DAMASK_EICMD/python/damask/_vtk.py

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import multiprocessing as mp
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from pathlib import Path
import pandas as pd
import numpy as np
import vtk
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from vtk.util.numpy_support import numpy_to_vtk as np_to_vtk
from vtk.util.numpy_support import numpy_to_vtkIdTypeArray as np_to_vtkIdTypeArray
from vtk.util.numpy_support import vtk_to_numpy as vtk_to_np
from . import util
from . import environment
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from . import Table
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class VTK:
"""
Spatial visualization (and potentially manipulation).
High-level interface to VTK.
"""
def __init__(self,geom):
"""
Set geometry and topology.
Parameters
----------
geom : subclass of vtk.vtkDataSet
Description of geometry and topology. Valid types are vtk.vtkRectilinearGrid,
vtk.vtkUnstructuredGrid, or vtk.vtkPolyData.
"""
self.geom = geom
@staticmethod
def from_rectilinearGrid(grid,size,origin=np.zeros(3)):
"""
Create VTK of type vtk.vtkRectilinearGrid.
This is the common type for results from the grid solver.
Parameters
----------
grid : numpy.ndarray of shape (3) of np.dtype = int
Number of cells.
size : numpy.ndarray of shape (3)
Physical length.
origin : numpy.ndarray of shape (3), optional
Spatial origin.
"""
geom = vtk.vtkRectilinearGrid()
geom.SetDimensions(*(grid+1))
coord = [np_to_vtk(np.linspace(origin[i],origin[i]+size[i],grid[i]+1),deep=True) for i in [0,1,2]]
[coord[i].SetName(n) for i,n in enumerate(['x','y','z'])]
geom.SetXCoordinates(coord[0])
geom.SetYCoordinates(coord[1])
geom.SetZCoordinates(coord[2])
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return VTK(geom)
@staticmethod
def from_unstructuredGrid(nodes,connectivity,cell_type):
"""
Create VTK of type vtk.vtkUnstructuredGrid.
This is the common type for results from FEM solvers.
Parameters
----------
nodes : numpy.ndarray of shape (:,3)
Spatial position of the nodes.
connectivity : numpy.ndarray of np.dtype = int
Cell connectivity (0-based), first dimension determines #Cells, second dimension determines #Nodes/Cell.
cell_type : str
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Name of the vtk.vtkCell subclass. Tested for TRIANGLE, QUAD, TETRA, and HEXAHEDRON.
"""
vtk_nodes = vtk.vtkPoints()
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vtk_nodes.SetData(np_to_vtk(nodes))
cells = vtk.vtkCellArray()
cells.SetNumberOfCells(connectivity.shape[0])
T = np.concatenate((np.ones((connectivity.shape[0],1),dtype=np.int64)*connectivity.shape[1],
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connectivity),axis=1).ravel()
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cells.SetCells(connectivity.shape[0],np_to_vtkIdTypeArray(T,deep=True))
geom = vtk.vtkUnstructuredGrid()
geom.SetPoints(vtk_nodes)
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geom.SetCells(eval(f'vtk.VTK_{cell_type.split("_",1)[-1].upper()}'),cells)
return VTK(geom)
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@staticmethod
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def from_polyData(points):
"""
Create VTK of type vtk.polyData.
This is the common type for point-wise data.
Parameters
----------
points : numpy.ndarray of shape (:,3)
Spatial position of the points.
"""
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vtk_points = vtk.vtkPoints()
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vtk_points.SetData(np_to_vtk(points))
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geom = vtk.vtkPolyData()
geom.SetPoints(vtk_points)
return VTK(geom)
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@staticmethod
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def from_file(fname,dataset_type=None):
"""
Create VTK from file.
Parameters
----------
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fname : str or pathlib.Path
Filename for reading. Valid extensions are .vtr, .vtu, .vtp, and .vtk.
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dataset_type : str, optional
Name of the vtk.vtkDataSet subclass when opening an .vtk file. Valid types are vtkRectilinearGrid,
vtkUnstructuredGrid, and vtkPolyData.
"""
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ext = Path(fname).suffix
if ext == '.vtk' or dataset_type:
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reader = vtk.vtkGenericDataObjectReader()
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reader.SetFileName(str(fname))
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reader.Update()
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if dataset_type is None:
raise TypeError('Dataset type for *.vtk file not given.')
elif dataset_type.lower().endswith('rectilineargrid'):
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geom = reader.GetRectilinearGridOutput()
elif dataset_type.lower().endswith('unstructuredgrid'):
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geom = reader.GetUnstructuredGridOutput()
elif dataset_type.lower().endswith('polydata'):
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geom = reader.GetPolyDataOutput()
else:
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raise TypeError(f'Unknown dataset type {dataset_type} for vtk file')
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else:
if ext == '.vtr':
reader = vtk.vtkXMLRectilinearGridReader()
elif ext == '.vtu':
reader = vtk.vtkXMLUnstructuredGridReader()
elif ext == '.vtp':
reader = vtk.vtkXMLPolyDataReader()
else:
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raise TypeError(f'Unknown file extension {ext}')
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reader.SetFileName(str(fname))
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reader.Update()
geom = reader.GetOutput()
return VTK(geom)
@staticmethod
def _write(writer):
"""Wrapper for parallel writing."""
writer.Write()
def write(self,fname,parallel=True):
"""
Write to file.
