917 lines
38 KiB
Python
917 lines
38 KiB
Python
import copy
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import multiprocessing as mp
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from functools import partial
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from os import path
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import numpy as np
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import h5py
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from scipy import ndimage,spatial
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import vtk
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from . import environment
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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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class Geom:
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"""Geometry definition for grid solvers."""
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def __init__(self,material,size,origin=[0.0,0.0,0.0],comments=[]):
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"""
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New geometry definition from array of material, size, and origin.
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Parameters
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----------
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material : numpy.ndarray
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Material index array (3D).
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size : list or numpy.ndarray
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Physical size of the geometry in meter.
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origin : list or numpy.ndarray, optional
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Physical origin of the geometry in meter.
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comments : list of str, optional
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Comment lines.
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"""
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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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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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if self.material.dtype in np.sctypes['float'] and \
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np.all(self.material == self.material.astype(int).astype(float)):
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self.material = self.material.astype(int)
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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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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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self.comments = [str(c) for c in comments] if isinstance(comments,list) else [str(comments)]
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def __repr__(self):
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"""Basic information on geometry definition."""
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return util.srepr([
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f'grid a b c: {util.srepr(self.grid, " x ")}',
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f'size x y z: {util.srepr(self.size, " x ")}',
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f'origin x y z: {util.srepr(self.origin," ")}',
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f'# materials: {self.N_materials}',
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f'max material: {np.nanmax(self.material)}',
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])
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def __copy__(self):
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"""Copy geometry."""
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return copy.deepcopy(self)
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def copy(self):
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"""Copy geometry."""
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return self.__copy__()
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def diff(self,other):
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"""
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Report property differences of self relative to other.
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Parameters
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----------
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other : Geom
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Geometry to compare self against.
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"""
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message = []
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if np.any(other.grid != self.grid):
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message.append(util.delete(f'grid a b c: {util.srepr(other.grid," x ")}'))
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message.append(util.emph( f'grid a b c: {util.srepr( self.grid," x ")}'))
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if not np.allclose(other.size,self.size):
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message.append(util.delete(f'size x y z: {util.srepr(other.size," x ")}'))
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message.append(util.emph( f'size x y z: {util.srepr( self.size," x ")}'))
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if not np.allclose(other.origin,self.origin):
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message.append(util.delete(f'origin x y z: {util.srepr(other.origin," ")}'))
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message.append(util.emph( f'origin x y z: {util.srepr( self.origin," ")}'))
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if other.N_materials != self.N_materials:
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message.append(util.delete(f'# materials: {other.N_materials}'))
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message.append(util.emph( f'# materials: { self.N_materials}'))
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if np.nanmax(other.material) != np.nanmax(self.material):
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message.append(util.delete(f'max material: {np.nanmax(other.material)}'))
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message.append(util.emph( f'max material: {np.nanmax( self.material)}'))
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return util.return_message(message)
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@property
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def grid(self):
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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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return np.unique(self.material).size
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@staticmethod
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def load(fname):
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"""
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Read a VTK rectilinear grid.
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Parameters
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----------
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fname : str or or pathlib.Path
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Geometry file to read.
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Valid extension is .vtr, it will be appended if not given.
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"""
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v = VTK.load(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr')
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comments = v.get_comments()
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grid = 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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return Geom(material = v.get('material').reshape(grid,order='F'),
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size = bbox[1] - bbox[0],
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origin = bbox[0],
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comments=comments)
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@staticmethod
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def load_ASCII(fname):
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"""
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Read a geom file.
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Parameters
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----------
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fname : str or file handle
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Geometry file to read.
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"""
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try:
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f = open(fname)
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except TypeError:
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f = fname
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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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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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raise TypeError('Header length information missing or invalid')
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content = f.readlines()
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comments = []
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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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key = items[0] if items else ''
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if key == 'grid':
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grid = 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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origin = np.array([float(dict(zip(items[1::2],items[2::2]))[i]) for i in ['x','y','z']])
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else:
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comments.append(line.strip())
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material = np.empty(grid.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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elif items[1].lower() == 'to':
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items = 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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i += len(items)
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if i != grid.prod():
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raise TypeError(f'Invalid file: expected {grid.prod()} entries, found {i}')
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if not np.any(np.mod(material,1) != 0.0): # no float present
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material = material.astype('int')
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return Geom(material.reshape(grid,order='F'),size,origin,comments)
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@staticmethod
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def load_DREAM3D(fname,base_group,point_data=None,material='FeatureIds'):
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"""
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Load a DREAM.3D file.
