Voxelization #1209

hadjiszs · 2016-09-30T13:18:55Z

PR Description

Algorithm

I traverse all voxels V of triangle bounding box and insert in digital set if V overlaps current triangle.
I use intersection target (samuli laine) to know if a voxel overlaps a triangle.

6-separated

foreach triangle ABC
    foreach blue segment S of intersection target set
        2D projection of ABC on the plane of normal N(x,y,z)
        corresponding to S, just by ignoring coordinate

        foreach voxel V of ABC bounding box
            2D projection of V
            if 2D V is inside 2D triangle ABC
                insert V in digitalSet

26-separated

It's the same algorithm but I do differently of 6-separated way for projections.

foreach triangle ABC
    foreach blue segment S of intersection target set
        compute e1 and e2 to have a base with each normal N(x,y,z)
        corresponding to S, so
            e1 = (-y, x, 0)
            e2 = (-xz, -yz, x^2)

        2D projection of A B and C on plane (0, e1, e2)
        foreach voxel V of ABC bounding box
            2D projection of V on plane (0, e1, e2)
            if 2D V is inside 2D triangle ABC
                insert V in digitalSet

Checklist

Unit-test of your feature with Catch.
Doxygen documentation of the code completed (classes, methods, types, members...)
Documentation module page added or updated.
New entry in the ChangeLog.md added.
No warning raised in Debug cmake mode (otherwise, Travis C.I. will fail).
All continuous integration tests pass (Travis & appveyor)

kerautret · 2016-09-30T13:53:45Z

Thanks! and also to the tools I look it this week end!

copyme · 2016-09-30T13:57:29Z

Can you provide information about the implemented algorithm?

dcoeurjo · 2016-09-30T13:59:35Z

@kerautret and @copyme please hold on. @hadjiszs is an intern I have at Lyon and the code is not ready for review.

I asked @hadjiszs to PR to be able to discuss on his code.

kerautret · 2016-09-30T14:01:02Z

ok let me know when ready but that nice idea ;)

minor change

… voxelization

dcoeurjo · 2016-10-03T09:24:43Z

@hadjiszs have you checked the « allow edits from maintainers » when you've created your Pull-Request ?

hadjiszs · 2016-10-03T10:28:15Z

@dcoeurjo sorry I didn't know this option, but it seems checked

screenshot:

dcoeurjo · 2016-10-12T16:39:45Z

@hadjiszs : since we do not optimize the intersection tests for adjacent triangles, I suggest to remove the mesh from the constructor and add a "voxelise(Mesh)" method.
You could thus voxelise different meshes and get a unique digital set at the end. What do you think?

hadjiszs · 2016-10-16T15:50:05Z

@dcoeurjo yes I think it's ok, maybe with a "add(Mesh)" method, and a voxelize() method?

to be able to do something like that:

MeshVoxelizer mv(...);

Mesh3 aMesh1(...);
Mesh3 aMesh2(...);
Mesh3 aMesh3(...);

mv.add(aMesh1);
mv.add(aMesh2);
mv.add(aMesh3);

mv.voxelize(); // to be able to have a parallelization on list of mesh in voxelize() method

by the way, I try to fix last build fail of travis, but I really don't understand error about DGtal::HDF5Reader https://travis-ci.org/DGtal-team/DGtal/jobs/167108444#L1111

dcoeurjo · 2016-10-16T16:09:28Z

Even simpler:

MeshVoxeliser mv(domain);

mv.voxelise (aMesh1);
mv.voxelise(aMesh2);

Point a(...),b(...),c(...);

//add a unique triangle
mv.voxelise(a,b,c);

..

no need to keep the meshes (or a ref to) as members.

dcoeurjo · 2016-10-16T16:09:56Z

Don't bother with the HDF5 issue, I'll have a look.

thx

hadjiszs · 2016-10-17T06:36:18Z

sorry I haven't explained my example,
it was to have a parallel processing on list of meshes within voxelize method

something like that (in voxelize method)

#omp parallel for // just for example with openmp syntax
foreach mesh M
    // .. voxelization of M into digitalSet

To let programmer add/remove meshes in MeshVoxelizer, and he chooses when he wants to run parallel voxelization of all current list of meshes he established. With that, he can have a parallel voxelization of a set of meshes

but, there is no parallelism in MeshVoxelizer yet, so my proposition is useless for now and I think it would be eventually for later, and I will do like you said as of now

dcoeurjo · 2016-10-19T07:26:15Z

I've updated the interface. Your tool may be deprecated now.

dcoeurjo · 2017-11-18T12:59:58Z

can someone review this dude too ?

…ation

kerautret

first part of the review I will finish it tomorrow ;)

kerautret · 2017-11-18T22:51:15Z

src/DGtal/shapes/doc/moduleMeshVoxelization.dox

+
+The approach is rather simple: Given a triangulated mesh, the
+MeshVoxlizer processes each triangle independently. If the triangle
+intersects a given @a template centered ot a given grid point, then


ot a given grid -> at a given grid

kerautret · 2017-11-18T22:53:59Z

src/DGtal/shapes/doc/moduleMeshVoxelization.dox

+
+\section sectVoxelization2 Basic Usage
+
+Given a Mesh @a aMesh, the MeshVoxelizer class is template by a


is templateD

kerautret · 2017-11-18T22:59:18Z

src/DGtal/shapes/doc/moduleMeshVoxelization.dox

+
+@snippet examples/shapes/exampleMeshVoxelizer.cpp MeshVoxelizerDig
+
+Once exported


"Once exported with :" ?

kerautret · 2017-11-18T23:01:47Z

src/DGtal/shapes/doc/moduleMeshVoxelization.dox

+
+we obtain the following voxel set:
+
+@image html resultCube.png "Resulting voxelSet (quad faces triangulated by the viewer)"


perhaps could you just use an export in off format and the visualize it with the DGtalTools meshViewer (to avoid to display triangle)..

by the way perhaps having another example with bunny or other will be nice to illustrate such new nice work ;)!

