[Paraview] Problem with numpy array

Sun Apr 22 05:10:19 EDT 2018

Now it works,
Maybe was a problem about the treatment of the vectors or the numpy library.

Thanks for the support,
Andrea

From: Andy Bauer [mailto:andy.bauer at kitware.com]
Sent: Thursday, April 19, 2018 15:23
To: Caffagni, Andrea
Cc: Oscar Wilsby; Cory Quammen; paraview at public.kitware.com
Subject: Re: [Paraview] Problem with numpy array

The Gradient of Unstructured Dataset does increase the tensor dimension. So a scalar, or 1 component array in VTK/PV, becomes a vector, or a 3 components array. Similarly, a vector becomes a 2nd order tensor, or 9 component array.
Andrea: could you try upgrading to ParaView 5.5 (available at paraview.org/download<http://paraview.org/download>) ? Some of the numpy support has been improved since 5.3. I tried your original Programmable Filter script and I got an eigenvectors and eigenvalues array:
import numpy as np
from numpy import linalg as LA
from paraview import numpy_support
input = inputs[0]

numPoints = input.GetNumberOfPoints()
print "number of points",numPoints
tensors = input.PointData['Gradients']
print "tensors[0:3]",tensors[0:3]
eigenvalues,eigenvectors = LA.eig(tensors)
print 'eigenvalues', eigenvalues[0]
print 'eigenvectors',eigenvectors[0]
output.PointData.append(eigenvalues,'eigenvalues')
output.PointData.append(eigenvectors,'eigenvectors')

Once you get PV 5.5, you can try loading the attached eigen.pvsm state file which worked for me if you want to test it out. Note that since I used the Gradient of Unstructured Dataset filter twice to go from a scalar array to a second order tensor before doing the programmable filter, I used Gradients2 for the output array name for the second order tensor.
Best,
Andy

On Thu, Apr 19, 2018 at 1:03 AM, Caffagni, Andrea <Andrea.Caffagni at ferrari.com<mailto:Andrea.Caffagni at ferrari.com>> wrote:
If I add simply the code suggested from you Oscar, my filters becomes:

import numpy as np
from numpy import linalg as LA
from paraview import numpy_support
from vtk.util import numpy_support
input = inputs[0]

numPoints = input.GetNumberOfPoints()
print "number of points",numPoints
#print "keys",input.GetPointData().keys()
tensorsVTK = input.PointData['Gradients']
tensorsNP=numpy_support.vtk_to_numpy(tensorsVTK)
#tensors[0,:,:]=np.diag((1,2,3))
#tensors[0,:,:]=[[1,-1,2],[2,-1,3],[0,0,1]]
print "tensors[0:3]",tensors[0:3]
eigenvalues,eigenvectors = LA.eig(tensorsNP)
print 'eigenvalues', eigenvalues[0]
print 'eigenvectors',eigenvectors[0]
output.PointData.append(eigenvalues,'eigenvalues')
output.PointData.append(eigenvectors,'eigenvectors')

I obtain the following Output:

Traceback (most recent call last):

File "<string>", line 22, in <module>

File "<string>", line 8, in RequestData

UnboundLocalError: local variable 'NumPy_data' referenced before assignment

Traceback (most recent call last):

File "<string>", line 22, in <module>

File "<string>", line 12, in RequestData

File "C:\Program Files\ParaView 5.3.0-Qt5-OpenGL2-Windows-64bit\bin\lib\site-packages\vtk\util\numpy_support.py", line 213, in vtk_to_numpy

typ = vtk_array.GetDataType()

AttributeError: 'VTKCompositeDataArray' object has no attribute 'GetDataType'

number of points 1

I need to reshape the vector or define the type?

Best Regards,
Andrea

From: Oscar Wilsby [mailto:ow222 at cam.ac.uk<mailto:ow222 at cam.ac.uk>]
Sent: Wednesday, April 18, 2018 21:14
To: Cory Quammen
Cc: Caffagni, Andrea; Andy Bauer; paraview at public.kitware.com<mailto:paraview at public.kitware.com>

Subject: Re: [Paraview] Problem with numpy array

Hi Andy,

I haven’t verified, but at a glance it looks like what you are passing to the the LA.eig function is not a 2D numpy array. Can you try doing np.asarray(tensors) or

from vtk.util.numpy_support import vtk_to_numpy

tensors = vtk_to_numpy(tensors)
and then pass that to LA.eig?