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Parameters
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----------
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fname : str
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Filename of the DREAM.3D file
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base_group : str
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Name of the group (folder) below 'DataContainers'. For example
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'SyntheticVolumeDataContainer'.
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point_data : str, optional
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Name of the group (folder) containing the point wise material data,
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for example 'CellData'. Defaults to None, in which case points consecutively numbered.
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material : str, optional
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Name of the dataset containing the material ID. Defaults to
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'FeatureIds'.
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"""
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root_dir ='DataContainers'
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f = h5py.File(fname, 'r')
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g = path.join(root_dir,base_group,'_SIMPL_GEOMETRY')
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size = f[path.join(g,'DIMENSIONS')][()] * f[path.join(g,'SPACING')][()]
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grid = f[path.join(g,'DIMENSIONS')][()]
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origin = f[path.join(g,'ORIGIN')][()]
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group_pointwise = path.join(root_dir,base_group,point_data)
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ma = np.arange(1,np.product(grid)+1,dtype=int) if point_data is None else \
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np.reshape(f[path.join(group_pointwise,material)],grid.prod())
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return Geom(ma.reshape(grid,order='F'),size,origin,util.execution_stamp('Geom','load_DREAM3D'))
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@staticmethod
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def from_table(table,coordinates,labels):
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"""
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Load an ASCII table.
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Parameters
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----------
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table : damask.Table
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Table that contains material information.
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coordinates : str
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Label of the column containing the spatial coordinates.
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labels : str or list of str
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Label(s) of the columns containing the material definition.
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Each unique combintation of values results in a material.
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"""
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t = table.sort_by([f'{i}_{coordinates}' for i in range(3,0,-1)])
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grid,size,origin = grid_filters.cell_coord0_gridSizeOrigin(t.get(coordinates))
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labels_ = [labels] if isinstance(labels,str) else labels
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_,unique_inverse = np.unique(np.hstack([t.get(l) for l in labels_]),return_inverse=True,axis=0)
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ma = unique_inverse.reshape(grid,order='F') + 1
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return Geom(ma,size,origin,util.execution_stamp('Geom','from_table'))
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@staticmethod
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def _find_closest_seed(seeds, weights, point):
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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(grid,size,seeds,weights,material=None,periodic=True):
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"""
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Generate geometry from Laguerre tessellation.
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Parameters
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----------
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grid : int numpy.ndarray of shape (3)
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Number of grid points in x,y,z direction.
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size : list or numpy.ndarray of shape (3)
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Physical size of the geometry in meter.
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seeds : numpy.ndarray of shape (:,3)
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Position of the seed points in meter. All points need to lay within the box.
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weights : numpy.ndarray of shape (seeds.shape[0])
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Weights of the seeds. Setting all weights to 1.0 gives a standard Voronoi tessellation.
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material : numpy.ndarray of shape (seeds.shape[0]), optional
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Material ID of the seeds. Defaults to None, in which case materials are
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consecutively numbered.
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periodic : Boolean, optional
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Perform a periodic tessellation. Defaults to True.
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"""
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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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seeds_p = np.vstack((seeds_p-np.array([0.,size[1],0.]),seeds_p,seeds_p+np.array([0.,size[1],0.])))
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seeds_p = np.vstack((seeds_p-np.array([0.,0.,size[2]]),seeds_p,seeds_p+np.array([0.,0.,size[2]])))
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coords = grid_filters.cell_coord0(grid*3,size*3,-size).reshape(-1,3)
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else:
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weights_p = weights
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seeds_p = seeds
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coords = grid_filters.cell_coord0(grid,size).reshape(-1,3)
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pool = mp.Pool(processes = int(environment.options['DAMASK_NUM_THREADS']))
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result = pool.map_async(partial(Geom._find_closest_seed,seeds_p,weights_p), [coord for coord in coords])
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pool.close()
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pool.join()
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material_ = np.array(result.get())
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if periodic:
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material_ = material_.reshape(grid*3)
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material_ = material_[grid[0]:grid[0]*2,grid[1]:grid[1]*2,grid[2]:grid[2]*2]%seeds.shape[0]
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else:
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material_ = material_.reshape(grid)
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return Geom(material = material_ if material is None else material[material_],
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size = size,
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comments = util.execution_stamp('Geom','from_Laguerre_tessellation'),
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)
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@staticmethod
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def from_Voronoi_tessellation(grid,size,seeds,material=None,periodic=True):
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"""
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Generate geometry from Voronoi tessellation.
