polishing
grid is interpreted again in the DAMASK meaning, i.e it specifies the number of cells, not the number of nodes
This commit is contained in:
Martin Diehl
parent
bb2019810a
commit
a6a73cdc0f
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@ -8,27 +8,50 @@ from vtk.util import numpy_support as nps
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from . import table
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from . import version
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class VTK: # capitals needed/preferred?
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class VTK:
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"""
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Manage vtk files.
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Spatial visualization (and potentially manipulation).
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tbd
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High-level interface to VTK.
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"""
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def __init__(self,geom):
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"""tbd."""
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"""
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Set geometry and topology.
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Parameters
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----------
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geom : subclass of vtk.vtkDataSet
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Description of geometry and topology. Valid types are vtk.vtkRectilinearGrid,
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vtk.vtkUnstructuredGrid, or vtk.vtkPolyData.
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"""
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self.geom = geom
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@staticmethod
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def from_rectilinearGrid(grid,size,origin=np.zeros(3)):
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"""Check https://blog.kitware.com/ghost-and-blanking-visibility-changes/ for missing data."""
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"""
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Create VTK of type vtk.vtkRectilinearGrid.
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This is the common type for results from the grid solver.
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Parameters
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----------
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grid : numpy.ndarray of shape (3) of np.dtype = int
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Number of cells.
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size : numpy.ndarray of shape (3)
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Physical length.
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origin : numpy.ndarray of shape (3), optional
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Spatial origin.
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"""
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coordArray = [vtk.vtkDoubleArray(),vtk.vtkDoubleArray(),vtk.vtkDoubleArray()]
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for dim in [0,1,2]:
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for c in np.linspace(origin[dim],origin[dim]+size[dim],grid[dim]):
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for c in np.linspace(origin[dim],origin[dim]+size[dim],grid[dim]+1):
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coordArray[dim].InsertNextValue(c)
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geom = vtk.vtkRectilinearGrid()
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geom.SetDimensions(*grid)
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geom.SetDimensions(*(grid+1))
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geom.SetXCoordinates(coordArray[0])
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geom.SetYCoordinates(coordArray[1])
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geom.SetZCoordinates(coordArray[2])
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@ -39,10 +62,18 @@ class VTK: # capitals needed/preferred?
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@staticmethod
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def from_unstructuredGrid(nodes,connectivity,cell_type):
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"""
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Create an unstructured grid (mesh).
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Create VTK of type vtk.vtkUnstructuredGrid.
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connectivity: 0 based at the moment, shape Ncell x N nodes
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cell_type: TRIANGLE, 'QUAD', 'TETRA','HEXAHEDRON'
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This is the common type for results from FEM solvers.
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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, 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, and HEXAHEDRON.
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"""
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vtk_nodes = vtk.vtkPoints()
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@ -62,6 +93,17 @@ class VTK: # capitals needed/preferred?
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@staticmethod
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def from_polyData(points):
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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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"""
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vtk_points= vtk.vtkPoints()
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vtk_points.SetData(nps.numpy_to_vtk(points))
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@ -79,16 +121,28 @@ class VTK: # capitals needed/preferred?
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@staticmethod
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def from_file(fname,ftype=None):
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"""
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Create VTK from file.
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Parameters
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----------
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fname : str
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Filename for reading. Valid extensions are .vtk, .vtr, .vtu, and .vtp.
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ftype : str, optional
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Name of the vtk.vtkDataSet subclass when opening an .vtk file. Valid types are vtkRectilinearGrid,
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vtkUnstructuredGrid, and vtkPolyData.
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"""
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ext = os.path.splitext(fname)[1]
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if ext == '.vtk':
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reader = vtk.vtkGenericDataObjectReader()
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reader.SetFileName(fname)
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reader.Update()
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if ftype.lower() == 'rectilineargrid':
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if 'rectilineargrid' in ftype.lower():
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geom = reader.GetRectilinearGridOutput()
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elif ftype.lower() == 'unstructuredgrid':
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elif 'unstructuredgrid' in ftype.lower():
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geom = reader.GetUnstructuredGridOutput()
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elif ftype.lower() == 'polydata':
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elif 'polydata' in ftype.lower():
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geom = reader.GetPolyDataOutput()
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else:
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raise Exception
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@ -109,8 +163,17 @@ class VTK: # capitals needed/preferred?
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return VTK(geom)
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# ToDo: If extension is given, check for consistency.
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def write(self,fname):
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"""ToDo: Check if given fileextension makes sense."""
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"""
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Write to file.
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Parameters
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----------
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fname : str
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Filename for writing.
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"""
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if (isinstance(self.geom,vtk.vtkRectilinearGrid)):
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writer = vtk.vtkXMLRectilinearGridWriter()
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elif(isinstance(self.geom,vtk.vtkUnstructuredGrid)):
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@ -127,18 +190,19 @@ class VTK: # capitals needed/preferred?
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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 pd.DataFrame and/or table
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def add(self,data,label=None):
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Npoints = self.geom.GetNumberOfPoints()
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Ncells = self.geom.GetNumberOfCells()
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"""Add data to either cells or points."""
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N_points = self.geom.GetNumberOfPoints()
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N_cells = self.geom.GetNumberOfCells()
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if isinstance(data,np.ndarray):
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shape = [data.shape[0],np.product(data.shape[1:],dtype=np.int)]
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d = nps.numpy_to_vtk(num_array=data.reshape(shape),deep=True)
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d = nps.numpy_to_vtk(num_array=data.reshape(data.shape[0],-1),deep=True)
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d.SetName(label)
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if shape[0] == Ncells:
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if data.shape[0] == N_cells:
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self.geom.GetCellData().AddArray(d)
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elif shape[0] == Npoints:
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elif data.shape[0] == N_points:
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self.geom.GetPointData().AddArray(d)
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elif isinstance(data,pd.DataFrame):
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pass
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@ -26,12 +26,12 @@ class Result:
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def __init__(self,fname):
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"""
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Opens an existing DADF5 file.
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Open an existing DADF5 file.
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Parameters
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----------
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fname : str
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name of the DADF5 file to be openend.
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name of the DADF5 file to be openend.
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"""
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with h5py.File(fname,'r') as f:
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@ -1029,7 +1029,7 @@ class Result:
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if mode.lower()=='cell':
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if self.structured:
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v = VTK.from_rectilinearGrid(self.grid+1,self.size,self.origin)
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v = VTK.from_rectilinearGrid(self.grid,self.size,self.origin)
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else:
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with h5py.File(self.fname,'r') as f:
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v = VTK.from_unstructuredGrid(f['/geometry/x_n'][()],
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