import os import warnings import multiprocessing as mp from pathlib import Path from typing import Union, Optional, Literal, List import numpy as np import vtk 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 Table class VTK: """ Spatial visualization (and potentially manipulation). High-level interface to VTK. """ def __init__(self, vtk_data: vtk.vtkImageData): """ New spatial visualization. Parameters ---------- vtk_data : subclass of vtk.vtkDataSet Description of geometry and topology, optionally with attached data. Valid types are vtk.vtkImageData, vtk.vtkUnstructuredGrid, vtk.vtkPolyData, and vtk.vtkRectilinearGrid. """ self.vtk_data = vtk_data @staticmethod #ITERABLES PROPER def from_image_data(cells: np.ndarray, size: np.ndarray, origin: Optional[np.ndarray] = np.zeros(3)) -> "VTK": """ Create VTK of type vtk.vtkImageData. This is the common type for grid solver results. Parameters ---------- cells : iterable of int, len (3) Number of cells along each dimension. size : iterable of float, len (3) Physical length along each dimension. origin : iterable of float, len (3), optional Coordinates of grid origin. Returns ------- new : damask.VTK VTK-based geometry without nodal or cell data. """ vtk_data = vtk.vtkImageData() vtk_data.SetDimensions(*(np.array(cells)+1)) vtk_data.SetOrigin(*(np.array(origin))) vtk_data.SetSpacing(*(size/cells)) return VTK(vtk_data) @staticmethod def from_rectilinear_grid(grid: np.ndarray, size: np.ndarray, origin: np.ndarray = np.zeros(3)) -> "VTK": """ Create VTK of type vtk.vtkRectilinearGrid. Parameters ---------- grid : iterable of int, len (3) Number of cells along each dimension. size : iterable of float, len (3) Physical length along each dimension. origin : iterable of float, len (3), optional Coordinates of grid origin. Returns ------- new : damask.VTK VTK-based geometry without nodal or cell data. """ warnings.warn('Support for vtr files will be removed in DAMASK 3.1.0', DeprecationWarning,2) vtk_data = vtk.vtkRectilinearGrid() vtk_data.SetDimensions(*(np.array(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'])] vtk_data.SetXCoordinates(coord[0]) vtk_data.SetYCoordinates(coord[1]) vtk_data.SetZCoordinates(coord[2]) return VTK(vtk_data) @staticmethod def from_unstructured_grid(nodes: np.ndarray, connectivity: np.ndarray, cell_type: str) -> "VTK": """ Create VTK of type vtk.vtkUnstructuredGrid. This is the common type for mesh solver results. 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 Name of the vtk.vtkCell subclass. Tested for TRIANGLE, QUAD, TETRA, and HEXAHEDRON. Returns ------- new : damask.VTK VTK-based geometry without nodal or cell data. """ vtk_nodes = vtk.vtkPoints() vtk_nodes.SetData(np_to_vtk(np.ascontiguousarray(nodes))) cells = vtk.vtkCellArray() cells.SetNumberOfCells(connectivity.shape[0]) T = np.concatenate((np.ones((connectivity.shape[0],1),dtype=np.int64)*connectivity.shape[1], connectivity),axis=1).ravel() cells.SetCells(connectivity.shape[0],np_to_vtkIdTypeArray(T,deep=True)) vtk_data = vtk.vtkUnstructuredGrid() vtk_data.SetPoints(vtk_nodes) cell_types = {'TRIANGLE':vtk.VTK_TRIANGLE, 'QUAD':vtk.VTK_QUAD, 'TETRA' :vtk.VTK_TETRA, 'HEXAHEDRON':vtk.VTK_HEXAHEDRON} vtk_data.SetCells(cell_types[cell_type.split("_",1)[-1].upper()],cells) return VTK(vtk_data) @staticmethod def from_poly_data(points: np.ndarray) -> "VTK": """ 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. Returns ------- new : damask.VTK VTK-based geometry without nodal or cell data. """ N = points.shape[0] vtk_points = vtk.vtkPoints() vtk_points.SetData(np_to_vtk(np.ascontiguousarray(points))) vtk_cells = vtk.vtkCellArray() vtk_cells.SetNumberOfCells(N) vtk_cells.SetCells(N,np_to_vtkIdTypeArray(np.stack((np.ones (N,dtype=np.int64), np.arange(N,dtype=np.int64)),axis=1).ravel(),deep=True)) vtk_data = vtk.vtkPolyData() vtk_data.SetPoints(vtk_points) vtk_data.SetVerts(vtk_cells) return VTK(vtk_data) @staticmethod def load(fname: Union[str, Path], dataset_type: Literal['vtkImageData', 'vtkRectilinearGrid', 'vtkUnstructuredGrid', 'vtkPolyData'] = None) -> "VTK": """ Load from VTK file. Parameters ---------- fname : str or pathlib.Path Filename for reading. Valid extensions are .vti, .vtr, .vtu, .vtp, and .vtk. dataset_type : {'vtkImageData', ''vtkRectilinearGrid', 'vtkUnstructuredGrid', 'vtkPolyData'}, optional Name of the vtk.vtkDataSet subclass when opening a .vtk file. Returns ------- loaded : damask.VTK VTK-based geometry from file. """ if not os.path.isfile(fname): # vtk has a strange error handling raise FileNotFoundError(f'No such file: {fname}') ext = Path(fname).suffix if ext == '.vtk' or dataset_type is not None: reader = vtk.vtkGenericDataObjectReader() reader.SetFileName(str(fname)) if dataset_type is None: raise TypeError('Dataset type for *.vtk file not given.') elif dataset_type.lower().endswith(('imagedata','image_data')): reader.Update() vtk_data = reader.GetStructuredPointsOutput() elif dataset_type.lower().endswith(('rectilineargrid','rectilinear_grid')): reader.Update() vtk_data = reader.GetRectilinearGridOutput() elif dataset_type.lower().endswith(('unstructuredgrid','unstructured_grid')): reader.Update() vtk_data = reader.GetUnstructuredGridOutput() elif dataset_type.lower().endswith(('polydata','poly_data')): reader.Update() vtk_data = reader.GetPolyDataOutput() else: raise TypeError(f'Unknown dataset type {dataset_type} for vtk file') else: if ext == '.vti': reader = vtk.vtkXMLImageDataReader() elif ext == '.vtr': reader = vtk.vtkXMLRectilinearGridReader() elif ext == '.vtu': reader = vtk.vtkXMLUnstructuredGridReader() elif ext == '.vtp': reader = vtk.vtkXMLPolyDataReader() else: raise TypeError(f'Unknown file extension {ext}') reader.SetFileName(str(fname)) reader.Update() vtk_data = reader.GetOutput() return VTK(vtk_data) @staticmethod def _write(writer): """Wrapper for parallel writing.""" writer.Write() def save(self, fname: Union[str, Path], parallel: bool = True, compress: bool = True): """ Save as VTK file. Parameters ---------- fname : str or pathlib.Path Filename for writing. parallel : bool, optional Write data in parallel background process. Defaults to True. compress : bool, optional Compress with zlib algorithm. Defaults to True. """ if isinstance(self.vtk_data,vtk.vtkImageData): writer = vtk.vtkXMLImageDataWriter() elif isinstance(self.vtk_data,vtk.vtkRectilinearGrid): writer = vtk.vtkXMLRectilinearGridWriter() elif isinstance(self.vtk_data,vtk.vtkUnstructuredGrid): writer = vtk.vtkXMLUnstructuredGridWriter() elif isinstance(self.vtk_data,vtk.vtkPolyData): writer = vtk.vtkXMLPolyDataWriter() default_ext = '.'+writer.GetDefaultFileExtension() ext = Path(fname).suffix writer.SetFileName(str(fname)+(default_ext if default_ext != ext else '')) if compress: writer.SetCompressorTypeToZLib() else: writer.SetCompressorTypeToNone() writer.SetDataModeToBinary() writer.SetInputData(self.vtk_data) if parallel: try: mp_writer = mp.Process(target=self._write,args=(writer,)) mp_writer.start() except TypeError: writer.Write() else: writer.Write() # Check https://blog.kitware.com/ghost-and-blanking-visibility-changes/ for missing data # Needs support for damask.Table def add(self, data: Union[np.ndarray, np.ma.MaskedArray], label: str = None): """ Add data to either cells or points. Parameters ---------- data : numpy.ndarray or numpy.ma.MaskedArray Data to add. First dimension needs to match either number of cells or number of points. label : str Data label. """ N_points = self.vtk_data.GetNumberOfPoints() N_cells = self.vtk_data.GetNumberOfCells() if isinstance(data,np.ndarray): if label is None: raise ValueError('No label defined for numpy.ndarray') N_data = data.shape[0] data_ = (data if not isinstance(data,np.ma.MaskedArray) else np.where(data.mask,data.fill_value,data)).reshape(N_data,-1) if data_.dtype in [np.double,np.longdouble]: d = np_to_vtk(data_.astype(np.single),deep=True) # avoid large files elif data_.dtype.type is np.str_: d = vtk.vtkStringArray() for s in np.squeeze(data_): d.InsertNextValue(s) else: d = np_to_vtk(data_,deep=True) d.SetName(label) if N_data == N_points: self.vtk_data.GetPointData().AddArray(d) elif N_data == N_cells: self.vtk_data.GetCellData().AddArray(d) else: raise ValueError(f'Cell / point count ({N_cells} / {N_points}) differs from data ({N_data}).') elif isinstance(data,Table): raise NotImplementedError('damask.Table') else: raise TypeError def get(self, label: str) -> np.ndarray: """ 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. Returns ------- data : numpy.ndarray Data stored under the given label. """ cell_data = self.vtk_data.GetCellData() for a in range(cell_data.GetNumberOfArrays()): if cell_data.GetArrayName(a) == label: try: return vtk_to_np(cell_data.GetArray(a)) except AttributeError: vtk_array = cell_data.GetAbstractArray(a) # string array point_data = self.vtk_data.GetPointData() for a in range(point_data.GetNumberOfArrays()): if point_data.GetArrayName(a) == label: try: return vtk_to_np(point_data.GetArray(a)) except AttributeError: vtk_array = point_data.GetAbstractArray(a) # string array try: # string array return np.array([vtk_array.GetValue(i) for i in range(vtk_array.GetNumberOfValues())]).astype(str) except UnboundLocalError: raise ValueError(f'Array "{label}" not found.') def get_comments(self) -> List[str]: """Return the comments.""" fielddata = self.vtk_data.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: Union[str, List[str]]): """ Set comments. Parameters ---------- comments : str or list of str Comments. """ s = vtk.vtkStringArray() s.SetName('comments') for c in [comments] if isinstance(comments,str) else comments: s.InsertNextValue(c) self.vtk_data.GetFieldData().AddArray(s) def add_comments(self, comments: Union[str, List[str]]): """ 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)) def __repr__(self) -> str: """ASCII representation of the VTK data.""" writer = vtk.vtkDataSetWriter() writer.SetHeader(f'# {util.execution_stamp("VTK")}') writer.WriteToOutputStringOn() writer.SetInputData(self.vtk_data) writer.Write() return writer.GetOutputString() def show(self) -> None: """ Render. See http://compilatrix.com/article/vtk-1 for further ideas. """ try: import wx _ = wx.App(False) # noqa width, height = wx.GetDisplaySize() except ImportError: try: import tkinter tk = tkinter.Tk() width = tk.winfo_screenwidth() height = tk.winfo_screenheight() tk.destroy() except Exception as e: width = 1024 height = 768 mapper = vtk.vtkDataSetMapper() mapper.SetInputData(self.vtk_data) actor = vtk.vtkActor() actor.SetMapper(mapper) ren = vtk.vtkRenderer() window = vtk.vtkRenderWindow() window.AddRenderer(ren) ren.AddActor(actor) ren.SetBackground(0.2,0.2,0.2) window.SetSize(width,height) iren = vtk.vtkRenderWindowInteractor() iren.SetRenderWindow(window) iren.Initialize() window.Render() iren.Start()