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