[Imstk-developers] Clearing surface mesh data on intialization

Fri Jul 28 11:11:54 EDT 2017

I don't see the issue then: Initialize is called first to setup vertices
and connectivity, then additional fields can be manually added (like
normals). Could you just make sure you keep adding the normals after
initializing the mesh?

Alexis Girault
R&D Engineer in Medical Computing
Kitware, Inc.

http://www.kitware.com
(919) 969-6990 x325

On Fri, Jul 28, 2017 at 11:08 AM, Milef, Nicholas Boris <milefn at rpi.edu>
wrote:

> @Alexis
> It's here, but I set up the normals afterwards right now since they get
> cleared on initialization:
> https://gitlab.kitware.com/iMSTK/iMSTK/blob/master/Base/Geometry/Reader/
> imstkAssimpMeshIO.cpp#L101
>
> @Sreekanth
> They can't really be recomputed afterwards. At that point, it would be up
> to the user to specify or recompute this once they can ensure the normals
> are correct. It can only be computed before the iMSTK normal calculation
> takes place. Otherwise the important information is lost.
>
> We could require the user to explicitly call the compute UV seams, but I
> have a feeling people just won't do this :)
> ------------------------------
> *From:* Sreekanth Arikatla [sreekanth.arikatla at kitware.com]
> *Sent:* Thursday, July 27, 2017 9:17 PM
>
> *To:* Milef, Nicholas Boris
> *Cc:* Alexis Girault; imstk-developers at imstk.org
> *Subject:* Re: [Imstk-developers] Clearing surface mesh data on
> intialization
>
> Hi Nick,
>             When you set new data shouldn't the seam vertices from the
> prior data be cleared too since they are invalid? If needed the seam
> vertices should be recomputed for the new data?
>
> On Thu, Jul 27, 2017 at 7:31 PM, Alexis Girault <
> alexis.girault at kitware.com> wrote:
>
>> Not where `clear` is called, where `initialize` is called. (What calls that
>> functio
>> <https://gitlab.kitware.com/iMSTK/iMSTK/blob/master/Base/Geometry/Mesh/imstkSurfaceMesh.cpp#L27-29>n
>> after you set up the normals: )
>>
>> Alexis Girault
>> R&D Engineer in Medical Computing
>> Kitware, Inc.
>>
>> http://www.kitware.com
>> (919) 969-6990 x325
>>
>> On Thu, Jul 27, 2017 at 6:44 PM, Milef, Nicholas Boris <milefn at rpi.edu>
>> wrote:
>>
>>> Yeah:
>>> https://gitlab.kitware.com/iMSTK/iMSTK/blob/master/Base/Geom
>>> etry/Mesh/imstkSurfaceMesh.cpp#L31
>>> https://gitlab.kitware.com/iMSTK/iMSTK/blob/master/Base/Geom
>>> etry/Mesh/imstkSurfaceMesh.cpp#L50
>>>
>>> ------------------------------
>>> *From:* Alexis Girault [alexis.girault at kitware.com]
>>> *Sent:* Thursday, July 27, 2017 6:42 PM
>>> *To:* Milef, Nicholas Boris; Sreekanth Arikatla
>>>
>>> *Cc:* imstk-developers at imstk.org
>>> *Subject:* Re: [Imstk-developers] Clearing surface mesh data on
>>> intialization
>>>
>>> Could you point us out in the code to where initialize is called which
>>> deletes your normals?
>>>
>>> On Thu, Jul 27, 2017, 18:37 Milef, Nicholas Boris <milefn at rpi.edu>
>>> wrote:
>>>
>>>> The issue is still there. I can put the UV seam code before all of the
>>>> clears, but if the user for some reason calls this function and gives
>>>> different vertices/triangles, then it won't work properly with the new
>>>> data. This is because the normals and the UV seam vertices won't correspond
>>>> to each other.
>>>> ------------------------------
>>>> *From:* Sreekanth Arikatla [sreekanth.arikatla at kitware.com]
>>>> *Sent:* Thursday, July 27, 2017 6:26 PM
>>>> *To:* Milef, Nicholas Boris
>>>>
>>>> *Cc:* Alexis Girault; imstk-developers at imstk.org
>>>> *Subject:* Re: [Imstk-developers] Clearing surface mesh data on
>>>> intialization
>>>> Not a problem!
