355 lines
11 KiB
Python
355 lines
11 KiB
Python
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_rectilinearGrid(grid,size,origin=np.zeros(3)):
|
|
"""
|
|
Create VTK of type vtk.vtkRectilinearGrid.
|
|
|
|
This is the common type for results from the grid solver.
|
|
|
|
Parameters
|
|
----------
|
|
grid : numpy.ndarray of shape (3) of np.dtype = int
|
|
Number of cells.
|
|
size : numpy.ndarray of shape (3)
|
|
Physical length.
|
|
origin : numpy.ndarray of shape (3), optional
|
|
Spatial origin.
|
|
|
|
"""
|
|
vtk_data = vtk.vtkRectilinearGrid()
|
|
vtk_data.SetDimensions(*(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_unstructuredGrid(nodes,connectivity,cell_type):
|
|
"""
|
|
Create VTK of type vtk.vtkUnstructuredGrid.
|
|
|
|
This is the common type for results from FEM solvers.
|
|
|
|
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_polyData(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.
|
|
|
|
"""
|
|
vtk_points = vtk.vtkPoints()
|
|
vtk_points.SetData(np_to_vtk(points))
|
|
|
|
vtk_data = vtk.vtkPolyData()
|
|
vtk_data.SetPoints(vtk_points)
|
|
|
|
return VTK(vtk_data)
|
|
|
|
|
|
@staticmethod
|
|
def from_file(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 an .vtk file. Valid types are vtkRectilinearGrid,
|
|
vtkUnstructuredGrid, and vtkPolyData.
|
|
|
|
"""
|
|
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 to_file(self,fname,parallel=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.
|
|
|
|
"""
|
|
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
|
|
if ext and ext != '.'+default_ext:
|
|
raise ValueError(f'Given extension {ext} does not match default .{default_ext}')
|
|
writer.SetFileName(str(Path(fname).with_suffix('.'+default_ext)))
|
|
writer.SetCompressorTypeToZLib()
|
|
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 need 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')
|
|
|
|
if data.dtype in [np.float64, np.float128]: # avoid large files
|
|
d = np_to_vtk(num_array=data.astype(np.float32).reshape(data.shape[0],-1),deep=True)
|
|
else:
|
|
d = np_to_vtk(num_array=data.reshape(data.shape[0],-1),deep=True)
|
|
d.SetName(label)
|
|
|
|
if data.shape[0] == N_cells:
|
|
self.vtk_data.GetCellData().AddArray(d)
|
|
elif data.shape[0] == N_points:
|
|
self.vtk_data.GetPointData().AddArray(d)
|
|
else:
|
|
raise ValueError(f'Invalid shape {data.shape[0]}')
|
|
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()
|