Merge branch 'typehints_vtk_util' into 'development'
02 Typehints vtk util See merge request damask/DAMASK!502
This commit is contained in:
Philip Eisenlohr
commit
160eb1c600
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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 Union, Optional, TextIO, List, Sequence
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from typing import Union, Optional, TextIO, List, Sequence, Literal
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from pathlib import Path
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import numpy as np
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@ -70,7 +70,7 @@ class Grid:
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])
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def __copy__(self) -> "Grid":
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def __copy__(self) -> 'Grid':
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"""Create deep copy."""
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return copy.deepcopy(self)
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@ -161,7 +161,7 @@ class Grid:
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@staticmethod
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def load(fname: Union[str, Path]) -> "Grid":
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def load(fname: Union[str, Path]) -> 'Grid':
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"""
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Load from VTK image data file.
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@ -190,7 +190,7 @@ class Grid:
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@typing. no_type_check
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@staticmethod
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def load_ASCII(fname)-> "Grid":
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def load_ASCII(fname)-> 'Grid':
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"""
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Load from geom file.
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@ -264,7 +264,7 @@ class Grid:
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@staticmethod
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def load_Neper(fname: Union[str, Path]) -> "Grid":
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def load_Neper(fname: Union[str, Path]) -> 'Grid':
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"""
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Load from Neper VTK file.
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@ -279,7 +279,7 @@ class Grid:
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Grid-based geometry from file.
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"""
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v = VTK.load(fname,'vtkImageData')
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v = VTK.load(fname,'ImageData')
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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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@ -292,7 +292,7 @@ class Grid:
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def load_DREAM3D(fname: Union[str, Path],
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feature_IDs: str = None, cell_data: str = None,
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phases: str = 'Phases', Euler_angles: str = 'EulerAngles',
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base_group: str = None) -> "Grid":
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base_group: str = None) -> 'Grid':
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"""
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Load DREAM.3D (HDF5) file.
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@ -354,7 +354,7 @@ class Grid:
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@staticmethod
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def from_table(table: Table,
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coordinates: str,
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labels: Union[str, Sequence[str]]) -> "Grid":
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labels: Union[str, Sequence[str]]) -> 'Grid':
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"""
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Create grid from ASCII table.
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@ -422,6 +422,7 @@ class Grid:
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Grid-based geometry from tessellation.
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"""
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weights_p: FloatSequence
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if periodic:
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weights_p = np.tile(weights,27) # Laguerre weights (1,2,3,1,2,3,...,1,2,3)
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seeds_p = np.vstack((seeds -np.array([size[0],0.,0.]),seeds, seeds +np.array([size[0],0.,0.])))
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@ -452,7 +453,7 @@ class Grid:
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size: FloatSequence,
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seeds: np.ndarray,
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material: IntSequence = None,
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periodic: bool = True) -> "Grid":
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periodic: bool = True) -> 'Grid':
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"""
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Create grid from Voronoi tessellation.
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@ -538,7 +539,7 @@ class Grid:
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surface: str,
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threshold: float = 0.0,
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periods: int = 1,
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materials: IntSequence = (0,1)) -> "Grid":
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materials: IntSequence = (0,1)) -> 'Grid':
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"""
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Create grid from definition of triply periodic minimal surface.
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@ -684,7 +685,7 @@ class Grid:
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fill: int = None,
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R: Rotation = Rotation(),
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inverse: bool = False,
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periodic: bool = True) -> "Grid":
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periodic: bool = True) -> 'Grid':
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"""
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Insert a primitive geometric object at a given position.
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@ -769,7 +770,7 @@ class Grid:
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)
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def mirror(self, directions: Sequence[str], reflect: bool = False) -> "Grid":
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def mirror(self, directions: Sequence[str], reflect: bool = False) -> 'Grid':
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"""
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Mirror grid along given directions.
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@ -821,7 +822,7 @@ class Grid:
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)
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def flip(self, directions: Sequence[str]) -> "Grid":
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def flip(self, directions: Union[Literal['x', 'y', 'z'], Sequence[Literal['x', 'y', 'z']]]) -> 'Grid':
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"""
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Flip grid along given directions.
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@ -851,7 +852,7 @@ class Grid:
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)
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def scale(self, cells: IntSequence, periodic: bool = True) -> "Grid":
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def scale(self, cells: IntSequence, periodic: bool = True) -> 'Grid':
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"""
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Scale grid to new cells.