>>>>
>>>> On Thu, Jul 27, 2017 at 6:22 PM, Milef, Nicholas Boris <milefn at rpi.edu>
>>>> wrote:
>>>>
>>>>> Yeah, sorry about that!
>>>>> ------------------------------
>>>>> *From:* Sreekanth Arikatla [sreekanth.arikatla at kitware.com]
>>>>> *Sent:* Thursday, July 27, 2017 6:20 PM
>>>>>
>>>>> *To:* Milef, Nicholas Boris
>>>>> *Cc:* Alexis Girault; imstk-developers at imstk.org
>>>>> *Subject:* Re: [Imstk-developers] Clearing surface mesh data on
>>>>> intialization
>>>>>
>>>>> I see, it must have reported Initialize methods from physics that are
>>>>> not related to this.
>>>>>
>>>>> On Thu, Jul 27, 2017 at 6:14 PM, Milef, Nicholas Boris <milefn at rpi.edu
>>>>> > wrote:
>>>>>
>>>>>> @Alexis But why should it be overwriting the normals? That's not
>>>>>> derived data.
>>>>>>
>>>>>> @Sreekanth I wasn't reading carefully enough. I tried to find all
>>>>>> references, but apparently Visual Studio finds everything with the same
>>>>>> name as the method, not necessarily the surface mesh's method. Sorry about
>>>>>> that.
>>>>>>
>>>>>> ------------------------------
>>>>>> *From:* Sreekanth Arikatla [sreekanth.arikatla at kitware.com]
>>>>>> *Sent:* Thursday, July 27, 2017 6:04 PM
>>>>>> *To:* Milef, Nicholas Boris
>>>>>> *Cc:* Alexis Girault; imstk-developers at imstk.org
>>>>>>
>>>>>> *Subject:* Re: [Imstk-developers] Clearing surface mesh data on
>>>>>> intialization
>>>>>>
>>>>>> Initialize is called at the setup phase by readers as well as when
>>>>>> the user creates the data. It is supposed to be only called only for
>>>>>> initialization and reinitialization with new data. Can you point me where
>>>>>> it is called in the physics?
>>>>>>
>>>>>> On Thu, Jul 27, 2017 at 5:57 PM, Milef, Nicholas Boris <
>>>>>> milefn at rpi.edu> wrote:
>>>>>>
>>>>>>> Actually, to clarify, I don't think it's a big deal if it's used in
>>>>>>> the physics classes, as long as it doesn't modify an already built mesh as
>>>>>>> I describe in the previous message. I don't know what type of impact the
>>>>>>> normals have in the physics classes.
>>>>>>> ------------------------------
>>>>>>> *From:* Imstk-developers [imstk-developers-bounces at imstk.org] on
>>>>>>> behalf of Milef, Nicholas Boris [milefn at rpi.edu]
>>>>>>> *Sent:* Thursday, July 27, 2017 5:53 PM
>>>>>>> *To:* Alexis Girault
>>>>>>>
>>>>>>> *Cc:* imstk-developers at imstk.org
>>>>>>> *Subject:* Re: [Imstk-developers] Clearing surface mesh data on
>>>>>>> intialization
>>>>>>>
>>>>>>> If it were only called in the readers, I wouldn't have a problem
>>>>>>> with it. But it's called in some of the physics classes too. It also clears
>>>>>>> data such as normals that's been set (i.e., by the readers). I need some of
>>>>>>> that data though to fix the UV seams.
>>>>>>>
>>>>>>> For meshes, Assimp is told to generate smooth normals and to join
>>>>>>> identical normals. For most vertices, this works as intended, but for
>>>>>>> vertices on UV seams, they can't be joined. Assimp smooths those vertices
>>>>>>> by treating them as a single vertex, which I would want as the intended
>>>>>>> behavior. So I need to go through all of the vertices and find the ones
>>>>>>> with the same normals and positions, but the normals get cleared by the
>>>>>>> initialize function. Assimp's behavior is correct (I can't think of another
>>>>>>> way we would want it to deal with these problems).
