DAMASK_EICMD/python/damask/geom.py

import os
from io import StringIO

import numpy as np
import vtk
from vtk.util import numpy_support

from . import util
from . import version


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

  def __init__(self,microstructure,size,origin=[0.0,0.0,0.0],homogenization=1,comments=[]):
    """
    New geometry definition from array of microstructures and size.

    Parameters
    ----------
    microstructure : numpy.ndarray
        microstructure array (3D)
    size : list or numpy.ndarray
        physical size of the microstructure in meter.
    origin : list or numpy.ndarray, optional
        physical origin of the microstructure in meter.
    homogenization : integer, optional
        homogenization index.
    comments : list of str, optional
        comments lines.

    """
    self.__transforms__ = \
    self.set_microstructure(microstructure)
    self.set_size(size)
    self.set_origin(origin)
    self.set_homogenization(homogenization)
    self.set_comments(comments)
    

  def __repr__(self):
    """Basic information on geometry definition."""
    return util.srepr([
           'grid     a b c:      {}'.format(' x '.join(map(str,self.get_grid  ()))),
           'size     x y z:      {}'.format(' x '.join(map(str,self.get_size  ()))),
           'origin   x y z:      {}'.format('   '.join(map(str,self.get_origin()))),
           'homogenization:      {}'.format(self.get_homogenization()),
           '# microstructures:   {}'.format(len(np.unique(self.microstructure))),
           'max microstructure:  {}'.format(np.nanmax(self.microstructure)),
          ])

  def update(self,microstructure=None,size=None,origin=None,rescale=False):
    """
    Updates microstructure and size.

    Parameters
    ----------
    microstructure : numpy.ndarray, optional
        microstructure array (3D).
    size : list or numpy.ndarray, optional
        physical size of the microstructure in meter.
    origin : list or numpy.ndarray, optional
        physical origin of the microstructure in meter.
    rescale : bool, optional
        ignore size parameter and rescale according to change of grid points.

    """
    grid_old    = self.get_grid()
    size_old    = self.get_size()
    origin_old  = self.get_origin()
    unique_old  = len(np.unique(self.microstructure))
    max_old     = np.nanmax(self.microstructure)
    
    if size is not None and rescale:
      raise ValueError('Either set size explicitly or rescale automatically')

    self.set_microstructure(microstructure)
    self.set_origin(origin)

    if size is not None:
      self.set_size(size)
    elif rescale:
      self.set_size(self.get_grid()/grid_old*self.size)

    message = ['grid     a b c:      {}'.format(' x '.join(map(str,grid_old)))]
    if np.any(grid_old != self.get_grid()):
      message[-1] = util.delete(message[-1])
      message.append(util.emph('grid     a b c:      {}'.format(' x '.join(map(str,self.get_grid())))))

    message.append('size     x y z:      {}'.format(' x '.join(map(str,size_old))))
    if np.any(size_old != self.get_size()):
      message[-1] = util.delete(message[-1])
      message.append(util.emph('size     x y z:      {}'.format(' x '.join(map(str,self.get_size())))))

    message.append('origin   x y z:      {}'.format('   '.join(map(str,origin_old))))
    if np.any(origin_old != self.get_origin()):
      message[-1] = util.delete(message[-1])
      message.append(util.emph('origin   x y z:      {}'.format('   '.join(map(str,self.get_origin())))))

    message.append('homogenization:      {}'.format(self.get_homogenization()))

    message.append('# microstructures:   {}'.format(unique_old))
    if unique_old != len(np.unique(self.microstructure)):
      message[-1] = util.delete(message[-1])
      message.append(util.emph('# microstructures:   {}'.format(len(np.unique(self.microstructure)))))

    message.append('max microstructure:  {}'.format(max_old))
    if max_old != np.nanmax(self.microstructure):
      message[-1] = util.delete(message[-1])
      message.append(util.emph('max microstructure:  {}'.format(np.nanmax(self.microstructure))))
    
    return util.return_message(message)

  def set_comments(self,comments):
    """
    Replaces all existing comments.

    Parameters
    ----------
    comments : list of str
        new comments.

    """
    self.comments = []
    self.add_comments(comments)
    
  def add_comments(self,comments):
    """
    Appends comments to existing comments.

    Parameters
    ----------
    comments : list of str
        new comments.

    """
    self.comments += [str(c) for c in comments] if isinstance(comments,list) else [str(comments)]

  def set_microstructure(self,microstructure):
    """
    Replaces the existing microstructure representation.

    Parameters
    ----------
    microstructure : numpy.ndarray
        microstructure array (3D).

    """
    if microstructure is not None:
      if len(microstructure.shape) != 3:
        raise ValueError('Invalid microstructure shape {}'.format(*microstructure.shape))
      elif microstructure.dtype not in np.sctypes['float'] + np.sctypes['int']:
        raise TypeError('Invalid data type {} for microstructure'.format(microstructure.dtype))
      else:
        self.microstructure = np.copy(microstructure)

  def set_size(self,size):
    """
    Replaces the existing size information.

    Parameters
    ----------
    size : list or numpy.ndarray
        physical size of the microstructure in meter.

    """
    if size is None:
      grid = np.asarray(self.microstructure.shape)
      self.size = grid/np.max(grid)
    else:
      if len(size) != 3 or any(np.array(size)<=0):
        raise ValueError('Invalid size {}'.format(*size))
      else:
        self.size = np.array(size)

  def set_origin(self,origin):
    """
    Replaces the existing origin information.

