[SOLVED] How to use the Sofa mesh partition tools?

[Pasquale94]

Hi everyone again, I am sorry if I make a lot of post and questions in these days.
One of my projects consist into simulate a pneumatic finger, made up of two different materials. In particular the overall structure, can be devided in a bottom part made by one material, and an upper part, which is made by a different one.
Of course, I have the surface mesh (file .obj) and the tetrahedral one (file .vtu).
I downloaded from the marketplace the “SOFA_mesh_partitioning_tools”(made by the CSIRO in Australia), and there some things that are not clear for me, because i am very new in mesh generation and partition.
First of all, i am following the file README.md, and I arrived at the point when the python script “test_mesh_generator_python2.py” have to be activated. When I try to call it in the command line, there is this following error, which i don’t understand why:

['openscad', '-osphere_0_0_skin.off', '-Dx=0', '-Dy=0', '-Dz=0', 'movable_sphere2.scad']
Traceback (most recent call last):
  File "test_mesh_generator_python2.py", line 13, in <module>
    subprocess.call(openscad_cmd.split())
  File "/usr/lib/python2.7/subprocess.py", line 172, in call
    return Popen(*popenargs, **kwargs).wait()
  File "/usr/lib/python2.7/subprocess.py", line 394, in __init__
    errread, errwrite)
  File "/usr/lib/python2.7/subprocess.py", line 1047, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

How can I resolve? What is the function of this code?

Then, when I type from the folder “Mesh_pipeline_exact_src” the command ./pipeline2 -i input_files_dir/input_files_demo/ -o output_files_dir/output_files_demo

this error will appear :

Input directory was set to input_files_dir/input_files_demo/.
Output directory was set to output_files_dir/output_files_demo.

prog_opts() done

"input_files_dir/input_files_demo/"is not a directory
tissues.size() = 0
segmentation fault (core dump created)

How can I fix it?

Then, seeing the examples, demo.scn and the finger_edited.py, I understood that my case, is closer to the application of the first scene, that plays with the local stiffness factors, but what I don’t uderstand how to make the mesh partitioning. Someone can guide me into do this?

[Hugo]

Dear @pasquale94

Many questions mean many investigation ongoing with SOFA! That’s good!
Since your question concerns the work from CSIRO and that I am not familiar with it (and apparently some error related to ‘openscad’), let me add Dr. Hockings to the discussions @NickHockings

Best

Hugo

[NickHock]

Hello @pasquale94

looking at the error messages, my first question is : do you have OpenSCAD installed ?
It is cross-platform and free-and-open-source, available here http://www.openscad.org/downloads.html .

Explanation:
The python script makes calls to OpenSCAD, to generate the set of intersecting surface meshes used in the demo.

Edit: I have just spotted that the file “movable_sphere2.scad” is missing from the repository. It is just the following OpenSCAD script:

module movable_sphere2()
{
translate([x,y,z])
sphere(20, $fs = 0.01);
}

movable_sphere2();

Please let me know how you get on.

Best,
Nick

[Pasquale94]

Thank you @nickhockings and @Hugo,

I resolved the first error but the second not. How is possible that it not find the input folder?

Thank you,
Pasquale

[NickHock]

@pasquale94,
It is looking for the input folder using a relative path from where “pipeline2” is run. Two ways it might not find the input folder (i) does the folder exist, (ii) is the relative path correct for where you are running the script.

In the Git repository “SOFA_mesh_partitioning_tools/mesh_pipeline/input_files_dir/input_files_demo/” is already populated with the input files (identical to what would be produced by the “test_mesh_generator_python2.py” script). The instructions imply that you would be in the “SOFA_mesh_partitioning_tools/mesh_pipeline/” directory when calling “Mesh_pipeline_exact_src/pipeline2 -i input_files_dir/input_files_demo/ -o output_files_dir/output_files_demo”

Best,
Nick

[Pasquale94]

Hi @NickHockings

Thank you for the explanation, but now I encountered another error:

terminate called after throwing an instance of 'CGAL::Assertion_exception'
  what():  CGAL ERROR: assertion violation!
Expr: !tree_.empty()
File: /usr/local/include/CGAL/Polyhedral_mesh_domain_3.h
Line: 730
Annullato (core dump creato)

It seems that the variable “tree_” is empty. How can I fix it?

[NickHock]

Hi @pasquale94,

tree_ is internal to CGAL. The problem will be further back in the execution.

Please send me all the terminal output from where you called

Mesh_pipeline_exact_src/pipeline2 -i input_files_dir/input_files_demo/ -o output_files_dir/output_files_demo

…

The main program prints out statements as each section completes.