Kind regards,

Oscar

On 18 Apr 2018, at 16:33, Cory Quammen <cory.quammen at kitware.com<mailto:cory.quammen at kitware.com>> wrote:

Hey Andy,

Does the GradientOfUnstructuredDataSet filter produce a tensor from an input vector field? My testing in ParaView indicates it doesn't , but I'm not super familiar with it.
Thanks,
Cory

On Wed, Apr 18, 2018 at 11:14 AM, Caffagni, Andrea <Andrea.Caffagni at ferrari.com<mailto:Andrea.Caffagni at ferrari.com>> wrote:
Dear Cory,
This is the complete message that I have obtained like output:

Traceback (most recent call last):
File "<string>", line 22, in <module>
File "<string>", line 14, in RequestData
File "C:\Program Files\ParaView 5.3.0-Qt5-OpenGL2-Windows-64bit\bin\lib\site-packages\numpy\linalg\linalg.py", line 1095, in eig
_assertRankAtLeast2(a)
File "C:\Program Files\ParaView 5.3.0-Qt5-OpenGL2-Windows-64bit\bin\lib\site-packages\numpy\linalg\linalg.py", line 202, in _assertRankAtLeast2
'at least two-dimensional' % len(a.shape))
numpy.linalg.linalg.LinAlgError: 0-dimensional array given. Array must be at least two-dimensional
number of points 1
tensors[0:3] [VTKArray([[[ 8.34616375, -23.89611435, 2.00894117],
[ 0.67995167, -23.11237526, 289.07113647],
[ 27.26550674, -231.06710815, 16.90883636]]], dtype=float32)]

From this, I have thought about the vtk array.

Best regards,
Andrea

From: Cory Quammen [mailto:cory.quammen at kitware.com<mailto:cory.quammen at kitware.com>]
Sent: Wednesday, April 18, 2018 15:11
To: Caffagni, Andrea
Cc: paraview at public.kitware.com<mailto:paraview at public.kitware.com>
Subject: Re: [Paraview] Problem with numpy array

Hi Andrea,

Besides the error message, what does your script print?

Thanks,
Cory

On Wed, Apr 18, 2018 at 2:14 AM, Caffagni, Andrea <Andrea.Caffagni at ferrari.com<mailto:Andrea.Caffagni at ferrari.com>> wrote:
Dear Users,
I need to solve an eigenproblem in a point of a CFD field.
Using the GradientOfUnstructuredDataSet I calculate the velocity gradient of my velocity field, than I isolate may point of interest and I have written the following ProgrammableFilter:

import numpy as np
from numpy import linalg as LA
from paraview import numpy_support
input = inputs[0]

numPoints = input.GetNumberOfPoints()
print "number of points",numPoints
tensors = input.PointData['Gradients']
print "tensors[0:3]",tensors[0:3]
eigenvalues,eigenvectors = LA.eig(tensors)
print 'eigenvalues', eigenvalues[0]
print 'eigenvectors',eigenvectors[0]
output.PointData.append(eigenvalues,'eigenvalues')
output.PointData.append(eigenvectors,'eigenvectors')

I have obtained the following error message:

Traceback (most recent call last):
File "<string>", line 22, in <module>
File "<string>", line 14, in RequestData
File "C:\Program Files\ParaView 5.3.0-Qt5-OpenGL2-Windows-64bit\bin\lib\site-packages\numpy\linalg\linalg.py", line 1095, in eig
_assertRankAtLeast2(a)
File "C:\Program Files\ParaView 5.3.0-Qt5-OpenGL2-Windows-64bit\bin\lib\site-packages\numpy\linalg\linalg.py", line 202, in _assertRankAtLeast2
'at least two-dimensional' % len(a.shape))
numpy.linalg.linalg.LinAlgError: 0-dimensional array given. Array must be at least two-dimensional

I imagine that the problem is linked to the vtk array, I need to convert my ‘Gradients’ matrix in a nparray?
Someone have the same problem?

Best Regards,
Andrea

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Questo messaggio è da intendersi esclusivamente ad uso del destinatario e può contenere informazioni che sono di natura privilegiata, confidenziale o non divulgabile secondo le leggi vigenti. Se il lettore del presente messaggio non è il destinatario designato, o il dipendente/agente responsabile per la consegna del messaggio al destinatario designato, si informa che ogni disseminazione, distribuzione o copiatura di questa comunicazione è vietata anche ai sensi della normativa vigente in materia di protezione dei dati personali. Se avete ricevuto questo messaggio per errore, vi preghiamo di notificarcelo immediatamente a mezzo e-mail di risposta e successivamente di procedere alla cancellazione di questa e-mail e relativi allegati dal vostro sistema.
_________________________________________________________________________________________________________________

This message is intended only for the use of the addressee and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is prohibited under the applicable data protection law. If you have received this e-mail by mistake, please notify us immediately by return e-mail and delete this e-mail and all attachments from your system.

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--
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Staff R&D Engineer
Kitware, Inc.
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