# [vtkusers] 3D numpy array to vtkDataSet

Cory Quammen cory.quammen at kitware.com
Mon Jul 20 23:07:28 EDT 2015

```Quentan,

Thank you for posting the excellent code sample. With it, I could see what
the problem was right away.

The problem is that vtkImageData has the notion of an origin, and you are
not setting it. By default, vtkImageData have a corner at (0, 0, 0), but
your function in numpy starts at (-1, -1, -1). By not setting the origin to
(-1, -1, -1), you are accidentally shifting your data. You'll need to set
the origin in your vtk_image_data via

vtk_image_data.SetOrigin(-1, -1, -1)

You'll also need to figure out your vtk_image_data's spacing. For the
x-component, this can be computed with

(x_max - x_min) / (x_dim - 1)

where x_{max, min} are the maximum and minimum x coordinate and x_dim is
the number of voxels in the x direction.

I hope that helps,
Cory

On Sun, Jul 19, 2015 at 1:40 PM, Quentan Qi <quentan at gmail.com> wrote:

> Dear Cory,
>
> I may fail to explain my problem, so I made an example
> <https://github.com/quentan/Test_ImageData> to show what I want to
> express, as you suggested. https://github.com/quentan/Test_ImageData
>
> This example generates a quadric with its implicit form: F(x,y,z) =
> a0*x^2 + a1*y^2 + a2*z^2 + a3*x*y + a4*y*z + a5*x*z + a6*x + a7*y + a8*z +
> a9
>
> perfectly.
>
> The right viewport renders the same quadric with a meshgrid generated with
> numpy. The meshgrid is converted to vtkFloatArray then to vtkImageData. Its
> shape is right, but locates at wrong position, which seems like it was
> scaled to some positive values.
>
> Note the small perpendicular coordinate lines in the corner.
>
> I guess the issue raises around line 120 - 123. If any other wrongs
> happen, point it for me, please.
>
> Cheers,
> Quentan
>
>
> On 18 Jul 2015, at 15:09, Cory Quammen <cory.quammen at kitware.com> wrote:
>
> Quentan,
>
> vtkImageData is in fact a subclass of vtkDataSet, so no conversion is
> needed. You said, "vtkImageData scales all points to positive integer
> values", but this should not be the case. Something strange is going on.
>
> Could you expand the code above into a complete example that can be run
> through vtkpython? That will make it easier to take a look. In particular,
> please add a part that shows the vtkImageData are being scaled to positive
> integers. It's fine if you fill the array with random values.
>
> Thanks,
> Cory
>
>
> On Sat, Jul 18, 2015 at 6:08 AM, Quentan Qi <quentan at gmail.com> wrote:
>
>> Hi there,
>>
>> I am going to read a set of discrete 3D points (float value, not int
>> value) and show both the points and the fitting surface via VTK’s implicit
>> functions, say vtkImplicitVolume or vtkImplicitDataSet.
>>
>> It works fine of the numpy arrary to vtkImageData conversion in the
>> following code, but is out of my mind how to convert it to vtkDataSet,
>> which is my requirement.
>>
>> ```Python
>>     # Convert numpy array to VTK array (vtkFloatArray)
>>     vtk_data_array = numpy_support.numpy_to_vtk(
>>         num_array=ndarray.transpose(2, 1, 0).ravel(),  # ndarray contains
>> the fitting result from the points. It is a 3D array
>>         deep=True,
>>         array_type=vtk.VTK_FLOAT)
>>
>>     # Convert the VTK array to vtkImageData
>>     img_vtk = vtk.vtkImageData()
>>     img_vtk.SetDimensions(ndarray.shape)
>>     img_vtk.SetSpacing(spacing[::-1])
>>     img_vtk.GetPointData().SetScalars(vtk_data_array)
>>
>>     # …
>>     implicit_volume = vtk.vtkImplicitVolume()  # I want a
>> vtkImplicitDataSet, whose input is a vtkDataSet
>>     implicit_volume.SetVolume(img_vtk)
>> ```
>>
>> Because vtkImageData scales all points to positive integer values so that
>> the rendering result mismatches the original points, I deem vtkDataSet or
>> its subclass can do it. Anybody knows how to convert?
>>
>> Cheers,
>> Quentan
>>
>> _______________________________________________
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>
>
> --
> Cory Quammen
> R&D Engineer
> Kitware, Inc.
>
>
>

--
Cory Quammen
R&D Engineer
Kitware, Inc.
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