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Parameters
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----------
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grid : int numpy.ndarray of shape (3)
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Number of grid points in x,y,z direction.
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size : list or numpy.ndarray of shape (3)
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Physical size of the geometry in meter.
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seeds : numpy.ndarray of shape (:,3)
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Position of the seed points in meter. All points need to lay within the box.
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material : numpy.ndarray of shape (seeds.shape[0]), optional
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Material ID of the seeds. Defaults to None, in which case materials are
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consecutively numbered.
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periodic : Boolean, optional
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Perform a periodic tessellation. Defaults to True.
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"""
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coords = grid_filters.cell_coord0(grid,size).reshape(-1,3)
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KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds)
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devNull,material_ = KDTree.query(coords)
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return Geom(material = (material_ if material is None else material[material_]).reshape(grid),
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size = size,
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comments = util.execution_stamp('Geom','from_Voronoi_tessellation'),
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)
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_minimal_surface = \
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{'Schwarz P': lambda x,y,z: np.cos(x) + np.cos(y) + np.cos(z),
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'Double Primitive': lambda x,y,z: ( 0.5 * (np.cos(x)*np.cos(y) + np.cos(y)*np.cos(z) + np.cos(z)*np.cos(x))
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+ 0.2 * (np.cos(2*x) + np.cos(2*y) + np.cos(2*z)) ),
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'Schwarz D': lambda x,y,z: ( np.sin(x)*np.sin(y)*np.sin(z)
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+ np.sin(x)*np.cos(y)*np.cos(z)
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+ np.cos(x)*np.cos(y)*np.sin(z)
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+ np.cos(x)*np.sin(y)*np.cos(z) ),
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'Complementary D': lambda x,y,z: ( np.cos(3*x+y)*np.cos(z) - np.sin(3*x-y)*np.sin(z) + np.cos(x+3*y)*np.cos(z)
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+ np.sin(x-3*y)*np.sin(z) + np.cos(x-y)*np.cos(3*z) - np.sin(x+y)*np.sin(3*z) ),
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'Double Diamond': lambda x,y,z: 0.5 * (np.sin(x)*np.sin(y)
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+ np.sin(y)*np.sin(z)
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+ np.sin(z)*np.sin(x)
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+ np.cos(x) * np.cos(y) * np.cos(z) ),
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'Dprime': lambda x,y,z: 0.5 * ( np.cos(x)*np.cos(y)*np.cos(z)
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+ np.cos(x)*np.sin(y)*np.sin(z)
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+ np.sin(x)*np.cos(y)*np.sin(z)
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+ np.sin(x)*np.sin(y)*np.cos(z)
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- np.sin(2*x)*np.sin(2*y)
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- np.sin(2*y)*np.sin(2*z)
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- np.sin(2*z)*np.sin(2*x) ) - 0.2,
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'Gyroid': lambda x,y,z: np.cos(x)*np.sin(y) + np.cos(y)*np.sin(z) + np.cos(z)*np.sin(x),
|
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'Gprime': lambda x,y,z : ( np.sin(2*x)*np.cos(y)*np.sin(z)
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+ np.sin(2*y)*np.cos(z)*np.sin(x)
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+ np.sin(2*z)*np.cos(x)*np.sin(y) ) + 0.32,
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'Karcher K': lambda x,y,z: ( 0.3 * ( np.cos(x) + np.cos(y) + np.cos(z)
|
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+ np.cos(x)*np.cos(y) + np.cos(y)*np.cos(z) + np.cos(z)*np.cos(x) )
|
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- 0.4 * ( np.cos(2*x) + np.cos(2*y) + np.cos(2*z) ) ) + 0.2,
|
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'Lidinoid': lambda x,y,z: 0.5 * ( np.sin(2*x)*np.cos(y)*np.sin(z)
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+ np.sin(2*y)*np.cos(z)*np.sin(x)
|
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+ np.sin(2*z)*np.cos(x)*np.sin(y)
|
||
- np.cos(2*x)*np.cos(2*y)
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- np.cos(2*y)*np.cos(2*z)
|
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- np.cos(2*z)*np.cos(2*x) ) + 0.15,
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'Neovius': lambda x,y,z: ( 3 * (np.cos(x)+np.cos(y)+np.cos(z))
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+ 4 * np.cos(x)*np.cos(y)*np.cos(z) ),
|
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'Fisher-Koch S': lambda x,y,z: ( np.cos(2*x)*np.sin( y)*np.cos( z)
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+ np.cos( x)*np.cos(2*y)*np.sin( z)
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+ np.sin( x)*np.cos( y)*np.cos(2*z) ),
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}
|
||
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||
|
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@staticmethod
|
||
def from_minimal_surface(grid,size,surface,threshold=0.0,periods=1,materials=(0,1)):
|
||
"""
|
||
Generate geometry from definition of triply periodic minimal surface.
