Merge branch 'typehints_grid' into 'development'

added fist typehints for _grid module

See merge request damask/DAMASK!474
This commit is contained in:
Daniel Otto de Mentock 2022-01-13 16:21:19 +00:00
commit a000e477cf
9 changed files with 247 additions and 187 deletions

View File

@ -205,7 +205,7 @@ class Colormap(mpl.colors.ListedColormap):
Returns
-------
color : np.ndarray, shape(...,4)
color : numpy.ndarray, shape(...,4)
RGBA values of interpolated color(s).
Examples

View File

@ -3,6 +3,9 @@ import copy
import warnings
import multiprocessing as mp
from functools import partial
import typing
from typing import Union, Optional, TextIO, List, Sequence
from pathlib import Path
import numpy as np
import pandas as pd
@ -13,7 +16,8 @@ from . import VTK
from . import util
from . import grid_filters
from . import Rotation
from . import Table
from ._typehints import FloatSequence, IntSequence
class Grid:
"""
@ -25,30 +29,34 @@ class Grid:
the physical size.
"""
def __init__(self,material,size,origin=[0.0,0.0,0.0],comments=[]):
def __init__(self,
material: np.ndarray,
size: FloatSequence,
origin: FloatSequence = np.zeros(3),
comments: Union[str, Sequence[str]] = []):
"""
New geometry definition for grid solvers.
Parameters
----------
material : numpy.ndarray of shape (:,:,:)
material : numpy.ndarray, shape (:,:,:)
Material indices. The shape of the material array defines
the number of cells.
size : list or numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of grid in meter.
origin : list or numpy.ndarray of shape (3), optional
Coordinates of grid origin in meter.
comments : list of str, optional
origin : sequence of float, len (3), optional
Coordinates of grid origin in meter. Defaults to [0.0,0.0,0.0].
comments : (list of) str, optional
Comments, e.g. history of operations.
"""
self.material = material
self.size = size
self.origin = origin
self.comments = comments
self.size = size # type: ignore
self.origin = origin # type: ignore
self.comments = comments # type: ignore
def __repr__(self):
def __repr__(self) -> str:
"""Basic information on grid definition."""
mat_min = np.nanmin(self.material)
mat_max = np.nanmax(self.material)
@ -62,14 +70,14 @@ class Grid:
])
def __copy__(self):
def __copy__(self) -> "Grid":
"""Create deep copy."""
return copy.deepcopy(self)
copy = __copy__
def __eq__(self,other):
def __eq__(self, other: object) -> bool:
"""
Test equality of other.
@ -79,22 +87,24 @@ class Grid:
Grid to compare self against.
"""
return (np.allclose(other.size,self.size)
if not isinstance(other, Grid):
return NotImplemented
return bool(np.allclose(other.size,self.size)
and np.allclose(other.origin,self.origin)
and np.all(other.cells == self.cells)
and np.all(other.material == self.material))
@property
def material(self):
def material(self) -> np.ndarray:
"""Material indices."""
return self._material
@material.setter
def material(self,material):
def material(self, material: np.ndarray):
if len(material.shape) != 3:
raise ValueError(f'invalid material shape {material.shape}')
elif material.dtype not in np.sctypes['float'] + np.sctypes['int']:
elif material.dtype not in np.sctypes['float'] and material.dtype not in np.sctypes['int']:
raise TypeError(f'invalid material data type {material.dtype}')
else:
self._material = np.copy(material)
@ -105,59 +115,59 @@ class Grid:
@property
def size(self):
def size(self) -> np.ndarray:
"""Physical size of grid in meter."""
return self._size
@size.setter
def size(self,size):
def size(self, size: FloatSequence):
if len(size) != 3 or any(np.array(size) < 0):
raise ValueError(f'invalid size {size}')
else:
self._size = np.array(size)
@property
def origin(self):
def origin(self) -> np.ndarray:
"""Coordinates of grid origin in meter."""
return self._origin
@origin.setter
def origin(self,origin):
def origin(self, origin: FloatSequence):
if len(origin) != 3:
raise ValueError(f'invalid origin {origin}')
else:
self._origin = np.array(origin)
@property
def comments(self):
def comments(self) -> List[str]:
"""Comments, e.g. history of operations."""
return self._comments
@comments.setter
def comments(self,comments):
def comments(self, comments: Union[str, Sequence[str]]):