I need to see these and the whole stack of errors that it gives you.

Best regards,
Nick

[Pasquale94]

Hello @NickHockings

I called the command Mesh_pipeline_exact_src/pipeline2 -i input_files_dir/input_files_demo/ -o output_files_dir/output_files_demo from the folder SOFA_mesh_partitioning_tools-master/mesh_pipeline, this is the output of the terminal:

Mesh_pipeline_exact_src/pipeline2 -i input_files_dir/input_files_demo/ -o output_files_dir/output_files_demo

Input directory was set to input_files_dir/input_files_demo/.
Output directory was set to output_files_dir/output_files_demo.

prog_opts() done

"input_files_dir/input_files_demo/" is a directory containing:
it->filename() : movable_sphere2_25_0_0_skin.off
it->filename() : sphere_0_0_s_kin.off
it->filename() : sphere_0_10_skin.off
it->filename() : sphere_0_30_skin.off
it->filename() : sphere_10_0_bone.off
it->filename() : sphere_10_10_bone.off
it->filename() : sphere_10_30_bone.off
it->filename() : sphere_20_30_tendon.off
it->filename() : sphere_30_30_ligament.off
it->filename() : tissues.yaml

 Reading a yaml file 

Adding : skin	10	tissues.size() : 1
Adding : bone	1000	tissues.size() : 2
Adding : tendon	100	tissues.size() : 3
Adding : ligament	100	tissues.size() : 4
Adding : muscle	10	tissues.size() : 5
Adding : loose_ct	1	tissues.size() : 6

"input_files_dir/input_files_demo/" : Reading meshes

   "input_files_dir/input_files_demo/movable_sphere2_25_0_0_skin.off"		s = movable_sphere2_25_0_0_skin.off	 e = .*skin.*
pushing back
skin->mesh_vec.size() = 1
s = movable_sphere2_25_0_0_skin.off	 e = .*bone.*
s = movable_sphere2_25_0_0_skin.off	 e = .*tendon.*
s = movable_sphere2_25_0_0_skin.off	 e = .*ligament.*
s = movable_sphere2_25_0_0_skin.off	 e = .*muscle.*
s = movable_sphere2_25_0_0_skin.off	 e = .*loose_ct.*

   "input_files_dir/input_files_demo/sphere_0_0_s_kin.off"		s = sphere_0_0_s_kin.off	 e = .*skin.*
s = sphere_0_0_s_kin.off	 e = .*bone.*
s = sphere_0_0_s_kin.off	 e = .*tendon.*
s = sphere_0_0_s_kin.off	 e = .*ligament.*
s = sphere_0_0_s_kin.off	 e = .*muscle.*
s = sphere_0_0_s_kin.off	 e = .*loose_ct.*

   "input_files_dir/input_files_demo/sphere_0_10_skin.off"		s = sphere_0_10_skin.off	 e = .*skin.*
pushing back
skin->mesh_vec.size() = 2
s = sphere_0_10_skin.off	 e = .*bone.*
s = sphere_0_10_skin.off	 e = .*tendon.*
s = sphere_0_10_skin.off	 e = .*ligament.*
s = sphere_0_10_skin.off	 e = .*muscle.*
s = sphere_0_10_skin.off	 e = .*loose_ct.*

   "input_files_dir/input_files_demo/sphere_0_30_skin.off"		s = sphere_0_30_skin.off	 e = .*skin.*
pushing back
skin->mesh_vec.size() = 3
s = sphere_0_30_skin.off	 e = .*bone.*
s = sphere_0_30_skin.off	 e = .*tendon.*
s = sphere_0_30_skin.off	 e = .*ligament.*
s = sphere_0_30_skin.off	 e = .*muscle.*
s = sphere_0_30_skin.off	 e = .*loose_ct.*

   "input_files_dir/input_files_demo/sphere_10_0_bone.off"		s = sphere_10_0_bone.off	 e = .*skin.*
s = sphere_10_0_bone.off	 e = .*bone.*
pushing back
bone->mesh_vec.size() = 1
s = sphere_10_0_bone.off	 e = .*tendon.*
s = sphere_10_0_bone.off	 e = .*ligament.*
s = sphere_10_0_bone.off	 e = .*muscle.*
s = sphere_10_0_bone.off	 e = .*loose_ct.*