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@ -898,7 +899,7 @@ class Grid:
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def clean(self,
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stencil: int = 3,
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selection: IntSequence = None,
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periodic: bool = True) -> "Grid":
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periodic: bool = True) -> 'Grid':
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"""
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Smooth grid by selecting most frequent material index within given stencil at each location.
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@ -938,7 +939,7 @@ class Grid:
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)
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def renumber(self) -> "Grid":
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def renumber(self) -> 'Grid':
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"""
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Renumber sorted material indices as 0,...,N-1.
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@ -957,7 +958,7 @@ class Grid:
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)
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def rotate(self, R: Rotation, fill: int = None) -> "Grid":
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def rotate(self, R: Rotation, fill: int = None) -> 'Grid':
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"""
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Rotate grid (pad if required).
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@ -997,7 +998,7 @@ class Grid:
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def canvas(self,
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cells: IntSequence = None,
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offset: IntSequence = None,
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fill: int = None) -> "Grid":
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fill: int = None) -> 'Grid':
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"""
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Crop or enlarge/pad grid.
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@ -1048,7 +1049,7 @@ class Grid:
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)
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def substitute(self, from_material: IntSequence, to_material: IntSequence) -> "Grid":
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def substitute(self, from_material: IntSequence, to_material: IntSequence) -> 'Grid':
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"""
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Substitute material indices.
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@ -1076,7 +1077,7 @@ class Grid:
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)
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def sort(self) -> "Grid":
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def sort(self) -> 'Grid':
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"""
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Sort material indices such that min(material) is located at (0,0,0).
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@ -1102,7 +1103,7 @@ class Grid:
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vicinity: int = 1,
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offset: int = None,
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trigger: IntSequence = [],
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periodic: bool = True) -> "Grid":
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periodic: bool = True) -> 'Grid':
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"""
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Offset material index of points in the vicinity of xxx.
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@ -2,6 +2,7 @@ import os
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import warnings
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import multiprocessing as mp
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from pathlib import Path
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from typing import Union, Literal, List
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import numpy as np
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import vtk
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@ -9,6 +10,7 @@ from vtk.util.numpy_support import numpy_to_vtk as np_to_vtk
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from vtk.util.numpy_support import numpy_to_vtkIdTypeArray as np_to_vtkIdTypeArray
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from vtk.util.numpy_support import vtk_to_numpy as vtk_to_np
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from ._typehints import FloatSequence, IntSequence
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from . import util
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from . import Table
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@ -20,7 +22,7 @@ class VTK:
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High-level interface to VTK.
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"""
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def __init__(self,vtk_data):
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def __init__(self, vtk_data: vtk.vtkDataSet):
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"""
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New spatial visualization.
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@ -36,7 +38,7 @@ class VTK:
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@staticmethod
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def from_image_data(cells,size,origin=np.zeros(3)):
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def from_image_data(cells: IntSequence, size: FloatSequence, origin: FloatSequence = np.zeros(3)) -> 'VTK':
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"""
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Create VTK of type vtk.vtkImageData.
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@ -60,13 +62,13 @@ class VTK:
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vtk_data = vtk.vtkImageData()
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vtk_data.SetDimensions(*(np.array(cells)+1))
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vtk_data.SetOrigin(*(np.array(origin)))
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vtk_data.SetSpacing(*(size/cells))
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vtk_data.SetSpacing(*(np.array(size)/np.array(cells)))
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return VTK(vtk_data)
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@staticmethod
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def from_rectilinear_grid(grid,size,origin=np.zeros(3)):
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def from_rectilinear_grid(grid: np.ndarray, size: FloatSequence, origin: FloatSequence = np.zeros(3)) -> 'VTK':
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"""
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Create VTK of type vtk.vtkRectilinearGrid.
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@ -98,7 +100,7 @@ class VTK:
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@staticmethod
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def from_unstructured_grid(nodes,connectivity,cell_type):
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def from_unstructured_grid(nodes: np.ndarray, connectivity: np.ndarray, cell_type: str) -> 'VTK':
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"""
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Create VTK of type vtk.vtkUnstructuredGrid.