    Parameters
    ----------
    origin : list or numpy.ndarray
        physical origin of the microstructure in meter

    """
    if origin is not None:
      if len(origin) != 3:
        raise ValueError('Invalid origin {}'.format(*origin))
      else:
        self.origin = np.array(origin)

  def set_homogenization(self,homogenization):
    """
    Replaces the existing homogenization index.

    Parameters
    ----------
    homogenization : integer
        homogenization index

    """
    if homogenization is not None:
      if not isinstance(homogenization,int) or homogenization < 1:
        raise TypeError('Invalid homogenization {}'.format(homogenization))
      else:
        self.homogenization = homogenization


  def get_microstructure(self):
    """Return the microstructure representation."""
    return np.copy(self.microstructure)

  def get_size(self):
    """Return the physical size in meter."""
    return np.copy(self.size)

  def get_origin(self):
    """Return the origin in meter."""
    return np.copy(self.origin)

  def get_grid(self):
    """Return the grid discretization."""
    return np.array(self.microstructure.shape)

  def get_homogenization(self):
    """Return the homogenization index."""
    return self.homogenization

  def get_comments(self):
    """Return the comments."""
    return self.comments[:]

  def get_header(self):
    """Return the full header (grid, size, origin, homogenization, comments)."""
    header =  ['{} header'.format(len(self.comments)+4)] + self.comments
    header.append('grid   a {} b {} c {}'.format(*self.get_grid()))
    header.append('size   x {} y {} z {}'.format(*self.get_size()))
    header.append('origin x {} y {} z {}'.format(*self.get_origin()))
    header.append('homogenization {}'.format(self.get_homogenization()))
    return header
      
  @classmethod
  def from_file(cls,fname):
    """
    Reads a geom file.

    Parameters
    ----------
    fname : str or file handle
        geometry file to read.

    """
    with (open(fname) if isinstance(fname,str) else fname) as f:
      f.seek(0)
      header_length,keyword = f.readline().split()[:2]
      header_length = int(header_length)
      content = f.readlines()

    if not keyword.startswith('head') or header_length < 3:
      raise TypeError('Header length information missing or invalid')

    comments = [] 
    for i,line in enumerate(content[:header_length]):
      items = line.lower().strip().split()
      key = items[0] if len(items) > 0 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']])
      elif key == 'homogenization':
        homogenization = int(items[1])
      else:
        comments.append(line.strip())

    microstructure = np.empty(grid.prod())                                                          # initialize as flat array
    i = 0
    for line in content[header_length:]:
      items = line.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))
      
      microstructure[i:i+len(items)] = items
      i += len(items)
    
    if i != grid.prod():
      raise TypeError('Invalid file: expected {} entries,found {}'.format(grid.prod(),i))
    
    microstructure = microstructure.reshape(grid,order='F')
    if not np.any(np.mod(microstructure.flatten(),1) != 0.0):                                       # no float present
      microstructure = microstructure.astype('int')
    
    return cls(microstructure.reshape(grid),size,origin,homogenization,comments)

  def to_file(self,fname):
    """
    Writes a geom file.

    Parameters
    ----------
    fname : str or file handle
        geometry file to write.

    """
    header = self.get_header()
    grid   = self.get_grid()
    format_string = '%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.microstructure))))) if self.microstructure.dtype == int \
               else '%g'
    np.savetxt(fname,
               self.microstructure.reshape([grid[0],np.prod(grid[1:])],order='F').T,
               header='\n'.join(header), fmt=format_string, comments='')


               
  def to_vtk(self,fname=None):
    """
    Generates vtk file.

    Parameters
    ----------
    fname : str, optional
        vtk file to write. If no file is given, a string is returned.

    """
    grid = self.get_grid() + np.ones(3,dtype=int)
    size = self.get_size()
    origin = self.get_origin()

    coords = [
              np.linspace(0,size[0],grid[0]) + origin[0],
              np.linspace(0,size[1],grid[1]) + origin[1],
              np.linspace(0,size[2],grid[2]) + origin[2]
             ]
    
    rGrid = vtk.vtkRectilinearGrid()
    coordArray = [vtk.vtkDoubleArray(),vtk.vtkDoubleArray(),vtk.vtkDoubleArray()]

    rGrid.SetDimensions(*grid)
    for d,coord in enumerate(coords):
      for c in coord:
        coordArray[d].InsertNextValue(c)

    rGrid.SetXCoordinates(coordArray[0])
    rGrid.SetYCoordinates(coordArray[1])
    rGrid.SetZCoordinates(coordArray[2])
    
    ms = numpy_support.numpy_to_vtk(num_array=self.microstructure.flatten(order='F'),
                                    array_type=vtk.VTK_INT if self.microstructure.dtype == int else vtk.VTK_FLOAT)
    ms.SetName('microstructure')
    rGrid.GetCellData().AddArray(ms)


    if fname is None:
      writer = vtk.vtkDataSetWriter()
      writer.SetHeader('damask.Geom '+version)
      writer.WriteToOutputStringOn()
    else:
      writer = vtk.vtkXMLRectilinearGridWriter()
      writer.SetCompressorTypeToZLib()
      writer.SetDataModeToBinary()
      
      ext = os.path.splitext(fname)[1]
      if ext == '':
        name = fname + '.' + writer.GetDefaultFileExtension()
      elif ext == writer.GetDefaultFileExtension():
        name = fname
      else:
        raise ValueError("unknown extension {}".format(ext))
      writer.SetFileName(name)
  
    writer.SetInputData(rGrid)
    writer.Write()

    if fname is None: return writer.GetOutputString()

               
  def show(self):
    """Show raw content (as in file)."""
    f=StringIO()
    self.to_file(f)
    f.seek(0)
    return ''.join(f.readlines())