   "input_files_dir/input_files_demo/sphere_10_10_bone.off"		s = sphere_10_10_bone.off	 e = .*skin.*
s = sphere_10_10_bone.off	 e = .*bone.*
pushing back
bone->mesh_vec.size() = 2
s = sphere_10_10_bone.off	 e = .*tendon.*
s = sphere_10_10_bone.off	 e = .*ligament.*
s = sphere_10_10_bone.off	 e = .*muscle.*
s = sphere_10_10_bone.off	 e = .*loose_ct.*

   "input_files_dir/input_files_demo/sphere_10_30_bone.off"		s = sphere_10_30_bone.off	 e = .*skin.*
s = sphere_10_30_bone.off	 e = .*bone.*
pushing back
bone->mesh_vec.size() = 3
s = sphere_10_30_bone.off	 e = .*tendon.*
s = sphere_10_30_bone.off	 e = .*ligament.*
s = sphere_10_30_bone.off	 e = .*muscle.*
s = sphere_10_30_bone.off	 e = .*loose_ct.*

   "input_files_dir/input_files_demo/sphere_20_30_tendon.off"		s = sphere_20_30_tendon.off	 e = .*skin.*
s = sphere_20_30_tendon.off	 e = .*bone.*
s = sphere_20_30_tendon.off	 e = .*tendon.*
pushing back
tendon->mesh_vec.size() = 1
s = sphere_20_30_tendon.off	 e = .*ligament.*
s = sphere_20_30_tendon.off	 e = .*muscle.*
s = sphere_20_30_tendon.off	 e = .*loose_ct.*

   "input_files_dir/input_files_demo/sphere_30_30_ligament.off"		s = sphere_30_30_ligament.off	 e = .*skin.*
s = sphere_30_30_ligament.off	 e = .*bone.*
s = sphere_30_30_ligament.off	 e = .*tendon.*
s = sphere_30_30_ligament.off	 e = .*ligament.*
pushing back
ligament->mesh_vec.size() = 1
s = sphere_30_30_ligament.off	 e = .*muscle.*
s = sphere_30_30_ligament.off	 e = .*loose_ct.*

   "input_files_dir/input_files_demo/tissues.yaml"		Not a .off file "input_files_dir/input_files_demo/tissues.yaml"

 Finished reading meshed 

 tissues.size() = 6
 tissues.begin()->name = skin
 tissues.begin()->mesh_vec.size() = 3
 
load_surface_meshes() done

out_dir = output_files_dir/output_files_demo
"output_files_dir/output_files_demo"is not a directory
subdomain_meshes.begin()->mesh_vec.begin()->is_empty()  = 0

tissue_it_a = 0

tissue_it_d = 1

tissue_it_d = 2

tissue_it_d = 3

 target patch : 1_0

tissue_it_a = 1

tissue_it_b = 0	
tissue_it_c = 0	continue
target.mesh_vec.at(1).is_empty() = 0

 target patch : 1_2
tissue_it_d = 0

tissue_it_d = 2

tissue_it_d = 3

 target patch : 2_0

tissue_it_a = 2

tissue_it_b = 0	
tissue_it_c = 0	continue

tissue_it_c = 1target.mesh_vec.at(1).is_empty() = 0

 target patch : 1_3
tissue_it_b = 1	
tissue_it_c = 0
tissue_it_c = 1	continue
target.mesh_vec.at(1).is_empty() = 0

 target patch : 2_3
tissue_it_d = 0

tissue_it_d = 1

tissue_it_d = 3

 target patch : 3_0

tissue_it_a = 3

tissue_it_b = 0	
tissue_it_c = 0	continue

tissue_it_c = 1
tissue_it_c = 2target.mesh_vec.at(1).is_empty() = 0

 target patch : 1_4
tissue_it_b = 1	
tissue_it_c = 0
tissue_it_c = 1	continue

tissue_it_c = 2target.mesh_vec.at(1).is_empty() = 0

tissue_it_b = 2	
tissue_it_c = 0
tissue_it_c = 1
tissue_it_c = 2	continue
target.mesh_vec.at(1).is_empty() = 0

