Unified object.comments as list[str]; simplifications of Python code
This commit is contained in:
Martin Diehl
Philip Eisenlohr
parent
c4883e2557
commit
dcdc4acbd5
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@ -399,7 +399,7 @@ class Colormap(mpl.colors.ListedColormap):
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"""
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labels = {'RGBA':4} if self.colors.shape[1] == 4 else {'RGB': 3}
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t = Table(labels,self.colors,f'Creator: {util.execution_stamp("Colormap")}')
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t = Table(labels,self.colors,[f'Creator: {util.execution_stamp("Colormap")}'])
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t.save(self._get_file_handle(fname,'.txt'))
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@ -4,7 +4,7 @@ import warnings
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import multiprocessing as mp
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from functools import partial
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import typing
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from typing import Optional, Union, TextIO, List, Sequence, Dict
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from typing import Optional, Union, TextIO, Sequence, Dict
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from pathlib import Path
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import numpy as np
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@ -18,9 +18,9 @@ from . import grid_filters
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from . import Rotation
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from . import Table
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from . import Colormap
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from ._typehints import FloatSequence, IntSequence, IntCollection, NumpyRngSeed
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from ._typehints import FloatSequence, IntSequence, NumpyRngSeed
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try:
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import numba as nb # type: ignore
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import numba as nb # type: ignore
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except ImportError:
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nb = False
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@ -63,11 +63,12 @@ class Grid:
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"""
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self.material = material
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self.size = size # type: ignore
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self.origin = origin # type: ignore
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self.size = size # type: ignore
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self.origin = origin # type: ignore
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self.initial_conditions = {} if initial_conditions is None else initial_conditions
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comments_ = [comments] if isinstance(comments,str) else comments
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self.comments = [] if comments_ is None else [str(c) for c in comments_]
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self.comments = [] if comments is None else \
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[comments] if isinstance(comments,str) else \
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[str(c) for c in comments]
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def __repr__(self) -> str:
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"""
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@ -183,17 +184,6 @@ class Grid:
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self._ic = ic
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@property
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def comments(self) -> List[str]:
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"""Comments, e.g. history of operations."""
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return self._comments
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@comments.setter
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def comments(self,
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comments: Union[str, Sequence[str]]):
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self._comments = [str(c) for c in comments] if isinstance(comments,Sequence) else [str(comments)]
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@property
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def cells(self) -> np.ndarray:
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"""Number of cells in x,y,z direction."""
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@ -226,14 +216,13 @@ class Grid:
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v = VTK.load(fname if str(fname).endswith('.vti') else str(fname)+'.vti')
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cells = np.array(v.vtk_data.GetDimensions())-1
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bbox = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
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comments = v.comments
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ic = {label:v.get(label).reshape(cells,order='F') for label in set(v.labels['Cell Data']) - {'material'}}
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return Grid(material = v.get('material').reshape(cells,order='F'),
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size = bbox[1] - bbox[0],
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origin = bbox[0],
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initial_conditions = ic,
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comments = comments,
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comments = v.comments,
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)
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@ -1103,7 +1092,7 @@ class Grid:
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def clean(self,
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distance: float = np.sqrt(3),
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selection: Optional[IntCollection] = None,
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selection: Optional[IntSequence] = None,
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invert_selection: bool = False,
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periodic: bool = True,
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rng_seed: Optional[NumpyRngSeed] = None) -> 'Grid':
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@ -1115,7 +1104,7 @@ class Grid:
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distance : float, optional
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Voxel distance checked for presence of other materials.
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Defaults to sqrt(3).
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selection : (collection of) int, optional
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selection : (sequence of) int, optional
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Material IDs to consider. Defaults to all.
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invert_selection : bool, optional
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Consider all material IDs except those in selection. Defaults to False.
