import os import multiprocessing as mp from pathlib import Path import pandas as pd 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 environment from . import Table class VTK: """ Spatial visualization (and potentially manipulation). High-level interface to VTK. """ def __init__(self,vtk_data): """ Initialize from vtk dataset. Parameters ---------- vtk_data : subclass of vtk.vtkDataSet Description of geometry and topology, optionally with attached data. Valid types are vtk.vtkRectilinearGrid, vtk.vtkUnstructuredGrid, or vtk.vtkPolyData. """ self.vtk_data = vtk_data @staticmethod def from_rectilinear_grid(grid,size,origin=np.zeros(3)): """ Create VTK of type vtk.vtkRectilinearGrid. This is the common type for grid solver results. Parameters ---------- grid : iterable of int, len (3) Number of cells along each dimension. size : iterable of float, len (3) Physical lengths along each dimension. origin : iterable of float, len (3), optional Spatial origin coordinates. """ 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,connectivity,cell_type): """ Create VTK of type vtk.vtkUnstructuredGrid. This is the common type for FEM 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. """ vtk_nodes = vtk.vtkPoints() 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], connectivity),axis=1).ravel() cells.SetCells(connectivity.shape[0],np_to_vtkIdTypeArray(T,deep=True)) vtk_data = vtk.vtkUnstructuredGrid() vtk_data.SetPoints(vtk_nodes) vtk_data.SetCells(eval(f'vtk.VTK_{cell_type.split("_",1)[-1].upper()}'),cells) return VTK(vtk_data) @staticmethod def from_poly_data(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. """ N = points.shape[0] vtk_points = vtk.vtkPoints() vtk_points.SetData(np_to_vtk(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,dataset_type=None): """ Create VTK from file. Parameters ---------- fname : str or pathlib.Path Filename for reading. Valid extensions are .vtr, .vtu, .vtp, and .vtk. dataset_type : str, optional Name of the vtk.vtkDataSet subclass when opening a .vtk file. Valid types are vtkRectilinearGrid, vtkUnstructuredGrid, and vtkPolyData. """ 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('rectilineargrid'): reader.Update() vtk_data = reader.GetRectilinearGridOutput() elif dataset_type.lower().endswith('unstructuredgrid'): reader.Update() vtk_data = reader.GetUnstructuredGridOutput() elif dataset_type.lower().endswith('polydata'): reader.Update() vtk_data = reader.GetPolyDataOutput() else: raise TypeError(f'Unknown dataset type {dataset_type} for vtk file') else: if 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,parallel=True,compress=True): """ Write to file. Parameters ---------- fname : str or pathlib.Path Filename for writing. parallel : boolean, 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.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 pd.DataFrame and/or table def add(self,data,label=None): """ Add data to either cells or points. Parameters ---------- data : numpy.ndarray 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] d = np_to_vtk((data.astype(np.float32) if data.dtype in [np.float64, np.float128] else data).reshape(N_data,-1),deep=True) # avoid large files 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,pd.DataFrame): raise NotImplementedError('pd.DataFrame') elif isinstance(data,Table): raise NotImplementedError('damask.Table') 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. """ cell_data = self.vtk_data.GetCellData() for a in range(cell_data.GetNumberOfArrays()): if cell_data.GetArrayName(a) == label: return vtk_to_np(cell_data.GetArray(a)) point_data = self.vtk_data.GetPointData() for a in range(point_data.GetNumberOfArrays()): if point_data.GetArrayName(a) == label: return vtk_to_np(point_data.GetArray(a)) raise ValueError(f'Array "{label}" not found.') def get_comments(self): """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): """ 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): """ 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): """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): """ Render. See http://compilatrix.com/article/vtk-1 for further ideas. """ 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(environment.screen_size[0],environment.screen_size[1]) iren = vtk.vtkRenderWindowInteractor() iren.SetRenderWindow(window) iren.Initialize() window.Render() iren.Start()