|
||
|
||
Parameters
|
||
----------
|
||
grid : int numpy.ndarray of shape (3)
|
||
Number of grid points in x,y,z direction.
|
||
size : list or numpy.ndarray of shape (3)
|
||
Physical size of the geometry in meter.
|
||
surface : str
|
||
Type of the minimal surface. See notes for details.
|
||
threshold : float, optional.
|
||
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
|
||
Material IDs. Defaults to (1,2).
|
||
|
||
Notes
|
||
-----
|
||
The following triply-periodic minimal surfaces are implemented:
|
||
- Schwarz P
|
||
- Double Primitive
|
||
- Schwarz D
|
||
- Complementary D
|
||
- Double Diamond
|
||
- Dprime
|
||
- Gyroid
|
||
- Gprime
|
||
- Karcher K
|
||
- Lidinoid
|
||
- Neovius
|
||
- Fisher-Koch S
|
||
|
||
References
|
||
----------
|
||
Surface curvature in triply-periodic minimal surface architectures as
|
||
a distinct design parameter in preparing advanced tissue engineering scaffolds
|
||
Sébastien B G Blanquer, Maike Werner, Markus Hannula, Shahriar Sharifi,
|
||
Guillaume P R Lajoinie, David Eglin, Jari Hyttinen, André A Poot, and Dirk W Grijpma
|
||
10.1088/1758-5090/aa6553
|
||
|
||
Triply Periodic Bicontinuous Cubic Microdomain Morphologies by Symmetries
|
||
Meinhard Wohlgemuth, Nataliya Yufa, James Hoffman, and Edwin L. Thomas
|
||
10.1021/ma0019499
|
||
|
||
Minisurf – A minimal surface generator for finite element modeling and additive manufacturing
|
||
Meng-Ting Hsieh, Lorenzo Valdevit
|
||
10.1016/j.simpa.2020.100026
|
||
|
||
"""
|
||
x,y,z = np.meshgrid(periods*2.0*np.pi*(np.arange(grid[0])+0.5)/grid[0],
|
||
periods*2.0*np.pi*(np.arange(grid[1])+0.5)/grid[1],
|
||
periods*2.0*np.pi*(np.arange(grid[2])+0.5)/grid[2],
|
||
indexing='ij',sparse=True)
|
||
return Geom(material = np.where(threshold < Geom._minimal_surface[surface](x,y,z),materials[1],materials[0]),
|
||
size = size,
|
||
comments = util.execution_stamp('Geom','from_minimal_surface'),
|
||
)
|
||
|
||
|
||
def save(self,fname,compress=True):
|
||
"""
|
||
Store as vtk rectilinear grid.
|
||
|
||
Parameters
|
||
----------
|
||
fname : str or or pathlib.Path
|
||
Filename to write. Valid extension is .vtr, it will be appended if not given.
|
||
compress : bool, optional
|
||
Compress with zlib algorithm. Defaults to True.
|
||
|
||
"""
|
||
v = VTK.from_rectilinearGrid(self.grid,self.size,self.origin)
|
||
v.add(self.material.flatten(order='F'),'material')
|
||
v.add_comments(self.comments)
|
||
|
||
v.save(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr',parallel=False,compress=compress)
|
||
|
||
|
||
def save_ASCII(self,fname):
|
||
"""
|
||
Write a geom file.
|
||
|
||
Parameters
|
||
----------
|
||
fname : str or file handle
|
||
Geometry file to write with extension '.geom'.
|
||
compress : bool, optional
|
||
Compress geometry with 'x of y' and 'a to b'.
|
||
|
||
"""
|
||
header = [f'{len(self.comments)+4} header'] + self.comments \
|
||
+ ['grid a {} b {} c {}'.format(*self.grid),
|
||
'size x {} y {} z {}'.format(*self.size),
|
||
'origin x {} y {} z {}'.format(*self.origin),
|
||
'homogenization 1',
|
||
]
|
||
|
||
format_string = '%g' if self.material.dtype in np.sctypes['float'] else \
|
||
'%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.material)))))
|
||
np.savetxt(fname,
|
||
self.material.reshape([self.grid[0],np.prod(self.grid[1:])],order='F').T,
|
||
header='\n'.join(header), fmt=format_string, comments='')
|
||
|
||
|
||
def show(self):
|
||
"""Show on screen."""
