Chimie Théorique » QMX

import numpy as np

from numpy.ctypeslib import ctypes

from vtk import vtkDataArray, vtkFloatArray, vtkDoubleArray

if ctypes is None:

    class CTypesEmulator:

        def __init__(self):

            self._SimpleCData = np.number

            self.c_float = np.float32

            self.c_double = np.float64

    try:

        import ctypes

    except ImportError:

        ctypes = CTypesEmulator()

# -------------------------------------------------------------------

class vtkNumPyBuffer:

    def __init__(self, data):

        self.strbuf = data.tostring()

        self.nitems = len(data.flat)

    def __len__(self):

        return self.nitems

    def get_pointer(self):

        # Any C/C++ method that requires a void * can be passed a Python

        # string. No check is done to ensure that the string is the correct

        # size, and the string's reference count is not incremented. Extreme

        # caution should be applied when using this feature.

        return self.strbuf

    def notify(self, obj, event):

        if event == 'DeleteEvent':

            del self.strbuf

        else:

            raise RuntimeError('Event not recognized.')

class vtkDataArrayFromNumPyBuffer:

    def __init__(self, vtk_class, ctype, data=None):

        assert issubclass(ctype, ctypes._SimpleCData)

        self.ctype = ctype

        self.vtk_da = vtk_class()

        assert isinstance(self.vtk_da, vtkDataArray)

        assert self.vtk_da.GetDataTypeSize() == np.nbytes[np.dtype(self.ctype)]

        if data is not None:

            self.read_numpy_array(data)

    def read_numpy_array(self, data):

        if not isinstance(data, np.ndarray):

            data = np.array(data, dtype=self.ctype)

        if data.dtype != self.ctype: # NB: "is not" gets it wrong

            data = data.astype(self.ctype)

        self.vtk_da.SetNumberOfComponents(data.shape[-1])

        # Passing the void* buffer to the C interface does not increase

        # its reference count, hence the buffer is deleted by Python when

        # the reference count of the string from tostring reaches zero.

        # Also, the boolean True tells VTK to save (not delete) the buffer

        # when the VTK data array is deleted - we want Python to do this.

        npybuf = vtkNumPyBuffer(data)

        self.vtk_da.SetVoidArray(npybuf.get_pointer(), len(npybuf), True)

        self.vtk_da.AddObserver('DeleteEvent', npybuf.notify)

    def get_output(self):

        return self.vtk_da

    def copy(self):

        vtk_da_copy = self.vtk_da.NewInstance()

        vtk_da_copy.SetNumberOfComponents(self.vtk_da.GetNumberOfComponents())

        vtk_da_copy.SetNumberOfTuples(self.vtk_da.GetNumberOfTuples())

        assert vtk_da_copy.GetSize() == self.vtk_da.GetSize()

        vtk_da_copy.DeepCopy(self.vtk_da)

        return vtk_da_copy

# -------------------------------------------------------------------

class vtkDataArrayFromNumPyArray(vtkDataArrayFromNumPyBuffer):

    """Class for reading vtkDataArray from 1D or 2D NumPy array.

    This class can be used to generate a vtkDataArray from a NumPy array.

    The NumPy array should be of the form <entries> x <number of components>

    where 'number of components' indicates the number of components in

    each entry in the vtkDataArray. Note that this form is also expected

    even in the case of only a single component.

    """

    def __init__(self, vtk_class, ctype, data=None, buffered=True):

        self.buffered = buffered

        vtkDataArrayFromNumPyBuffer.__init__(self, vtk_class, ctype, data)

    def read_numpy_array(self, data):

        """Read vtkDataArray from NumPy array"""

        if not isinstance(data, np.ndarray):

            data = np.array(data, dtype=self.ctype)

        if data.dtype != self.ctype: # NB: "is not" gets it wrong

            data = data.astype(self.ctype)

        if data.ndim == 1:

            data = data[:, np.newaxis]

        elif data.ndim != 2:

            raise ValueError('Data must be a 1D or 2D NumPy array.')

        if self.buffered:

            vtkDataArrayFromNumPyBuffer.read_numpy_array(self, data)

        else:

            self.vtk_da.SetNumberOfComponents(data.shape[-1])

            self.vtk_da.SetNumberOfTuples(data.shape[0])

            for i, d_c in enumerate(data):

                for c, d in enumerate(d_c):

                    self.vtk_da.SetComponent(i, c, d)

class vtkFloatArrayFromNumPyArray(vtkDataArrayFromNumPyArray):

    def __init__(self, data):

        vtkDataArrayFromNumPyArray.__init__(self, vtkFloatArray,

                                            ctypes.c_float, data)

class vtkDoubleArrayFromNumPyArray(vtkDataArrayFromNumPyArray):

    def __init__(self, data):

        vtkDataArrayFromNumPyArray.__init__(self, vtkDoubleArray,

                                            ctypes.c_double, data)

# -------------------------------------------------------------------

class vtkDataArrayFromNumPyMultiArray(vtkDataArrayFromNumPyBuffer):

    """Class for reading vtkDataArray from a multi-dimensional NumPy array.

    This class can be used to generate a vtkDataArray from a NumPy array.

    The NumPy array should be of the form <gridsize> x <number of components>

    where 'number of components' indicates the number of components in

    each gridpoint in the vtkDataArray. Note that this form is also expected

    even in the case of only a single component.

    """

    def __init__(self, vtk_class, ctype, data=None, buffered=True):

        self.buffered = buffered

        vtkDataArrayFromNumPyBuffer.__init__(self, vtk_class, ctype, data)

    def read_numpy_array(self, data):

        """Read vtkDataArray from NumPy array"""

        if not isinstance(data, np.ndarray):

            data = np.array(data, dtype=self.ctype)

        if data.dtype != self.ctype: # NB: "is not" gets it wrong

            data = data.astype(self.ctype)

        if data.ndim <=2:

            raise Warning('This is inefficient for 1D and 2D NumPy arrays. ' +

                          'Use a vtkDataArrayFromNumPyArray subclass instead.')

        if self.buffered:

            # This is less than ideal, but will not copy data (uses views).

            # To get the correct ordering, the grid dimensions have to be

            # transposed without moving the last dimension (the components).

            n = data.ndim-1

            for c in range(n//2):

                data = data.swapaxes(c,n-1-c)

            vtkDataArrayFromNumPyBuffer.read_numpy_array(self, data)

        else:

            self.vtk_da.SetNumberOfComponents(data.shape[-1])

            self.vtk_da.SetNumberOfTuples(np.prod(data.shape[:-1]))

            for c, d_T in enumerate(data.T):

                for i, d in enumerate(d_T.flat):

                    self.vtk_da.SetComponent(i, c, d)

class vtkFloatArrayFromNumPyMultiArray(vtkDataArrayFromNumPyMultiArray):

    def __init__(self, data):

        vtkDataArrayFromNumPyMultiArray.__init__(self, vtkFloatArray,

                                                 ctypes.c_float, data)

class vtkDoubleArrayFromNumPyMultiArray(vtkDataArrayFromNumPyMultiArray):

    def __init__(self, data):

        vtkDataArrayFromNumPyMultiArray.__init__(self, vtkDoubleArray,

                                                 ctypes.c_double, data)