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@ -138,7 +140,7 @@ class VTK:
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@staticmethod
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def from_poly_data(points):
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def from_poly_data(points: np.ndarray) -> 'VTK':
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"""
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Create VTK of type vtk.polyData.
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@ -172,15 +174,17 @@ class VTK:
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@staticmethod
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def load(fname,dataset_type=None):
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def load(fname: Union[str, Path],
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dataset_type: Literal['ImageData', 'UnstructuredGrid', 'PolyData'] = None) -> 'VTK':
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"""
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Load from VTK file.
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Parameters
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----------
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fname : str or pathlib.Path
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Filename for reading. Valid extensions are .vti, .vtr, .vtu, .vtp, and .vtk.
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dataset_type : {'vtkImageData', ''vtkRectilinearGrid', 'vtkUnstructuredGrid', 'vtkPolyData'}, optional
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Filename for reading.
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Valid extensions are .vti, .vtr, .vtu, .vtp, and .vtk.
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dataset_type : {'ImageData', 'UnstructuredGrid', 'PolyData'}, optional
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Name of the vtk.vtkDataSet subclass when opening a .vtk file.
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Returns
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@ -234,7 +238,7 @@ class VTK:
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def _write(writer):
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"""Wrapper for parallel writing."""
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writer.Write()
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def save(self,fname,parallel=True,compress=True):
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def save(self, fname: Union[str, Path], parallel: bool = True, compress: bool = True):
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"""
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Save as VTK file.
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@ -280,7 +284,7 @@ class VTK:
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# Check https://blog.kitware.com/ghost-and-blanking-visibility-changes/ for missing data
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# Needs support for damask.Table
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def add(self,data,label=None):
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def add(self, data: Union[np.ndarray, np.ma.MaskedArray], label: str = None):
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"""
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Add data to either cells or points.
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@ -327,7 +331,7 @@ class VTK:
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raise TypeError
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def get(self,label):
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def get(self, label: str) -> np.ndarray:
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"""
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Get either cell or point data.
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@ -369,7 +373,7 @@ class VTK:
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raise ValueError(f'Array "{label}" not found.')
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def get_comments(self):
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def get_comments(self) -> List[str]:
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"""Return the comments."""
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fielddata = self.vtk_data.GetFieldData()
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for a in range(fielddata.GetNumberOfArrays()):
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|
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@ -379,7 +383,7 @@ class VTK:
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return []
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def set_comments(self,comments):
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def set_comments(self, comments: Union[str, List[str]]):
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"""
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Set comments.
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@ -396,7 +400,7 @@ class VTK:
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self.vtk_data.GetFieldData().AddArray(s)
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def add_comments(self,comments):
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def add_comments(self, comments: Union[str, List[str]]):
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"""
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Add comments.
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|
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@ -409,7 +413,7 @@ class VTK:
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self.set_comments(self.get_comments() + ([comments] if isinstance(comments,str) else comments))
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def __repr__(self):
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def __repr__(self) -> str:
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"""ASCII representation of the VTK data."""
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writer = vtk.vtkDataSetWriter()
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writer.SetHeader(f'# {util.execution_stamp("VTK")}')
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|
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@ -419,7 +423,7 @@ class VTK:
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return writer.GetOutputString()
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def show(self) -> None:
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def show(self):
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"""
|
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Render.
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|
|
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|
|
@ -79,7 +79,7 @@ def from_Poisson_disc(size: _FloatSequence, N_seeds: int, N_candidates: int, dis
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s = 1
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i = 0
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progress = _util._ProgressBar(N_seeds+1,'',50)
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progress = _util.ProgressBar(N_seeds+1,'',50)
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while s < N_seeds:
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i += 1
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candidates = rng.random((N_candidates,3))*_np.broadcast_to(size,(N_candidates,3))
|
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|
|
|
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|
|
@ -7,12 +7,16 @@ import subprocess
|
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import shlex
|
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import re
|
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import fractions
|
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import collections.abc as abc
|
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from functools import reduce
|
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from typing import Union, Tuple, Iterable, Callable, Dict, List, Any, Literal, Optional
|
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from pathlib import Path
|
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|
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import numpy as np
|
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import h5py
|
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|
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from . import version
|
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from ._typehints import FloatSequence
|
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# limit visibility
|
||||
__all__=[
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|
|
@ -50,16 +54,16 @@ _colors = {
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|||
####################################################################################################
|
||||
# Functions
|
||||
####################################################################################################
|
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def srepr(arg,glue = '\n'):
|
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def srepr(msg, glue: str = '\n') -> str:
|
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r"""
|
||||
Join items with glue string.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
arg : iterable
|
||||
msg : object with __repr__ or sequence of objects with __repr__
|
||||
Items to join.