self._comments = [str(c) for c in comments] if isinstance(comments,list) else [str(comments)]
@property
def cells(self):
def cells(self) -> np.ndarray:
"""Number of cells in x,y,z direction."""
return np.asarray(self.material.shape)
@property
def N_materials(self):
def N_materials(self) -> int:
"""Number of (unique) material indices within grid."""
return np.unique(self.material).size
@staticmethod
def load(fname):
def load(fname: Union[str, Path]) -> "Grid":
"""
Load from VTK image data file.
Parameters
----------
fname : str or or pathlib.Path
fname : str or pathlib.Path
Grid file to read. Valid extension is .vti, which will be appended
if not given.
@ -178,8 +188,9 @@ class Grid:
comments=comments)
@typing. no_type_check
@staticmethod
def load_ASCII(fname):
def load_ASCII(fname)-> "Grid":
"""
Load from geom file.
@ -198,15 +209,17 @@ class Grid:
"""
warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.0.0', DeprecationWarning,2)
try:
if isinstance(fname, (str, Path)):
f = open(fname)
except TypeError:
elif isinstance(fname, TextIO):
f = fname
else:
raise TypeError
f.seek(0)
try:
header_length,keyword = f.readline().split()[:2]
header_length = int(header_length)
header_length_,keyword = f.readline().split()[:2]
header_length = int(header_length_)
except ValueError:
header_length,keyword = (-1, 'invalid')
if not keyword.startswith('head') or header_length < 3:
@ -226,19 +239,19 @@ class Grid:
else:
comments.append(line.strip())
material = np.empty(cells.prod()) # initialize as flat array
material = np.empty(int(cells.prod())) # initialize as flat array
i = 0
for line in content[header_length:]:
items = line.split('#')[0].split()
if len(items) == 3:
if items[1].lower() == 'of':
items = np.ones(int(items[0]))*float(items[2])
material_entry = np.ones(int(items[0]))*float(items[2])
elif items[1].lower() == 'to':
items = np.linspace(int(items[0]),int(items[2]),
material_entry = np.linspace(int(items[0]),int(items[2]),
abs(int(items[2])-int(items[0]))+1,dtype=float)
else: items = list(map(float,items))
else: items = list(map(float,items))
material[i:i+len(items)] = items
else: material_entry = list(map(float, items))
else: material_entry = list(map(float, items))
material[i:i+len(material_entry)] = material_entry
i += len(items)
if i != cells.prod():
@ -251,13 +264,13 @@ class Grid:
@staticmethod
def load_Neper(fname):
def load_Neper(fname: Union[str, Path]) -> "Grid":
"""
Load from Neper VTK file.
Parameters
----------
fname : str, pathlib.Path, or file handle
fname : str or pathlib.Path
Geometry file to read.
Returns
@ -276,10 +289,10 @@ class Grid:
@staticmethod
def load_DREAM3D(fname,
feature_IDs=None,cell_data=None,
phases='Phases',Euler_angles='EulerAngles',
base_group=None):
def load_DREAM3D(fname: Union[str, Path],
feature_IDs: str = None, cell_data: str = None,
phases: str = 'Phases', Euler_angles: str = 'EulerAngles',
base_group: str = None) -> "Grid":
"""
Load DREAM.3D (HDF5) file.
@ -290,24 +303,24 @@ class Grid:
Parameters
----------
fname : str
fname : str or or pathlib.Path
Filename of the DREAM.3D (HDF5) file.
feature_IDs : str
feature_IDs : str, optional
Name of the dataset containing the mapping between cells and
grain-wise data. Defaults to 'None', in which case cell-wise
data is used.
cell_data : str
cell_data : str, optional
Name of the group (folder) containing cell-wise data. Defaults to
None in wich case it is automatically detected.
phases : str
phases : str, optional
Name of the dataset containing the phase ID. It is not used for
grain-wise data, i.e. when feature_IDs is not None.
Defaults to 'Phases'.
Euler_angles : str
Euler_angles : str, optional
Name of the dataset containing the crystallographic orientation as
Euler angles in radians It is not used for grain-wise data, i.e.
when feature_IDs is not None. Defaults to 'EulerAngles'.
base_group : str
base_group : str, optional
Path to the group (folder) that contains geometry (_SIMPL_GEOMETRY),
and grain- or cell-wise data. Defaults to None, in which case
it is set as the path that contains _SIMPL_GEOMETRY/SPACING.
@ -339,7 +352,9 @@ class Grid:
@staticmethod
def from_table(table,coordinates,labels):