|
||
v = VTK.from_rectilinearGrid(self.grid,self.size,self.origin)
|
||
v.show()
|
||
|
||
|
||
def add_primitive(self,dimension,center,exponent,
|
||
fill=None,R=Rotation(),inverse=False,periodic=True):
|
||
"""
|
||
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, grid point locations (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, grid point
|
||
locations (cell centers) are addressed.
|
||
If given as floats, coordinates are addressed.
|
||
exponent : numpy.ndarray of shape(3) or float
|
||
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)
|
||
fill : int, optional
|
||
Fill value for primitive. Defaults to material.max() + 1.
|
||
R : damask.Rotation, optional
|
||
Rotation of primitive. Defaults to no rotation.
|
||
inverse : Boolean, optional
|
||
Retain original materials within primitive and fill outside.
|
||
Defaults to False.
|
||
periodic : Boolean, optional
|
||
Repeat primitive over boundaries. Defaults to True.
|
||
|
||
"""
|
||
# normalized 'radius' and center
|
||
r = np.array(dimension)/self.grid/2.0 if np.array(dimension).dtype in np.sctypes['int'] else \
|
||
np.array(dimension)/self.size/2.0
|
||
c = (np.array(center) + .5)/self.grid if np.array(center).dtype in np.sctypes['int'] else \
|
||
(np.array(center) - self.origin)/self.size
|
||
|
||
coords = grid_filters.cell_coord0(self.grid,np.ones(3)) \
|
||
- ((np.ones(3)-(1./self.grid if np.array(center).dtype in np.sctypes['int'] else 0))*0.5 if periodic else c) # periodic center is always at CoG
|
||
coords_rot = R.broadcast_to(tuple(self.grid))@coords
|
||
|
||
with np.errstate(all='ignore'):
|
||
mask = np.sum(np.power(coords_rot/r,2.0**np.array(exponent)),axis=-1) > 1.0
|
||
|
||
if periodic: # translate back to center
|
||
mask = np.roll(mask,((c-np.ones(3)*.5)*self.grid).astype(int),(0,1,2))
|
||
|
||
fill_ = np.full_like(self.material,np.nanmax(self.material)+1 if fill is None else fill)
|
||
|
||
return Geom(material = np.where(np.logical_not(mask) if inverse else mask, self.material,fill_),
|
||
size = self.size,
|
||
origin = self.origin,
|
||
comments = self.comments+[util.execution_stamp('Geom','add_primitive')],
|
||
)
|
||
|
||
|
||
def mirror(self,directions,reflect=False):
|
||
"""
|
||
Mirror geometry along given directions.
|
||
|
||
Parameters
|
||
----------
|
||
directions : iterable containing str
|
||
Direction(s) along which the geometry is mirrored.
|
||
Valid entries are 'x', 'y', 'z'.
|
||
reflect : bool, optional
|
||
Reflect (include) outermost layers. Defaults to False.
|
||
|
||
"""
|
||
valid = ['x','y','z']
|
||
if not set(directions).issubset(valid):
|
||
raise ValueError(f'Invalid direction {set(directions).difference(valid)} specified.')
|
||
|
||
limits = [None,None] if reflect else [-2,0]
|
||
mat = self.material.copy()
|
||
|
||
if 'x' in directions:
|
||
mat = np.concatenate([mat,mat[limits[0]:limits[1]:-1,:,:]],0)
|
||
if 'y' in directions:
|
||
mat = np.concatenate([mat,mat[:,limits[0]:limits[1]:-1,:]],1)
|
||
if 'z' in directions:
|
||
mat = np.concatenate([mat,mat[:,:,limits[0]:limits[1]:-1]],2)
|
||
|
||
return Geom(material = mat,
|
||
size = self.size/self.grid*np.asarray(mat.shape),
|
||
origin = self.origin,
|
||
comments = self.comments+[util.execution_stamp('Geom','mirror')],
|
||
)
|
||
|
||
|
||
def flip(self,directions):
|
||
"""
|
||
Flip geometry along given directions.
|
||
|
||
Parameters
|
||
----------
|
||
directions : iterable containing str
|
||
Direction(s) along which the geometry is flipped.
|
||
Valid entries are 'x', 'y', 'z'.
