[Kiwiviewer] write volume data with 3D surface

[Pat Marion]

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