def from_table(table: Table,
coordinates: str,
labels: Union[str, Sequence[str]]) -> "Grid":
"""
Create grid from ASCII table.
@ -350,7 +365,7 @@ class Grid:
coordinates : str
Label of the vector column containing the spatial coordinates.
Need to be ordered (1./x fast, 3./z slow).
labels : str or list of str
labels : (list of) str
Label(s) of the columns containing the material definition.
Each unique combination of values results in one material ID.
@ -372,28 +387,33 @@ class Grid:
@staticmethod
def _find_closest_seed(seeds, weights, point):
def _find_closest_seed(seeds: np.ndarray, weights: np.ndarray, point: np.ndarray) -> np.integer:
return np.argmin(np.sum((np.broadcast_to(point,(len(seeds),3))-seeds)**2,axis=1) - weights)
@staticmethod
def from_Laguerre_tessellation(cells,size,seeds,weights,material=None,periodic=True):
def from_Laguerre_tessellation(cells: IntSequence,
size: FloatSequence,
seeds: np.ndarray,
weights: FloatSequence,
material: IntSequence = None,
periodic: bool = True):
"""
Create grid from Laguerre tessellation.
Parameters
----------
cells : int numpy.ndarray of shape (3)
cells : sequence of int, len (3)
Number of cells in x,y,z direction.
size : list or numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the grid in meter.
seeds : numpy.ndarray of shape (:,3)
seeds : numpy.ndarray, shape (:,3)
Position of the seed points in meter. All points need to lay within the box.
weights : numpy.ndarray of shape (seeds.shape[0])
weights : sequence of float, len (seeds.shape[0])
Weights of the seeds. Setting all weights to 1.0 gives a standard Voronoi tessellation.
material : numpy.ndarray of shape (seeds.shape[0]), optional
material : sequence of int, len (seeds.shape[0]), optional
Material ID of the seeds.
Defaults to None, in which case materials are consecutively numbered.
periodic : Boolean, optional
periodic : bool, optional
Assume grid to be periodic. Defaults to True.
Returns
@ -421,29 +441,33 @@ class Grid:
if periodic: material_ %= len(weights)
return Grid(material = material_ if material is None else material[material_],
return Grid(material = material_ if material is None else np.array(material)[material_],
size = size,
comments = util.execution_stamp('Grid','from_Laguerre_tessellation'),
)
@staticmethod
def from_Voronoi_tessellation(cells,size,seeds,material=None,periodic=True):
def from_Voronoi_tessellation(cells: IntSequence,
size: FloatSequence,
seeds: np.ndarray,
material: IntSequence = None,
periodic: bool = True) -> "Grid":
"""
Create grid from Voronoi tessellation.
Parameters
----------
cells : int numpy.ndarray of shape (3)
cells : sequence of int, len (3)
Number of cells in x,y,z direction.
size : list or numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the grid in meter.
seeds : numpy.ndarray of shape (:,3)
seeds : numpy.ndarray, shape (:,3)
Position of the seed points in meter. All points need to lay within the box.
material : numpy.ndarray of shape (seeds.shape[0]), optional
material : sequence of int, len (seeds.shape[0]), optional
Material ID of the seeds.
Defaults to None, in which case materials are consecutively numbered.
periodic : Boolean, optional
periodic : bool, optional
Assume grid to be periodic. Defaults to True.
Returns
@ -460,7 +484,7 @@ class Grid:
except TypeError:
material_ = tree.query(coords, n_jobs = int(os.environ.get('OMP_NUM_THREADS',4)))[1] # scipy <1.6
return Grid(material = (material_ if material is None else material[material_]).reshape(cells),
return Grid(material = (material_ if material is None else np.array(material)[material_]).reshape(cells),
size = size,
comments = util.execution_stamp('Grid','from_Voronoi_tessellation'),
)
@ -509,15 +533,20 @@ class Grid:
@staticmethod
def from_minimal_surface(cells,size,surface,threshold=0.0,periods=1,materials=(0,1)):
def from_minimal_surface(cells: IntSequence,
size: FloatSequence,
surface: str,
threshold: float = 0.0,
periods: int = 1,
materials: IntSequence = (0,1)) -> "Grid":
"""
Create grid from definition of triply periodic minimal surface.
Parameters
----------
cells : int numpy.ndarray of shape (3)
cells : sequence of int, len (3)
Number of cells in x,y,z direction.
