485 lines
16 KiB
Python
485 lines
16 KiB
Python
import os
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import warnings
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import multiprocessing as mp
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from pathlib import Path
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from typing import Union, Literal, List
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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 ._typehints import FloatSequence, IntSequence
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from . import util
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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,
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vtk_data: vtk.vtkDataSet):
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"""
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New spatial visualization.
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Parameters
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----------
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vtk_data : subclass of vtk.vtkDataSet
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Description of geometry and topology, optionally with attached data.
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Valid types are vtk.vtkImageData, vtk.vtkUnstructuredGrid,
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vtk.vtkPolyData, and vtk.vtkRectilinearGrid.
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"""
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self.vtk_data = vtk_data
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@staticmethod
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def from_image_data(cells: IntSequence,
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size: FloatSequence,
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origin: FloatSequence = np.zeros(3)) -> 'VTK':
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"""
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Create VTK of type vtk.vtkImageData.
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This is the common type for grid solver results.
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Parameters
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----------
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cells : iterable of int, len (3)
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Number of cells along each dimension.
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size : iterable of float, len (3)
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Physical length along each dimension.
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origin : iterable of float, len (3), optional
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Coordinates of grid origin.
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Returns
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-------
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new : damask.VTK
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VTK-based geometry without nodal or cell data.
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"""
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vtk_data = vtk.vtkImageData()
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vtk_data.SetDimensions(*(np.array(cells)+1))
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vtk_data.SetOrigin(*(np.array(origin)))
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vtk_data.SetSpacing(*(np.array(size)/np.array(cells)))
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return VTK(vtk_data)
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@staticmethod
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def from_rectilinear_grid(grid: np.ndarray,
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size: FloatSequence,
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origin: FloatSequence = np.zeros(3)) -> 'VTK':
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"""
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Create VTK of type vtk.vtkRectilinearGrid.
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Parameters
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----------
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grid : iterable of int, len (3)
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Number of cells along each dimension.
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size : iterable of float, len (3)
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Physical length along each dimension.
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origin : iterable of float, len (3), optional
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Coordinates of grid origin.
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Returns
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-------
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new : damask.VTK
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VTK-based geometry without nodal or cell data.
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"""
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warnings.warn('Support for vtr files will be removed in DAMASK 3.1.0', DeprecationWarning,2)
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vtk_data = vtk.vtkRectilinearGrid()
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vtk_data.SetDimensions(*(np.array(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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vtk_data.SetXCoordinates(coord[0])
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vtk_data.SetYCoordinates(coord[1])
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vtk_data.SetZCoordinates(coord[2])
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return VTK(vtk_data)
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@staticmethod
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def from_unstructured_grid(nodes: np.ndarray,
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connectivity: np.ndarray,
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cell_type: str) -> 'VTK':
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"""
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Create VTK of type vtk.vtkUnstructuredGrid.
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This is the common type for mesh solver results.
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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,
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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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Returns
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-------
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new : damask.VTK
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VTK-based geometry without nodal or cell data.
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"""
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vtk_nodes = vtk.vtkPoints()
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vtk_nodes.SetData(np_to_vtk(np.ascontiguousarray(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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vtk_data = vtk.vtkUnstructuredGrid()
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vtk_data.SetPoints(vtk_nodes)
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cell_types = {'TRIANGLE':vtk.VTK_TRIANGLE, 'QUAD':vtk.VTK_QUAD,
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'TETRA' :vtk.VTK_TETRA, 'HEXAHEDRON':vtk.VTK_HEXAHEDRON}
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vtk_data.SetCells(cell_types[cell_type.split("_",1)[-1].upper()],cells)
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return VTK(vtk_data)
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@staticmethod
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def from_poly_data(points: np.ndarray) -> 'VTK':
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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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Returns
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-------
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new : damask.VTK
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VTK-based geometry without nodal or cell data.
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"""
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N = points.shape[0]
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vtk_points = vtk.vtkPoints()
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vtk_points.SetData(np_to_vtk(np.ascontiguousarray(points)))
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vtk_cells = vtk.vtkCellArray()
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vtk_cells.SetNumberOfCells(N)
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vtk_cells.SetCells(N,np_to_vtkIdTypeArray(np.stack((np.ones (N,dtype=np.int64),
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np.arange(N,dtype=np.int64)),axis=1).ravel(),deep=True))
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vtk_data = vtk.vtkPolyData()
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vtk_data.SetPoints(vtk_points)
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vtk_data.SetVerts(vtk_cells)
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return VTK(vtk_data)
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@staticmethod
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def load(fname: Union[str, Path],
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dataset_type: Literal['ImageData', 'UnstructuredGrid', 'PolyData'] = None) -> 'VTK':
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"""
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Load from VTK 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.
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Valid extensions are .vti, .vtr, .vtu, .vtp, and .vtk.
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dataset_type : {'ImageData', 'UnstructuredGrid', 'PolyData'}, optional
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Name of the vtk.vtkDataSet subclass when opening a .vtk file.
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Returns
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-------
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loaded : damask.VTK
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VTK-based geometry from file.
