"""This module provides classes that allow numpy style access to VTK datasets. See examples at bottom. """ from contextlib import suppress from vtkmodules.vtkCommonCore import vtkPoints, vtkAbstractArray, vtkDataArray from vtkmodules.vtkCommonDataModel import ( vtkCellArray, vtkDataObject, vtkFieldData, vtkDataSetAttributes, vtkPointData, vtkCellData, vtkDataObject, vtkImageData, vtkMultiBlockDataSet, vtkPolyData, vtkStructuredGrid, vtkRectilinearGrid, vtkUnstructuredGrid, vtkOverlappingAMR, vtkPartitionedDataSet, vtkPartitionedDataSetCollection, ) import weakref NUMPY_AVAILABLE = False with suppress(ImportError): import numpy from vtkmodules.numpy_interface import dataset_adapter as dsa NUMPY_AVAILABLE = True class FieldDataBase(object): def __init__(self): self.association = None self.dataset = None def __getitem__(self, idx): """Implements the [] operator. Accepts an array name or index.""" return self.get_array(idx) def __setitem__(self, name, value): """Implements the [] operator. Accepts an array name or index.""" return self.set_array(name, value) def get_array(self, idx): "Given an index or name, returns a VTKArray." if isinstance(idx, int) and idx >= self.GetNumberOfArrays(): raise IndexError("array index out of range") vtkarray = super().GetArray(idx) if not NUMPY_AVAILABLE: return vtkarray if vtkarray else self.GetAbstractArray(idx) if not vtkarray: vtkarray = self.GetAbstractArray(idx) if vtkarray: return vtkarray return dsa.NoneArray array = dsa.vtkDataArrayToVTKArray(vtkarray, self.dataset) array.Association = self.association return array def __contains__(self, aname): """Returns true if the container contains arrays with the given name, false otherwise""" return self.HasArray(aname) def keys(self): """Returns the names of the arrays as a list.""" kys = [] narrays = self.GetNumberOfArrays() for i in range(narrays): name = self.GetAbstractArray(i).GetName() if name: kys.append(name) return tuple(kys) def values(self): """Returns the arrays as a tuple.""" vals = [] narrays = self.GetNumberOfArrays() for i in range(narrays): a = self.get_array(i) if a.GetName(): vals.append(a) return tuple(vals) def items(self): """Returns a tuple of pairs (name, array)""" pairs = [] narrays = self.GetNumberOfArrays() for i in range(narrays): arr = self.get_array(i) name = arr.GetName() if name: pairs.append((name, arr)) return tuple(pairs) def set_array(self, name, narray): """Appends a new array to the dataset attributes.""" if not NUMPY_AVAILABLE: if isinstance(narray, vtkAbstractArray): narray.SetName(name) self.AddArray(narray) return if narray is dsa.NoneArray: # if NoneArray, nothing to do. return if self.association == vtkDataObject.POINT: arrLength = self.dataset.GetNumberOfPoints() elif self.association == vtkDataObject.CELL: arrLength = self.dataset.GetNumberOfCells() elif ( self.association == vtkDataObject.ROW and self.dataset.GetNumberOfColumns() > 0 ): arrLength = self.dataset.GetNumberOfRows() else: if not isinstance(narray, numpy.ndarray): arrLength = 1 else: arrLength = narray.shape[0] # Fixup input array length: if ( not isinstance(narray, numpy.ndarray) or numpy.ndim(narray) == 0 ): # Scalar input dtype = narray.dtype if isinstance(narray, numpy.ndarray) else type(narray) tmparray = numpy.empty(arrLength, dtype=dtype) tmparray.fill(narray) narray = tmparray elif narray.shape[0] != arrLength: # Vector input components = 1 for l in narray.shape: components *= l tmparray = numpy.empty((arrLength, components), dtype=narray.dtype) tmparray[:] = narray.flatten() narray = tmparray shape = narray.shape if len(shape) == 3: # Array of matrices. We need to make sure the order in memory is right. # If column order (c order), transpose. VTK wants row order (fortran # order). The deep copy later will make sure that the array is contiguous. # If row order but not contiguous, transpose so that the deep copy below # does not happen. size = narray.dtype.itemsize if (narray.strides[1] / size == 3 and narray.strides[2] / size == 1) or ( narray.strides[1] / size == 1 and narray.strides[2] / size == 3 and not narray.flags.contiguous ): narray = narray.transpose(0, 2, 1) # If array is not contiguous, make a deep copy that is contiguous if not narray.flags.contiguous: narray = numpy.ascontiguousarray(narray) # Flatten array of matrices to array of vectors if len(shape) == 3: narray = narray.reshape(shape[0], shape[1] * shape[2]) # this handle the case when an input array is directly appended on the # output. We want to make sure that the array added to the output is not # referring to the input dataset. copy = dsa.VTKArray(narray) try: copy.VTKObject = narray.VTKObject except AttributeError: pass arr = dsa.numpyTovtkDataArray(copy, name) self.AddArray(arr) def __eq__(self, other: object) -> bool: """Test dict-like equivalency.""" # here we check if other is the same class or a subclass of self. if not isinstance(other, type(self)): return False if self is other: return True """ If numpy is not available, only check for identity without comparing contents of the data arrays """ if not NUMPY_AVAILABLE: return False if set(self.keys()) != set(other.keys()): return False # verify the value of the arrays for key, value in other.items(): if not numpy.array_equal(value, self[key]): return False return True def __iter__(self): return iter(self.keys()) def __len__(self): return self.GetNumberOfArrays() @vtkFieldData.override class FieldData(FieldDataBase, vtkFieldData): pass class DataSetAttributesBase(FieldDataBase): pass @vtkDataSetAttributes.override class DataSetAttributes(DataSetAttributesBase, vtkDataSetAttributes): def __eq__(self, other: object) -> bool: """Test dict-like equivalency.""" if not super().__eq__(other): return False for attr in [ "GetScalars", "GetVectors", "GetNormals", "GetTangents", "GetTCoords", "GetTensors", "GetGlobalIds", "GetPedigreeIds", "GetRationalWeights", "GetHigherOrderDegrees", "GetProcessIds", ]: self_attr = getattr(self, attr)() other_attr = getattr(other, attr)() if self_attr and other_attr: if self_attr.GetName() != other_attr.GetName(): return False elif self_attr != other_attr: return False return True @vtkPointData.override class PointData(DataSetAttributesBase, vtkPointData): pass @vtkCellData.override class CellData(DataSetAttributesBase, vtkCellData): pass class CompositeDataSetAttributesIterator(object): def __init__(self, cdsa): self._cdsa = cdsa if cdsa: self._itr = iter(cdsa.keys()) else: self._itr = None def __iter__(self): return self def __next__(self): if not self._cdsa: raise StopIteration name = next(self._itr) return self._cdsa[name] def next(self): return self.__next__() class CompositeDataSetAttributes(object): """This is a python friendly wrapper for vtkDataSetAttributes for composite datasets. Since composite datasets themselves don't have attribute data, but the attribute data is associated with the leaf nodes in the composite dataset, this class simulates a DataSetAttributes interface by taking a union of DataSetAttributes associated with all leaf nodes.""" def __init__(self, dataset, association): self.DataSet = dataset self.Association = association self.ArrayNames = [] self.Arrays = {} # build the set of arrays available in the composite dataset. Since # composite datasets can have partial arrays, we need to iterate over # all non-null blocks in the dataset. self.__determine_arraynames() def __determine_arraynames(self): array_set = set() array_list = [] for dataset in self.DataSet: dsa = dataset.GetAttributesAsFieldData(self.Association) for array_name in dsa.keys(): if array_name not in array_set: array_set.add(array_name) array_list.append(array_name) self.ArrayNames = array_list def modified(self): """Rescans the contained dataset to update the internal list of arrays.""" self.__determine_arraynames() def __contains__(self, aname): """Returns true if the container contains arrays with the given name, false otherwise""" return aname in self.ArrayNames def keys(self): """Returns the names of the arrays as a tuple.""" return tuple(self.ArrayNames) def values(self): """Returns all the arrays as a tuple.""" arrays = [] for array in self: arrays.append(array) return tuple(arrays) def items(self): """Returns (name, array) pairs as a tuple.""" items = [] for name in self.keys(): items.append((name, self[name])) return tuple(items) def __getitem__(self, idx): """Implements the [] operator. Accepts an array name.""" return self.get_array(idx) def __setitem__(self, name, narray): """Implements the [] operator. Accepts