size : list or numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the grid in meter.
surface : str
Type of the minimal surface. See notes for details.
@ -525,7 +554,7 @@ class Grid:
Threshold of the minimal surface. Defaults to 0.0.
periods : integer, optional.
Number of periods per unit cell. Defaults to 1.
materials : (int, int), optional
materials : sequence of int, len (2)
Material IDs. Defaults to (0,1).
Returns
@ -566,22 +595,21 @@ class Grid:
>>> import numpy as np
>>> import damask
>>> damask.Grid.from_minimal_surface(np.array([64]*3,int),np.ones(3),
... 'Gyroid')
cells a b c: 64 x 64 x 64
size x y z: 1.0 x 1.0 x 1.0
origin x y z: 0.0 0.0 0.0
>>> damask.Grid.from_minimal_surface([64]*3,np.ones(3)*1.e-4,'Gyroid')
cells : 64 x 64 x 64
size : 0.0001 x 0.0001 x 0.0001 /
origin: 0.0 0.0 0.0 / m
# materials: 2
Minimal surface of 'Neovius' type. non-default material IDs.
>>> import numpy as np
>>> import damask
>>> damask.Grid.from_minimal_surface(np.array([80]*3,int),np.ones(3),
>>> damask.Grid.from_minimal_surface([80]*3,np.ones(3)*5.e-4,
... 'Neovius',materials=(1,5))
cells a b c: 80 x 80 x 80
size x y z: 1.0 x 1.0 x 1.0
origin x y z: 0.0 0.0 0.0
cells : 80 x 80 x 80
size : 0.0005 x 0.0005 x 0.0005 /
origin: 0.0 0.0 0.0 / m
# materials: 2 (min: 1, max: 5)
"""
@ -595,7 +623,7 @@ class Grid:
)
def save(self,fname,compress=True):
def save(self, fname: Union[str, Path], compress: bool = True):
"""
Save as VTK image data file.
@ -611,10 +639,10 @@ class Grid:
v.add(self.material.flatten(order='F'),'material')
v.add_comments(self.comments)
v.save(fname if str(fname).endswith('.vti') else str(fname)+'.vti',parallel=False,compress=compress)
v.save(fname,parallel=False,compress=compress)
def save_ASCII(self,fname):
def save_ASCII(self, fname: Union[str, TextIO]):
"""
Save as geom file.
@ -644,26 +672,33 @@ class Grid:
header='\n'.join(header), fmt=format_string, comments='')
def show(self):
def show(self) -> None:
"""Show on screen."""
VTK.from_rectilinear_grid(self.cells,self.size,self.origin).show()
def add_primitive(self,dimension,center,exponent,
fill=None,R=Rotation(),inverse=False,periodic=True):
def add_primitive(self,
dimension: Union[FloatSequence, IntSequence],
center: Union[FloatSequence, IntSequence],
exponent: Union[FloatSequence, float],
fill: int = None,
R: Rotation = Rotation(),
inverse: bool = False,
periodic: bool = True) -> "Grid":
"""
Insert a primitive geometric object at a given position.
Parameters
----------
dimension : int or float numpy.ndarray of shape (3)
Dimension (diameter/side length) of the primitive. If given as
integers, cell centers are addressed.
If given as floats, coordinates are addressed.
center : int or float numpy.ndarray of shape (3)
Center of the primitive. If given as integers, cell centers are addressed.
If given as floats, coordinates in space are addressed.
exponent : numpy.ndarray of shape (3) or float
dimension : sequence of int or float, len (3)
Dimension (diameter/side length) of the primitive.
If given as integers, cell centers are addressed.
If given as floats, physical coordinates are addressed.
center : sequence of int or float, len (3)
Center of the primitive.
If given as integers, cell centers are addressed.
If given as floats, physical coordinates are addressed.
exponent : float or sequence of float, len (3)
Exponents for the three axes.
0 gives octahedron (ǀxǀ^(2^0) + ǀyǀ^(2^0) + ǀzǀ^(2^0) < 1)
1 gives sphere (ǀxǀ^(2^1) + ǀyǀ^(2^1) + ǀzǀ^(2^1) < 1)
@ -671,10 +706,10 @@ class Grid:
Fill value for primitive. Defaults to material.max()+1.
R : damask.Rotation, optional
Rotation of primitive. Defaults to no rotation.
inverse : Boolean, optional
inverse : bool, optional
Retain original materials within primitive and fill outside.
Defaults to False.
periodic : Boolean, optional
periodic : bool, optional
Assume grid to be periodic. Defaults to True.
Returns
@ -690,9 +725,9 @@ class Grid:
>>> import damask
>>> g = damask.Grid(np.zeros([64]*3,int), np.ones(3)*1e-4)
>>> g.add_primitive(np.ones(3)*5e-5,np.ones(3)*5e-5,1)
cells a b c: 64 x 64 x 64
size x y z: 0.0001 x 0.0001 x 0.0001
origin x y z: 0.0 0.0 0.0
cells : 64 x 64 x 64
size : 0.0001 x 0.0001 x 0.0001 /
