added fist typehints for _grid module
This commit is contained in:
Daniel Otto de Mentock
parent
65c4417a20
commit
5558c301fa
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@ -3,6 +3,8 @@ import copy
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import warnings
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import multiprocessing as mp
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from functools import partial
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from typing import Union, Optional, TextIO, List, Sequence
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from pathlib import Path
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import numpy as np
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import pandas as pd
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@ -13,7 +15,7 @@ from . import VTK
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from . import util
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from . import grid_filters
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from . import Rotation
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from . import Table
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class Grid:
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"""
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@ -25,7 +27,11 @@ class Grid:
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the physical size.
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"""
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def __init__(self,material,size,origin=[0.0,0.0,0.0],comments=[]):
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def __init__(self,
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material: np.ndarray,
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size,
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origin = [0.0,0.0,0.0],
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comments = []):
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"""
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New geometry definition for grid solvers.
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@ -43,12 +49,12 @@ class Grid:
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"""
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self.material = material
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self.size = size
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self.origin = origin
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self._size = size
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self._origin = origin
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self.comments = comments
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def __repr__(self):
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def __repr__(self) -> str:
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"""Basic information on grid definition."""
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mat_min = np.nanmin(self.material)
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mat_max = np.nanmax(self.material)
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@ -62,14 +68,14 @@ class Grid:
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])
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def __copy__(self):
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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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copy = __copy__
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def __eq__(self,other):
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def __eq__(self, other):
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"""
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Test equality of other.
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@ -79,6 +85,8 @@ class Grid:
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Grid to compare self against.
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"""
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if not isinstance(other, Grid):
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raise TypeError
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return (np.allclose(other.size,self.size)
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and np.allclose(other.origin,self.origin)
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and np.all(other.cells == self.cells)
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@ -86,15 +94,15 @@ class Grid:
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@property
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def material(self):
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def material(self) -> np.ndarray:
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"""Material indices."""
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return self._material
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@material.setter
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def material(self,material):
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def material(self, material: np.ndarray):
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if len(material.shape) != 3:
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raise ValueError(f'invalid material shape {material.shape}')
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elif material.dtype not in np.sctypes['float'] + np.sctypes['int']:
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elif material.dtype not in np.sctypes['float'] and material.dtype not in np.sctypes['int']:
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raise TypeError(f'invalid material data type {material.dtype}')
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else:
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self._material = np.copy(material)
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@ -105,53 +113,53 @@ class Grid:
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@property
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def size(self):
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def size(self) -> np.ndarray:
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"""Physical size of grid in meter."""
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return self._size
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@size.setter
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def size(self,size):
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def size(self, size: Union[Sequence[float], np.ndarray]):
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if len(size) != 3 or any(np.array(size) < 0):
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raise ValueError(f'invalid size {size}')
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else:
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self._size = np.array(size)
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@property
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def origin(self):
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def origin(self) -> Union[Sequence[float], np.ndarray]:
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"""Coordinates of grid origin in meter."""
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return self._origin
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@origin.setter
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def origin(self,origin):
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def origin(self, origin: np.ndarray):
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if len(origin) != 3:
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raise ValueError(f'invalid origin {origin}')
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else:
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self._origin = np.array(origin)
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@property
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def comments(self):
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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,comments):
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def comments(self, comments: Union[str, Sequence[str]]):
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self._comments = [str(c) for c in comments] if isinstance(comments,list) else [str(comments)]
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@property
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def cells(self):
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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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return np.asarray(self.material.shape)
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@property
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def N_materials(self):
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def N_materials(self) -> int:
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"""Number of (unique) material indices within grid."""
