DAMASK_EICMD/python/damask/_geom.py

import copy
import multiprocessing as mp
from functools import partial
from os import path
import warnings

import numpy as np
import pandas as pd
import h5py
from scipy import ndimage,spatial

from . import environment
from . import VTK
from . import util
from . import grid_filters
from . import Rotation


class Geom:
    """Geometry definition for grid solvers."""

    def __init__(self,material,size,origin=[0.0,0.0,0.0],comments=[]):
        """
        New geometry definition from array of materials, size, and origin.

        Parameters
        ----------
        material : numpy.ndarray
            Material index array (3D).
        size : list or numpy.ndarray
            Physical size of the geometry in meter.
        origin : list or numpy.ndarray, optional
            Physical origin of the geometry in meter.
        comments : list of str, optional
            Comment lines.

        """
        self.material = material
        self.size     = size
        self.origin   = origin
        self.comments = comments


    def __repr__(self):
        """Basic information on geometry definition."""
        return util.srepr([
               f'grid     a b c:  {util.srepr(self.grid,  " x ")}',
               f'size     x y z:  {util.srepr(self.size,  " x ")}',
               f'origin   x y z:  {util.srepr(self.origin,"   ")}',
               f'# materials:     {self.N_materials}',
               f'max material:    {np.nanmax(self.material)}',
              ])


    def __copy__(self):
        """Copy geometry."""
        return copy.deepcopy(self)


    def copy(self):
        """Copy geometry."""
        return self.__copy__()


    def diff(self,other):
        """
        Report property differences of self relative to other.

        Parameters
        ----------
        other : Geom
            Geometry to compare self against.

        """
        message = []
        if np.any(other.grid != self.grid):
            message.append(util.deemph(f'grid     a b c:     {util.srepr(other.grid," x ")}'))
            message.append(util.emph(  f'grid     a b c:     {util.srepr( self.grid," x ")}'))

        if not np.allclose(other.size,self.size):
            message.append(util.deemph(f'size     x y z:     {util.srepr(other.size," x ")}'))
            message.append(util.emph(  f'size     x y z:     {util.srepr( self.size," x ")}'))

        if not np.allclose(other.origin,self.origin):
            message.append(util.deemph(f'origin   x y z:     {util.srepr(other.origin,"   ")}'))
            message.append(util.emph(  f'origin   x y z:     {util.srepr( self.origin,"   ")}'))

        if other.N_materials != self.N_materials:
            message.append(util.deemph(f'# materials:        {other.N_materials}'))
            message.append(util.emph(  f'# materials:        { self.N_materials}'))

        if np.nanmax(other.material) != np.nanmax(self.material):
            message.append(util.deemph(f'max material:       {np.nanmax(other.material)}'))
            message.append(util.emph(  f'max material:       {np.nanmax( self.material)}'))

        return util.return_message(message)


    @property
    def material(self):
        """Material indices."""
        return self._material

    @material.setter
    def material(self,material):
        if len(material.shape) != 3:
            raise ValueError(f'Invalid material shape {material.shape}.')
        elif material.dtype not in np.sctypes['float'] + np.sctypes['int']:
            raise TypeError(f'Invalid material data type {material.dtype}.')
        else:
            self._material = np.copy(material)

            if self.material.dtype in np.sctypes['float'] and \
               np.all(self.material == self.material.astype(int).astype(float)):
                self._material = self.material.astype(int)


    @property
    def size(self):
        """Physical size of geometry in meter."""
        return self._size

    @size.setter
    def size(self,size):
        if len(size) != 3 or any(np.array(size) <= 0):
            raise ValueError(f'Invalid size {size}.')
        else:
            self._size = np.array(size)

    @property
    def origin(self):
        """Coordinates of geometry origin in meter."""
        return self._origin

    @origin.setter
    def origin(self,origin):
        if len(origin) != 3:
            raise ValueError(f'Invalid origin {origin}.')
        else:
            self._origin = np.array(origin)

    @property
    def comments(self):
        """Comments/history of geometry."""
        return self._comments

    @comments.setter
    def comments(self,comments):
        self._comments = [str(c) for c in comments] if isinstance(comments,list) else [str(comments)]


    @property
    def grid(self):
        """Grid dimension of geometry."""
        return np.asarray(self.material.shape)


    @property
    def N_materials(self):
        """Number of (unique) material indices within geometry."""
        return np.unique(self.material).size


    @staticmethod
    def load(fname):
        """
        Read a VTK rectilinear grid.