an array name.""" return self.set_array(name, narray) def set_array(self, name, narray): """Appends a new array to the composite dataset attributes.""" if not NUMPY_AVAILABLE: # don't know how to handle composite dataset attribute when numpy not around raise NotImplementedError("Only available with numpy") if narray is dsa.NoneArray: # if NoneArray, nothing to do. return added = False if not isinstance(narray, dsa.VTKCompositeDataArray): # Scalar input for ds in self.DataSet: ds.GetAttributesAsFieldData(self.Association).set_array(name, narray) added = True if added: self.ArrayNames.append(name) # don't add the narray since it's a scalar. GetArray() will create a # VTKCompositeArray on-demand. else: for ds, array in zip(self.DataSet, narray.Arrays): if array is not None: ds.GetAttributesAsFieldData(self.Association).set_array(name, array) added = True if added: self.ArrayNames.append(name) self.Arrays[name] = weakref.ref(narray) def get_array(self, idx): """Given a name, returns a VTKCompositeArray.""" arrayname = idx if not NUMPY_AVAILABLE: # don't know how to handle composite dataset attribute when numpy not around raise NotImplementedError("Only available with numpy") if arrayname not in self.ArrayNames: return dsa.NoneArray if arrayname not in self.Arrays or self.Arrays[arrayname]() is None: array = dsa.VTKCompositeDataArray( dataset=self.DataSet, name=arrayname, association=self.Association ) self.Arrays[arrayname] = weakref.ref(array) else: array = self.Arrays[arrayname]() return array def __iter__(self): """Iterators on keys""" return iter(self.ArrayNames) def __len__(self): return len(self.ArrayNames) # class DataSet(DataObjectBase): class DataSet(object): def __init__(self, **kwargs) -> None: self._numpy_attrs = [] @property def point_data(self): pd = super().GetPointData() pd.dataset = self pd.association = self.POINT return pd @property def cell_data(self): cd = super().GetCellData() cd.dataset = self cd.association = self.CELL return cd @property def field_data(self): fd = super().GetFieldData() if fd: fd.dataset = self fd.association = self.FIELD return fd def __eq__(self, other: object) -> bool: """Test equivalency between data objects.""" if not isinstance(self, type(other)): return False if self is other: return True """ If numpy is not available, only check for identity without comparing contents of the data arrays """ if not NUMPY_AVAILABLE: return False for attr in self._numpy_attrs: if hasattr(self, attr): if not numpy.array_equal(getattr(self, attr), getattr(other, attr)): return False for attr in ["field_data", "point_data", "cell_data"]: if getattr(self, attr) != getattr(other, attr): return False return True def convert_to_unstructured_grid(self): from vtkmodules.vtkFiltersCore import vtkExtractCells ecells = vtkExtractCells() ecells.SetInputData(self) ecells.ExtractAllCellsOn() ecells.Update() return ecells.GetOutput() class PointSet(DataSet): def __init__(self, **kwargs) -> None: DataSet.__init__(self, **kwargs) self._numpy_attrs.append("points") @property def points(self): pts = self.GetPoints() if not NUMPY_AVAILABLE: return pts if not pts or not pts.GetData(): return None return dsa.vtkDataArrayToVTKArray(pts.GetData()) @points.setter def points(self, points): if isinstance(points, vtkPoints): self.SetPoints(points) return if not NUMPY_AVAILABLE: raise ValueError("Expect vtkPoints") pts = dsa.numpyTovtkDataArray(points, "points") vtkpts = vtkPoints() vtkpts.SetData(pts) self.SetPoints(vtkpts) @vtkUnstructuredGrid.override class UnstructuredGrid(PointSet, vtkUnstructuredGrid): def __init__(self, **kwargs): PointSet.__init__(self, **kwargs) vtkUnstructuredGrid.__init__(self, **kwargs) @property def cells(self): ca = self.GetCells() conn_vtk = ca.GetConnectivityArray() offsets_vtk = ca.GetOffsetsArray() ct_vtk = self.GetCellTypesArray() if not NUMPY_AVAILABLE: return { "connectivity": conn_vtk, "offsets": offsets_vtk, "cell_types": ct_vtk, } conn = dsa.vtkDataArrayToVTKArray(conn_vtk) offsets = dsa.vtkDataArrayToVTKArray(offsets_vtk) ct = dsa.vtkDataArrayToVTKArray(ct_vtk) return {"connectivity": conn, "offsets": offsets, "cell_types": ct} @cells.setter def cells(self, cells): ca = vtkCellArray() if not NUMPY_AVAILABLE: ca.SetData(cells["offsets"], cells["connectivity"]) self.SetCells(cells["cell_types"], ca) return conn_vtk = dsa.numpyTovtkDataArray(cells["connectivity"]) offsets_vtk = dsa.numpyTovtkDataArray(cells["offsets"]) cell_types_vtk = dsa.numpyTovtkDataArray(cells["cell_types"]) ca.SetData(offsets_vtk, conn_vtk) self.SetCells(cell_types_vtk, ca) @vtkImageData.override class ImageData(DataSet, vtkImageData): def __init__(self, **kwargs): DataSet.