[Paraview] Use case Paraview-Selection

Wed Apr 21 17:18:50 EDT 2010

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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>>>>>
>>>
>>>
>
>