of) int or None
Entity to transform into list.
Returns
-------
transformed : list
Entity transformed into list.
"""
return [] if arg is None else list(arg) if isinstance(arg,(_np.ndarray,_Collection)) else [arg]
####################################################################################################
# Classes
####################################################################################################

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@ -17,11 +17,13 @@ from damask import grid_filters
@pytest.fixture
def default():
"""Simple geometry."""
x=np.concatenate((np.ones(40,dtype=int),
np.arange(2,42),
np.ones(40,dtype=int)*2,
np.arange(1,41))).reshape(8,5,4,order='F')
return Grid(x,[8e-6,5e-6,4e-6])
g = np.array([8,5,4])
l = np.prod(g[:2])
return Grid(np.concatenate((np.ones (l,dtype=int),
np.arange(l,dtype=int)+2,
np.ones (l,dtype=int)*2,
np.arange(l,dtype=int)+1)).reshape(g,order='F'),
g*1e-6)
@pytest.fixture
def random():
@ -166,15 +168,15 @@ class TestGrid:
@pytest.mark.parametrize('periodic',[True,False])
def test_clean_reference(self,default,update,ref_path,distance,selection,periodic):
current = default.clean(distance,selection,periodic=periodic,rng_seed=0)
reference = ref_path/f'clean_{distance}_{"+".join(map(str,util.aslist(selection)))}_{periodic}.vti'
reference = ref_path/f'clean_{distance}_{util.srepr(selection,"+")}_{periodic}.vti'
if update:
current.save(reference)
assert Grid.load(reference) == current
@pytest.mark.parametrize('selection',[list(np.random.randint(1,20,6)),set(np.random.randint(1,20,6)),np.random.randint(1,20,6)])
@pytest.mark.parametrize('selection',[list(np.random.randint(1,20,6)),np.random.randint(1,20,6)])
@pytest.mark.parametrize('invert',[True,False])
def test_clean_invert(self,default,selection,invert):
selection_inverse = set(default.material.flatten()) - set(selection)
selection_inverse = np.setdiff1d(default.material,selection)
assert default.clean(selection=selection,invert_selection=invert,rng_seed=0) == \
default.clean(selection=selection_inverse,invert_selection=not invert,rng_seed=0)
@ -351,10 +353,10 @@ class TestGrid:
assert np.all(m2==grid.material)
@pytest.mark.parametrize('selection',[list(np.random.randint(1,20,6)),set(np.random.randint(1,20,6)),np.random.randint(1,20,6)])
@pytest.mark.parametrize('selection',[list(np.random.randint(1,20,6)),np.random.randint(1,20,6)])
@pytest.mark.parametrize('invert',[True,False])
def test_vicinity_offset_invert(self,random,selection,invert):
selection_inverse = set(random.material.flatten()) - set(selection)
selection_inverse = np.setdiff1d(random.material,selection)
assert random.vicinity_offset(selection=selection ,invert_selection=not invert) == \
random.vicinity_offset(selection=selection_inverse,invert_selection= invert)

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@ -393,7 +393,7 @@ class TestResult:
result.export_VTK(output,target_dir=tmp_path,parallel=False)
fname = fname.split('.')[0]+f'_inc{(inc if type(inc) == int else inc[0]):0>2}.vti'
v = VTK.load(tmp_path/fname)
v.comments = 'n/a'
v.comments = ['n/a']
v.save(tmp_path/fname,parallel=False)
with open(tmp_path/fname) as f:
cur = hashlib.md5(f.read().encode()).hexdigest()

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@ -6,7 +6,6 @@ from damask import Rotation
from damask import Table
from damask import _rotation
from damask import grid_filters
from damask import util
from damask import tensor
n = 1000
@ -1151,19 +1150,22 @@ class TestRotation:
@pytest.mark.parametrize('sigma',[5,10,15,20])
@pytest.mark.parametrize('shape',[1000,10000,100000,(10,100)])
def test_from_fiber_component(self,sigma,shape):
def astuple(a):
return tuple(a) if hasattr(a,'__len__') else (a,)
p = []
for run in range(5):
for run in range(9):
alpha = np.arccos(np.random.random()),np.random.random()*2*np.pi
beta = np.arccos(np.random.random()),np.random.random()*2*np.pi
f_in_C = np.array([np.sin(alpha[0])*np.cos(alpha[1]), np.sin(alpha[0])*np.sin(alpha[1]), np.cos(alpha[0])])
f_in_S = np.array([np.sin( beta[0])*np.cos( beta[1]), np.sin( beta[0])*np.sin( beta[1]), np.cos( beta[0])])
ax = np.append(np.cross(f_in_C,f_in_S), - np.arccos(np.dot(f_in_C,f_in_S)))
n = Rotation.from_axis_angle(ax if ax[3] > 0.0 else ax*-1.0 ,normalize=True) # rotation to align fiber axis in crystal and sample system
n = Rotation.from_axis_angle(ax if ax[3] > 0.0 else -ax,normalize=True) # rotation to align fiber axis in crystal and sample system
o = Rotation.from_fiber_component(alpha,beta,np.radians(sigma),shape,False)
angles = np.arccos(np.clip(np.dot(o@np.broadcast_to(f_in_S,tuple(util.aslist(shape))+(3,)),n@f_in_S),-1,1))
dist = np.array(angles) * (np.random.randint(0,2,util.aslist(shape))*2-1)
angles = np.arccos(np.clip(np.dot(o@np.broadcast_to(f_in_S,astuple(shape)+(3,)),n@f_in_S),-1,1))
dist = np.array(angles) * (np.random.randint(0,2,shape)*2-1)
p.append(stats.normaltest(dist)[1])

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@ -217,7 +217,7 @@ class TestVTK:
def test_comments(self,tmp_path,default):
default.comments += 'this is a comment'
default.comments += ['this is a comment']
default.save(tmp_path/'with_comments',parallel=False)
new = VTK.load(tmp_path/'with_comments.vti')
assert new.comments == ['this is a comment']

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@ -25,6 +25,17 @@ class TestUtil:
with pytest.raises(RuntimeError):
util.run('false')
@pytest.mark.parametrize('input,glue,quote,output',
[
(None,'',False,'None'),
([None,None],'\n',False,'None\nNone'),
([-0.5,0.5],'=',False,'-0.5=0.5'),
([1,2,3],'_',False,'1_2_3'),
([1,2,3],'/',True,'"1"/"2"/"3"'),
])
def test_srepr(self,input,glue,quote,output):
assert output == util.srepr(input,glue,quote)
@pytest.mark.parametrize('input,output',
[
([0,-2],[0,-1]),
@ -32,7 +43,6 @@ class TestUtil:
([1./2.,1./3.],[3,2]),
([2./3.,1./2.,1./3.],[4,3,2]),
])
def test_scale2coprime(self,input,output):
assert np.allclose(util.scale_to_coprime(np.array(input)),
np.array(output).astype(int))
@ -134,10 +144,6 @@ class TestUtil:
def test_decorate(self,style):
assert 'DAMASK' in style('DAMASK')
@pytest.mark.parametrize('lst',[1,[1,2],set([1,2,3]),np.arange(4)])
def test_aslist(self,lst):
assert len(util.aslist(lst)) > 0
@pytest.mark.parametrize('complete',[True,False])
def test_D3D_base_group(self,tmp_path,complete):
base_group = ''.join(random.choices('DAMASK', k=10))