Parameters
----------
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fname : str or pathlib.Path
Filename for writing.
parallel : boolean, optional
Write data in parallel background process. Defaults to True.
"""
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if isinstance(self.geom,vtk.vtkRectilinearGrid):
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writer = vtk.vtkXMLRectilinearGridWriter()
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elif isinstance(self.geom,vtk.vtkUnstructuredGrid):
writer = vtk.vtkXMLUnstructuredGridWriter()
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elif isinstance(self.geom,vtk.vtkPolyData):
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writer = vtk.vtkXMLPolyDataWriter()
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default_ext = writer.GetDefaultFileExtension()
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ext = Path(fname).suffix
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if ext and ext != '.'+default_ext:
raise ValueError(f'Given extension {ext} does not match default .{default_ext}')
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writer.SetFileName(str(Path(fname).with_suffix('.'+default_ext)))
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writer.SetCompressorTypeToZLib()
writer.SetDataModeToBinary()
writer.SetInputData(self.geom)
if parallel:
try:
mp_writer = mp.Process(target=self._write,args=(writer,))
mp_writer.start()
except TypeError:
writer.Write()
else:
writer.Write()
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# Check https://blog.kitware.com/ghost-and-blanking-visibility-changes/ for missing data
# Needs support for pd.DataFrame and/or table
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def add(self,data,label=None):
"""
Add data to either cells or points.
Parameters
----------
data : numpy.ndarray
Data to add. First dimension need to match either
number of cells or number of points
label : str
Data label.
"""
N_points = self.geom.GetNumberOfPoints()
N_cells = self.geom.GetNumberOfCells()
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if isinstance(data,np.ndarray):
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if label is None:
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raise ValueError('No label defined for numpy.ndarray')
if data.dtype in [np.float64, np.float128]: # avoid large files
d = np_to_vtk(num_array=data.astype(np.float32).reshape(data.shape[0],-1),deep=True)
else:
d = np_to_vtk(num_array=data.reshape(data.shape[0],-1),deep=True)
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d.SetName(label)
if data.shape[0] == N_cells:
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self.geom.GetCellData().AddArray(d)
elif data.shape[0] == N_points:
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self.geom.GetPointData().AddArray(d)
else:
raise ValueError(f'Invalid shape {data.shape[0]}')
elif isinstance(data,pd.DataFrame):
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raise NotImplementedError('pd.DataFrame')
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elif isinstance(data,Table):
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raise NotImplementedError('damask.Table')
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else:
raise TypeError
def get(self,label):
"""
Get either cell or point data.
Cell data takes precedence over point data, i.e. this
function assumes that labels are unique among cell and
point data.
Parameters
----------
label : str
Data label.
"""
celldata = self.geom.GetCellData()
for a in range(celldata.GetNumberOfArrays()):
if celldata.GetArrayName(a) == label:
return vtk_to_np(celldata.GetArray(a))
pointdata = self.geom.GetPointData()
for a in range(celldata.GetNumberOfArrays()):
if pointdata.GetArrayName(a) == label:
return vtk_to_np(pointdata.GetArray(a))
raise ValueError(f'array "{label}" not found')
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def get_comments(self):
"""Return the comments."""
fielddata = self.geom.GetFieldData()
for a in range(fielddata.GetNumberOfArrays()):
if fielddata.GetArrayName(a) == 'comments':
comments = fielddata.GetAbstractArray(a)
return [comments.GetValue(i) for i in range(comments.GetNumberOfValues())]
return []
def set_comments(self,comments):
"""
Set Comments.
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Parameters
----------
comments : str or list of str
Comments.
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"""
s = vtk.vtkStringArray()
s.SetName('comments')
for c in [comments] if isinstance(comments,str) else comments:
s.InsertNextValue(c)
self.geom.GetFieldData().AddArray(s)
def add_comments(self,comments):
"""
Add Comments.
Parameters
----------
comments : str or list of str
Comments to add.
"""
self.set_comments(self.get_comments + ([comments] if isinstance(comments,str) else comments))
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def __repr__(self):
"""ASCII representation of the VTK data."""
writer = vtk.vtkDataSetWriter()
writer.SetHeader(f'# {util.version_date("VTK")}')
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writer.WriteToOutputStringOn()
writer.SetInputData(self.geom)
writer.Write()
return writer.GetOutputString()
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def show(self):
"""
Render.
See http://compilatrix.com/article/vtk-1 for further ideas.
"""
mapper = vtk.vtkDataSetMapper()
mapper.SetInputData(self.geom)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
ren = vtk.vtkRenderer()
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window = vtk.vtkRenderWindow()
window.AddRenderer(ren)
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ren.AddActor(actor)
ren.SetBackground(0.2,0.2,0.2)
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window.SetSize(environment.screen_size[0],environment.screen_size[1])
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iren = vtk.vtkRenderWindowInteractor()
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iren.SetRenderWindow(window)
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iren.Initialize()
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window.Render()
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iren.Start()