[Paraview] vtkDoubleArray with >3 components

Bruce Jones bruce.david.jones at gmail.com
Thu Jul 23 13:36:17 EDT 2015 

Ok the solution was embarrasingly simple... When specifying the array size
I had specified the number of tuples, where I was supposed to specify
numTuples*numComponents

Thanks for the help anyway.

Bruce

On Wed, 22 Jul 2015 at 14:28 Bruce Jones <bruce.david.jones at gmail.com>
wrote:

> Hey Guys,
>
> I have created a minimum working example (attached). This example is built
> as a paraview plugin, build environment specified below. The plugin takes
> point data as input (sample attached), and just does the memory allocation
> and creation of output arrays as I have previously described. On my
> machine, as soon as I apply the filter, paraview crashes. Commenting line
> 107 in vtkHeapCorruption.cxx allows the filter to run, but the output is
> then limited to single component arrays, where some of the input arrays
> have 3 or 9 components.
>
> QT 4.8.6, Visual Studio 2010, Built against Paraview commit SHA1
> ID: 70155c17cfe7c2f547bb25ddb859a65518896ee3
>
> On Wed, 22 Jul 2015 at 11:21 Bruce Jones <bruce.david.jones at gmail.com>
> wrote:
>
>> Thanks Berk,
>>
>> I have tried with both zero and 1 as the save argument and am getting the
>> same behavior. As before, if I comment the SetNumberOfComponents call (or
>> set number of components to 1) everything works, except I only have single
>> component arrays in the output.
>>
>> I'm going to put together a minimum working example with the issue this
>> afternoon so that I can show you guys in more detail.
>>
>> Cheers,
>> Bruce
>>
>> On Wed, 22 Jul 2015 at 11:09 Berk Geveci <berk.geveci at kitware.com> wrote:
>>
>>> The solution is in the documentation:
>>>
>>>   // This method lets the user specify data to be held by the array.  The
>>>   // array argument is a pointer to the data.  size is the size of the
>>>   // array supplied by the user.  Set save to 1 to keep the class from
>>>   // deleting the array when it cleans up or reallocates memory.  The
>>> class
>>>   // uses the actual array provided; it does not copy the data from the
>>>   // suppled array. If specified, the delete method determines how the
>>> data
>>>   // array will be deallocated. If the delete method is
>>>   // VTK_DATA_ARRAY_FREE, free() will be used. If the delete method is
>>>   // DELETE, delete[] will be used. The default is FREE.
>>>
>>> You are passing 0 for the "save" argument, which means that VTK will
>>> delete the array when the VTK array object is deleted, which would cause a
>>> double delete/free. Use 1 as the second argument of SetArray() if you are
>>> managing the memory. Also, make sure that the VTK array is not used after
>>> you free your array.
>>>
>>> Best,
>>> -berk
>>>
>>> On Wed, Jul 22, 2015 at 9:56 AM, Bruce Jones <
>>> bruce.david.jones at gmail.com> wrote:
>>>
>>>> Hi Guys,
>>>>
>>>> I have just tried it as you suggested, doing SetNumberOfComponents then
>>>> SetArray, without doing SetNumberOfTuples. Unfortunately I am still getting
>>>> the same behaviour.
>>>>
>>>> Cheers,
>>>> Bruce
>>>>
>>>> On Wed, 22 Jul 2015 at 09:44 Berk Geveci <berk.geveci at kitware.com>
>>>> wrote:
>>>>
>>>>> Actually, don't call SetNumberOfTuples() at all if you are using
>>>>> SetArray(). It will unnecessarily allocate memory if you call it before
>>>>> SetArray().
>>>>>
>>>>> -berk
>>>>>
>>>>> On Wed, Jul 22, 2015 at 9:40 AM, Shawn Waldon <
>>>>> shawn.waldon at kitware.com> wrote:
>>>>>
>>>>>> Hi Bruce,
>>>>>>
>>>>>> SetNumberOfTuples reallocates the internal datastructure of the data
>>>>>> array to be the new required size based on the new number of components and
>>>>>> number of tuples.  This (combined with trying to clean up the old data from
>>>>>> SetArray) may be causing the heap corruption you are seeing.  Try setting
>>>>>> the number of components and number of tuples before adding the data to the
>>>>>> array.
>>>>>>
>>>>>> HTH,
>>>>>> Shawn
>>>>>>
>>>>>> On Tue, Jul 21, 2015 at 1:37 PM, Bruce Jones <
>>>>>> bruce.david.jones at gmail.com> wrote:
>>>>>>
>>>>>>> Hi Cory,
>>>>>>>
>>>>>>> Sorry for the delayed response, I've hit another more serious bug
>>>>>>> which has been diverting my attention from this.
>>>>>>>
>>>>>>> Thanks for the state file, I haven't got it to work as I don't have
>>>>>>> numpy set up, but I have also got this working with 9 component arrays in
>>>>>>> paraview using a python script. However, I am now trying to port my python
>>>>>>> plugin to c++ which is where I am seeing the error.
>>>>>>>
>>>>>>> In my plugin I want to output a vtkarray for each vtkarray in the
>>>>>>> input dataset. The values in the output vtkarrays are interpolated from
>>>>>>> those in the input vtkarrays. Rather than working directly on vtkarray
>>>>>>> objects, I am allocating c++ arrays for each vtkarray, performing the
>>>>>>> interpolation, then creating vtkDoubleArrays and using SetArray to pass a
>>>>>>> pointer to my allocated c++ arrays to the output vtkarrays. The code for
>>>>>>> setting up the output vtkarrays is roughly as follows
>>>>>>>
