[Paraview] Use case Paraview-Selection

Christian Werner christian.werner at rwth-aachen.de
Thu Apr 22 03:19:14 EDT 2010


Yep, I know the Find Data and it's quite nice to have. I mean something 
still more simple. In my use case i wrote:

"...The object will highlight so the user can always see which objects
have already been selected..."


which could be realized with some kind of "RegionID" selector. So one 
click and -BAM- all points with same ID selected.

Best regards,
Christian


Utkarsh Ayachit wrote:
> Glad it works.
>
> What do you mean by "a pick selects all cells with same ID" ? Is ID a
> cell array? If so, you can already do so using the  Edit | "Find Data"
> dialog
>  [ http://www.paraview.org/Wiki/Find_Data_using_Queries ]
>
> Utkarsh
>
>
> On Wed, Apr 21, 2010 at 5:10 PM, Christian Werner
> <christian.werner at rwth-aachen.de> wrote:
>   
>> This works perfectly, thank you very much! The processing is getting really
>> professional now.
>>
>> As for the selection tools, should I just go ahead and write a feature
>> request? (a pick selects all cells with same ID / enable multiselect so you
>> do not have to use the Ctrl-Key anymore)
>>
>> Best regards,
>> Christian
>>
>>
>>
>> Utkarsh Ayachit wrote:
>>     
>>> Christian,
>>>
>>> Attached is simple python script (that you can encapsulate as a macro)
>>> to which you can add code to processes the extract points however you
>>> like. I am simply writing them out to a file.
>>>
>>> To use this script, do the following (to keep it simple I am using the
>>> Sphere source as an example, no reason why it won't work with your
>>> data).
>>> 1> Create Sphere source
>>> 2> Create a selection of points or cells
>>> 3> Open Python Shell and run the attached script.
>>>
>>> As as result, you'll have a mygrid.vtu file written out with the
>>> extracted points(or cells). No 3 seconds waits, no errors writing
>>> files, no need for the user to create extract selection filter.
>>>
>>> Using the python macros capability, you can make this script a
>>> trigger-able from a toolbutton.
>>>
>>> Utkarsh
>>>
>>> On Wed, Apr 21, 2010 at 8:55 AM, Christian Werner
>>> <christian.werner at rwth-aachen.de> wrote:
>>>
>>>       
>>>> Hi!
>>>>
>>>> I made a new topic about that selection thing. Here is my use-case:
>>>>
>>>> Overview: We have volumetric data of metal components. These components
>>>> contain unwanted defects (holes that appear during the casting process).
>>>> These holes are visible as dark regions (objects) in the data.
>>>> Unfortunately, there are other structures in the metal that are also dark
>>>> (graphite). After a few image processing steps many of those objects
>>>> (defects and graphite) are segmented out of the originial volume data. A
>>>> contouring (and connectivity filtering) yields a nice visualization of
>>>> those
>>>> objects.
>>>>
>>>> Use Case: Select defects
>>>> Goal: The user selects the defects out of the many presented objects.
>>>>
>>>> Details: Due to the extremely cool features of Paraview, the user is able
>>>> to
>>>> mix the views of all extracted objects and the original volume data (see
>>>> image) to easily verify which object is a defect and which one is
>>>> graphite.
>>>> When the user identifies an object as a defect, he marks it by a simple
>>>> click. The object will highlight so the user can always see which objects
>>>> have already been selected. When the user is done selecting all defects,
>>>> he
>>>> clicks on the "Measure Defects" button. A database containing all
>>>> necessary
>>>> information on the defects (centroid, total volume, volume
>>>> percentage,...)
>>>> will automatically be created and saved in a secret place.
>>>>
>>>> Remark:
>>>> The "Measure Defects Button" will call a Python macro that desperately
>>>> tries
>>>> to extract the selected objects (points). These points are needed for
>>>> correspondance to the original volume data that is actually being
>>>> analyzed
>>>> (the mean grey value of a defect and such are important quantities).
>>>> Certainly, one single point per object suffices for this correspondance.