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return np.unique(self.material).size
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@staticmethod
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def load(fname):
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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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@ -198,15 +206,17 @@ class Grid:
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"""
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warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning,2)
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try:
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if isinstance(fname, (str, Path)):
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f = open(fname)
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except TypeError:
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elif isinstance(fname, TextIO):
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f = fname
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else:
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raise TypeError
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f.seek(0)
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try:
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header_length,keyword = f.readline().split()[:2]
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header_length = int(header_length)
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header_length_,keyword = f.readline().split()[:2]
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header_length = int(header_length_)
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except ValueError:
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header_length,keyword = (-1, 'invalid')
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if not keyword.startswith('head') or header_length < 3:
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@ -215,10 +225,10 @@ class Grid:
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comments = []
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content = f.readlines()
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for i,line in enumerate(content[:header_length]):
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items = line.split('#')[0].lower().strip().split()
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items: List[str] = line.split('#')[0].lower().strip().split()
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key = items[0] if items else ''
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if key == 'grid':
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cells = np.array([ int(dict(zip(items[1::2],items[2::2]))[i]) for i in ['a','b','c']])
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cells = np.array([int(dict(zip(items[1::2],items[2::2]))[i]) for i in ['a','b','c']])
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elif key == 'size':
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size = np.array([float(dict(zip(items[1::2],items[2::2]))[i]) for i in ['x','y','z']])
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elif key == 'origin':
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@ -226,19 +236,19 @@ class Grid:
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else:
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comments.append(line.strip())
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material = np.empty(cells.prod()) # initialize as flat array
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material = np.empty(int(cells.prod())) # initialize as flat array
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i = 0
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for line in content[header_length:]:
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items = line.split('#')[0].split()
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if len(items) == 3:
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if items[1].lower() == 'of':
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items = np.ones(int(items[0]))*float(items[2])
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material_entry = np.ones(int(items[0]))*float(items[2])
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elif items[1].lower() == 'to':
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items = np.linspace(int(items[0]),int(items[2]),
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material_entry = np.linspace(int(items[0]),int(items[2]),
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abs(int(items[2])-int(items[0]))+1,dtype=float)
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else: items = list(map(float,items))
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else: items = list(map(float,items))
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material[i:i+len(items)] = items
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else: material_entry = list(map(float, items))
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else: material_entry = list(map(float, items))
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material[i:i+len(material_entry)] = material_entry
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i += len(items)
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if i != cells.prod():
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@ -251,7 +261,7 @@ class Grid:
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@staticmethod
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def load_Neper(fname):
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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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@ -276,10 +286,10 @@ class Grid:
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@staticmethod
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def load_DREAM3D(fname,
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feature_IDs=None,cell_data=None,
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phases='Phases',Euler_angles='EulerAngles',
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base_group=None):
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def load_DREAM3D(fname: str,
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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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"""
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Load DREAM.3D (HDF5) file.
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@ -339,7 +349,7 @@ class Grid:
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@staticmethod
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def from_table(table,coordinates,labels):
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def from_table(table: Table, coordinates: str, labels: Union[str, Sequence[str]]) -> "Grid":
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"""
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Create grid from ASCII table.
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@ -372,11 +382,16 @@ class Grid:
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@staticmethod
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def _find_closest_seed(seeds, weights, point):
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def _find_closest_seed(seeds: np.ndarray, weights: np.ndarray, point: np.ndarray) -> np.integer:
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return np.argmin(np.sum((np.broadcast_to(point,(len(seeds),3))-seeds)**2,axis=1) - weights)
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@staticmethod
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def from_Laguerre_tessellation(cells,size,seeds,weights,material=None,periodic=True):
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def from_Laguerre_tessellation(cells,
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size,
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seeds,
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weights,
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material = None,
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periodic = True):
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"""
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Create grid from Laguerre tessellation.
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@ -412,7 +427,6 @@ class Grid:
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seeds_p = seeds
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coords = grid_filters.coordinates0_point(cells,size).reshape(-1,3)
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pool = mp.Pool(int(os.environ.get('OMP_NUM_THREADS',4)))
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result = pool.map_async(partial(Grid._find_closest_seed,seeds_p,weights_p), coords)
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pool.close()
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@ -428,7 +442,11 @@ class Grid:
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@staticmethod
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def from_Voronoi_tessellation(cells,size,seeds,material=None,periodic=True):
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def from_Voronoi_tessellation(cells: np.ndarray,
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size: Union[Sequence[float], np.ndarray],
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seeds: np.ndarray,
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material: np.ndarray = None,
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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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@ -509,7 +527,12 @@ class Grid:
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@staticmethod
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def from_minimal_surface(cells,size,surface,threshold=0.0,periods=1,materials=(0,1)):
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def from_minimal_surface(cells: np.ndarray,
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size: Union[Sequence[float], np.ndarray],
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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: tuple = (0,1)) -> "Grid":
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"""
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Create grid from definition of triply periodic minimal surface.
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@ -595,7 +618,7 @@ class Grid:
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)
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def save(self,fname,compress=True):
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def save(self, fname: Union[str, Path], compress: bool = True):
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"""
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Save as VTK image data file.
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@ -614,7 +637,7 @@ class Grid:
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v.save(fname if str(fname).endswith('.vti') else str(fname)+'.vti',parallel=False,compress=compress)
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def save_ASCII(self,fname):
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def save_ASCII(self, fname: Union[str, TextIO]):
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"""
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Save as geom file.
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@ -649,8 +672,14 @@ class Grid:
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VTK.from_rectilinear_grid(self.cells,self.size,self.origin).show()
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def add_primitive(self,dimension,center,exponent,
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fill=None,R=Rotation(),inverse=False,periodic=True):
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def add_primitive(self,
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dimension: np.ndarray,
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center: np.ndarray,
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exponent: Union[np.ndarray, float],
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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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"""
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Insert a primitive geometric object at a given position.
