Re: [MORPHMET] Re: How to export .obj with textures as .ply with colours for morphometric analyses?

[M. Viviana Toro Ibacache]

Dear Patrick,

I apologise for the late reply. The software I used to do the procedure is
Geomagic Studio, version 2012, 64-bits.

Best wishes,
Viviana

2016-09-19 5:19 GMT-03:00 lv xiao :

> Hi Dr. Viviana, thank you very much for your exposition. I noted that
> there are several softwares in Geomagic, such as Geomagic Design, Geomagic
> Freeform, and Geomagic Wrap. May I know which Geomagic software did you
> use? Thank you very much!
>
> Best regards,
> Patrick WEN
>
> On Wednesday, 14 September 2016 18:11:12 UTC+8, mtoroibacache wrote:
>>
>> Dear Colleagues,
>>
>> I really appreciate your help with this. Indeed, there is a bit of
>> everything you mentioned in both the problem and the solution. I will try
>> to summarise it in case it can help someone else:
>>
>> - File names: Indeed I had problems in the past with .obj files whose
>> names had spaces, as Thomas mentioned. This was not the case though (I
>> learned my lesson), but it could happen to someone else.
>>
>> - Lack of software to do this in a very reliable way: as Bill mentioned,
>> there might be issues with accuracy by transforming an .obj with texture to
>> a coloured .ply. I will explore the use of Blender directly in .obj files
>> for landmark placing. I am not too worried about my data as the landmark
>> configuration corresponds to human faces (the texture will guide me in
>> placing landmarks in some curved places), where in my experience geometry
>> dimensions exceed small inaccuracies. But it is definitely something to
>> bear in  mind. Of course, I shall run tests to assess the effect of
>> measurement error on my data.
>>
>> - The .obj texture files: a big problem seemed to be that the original
>> data had three .jpg files depicting texture. As Pablo mentioned, the
>> "standard" texture should be one file. So...
>>
>> - ... Geomagic comes to rescue (maybe Blender does this too?): Anneke
>> suggested to use Geomagic, which indeed helps a lot. Antonio took my files
>> and helped me to generate in Geomagic the single-.png-file texture, which
>> can then be used to produce coloured .ply and .wrl files in Meshlab that
>> can be opened in Avizo (.wrl, for which an extra step in Geomagic is
>> needed), and in the R packages Geomorph and Morpho for landmark placing.
>>
>> About Joes's comment, I do not believe .stl can hold colours, but I do
>> not have too much experience with the .stl format. The .obj format (as well
>> as .ply) has a relatively simple structure that describes the position in
>> space of faces and vertices plus other stuff and can be created "by hand"
>> using a text editor such as Notepad (I am sure you might have checked this
>> but just in case https://en.wikipedia.org/wiki/Wavefront_.obj_file). I
>> have written .ply files in the past that worked very well for doing
>> morphometric analyses in R.
>>
>> So, again thanks everyone for all the help!
>>
>> Best wishes,
>> Viviana
>>
>>
>> 2016-09-07 21:35 GMT+02:00 pablo.diaz.jarufe :
>>
>>> Hello Viviana
>>> Working with DAVID I noticed that the textures of the OBJ files. are
>>> saved in PNG format, not in JPG; and all the views are in the same
>>> file. There is any way to create this kind of PNG. file with your
>>> pictures?. May be this correction could work fine in meshlab.
>>> I hope this information will be useful
>>> Best
>>>
>>>
>>> El jueves, 1 de septiembre de 2016, 8:31:47 (UTC-3), mtoroibacache
>>> escribió:

 Deal Morphometricians,

 I have .obj files with textures from three .jpg photos. I can load and
 see the textures very nicely in Meshlab, but I need the textures to be
 transformed into a coloured .ply file to do geometric morphometric analyses
 (the landmarks are represented in the textures). So far it has not worked
 doing it from Meshlab, so my questions are:

 - I know I can place landmarks in Meshlab using the .obj file, but when
 I do it, the software crashes. any thoughts? the .obj file is 16 Mb big. Is
 there a limit to files size in Meshlab? I would rather not to downsample
 the mesh to not lose anatomical details.