        Parameters
        ----------
        fname : str or or pathlib.Path
            Geometry file to read.
            Valid extension is .vtr, which will be appended if not given.

        """
        v = VTK.load(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr')
        comments = v.get_comments()
        grid = np.array(v.vtk_data.GetDimensions())-1
        bbox = np.array(v.vtk_data.GetBounds()).reshape(3,2).T

        return Geom(material = v.get('material').reshape(grid,order='F'),
                    size = bbox[1] - bbox[0],
                    origin = bbox[0],
                    comments=comments)


    @staticmethod
    def load_ASCII(fname):
        """
        Read a geom file.

        Storing geometry files in ASCII format is deprecated.
        This function will be removed in a future version of DAMASK.

        Parameters
        ----------
        fname : str, pathlib.Path, or file handle
            Geometry file to read.

        """
        warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning)
        try:
            f = open(fname)
        except TypeError:
            f = fname

        f.seek(0)
        try:
            header_length,keyword = f.readline().split()[:2]
            header_length = int(header_length)
        except ValueError:
            header_length,keyword = (-1, 'invalid')
        if not keyword.startswith('head') or header_length < 3:
            raise TypeError('Header length information missing or invalid')

        comments = []
        content = f.readlines()
        for i,line in enumerate(content[:header_length]):
            items = line.split('#')[0].lower().strip().split()
            key = items[0] if items else ''
            if   key == 'grid':
                grid   = np.array([  int(dict(zip(items[1::2],items[2::2]))[i]) for i in ['a','b','c']])
            elif key == 'size':
                size   = np.array([float(dict(zip(items[1::2],items[2::2]))[i]) for i in ['x','y','z']])
            elif key == 'origin':
                origin = np.array([float(dict(zip(items[1::2],items[2::2]))[i]) for i in ['x','y','z']])
            else:
                comments.append(line.strip())

        material = np.empty(grid.prod())                                                            # initialize as flat array
        i = 0
        for line in content[header_length:]:
            items = line.split('#')[0].split()
            if len(items) == 3:
                if   items[1].lower() == 'of':
                    items = np.ones(int(items[0]))*float(items[2])
                elif items[1].lower() == 'to':
                    items = np.linspace(int(items[0]),int(items[2]),
                                        abs(int(items[2])-int(items[0]))+1,dtype=float)
                else:                        items = list(map(float,items))
            else:                            items = list(map(float,items))
            material[i:i+len(items)] = items
            i += len(items)

        if i != grid.prod():
            raise TypeError(f'Invalid file: expected {grid.prod()} entries, found {i}')

        if not np.any(np.mod(material,1) != 0.0):                                                   # no float present
            material = material.astype('int') - (1 if material.min() > 0 else 0)

        return Geom(material.reshape(grid,order='F'),size,origin,comments)


    @staticmethod
    def load_DREAM3D(fname,base_group,point_data=None,material='FeatureIds'):
        """
        Load a DREAM.3D file.

        Parameters
        ----------
        fname : str
            Filename of the DREAM.3D file
        base_group : str
            Name of the group (folder) below 'DataContainers',
            for example 'SyntheticVolumeDataContainer'.
        point_data : str, optional
            Name of the group (folder) containing the pointwise material data,
            for example 'CellData'. Defaults to None, in which case points are consecutively numbered.
        material : str, optional
            Name of the dataset containing the material ID.
            Defaults to 'FeatureIds'.

        """
        root_dir ='DataContainers'
        f = h5py.File(fname, 'r')
        g = path.join(root_dir,base_group,'_SIMPL_GEOMETRY')
        grid   = f[path.join(g,'DIMENSIONS')][()]
        size   = f[path.join(g,'SPACING')][()] * grid
        origin = f[path.join(g,'ORIGIN')][()]

        ma = np.arange(grid.prod(),dtype=int) \
             if point_data is None else \
             np.reshape(f[path.join(root_dir,base_group,point_data,material)],grid.prod())

        return Geom(ma.reshape(grid,order='F'),size,origin,util.execution_stamp('Geom','load_DREAM3D'))


    @staticmethod
    def from_table(table,coordinates,labels):
        """
        Derive geometry from an ASCII table.

