[vtkusers] Possible Bug in vtkXMLReader when reading timeseries

Mon Sep 26 10:43:37 EDT 2016

One more thing, Simon. Could you contribute a small data set with more than
one time step so that we can add a test that uses it?

Thanks,
Cory

On Mon, Sep 26, 2016 at 10:39 AM, Cory Quammen <cory.quammen at kitware.com>
wrote:

> Simon,
>
> Might you be able to try TJ's merge request and see if it restores the
> functionality you expected?
>
> Thanks,
> Cory
>
> On Mon, Sep 26, 2016 at 9:34 AM, T.J. Corona <tj.corona at kitware.com>
> wrote:
>
>> Hi Simon,
>>
>> I have created a MR (https://gitlab.kitware.com/vt
>> k/vtk/merge_requests/2007) that reverts the addition of an
>> exit-with-error when data arrays have the same name.
>>
>> Cory,
>>
>> I believe this MR also accounts for the segfault you originally reported
>> when reading in data arrays that have duplicate names.
>>
>> Sincerely,
>> T.J.
>>
>> Thomas J. Corona, Ph.D.
>> Kitware, Inc.
>> R&D Engineer
>> 21 Corporate Drive
>> Clifton Park, NY 12065-8662
>> Phone: 518-881-4443
>>
>> On Sep 23, 2016, at 1:41 PM, Cory Quammen <cory.quammen at kitware.com>
>> wrote:
>>
>> Simon,
>>
>> Thanks for your sleuthing and bug report. I don't believe your use case
>> was known when merge request !488 was merged.
>>
>> TJ,
>>
>> Can you have a look at Simon's issue?
>>
>> Thanks,
>> Cory
>>
>> On Fri, Sep 23, 2016 at 12:07 PM, Simon Praetorius <
>> Simon.Praetorius at tu-dresden.de> wrote:
>>
>>> I have found an old issue in the mantis bug-tracker addressing this
>>> topic: #15723
>>>
>>> The answer was: "VTK file format does not support saving several time
>>> steps in a file" and a reference to the file-format description was given.
>>> This description (version 4.2.) is definitely not complete, thus it can not
>>> be an indicator for a support of writing timeseries or not.
>>>
>>> Although the file-format description does not show support for
>>> timeseries, at least in older vtk versions (before 6.3) it was supported.
>>> The source code of the XMLreader shows all the necessary parts to read the
>>> time-series, all the corresponding attributes are interpreted. The only
>>> problem is a change in the handling of duplicate names. This was done about
>>> a year ago in merge request !488. Since there is no test that reads back
>>> the files generated by `IO/XML/Testing/Cxx/TestXMLCInterface.c` no
>>> error could be detected. The corresponding test to create the file was
>>> removed in June 2016.
>>>
>>> Thus, the questions are:
>>> - Is this feature quietly removed from VTK, or removed by accident since
>>> only few people use it?
>>> - Is the documentation of the file-format incomplete or the
>>> implementation simply not cleaned up?
>>> - Should the test for duplicate array names be rewritten in order to
>>> allow timeseries again?
>>> - There should be at least a comment in the file-format description that
>>> duplicate array names are not allowed!
>>>
>>> Maybe this issue could be forwarded to the developer mailing list.
>>>
>>> Simon
>>>
>>>
>>> Zitat von Simon Praetorius <Simon.Praetorius at tu-dresden.de>:
>>>
>>>
>>> Hi,
>>>>
>>>> When reading a VTK XML-file that includes timesteps, the
>>>> `vtkXMLDataReader:282` throws an error that multiple arrays with the same
>>>> name are present in the file. In general this is a valid test and the error
>>>> is correct, except for the case that multiple timesteps are written in the
>>>> file. An example file can be created by the test
>>>> `IO/XML/Testing/Cxx/TestXMLCInterface.c`:
>>>>
>>>> ```xml
>>>> <Piece NumberOfPoints="8" NumberOfCells="1">
>>>>   <PointData Scalars="example data">
>>>>     <DataArray type="Float32" Name="example data" TimeStep="0"
>>>> format="appended" RangeMin="0" RangeMax="0" offset="0" />
>>>>     <DataArray type="Float32" Name="example data" TimeStep="1"
>>>> format="appended" RangeMin="1" RangeMax="1" offset="240" />
>>>>     <!-- ... -->
>>>>   </PointData>
>>>> </Piece>
>>>> ```
>>>> Here all DataArrays refer to the same dataset at different timesteps.
>>>>
>>>> Reading back this file, using a `VTLXMLUnstructuredGridReader` (e.g.
>>>> `Examples/IO/Cxx/DumpXMLFile.cxx`), produced the error above:
>>>>
>>>> ```
>>>> vtkXMLDataReader.cxx, line 282: Duplicate array names.
>>>> ```
>>>>
>>>> Writing TimeSteps seems to be supported by the XMLReader and the
>>>> XMLWriter. Maybe the `vtkXMLWriterC` is not valid/compatible any more? Is
>>>> the structure of the vtk format changed when writing timeseries, compared
>>>> to the xml-code shown above?
>>>> (I'm referring to the VTK version 7.0.0, when naming line-numbers.)
>>>>
>>>>
>>>> This issue refers to an old ParaView issue #5542 (
>>>> http://www.paraview.org/Bug/view.php?id=5542). The file was readable
>>>> with at least vtk-5.2 and paraview-3.6.2.
>>>>
>>>> Simon
>>>>
>>>> --
>>>> Dr. Simon Praetorius
>>>> Institut für Wissenschaftliches Rechnen
>>>> Fachrichtung Mathematik
>>>> Technische Universität Dresden
>>>> Tel.: TUD-42377
>>>> Mail: simon.praetorius at tu-dresden.de
>>>> Web: www.math.tu-dresden.de/~spraetor
>>>>
>>>
>>>
>>>
>>> --
>>> Dr. Simon Praetorius
>>> Institut für Wissenschaftliches Rechnen
>>> Fachrichtung Mathematik
>>> Technische Universität Dresden
>>> Tel.: TUD-42377
>>> Mail: simon.praetorius at tu-dresden.de
>>> Web: www.math.tu-dresden.de/~spraetor
>>>
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>>
>>
>> --
>> Cory Quammen
>> Staff R&D Engineer
>> Kitware, Inc.
>>
>>
>>
>
>
> --
> Cory Quammen
> Staff R&D Engineer
> Kitware, Inc.
>

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