579 lines
19 KiB
Python
579 lines
19 KiB
Python
import os
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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, Sequence
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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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from . import Colormap
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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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def __repr__(self) -> str:
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"""Give short human-readable summary."""
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info = [self.vtk_data.__vtkname__]
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for data in ['Cell Data', 'Point Data']:
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if data == 'Cell Data': info.append(f'\n# cells: {self.N_cells}')
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if data == 'Point Data': info.append(f'\n# points: {self.N_points}')
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if data in self.labels:
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info += [f' - {l}' for l in self.labels[data]]
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return util.srepr(info)
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def __eq__(self,
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other: object) -> bool:
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"""
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Equal to other.
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Parameters
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----------
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other : damask.VTK
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VTK to check for equality.
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"""
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if not isinstance(other, VTK):
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return NotImplemented
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return self.as_ASCII() == other.as_ASCII()
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def copy(self):
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if isinstance(self.vtk_data,vtk.vtkImageData):
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dup = vtk.vtkImageData()
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elif isinstance(self.vtk_data,vtk.vtkUnstructuredGrid):
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dup = vtk.vtkUnstructuredGrid()
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elif isinstance(self.vtk_data,vtk.vtkPolyData):
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dup = vtk.vtkPolyData()
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elif isinstance(self.vtk_data,vtk.vtkRectilinearGrid):
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dup = vtk.vtkRectilinearGrid()
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else:
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raise TypeError
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dup.DeepCopy(self.vtk_data)
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return VTK(dup)
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@property
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def comments(self) -> List[str]:
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"""Return the comments."""
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field_data = self.vtk_data.GetFieldData()
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for a in range(field_data.GetNumberOfArrays()):
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if field_data.GetArrayName(a) == 'comments':
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comments = field_data.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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@comments.setter
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def comments(self,
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comments: Union[str, Sequence[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 util.tail_repack(comments,self.comments):
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s.InsertNextValue(c)
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self.vtk_data.GetFieldData().AddArray(s)
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@property
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def N_points(self) -> int:
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"""Number of points in vtkdata."""
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return self.vtk_data.GetNumberOfPoints()
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@property
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def N_cells(self) -> int:
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"""Number of cells in vtkdata."""
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return self.vtk_data.GetNumberOfCells()
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@property
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def labels(self):
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"""Labels of datasets."""
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labels = {}
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cell_data = self.vtk_data.GetCellData()
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if c := [cell_data.GetArrayName(a) for a in range(cell_data.GetNumberOfArrays())]:
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labels['Cell Data'] = c
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point_data = self.vtk_data.GetPointData()
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if p := [point_data.GetArrayName(a) for a in range(point_data.GetNumberOfArrays())]:
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labels['Point Data'] = p
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return labels
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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_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, 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, 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 from_rectilinear_grid(grid: FloatSequence) -> '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 : iterables of floats, len (3)
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Grid coordinates along x, y, and z directions.
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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.vtkRectilinearGrid()
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vtk_data.SetDimensions(*map(len,grid))
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coord = [np_to_vtk(np.array(grid[i]),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 load(fname: Union[str, Path],
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dataset_type: Literal['ImageData', 'UnstructuredGrid', 'PolyData', 'RectilinearGrid'] = 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, .vtu, .vtp, .vtr, and .vtk.
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dataset_type : {'ImageData', 'UnstructuredGrid', 'PolyData', 'RectilinearGrid'}, 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 Path(fname).expanduser().is_file(): # vtk has a strange error handling
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raise FileNotFoundError(f'file "{fname}" not found')
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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(Path(fname).expanduser()))
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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(('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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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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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 == '.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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elif ext == '.vtr':
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reader = vtk.vtkXMLRectilinearGridReader()
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else:
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raise TypeError(f'unknown file extension "{ext}"')
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reader.SetFileName(str(Path(fname).expanduser()))
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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 as_ASCII(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 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.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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elif isinstance(self.vtk_data,vtk.vtkRectilinearGrid):
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writer = vtk.vtkXMLRectilinearGridWriter()
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default_ext = '.'+writer.GetDefaultFileExtension()
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ext = Path(fname).suffix
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writer.SetFileName(str(Path(fname).expanduser())+(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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def add(self,
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data: Union[np.ndarray, np.ma.MaskedArray, 'Table'],
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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, numpy.ma.MaskedArray, or damask.Table
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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, optional if data is damask.Table
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Data label.