        Parameters
        ----------
        table : damask.Table
            Table that contains material information.
        coordinates : str
            Label of the vector column containing the spatial coordinates.
            Need to be ordered (1./x fast, 3./z slow).
        labels : str or list of str
            Label(s) of the columns containing the material definition.
            Each unique combintation of values results in one material ID.

        """
        grid,size,origin = grid_filters.cell_coord0_gridSizeOrigin(table.get(coordinates))

        labels_ = [labels] if isinstance(labels,str) else labels
        unique,unique_inverse = np.unique(np.hstack([table.get(l) for l in labels_]),return_inverse=True,axis=0)

        ma = np.arange(grid.prod()) if len(unique) == grid.prod() else \
             np.arange(unique.size)[np.argsort(pd.unique(unique_inverse))][unique_inverse]

        return Geom(ma.reshape(grid,order='F'),size,origin,util.execution_stamp('Geom','from_table'))


    @staticmethod
    def _find_closest_seed(seeds, weights, point):
        return np.argmin(np.sum((np.broadcast_to(point,(len(seeds),3))-seeds)**2,axis=1) - weights)

    @staticmethod
    def from_Laguerre_tessellation(grid,size,seeds,weights,material=None,periodic=True):
        """
        Generate geometry from Laguerre tessellation.

        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.
        seeds : numpy.ndarray of shape (:,3)
            Position of the seed points in meter. All points need to lay within the box.
        weights : numpy.ndarray of shape (seeds.shape[0])
            Weights of the seeds. Setting all weights to 1.0 gives a standard Voronoi tessellation.
        material : numpy.ndarray of shape (seeds.shape[0]), optional
            Material ID of the seeds.
            Defaults to None, in which case materials are consecutively numbered.
        periodic : Boolean, optional
            Perform a periodic tessellation. Defaults to True.

        """
        if periodic:
            weights_p = np.tile(weights,27)                                                         # Laguerre weights (1,2,3,1,2,3,...,1,2,3)
            seeds_p = np.vstack((seeds  -np.array([size[0],0.,0.]),seeds,  seeds  +np.array([size[0],0.,0.])))
            seeds_p = np.vstack((seeds_p-np.array([0.,size[1],0.]),seeds_p,seeds_p+np.array([0.,size[1],0.])))
            seeds_p = np.vstack((seeds_p-np.array([0.,0.,size[2]]),seeds_p,seeds_p+np.array([0.,0.,size[2]])))
            coords  = grid_filters.cell_coord0(grid*3,size*3,-size).reshape(-1,3)
        else:
            weights_p = weights
            seeds_p   = seeds
            coords    = grid_filters.cell_coord0(grid,size).reshape(-1,3)

        pool = mp.Pool(processes = int(environment.options['DAMASK_NUM_THREADS']))
        result = pool.map_async(partial(Geom._find_closest_seed,seeds_p,weights_p), [coord for coord in coords])
        pool.close()
        pool.join()
        material_ = np.array(result.get())

        if periodic:
            material_ = material_.reshape(grid*3)
            material_ = material_[grid[0]:grid[0]*2,grid[1]:grid[1]*2,grid[2]:grid[2]*2]%seeds.shape[0]
        else:
            material_ = material_.reshape(grid)

        return Geom(material = material_ if material is None else material[material_],
                    size     = size,
                    comments = util.execution_stamp('Geom','from_Laguerre_tessellation'),
                   )


    @staticmethod
    def from_Voronoi_tessellation(grid,size,seeds,material=None,periodic=True):
        """
        Generate geometry from Voronoi tessellation.

        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.
        seeds : numpy.ndarray of shape (:,3)
            Position of the seed points in meter. All points need to lay within the box.
        material : numpy.ndarray of shape (seeds.shape[0]), optional
            Material ID of the seeds.
            Defaults to None, in which case materials are consecutively numbered.
        periodic : Boolean, optional
            Perform a periodic tessellation. Defaults to True.