__init__(self, **kwargs) vtkImageData.__init__(self, **kwargs) @vtkPolyData.override class PolyData(PointSet, vtkPolyData): def __init__(self, **kwargs) -> None: PointSet.__init__(self, **kwargs) vtkPolyData.__init__(self, **kwargs) self._numpy_attrs.extend(["verts", "lines", "strips", "polys"]) @property def verts_arrays(self): ca = self.GetVerts() conn_vtk = ca.GetConnectivityArray() offsets_vtk = ca.GetOffsetsArray() if not NUMPY_AVAILABLE: return { "connectivity": conn_vtk, "offsets": offsets_vtk, } conn = dsa.vtkDataArrayToVTKArray(conn_vtk) offsets = dsa.vtkDataArrayToVTKArray(offsets_vtk) return {"connectivity": conn, "offsets": offsets} @property def lines_arrays(self): ca = self.GetLines() conn_vtk = ca.GetConnectivityArray() offsets_vtk = ca.GetOffsetsArray() if not NUMPY_AVAILABLE: return { "connectivity": conn_vtk, "offsets": offsets_vtk, } conn = dsa.vtkDataArrayToVTKArray(conn_vtk) offsets = dsa.vtkDataArrayToVTKArray(offsets_vtk) return {"connectivity": conn, "offsets": offsets} @property def strips_arrays(self): ca = self.GetStrips() conn_vtk = ca.GetConnectivityArray() offsets_vtk = ca.GetOffsetsArray() if not NUMPY_AVAILABLE: return { "connectivity": conn_vtk, "offsets": offsets_vtk, } conn = dsa.vtkDataArrayToVTKArray(conn_vtk) offsets = dsa.vtkDataArrayToVTKArray(offsets_vtk) return {"connectivity": conn, "offsets": offsets} @property def polys_arrays(self): ca = self.GetPolys() conn_vtk = ca.GetConnectivityArray() offsets_vtk = ca.GetOffsetsArray() if not NUMPY_AVAILABLE: return { "connectivity": conn_vtk, "offsets": offsets_vtk, } conn = dsa.vtkDataArrayToVTKArray(conn_vtk) offsets = dsa.vtkDataArrayToVTKArray(offsets_vtk) return {"connectivity": conn, "offsets": offsets} @vtkRectilinearGrid.override class RectilinearGrid(DataSet, vtkRectilinearGrid): def __init__(self, **kwargs) -> None: DataSet.__init__(self, **kwargs) vtkRectilinearGrid.__init__(self, **kwargs) self._numpy_attrs.extend(["x_coordinates", "y_coordinates", "z_coordinates"]) @property def x_coordinates(self): pts = self.GetXCoordinates() if not NUMPY_AVAILABLE: return pts if not pts: return None return dsa.vtkDataArrayToVTKArray(pts) @x_coordinates.setter def x_coordinates(self, points): if isinstance(points, vtkDataArray): self.SetXCoordinates(points) return if not NUMPY_AVAILABLE: raise ValueError("Expect vtkDataArray") pts = dsa.numpyTovtkDataArray(points, "x_coords") self.SetXCoordinates(pts) @property def y_coordinates(self): pts = self.GetYCoordinates() if not NUMPY_AVAILABLE: return pts if not pts: return None return dsa.vtkDataArrayToVTKArray(pts) @y_coordinates.setter def y_coordinates(self, points): if isinstance(points, vtkDataArray): self.SetYCoordinates(points) return if not NUMPY_AVAILABLE: raise ValueError("Expect vtkDataArray") pts = dsa.numpyTovtkDataArray(points, "y_coords") self.SetYCoordinates(pts) @property def z_coordinates(self): pts = self.GetZCoordinates() if not NUMPY_AVAILABLE: return pts if not pts: return None return dsa.vtkDataArrayToVTKArray(pts) @z_coordinates.setter def z_coordinates(self, points): if isinstance(points, vtkDataArray): self.SetZCoordinates(points) return if not NUMPY_AVAILABLE: raise ValueError("Expect vtkDataArray") pts = dsa.numpyTovtkDataArray(points, "z_coords") self.SetZCoordinates(pts) class CompositeDataIterator(object): """Wrapper for a vtkCompositeDataIterator class to satisfy the python iterator protocol. This iterator iterates over non-empty leaf nodes. To iterate over empty or non-leaf nodes, use the vtkCompositeDataIterator directly. """ def __init__(self, cds): self.Iterator = cds.NewIterator() if self.Iterator: self.Iterator.UnRegister(None) self.Iterator.GoToFirstItem() def __iter__(self): return self def __next__(self): if not self.Iterator: raise StopIteration if self.Iterator.IsDoneWithTraversal(): raise StopIteration retVal = self.Iterator.GetCurrentDataObject() self.Iterator.GoToNextItem() return retVal def next(self): return self.