origin: 0.0 0.0 0.0 / m
# materials: 2
Add a cube at the origin.
@ -701,9 +736,9 @@ class Grid:
>>> import damask
>>> g = damask.Grid(np.zeros([64]*3,int), np.ones(3)*1e-4)
>>> g.add_primitive(np.ones(3,int)*32,np.zeros(3),np.inf)
cells a b c: 64 x 64 x 64
size x y z: 0.0001 x 0.0001 x 0.0001
origin x y z: 0.0 0.0 0.0
cells : 64 x 64 x 64
size : 0.0001 x 0.0001 x 0.0001 /
origin: 0.0 0.0 0.0 / m
# materials: 2
"""
@ -734,13 +769,13 @@ class Grid:
)
def mirror(self,directions,reflect=False):
def mirror(self, directions: Sequence[str], reflect: bool = False) -> "Grid":
"""
Mirror grid along given directions.
Parameters
----------
directions : iterable containing str
directions : (sequence of) str
Direction(s) along which the grid is mirrored.
Valid entries are 'x', 'y', 'z'.
reflect : bool, optional
@ -759,9 +794,9 @@ class Grid:
>>> import damask
>>> g = damask.Grid(np.zeros([32]*3,int), np.ones(3)*1e-4)
>>> g.mirror('xy',True)
cells a b c: 64 x 64 x 32
size x y z: 0.0002 x 0.0002 x 0.0001
origin x y z: 0.0 0.0 0.0
cells : 64 x 64 x 32
size : 0.0002 x 0.0002 x 0.0001 /
origin: 0.0 0.0 0.0 / m
# materials: 1
"""
@ -769,7 +804,7 @@ class Grid:
if not set(directions).issubset(valid):
raise ValueError(f'invalid direction {set(directions).difference(valid)} specified')
limits = [None,None] if reflect else [-2,0]
limits: Sequence[Optional[int]] = [None,None] if reflect else [-2,0]
mat = self.material.copy()
if 'x' in directions:
@ -786,13 +821,13 @@ class Grid:
)
def flip(self,directions):
def flip(self, directions: Sequence[str]) -> "Grid":
"""
Flip grid along given directions.
Parameters
----------
directions : iterable containing str
directions : (sequence of) str
Direction(s) along which the grid is flipped.
Valid entries are 'x', 'y', 'z'.
@ -815,15 +850,15 @@ class Grid:
)
def scale(self,cells,periodic=True):
def scale(self, cells: IntSequence, periodic: bool = True) -> "Grid":
"""
Scale grid to new cells.
Parameters
----------
cells : numpy.ndarray of shape (3)
cells : sequence of int, len (3)
Number of cells in x,y,z direction.
periodic : Boolean, optional
periodic : bool, optional
Assume grid to be periodic. Defaults to True.
Returns
@ -839,9 +874,9 @@ class Grid:
>>> import damask
>>> g = damask.Grid(np.zeros([32]*3,int),np.ones(3)*1e-4)
>>> g.scale(g.cells*2)
cells a b c: 64 x 64 x 64
size x y z: 0.0001 x 0.0001 x 0.0001
origin x y z: 0.0 0.0 0.0
cells : 64 x 64 x 64
size : 0.0001 x 0.0001 x 0.0001 /
origin: 0.0 0.0 0.0 / m
# materials: 1
"""
@ -859,7 +894,10 @@ class Grid:
)
def clean(self,stencil=3,selection=None,periodic=True):
def clean(self,
stencil: int = 3,
selection: IntSequence = None,
periodic: bool = True) -> "Grid":
"""
Smooth grid by selecting most frequent material index within given stencil at each location.
@ -867,9 +905,9 @@ class Grid:
----------
stencil : int, optional
Size of smoothing stencil.
selection : list, optional
selection : sequence of int, optional
Field values that can be altered. Defaults to all.
periodic : Boolean, optional
periodic : bool, optional
Assume grid to be periodic. Defaults to True.
Returns
@ -878,7 +916,7 @@ class Grid:
Updated grid-based geometry.
"""
def mostFrequent(arr,selection=None):
def mostFrequent(arr: np.ndarray, selection = None):
me = arr[arr.size//2]
if selection is None or me in selection:
unique, inverse = np.unique(arr, return_inverse=True)
@ -899,7 +937,7 @@ class Grid:
)
def renumber(self):
def renumber(self) -> "Grid":
"""
Renumber sorted material indices as 0,...,N-1.
@ -918,7 +956,7 @@ class Grid:
)
def rotate(self,R,fill=None):
def rotate(self, R: Rotation, fill: int = None) -> "Grid":
"""
Rotate grid (pad if required).
@ -926,7 +964,7 @@ class Grid:
----------
R : damask.Rotation
Rotation to apply to the grid.
fill : int or float, optional
fill : int, optional
Material index to fill the corners. Defaults to material.max() + 1.
Returns
@ -956,17 +994,20 @@ class Grid:
)
def canvas(self,cells=None,offset=None,fill=None):
def canvas(self,
cells: IntSequence = None,
offset: IntSequence = None,
fill: int = None) -> "Grid":
"""
Crop or enlarge/pad grid.
Parameters
----------
cells : numpy.ndarray of shape (3)
