[vtkusers] PCA on vtkImageData

[David Gobbi]

Hi Andrew,

My best guess is that the internal points are there, but ParaView is only
showing the surface.  From python you can call GetNumberOfPoints() on the
data set to check if the number of points matches what you expect.

 - David

On Mon, Nov 17, 2014 at 10:25 AM, Andrew Crozier <
andrew.crozier at medunigraz.at> wrote:

>  I wrote it out with vtkUnstructuredGridWriter and loaded it up in
> Paraview. Showing it there with a 'Points' or '3D Glyphs' representation
> shows only vertices on the external surface of the specified region.
>
> (Python) code I used to generate:
>
> tf = vtk.vtkThreshold()
> tf.SetInput(img)
> tf.ThresholdBetween(1.5,2.5)
> tf.Update()
> op = tf.GetOutput()
>
> writer = vtk.vtkUnstructuredGridWriter()
> writer.SetFileName('thresh.vtk')
> writer.SetInput(op)
> writer.Write()
>
> Andrew
>
>
> On 17/11/14 17:40, David Gobbi wrote:
>
> Hi Andrew,
>
>  It should export all the points in the volume, as long as they are
> within the applied thresholds.  What is your evidence that it's only
> exporting the boundary?
>
>   - David
>
> On Mon, Nov 17, 2014 at 9:34 AM, Andrew Crozier <
> andrew.crozier at medunigraz.at> wrote:
>
>>  Hi David,
>>
>> Thanks for the suggestion. I looked at the vtkThreshold filer, however it
>> appears to export the boundary of the thresholded volume, whereas I require
>> all points inside the volume. Have you any idea of how to achieve that?
>>
>> BW,
>> Andrew
>>
>>
>> On 17/11/14 17:16, David Gobbi wrote:
>>
>> Hi Andrew,
>>
>>  The vtkThreshold filter will extract only the cells with the desired
>> scalar values, and will output them as an unstructured grid.  It
>> isn't exactly what you want because it extracts cells, rather than
>> points, but it might be worth a shot.
>>
>>   - David
>>
>> On Mon, Nov 17, 2014 at 8:28 AM, Andrew Crozier <
>> andrew.crozier at medunigraz.at> wrote:
>>
>>> Hi,
>>>
>>> I am trying to evaluate the principal components of a strucutre in a 3D
>>> volume image, to determine its spatial alignment for use in an automatic
>>> processing pipeline.
>>>
>>> The input is a vtkImageData, with multiple integer values (say, 0, 1, 2
>>> and 3), and I want to perform PCA on the positions of all voxels with value
>>> 2, for example.
>>>
>>> I have looked at vtkPCAAnalysisFilter, and this requires an input of
>>> vtkPointSet. vtkImageDataToPointSet converts a vtkImageData to a
>>> vtkStructuredGrid, however I expect this to include all points in the
>>> original image. At the moment I seem to be missing some way of filtering
>>> out the points other than those of value 2.
>>>
>>> Any help provided for this would be greatly appreciated!
>>>
>>> Best wishes,
>>> Andrew Crozier
>>>
>>>
>>   --
>> ------------------------------
>> *Andrew Crozier*
>> andrew.crozier at medunigraz.at
>>
>> Postdoctoral Researcher
>> Institute for Biophysics
>> Medical University of Graz
>>
>
>
> --
> ------------------------------
> *Andrew Crozier*
> andrew.crozier at medunigraz.at
>
> Postdoctoral Researcher
> Institute for Biophysics
> Medical University of Graz
>
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