>>>>
>>>>
>>>> Best regards,
>>>> Christian
>>>>
>>>>
>>>> Utkarsh Ayachit schrieb:
>>>>
>>>>         
>>>>> Christian,
>>>>>
>>>>> O-oh! We can't have our users going mad now can we :). Guess we are
>>>>> looking at this the wrong way, instead of working from the solution,
>>>>> let's start with the problem/use-case. Can you describe your use-case
>>>>> as simply as possibly. What's the goal here? What is the user doing?
>>>>>
>>>>> Utkarsh
>>>>>
>>>>> On Mon, Apr 19, 2010 at 11:20 AM, Christian Werner
>>>>> <christian.werner at rwth-aachen.de> wrote:
>>>>>
>>>>>
>>>>>           
>>>>>> Does that mean that I have to create a selection with explicitly
>>>>>> defining
>>>>>> the points? Oh man... Then I can forget the whole thing anyway.
>>>>>>
>>>>>> Everything is so nice about Paraview, but this selection thing is
>>>>>> driving
>>>>>> me
>>>>>> mad.
>>>>>>
>>>>>> It's still all about making it as easy as possible for the user to
>>>>>> select
>>>>>> objects out of Polydata and let a plugin analyze these objects. As it
>>>>>> seems
>>>>>> now, the user has to:
>>>>>>
>>>>>> 1) Ctrl+Click matching objects one after another (already dangerours,
>>>>>> because you might forget to hold down Ctrl when selecting)
>>>>>> 2) go to Filter->Recent->ExtractSelection
>>>>>> 3) wait at least 3 seconds
>>>>>> 4) call a plugin that writes the extracted points' coordinates and
>>>>>> their
>>>>>> ID
>>>>>> to a file
>>>>>> 5) call the analyzing plugin that reads out the file (to get the
>>>>>> RegionID
>>>>>> and coordinates) and does the analysing stuff (in ITK)
>>>>>>
>>>>>> I have found a way to do that "wait 3 seconds" in Python using a
>>>>>> thread(!)
>>>>>> which checks the time and joins after some seconds. Using sleep(5)
>>>>>> simply
>>>>>> froze everything and postponed the segmentation fault (which clearly
>>>>>> comes
>>>>>> from my writer that doesn't have input). Another possibility would be
>>>>>> to
>>>>>> modify vtkExtractSelection to suite my needs, but I won't do that,
>>>>>> since
>>>>>> I
>>>>>> don't have time for that anymore. This workaround has to do.
>>>>>>
>>>>>> Anyway, Paraview, VTK and ITK are really nice, I am glad I found these
>>>>>> open-source tools.
>>>>>>
>>>>>> Best regards,
>>>>>> Christian
>>>>>>
>>>>>>
>>>>>>
>>>>>> Utkarsh Ayachit schrieb:
>>>>>>
>>>>>>
>>>>>>             
>>>>>>> Does your data have time? If not, you don't need to specify the
>>>>>>> time=10000 attribute at all. So SelectionWriter is the thing that's
>>>>>>> coming from your plugin? Does it support writing empty datasets?  Can
>>>>>>> you attach a debugger and see where is crashes? Are you sure it's not
>>>>>>> crashing in the writer? I dont' see why UpdatePipeline() on extract
>>>>>>> selection would crash. Instead of using a macro, try manually typing
>>>>>>> the text in the python shell to see exactly what line causes the
>>>>>>> segfault.
>>>>>>>
>>>>>>> BTW, ExtractSelection needs two inputs: 'Input" and "Selection" where
>>>>>>> Selection is set to the SelectionQuerySource proxy.
>>>>>>>
>>>>>>> Utkarsh
>>>>>>>
>>>>>>> On Mon, Apr 19, 2010 at 10:34 AM, Christian Werner
>>>>>>> <christian.werner at rwth-aachen.de> wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>               
>>>>>>>> I am afraid UpdatePipeline doesn't help, even if I set the time to
>>>>>>>> some
>>>>>>>> high
>>>>>>>> value. Paraview crashes right in the moment where I start this macro:
>>>>>>>>
>>>>>>>> extract=ExtractSelection(Input=ConnectivityFilter)
>>>>>>>>
>>>>>>>> UpdatePipeline(time= 10000, proxy=extract)
>>>>>>>>
>>>>>>>> mFilename = destPath + str( time() )
>>>>>>>>
>>>>>>>> swriter=SelectionWriter(Input=extract)
>>>>>>>>
>>>>>>>> swriter.FileName=mFilename
>>>>>>>>
>>>>>>>> swriter.UpdatePipeline()
>>>>>>>>
>>>>>>>>
>>>>>>>> When I manually select Fiters->ExtractSelection and then do:
>>>>>>>>
>>>>>>>> mFilename = destPath + str( time() )
>>>>>>>>
>>>>>>>> swriter=SelectionWriter()
>>>>>>>>
>>>>>>>> swriter.FileName=mFilename
>>>>>>>>
>>>>>>>> swriter.UpdatePipeline()
>>>>>>>>
>>>>>>>>