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"""
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def _add_array(vtk_data,
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data: np.ndarray,
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label: str):
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N_data = data.shape[0]
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data_ = data.reshape(N_data,-1) \
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.astype(np.single if data.dtype in [np.double,np.longdouble] else data.dtype)
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if 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 == vtk_data.GetNumberOfPoints():
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vtk_data.GetPointData().AddArray(d)
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elif N_data == vtk_data.GetNumberOfCells():
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vtk_data.GetCellData().AddArray(d)
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else:
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raise ValueError(f'data count mismatch ({N_data} ≠ {self.N_points} & {self.N_cells})')
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|
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dup = self.copy()
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if isinstance(data,np.ndarray):
|
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if label is not None:
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_add_array(dup.vtk_data,
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np.where(data.mask,data.fill_value,data) if isinstance(data,np.ma.MaskedArray) else data,
|
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label)
|
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else:
|
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raise ValueError('no label defined for numpy.ndarray')
|
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elif isinstance(data,Table):
|
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for l in data.labels:
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_add_array(dup.vtk_data,data.get(l),l)
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else:
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raise TypeError
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|
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return dup
|
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|
|
|
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def get(self,
|
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label: str) -> np.ndarray:
|
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"""
|
|
Get either cell or point data.
|
|
|
|
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.
|
|
|
|
Parameters
|
|
----------
|
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label : str
|
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Data label.
|
|
|
|
Returns
|
|
-------
|
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data : numpy.ndarray
|
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Data stored under the given label.
|
|
|
|
"""
|
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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))
|
|
except AttributeError:
|
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vtk_array = cell_data.GetAbstractArray(a) # string array
|
|
|
|
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))
|
|
except AttributeError:
|
|
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)
|
|
except UnboundLocalError:
|
|
raise KeyError(f'array "{label}" not found')
|
|
|
|
|
|
def show(self,
|
|
label: str = None,
|
|
colormap: Union[Colormap, str] = 'cividis'):
|
|
"""
|
|
Render.
|
|
|
|
Parameters
|
|
----------
|
|
label : str, optional
|
|
Label of the dataset to show.
|
|
colormap : damask.Colormap or str, optional
|
|
Colormap for visualization of dataset. Defaults to 'cividis'.
|
|
|
|
Notes
|
|
-----
|
|
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:
|
|
width = 1024
|
|
height = 768
|
|
|
|
lut = vtk.vtkLookupTable()
|
|
colormap_ = Colormap.from_predefined(colormap) if isinstance(colormap,str) else \
|
|
colormap
|
|
lut.SetNumberOfTableValues(len(colormap_.colors))
|
|
for i,c in enumerate(colormap_.colors):
|
|
lut.SetTableValue(i,c if len(c)==4 else np.append(c,1.0))
|
|
lut.Build()
|
|
|
|
self.vtk_data.GetCellData().SetActiveScalars(label)
|
|
mapper = vtk.vtkDataSetMapper()
|
|
mapper.SetInputData(self.vtk_data)
|
|
mapper.SetLookupTable(lut)
|
|
mapper.SetScalarRange(self.vtk_data.GetScalarRange())
|
|
|
|
actor = vtk.vtkActor()
|
|
actor.SetMapper(mapper)
|
|
actor.GetProperty().SetColor(230/255,150/255,68/255)
|
|
|
|
ren = vtk.vtkRenderer()
|
|
ren.AddActor(actor)
|
|
if label is None:
|
|
ren.SetBackground(67/255,128/255,208/255)
|
|
else:
|
|
colormap_vtk = vtk.vtkScalarBarActor()
|
|
colormap_vtk.SetLookupTable(lut)
|
|
colormap_vtk.SetTitle(label)
|
|
colormap_vtk.SetMaximumWidthInPixels(width//100)
|
|
ren.AddActor2D(colormap_vtk)
|
|
ren.SetBackground(0.3,0.3,0.3)
|
|
|
|
window = vtk.vtkRenderWindow()
|
|
window.AddRenderer(ren)
|
|
window.SetSize(width,height)
|
|
window.SetWindowName(util.execution_stamp('VTK','show'))
|
|
|
|
iren = vtk.vtkRenderWindowInteractor()
|
|
iren.SetRenderWindow(window)
|
|
if os.name == 'posix' and 'DISPLAY' not in os.environ:
|
|
print('Found no rendering device')
|
|
else:
|
|
window.Render()
|
|
iren.Start()
|