DAMASK_EICMD/python/damask/geom.py

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import os
from io import StringIO
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import numpy as np
import vtk
from vtk.util import numpy_support
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from . import util
from . import version
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class Geom():
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"""Geometry definition for grid solvers."""
def __init__(self,microstructure,size,origin=[0.0,0.0,0.0],homogenization=1,comments=[]):
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"""
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)
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def __repr__(self):
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"""Basic information on geometry definition."""
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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()))),
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'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):
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"""
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()
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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)
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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())))))
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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())))))
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message.append('homogenization: {}'.format(self.get_homogenization()))
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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)))))
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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):
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"""
Replaces all existing comments.
Parameters
----------
comments : list of str
new comments.
"""
self.comments = []
self.add_comments(comments)
def add_comments(self,comments):
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"""
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)]
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def set_microstructure(self,microstructure):
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"""
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))
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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)
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def set_size(self,size):
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"""
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):
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"""
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):
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"""
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
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def get_microstructure(self):
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"""Return the microstructure representation."""
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return np.copy(self.microstructure)
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def get_size(self):
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"""Return the physical size in meter."""
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return np.copy(self.size)
def get_origin(self):
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"""Return the origin in meter."""
return np.copy(self.origin)
def get_grid(self):
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"""Return the grid discretization."""
return np.array(self.microstructure.shape)
def get_homogenization(self):
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"""Return the homogenization index."""
return self.homogenization
def get_comments(self):
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"""Return the comments."""
return self.comments[:]
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def get_header(self):
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"""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):
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"""
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())
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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)
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if i != grid.prod():
raise TypeError('Invalid file: expected {} entries,found {}'.format(grid.prod(),i))
microstructure = microstructure.reshape(grid,order='F')
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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):
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"""
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):
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"""
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()
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def show(self):
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"""Show raw content (as in file)."""
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f=StringIO()
self.to_file(f)
f.seek(0)
return ''.join(f.readlines())