[Paraview-developers] Python programmable source acting as filereader

[Daan van Vugt]

Hi Utkarsh,

I managed to fix all of the aforementioned. There is just one problem left,
when I import h5py.
There is no h5py included in the paraview python installation, right? I'm
not married to this specific module, so alternatives are also okay.

ImportError: /usr/lib/python2.7/site-packages/h5py/_errors.so: undefined
symbol: PyUnicodeUCS4_DecodeUTF8
Traceback (most recent call last):
  File "<string>", line 20, in <module>
  File "<string>", line 1510, in RequestData
  File "/usr/lib/python2.7/site-packages/h5py/__init__.py", line 24, in
<module>
    from . import _errors

See also:
http://stackoverflow.com/questions/16871799/trying-to-import-a-module-undefined-symbol-pyunicodeucs4-decodeutf8
This means that the paraview included python installation is UCS2, which is
incompatible with my local version.

Do you have a suggestion for where on the wiki to document the
fileseriesreader I have built?

Daan

On Wed, Jan 25, 2017 at 8:53 AM, Daan van Vugt <daanvanvugt at gmail.com>
wrote:

> Hi Utkarsh,
>
> I think I can make that work. Is there any way to get a filename pattern
> (or list of files) in a nice way through the GUI?
>
> Also I'm having trouble accessing the Properties set in my script when
> using it with python_filter_generator.py
>
> Daan
>
> On Tue, Jan 24, 2017 at 5:15 PM, Utkarsh Ayachit <
> utkarsh.ayachit at kitware.com> wrote:
>
>> Daan,
>>
>> I didn't notice this earlier, but you're using a vtkProgrammableFilter
>> together with a vtkFileSeriesReader. That, I am afraid is not current
>> supported. You're better off adding support to reading the multiple files
>> to your Programamble Source itself. The ParaView guide does provide an
>> example for a reading a file series of csv files as a time series (Section
>> 13.2.2). That should give you pointers to update your Python script. Let me
>> know if you need additional pointers.
>>
>> Utkarsh
>>
>> On Tue, Jan 24, 2017 at 10:22 AM, Daan van Vugt <daanvanvugt at gmail.com>
>> wrote:
>>
>>> Hi Utkarsh,
>>>
>>> When I do that I get a segfault, with the following backtrace:
>>>
>>> =========================================================
>>> Process id 7407 Caught SIGSEGV at 0x0 address not mapped to object
>>> Program Stack:
>>> WARNING: The stack trace will not use advanced capabilities because this
>>> is a release build.
>>> 0x7f27d2933080 : ??? [(???) ???:-1]
>>> 0x7f27d242a536 : vtkProgrammableFilter::RequestData(vtkInformation*,
>>> vtkInformationVector**, vtkInformationVector*)
>>> [(libvtkFiltersProgrammable-pv5.2.so.1) ???:-1]
>>> 0x7f27d26f7880 : vtkPythonProgrammableFilter::ProcessRequest(vtkInformation*,
>>> vtkInformationVector**, vtkInformationVector*)
>>> [(libvtkPVClientServerCoreCore-pv5.2.so.1) ???:-1]
>>> 0x7f27c93e3e1b : vtkFileSeriesReader::RequestData(vtkInformation*,
>>> vtkInformationVector**, vtkInformationVector*)
>>> [(libvtkPVVTKExtensionsDefault-pv5.2.so.1) ???:-1]
>>>
>>> (this occurs before any of my python code has been executed)
>>>
>>> Thanks,
>>> Daan
>>>
>>> On Tue, Jan 24, 2017 at 3:39 PM, Utkarsh Ayachit <
>>> utkarsh.ayachit at kitware.com> wrote:
>>>
>>>> Daan,
>>>>
>>>> Can you try changing the `si_class` attribute in the XML for the proxy
>>>> to be `vtkSIMetaReaderProxy`? I suspect the classname was changed at some
>>>> point. If that works, I can update the Wiki.
>>>>
>>>> Thanks
>>>> Utkarsh
>>>>
>>>> On Thu, Jan 19, 2017 at 11:01 AM, Daan van Vugt <daanvanvugt at gmail.com>
>>>> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I would like to create a plugin that uses h5py and numpy to read a
>>>>> file, do some operations on it and return VTK objects.
>>>>> Would it be possible to do the same thing as
>>>>> http://www.paraview.org/Wiki/Animating_legacy_VTK_file_serie
>>>>> s#Making_custom_readers_work_with_file_series
>>>>> but instead of using a vtkPDataSetReader use a
>>>>> vtkPythonProgrammableSource?
>>>>>
>>>>> I have made a (very naive) try, attached to this post.
>>>>> When using this to read a series of files I get the errors (version
>>>>> 5.2.0 64-bit) shown below.
>>>>> To test, just use any hdf5 file. (.h5)
>>>>>
>>>>> Thanks for any help,
>>>>> Daan
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ERROR: In /home/buildslave/dashboards/buildbot/paraview-pvbinsdash-lin
>>>>> ux-shared-release_opengl2_qt4_superbuild/source-paraview/Par
>>>>> aViewCore/ServerImplementation/Core/vtkPVSessionCore.cxx, line 439
>>>>> vtkPVSessionCore (0x100da30): Failed to instantiate
>>>>> vtkSIFileSeriesReaderProxy
>>>>>
>>>>>
>>>>> global_id: 4875
>>>>> location: 2
>>>>> [paraview_protobuf.DefinitionHeader.client_class]: "vtkSMSourceProxy"
>>>>> [paraview_protobuf.DefinitionHeader.server_class]:
>>>>> "vtkSIFileSeriesReaderProxy"
>>>>> [paraview_protobuf.ProxyState.xml_group]: "sources"
>>>>> [paraview_protobuf.ProxyState.xml_name]: "JorekReadH5"
>>>>> [paraview_protobuf.ProxyState.subproxy] {
>>>>>   name: "Reader"
>>>>>   global_id: 4864
>>>>> }
>>>>> ############ ABORT #############
>>>>> ERROR: In /home/buildslave/dashboards/buildbot/paraview-pvbinsdash-lin
>>>>> ux-shared-release_opengl2_qt4_superbuild/source-paraview/Par
>>>>> aViewCore/ServerImplementation/Core/vtkPVSessionCore.cxx, line 794
>>>>> vtkPVSessionCore (0x100da30): No object with global-id: 4875
>>>>>
>>>>>
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