 target patch : 3_4
tissue_it_d = 0

tissue_it_d = 1

tissue_it_d = 2

 target patch : 4_0
generate_subdomain_meshes() done

 idx = 0, new_pair_vec.size() = 2
 idx = 1, new_pair_vec.size() = 3
 idx = 2, new_pair_vec.size() = 4
 idx = 3, new_pair_vec.size() = 5
 idx = 4, new_pair_vec.size() = 6
 idx = 5, new_pair_vec.size() = 7
 idx = 6, new_pair_vec.size() = 8
 idx = 7, new_pair_vec.size() = 9
 idx = 8, new_pair_vec.size() = 10
pair_vec[0] = (1,0)
pair_vec[1] = (1,2)
pair_vec[2] = (2,0)
pair_vec[3] = (1,3)
pair_vec[4] = (2,3)
pair_vec[5] = (3,0)
pair_vec[6] = (1,4)
pair_vec[7] = (3,4)
pair_vec[8] = (4,0)
new_pair_vec[0] = (1,0)
new_pair_vec[1] = (1,0)
new_pair_vec[2] = (1,2)
new_pair_vec[3] = (2,0)
new_pair_vec[4] = (1,3)
new_pair_vec[5] = (2,3)
new_pair_vec[6] = (3,0)
new_pair_vec[7] = (1,4)
new_pair_vec[8] = (3,4)
new_pair_vec[9] = (4,0)
mkvec_cc() done

patch_vec.size() = 10	pair_vec.size() = 10

 Wrote filename :output_files_dir/output_files_demo/patch0.off
i=0	patch_vec.at(i).is_valid()  = 1	patch_vec.at(i).is_empty()  = 0	patch_vec.at(i).number_of_faces   1201
	patches.at(i).is_valid()  = 1	patches.at(i).is_empty()  = 1	patches.at(i).size_of_facets()  = 0	patches.at(i) num facets  = 0	patch_vec.at(i).number_of_faces   1201

 Wrote filename :output_files_dir/output_files_demo/patch1.off
i=1	patch_vec.at(i).is_valid()  = 1	patch_vec.at(i).is_empty()  = 0	patch_vec.at(i).number_of_faces   764
	patches.at(i).is_valid()  = 1	patches.at(i).is_empty()  = 1	patches.at(i).size_of_facets()  = 0	patches.at(i) num facets  = 0	patch_vec.at(i).number_of_faces   764

 Wrote filename :output_files_dir/output_files_demo/patch2.off
i=2	patch_vec.at(i).is_valid()  = 1	patch_vec.at(i).is_empty()  = 0	patch_vec.at(i).number_of_faces   1131
	patches.at(i).is_valid()  = 1	patches.at(i).is_empty()  = 1	patches.at(i).size_of_facets()  = 0	patches.at(i) num facets  = 0	patch_vec.at(i).number_of_faces   1131

 Wrote filename :output_files_dir/output_files_demo/patch3.off
i=3	patch_vec.at(i).is_valid()  = 1	patch_vec.at(i).is_empty()  = 0	patch_vec.at(i).number_of_faces   1398
	patches.at(i).is_valid()  = 1	patches.at(i).is_empty()  = 1	patches.at(i).size_of_facets()  = 0	patches.at(i) num facets  = 0	patch_vec.at(i).number_of_faces   1398

 Wrote filename :output_files_dir/output_files_demo/patch4.off
i=4	patch_vec.at(i).is_valid()  = 1	patch_vec.at(i).is_empty()  = 0	patch_vec.at(i).number_of_faces   96
	patches.at(i).is_valid()  = 1	patches.at(i).is_empty()  = 1	patches.at(i).size_of_facets()  = 0	patches.at(i) num facets  = 0	patch_vec.at(i).number_of_faces   96

 Wrote filename :output_files_dir/output_files_demo/patch5.off
i=5	patch_vec.at(i).is_valid()  = 1	patch_vec.at(i).is_empty()  = 0	patch_vec.at(i).number_of_faces   415
	patches.at(i).is_valid()  = 1	patches.at(i).is_empty()  = 1	patches.at(i).size_of_facets()  = 0	patches.at(i) num facets  = 0	patch_vec.at(i).number_of_faces   415

 Wrote filename :output_files_dir/output_files_demo/patch6.off
i=6	patch_vec.at(i).is_valid()  = 1	patch_vec.at(i).is_empty()  = 0	patch_vec.at(i).number_of_faces   431
	patches.at(i).is_valid()  = 1	patches.at(i).is_empty()  = 1	patches.at(i).size_of_facets()  = 0	patches.at(i) num facets  = 0	patch_vec.at(i).number_of_faces   431

 Wrote filename :output_files_dir/output_files_demo/patch7.off
i=7	patch_vec.at(i).is_valid()  = 1	patch_vec.at(i).is_empty()  = 0	patch_vec.at(i).number_of_faces   118
	patches.at(i).is_valid()  = 1	patches.at(i).is_empty()  = 1	patches.at(i).size_of_facets()  = 0	patches.at(i) num facets  = 0	patch_vec.at(i).number_of_faces   118