        """
        coords = grid_filters.cell_coord0(grid,size).reshape(-1,3)
        KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds)
        devNull,material_ = KDTree.query(coords)

        return Geom(material = (material_ if material is None else material[material_]).reshape(grid),
                    size     = size,
                    comments = util.execution_stamp('Geom','from_Voronoi_tessellation'),
                   )


    _minimal_surface = \
        {'Schwarz P':        lambda x,y,z: np.cos(x) + np.cos(y) + np.cos(z),
         '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))
                                           + 0.2 * (np.cos(2*x) + np.cos(2*y) + np.cos(2*z)) ),
         'Schwarz D':        lambda x,y,z: ( np.sin(x)*np.sin(y)*np.sin(z)
                                           + np.sin(x)*np.cos(y)*np.cos(z)
                                           + np.cos(x)*np.cos(y)*np.sin(z)
                                           + np.cos(x)*np.sin(y)*np.cos(z) ),
         '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)
                                           + np.sin(x-3*y)*np.sin(z) + np.cos(x-y)*np.cos(3*z) - np.sin(x+y)*np.sin(3*z) ),
         'Double Diamond':   lambda x,y,z: 0.5 * (np.sin(x)*np.sin(y)
                                                + np.sin(y)*np.sin(z)
                                                + np.sin(z)*np.sin(x)
                                                + np.cos(x) * np.cos(y) * np.cos(z) ),
         'Dprime':           lambda x,y,z: 0.5 * ( np.cos(x)*np.cos(y)*np.cos(z)
                                                 + np.cos(x)*np.sin(y)*np.sin(z)
                                                 + np.sin(x)*np.cos(y)*np.sin(z)
                                                 + np.sin(x)*np.sin(y)*np.cos(z)
                                                 - np.sin(2*x)*np.sin(2*y)
                                                 - np.sin(2*y)*np.sin(2*z)
                                                 - np.sin(2*z)*np.sin(2*x) ) - 0.2,
         'Gyroid':           lambda x,y,z: np.cos(x)*np.sin(y) + np.cos(y)*np.sin(z) + np.cos(z)*np.sin(x),
         'Gprime':           lambda x,y,z : ( np.sin(2*x)*np.cos(y)*np.sin(z)
                                            + np.sin(2*y)*np.cos(z)*np.sin(x)
                                            + np.sin(2*z)*np.cos(x)*np.sin(y) ) + 0.32,
         'Karcher K':        lambda x,y,z: ( 0.3 * ( np.cos(x)           + np.cos(y)           + np.cos(z)
                                                   + np.cos(x)*np.cos(y) + np.cos(y)*np.cos(z) + np.cos(z)*np.cos(x) )
                                           - 0.4 * ( np.cos(2*x)         + np.cos(2*y)         + np.cos(2*z) ) ) + 0.2,
         'Lidinoid':         lambda x,y,z: 0.5 * ( np.sin(2*x)*np.cos(y)*np.sin(z)
                                                 + np.sin(2*y)*np.cos(z)*np.sin(x)
                                                 + np.sin(2*z)*np.cos(x)*np.sin(y)
                                                 - np.cos(2*x)*np.cos(2*y)
                                                 - np.cos(2*y)*np.cos(2*z)
                                                 - np.cos(2*z)*np.cos(2*x) ) + 0.15,
         'Neovius':          lambda x,y,z: ( 3 * (np.cos(x)+np.cos(y)+np.cos(z))
                                           + 4 * np.cos(x)*np.cos(y)*np.cos(z) ),
         'Fisher-Koch S':    lambda x,y,z: ( np.cos(2*x)*np.sin(  y)*np.cos(  z)
                                           + np.cos(  x)*np.cos(2*y)*np.sin(  z)
                                           + np.sin(  x)*np.cos(  y)*np.cos(2*z) ),
      }


    @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
        ----------
        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
        Surface curvature in triply-periodic minimal surface architectures as
        a distinct design parameter in preparing advanced tissue engineering scaffolds
        https://doi.org/10.1088/1758-5090/aa6553

        Meinhard Wohlgemuth, Nataliya Yufa, James Hoffman, and Edwin L. Thomas
        Triply Periodic Bicontinuous Cubic Microdomain Morphologies by Symmetries
        https://doi.org/10.1021/ma0019499

        Meng-Ting Hsieh, Lorenzo Valdevit
        Minisurf – A minimal surface generator for finite element modeling and additive manufacturing
        https://doi.org/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 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_rectilinear_grid(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.

        Storing geometry files in ASCII format is deprecated.
        This function will be removed in a future version of DAMASK.