|
||
|
||
"""
|
||
valid = ['x','y','z']
|
||
if not set(directions).issubset(valid):
|
||
raise ValueError(f'Invalid direction {set(directions).difference(valid)} specified.')
|
||
|
||
mat = np.flip(self.material, (valid.index(d) for d in directions if d in valid))
|
||
|
||
return Geom(material = mat,
|
||
size = self.size,
|
||
origin = self.origin,
|
||
comments = self.comments+[util.execution_stamp('Geom','flip')],
|
||
)
|
||
|
||
|
||
def scale(self,grid,periodic=True):
|
||
"""
|
||
Scale geometry to new grid.
|
||
|
||
Parameters
|
||
----------
|
||
grid : numpy.ndarray of shape (3)
|
||
Number of grid points in x,y,z direction.
|
||
periodic : Boolean, optional
|
||
Assume geometry to be periodic. Defaults to True.
|
||
|
||
"""
|
||
return Geom(material = ndimage.interpolation.zoom(
|
||
self.material,
|
||
grid/self.grid,
|
||
output=self.material.dtype,
|
||
order=0,
|
||
mode=('wrap' if periodic else 'nearest'),
|
||
prefilter=False
|
||
),
|
||
size = self.size,
|
||
origin = self.origin,
|
||
comments = self.comments+[util.execution_stamp('Geom','scale')],
|
||
)
|
||
|
||
|
||
def clean(self,stencil=3,selection=None,periodic=True):
|
||
"""
|
||
Smooth geometry by selecting most frequent material index within given stencil at each location.
|
||
|
||
Parameters
|
||
----------
|
||
stencil : int, optional
|
||
Size of smoothing stencil.
|
||
selection : list, optional
|
||
Field values that can be altered. Defaults to all.
|
||
periodic : Boolean, optional
|
||
Assume geometry to be periodic. Defaults to True.
|
||
|
||
"""
|
||
def mostFrequent(arr,selection=None):
|
||
me = arr[arr.size//2]
|
||
if selection is None or me in selection:
|
||
unique, inverse = np.unique(arr, return_inverse=True)
|
||
return unique[np.argmax(np.bincount(inverse))]
|
||
else:
|
||
return me
|
||
|
||
return Geom(material = ndimage.filters.generic_filter(
|
||
self.material,
|
||
mostFrequent,
|
||
size=(stencil if selection is None else stencil//2*2+1,)*3,
|
||
mode=('wrap' if periodic else 'nearest'),
|
||
extra_keywords=dict(selection=selection),
|
||
).astype(self.material.dtype),
|
||
size = self.size,
|
||
origin = self.origin,
|
||
comments = self.comments+[util.execution_stamp('Geom','clean')],
|
||
)
|
||
|
||
|
||
def renumber(self):
|
||
"""Renumber sorted material indices to 1,...,N."""
|
||
renumbered = np.empty(self.grid,dtype=self.material.dtype)
|
||
for i, oldID in enumerate(np.unique(self.material)):
|
||
renumbered = np.where(self.material == oldID, i+1, renumbered)
|
||
|
||
return Geom(material = renumbered,
|
||
size = self.size,
|
||
origin = self.origin,
|
||
comments = self.comments+[util.execution_stamp('Geom','renumber')],
|
||
)
|
||
|
||
|
||
def rotate(self,R,fill=None):
|
||
"""
|
||
Rotate geometry (pad if required).
|
||
|
||
Parameters
|
||
----------
|
||
R : damask.Rotation
|
||
Rotation to apply to the geometry.
|
||
fill : int or float, optional
|
||
Material index to fill the corners. Defaults to material.max() + 1.
|
||
|
||
"""
|
||
if fill is None: fill = np.nanmax(self.material) + 1
|
||
dtype = float if np.isnan(fill) or int(fill) != fill or self.material.dtype==np.float else int
|
||
|
||
Eulers = R.as_Eulers(degrees=True)
|
||
material_in = self.material.copy()
|
||
|
||
# These rotations are always applied in the reference coordinate system, i.e. (z,x,z) not (z,x',z'')
|
||
# see https://www.cs.utexas.edu/~theshark/courses/cs354/lectures/cs354-14.pdf
|
||
for angle,axes in zip(Eulers[::-1], [(0,1),(1,2),(0,1)]):
|
||
material_out = ndimage.rotate(material_in,angle,axes,order=0,
|
||
prefilter=False,output=dtype,cval=fill)
|
||
if np.prod(material_in.shape) == np.prod(material_out.shape):
|
||
# avoid scipy interpolation errors for rotations close to multiples of 90°
|
||
material_in = np.rot90(material_in,k=np.rint(angle/90.).astype(int),axes=axes)
|
||
else:
|
||
material_in = material_out
|
||
|
||
origin = self.origin-(np.asarray(material_in.shape)-self.grid)*.5 * self.size/self.grid
|
||
|
||
return Geom(material = material_in,
|
||
size = self.size/self.grid*np.asarray(material_in.shape),
|
||
origin = origin,
|
||
comments = self.comments+[util.execution_stamp('Geom','rotate')],
|
||
)
|
||
|
||
|
||
def canvas(self,grid=None,offset=None,fill=None):
|
||
"""
|
||
Crop or enlarge/pad geometry.