__next__() def __getattr__(self, name): """Returns attributes from the vtkCompositeDataIterator.""" return getattr(self.Iterator, name) class CompositeDataSetBase(object): """A wrapper for vtkCompositeData and subclasses that makes it easier to access Point/Cell/Field data as VTKCompositeDataArrays. It also provides a Python type iterator.""" def __init__(self, **kwargs): self._PointData = None self._CellData = None self._FieldData = None self._Points = None def __iter__(self): "Creates an iterator for the contained datasets." return CompositeDataIterator(self) def get_attributes(self, type): """Returns the attributes specified by the type as a CompositeDataSetAttributes instance.""" return CompositeDataSetAttributes(self, type) @property def point_data(self): "Returns the point data as a DataSetAttributes instance." if self._PointData is None or self._PointData() is None: pdata = self.get_attributes(vtkDataObject.POINT) self._PointData = weakref.ref(pdata) return self._PointData() @property def cell_data(self): "Returns the cell data as a DataSetAttributes instance." if self._CellData is None or self._CellData() is None: cdata = self.get_attributes(vtkDataObject.CELL) self._CellData = weakref.ref(cdata) return self._CellData() @property def field_data(self): "Returns the field data as a DataSetAttributes instance." if self._FieldData is None or self._FieldData() is None: fdata = self.get_attributes(vtkDataObject.FIELD) self._FieldData = weakref.ref(fdata) return self._FieldData() @property def points(self): "Returns the points as a VTKCompositeDataArray instance." if not NUMPY_AVAILABLE: # don't know how to handle composite dataset when numpy not around raise NotImplementedError("Only available with numpy") if self._Points is None or self._Points() is None: pts = [] for ds in self: try: _pts = ds.Points except AttributeError: _pts = None if _pts is None: pts.append(dsa.NoneArray) else: pts.append(_pts) if len(pts) == 0 or all([a is dsa.NoneArray for a in pts]): cpts = dsa.NoneArray else: cpts = dsa.VTKCompositeDataArray(pts, dataset=self) self._Points = weakref.ref(cpts) return self._Points() @vtkPartitionedDataSet.override class PartitionedDataSet(CompositeDataSetBase, vtkPartitionedDataSet): def append(self, dataset): self.SetPartition(self.GetNumberOfPartitions(), dataset) @vtkPartitionedDataSetCollection.override class PartitionedDataSetCollection(CompositeDataSetBase, vtkPartitionedDataSetCollection): def append(self, dataset): self.SetPartitionedDataSet(self.GetNumberOfPartitionedDataSets(), dataset) @vtkOverlappingAMR.override class OverlappingAMR(CompositeDataSetBase, vtkOverlappingAMR): pass @vtkMultiBlockDataSet.override class MultiBlockDataSet(CompositeDataSetBase, vtkMultiBlockDataSet): pass @vtkStructuredGrid.override class StructuredGrid(PointSet, vtkStructuredGrid): def __init__(self, **kwargs): PointSet.__init__(self, **kwargs) vtkStructuredGrid.__init__(self, **kwargs) @property def x_coordinates(self): if not NUMPY_AVAILABLE: raise NotImplementedError("Only available with numpy") dims = [0,0,0] self.GetDimensions(dims) return self.points[:, 0].reshape(dims, order="F") @property def y_coordinates(self): if not NUMPY_AVAILABLE: raise NotImplementedError("Only available with numpy") dims = [0,0,0] self.GetDimensions(dims) return self.points[:, 1].reshape(dims, order="F") @property def z_coordinates(self): if not NUMPY_AVAILABLE: raise NotImplementedError("Only available with numpy") dims = [0,0,0] self.GetDimensions(dims) return self.points[:, 2].reshape(dims, order="F") # ----------------------------------------------------------------------------- # Handle pickle registration # ----------------------------------------------------------------------------- with suppress(ImportError): import copyreg from vtkmodules.util.pickle_support import serialize_VTK_data_object copyreg.pickle(PolyData, serialize_VTK_data_object) copyreg.pickle(UnstructuredGrid, serialize_VTK_data_object) copyreg.pickle(ImageData, serialize_VTK_data_object) copyreg.pickle(PartitionedDataSet, serialize_VTK_data_object) copyreg.pickle(StructuredGrid, serialize_VTK_data_object)