cells : sequence of int, len (3), optional
Number of cells x,y,z direction.
offset : numpy.ndarray of shape (3)
offset : sequence of int, len (3), optional
Offset (measured in cells) from old to new grid [0,0,0].
fill : int or float, optional
fill : int, optional
Material index to fill the background. Defaults to material.max() + 1.
Returns
@ -981,42 +1022,43 @@ class Grid:
>>> import numpy as np
>>> import damask
>>> g = damask.Grid(np.zeros([32]*3,int),np.ones(3)*1e-4)
>>> g.canvas(np.array([32,32,16],int))
cells a b c: 33 x 32 x 16
size x y z: 0.0001 x 0.0001 x 5e-05
origin x y z: 0.0 0.0 0.0
>>> g.canvas([32,32,16])
cells : 33 x 32 x 16
size : 0.0001 x 0.0001 x 5e-05 /
origin: 0.0 0.0 0.0 / m
# materials: 1
"""
if offset is None: offset = 0
offset_ = np.array(offset,int) if offset is not None else np.zeros(3,int)
cells_ = np.array(cells,int) if cells is not None else self.cells
if fill is None: fill = np.nanmax(self.material) + 1
dtype = float if int(fill) != fill or self.material.dtype in np.sctypes['float'] else int
canvas = np.full(self.cells if cells is None else cells,fill,dtype)
canvas = np.full(cells_,fill,dtype)
LL = np.clip( offset, 0,np.minimum(self.cells, cells+offset))
UR = np.clip( offset+cells, 0,np.minimum(self.cells, cells+offset))
ll = np.clip(-offset, 0,np.minimum( cells,self.cells-offset))
ur = np.clip(-offset+self.cells,0,np.minimum( cells,self.cells-offset))
LL = np.clip( offset_, 0,np.minimum(self.cells, cells_+offset_))
UR = np.clip( offset_+cells_, 0,np.minimum(self.cells, cells_+offset_))
ll = np.clip(-offset_, 0,np.minimum( cells_,self.cells-offset_))
ur = np.clip(-offset_+self.cells,0,np.minimum( cells_,self.cells-offset_))
canvas[ll[0]:ur[0],ll[1]:ur[1],ll[2]:ur[2]] = self.material[LL[0]:UR[0],LL[1]:UR[1],LL[2]:UR[2]]
return Grid(material = canvas,
size = self.size/self.cells*np.asarray(canvas.shape),
origin = self.origin+offset*self.size/self.cells,
origin = self.origin+offset_*self.size/self.cells,
comments = self.comments+[util.execution_stamp('Grid','canvas')],
)
def substitute(self,from_material,to_material):
def substitute(self, from_material: IntSequence, to_material: IntSequence) -> "Grid":
"""
Substitute material indices.
Parameters
----------
from_material : iterable of ints
from_material : sequence of int
Material indices to be substituted.
to_material : iterable of ints
to_material : sequence of int
New material indices.
Returns
@ -1038,7 +1080,7 @@ class Grid:
)
def sort(self):
def sort(self) -> "Grid":
"""
Sort material indices such that min(material) is located at (0,0,0).
@ -1060,7 +1102,11 @@ class Grid:
)
def vicinity_offset(self,vicinity=1,offset=None,trigger=[],periodic=True):
def vicinity_offset(self,
vicinity: int = 1,
offset: int = None,
trigger: IntSequence = [],
periodic: bool = True) -> "Grid":
"""
Offset material index of points in the vicinity of xxx.
@ -1076,10 +1122,10 @@ class Grid:
offset : int, optional
Offset (positive or negative) to tag material indices,
defaults to material.max()+1.
trigger : list of ints, optional
trigger : sequence of int, optional
List of material indices that trigger a change.
Defaults to [], meaning that any different neighbor triggers a change.
periodic : Boolean, optional
periodic : bool, optional
Assume grid to be periodic. Defaults to True.
Returns
@ -1088,8 +1134,7 @@ class Grid:
Updated grid-based geometry.
"""
def tainted_neighborhood(stencil,trigger):
def tainted_neighborhood(stencil: np.ndarray, trigger):
me = stencil[stencil.shape[0]//2]
return np.any(stencil != me if len(trigger) == 0 else
np.in1d(stencil,np.array(list(set(trigger) - {me}))))
@ -1108,15 +1153,15 @@ class Grid:
)
def get_grain_boundaries(self,periodic=True,directions='xyz'):
def get_grain_boundaries(self, periodic: bool = True, directions: Sequence[str] = 'xyz'):
"""
Create VTK unstructured grid containing grain boundaries.
Parameters
----------
periodic : Boolean, optional
periodic : bool, optional
Assume grid to be periodic. Defaults to True.
directions : iterable containing str, optional
directions : (sequence of) string, optional
Direction(s) along which the boundaries are determined.
Valid entries are 'x', 'y', 'z'. Defaults to 'xyz'.