|
||||
glue : str, optional
|
||||
Glue used for joining operation. Defaults to \n.
|
||||
Glue used for joining operation. Defaults to '\n'.
|
||||
|
||||
Returns
|
||||
-------
|
||||
|
|
@ -67,21 +71,21 @@ def srepr(arg,glue = '\n'):
|
|||
String representation of the joined items.
|
||||
|
||||
"""
|
||||
if (not hasattr(arg, 'strip') and
|
||||
(hasattr(arg, '__getitem__') or
|
||||
hasattr(arg, '__iter__'))):
|
||||
return glue.join(str(x) for x in arg)
|
||||
if (not hasattr(msg, 'strip') and
|
||||
(hasattr(msg, '__getitem__') or
|
||||
hasattr(msg, '__iter__'))):
|
||||
return glue.join(str(x) for x in msg)
|
||||
else:
|
||||
return arg if isinstance(arg,str) else repr(arg)
|
||||
return msg if isinstance(msg,str) else repr(msg)
|
||||
|
||||
|
||||
def emph(what):
|
||||
def emph(msg) -> str:
|
||||
"""
|
||||
Format with emphasis.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
what : object with __repr__ or iterable of objects with __repr__.
|
||||
msg : object with __repr__ or sequence of objects with __repr__
|
||||
Message to format.
|
||||
|
||||
Returns
|
||||
|
|
@ -90,15 +94,15 @@ def emph(what):
|
|||
Formatted string representation of the joined items.
|
||||
|
||||
"""
|
||||
return _colors['bold']+srepr(what)+_colors['end_color']
|
||||
return _colors['bold']+srepr(msg)+_colors['end_color']
|
||||
|
||||
def deemph(what):
|
||||
def deemph(msg) -> str:
|
||||
"""
|
||||
Format with deemphasis.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
what : object with __repr__ or iterable of objects with __repr__.
|
||||
msg : object with __repr__ or sequence of objects with __repr__
|
||||
Message to format.
|
||||
|
||||
Returns
|
||||
|
|
@ -107,15 +111,15 @@ def deemph(what):
|
|||
Formatted string representation of the joined items.
|
||||
|
||||
"""
|
||||
return _colors['dim']+srepr(what)+_colors['end_color']
|
||||
return _colors['dim']+srepr(msg)+_colors['end_color']
|
||||
|
||||
def warn(what):
|
||||
def warn(msg) -> str:
|
||||
"""
|
||||
Format for warning.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
what : object with __repr__ or iterable of objects with __repr__.
|
||||
msg : object with __repr__ or sequence of objects with __repr__
|
||||
Message to format.
|
||||
|
||||
Returns
|
||||
|
|
@ -124,15 +128,15 @@ def warn(what):
|
|||
Formatted string representation of the joined items.
|
||||
|
||||
"""
|
||||
return _colors['warning']+emph(what)+_colors['end_color']
|
||||
return _colors['warning']+emph(msg)+_colors['end_color']
|
||||
|
||||
def strikeout(what):
|
||||
def strikeout(msg) -> str:
|
||||
"""
|
||||
Format as strikeout.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
what : object with __repr__ or iterable of objects with __repr__.
|
||||
msg : object with __repr__ or iterable of objects with __repr__
|
||||
Message to format.
|
||||
|
||||
Returns
|
||||
|
|
@ -141,10 +145,10 @@ def strikeout(what):
|
|||
Formatted string representation of the joined items.
|
||||
|
||||
"""
|
||||
return _colors['crossout']+srepr(what)+_colors['end_color']
|
||||
return _colors['crossout']+srepr(msg)+_colors['end_color']
|
||||
|
||||
|
||||
def run(cmd,wd='./',env=None,timeout=None):
|
||||
def run(cmd: str, wd: str = './', env: Dict[str, str] = None, timeout: int = None) -> Tuple[str, str]:
|
||||
"""
|
||||
Run a command.