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@ -1136,8 +1125,8 @@ class Grid:
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"""
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def most_frequent(stencil: np.ndarray,
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selection: Union[None,set],
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rng: np.random.Generator):
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selection: Union[None,np.ndarray],
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rng: np.random.Generator):
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me = stencil[stencil.size//2]
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if selection is None or me in selection:
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unique, counts = np.unique(stencil,return_counts=True)
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@ -1152,8 +1141,8 @@ class Grid:
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xx,yy,zz = np.meshgrid(ext,ext,ext)
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footprint = xx**2+yy**2+zz**2 <= distance**2+distance*1e-8
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selection_ = None if selection is None else \
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set(self.material.flatten()) - set(util.aslist(selection)) if invert_selection else \
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set(self.material.flatten()) & set(util.aslist(selection))
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np.setdiff1d(self.material,selection) if invert_selection else \
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np.intersect1d(self.material,selection)
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material = ndimage.generic_filter(
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self.material,
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most_frequent,
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@ -1265,7 +1254,7 @@ class Grid:
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def vicinity_offset(self,
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distance: float = np.sqrt(3),
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offset: Optional[int] = None,
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selection: Optional[IntCollection] = None,
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selection: Optional[IntSequence] = None,
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invert_selection: bool = False,
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periodic: bool = True) -> 'Grid':
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"""
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@ -1282,7 +1271,7 @@ class Grid:
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offset : int, optional
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Offset (positive or negative) to tag material IDs.
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Defaults to material.max()+1.
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selection : (collection of) int, optional
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selection : (sequence of) int, optional
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Material IDs that trigger an offset.
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Defaults to any other than own material ID.
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invert_selection : bool, optional
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@ -1315,8 +1304,8 @@ class Grid:
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footprint = xx**2+yy**2+zz**2 <= distance**2+distance*1e-8
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offset_ = np.nanmax(self.material)+1 if offset is None else offset
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selection_ = None if selection is None else \
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np.array(list(set(self.material.flatten()) - set(util.aslist(selection)))) if invert_selection else \
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np.array(list(set(self.material.flatten()) & set(util.aslist(selection))))
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np.setdiff1d(self.material,selection) if invert_selection else \
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np.intersect1d(self.material,selection)
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mask = ndimage.generic_filter(self.material,
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tainted_neighborhood,
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@ -1874,7 +1874,7 @@ class Result:
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if self.version_minor >= 13:
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creator = f.attrs['creator'] if h5py3 else f.attrs['creator'].decode()
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created = f.attrs['created'] if h5py3 else f.attrs['created'].decode()
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v.comments += f'{creator} ({created})'
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v.comments += [f'{creator} ({created})']
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for inc in util.show_progress(self.visible['increments']):
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@ -29,8 +29,9 @@ class Table:
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Additional, human-readable information.
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"""
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comments_ = [comments] if isinstance(comments,str) else comments
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self.comments = [] if comments_ is None else [str(c) for c in comments_]
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self.comments = [] if comments is None else \
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[comments] if isinstance(comments,str) else \
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[str(c) for c in comments]
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self.shapes = { k:(v,) if isinstance(v,(np.int64,np.int32,int)) else v for k,v in shapes.items() }
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self.data = pd.DataFrame(data=data)
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self._relabel('uniform')
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@ -185,16 +186,6 @@ class Table:
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self.data.columns = self._label(self.shapes,how) # type: ignore
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def _add_comment(self,
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label: str,
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shape: Tuple[int, ...],
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info: Optional[str] = None):
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if info is not None:
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specific = f'{label}{" "+str(shape) if np.prod(shape,dtype=np.int64) > 1 else ""}: {info}'
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general = util.execution_stamp('Table')
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self.comments.append(f'{specific} / {general}')
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def isclose(self,
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other: 'Table',
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rtol: float = 1e-5,
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@ -402,13 +393,15 @@ class Table:
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Updated table.
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"""
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dup = self.copy()
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dup._add_comment(label, data.shape[1:], info)
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def add_comment(label: str, shape: Tuple[int, ...],info: str) -> List[str]:
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specific = f'{label}{" "+str(shape) if np.prod(shape,dtype=np.int64) > 1 else ""}: {info}'
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general = util.execution_stamp('Table')
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return [f'{specific} / {general}']
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if m := re.match(r'(.*)\[((\d+,)*(\d+))\]',label):
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key = m.group(1)
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else:
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key = label
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dup = self.copy()
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if info is not None: self.comments += add_comment(label,data.shape[1:],info)
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key = m.group(1) if (m := re.match(r'(.*)\[((\d+,)*(\d+))\]',label)) else label
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if key in dup.shapes:
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@ -1,6 +1,6 @@
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"""Functionality for typehints."""