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"""
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if not os.path.isfile(fname): # vtk has a strange error handling
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raise FileNotFoundError(f'No such file: {fname}')
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if (ext := Path(fname).suffix) == '.vtk' or dataset_type is not None:
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reader = vtk.vtkGenericDataObjectReader()
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reader.SetFileName(str(fname))
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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(('imagedata','image_data')):
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reader.Update()
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vtk_data = reader.GetStructuredPointsOutput()
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elif dataset_type.lower().endswith(('rectilineargrid','rectilinear_grid')):
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reader.Update()
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vtk_data = reader.GetRectilinearGridOutput()
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elif dataset_type.lower().endswith(('unstructuredgrid','unstructured_grid')):
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reader.Update()
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vtk_data = reader.GetUnstructuredGridOutput()
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elif dataset_type.lower().endswith(('polydata','poly_data')):
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reader.Update()
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vtk_data = 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 == '.vti':
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reader = vtk.vtkXMLImageDataReader()
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elif 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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vtk_data = reader.GetOutput()
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return VTK(vtk_data)
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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 save(self,
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fname: Union[str, Path],
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parallel: bool = True,
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compress: bool = True):
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"""
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Save as VTK 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 : bool, optional
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Write data in parallel background process. Defaults to True.
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compress : bool, optional
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Compress with zlib algorithm. Defaults to True.
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"""
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if isinstance(self.vtk_data,vtk.vtkImageData):
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writer = vtk.vtkXMLImageDataWriter()
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elif isinstance(self.vtk_data,vtk.vtkRectilinearGrid):
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writer = vtk.vtkXMLRectilinearGridWriter()
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elif isinstance(self.vtk_data,vtk.vtkUnstructuredGrid):
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writer = vtk.vtkXMLUnstructuredGridWriter()
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elif isinstance(self.vtk_data,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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writer.SetFileName(str(fname)+(default_ext if default_ext != ext else ''))
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if compress:
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writer.SetCompressorTypeToZLib()
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else:
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writer.SetCompressorTypeToNone()
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writer.SetDataModeToBinary()
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writer.SetInputData(self.vtk_data)
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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 damask.Table
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def add(self,
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data: Union[np.ndarray, np.ma.MaskedArray],
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label: str = 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 or numpy.ma.MaskedArray
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Data to add. First dimension needs 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.vtk_data.GetNumberOfPoints()
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N_cells = self.vtk_data.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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N_data = data.shape[0]
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data_ = (data if not isinstance(data,np.ma.MaskedArray) else
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np.where(data.mask,data.fill_value,data)).reshape(N_data,-1)
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if data_.dtype in [np.double,np.longdouble]:
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d = np_to_vtk(data_.astype(np.single),deep=True) # avoid large files
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elif data_.dtype.type is np.str_:
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d = vtk.vtkStringArray()
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for s in np.squeeze(data_):
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d.InsertNextValue(s)
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else:
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d = np_to_vtk(data_,deep=True)
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d.SetName(label)
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if N_data == N_points:
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self.vtk_data.GetPointData().AddArray(d)
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elif N_data == N_cells:
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self.vtk_data.GetCellData().AddArray(d)
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else:
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raise ValueError(f'Cell / point count ({N_cells} / {N_points}) differs from data ({N_data}).')
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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,
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label: str) -> np.ndarray:
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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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Returns
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-------
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data : numpy.ndarray
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Data stored under the given label.
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"""
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cell_data = self.vtk_data.GetCellData()
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for a in range(cell_data.GetNumberOfArrays()):
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if cell_data.GetArrayName(a) == label:
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try:
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return vtk_to_np(cell_data.GetArray(a))
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except AttributeError:
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vtk_array = cell_data.GetAbstractArray(a) # string array
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point_data = self.vtk_data.GetPointData()
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for a in range(point_data.GetNumberOfArrays()):
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if point_data.GetArrayName(a) == label:
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try:
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return vtk_to_np(point_data.GetArray(a))
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except AttributeError:
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vtk_array = point_data.GetAbstractArray(a) # string array
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try:
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# string array
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return np.array([vtk_array.GetValue(i) for i in range(vtk_array.GetNumberOfValues())]).astype(str)
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except UnboundLocalError:
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raise ValueError(f'Array "{label}" not found.')
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def get_comments(self) -> List[str]:
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"""Return the comments."""
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fielddata = self.vtk_data.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,
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comments: Union[str, List[str]]):
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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.vtk_data.GetFieldData().AddArray(s)
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def add_comments(self,
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comments: Union[str, List[str]]):
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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) -> str:
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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.vtk_data)
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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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try:
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import wx
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_ = wx.App(False) # noqa
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width, height = wx.GetDisplaySize()
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except ImportError:
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try:
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import tkinter
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tk = tkinter.Tk()
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width = tk.winfo_screenwidth()
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height = tk.winfo_screenheight()
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tk.destroy()
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except Exception:
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width = 1024
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height = 768
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mapper = vtk.vtkDataSetMapper()
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mapper.SetInputData(self.vtk_data)
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actor = vtk.vtkActor()
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actor.SetMapper(mapper)
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actor.GetProperty().SetColor(230/255,150/255,68/255)
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ren = vtk.vtkRenderer()
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ren.AddActor(actor)
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ren.SetBackground(67/255,128/255,208/255)
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window = vtk.vtkRenderWindow()
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window.AddRenderer(ren)
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window.SetSize(width,height)
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window.SetWindowName(util.execution_stamp('VTK','show'))
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iren = vtk.vtkRenderWindowInteractor()
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iren.SetRenderWindow(window)
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if os.name == 'posix' and 'DISPLAY' not in os.environ:
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print('Found no rendering device')
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else:
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window.Render()
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iren.Start()
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