 - When using the Transfer Texture to Vertex Color function, the texture
 gets messed. It seems from web forums that Mshlab takes only one of the (in
 this case) three .jpg files to do the colouring of the .ply mesh. Does
 anybody know how to fix this? Another freeware software?

 - Is there any landmark acquisition software that loads .obj files with
 textures? So far, I have not been able to do it in Landmark Editor, Evan
 toolbox, Avizo, Morpho nor Geomorph.

 Any help is greatly appreciated.

 Best (y saludos),
 Viviana



 --

 *Viviana Toro-Ibacache DDS MSc PhD*
 Profesora Asistente *(Assistant Professor)*
 Centro de Análisis Cuantitativo en Antropología Dental (CA2)
 Unidad de Anatomía, Instituto de Investigación en Ciencias Odontológicas

Re: [MORPHMET] Re: How to export .obj with textures as .ply with colours for morphometric analyses?

[M. Viviana Toro Ibacache]

Dear Colleagues,

I really appreciate your help with this. Indeed, there is a bit of
everything you mentioned in both the problem and the solution. I will try
to summarise it in case it can help someone else:

- File names: Indeed I had problems in the past with .obj files whose names
had spaces, as Thomas mentioned. This was not the case though (I learned my
lesson), but it could happen to someone else.

- Lack of software to do this in a very reliable way: as Bill mentioned,
there might be issues with accuracy by transforming an .obj with texture to
a coloured .ply. I will explore the use of Blender directly in .obj files
for landmark placing. I am not too worried about my data as the landmark
configuration corresponds to human faces (the texture will guide me in
placing landmarks in some curved places), where in my experience geometry
dimensions exceed small inaccuracies. But it is definitely something to
bear in  mind. Of course, I shall run tests to assess the effect of
measurement error on my data.

- The .obj texture files: a big problem seemed to be that the original data
had three .jpg files depicting texture. As Pablo mentioned, the "standard"
texture should be one file. So...

- ... Geomagic comes to rescue (maybe Blender does this too?): Anneke
suggested to use Geomagic, which indeed helps a lot. Antonio took my files
and helped me to generate in Geomagic the single-.png-file texture, which
can then be used to produce coloured .ply and .wrl files in Meshlab that
can be opened in Avizo (.wrl, for which an extra step in Geomagic is
needed), and in the R packages Geomorph and Morpho for landmark placing.

About Joes's comment, I do not believe .stl can hold colours, but I do not
have too much experience with the .stl format. The .obj format (as well as
.ply) has a relatively simple structure that describes the position in
space of faces and vertices plus other stuff and can be created "by hand"
using a text editor such as Notepad (I am sure you might have checked this
but just in case https://en.wikipedia.org/wiki/Wavefront_.obj_file). I have
written .ply files in the past that worked very well for doing morphometric
analyses in R.

So, again thanks everyone for all the help!

Best wishes,
Viviana


2016-09-07 21:35 GMT+02:00 pablo.diaz.jarufe :

> Hello Viviana
> Working with DAVID I noticed that the textures of the OBJ files. are
> saved in PNG format, not in JPG; and all the views are in the same file.
> There is any way to create this kind of PNG. file with your pictures?. May
> be this correction could work fine in meshlab.
> I hope this information will be useful
> Best
>
>
> El jueves, 1 de septiembre de 2016, 8:31:47 (UTC-3), mtoroibacache
> escribió:
>>
>> Deal Morphometricians,
>>
>> I have .obj files with textures from three .jpg photos. I can load and
>> see the textures very nicely in Meshlab, but I need the textures to be
>> transformed into a coloured .ply file to do geometric morphometric analyses
>> (the landmarks are represented in the textures). So far it has not worked
>> doing it from Meshlab, so my questions are:
>>
>> - I know I can place landmarks in Meshlab using the .obj file, but when I
>> do it, the software crashes. any thoughts? the .obj file is 16 Mb big. Is
>> there a limit to files size in Meshlab? I would rather not to downsample
>> the mesh to not lose anatomical details.
>>
>> - When using the Transfer Texture to Vertex Color function, the texture
>> gets messed. It seems from web forums that Mshlab takes only one of the (in
>> this case) three .jpg files to do the colouring of the .ply mesh. Does
>> anybody know how to fix this? Another freeware software?
>>
>> - Is there any landmark acquisition software that loads .obj files with
>> textures? So far, I have not been able to do it in Landmark Editor, Evan
>> toolbox, Avizo, Morpho nor Geomorph.
>>
>> Any help is greatly appreciated.
>>
>> Best (y saludos),
>> Viviana
>>
>>
>>
>> --
>>
>> *Viviana Toro-Ibacache DDS MSc PhD*
>> Profesora Asistente *(Assistant Professor)*
>> Centro de Análisis Cuantitativo en Antropología Dental (CA2)
>> Unidad de Anatomía, Instituto de Investigación en Ciencias Odontológicas
>> Facultad de Odontología Universidad de Chile
>>
>> Dirección:  Sergio Livingstone Pohlhammer 943
>> *(address)*   Independencia, Región Metropolitana
>>  Chile
>> Email:mtoroi...@odontologia.uchile.cl
>> Web: www.researchgate.net/profile/Viviana_Toro_Ibacache/
>>  www.cienciaymemoria.cl/staff.html
>>
> --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
> ---
> You received this message because you are subscribed to the Google Groups
> "MORPHMET" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to morphmet+unsubscr...@morphometrics.org.
>