 Wrote filename :output_files_dir/output_files_demo/patch8.off
i=8	patch_vec.at(i).is_valid()  = 1	patch_vec.at(i).is_empty()  = 0	patch_vec.at(i).number_of_faces   362
	patches.at(i).is_valid()  = 1	patches.at(i).is_empty()  = 1	patches.at(i).size_of_facets()  = 0	patches.at(i) num facets  = 0	patch_vec.at(i).number_of_faces   362

 Wrote filename :output_files_dir/output_files_demo/patch9.off
i=9	patch_vec.at(i).is_valid()  = 1	patch_vec.at(i).is_empty()  = 0	patch_vec.at(i).number_of_faces   696
	patches.at(i).is_valid()  = 1	patches.at(i).is_empty()  = 1	patches.at(i).size_of_facets()  = 0	patches.at(i) num facets  = 0	patch_vec.at(i).number_of_faces   696

pair_vec[0] = (1,0)
pair_vec[1] = (1,0)
pair_vec[2] = (1,2)
pair_vec[3] = (2,0)
pair_vec[4] = (1,3)
pair_vec[5] = (2,3)
pair_vec[6] = (3,0)
pair_vec[7] = (1,4)
pair_vec[8] = (3,4)
pair_vec[9] = (4,0)

Generating domain

terminate called after throwing an instance of 'CGAL::Assertion_exception'
  what():  CGAL ERROR: assertion violation!
Expr: !tree_.empty()
File: /usr/local/include/CGAL/Polyhedral_mesh_domain_3.h
Line: 730
Annullato (core dump creato)

Thank you for the support,

Pasquale.

[NickHock]

Hi @pasquale94

I think the fault is here :

out_dir = output_files_dir/output_files_demo
“output_files_dir/output_files_demo”is not a directory
subdomain_meshes.begin()->mesh_vec.begin()->is_empty() = 0

You need to create the directory “output_files_dir/output_files_demo”.
(This is partly because Git does not like me leaving an empty directory in the repository.)

Best regards,
Nick

[Pasquale94]

Hi @NickHockings

Thank you for the support! It works now… But I still have a question.
I want to make a mesh partition of a soft robotic finger, because it is made by two different material. So, my question is, How to do that, how I can differentiate the domains that I want in the mesh? And then, I have to do this with the surface mesh or the volumetric one?

I am sorry fo all this question, but I am very new in this field.
Happy Sunday!

Pasquale.

[NickHock]

Hi @pasquale94,

Good to hear that you have it working now.

Short answer:
The domains are differentiated by keywords in their file names, defined in the .yaml file. The input files need to be .off surface meshes.

Long Answer:

The way that it works is that it takes in a set of surface meshes, and uses them to define the partitioned tetrahedral mesh that it generates.

The surface meshes are divided into one group for each material. A surface mesh is identified as belonging to a particular material by the keyword at the end of its filename. e.g. “myFirstMesh_bone.ply” and “mySecondMesh_bone.ply” are both in the “bone” group. The members of each group are ‘union’ed to make a single surface mesh for each material.

These surface meshes defining each material are the subtracted from each other in order of precedence. The keywords of the materials and their order of precedence is defined in the .yaml file. The result of this step is a set of surface patch meshes that define the boundaries between each material.

The final step uses these patches to generate the partitioned tetrahedral mesh.
Note there are “mesh specification options” that define qualities of the tetrahedral mesh, including element size and facet angle. The right values depend on the scale of your input meshes, and the resolution you desire for the partitioned tetrahedral mesh.

After that you need to follow the “Building a SOFA scene with a partitioned mesh:” instructions. Look at the “multi-stiffness_FEM_demo\demo.scn” file to see how the partitioned mesh is used, and don’t forget to do the “Manual editing of .vtu file xml tags 64bit -> 32bit”.

Best regards,
Nick

[Pasquale94]

Hi @NickHockings

Thank you for all the support, noe I understand and all my doubts are clear, I alo created my partitioned mesh and everything works. Thank you very much!

Best,
Pasquale.

[NickHock]

Hi @pasquale94,

That’s great to hear. Please send screen shots and videos to @hugo. He is always looking for images for the SOFA gallery. NB the SOFA GUI has options for capturing video.

Best,
Nick

[Hugo]

Ouh yeah! Do not hesitate to send me videos so that I can highlight both of your work!
Congrats @pasquale94 and @NickHockings for helping so much!

Hugo

[Pasquale94]

Hello @NickHockings and @Hugo.

The projects are at an early stage for now, but in the next months we have other results, and our group is growing, so of course we will send you our highlights and material.

Thank you for the interest!

Best,
Pasquale Ferrentino.

[Author]

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