View File

@ -393,8 +393,8 @@ class Orientation(Rotation,Crystal):
Returns
-------
in : numpy.ndarray of quaternion.shape
Boolean array indicating whether Rodrigues-Frank vector falls into fundamental zone.
in : numpy.ndarray of bool, quaternion.shape
Whether Rodrigues-Frank vector falls into fundamental zone.
Notes
-----
@ -437,8 +437,8 @@ class Orientation(Rotation,Crystal):
Returns
-------
in : numpy.ndarray of quaternion.shape
Boolean array indicating whether Rodrigues-Frank vector falls into disorientation FZ.
in : numpy.ndarray of bool, quaternion.shape
Whether Rodrigues-Frank vector falls into disorientation FZ.
References
----------
@ -651,8 +651,8 @@ class Orientation(Rotation,Crystal):
Returns
-------
in : numpy.ndarray of shape (...)
Boolean array indicating whether vector falls into SST.
in : numpy.ndarray, shape (...)
Whether vector falls into SST.
"""
if not isinstance(vector,np.ndarray) or vector.shape[-1] != 3:

View File

@ -1817,7 +1817,7 @@ class Result:
output : (list of) str, optional
Names of the datasets to export to the file.
Defaults to '*', in which case all datasets are exported.
overwrite : boolean, optional
overwrite : bool, optional
Overwrite existing configuration files.
Defaults to False.

View File

@ -671,7 +671,7 @@ class Rotation:
----------
q : numpy.ndarray of shape (...,4)
Unit quaternion (q_0, q_1, q_2, q_3) in positive real hemisphere, i.e. ǀqǀ = 1, q_0 0.
accept_homomorph : boolean, optional
accept_homomorph : bool, optional
Allow homomorphic variants, i.e. q_0 < 0 (negative real hemisphere).
Defaults to False.
P : int {-1,1}, optional
@ -706,7 +706,7 @@ class Rotation:
phi : numpy.ndarray of shape (...,3)
Euler angles (φ_1 [0,2π], ϕ [0,π], φ_2 [0,2π])
or (φ_1 [0,360], ϕ [0,180], φ_2 [0,360]) if degrees == True.
degrees : boolean, optional
degrees : bool, optional
Euler angles are given in degrees. Defaults to False.
Notes
@ -737,9 +737,9 @@ class Rotation:
axis_angle : numpy.ndarray of shape (...,4)
Axis and angle (n_1, n_2, n_3, ω) with ǀnǀ = 1 and ω [0,π]
or ω [0,180] if degrees == True.
degrees : boolean, optional
degrees : bool, optional
Angle ω is given in degrees. Defaults to False.
normalize: boolean, optional
normalize: bool, optional
Allow ǀnǀ 1. Defaults to False.
P : int {-1,1}, optional
Sign convention. Defaults to -1.
@ -773,9 +773,9 @@ class Rotation:
----------
basis : numpy.ndarray of shape (...,3,3)
Three three-dimensional lattice basis vectors.
orthonormal : boolean, optional
orthonormal : bool, optional
Basis is strictly orthonormal, i.e. is free of stretch components. Defaults to True.
reciprocal : boolean, optional
reciprocal : bool, optional
Basis vectors are given in reciprocal (instead of real) space. Defaults to False.
"""
@ -851,7 +851,7 @@ class Rotation:
----------
rho : numpy.ndarray of shape (...,4)
RodriguesFrank vector (n_1, n_2, n_3, tan(ω/2)) with ǀnǀ = 1 and ω [0,π].
normalize : boolean, optional
normalize : bool, optional
Allow ǀnǀ 1. Defaults to False.
P : int {-1,1}, optional
Sign convention. Defaults to -1.
@ -977,9 +977,9 @@ class Rotation:
N : integer, optional
Number of discrete orientations to be sampled from the given ODF.
Defaults to 500.
degrees : boolean, optional
degrees : bool, optional
Euler space grid coordinates are in degrees. Defaults to True.
fractions : boolean, optional
fractions : bool, optional
ODF values correspond to volume fractions, not probability densities.
Defaults to True.
rng_seed: {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
@ -1033,7 +1033,7 @@ class Rotation:
Standard deviation of (Gaussian) misorientation distribution.
N : int, optional
Number of samples. Defaults to 500.
degrees : boolean, optional
degrees : bool, optional
sigma is given in degrees. Defaults to True.
rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
A seed to initialize the BitGenerator.
@ -1072,7 +1072,7 @@ class Rotation:
Defaults to 0.
N : int, optional
Number of samples. Defaults to 500.
degrees : boolean, optional
degrees : bool, optional
sigma, alpha, and beta are given in degrees.
rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
A seed to initialize the BitGenerator.

