convert VTK array to numpy array

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1

I have a VTKArray
VTKArray([ -3.17113447, -16.9386692 , 16.73578644], dtype=float32)
I’m trying to convert this to a numpy array

from vtk.util.numpy_support import vtk_to_numpy

vtk_to_numpy(edgeNode0_pos)
error:
(self.class.name, name))
AttributeError: ‘VTKArray’ object has no attribute ‘GetDataType’

Any help on how to resolve this error will be useful.

1 Like
2

That VTKArray is a numpy array - its a helper class that wraps the numpy.ndarray class. vtk.util.numpy_support.vtk_to_numpy converts vtkDataArrays into VTKArrays.

Try:

isinstance(edgeNode0_pos, np.ndarray)
1 Like
3

I would like to convert the VTKArray into a numpy array anyway. Like a proper numpy array, no wrappers. Is that possible? I don’t understand how isinstance helps here.

Sorry for piggybacking on this old question, it just exactly describes what I’m looking for.

1 Like
4

The following two functions may help.

def vtkToNumpy(data):
    temp = vtk_to_numpy(data.GetPointData().GetScalars())
    dims = data.GetDimensions()
    component = data.GetNumberOfScalarComponents()
    if component == 1:
        numpy_data = temp.reshape(dims[2], dims[1], dims[0])
        numpy_data = numpy_data.transpose(2,1,0)
    elif component == 3 or component == 4:
        if dims[2] == 1: # a 2D RGB image
            numpy_data = temp.reshape(dims[1], dims[0], component)
            numpy_data = numpy_data.transpose(0, 1, 2)
            numpy_data = np.flipud(numpy_data)
        else:
            raise RuntimeError('unknow type')
    return numpy_data

def numpyToVTK(data, multi_component=False, type='float'):
    '''
    multi_components: rgb has 3 components
    type：float or char
    '''
    if type == 'float':
        data_type = vtk.VTK_FLOAT
    elif type == 'char':
        data_type = vtk.VTK_UNSIGNED_CHAR
    else:
        raise RuntimeError('unknown type')
    if multi_component == False:
        if len(data.shape) == 2:
            data = data[:, :, np.newaxis]
        flat_data_array = data.transpose(2,1,0).flatten()
        vtk_data = numpy_to_vtk(num_array=flat_data_array, deep=True, array_type=data_type)
        shape = data.shape
    else:
        assert len(data.shape) == 3, 'only test for 2D RGB'
        flat_data_array = data.transpose(1, 0, 2)
        flat_data_array = np.reshape(flat_data_array, newshape=[-1, data.shape[2]])
        vtk_data = numpy_to_vtk(num_array=flat_data_array, deep=True, array_type=data_type)
        shape = [data.shape[0], data.shape[1], 1]
    img = vtk.vtkImageData()
    img.GetPointData().SetScalars(vtk_data)
    img.SetDimensions(shape[0], shape[1], shape[2])
    return img
3 Likes
5

Converting the VTKArray into a proper numpy array can done as follows:

>>> points
VTKArray([[  7.881,  99.893,  31.901]], dtype=float32)
>>> import numpy as np
>>> np.array(points)
array([[ 7.881, 99.893, 31.901]], dtype=float32)