[vtkusers] PCA on vtkImageData

[Andrew Crozier]

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 <mailto: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
>>     <mailto: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 <mailto: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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