>>>>>>>                 vtkPointData *pointData = input->GetPointData();
>>>>>>>                 vtkDataArray *dArray = pointData->GetArray(i);
>>>>>>> vtkDoubleArray *vtkDArrayAve = vtkDoubleArray::New();
>>>>>>> vtkDArrayAve->SetName(dArray->GetName());
>>>>>>> vtkDArrayAve->SetArray(dArraysAve[i],hgrid->GetTotalCells(),0);
>>>>>>> vtkDArrayAve->SetNumberOfComponents(numComponents[i]);
>>>>>>> vtkDArrayAve->SetNumberOfTuples(hgrid->GetTotalCells());
>>>>>>> output->GetPointData()->AddArray(vtkDArrayAve);
>>>>>>>
>>>>>>> dArraysAve is an array of pointers pointing to my c++ arrays
>>>>>>> hgrid->GetTotalCells() returns the number of data points for my
>>>>>>> output
>>>>>>>
>>>>>>> I also have another mode of operation for this plugin, where I
>>>>>>> perform the interpolation differently, in that function, if I make the call
>>>>>>> to SetNumberOfComponents() some heap corruption occurs and I get a segfault
>>>>>>> when I try to subsequently free my c++ arrays. Commenting out the call to
>>>>>>> SetNumberOfComponents avoids the segfault, but then I am limited to single
>>>>>>> component arrays. This is the more serious bug I mentioned, initially I
>>>>>>> figured they were unrelated, but I can't deny the number of components
>>>>>>> coincidence.
>>>>>>>
>>>>>>> Cheers,
>>>>>>> Bruce
>>>>>>>
>>>>>>> On Thu, 16 Jul 2015 at 14:41 Cory Quammen <cory.quammen at kitware.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hi Bruce,
>>>>>>>>
>>>>>>>> I have attached a ParaView state file with a Programmable Source
>>>>>>>> that produces a vtkPolyData with 100 random points and a point data array
>>>>>>>> with 9 components. It seems to display the various component ranges just
>>>>>>>> fine.
>>>>>>>>
>>>>>>>> Best,
>>>>>>>> Cory
>>>>>>>>
>>>>>>>> On Thu, Jul 16, 2015 at 11:14 AM, Cory Quammen <
>>>>>>>> cory.quammen at kitware.com> wrote:
>>>>>>>>
>>>>>>>>> Hi Bruce,
>>>>>>>>>
>>>>>>>>> I haven't seen this, but ParaView may be interpreting this array
>>>>>>>>> as a tensor field. Do you have a smallish test data file that you can share
>>>>>>>>> that shows the problem?
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>> Cory
>>>>>>>>>
>>>>>>>>> On Sat, Jul 11, 2015 at 11:14 AM, Bruce Jones <
>>>>>>>>> bruce.david.jones at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> I am creating vtkDoubleArrays based on averaging some input data
>>>>>>>>>> to a reduced set of points. The input data includes various vtk arrays
>>>>>>>>>> which have 1, 3 and 9 components.
>>>>>>>>>>
>>>>>>>>>> After averaging, I am writing the data to c++ arrays, and
>>>>>>>>>> creating a new vtkDoubleArray using the SetArray() function to pass the c++
>>>>>>>>>> arrays. This works fine for 1 and 3 component arrays, however for the 9
>>>>>>>>>> component arrays paraview shows that every element is set to 0.
>>>>>>>>>>
>>>>>>>>>> If I hardcode it so that 9 component arrays become 3 component
>>>>>>>>>> arrays (reading only the first 3 components from the input array), then I
>>>>>>>>>> get the correct data for the first 3 components, though I obviously need
>>>>>>>>>> the other 6 components in the end.
>>>>>>>>>>
>>>>>>>>>> Has anyone encountered this before?
>>>>>>>>>>
>>>>>>>>>> Cheers,
>>>>>>>>>> Bruce
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> Powered by www.kitware.com
>>>>>>>>>>
>>>>>>>>>> Visit other Kitware open-source projects at
>>>>>>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>>>>>>
>>>>>>>>>> Please keep messages on-topic and check the ParaView Wiki at:
>>>>>>>>>> http://paraview.org/Wiki/ParaView
>>>>>>>>>>
>>>>>>>>>> Search the list archives at:
>>>>>>>>>> http://markmail.org/search/?q=ParaView
>>>>>>>>>>
>>>>>>>>>> Follow this link to subscribe/unsubscribe:
>>>>>>>>>> http://public.kitware.com/mailman/listinfo/paraview
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Cory Quammen
>>>>>>>>> R&D Engineer
>>>>>>>>> Kitware, Inc.
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Cory Quammen
>>>>>>>> R&D Engineer
>>>>>>>> Kitware, Inc.
>>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Powered by www.kitware.com
>>>>>>>
>>>>>>> Visit other Kitware open-source projects at
>>>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>>>
>>>>>>> Please keep messages on-topic and check the ParaView Wiki at:
>>>>>>> http://paraview.org/Wiki/ParaView
>>>>>>>
>>>>>>> Search the list archives at: http://markmail.org/search/?q=ParaView
>>>>>>>
>>>>>>> Follow this link to subscribe/unsubscribe:
>>>>>>> http://public.kitware.com/mailman/listinfo/paraview
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Powered by www.kitware.com
>>>>>>
>>>>>> Visit other Kitware open-source projects at
>>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>>
>>>>>> Please keep messages on-topic and check the ParaView Wiki at:
>>>>>> http://paraview.org/Wiki/ParaView
>>>>>>
>>>>>> Search the list archives at: http://markmail.org/search/?q=ParaView
>>>>>>
>>>>>> Follow this link to subscribe/unsubscribe:
>>>>>> http://public.kitware.com/mailman/listinfo/paraview
>>>>>>
>>>>>>
>>>>>
>>>
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