|
||||
|
||||
|
|
@ -153,7 +157,7 @@ def run(cmd,wd='./',env=None,timeout=None):
|
|||
cmd : str
|
||||
Command to be executed.
|
||||
wd : str, optional
|
||||
Working directory of process. Defaults to ./ .
|
||||
Working directory of process. Defaults to './'.
|
||||
env : dict, optional
|
||||
Environment for execution.
|
||||
timeout : integer, optional
|
||||
|
|
@ -185,7 +189,7 @@ def run(cmd,wd='./',env=None,timeout=None):
|
|||
execute = run
|
||||
|
||||
|
||||
def natural_sort(key):
|
||||
def natural_sort(key: str) -> List[Union[int, str]]:
|
||||
"""
|
||||
Natural sort.
|
||||
|
||||
|
|
@ -200,7 +204,10 @@ def natural_sort(key):
|
|||
return [ convert(c) for c in re.split('([0-9]+)', key) ]
|
||||
|
||||
|
||||
def show_progress(iterable,N_iter=None,prefix='',bar_length=50):
|
||||
def show_progress(iterable: Iterable,
|
||||
N_iter: int = None,
|
||||
prefix: str = '',
|
||||
bar_length: int = 50) -> Any:
|
||||
"""
|
||||
Decorate a loop with a progress bar.
|
||||
|
||||
|
|
@ -208,39 +215,49 @@ def show_progress(iterable,N_iter=None,prefix='',bar_length=50):
|
|||
|
||||
Parameters
|
||||
----------
|
||||
iterable : iterable or function with yield statement
|
||||
Iterable (or function with yield statement) to be decorated.
|
||||
iterable : iterable
|
||||
Iterable to be decorated.
|
||||
N_iter : int, optional
|
||||
Total number of iterations. Required unless obtainable as len(iterable).
|
||||
Total number of iterations. Required if iterable is not a sequence.
|
||||
prefix : str, optional
|
||||
Prefix string.
|
||||
bar_length : int, optional
|
||||
Length of progress bar in characters. Defaults to 50.
|
||||
|
||||
"""
|
||||
if N_iter in [0,1] or (hasattr(iterable,'__len__') and len(iterable) <= 1):
|
||||
if isinstance(iterable,abc.Sequence):
|
||||
if N_iter is None:
|
||||
N = len(iterable)
|
||||
else:
|
||||
raise ValueError('N_iter given for sequence')
|
||||
else:
|
||||
if N_iter is None:
|
||||
raise ValueError('N_iter not given')
|
||||
else:
|
||||
N = N_iter
|
||||
|
||||
if N <= 1:
|
||||
for item in iterable:
|
||||
yield item
|
||||
else:
|
||||
status = _ProgressBar(N_iter if N_iter is not None else len(iterable),prefix,bar_length)
|
||||
|
||||
status = ProgressBar(N,prefix,bar_length)
|
||||
for i,item in enumerate(iterable):
|
||||
yield item
|
||||
status.update(i)
|
||||
|
||||
|
||||
def scale_to_coprime(v):
|
||||
def scale_to_coprime(v: FloatSequence) -> np.ndarray:
|
||||
"""
|
||||
Scale vector to co-prime (relatively prime) integers.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
v : numpy.ndarray of shape (:)
|
||||
v : sequence of float, len (:)
|
||||
Vector to scale.
|
||||
|
||||
Returns
|
||||
-------
|
||||
m : numpy.ndarray of shape (:)
|
||||
m : numpy.ndarray, shape (:)
|
||||
Vector scaled to co-prime numbers.
|
||||
|
||||
"""
|
||||
|
|
@ -257,17 +274,21 @@ def scale_to_coprime(v):
|
|||
except AttributeError:
|
||||
return a * b // np.gcd(a, b)
|
||||
|
||||
m = (np.array(v) * reduce(lcm, map(lambda x: int(get_square_denominator(x)),v)) ** 0.5).astype(int)
|
||||
v_ = np.array(v)
|
||||
m = (v_ * reduce(lcm, map(lambda x: int(get_square_denominator(x)),v_))**0.5).astype(int)
|
||||
m = m//reduce(np.gcd,m)
|
||||
|
||||
with np.errstate(invalid='ignore'):
|
||||
if not np.allclose(np.ma.masked_invalid(v/m),v[np.argmax(abs(v))]/m[np.argmax(abs(v))]):
|
||||
raise ValueError(f'Invalid result {m} for input {v}. Insufficient precision?')