View File

@ -28,8 +28,8 @@ class VTK:
----------
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.
Valid types are vtk.vtkImageData, vtk.vtkUnstructuredGrid,
vtk.vtkPolyData, and vtk.vtkRectilinearGrid.
"""
self.vtk_data = vtk_data
@ -242,7 +242,7 @@ class VTK:
----------
fname : str or pathlib.Path
Filename for writing.
parallel : boolean, optional
parallel : bool, optional
Write data in parallel background process. Defaults to True.
compress : bool, optional
Compress with zlib algorithm. Defaults to True.
@ -419,7 +419,7 @@ class VTK:
return writer.GetOutputString()
def show(self):
def show(self) -> None:
"""
Render.

View File

@ -61,7 +61,7 @@ def from_Poisson_disc(size: _FloatSequence, N_seeds: int, N_candidates: int, dis
Number of candidates to consider for finding best candidate.
distance : float
Minimum acceptable distance to other seeds.
periodic : boolean, optional
periodic : bool, optional
Calculate minimum distance for periodically repeated grid.
rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
A seed to initialize the BitGenerator. Defaults to None.
@ -99,8 +99,8 @@ def from_Poisson_disc(size: _FloatSequence, N_seeds: int, N_candidates: int, dis
return coords
def from_grid(grid, selection: _IntSequence = None,
invert: bool = False, average: bool = False, periodic: bool = True) -> _Tuple[_np.ndarray, _np.ndarray]:
def from_grid(grid, selection: _IntSequence = None, invert_selection: bool = False,
average: bool = False, periodic: bool = True) -> _Tuple[_np.ndarray, _np.ndarray]:
"""
Create seeds from grid description.
@ -110,11 +110,11 @@ def from_grid(grid, selection: _IntSequence = None,
Grid from which the material IDs are used as seeds.
selection : sequence of int, optional
Material IDs to consider.
invert : boolean, false
invert_selection : bool, optional
Consider all material IDs except those in selection. Defaults to False.
average : boolean, optional
average : bool, optional
Seed corresponds to center of gravity of material ID cloud.
periodic : boolean, optional
periodic : bool, optional
Center of gravity accounts for periodic boundaries.
Returns
@ -125,7 +125,7 @@ def from_grid(grid, selection: _IntSequence = None,
"""
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,selection,invert=invert).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:

View File

@ -237,12 +237,27 @@ class TestGrid:
modified)
def test_canvas(self,default):
def test_canvas_extend(self,default):
cells = default.cells
grid_add = np.random.randint(0,30,(3))
modified = default.canvas(cells + grid_add)
cells_add = np.random.randint(0,30,(3))
modified = default.canvas(cells + cells_add)
assert np.all(modified.material[:cells[0],:cells[1],:cells[2]] == default.material)
@pytest.mark.parametrize('sign',[+1,-1])
@pytest.mark.parametrize('extra_offset',[0,-1])
def test_canvas_move_out(self,sign,extra_offset):
g = Grid(np.zeros(np.random.randint(3,30,(3)),int),np.ones(3))
o = sign*np.ones(3)*g.cells.min() +extra_offset*sign
if extra_offset == 0:
assert np.all(g.canvas(offset=o).material == 1)
else:
assert np.all(np.unique(g.canvas(offset=o).material) == (0,1))
def test_canvas_cells(self,default):
g = Grid(np.zeros(np.random.randint(3,30,(3)),int),np.ones(3))
cells = np.random.randint(1,30,(3))
offset = np.random.randint(-30,30,(3))
assert np.all(g.canvas(cells,offset).cells == cells)
@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)))])

View File

@ -67,5 +67,5 @@ class TestSeeds:
coords = seeds.from_random(size,N_seeds,cells)
grid = Grid.from_Voronoi_tessellation(cells,size,coords)
selection=np.random.randint(N_seeds)+1
coords,material = seeds.from_grid(grid,average=average,periodic=periodic,invert=invert,selection=[selection])
coords,material = seeds.from_grid(grid,average=average,periodic=periodic,invert_selection=invert,selection=[selection])
assert selection not in material if invert else (selection==material).all()