-- 

*Viviana Toro-Ibacache DDS MSc PhD*
Profesora Asistente *(Assistant Professor)*
Centro de Análisis Cuantitativo en 

Re: [MORPHMET] How to export .obj with textures as .ply with colours for morphometric analyses?

[M. Viviana Toro Ibacache]

Dear Anneke,

Geomagic seems to read the three files and saves them to generate a .wrl
(not .ply) file that has indeed colours, although they are not in the right
place. But that is a good start. I assume there is a Geomagic setting to
generate the file I am missing so I will keep on trying. Luckily in the lab
I currently am there is Geomagic... a freware option for everyone would
always be great!

Thanks and best wishes,
Viviana

2016-09-07 16:39 GMT+02:00 Anneke van Heteren <a.h.vanhete...@gmail.com>:

> Dear Viviana,
>
> Have you tried geomagic? It has been a while since I last used this
> program so I forgot the details, but it is capable of importing obj files
> with textures and then exporting coloured ply files. Like I said, I forgot
> the exact steps you would have to take, but I have done it before, so it is
> certainly possible.
> I hope that somewhat helps you.
>
> Best wishes,
>
> Anneke van Heteren
> On Sep 2, 2016 2:54 PM, "Antonio Profico" <antonio.prof...@uniroma1.it>
> wrote:
>
> Dear Viviana,
>
> you can export the 3D model from MeshLab as wrl format (export mesh as).
> After, you can open and display the new mesh in Avizo (Display Open
> Inventor Scene). In this way you can acquire the landmark in Avizo.
>
> Best,
> Antonio
>
>
> 2016-09-01 13:31 GMT+02:00 M. Viviana Toro Ibacache <
> mtoroibaca...@odontologia.uchile.cl>:
>
>> Deal Morphometricians,
>>
>> I have .obj files with textures from three .jpg photos. I can load and
>> see the textures very nicely in Meshlab, but I need the textures to be
>> transformed into a coloured .ply file to do geometric morphometric analyses
>> (the landmarks are represented in the textures). So far it has not worked
>> doing it from Meshlab, so my questions are:
>>
>> - I know I can place landmarks in Meshlab using the .obj file, but when I
>> do it, the software crashes. any thoughts? the .obj file is 16 Mb big. Is
>> there a limit to files size in Meshlab? I would rather not to downsample
>> the mesh to not lose anatomical details.
>>
>> - When using the Transfer Texture to Vertex Color function, the texture
>> gets messed. It seems from web forums that Mshlab takes only one of the (in
>> this case) three .jpg files to do the colouring of the .ply mesh. Does
>> anybody know how to fix this? Another freeware software?
>>
>> - Is there any landmark acquisition software that loads .obj files with
>> textures? So far, I have not been able to do it in Landmark Editor, Evan
>> toolbox, Avizo, Morpho nor Geomorph.
>>
>> Any help is greatly appreciated.
>>
>> Best (y saludos),
>> Viviana
>>
>>
>>
>> --
>>
>> *Viviana Toro-Ibacache DDS MSc PhD*
>> Profesora Asistente *(Assistant Professor)*
>> Centro de Análisis Cuantitativo en Antropología Dental (CA2)
>> Unidad de Anatomía, Instituto de Investigación en Ciencias Odontológicas
>> Facultad de Odontología Universidad de Chile
>>
>> Dirección:  Sergio Livingstone Pohlhammer 943
>> *(address)*   Independencia, Región Metropolitana
>>  Chile
>> Email:mtoroibaca...@odontologia.uchile.cl
>> Web: www.researchgate.net/profile/Viviana_Toro_Ibacache/
>>  www.cienciaymemoria.cl/staff.html
>>
>> --
>> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
>> ---
>> You received this message because you are subscribed to the Google Groups
>> "MORPHMET" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to morphmet+unsubscr...@morphometrics.org.
>>
>
>
>
> --
> __
>
> Antonio Profico
> PhD
> Department of Environmental Biology – Dipartimento di Biologia Ambientale
> SAPIENZA Università di Roma
>
> Lab.  06 4991 2690
> Mob. 3293440766
>
> --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
> ---
> You received this message because you are subscribed to the Google Groups
> "MORPHMET" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to morphmet+unsubscr...@morphometrics.org.
>
>