|
||||
if not np.allclose(np.ma.masked_invalid(v_/m),v_[np.argmax(abs(v_))]/m[np.argmax(abs(v_))]):
|
||||
raise ValueError(f'Invalid result {m} for input {v_}. Insufficient precision?')
|
||||
|
||||
return m
|
||||
|
||||
|
||||
def project_equal_angle(vector,direction='z',normalize=True,keepdims=False):
|
||||
def project_equal_angle(vector: np.ndarray,
|
||||
direction: Literal['x', 'y', 'z'] = 'z',
|
||||
normalize: bool = True,
|
||||
keepdims: bool = False) -> np.ndarray:
|
||||
"""
|
||||
Apply equal-angle projection to vector.
|
||||
|
||||
|
|
@ -275,9 +296,8 @@ def project_equal_angle(vector,direction='z',normalize=True,keepdims=False):
|
|||
----------
|
||||
vector : numpy.ndarray, shape (...,3)
|
||||
Vector coordinates to be projected.
|
||||
direction : str
|
||||
Projection direction 'x', 'y', or 'z'.
|
||||
Defaults to 'z'.
|
||||
direction : {'x', 'y', 'z'}
|
||||
Projection direction. Defaults to 'z'.
|
||||
normalize : bool
|
||||
Ensure unit length of input vector. Defaults to True.
|
||||
keepdims : bool
|
||||
|
|
@ -309,7 +329,10 @@ def project_equal_angle(vector,direction='z',normalize=True,keepdims=False):
|
|||
return np.roll(np.block([v[...,:2]/(1.0+np.abs(v[...,2:3])),np.zeros_like(v[...,2:3])]),
|
||||
-shift if keepdims else 0,axis=-1)[...,:3 if keepdims else 2]
|
||||
|
||||
def project_equal_area(vector,direction='z',normalize=True,keepdims=False):
|
||||
def project_equal_area(vector: np.ndarray,
|
||||
direction: Literal['x', 'y', 'z'] = 'z',
|
||||
normalize: bool = True,
|
||||
keepdims: bool = False) -> np.ndarray:
|
||||
"""
|
||||
Apply equal-area projection to vector.
|
||||
|
||||
|
|
@ -317,9 +340,8 @@ def project_equal_area(vector,direction='z',normalize=True,keepdims=False):
|
|||
----------
|
||||
vector : numpy.ndarray, shape (...,3)
|
||||
Vector coordinates to be projected.
|
||||
direction : str
|
||||
Projection direction 'x', 'y', or 'z'.
|
||||
Defaults to 'z'.
|
||||
direction : {'x', 'y', 'z'}
|
||||
Projection direction. Defaults to 'z'.
|
||||
normalize : bool
|
||||
Ensure unit length of input vector. Defaults to True.
|
||||
keepdims : bool
|
||||
|
|
@ -351,15 +373,14 @@ def project_equal_area(vector,direction='z',normalize=True,keepdims=False):
|
|||
return np.roll(np.block([v[...,:2]/np.sqrt(1.0+np.abs(v[...,2:3])),np.zeros_like(v[...,2:3])]),
|
||||
-shift if keepdims else 0,axis=-1)[...,:3 if keepdims else 2]
|
||||
|
||||
|
||||
def execution_stamp(class_name,function_name=None):
|
||||
def execution_stamp(class_name: str, function_name: str = None) -> str:
|
||||
"""Timestamp the execution of a (function within a) class."""
|
||||
now = datetime.datetime.now().astimezone().strftime('%Y-%m-%d %H:%M:%S%z')
|
||||
_function_name = '' if function_name is None else f'.{function_name}'
|
||||
return f'damask.{class_name}{_function_name} v{version} ({now})'
|
||||
|
||||
|
||||
def hybrid_IA(dist,N,rng_seed=None):
|
||||
def hybrid_IA(dist: np.ndarray, N: int, rng_seed = None) -> np.ndarray:
|
||||
"""
|
||||
Hybrid integer approximation.