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from typing import Sequence, Union, Literal, TextIO, Collection
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from typing import Sequence, Union, Literal, TextIO
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from pathlib import Path
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import numpy as np
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@ -8,7 +8,6 @@ import numpy as np
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FloatSequence = Union[np.ndarray,Sequence[float]]
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IntSequence = Union[np.ndarray,Sequence[int]]
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IntCollection = Union[np.ndarray,Collection[int]]
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FileHandle = Union[TextIO, str, Path]
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CrystalFamily = Union[None,Literal['triclinic', 'monoclinic', 'orthorhombic', 'tetragonal', 'hexagonal', 'cubic']]
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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:
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@comments.setter
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def comments(self,
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comments: Union[str, Sequence[str]]):
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comments: Sequence[str]):
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"""
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Set comments.
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Parameters
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----------
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comments : (sequence of) str
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comments : sequence of str
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Comments.
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"""
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s = vtk.vtkStringArray()
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s.SetName('comments')
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comments_ = util.tail_repack(comments,self.comments) if comments[:len(self.comments)] == self.comments else \
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[comments] if isinstance(comments,str) else \
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comments
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for c in comments_:
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for c in comments:
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s.InsertNextValue(c)
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self.vtk_data.GetFieldData().AddArray(s)
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@ -478,13 +475,13 @@ class VTK:
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_add_array(dup.vtk_data,
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label,
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np.where(data.mask,data.fill_value,data) if isinstance(data,np.ma.MaskedArray) else data)
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if info is not None: dup.comments += f'{label}: {info}'
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if info is not None: dup.comments += [f'{label}: {info}']
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else:
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raise ValueError('no label defined for data')
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elif isinstance(table,Table):
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for l in table.labels:
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_add_array(dup.vtk_data,l,table.get(l))
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if info is not None: dup.comments += f'{l}: {info}'
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if info is not None: dup.comments += [f'{l}: {info}']
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else:
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raise TypeError
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@ -6,7 +6,7 @@ from scipy import spatial as _spatial
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import numpy as _np
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from ._typehints import FloatSequence as _FloatSequence, IntSequence as _IntSequence, \
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NumpyRngSeed as _NumpyRngSeed, IntCollection as _IntCollection
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NumpyRngSeed as _NumpyRngSeed
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from . import util as _util
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from . import grid_filters as _grid_filters
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@ -106,7 +106,7 @@ def from_Poisson_disc(size: _FloatSequence,
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def from_grid(grid,
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selection: _Optional[_IntCollection] = None,
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selection: _Optional[_IntSequence] = None,
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invert_selection: bool = False,
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average: bool = False,
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periodic: bool = True) -> _Tuple[_np.ndarray, _np.ndarray]:
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@ -117,7 +117,7 @@ def from_grid(grid,
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----------
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grid : damask.Grid
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Grid from which the material IDs are used as seeds.
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selection : (collection of) int, optional
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selection : (sequence of) int, optional
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Material IDs to consider.
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invert_selection : bool, optional
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Consider all material IDs except those in selection. Defaults to False.