>>>>>>> ------------------------------
>>>>>>> *From:* Alexis Girault [alexis.girault at kitware.com]
>>>>>>> *Sent:* Thursday, July 27, 2017 5:26 PM
>>>>>>> *To:* Milef, Nicholas Boris
>>>>>>> *Cc:* Sreekanth Arikatla; imstk-developers at imstk.org
>>>>>>> *Subject:* Re: [Imstk-developers] Clearing surface mesh data on
>>>>>>> intialization
>>>>>>>
>>>>>>> Is `initialize` only used in the readers currently? I believe the
>>>>>>> goal of that function was just to set vertices, triangles, or any other
>>>>>>> topology information needed in a single function. It should only be used
>>>>>>> after the constructor as a utility as far as I understand, so there
>>>>>>> shouldn't be data already set in the mesh at that point.
>>>>>>>
>>>>>>> When/where is this function currently called and creating an issue
>>>>>>> in your case?
>>>>>>>
>>>>>>> Also, I think the `clear `should only delete the derived data
>>>>>>> computed by the initialization input. Is it doing more than that now which
>>>>>>> would explain why it deletes your data?
>>>>>>>
>>>>>>> I think having an `initialize` function that clears derived data
>>>>>>> fields and set core parameters is good, we need to make sure it is called
>>>>>>> at a good place and does not remove some unexpected fields (but I just
>>>>>>> think it should be called before you try to set any data in it)
>>>>>>>
>>>>>>> Alexis Girault
>>>>>>> R&D Engineer in Medical Computing
>>>>>>> Kitware, Inc.
>>>>>>>
>>>>>>> http://www.kitware.com
>>>>>>> (919) 969-6990 x325
>>>>>>>
>>>>>>> On Thu, Jul 27, 2017 at 5:03 PM, Milef, Nicholas Boris <
>>>>>>> milefn at rpi.edu> wrote:
>>>>>>>
>>>>>>>> For now, I can just put the seam computation before the clear.
>>>>>>>> However, this will break if the vertex order changes or something like
>>>>>>>> that. Basically, what I'm trying to say is that I would want users to know
>>>>>>>> explicitly if they're messing up their data. A reinitialize function
>>>>>>>> doesn't convey this imo.
>>>>>>>> ------------------------------
>>>>>>>> *From:* Imstk-developers [imstk-developers-bounces at imstk.org] on
>>>>>>>> behalf of Milef, Nicholas Boris [milefn at rpi.edu]
>>>>>>>> *Sent:* Thursday, July 27, 2017 4:47 PM
>>>>>>>> *To:* Sreekanth Arikatla
>>>>>>>>
>>>>>>>> *Cc:* imstk-developers at imstk.org
>>>>>>>> *Subject:* Re: [Imstk-developers] Clearing surface mesh data on
>>>>>>>> intialization
>>>>>>>>
>>>>>>>> I guess where I'm stuck at is why we have an initialize function to
>>>>>>>> begin with. I still can't think of a use-case where we can't either 1) make
>>>>>>>> a new mesh or 2) modify the components of the old mesh.
>>>>>>>> ------------------------------
>>>>>>>> *From:* Sreekanth Arikatla [sreekanth.arikatla at kitware.com]
>>>>>>>> *Sent:* Thursday, July 27, 2017 4:37 PM
>>>>>>>> *To:* Milef, Nicholas Boris
>>>>>>>> *Cc:* imstk-developers at imstk.org
>>>>>>>> *Subject:* Re: [Imstk-developers] Clearing surface mesh data on
>>>>>>>> intialization
>>>>>>>>
>>>>>>>> Hi Nick,
>>>>>>>>             If you want to preserve the normals, you can add
>>>>>>>> normals to the Initialize function arg. If the normals are supplied,
>>>>>>>> initialize clears the previous data before assigning.
>>>>>>>>
>>>>>>>> On Thu, Jul 27, 2017 at 4:01 PM, Milef, Nicholas Boris <
>>>>>>>> milefn at rpi.edu> wrote:
>>>>>>>>
>>>>>>>>> No, I don't. I need to preserve the original normals that ASSIMP
>>>>>>>>> imports because ASSIMP calculates the normals correctly. Otherwise, I can't
>>>>>>>>> identify the UV seams.
>>>>>>>>>
>>>>>>>>> I can just do this computation in the SurfaceMeshRenderDelegate,
>>>>>>>>> but I'm not sure if the normals are used elsewhere after reinitializing the
>>>>>>>>> meshes. But isn't reinitializing a mesh dangerous in a multithreaded
>>>>>>>>> environment anyway?