|
||||
|
||||
|
|
@ -387,7 +408,10 @@ def hybrid_IA(dist,N,rng_seed=None):
|
|||
return np.repeat(np.arange(len(dist)),repeats)[np.random.default_rng(rng_seed).permutation(N_inv_samples)[:N]]
|
||||
|
||||
|
||||
def shapeshifter(fro,to,mode='left',keep_ones=False):
|
||||
def shapeshifter(fro: Tuple[int, ...],
|
||||
to: Tuple[int, ...],
|
||||
mode: Literal['left','right'] = 'left',
|
||||
keep_ones: bool = False) -> Tuple[Optional[int], ...]:
|
||||
"""
|
||||
Return dimensions that reshape 'fro' to become broadcastable to 'to'.
|
||||
|
||||
|
|
@ -398,9 +422,9 @@ def shapeshifter(fro,to,mode='left',keep_ones=False):
|
|||
to : tuple
|
||||
Target shape of array after broadcasting.
|
||||
len(to) cannot be less than len(fro).
|
||||
mode : str, optional
|
||||
mode : {'left', 'right'}, optional
|
||||
Indicates whether new axes are preferably added to
|
||||
either 'left' or 'right' of the original shape.
|
||||
either left or right of the original shape.
|
||||
Defaults to 'left'.
|
||||
keep_ones : bool, optional
|
||||
Treat '1' in fro as literal value instead of dimensional placeholder.
|
||||
|
|
@ -434,21 +458,22 @@ def shapeshifter(fro,to,mode='left',keep_ones=False):
|
|||
fro = (1,) if not len(fro) else fro
|
||||
to = (1,) if not len(to) else to
|
||||
try:
|
||||
grp = re.match(beg[mode]
|
||||
match = re.match(beg[mode]
|
||||
+f',{sep[mode]}'.join(map(lambda x: f'{x}'
|
||||
if x>1 or (keep_ones and len(fro)>1) else
|
||||
'\\d+',fro))
|
||||
+f',{end[mode]}',
|
||||
','.join(map(str,to))+',').groups()
|
||||
except AttributeError:
|
||||
+f',{end[mode]}',','.join(map(str,to))+',')
|
||||
assert match
|
||||
grp = match.groups()
|
||||
except AssertionError:
|
||||
raise ValueError(f'Shapes can not be shifted {fro} --> {to}')
|
||||
fill = ()
|
||||
fill: Tuple[Optional[int], ...] = ()
|
||||
for g,d in zip(grp,fro+(None,)):
|
||||
fill += (1,)*g.count(',')+(d,)
|
||||
return fill[:-1]
|
||||
|
||||
|
||||
def shapeblender(a,b):
|
||||
def shapeblender(a: Tuple[int, ...], b: Tuple[int, ...]) -> Tuple[int, ...]:
|
||||
"""
|
||||
Return a shape that overlaps the rightmost entries of 'a' with the leftmost of 'b'.
|
||||
|
||||
|
|
@ -476,7 +501,7 @@ def shapeblender(a,b):
|
|||
return a + b[i:]
|
||||
|
||||
|
||||
def extend_docstring(extra_docstring):
|
||||
def extend_docstring(extra_docstring: str) -> Callable:
|
||||
"""
|
||||
Decorator: Append to function's docstring.
|
||||
|
||||
|
|
@ -492,7 +517,7 @@ def extend_docstring(extra_docstring):
|
|||
return _decorator
|
||||
|
||||
|
||||
def extended_docstring(f,extra_docstring):
|
||||
def extended_docstring(f: Callable, extra_docstring: str) -> Callable:
|
||||
"""
|
||||
Decorator: Combine another function's docstring with a given docstring.
|
||||
|
||||
|
|
@ -510,7 +535,7 @@ def extended_docstring(f,extra_docstring):
|
|||
return _decorator
|
||||
|
||||
|
||||
def DREAM3D_base_group(fname):
|
||||
def DREAM3D_base_group(fname: Union[str, Path]) -> str:
|
||||
"""
|
||||
Determine the base group of a DREAM.3D file.
|
||||
|
||||
|
|
@ -536,7 +561,7 @@ def DREAM3D_base_group(fname):
|
|||
|
||||
return base_group
|
||||
|
||||
def DREAM3D_cell_data_group(fname):
|
||||
def DREAM3D_cell_data_group(fname: Union[str, Path]) -> str:
|
||||
"""
|
||||
Determine the cell data group of a DREAM.3D file.