|
||
|
||
Parameters
|
||
----------
|
||
grid : numpy.ndarray of shape (3)
|
||
Number of grid points in x,y,z direction.
|
||
offset : numpy.ndarray of shape (3)
|
||
Offset (measured in grid points) from old to new geometry [0,0,0].
|
||
fill : int or float, optional
|
||
Material index to fill the background. Defaults to material.max() + 1.
|
||
|
||
"""
|
||
if offset is None: offset = 0
|
||
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.grid if grid is None else grid,fill,dtype)
|
||
|
||
LL = np.clip( offset, 0,np.minimum(self.grid, grid+offset))
|
||
UR = np.clip( offset+grid, 0,np.minimum(self.grid, grid+offset))
|
||
ll = np.clip(-offset, 0,np.minimum( grid,self.grid-offset))
|
||
ur = np.clip(-offset+self.grid,0,np.minimum( grid,self.grid-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 Geom(material = canvas,
|
||
size = self.size/self.grid*np.asarray(canvas.shape),
|
||
origin = self.origin+offset*self.size/self.grid,
|
||
comments = self.comments+[util.execution_stamp('Geom','canvas')],
|
||
)
|
||
|
||
|
||
def substitute(self,from_material,to_material):
|
||
"""
|
||
Substitute material indices.
|
||
|
||
Parameters
|
||
----------
|
||
from_material : iterable of ints
|
||
Material indices to be substituted.
|
||
to_material : iterable of ints
|
||
New material indices.
|
||
|
||
"""
|
||
substituted = self.material.copy()
|
||
for from_ms,to_ms in zip(from_material,to_material):
|
||
substituted[self.material==from_ms] = to_ms
|
||
|
||
return Geom(material = substituted,
|
||
size = self.size,
|
||
origin = self.origin,
|
||
comments = self.comments+[util.execution_stamp('Geom','substitute')],
|
||
)
|
||
|
||
|
||
def vicinity_offset(self,vicinity=1,offset=None,trigger=[],periodic=True):
|
||
"""
|
||
Offset material index of points in the vicinity of xxx.
|
||
|
||
Different from themselves (or listed as triggers) within a given (cubic) vicinity,
|
||
i.e. within the region close to a grain/phase boundary.
|
||
ToDo: use include/exclude as in seeds.from_geom
|
||
|
||
Parameters
|
||
----------
|
||
vicinity : int, optional
|
||
Voxel distance checked for presence of other materials.
|
||
Defaults to 1.
|
||
offset : int, optional
|
||
Offset (positive or negative) to tag material indices,
|
||
defaults to material.max() + 1.
|
||
trigger : list of ints, optional
|
||
List of material indices that trigger a change.
|
||
Defaults to [], meaning that any different neighbor triggers a change.
|
||
periodic : Boolean, optional
|
||
Assume geometry to be periodic. Defaults to True.
|
||
|
||
"""
|
||
def tainted_neighborhood(stencil,trigger):
|
||
|
||
me = stencil[stencil.shape[0]//2]
|
||
if len(trigger) == 0:
|
||
return np.any(stencil != me)
|
||
if me in trigger:
|
||
trigger = set(trigger)
|
||
trigger.remove(me)
|
||
trigger = list(trigger)
|
||
return np.any(np.in1d(stencil,np.array(trigger)))
|
||
|
||
offset_ = np.nanmax(self.material) if offset is None else offset
|
||
mask = ndimage.filters.generic_filter(self.material,
|
||
tainted_neighborhood,
|
||
size=1+2*vicinity,
|
||
mode='wrap' if periodic else 'nearest',
|
||
extra_keywords={'trigger':trigger})
|
||
|
||
return Geom(material = np.where(mask, self.material + offset_,self.material),
|
||
size = self.size,
|
||
origin = self.origin,
|
||
comments = self.comments+[util.execution_stamp('Geom','vicinity_offset')],
|
||
)
|
||
|
||
def ShowGB(self,periodic=False):
|
||
"""
|
||
Create an extra VTK file to show grain boundaries as feature edges.