>>>>>>>>> ------------------------------
>>>>>>>>> *From:* Sreekanth Arikatla [sreekanth.arikatla at kitware.com]
>>>>>>>>> *Sent:* Thursday, July 27, 2017 3:55 PM
>>>>>>>>>
>>>>>>>>> *To:* Milef, Nicholas Boris
>>>>>>>>> *Cc:* imstk-developers at imstk.org
>>>>>>>>> *Subject:* Re: [Imstk-developers] Clearing surface mesh data on
>>>>>>>>> intialization
>>>>>>>>>
>>>>>>>>> It could be used in some cases depending on the scenario. Do you
>>>>>>>>> plan to call this at every frame?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Thu, Jul 27, 2017 at 3:53 PM, Milef, Nicholas Boris <
>>>>>>>>> milefn at rpi.edu> wrote:
>>>>>>>>>
>>>>>>>>>> Is that a useful use case though? Why not just make a new mesh?
>>>>>>>>>> ------------------------------
>>>>>>>>>> *From:* Sreekanth Arikatla [sreekanth.arikatla at kitware.com]
>>>>>>>>>> *Sent:* Thursday, July 27, 2017 3:52 PM
>>>>>>>>>> *To:* Milef, Nicholas Boris
>>>>>>>>>> *Cc:* imstk-developers at imstk.org
>>>>>>>>>> *Subject:* Re: [Imstk-developers] Clearing surface mesh data on
>>>>>>>>>> intialization
>>>>>>>>>>
>>>>>>>>>> Hi Nick,
>>>>>>>>>>             This is cleared in case one wants to reinitialize the
>>>>>>>>>> mesh with a different data. Initialize should only be called at
>>>>>>>>>> initilization or at runtime if the mesh data itself changes.
>>>>>>>>>>
>>>>>>>>>> On Thu, Jul 27, 2017 at 3:31 PM, Milef, Nicholas Boris <
>>>>>>>>>> milefn at rpi.edu> wrote:
>>>>>>>>>>
>>>>>>>>>>> I'm modifying the SurfaceMesh class currently, but why is all
>>>>>>>>>>> the data cleared on initialization? Is this necessary? I ask because I need
>>>>>>>>>>> this data to correct for the normals seams.
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Imstk-developers mailing list
>>>>>>>>>>> Imstk-developers at imstk.org
>>>>>>>>>>> http://public.kitware.com/mailman/listinfo/imstk-developers
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> Sreekanth Arikatla, Ph.D.,
>>>>>>>>>> Senior R&D Engineer,
>>>>>>>>>> Kitware, Inc. <http://www.kitware.com>, Carrboro, NC.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Sreekanth Arikatla, Ph.D.,
>>>>>>>>> Senior R&D Engineer,
>>>>>>>>> Kitware, Inc. <http://www.kitware.com>, Carrboro, NC.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Sreekanth Arikatla, Ph.D.,
>>>>>>>> Senior R&D Engineer,
>>>>>>>> Kitware, Inc. <http://www.kitware.com>, Carrboro, NC.
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Imstk-developers mailing list
>>>>>>>> Imstk-developers at imstk.org
>>>>>>>> http://public.kitware.com/mailman/listinfo/imstk-developers
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Imstk-developers mailing list
>>>>>>> Imstk-developers at imstk.org
>>>>>>> http://public.kitware.com/mailman/listinfo/imstk-developers
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Sreekanth Arikatla, Ph.D.,
>>>>>> Senior R&D Engineer,
>>>>>> Kitware, Inc. <http://www.kitware.com>, Carrboro, NC.
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Sreekanth Arikatla, Ph.D.,
>>>>> Senior R&D Engineer,
>>>>> Kitware, Inc. <http://www.kitware.com>, Carrboro, NC.
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Sreekanth Arikatla, Ph.D.,
>>>> Senior R&D Engineer,
>>>> Kitware, Inc. <http://www.kitware.com>, Carrboro, NC.
>>>>
>>>>
>>
>
>
> --
> Sreekanth Arikatla, Ph.D.,
> Senior R&D Engineer,
> Kitware, Inc. <http://www.kitware.com>, Carrboro, NC.
>
>
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