-- 

*Viviana Toro-Ibacache DDS MSc PhD*
Profesora Asistente *(Assistant Professor)*
Centro de Análisis Cuantitativo en Antropología Dental (CA2)
Unidad de Anatomía, Instituto de Investigación en Ciencias Odontológicas
Facultad de Odontología Universidad de Chile

Dirección:  Sergio Livingstone Pohlhammer 943
*(address)*   Independencia, Región Metropolitana
 Chile
Email:mtoroibaca...@odontologia.uchile.cl
Web: www.researchgate.net/profile/Viviana_Toro_Ibacache/
 www.cienciaymemoria.cl/staff.html

-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.org
--- 
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Re: [MORPHMET] How to export .obj with textures as .ply with colours for morphometric analyses?

[M. Viviana Toro Ibacache]

Dear Bill,

Thanks for your comment. I can now have these considerations for this type
of data (as opposed to think that there was some mesh-exporting method I
was missing).

Best wishes,

Viviana


2016-09-02 14:20 GMT+02:00 Bill Sellers <w...@mac.com>:

> This is actually quite a tricky thing to do. Texturing in OBJ files maps
> part of an image onto a surface triangle. There are no vertices associated
> with the colours. PLY files work differently and each vertex has its own
> colour. To recreate the textures in a PLY file you would need to create a
> new vertex for each pixel in the OBJ file. That would make the file very
> much larger and involve a moderate amount of geometric calculation. I don't
> know of any software package that will do this for you (it isn't
> particularly hard but I doubt there is much demand). However there are
> plenty of software packages that will read textured OBJ files and let you
> make measurements of points on faces (Blender can do this for example). The
> problem is that the process isn't streamlined to make taking large numbers
> of measurements particularly quick and easy. Also I would worry that you
> are losing quite a lot of accuracy in this approach because the 3D position
> will just be linearly interpolated from the vertices and this may give you
> a false sense of the precision of the technique.
>
> Cheers
> Bill
> --
> Bill Sellers, Tel: 01612751719, Mobile: 07857655786,
> http://www.animalsimulation.org
> University of Manchester, D1239 Michael Smith Building, Manchester, M13
> 9PT.
>
> On 01/09/2016 12:31, M. Viviana Toro Ibacache wrote:
>
>> Deal Morphometricians,
>>
>> I have .obj files with textures from three .jpg photos. I can load and
>> see the textures very nicely in Meshlab, but I need the textures to be
>> transformed into a coloured .ply file to do geometric morphometric analyses
>> (the landmarks are represented in the textures). So far it has not worked
>> doing it from Meshlab, so my questions are:
>>
>> - I know I can place landmarks in Meshlab using the .obj file, but when I
>> do it, the software crashes. any thoughts? the .obj file is 16 Mb big. Is
>> there a limit to files size in Meshlab? I would rather not to downsample
>> the mesh to not lose anatomical details.
>>
>> - When using the Transfer Texture to Vertex Color function, the texture
>> gets messed. It seems from web forums that Mshlab takes only one of the (in
>> this case) three .jpg files to do the colouring of the .ply mesh. Does
>> anybody know how to fix this? Another freeware software?
>>
>> - Is there any landmark acquisition software that loads .obj files with
>> textures? So far, I have not been able to do it in Landmark Editor, Evan
>> toolbox, Avizo, Morpho nor Geomorph.