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@ -734,7 +763,7 @@ class Grid:
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)
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def mirror(self,directions,reflect=False):
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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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@ -769,7 +798,7 @@ class Grid:
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if not set(directions).issubset(valid):
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raise ValueError(f'invalid direction {set(directions).difference(valid)} specified')
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limits = [None,None] if reflect else [-2,0]
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limits: Sequence[Optional[int]] = [None,None] if reflect else [-2,0]
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mat = self.material.copy()
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if 'x' in directions:
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@ -786,7 +815,7 @@ class Grid:
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)
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def flip(self,directions):
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def flip(self, directions: Sequence[str]) -> "Grid":
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"""
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Flip grid along given directions.
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@ -815,7 +844,7 @@ class Grid:
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)
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def scale(self,cells,periodic=True):
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def scale(self, cells: np.ndarray, periodic: bool = True) -> "Grid":
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"""
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Scale grid to new cells.
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@ -859,7 +888,7 @@ class Grid:
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)
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def clean(self,stencil=3,selection=None,periodic=True):
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def clean(self, stencil: int = 3, selection: Sequence[float] = None, 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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@ -878,7 +907,7 @@ class Grid:
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Updated grid-based geometry.
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"""
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def mostFrequent(arr,selection=None):
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def mostFrequent(arr, selection = None):
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me = arr[arr.size//2]
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if selection is None or me in selection:
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unique, inverse = np.unique(arr, return_inverse=True)
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@ -899,7 +928,7 @@ class Grid:
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)
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def renumber(self):
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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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@ -918,7 +947,7 @@ class Grid:
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)
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def rotate(self,R,fill=None):
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def rotate(self, R: Rotation, fill: Union[int, float] = None) -> "Grid":
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"""
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Rotate grid (pad if required).
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@ -956,7 +985,7 @@ class Grid:
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)
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def canvas(self,cells=None,offset=None,fill=None):
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def canvas(self, cells = None, offset = None, fill = None):
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"""
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Crop or enlarge/pad grid.
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@ -1008,7 +1037,7 @@ class Grid:
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)
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def substitute(self,from_material,to_material):
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def substitute(self, from_material: np.ndarray, to_material: np.ndarray) -> "Grid":
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"""
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Substitute material indices.
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@ -1025,7 +1054,7 @@ class Grid:
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Updated grid-based geometry.
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"""
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def mp(entry,mapper):
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def mp(entry, mapper):
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return mapper[entry] if entry in mapper else entry
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mp = np.vectorize(mp)
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@ -1038,7 +1067,7 @@ class Grid:
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)
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def sort(self):
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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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@ -1060,7 +1089,11 @@ class Grid:
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)
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def vicinity_offset(self,vicinity=1,offset=None,trigger=[],periodic=True):
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def vicinity_offset(self,
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vicinity: int = 1,
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offset: int = None,
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trigger: Sequence[int] = [],
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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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@ -1088,8 +1121,7 @@ class Grid:
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Updated grid-based geometry.
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"""
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def tainted_neighborhood(stencil,trigger):
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def tainted_neighborhood(stencil, trigger):
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me = stencil[stencil.shape[0]//2]
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return np.any(stencil != me if len(trigger) == 0 else
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np.in1d(stencil,np.array(list(set(trigger) - {me}))))
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@ -1108,7 +1140,7 @@ class Grid:
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)
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def get_grain_boundaries(self,periodic=True,directions='xyz'):
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def get_grain_boundaries(self, periodic = True, directions = 'xyz'):
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"""
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Create VTK unstructured grid containing grain boundaries.
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@ -130,9 +130,9 @@ def gradient(size: _np.ndarray, f: _np.ndarray) -> _np.ndarray:
|
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return _np.fft.irfftn(grad_,axes=(0,1,2),s=f.shape[:3])
|
||||
|
||||
|
||||
def coordinates0_point(cells: Union[ _np.ndarray,Sequence[int]],
|
||||
size: _np.ndarray,
|
||||
origin: _np.ndarray = _np.zeros(3)) -> _np.ndarray:
|
||||
def coordinates0_point(cells: Union[_np.ndarray, Sequence[int]],
|
||||
size: Union[_np.ndarray, Sequence[float]],
|
||||
origin: Union[_np.ndarray, Sequence[float]] = _np.zeros(3)) -> _np.ndarray:
|
||||
"""
|
||||
Cell center positions (undeformed).
|
||||
|
||||
|
|
@ -305,9 +305,9 @@ def cellsSizeOrigin_coordinates0_point(coordinates0: _np.ndarray,
|
|||
return (cells,size,origin)
|
||||
|
||||
|
||||
def coordinates0_node(cells: Union[_np.ndarray,Sequence[int]],
|
||||
size: _np.ndarray,
|
||||
origin: _np.ndarray = _np.zeros(3)) -> _np.ndarray:
|
||||
def coordinates0_node(cells: Union[_np.ndarray, Sequence[int]],
|
||||
size: Union[_np.ndarray, Sequence[int]],
|
||||
origin: Union[_np.ndarray, Sequence[int]] = _np.zeros(3)) -> _np.ndarray:
|
||||
"""
|
||||
Nodal positions (undeformed).
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue