Re: [iso2mesh-users] Problem with node coordinates - mesh size

[Qianqian Fang]

On 04/18/2013 05:37 AM, Neis Alexander Lugo Ramirez wrote:
> Hi Qianqian and hi all,
>
> I've been working with Iso2mesh to generate a volumetric mesh that
> later will be imported to Abaqus. The input that I'm using is a 3D
> binary array which I've obtained from a different Matlab code (that
> basically creates the 3D array based on a full set of images).
>
> My question is: How can I control the size of the mesh in terms of
> measures (micrometers, mm, cm)? When I import the geometry to Abaqus,
> I'm getting nodes coordinates that don't match with the original size
> of my sample. I don't even know if Iso2mesh is using 'mm' or 'cm' to
> generate the coordinates. Is there a way to control these parameters?
>

hi Neis

the output mesh from v2m/v2s is defined in the input volumetric grid space.
In other words, the unit of the coordinates is in "grid/voxel" unit.

if your voxel dimension has a physical unit, you should scale the x/y/z
of the node array to convert the mesh from the grid space to the physical
space.


> PD: I've been playing with different values such as 'distbound',
> 'angbound' and 'radbound', but apparently these parameters control the
> mesh density (i.e. coarse or refined mesh but the size is still the same).

distbound/radbound are also defined in the grid/voxel unit;
angbound is defined with a radian unit.

let me know if these answer your question.

Qianqian

>
> I will appreciate if any of you can help me
>
> Thank you
>
> And please receive my best regards,
>
> Neis
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[Neis Alexander Lugo Ramirez]

Hi Qianqian,

Thanks for your reply!

My images are supposed to have a 2.7 micrometers voxel sixe. I've now used the options 'opt.A' and 'opt.B' to scale the original array to 2.7 micrometers. I don't know if I did it right, but apparently is working. I basically used opt.A=diag([2.7,2.7,2.7]) and opt.B=zeros(3,1) as you had previously proposed in a different topic to another person. Hopefully, this is ok.

Another doubt that I have, it is related with the parameters distbound, radbound and angbound. If I want to have tetrahedral elements of about the same size (equilateral), would it be correct the following:
angbound=60 degrees (that is the angle in an equilateral triangle)
distbound=0 (as the circumcenter of the triangle coincides with the center of the Delaunay circumference) 
radbound=I've measured the radius of the Delaunay circle?

I think the mesh that I'm obtainig is too coarse.

I hope for your answer

Regards,

PD: Thanks for your reply and for creating this amazing tool. It's been extremely useful in my master thesis research.

On Thursday, April 18, 2013 11:37:00 AM UTC+2, Neis Alexander Lugo Ramirez wrote:

Hi Qianqian and hi all,

I've been working with Iso2mesh to generate a volumetric mesh that later will be imported to Abaqus. The input that I'm using is a 3D binary array which I've obtained from a different Matlab code (that basically creates the 3D array based on a full set of images).

My question is: How can I control the size of the mesh in terms of measures (micrometers, mm, cm)? When I import the geometry to Abaqus, I'm getting nodes coordinates that don't match with the original size of my sample. I don't even know if Iso2mesh is using 'mm' or 'cm' to generate the coordinates. Is there a way to control these parameters?

PD: I've been playing with different values such as 'distbound', 'angbound' and 'radbound', but apparently these parameters control the mesh density (i.e. coarse or refined mesh but the size is still the same).

[Qianqian Fang]

On 04/19/2013 03:50 AM, Neis Alexander Lugo Ramirez wrote:

Hi Qianqian,

Thanks for your reply!

My images are supposed to have a 2.7 micrometers voxel sixe. I've now used the options 'opt.A' and 'opt.B' to scale the original array to 2.7 micrometers. I don't know if I did it right, but apparently is working. I basically used opt.A=diag([2.7,2.7,2.7]) and opt.B=zeros(3,1) as you had previously proposed in a different topic to another person. Hopefully, this is ok.

yes, that seems to be correct.

Another doubt that I have, it is related with the parameters distbound, radbound and angbound. If I want to have tetrahedral elements of about the same size (equilateral), would it be correct the following:
angbound=60 degrees (that is the angle in an equilateral triangle)
distbound=0 (as the circumcenter of the triangle coincides with the center of the Delaunay circumference) 
radbound=I've measured the radius of the Delaunay circle?

the explanations of these parameters can be found in this link:

http://www.cgal.org/Manual/latest/doc_html/cgal_manual/Surface_mesher/Chapter_main.html#Subsection_48.3.1

the settings you pass to iso2mesh will be simply passed on to
the cgal utilities to interpret.

for your purposes, I believe you should set distbound to a
large number (which will effectively ignore this constraint), and set
radbound to the radius of a sphere enclosing an element of
your target size V (basically, r=~ sqrt(3)/2*[(2*V)^(1/3)], see [1])

although angbound=60 looks right for your requirement, the
mesher will likely fail to converge within finite time.

I think the mesh that I'm obtainig is too coarse.

recently, Peter Varga helped me create an updated cgalmesh
binary. It has better sizing field control, see svn commit logs:

http://iso2mesh.svn.sourceforge.net/viewvc/iso2mesh?view=revision&revision=398
http://iso2mesh.svn.sourceforge.net/viewvc/iso2mesh?view=revision&revision=400

if you are interested, please check out the latest svn to test.
an example to use the new features can be found here:

http://iso2mesh.svn.sourceforge.net/viewvc/iso2mesh/trunk/iso2mesh/sample/demo_label_sizing.m?view=markup&pathrev=400

Qianqian


[1] http://www.kjmaclean.com/Geometry/StarTetrahedron.html

I hope for your answer

Regards,

PD: Thanks for your reply and for creating this amazing tool. It's been extremely useful in my master thesis research.


On Thursday, April 18, 2013 11:37:00 AM UTC+2, Neis Alexander Lugo Ramirez wrote:

Hi Qianqian and hi all,

I've been working with Iso2mesh to generate a volumetric mesh that later will be imported to Abaqus. The input that I'm using is a 3D binary array which I've obtained from a different Matlab code (that basically creates the 3D array based on a full set of images).

My question is: How can I control the size of the mesh in terms of measures (micrometers, mm, cm)? When I import the geometry to Abaqus, I'm getting nodes coordinates that don't match with the original size of my sample. I don't even know if Iso2mesh is using 'mm' or 'cm' to generate the coordinates. Is there a way to control these parameters?

PD: I've been playing with different values such as 'distbound', 'angbound' and 'radbound', but apparently these parameters control the mesh density (i.e. coarse or refined mesh but the size is still the same).

I will appreciate if any of you can help me

Thank you
 
And please receive my best regards,

Neis

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[Neis Alexander Lugo Ramirez]

Hi Qianqian,

Thank you for your response! I've now understood some things. May I ask you something else? Is the 'cgalmesh' option valid even if I'm using the 'opt' parameter? I've encountered some errors trying to run vol2mesh with both parameters activated. Why is that?