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@ -134,7 +134,7 @@ def from_grid(grid,
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"""
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material = grid.material.reshape((-1,1),order='F')
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mask = _np.full(grid.cells.prod(),True,dtype=bool) if selection is None else \
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_np.isin(material,_util.aslist(selection),invert=invert_selection).flatten()
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_np.isin(material,selection,invert=invert_selection).flatten()
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coords = _grid_filters.coordinates0_point(grid.cells,grid.size).reshape(-1,3,order='F')
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if not average:
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@ -11,16 +11,15 @@ import fractions as _fractions
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from collections import abc as _abc
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from functools import reduce as _reduce, partial as _partial
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from typing import Optional as _Optional, Callable as _Callable, Union as _Union, Iterable as _Iterable, \
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Sequence as _Sequence, Dict as _Dict, List as _List, Tuple as _Tuple, Literal as _Literal, \
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Any as _Any, Collection as _Collection, TextIO as _TextIO
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Dict as _Dict, List as _List, Tuple as _Tuple, Literal as _Literal, \
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Any as _Any, TextIO as _TextIO
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from pathlib import Path as _Path
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import numpy as _np
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import h5py as _h5py
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from . import version as _version
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from ._typehints import FloatSequence as _FloatSequence, NumpyRngSeed as _NumpyRngSeed, IntCollection as _IntCollection, \
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FileHandle as _FileHandle
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from ._typehints import FloatSequence as _FloatSequence, NumpyRngSeed as _NumpyRngSeed, FileHandle as _FileHandle
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# https://svn.blender.org/svnroot/bf-blender/trunk/blender/build_files/scons/tools/bcolors.py
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# https://stackoverflow.com/questions/287871
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@ -786,54 +785,6 @@ def dict_flatten(d: _Dict) -> _Dict:
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return new
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def tail_repack(extended: _Union[str, _Sequence[str]],
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existing: _List[str] = []) -> _List[str]:
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"""
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Repack tailing characters into single string if all are new.
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Parameters
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----------
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extended : (sequence of) str
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Extended string list with potentially autosplitted tailing string relative to `existing`.
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existing : list of str
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Base string list.
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Returns
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-------
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repacked : list of str
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Repacked version of `extended`.
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Examples
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--------
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>>> tail_repack(['a','new','e','n','t','r','y'],['a','new'])
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['a','new','entry']
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>>> tail_repack(['a','new','shiny','e','n','t','r','y'],['a','new'])
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['a','new','shiny','e','n','t','r','y']
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"""
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new = extended[len(existing):]
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return [extended] if isinstance(extended,str) else \
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existing + list([''.join(new)] if _np.prod([len(i) for i in new]) == 1 else new)
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def aslist(arg: _Union[_IntCollection, int, None]) -> _List:
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"""
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Transform argument to list.
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Parameters
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----------
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arg : (collection of) int or None
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Entity to transform into list.
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Returns
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-------
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transformed : list
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Entity transformed into list.
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"""
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return [] if arg is None else list(arg) if isinstance(arg,(_np.ndarray,_Collection)) else [arg]
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####################################################################################################
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# Classes
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####################################################################################################
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@ -17,11 +17,13 @@ from damask import grid_filters
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@pytest.fixture
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def default():
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"""Simple geometry."""
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x=np.concatenate((np.ones(40,dtype=int),
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np.arange(2,42),
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np.ones(40,dtype=int)*2,
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np.arange(1,41))).reshape(8,5,4,order='F')
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return Grid(x,[8e-6,5e-6,4e-6])
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g = np.array([8,5,4])
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l = np.prod(g[:2])
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return Grid(np.concatenate((np.ones (l,dtype=int),
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np.arange(l,dtype=int)+2,
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np.ones (l,dtype=int)*2,
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np.arange(l,dtype=int)+1)).reshape(g,order='F'),
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g*1e-6)
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@pytest.fixture
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def random():
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@ -166,15 +168,15 @@ class TestGrid:
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@pytest.mark.parametrize('periodic',[True,False])
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def test_clean_reference(self,default,update,ref_path,distance,selection,periodic):
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current = default.clean(distance,selection,periodic=periodic,rng_seed=0)
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reference = ref_path/f'clean_{distance}_{"+".join(map(str,util.aslist(selection)))}_{periodic}.vti'
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reference = ref_path/f'clean_{distance}_{util.srepr(selection,"+")}_{periodic}.vti'
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if update:
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current.save(reference)
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assert Grid.load(reference) == current
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@pytest.mark.parametrize('selection',[list(np.random.randint(1,20,6)),set(np.random.randint(1,20,6)),np.random.randint(1,20,6)])
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@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)
|
||||
|
||||
|
|
|
|||
|
|
@ -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()
|
||||
|
|
|
|||
|
|
@ -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])
|
||||
|
||||
|
|
|
|||
|
|
@ -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']
|
||||
|
|
|
|||
|
|
@ -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))
|
||||
|
|
|
|||
Loading…
Reference in New Issue