[Kiwiviewer] write volume data with 3D surface

João Domingos joao.sousa.domingos at gmail.com
Mon Sep 3 20:31:05 EDT 2012 

Pat,

I have 2 arrays in the vtkPolyData:

  Number Of Arrays: 2
  Array 0 name = ImageScalars
  Array 1 name = Normals

Deleting both does not change that.. It is still red. (I have not tried in
Paraview)

Regarding scene description files, i Meant, is there a way to make the
.kiwi visible in the Open Data (builtin example scenes) menu? I guess, with
your answer you meant no. Well, something for you guys to take into
consideration for the next version.

Many thanks,
Joao



On 3 September 2012 22:46, Pat Marion <pat.marion at kitware.com> wrote:

> Hi Joao,
>
> Oh, perhaps this surface has a point data attribute array, like point ids
> or something?  Can you open the vtp file in ParaView and see if it has an
> attribute array?  If so, KiwiViewer will color the points using the
> attribute array.  There is no way to disable that and use solid coloring,
> and no way to use opacity.  If you delete the attribute array, then solid
> coloring and opacity should work.  You could do this in your pipeline, if
> you're using a c++ vtk pipeline, like:
>
> // get the poly data at the end of the pipeline
> vtkPolyData* myData = contourFilter->GetOutput();
>
> // remove all point data arrays
> while (myData->GetPointData()->GetNumberOfArrays())
>   myData->GetPointData()->RemoveArray(0);
>
>
> Regarding scene description files, KiwiViewer doesn't actually use any
> .kiwi files for the builtin example scenes.  Most of the builtin datasets
> are just regular surfaces.  The textured earth, brain atlas, and can
> animation are special purpose demos, and can't be described using the
> simple .kiwi file format.
>
> Pat
>
>
>
> On Mon, Sep 3, 2012 at 4:14 PM, João Domingos <
> joao.sousa.domingos at gmail.com> wrote:
>
>> Hey Pat,
>>
>> Did some more testing and apparently the app is working fine. I was able
>> to change colors and opacity of several datasets, except on the surface I
>> told you about. The problem happens when you have an output of the
>> following pipeline type:
>>
>> vtkPolyData()(a mesh of points) -> vtkSurfaceReconstructionFilter() ->
>> vtkContourFilter()
>>
>> On the computer (meaning under normal VTK usage), this final vtkPolyData
>> output can be represented with a different opacity
>> (surf.GetProperty().SetOpacity(0.6) works), but color will always be red
>> (surf.GetProperty().SetColor(0,1,0) does nothing). On the KiwiViewer color
>> change again does not work for this surface (it is always red as in the
>> computer) but, unexpectedly, opacity also doesn't work. Besides this
>> specific case, I could represent my remaining datasets successfully and
>> change colors and opacities.
>>
>> One question, is there a way of including the scene description files
>> (.kiwi) with the examples KiwiViewer already has?
>>
>> Many thanks,
>> Joao
>>
>>
>>
>>
>>
>>
>>
>> On 31 August 2012 20:06, João Domingos <joao.sousa.domingos at gmail.com>wrote:
>>
>>> Hi Pat,
>>>
>>> Good to hear from you. I tried what you gave me and still the 3D model
>>> is completely red (tried opacity of 0.1). I'm using KiwiViewer from Android
>>> app store on a Galaxy S3. Eventually I will try to compile my own version.
>>> Do you have any more ideas for the opacity to work? Also, are those the
>>> only settings we can program without compiling a copy? The 'model-tapping
>>> to disappear function' I told you about can be simply coded in a .kiwi
>>> metafile as well?
>>>
>>> Many thanks for your time,
>>> Joao
>>>
>>>
>>>
>>> On 31 August 2012 16:17, Pat Marion <pat.marion at kitware.com> wrote:
>>>
>>>> Hi,
>>>>
>>>> Sorry I did not notice your emails earlier!  Regarding the transparency
>>>> bug, could you try reformating your .kiwi metafile so it lists the volume
>>>> first, then the surface, and add commas for each empty column, like this:
>>>>
>>>> filename,r,g,b,a
>>>> 37fr15.mha,,,,
>>>> LV_surface.vtp,1.0,0.0,0.0,0.5
>>>>
>>>> Does that work any better?  I've done a metafile just like this before
>>>> with transparency on the surface and it worked correctly for me, but I can
>>>> try again.  Are you using KiwiViewer from the Android app store, or did you
>>>> compile your own copy for Android or iOS?
>>>>
>>>> For the brain atlas, I hope that in future releases the demo can be
>>>> easily configurable for new models.  Right now you could edit the
>>>> models.txt file and replace the filenames, colors, and labels with your
>>>> own, but the demo does require the skin and skull models to be present, and
>>>> the initial position & scale of the clipping plane is hard coded.
>>>>
>>>> Pat
>>>>
>>>>
>>>>
>>>> On Fri, Aug 31, 2012 at 2:55 AM, João Domingos <
>>>> joao.sousa.domingos at gmail.com> wrote:
>>>>
>>>>> Any help please?
>>>>>
>>>>> Many thanks for your time,
>>>>> Domingos
>>>>>
>>>>>
>>>>>
>>>>> On 26 August 2012 20:53, João Domingos <joao.sousa.domingos at gmail.com>wrote:
>>>>>
>>>>>> Also, just like in the SPL-PNL Brain Atlas, can someone please tell
>>>>>> me how do you program a specific surface (ex: brain structure) to show its
>>>>>> legend and appear/disappear when touched? Would like to program that
>>>>>> function into my surface so that it could appear disappear from a metafile
>>>>>> volume (still with slicing capability embedded).
>>>>>>
>>>>>> Many thanks,
>>>>>> Domingos
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 25 August 2012 17:07, João Domingos <joao.sousa.domingos at gmail.com
>>>>>> > wrote:
>>>>>>
>>>>>>> Dear all,
>>>>>>>
>>>>>>> I was able to load both a metafile and a surface with the following
>>>>>>> instructions:
>>>>>>>
>>>>>>> filename,r,g,b,a
>>>>>>> LV_surface.vtp,1,0,0,0.5
>>>>>>> 37fr15.mha
>>>>>>>
>>>>>>> Another question: in the presence of a metafile volume, the transparency
>>>>>>> is not working on the surface. Do you know why? I have tried by putting
>>>>>>> everything 1 in the .mha.. but it is the same, no opacity change on the
>>>>>>> surface.
>>>>>>>
>>>>>>> Many thanks,
>>>>>>> Joao Domingos
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 25 August 2012 07:33, João Domingos <
>>>>>>> joao.sousa.domingos at gmail.com> wrote:
>>>>>>>
>>>>>>>> Dear all,
>>>>>>>>
>>>>>>>> I have opened (on a PC) a 3D volume and fitted a 3D surface and now
>>>>>>>> I would like to save both into a file so that I can open it in the
>>>>>>>> KiwiViewer. In the latter I can open the .mha (.raw) volume and my
>>>>>>>> surface.vtp file. The problem is, both are opened separately. Is there a
>>>>>>>> way to save both on the same file and then open both at the same time with
>>>>>>>> KiwiViewer?
>>>>>>>>
>>>>>>>>
>>>>>>>> Many thanks,
>>>>>>>> Domingos
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Kiwiviewer mailing list
>>>>> Kiwiviewer at public.kitware.com
>>>>> http://public.kitware.com/cgi-bin/mailman/listinfo/kiwiviewer
>>>>>
>>>>>
>>>>
>>>
>>
>
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