[Paraview] My own filter as part of pipeline for coprocessing raises "name not defined" error

Tue Oct 1 14:18:34 EDT 2013

Hi Hong,

I don't think you want to do VTK Python wrapping of your class. What you
want is to have the proxy to the filter Python wrapped such that it's
available when you import paraview.simple. This is what's needed for
Catalyst Python pipelines. I don't think you're properly initializing the
plugins from the previous directions I sent. You may want to look at
http://public.kitware.com/pipermail/paraview-developers/2013-September/002499.html

As a side note, the gradient of unstructured data set filter can compute
vorticity as well. It does require a vtkDataArray with three components to
use though.

Regards,
Andy

On Mon, Sep 30, 2013 at 5:06 PM, Hong Yi <hongyi at renci.org> wrote:

>  Thanks, Andy. The CMakeLists.txt for my plugin is copied below with
> newly added lines for python wrapping in orange:
>
> -----------------------------
> if(NOT ParaView_SOURCE_DIR)
>   find_package(ParaView)
>   include("${PARAVIEW_USE_FILE}")
>   include (ParaViewPlugins)
> else()
>   # we're building from within ParaView Source.
> endif()
>
> include_directories(${VTK_INCLUDE_DIRS})
> include(wrap-python.cmake)
>
> # create a paraview plugin containing server manager xml and the server
> # manager classes to build
> # this plugin can be loaded on the server side
>
> ADD_PARAVIEW_PLUGIN(SMVorticity "1.0"
>   SERVER_MANAGER_XML VorticityFilter.xml
>   SERVER_MANAGER_SOURCES VorticityFilter.cxx)
>
> target_link_libraries(SMVorticity ${deps})
>
> if(VTK_WRAP_PYTHON)
>   wrap_python(SMVorticity "${sources}")
> endif()
> -----------------------------
>
> The orange lines are added by following
> http://www.paraview.org/pipermail/paraview/2012-May/024855.html which
> works well and builds my filter and also wraps it in Python (i.e., it
> generates libSMVorticity.a and libSMVorticityPythonD.a). I have also
> verified the plugin is indeed loaded into pvserver and pvpython in paraview
> built bin directory.
>
> However, I still got "name not defined" error in coprocessing script when
> creating this filter by name "VorticityOfUnstructuredDataSet" in python
> script. I have a couple of specific questions I am currently investigating
> and hoping to get some inputs from experts in the list:
>
> 1. I am not sure where this name "VorticityOfUnstructuredDataSet"
> (exported by coprocessing script generator plugin) comes from, the only
> clue I can see is in plugin.cmake, where the plugin is specified with
> DESCRIPTION "Vorticity Of Unstructured DataSet" and in VorticityFilter.xml,
> where the plugin is given a label of "Vorticity Of Unstructured DataSet."
> Should this name be defined somewhere such as in some python file in
> paraview python site-packages?
>
> 2. I did try to add PV_PLUGIN_IMPORT macros to the adaptor since I am
> using Catalyst, however, the plugin symbol "pv_plugin_instance_SMVorticity"
> is undefined in the adaptor static lib (the same plugin symbol is defined
> in pvserver), hence I got an undefined error when linking simulation code
> to the adaptor. I did try to add my plugin static lib (in which the plugin
> symbol is defined) to the adaptor target via target_link_libraries before
> linking to vtkPVPythonCatalyst, but that does not seem to take any effect.
> For some reason I am still investigating, my plugin lib does not get to
> link to the adaptor via target_link_libraries. What I did is to go to src
> directory in the cross target and modified CMakeLists.txt for
> PhastaAdaptor, then went to corresponding paraview-build directory, and did
> "make clean" followed by "make" to rebuild PhastaAdaptor lib. Is there
> something obvious that I did not do correctly?
>
> Thanks for any inputs!
>
> Hong
>
>
>  ------------------------------
> *From:* Andy Bauer [andy.bauer at kitware.com]
> *Sent:* Friday, September 27, 2013 3:00 PM
> *To:* Hong Yi
> *Cc:* David E DeMarle; paraview at paraview.org
>
> *Subject:* Re: [Paraview] My own filter as part of pipeline for
> coprocessing raises "name not defined" error
>
>    Can you share your plugin or at least the CMakeLists.txt for your
> plugin? Have you tried with any other plugins that get packaged with
> ParaView to see if they work?
>
>  If you're using Catalyst, I would suggest adding in the
> PV_PLUGIN_IMPORT_INIT macros to the adaptor.
>
>  Andy
>
>
> On Thu, Sep 26, 2013 at 3:40 PM, Hong Yi <hongyi at renci.org> wrote:
>
>>   Thanks! I did put my plugin inside ParaView/Plugins in the same way as
>> other Plugins, and enabled it when building ParaView superbuild on
>> Titan. I can see the static lib for the Plugin is built in paraview-build/lib
>> directory. And yes, I did use a plugin and load it via Tools|ManagePlugins when creating python
>> coprocessing script. However, it looks like my plugin is not loaded
>> automatically even though it is built by ParaView superbuild. Perhaps I
>> should still follow the link
>> http://www.paraview.org/Wiki/ParaView/Plugin_HowTo#Plugins_in_Static_Applications but
>> I am having some difficulty in following the info in the link to do what is
>> suggested. Specifically, to what file should I insert two macros? It does
>> not sound right to insert them into my custom plugin cxx file. Where should
>> I add two macros to get my custom filter plugin to be loaded and wrapper
>> into python module? I see "LoadPlugin" function defined in simple.py to
>> call servermanager.LoadPlugin(filename, remote) which I am thinking perhaps
>> should be called to load my plugin before my python coprocessing script is
>> executed, but not sure whether this is the case or not.
>>
>>
>>
>> Thanks for any suggestions!
>>
>>
>>  Hong
>>
>>
>>
>>
>>
>> *From:* David E DeMarle [mailto:dave.demarle at kitware.com]
>> *Sent:* Thursday, September 26, 2013 1:28 PM
>> *To:* Andy Bauer
>> *Cc:* Hong Yi; paraview at paraview.org
>> *Subject:* Re: [Paraview] My own filter as part of pipeline for
>> coprocessing raises "name not defined" error
>>
>>
>>
>> Utkarsh pointed out that you still need to follow
>> http://www.paraview.org/Wiki/ParaView/Plugin_HowTo#Plugins_in_Static_Applications
>>
>> when the plugin is external to ParaView. If you put your plugin inside
>> ParaView/Plugins, then it is done automatically.
>>
>>
>>  David E DeMarle
>> Kitware, Inc.
>> R&D Engineer
>> 21 Corporate Drive
>> Clifton Park, NY 12065-8662
>> Phone: 518-881-4909
>>
>>
>>
>> On Thu, Sep 26, 2013 at 12:23 PM, David E DeMarle <
>> dave.demarle at kitware.com> wrote:
>>
>> I think that information is out of date. I believe that is done
>> automatically now.
>>
>>
>>
>> Otherwise Andy is right. Putting the filter inside a plugin a good way to
>> go. The plugin infrastructure will make it so that when you provide the XML
>> that describes your vtk class, ParaView's build system will automatically
>> wrap it into a proxy and python class so that ParaView will be able to use
>> it.
>>
>>
>>
>> Also, I recommend trying it on a local static build first. That way the
>> build time will be less and development will be quicker. Once you can load
>> you plugin locally, then you should only have to compile on titan once.
>>
>>
>>
>>
>>  David E DeMarle
>> Kitware, Inc.
>> R&D Engineer
>> 21 Corporate Drive
>> Clifton Park, NY 12065-8662
>> Phone: 518-881-4909
>>
>>
>>
>> On Wed, Sep 25, 2013 at 10:34 PM, Andy Bauer <andy.bauer at kitware.com>
>> wrote:
>>
>> Did you use a plugin to add in your custom filter when creating the
>> Python co-processing script? I'm not sure how plugins are "loaded" for
>> static builds but you may want to look at
>> http://www.paraview.org/Wiki/ParaView/Plugin_HowTo#Plugins_in_Static_Applications.
>> If that doesn't work, we'll have to figure out some other way to do it.
>>
>> Andy
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On Wed, Sep 25, 2013 at 9:16 PM, Hong Yi <hongyi at renci.org> wrote:
>>
>>   Hello,
>>
>> I set up a pipeline that used a custom filter I developed and exported it
>> as a python script for coprocessing. I have made sure the static library
>> for my custom filter is built and available in paraview-build/lib
>> directory, and I have also linked this custom filter static library along
>> with Catalyst libs to the simulation code for coprocessing. However, when I
>> run the simulation linked with ParaView coprocessing for in-situ
>> visualization, I got "NameError: name 'MyCustomizedFilterName' is not
>> defined" error when the line of my customized filter in my python
>> coprocessing script is read in for pipeline coprocessing. What should I do
>> to get my custom filter wrapped in python so that it can be recognized and
>> used as part of the python pipeline script for coprocessing? Any advice and
>> suggestions are very much appreciated.
>>
>> Thanks,
>>
>> Hong
>>
>>
>>
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