|
||
|
||
Parameters
|
||
----------
|
||
periodic : Boolean, optional
|
||
Show boundaries at periodic nodes too. Defaults to False.
|
||
|
||
"""
|
||
v = VTK.from_polyData(grid_filters.node_coord0(self.grid,self.size,self.origin).reshape(-1,3,order='F'))
|
||
cells = vtk.vtkCellArray()
|
||
|
||
index={}
|
||
nodes={}
|
||
nodes_PBC={}
|
||
if periodic:
|
||
nodes_PBC['0']=np.array([])
|
||
nodes_PBC['1']=np.array([])
|
||
nodes_PBC['2']=np.array([])
|
||
else:
|
||
nodes_PBC['0']=np.concatenate((
|
||
np.arange(0 , np.prod(self.grid+1) , (self.grid[0]+1) ),
|
||
np.arange(self.grid[0] , np.prod(self.grid+1) , (self.grid[0]+1) ) ))
|
||
nodes_PBC['2']=np.concatenate((
|
||
np.arange(0 , np.prod(self.grid[:2]+1) , 1 ),
|
||
np.arange(np.prod(self.grid+1) - np.prod(self.grid[:2]+1), \
|
||
np.prod(self.grid+1) , 1 ) ))
|
||
nodes_PBC['1']=np.concatenate((
|
||
np.concatenate([np.arange((i)*np.prod(self.grid[:2]+1), \
|
||
(i)*np.prod(self.grid[:2]+1)+ (self.grid[0]+1)) for i in range(self.grid[2]+1)]) ,
|
||
np.concatenate([np.arange( (i+1)*np.prod(self.grid[:2]+1)-(self.grid[0]+1),\
|
||
(i+1)*np.prod(self.grid[:2]+1)) for i in range(self.grid[2]+1)]) ))
|
||
|
||
for d_s in [0,1,2]:
|
||
base_nodes = np.where(self.material==np.roll(self.material,1,d_s),False,True)
|
||
for d in [0,1,2]:
|
||
if d_s == d:
|
||
base_nodes = np.concatenate((base_nodes,np.take(base_nodes,[0],d)),d)
|
||
else:
|
||
base_nodes = np.concatenate((base_nodes,np.logical_and(np.take(base_nodes,[0],d),False)),d)
|
||
nodes['{}'.format(d_s)]= np.argwhere(base_nodes.flatten(order='F'))[:,0]
|
||
index['{}'.format(d_s)]=np.isin(nodes['{}'.format(d_s)],nodes_PBC['{}'.format(d_s)],assume_unique=True,invert=True)
|
||
|
||
for p in nodes['0'][index['0']]:
|
||
q = vtk.vtkQuad()
|
||
q.GetPointIds().SetId(0, p)
|
||
q.GetPointIds().SetId(1, p+(self.grid[0]+1))
|
||
q.GetPointIds().SetId(2, p+np.prod(self.grid[:2]+1)+(self.grid[0]+1))
|
||
q.GetPointIds().SetId(3, p+np.prod(self.grid[:2]+1))
|
||
cells.InsertNextCell(q)
|
||
|
||
for p in nodes['1'][index['1']]:
|
||
q = vtk.vtkQuad()
|
||
q.GetPointIds().SetId(0, p)
|
||
q.GetPointIds().SetId(1, p+np.prod(self.grid[:2]+1))
|
||
q.GetPointIds().SetId(2, p+np.prod(self.grid[:2]+1)+1)
|
||
q.GetPointIds().SetId(3, p+1)
|
||
cells.InsertNextCell(q)
|
||
|
||
for p in nodes['2'][index['2']]:
|
||
q = vtk.vtkQuad()
|
||
q.GetPointIds().SetId(0, p)
|
||
q.GetPointIds().SetId(1, p+1)
|
||
q.GetPointIds().SetId(2, p+(self.grid[0]+1)+1)
|
||
q.GetPointIds().SetId(3, p+(self.grid[0]+1))
|
||
cells.InsertNextCell(q)
|
||
|
||
v.vtk_data.SetPolys(cells)
|
||
v.save('GrainBoundaries')
|
||
|
||
|