>>>>>>>> everything works fine.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Utkarsh Ayachit schrieb:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>                 
>>>>>>>>> You can simply call UpdatePipeline() as follows:
>>>>>>>>>
>>>>>>>>> from paraview.simple import *
>>>>>>>>> ....
>>>>>>>>> UpdatePipeline(proxy=extractSelectionSource)
>>>>>>>>>
>>>>>>>>> This will update the extract selection filter explicitly. Look at
>>>>>>>>> help(UpdatePipeline) for details.
>>>>>>>>>
>>>>>>>>> Utkarsh
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Sun, Apr 18, 2010 at 3:38 PM, Christian Werner
>>>>>>>>> <christian.werner at rwth-aachen.de> wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>                   
>>>>>>>>>> Hi Utkarsh,
>>>>>>>>>>
>>>>>>>>>> these are great news. I tried the python trace but not in
>>>>>>>>>> combination
>>>>>>>>>> with
>>>>>>>>>> the extraction (what I acutally do need anyway....)
>>>>>>>>>>
>>>>>>>>>> As you might remember I am working around the "lack" of possibilty
>>>>>>>>>> to
>>>>>>>>>> select
>>>>>>>>>> whole objects (cells with same RegionID). With the given
>>>>>>>>>> SelectionQuerySource this workaround is complete.
>>>>>>>>>>
>>>>>>>>>> There remains one issue: At some point I call an ExtractSelection()
>>>>>>>>>> in
>>>>>>>>>> Python that is followed by a call to a vtk-Plugin (which writes the
>>>>>>>>>> point
>>>>>>>>>> data of the selected points to disk). The resulting file is empty,
>>>>>>>>>> because
>>>>>>>>>> the Extraction takes a few seconds and obviously the plugin has no
>>>>>>>>>> valid
>>>>>>>>>> input when being executed. Paraview also crashes as a consequence.
>>>>>>>>>> When
>>>>>>>>>> I
>>>>>>>>>> am
>>>>>>>>>> doing this manually (trigger ExtractSelection, wait until it's
>>>>>>>>>> done,
>>>>>>>>>> call
>>>>>>>>>> the vtk Plugin to write the point data) everything works fine. I
>>>>>>>>>> could
>>>>>>>>>> just
>>>>>>>>>> go ahead and do a dull time.sleep(3) between the extraction and the
>>>>>>>>>> call
>>>>>>>>>> to
>>>>>>>>>> the plugin, but this certainly isn't good programming style.
>>>>>>>>>>
>>>>>>>>>> What can I do instead?
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Best regards,
>>>>>>>>>> Christian
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Utkarsh Ayachit wrote:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>                     
>>>>>>>>>>> Yes, you can use the "SelectionQuerySource" to construct your
>>>>>>>>>>> query
>>>>>>>>>>> as
>>>>>>>>>>> follows:
>>>>>>>>>>>
>>>>>>>>>>> selection_source_540 = SelectionQuerySource( InsideOut=0,
>>>>>>>>>>> ArrayName='', HierarchicalLevel=-1, ProcessID=-1,
>>>>>>>>>>> ContainingCells=0,
>>>>>>>>>>> DoubleValues=None, HierarchicalIndex=-1, FieldType='CELL',
>>>>>>>>>>> ArrayComponent=0, Operator='IS_ONE_OF', TermMode='ID',
>>>>>>>>>>> CompositeIndex=-1, IdTypeValues=0 )
>>>>>>>>>>>
>>>>>>>>>>> You can use the python trace recorder functionality to determine
>>>>>>>>>>> how
>>>>>>>>>>> to create the query. You will, however have to "Extract Selection"
>>>>>>>>>>> from the query (and hit apply) before the selection_source object
>>>>>>>>>>> will
>>>>>>>>>>> appear in the trace.
>>>>>>>>>>>
>>>>>>>>>>> Utkarsh
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Sat, Apr 17, 2010 at 9:32 AM, Christian Werner
>>>>>>>>>>> <christian.werner at rwth-aachen.de> wrote:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>                       
>>>>>>>>>>>> Hello!
>>>>>>>>>>>>
>>>>>>>>>>>> Is there any chance that the new Edit->Find Data functionality is
>>>>>>>>>>>> available
>>>>>>>>>>>> in Python-Scripting?
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Best regards,
>>>>>>>>>>>> Christian
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>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>                         
>>>>>>>>>>                     
>>>>>>>>                 
>>>>>> _______________________________________________
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>>>>>>
>>>>>>
>>>>>>             
>>>>         
>>     



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