|
||||
|
||||
|
|
@ -568,18 +593,18 @@ def DREAM3D_cell_data_group(fname):
|
|||
return cell_data_group
|
||||
|
||||
|
||||
def Bravais_to_Miller(*,uvtw=None,hkil=None):
|
||||
def Bravais_to_Miller(*, uvtw: np.ndarray = None, hkil: np.ndarray = None) -> np.ndarray:
|
||||
"""
|
||||
Transform 4 Miller–Bravais indices to 3 Miller indices of crystal direction [uvw] or plane normal (hkl).
|
||||
|
||||
Parameters
|
||||
----------
|
||||
uvtw|hkil : numpy.ndarray of shape (...,4)
|
||||
uvtw|hkil : numpy.ndarray, shape (...,4)
|
||||
Miller–Bravais indices of crystallographic direction [uvtw] or plane normal (hkil).
|
||||
|
||||
Returns
|
||||
-------
|
||||
uvw|hkl : numpy.ndarray of shape (...,3)
|
||||
uvw|hkl : numpy.ndarray, shape (...,3)
|
||||
Miller indices of [uvw] direction or (hkl) plane normal.
|
||||
|
||||
"""
|
||||
|
|
@ -595,18 +620,18 @@ def Bravais_to_Miller(*,uvtw=None,hkil=None):
|
|||
return np.einsum('il,...l',basis,axis)
|
||||
|
||||
|
||||
def Miller_to_Bravais(*,uvw=None,hkl=None):
|
||||
def Miller_to_Bravais(*, uvw: np.ndarray = None, hkl: np.ndarray = None) -> np.ndarray:
|
||||
"""
|
||||
Transform 3 Miller indices to 4 Miller–Bravais indices of crystal direction [uvtw] or plane normal (hkil).
|
||||
|
||||
Parameters
|
||||
----------
|
||||
uvw|hkl : numpy.ndarray of shape (...,3)
|
||||
uvw|hkl : numpy.ndarray, shape (...,3)
|
||||
Miller indices of crystallographic direction [uvw] or plane normal (hkl).
|
||||
|
||||
Returns
|
||||
-------
|
||||
uvtw|hkil : numpy.ndarray of shape (...,4)
|
||||
uvtw|hkil : numpy.ndarray, shape (...,4)
|
||||
Miller–Bravais indices of [uvtw] direction or (hkil) plane normal.
|
||||
|
||||
"""
|
||||
|
|
@ -624,7 +649,7 @@ def Miller_to_Bravais(*,uvw=None,hkl=None):
|
|||
return np.einsum('il,...l',basis,axis)
|
||||
|
||||
|
||||
def dict_prune(d):
|
||||
def dict_prune(d: Dict) -> Dict:
|
||||
"""
|
||||
Recursively remove empty dictionaries.
|
||||
|
||||
|
|
@ -650,7 +675,7 @@ def dict_prune(d):
|
|||
return new
|
||||
|
||||
|
||||
def dict_flatten(d):
|
||||
def dict_flatten(d: Dict) -> Dict:
|
||||
"""
|
||||
Recursively remove keys of single-entry dictionaries.
|
||||
|
||||
|
|
@ -678,14 +703,14 @@ def dict_flatten(d):
|
|||
####################################################################################################
|
||||
# Classes
|
||||
####################################################################################################
|
||||
class _ProgressBar:
|
||||
class ProgressBar:
|
||||
"""
|
||||
Report progress of an interation as a status bar.
|
||||
|
||||
Works for 0-based loops, ETA is estimated by linear extrapolation.
|
||||
"""
|
||||
|
||||
def __init__(self,total,prefix,bar_length):
|
||||
def __init__(self, total: int, prefix: str, bar_length: int):
|
||||
"""
|
||||
Set current time as basis for ETA estimation.
|
||||
|
||||
|
|
@ -708,7 +733,7 @@ class _ProgressBar:
|
|||
sys.stderr.write(f"{self.prefix} {'░'*self.bar_length} 0% ETA n/a")
|
||||
sys.stderr.flush()
|
||||
|
||||
def update(self,iteration):
|
||||
def update(self, iteration: int) -> None:
|
||||
|
||||
fraction = (iteration+1) / self.total
|
||||
filled_length = int(self.bar_length * fraction)
|
||||
|
|
|
|||
Loading…
Reference in New Issue