[Paraview] Use case Paraview-Selection

Wed Apr 21 13:54:57 EDT 2010

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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