>>
>> Any help is greatly appreciated.
>>
>> Best (y saludos),
>> Viviana
>>
>>
>>
>> --
>> *
>> Viviana Toro-Ibacache DDS MSc PhD*
>> Profesora Asistente /(Assistant Professor)/
>> Centro de Análisis Cuantitativo en Antropología Dental (CA2)
>> Unidad de Anatomía, Instituto de Investigación en Ciencias Odontológicas
>> Facultad de Odontología Universidad de Chile
>>
>> Dirección:  Sergio Livingstone Pohlhammer 943
>> /(address)/   Independencia, Región Metropolitana
>>  Chile
>> Email:mtoroibaca...@odontologia.uchile.cl > mtoroibaca...@odontologia.uchile.cl>
>> Web: www.researchgate.net/profile/Viviana_Toro_Ibacache/ <
>> http://www.researchgate.net/profile/Viviana_Toro_Ibacache/>
>>  www.cienciaymemoria.cl/staff.html <
>> http://www.cienciaymemoria.cl/staff.html>
>>
>> --
>> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
>> ---
>> You received this message because you are subscribed to the Google Groups
>> "MORPHMET" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to morphmet+unsubscr...@morphometrics.org > morphmet+unsubscr...@morphometrics.org>.
>>
>
> --
> MORPHMET may be accessed via its webpage at http://www.morphometrics.org
> --- You received this message because you are subscribed to the Google
> Groups "MORPHMET" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to morphmet+unsubscr...@morphometrics.org.
>
>


-- 

*Viviana Toro-Ibacache DDS MSc PhD*
Profesora Asistente *(Assistant Professor)*
Centro de Análisis Cuantitativo en Antropología Dental (CA2)
Unidad de Anatomía, Instituto de Investigación en Ciencias Odontológicas
Facultad de Odontología Un

[MORPHMET] How to export .obj with textures as .ply with colours for morphometric analyses?

[M. Viviana Toro Ibacache]

Deal Morphometricians,

I have .obj files with textures from three .jpg photos. I can load and see
the textures very nicely in Meshlab, but I need the textures to be
transformed into a coloured .ply file to do geometric morphometric analyses
(the landmarks are represented in the textures). So far it has not worked
doing it from Meshlab, so my questions are:

- I know I can place landmarks in Meshlab using the .obj file, but when I
do it, the software crashes. any thoughts? the .obj file is 16 Mb big. Is
there a limit to files size in Meshlab? I would rather not to downsample
the mesh to not lose anatomical details.

- When using the Transfer Texture to Vertex Color function, the texture
gets messed. It seems from web forums that Mshlab takes only one of the (in
this case) three .jpg files to do the colouring of the .ply mesh. Does
anybody know how to fix this? Another freeware software?

- Is there any landmark acquisition software that loads .obj files with
textures? So far, I have not been able to do it in Landmark Editor, Evan
toolbox, Avizo, Morpho nor Geomorph.

Any help is greatly appreciated.

Best (y saludos),
Viviana



-- 

*Viviana Toro-Ibacache DDS MSc PhD*
Profesora Asistente *(Assistant Professor)*
Centro de Análisis Cuantitativo en Antropología Dental (CA2)
Unidad de Anatomía, Instituto de Investigación en Ciencias Odontológicas
Facultad de Odontología Universidad de Chile

Dirección:  Sergio Livingstone Pohlhammer 943
*(address)*   Independencia, Región Metropolitana
 Chile
Email:mtoroibaca...@odontologia.uchile.cl
Web: www.researchgate.net/profile/Viviana_Toro_Ibacache/
 www.cienciaymemoria.cl/staff.html

-- 
MORPHMET may be accessed via its webpage at http://www.morphometrics.org
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