        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'.

        """
        warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning)
        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."""
        VTK.from_rectilinear_grid(self.grid,self.size,self.origin).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
            coordinates (cell centers) are addressed.
            If given as floats, coordinates in space 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.

        """
        # radius and center
        r = np.array(dimension)/2.0*self.size/self.grid if np.array(dimension).dtype in np.sctypes['int'] else \
            np.array(dimension)/2.0
        c = (np.array(center) + .5)*self.size/self.grid if np.array(center).dtype    in np.sctypes['int'] else \
            (np.array(center) - self.origin)

        coords = grid_filters.cell_coord0(self.grid,self.size,
                                          -(0.5*(self.size + (self.size/self.grid
                                                              if np.array(center).dtype in np.sctypes['int'] else
                                                              0)) if periodic else c))
        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/self.size-0.5)*self.grid).round().astype(int),(0,1,2))

        return Geom(material = np.where(np.logical_not(mask) if inverse else mask,
                                        self.material,
                                        np.nanmax(self.material)+1 if fill is None else 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 as 0,...,N-1."""
        _,renumbered = np.unique(self.material,return_inverse=True)

        return Geom(material = renumbered.reshape(self.grid),
                    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_Euler_angles(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.

        """
        def mp(entry,mapper):
            return mapper[entry] if entry in mapper else entry

        mp = np.vectorize(mp)
        mapper = dict(zip(from_material,to_material))

        return Geom(material = mp(self.material,mapper).reshape(self.grid),
                    size     = self.size,
                    origin   = self.origin,
                    comments = self.comments+[util.execution_stamp('Geom','substitute')],
                   )


    def sort(self):
        """Sort material indices such that min(material) is located at (0,0,0)."""
        a = self.material.flatten(order='F')
        from_ma = pd.unique(a)
        sort_idx = np.argsort(from_ma)
        ma = np.unique(a)[sort_idx][np.searchsorted(from_ma,a,sorter = sort_idx)]

        return Geom(material = ma.reshape(self.grid,order='F'),
                    size     = self.size,
                    origin   = self.origin,
                    comments = self.comments+[util.execution_stamp('Geom','sort')],
                   )


    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]
            return np.any(stencil != me
                          if len(trigger) == 0 else
                          np.in1d(stencil,np.array(list(set(trigger) - {me}))))

        offset_ = np.nanmax(self.material)+1 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 get_grain_boundaries(self,periodic=True,directions='xyz'):
        """
        Create VTK unstructured grid containing grain boundaries.

        Parameters
        ----------
        periodic : bool, optional
            Show boundaries across periodicity. Defaults to True.
        directions : iterable containing str, optional
            Direction(s) along which the geometry is mirrored.
            Valid entries are 'x', 'y', 'z'. Defaults to 'xyz'.

        """
        valid = ['x','y','z']
        if not set(directions).issubset(valid):
            raise ValueError(f'Invalid direction {set(directions).difference(valid)} specified.')

        o = [[0, self.grid[0]+1,           np.prod(self.grid[:2]+1)+self.grid[0]+1, np.prod(self.grid[:2]+1)],
             [0, np.prod(self.grid[:2]+1), np.prod(self.grid[:2]+1)+1,              1],
             [0, 1,                        self.grid[0]+1+1,                        self.grid[0]+1]] # offset for connectivity

        connectivity = []
        for i,d in enumerate(['x','y','z']):
            if d not in directions: continue
            mask = self.material != np.roll(self.material,1,i)
            for j in [0,1,2]:
                mask = np.concatenate((mask,np.take(mask,[0],j)*(i==j)),j)
            if i == 0 and not periodic: mask[0,:,:] = mask[-1,:,:] = False
            if i == 1 and not periodic: mask[:,0,:] = mask[:,-1,:] = False
            if i == 2 and not periodic: mask[:,:,0] = mask[:,:,-1] = False

            base_nodes = np.argwhere(mask.flatten(order='F')).reshape(-1,1)
            connectivity.append(np.block([base_nodes + o[i][k] for k in range(4)]))

        coords = grid_filters.node_coord0(self.grid,self.size,self.origin).reshape(-1,3,order='F')
        return VTK.from_unstructured_grid(coords,np.vstack(connectivity),'QUAD')