Here are some examples given from my tests that you can use:
(obtained by using bunny at scale 1 but manually changing scale of bunny (basicEditMesh --scale 300 -I bunny.off -o test.off and by using 6 and 26 template)

if you use an imported mesh in the examples simply use:

#include <DGtal/io/readers/MeshReader.h> aMesh << "bunny.off";

and then simply output in sdp format and display it with 3dSDPViewer for instance.

kerautret · 2017-11-18T23:15:16Z

src/DGtal/shapes/doc/moduleMeshVoxelization.dox

+
+We then create a voxelization of a scaled version of the cube onto a
+@f$ 128^3@f$ domain:
+


could you add the header mention (#include "DGtal/shapes/MeshVoxelizer.h") just before this code ?

kerautret

done, that is nice new features!
Just see some small assert add for the domain and then we can merge.

kerautret · 2017-11-19T08:50:51Z

src/DGtal/shapes/IntersectionTarget.h

+  /**
+     Description of template class 'IntersectionTarget'
+
+     \brief Aim: A class for intersection target used on voxelization


"used for" ?
and mention MeshVoxelizer in parenthesis @see MeshVoxelizer ?

kerautret · 2017-11-19T09:18:43Z

src/DGtal/shapes/MeshVoxelizer.h

+     * @param [out] outputSet the set that collects the voxels.
+     * @param [in] aMesh the mesh to voxelize (vertex coordinates will
+     * be casted to @e PointR3 points.
+     * @param [in] scaleFactor the scale factor to apply to the mesh


for this parameter perhaps you have to alter to be careful to not use a value compatible with the domain of the digital set, else we have an error... (or/and detect it explicitly later ?)

what do you mean ?
That the scale may induce voxels outside the set domain ?

sorry something was auto completed with my editor, or I was very tired ;)
I was thinking that you could add a user warning in the doc to avoid this potential error. But with the last change, we can simply mention that outside domain voxel are ignored ?

kerautret · 2017-11-19T09:19:10Z

src/DGtal/shapes/MeshVoxelizer.h

+     * @param [in] a the first point of the triangle
+     * @param [in] b the second point of the triangle
+     * @param [in] c the third point of the triangle
+     * @param [in] scaleFactor the scale factor to apply to the triangle (default=1.0)


kerautret · 2017-11-19T09:28:45Z

src/DGtal/shapes/MeshVoxelizer.ih

+
+          // check if current voxel projection is inside ABC projection
+          if(pointIsInside2DTriangle(AA, BB, CC, pp) != OUTSIDE)
+            outputSet.insert(v);


here I got an error if the scaleFactor is too large (v is outside the output domain, see previous remarks).

kerautret · 2017-11-19T09:40:32Z

src/DGtal/shapes/MeshVoxelizer.ih

+  A = a*scaleFactor;
+  B = b*scaleFactor;
+  C = c*scaleFactor;
+


perhaps add an assert to check if the points are in the digital set domain ?

yeah thanks.

Ok I've slightly changed the interface: I first check that the voxel is inside the domain or not before the insert. Hence, no more issue with the domain but if a voxel is outside the set, it is simply skipped.
Fine for you ?

dcoeurjo · 2017-11-20T08:31:34Z

Thanks for your comments.

dcoeurjo · 2017-11-20T08:32:49Z

Could you please generate the images with the bunny and 2 digitizations using different resolution (I'm not familiar with the mesh viewer) ?
This would be very nice for the module doc.

…ation

kerautret · 2017-11-20T13:09:39Z

Could you please generate the images with the bunny and 2 digitizations using different resolution (I'm not familiar with the mesh viewer) ?
This would be very nice for the module doc.

yes is what you want ?

dcoeurjo · 2017-11-23T10:47:51Z

thx @kerautret

dcoeurjo · 2017-11-24T08:36:00Z

I've updated the doc with the bunny images. Would it be fine for you ?

dcoeurjo · 2017-12-02T10:07:06Z

@kerautret is it fine for you?

kerautret

yes nice thanks just a typo, sorry for the delay ;(

kerautret · 2017-12-02T10:31:14Z

src/DGtal/shapes/doc/moduleMeshVoxelization.dox

@@ -84,6 +84,11 @@ be automatically triangulated using a naive fan approach. Hence, if
 the face in not planar and/or convex, the resulting digitization might
 be incorrect.

+Here you have another example with a more complex mesh (using DGtaltools tools for visualization):
+
+@image html bunnies.png "Voxelization at different resolution of a Stanford Bunny."


different resolutionS ?

kerautret · 2017-12-02T12:47:54Z

thanks looks fine, just waiting for travis and merging....

dcoeurjo · 2017-12-04T12:41:28Z

travis done ;)
merging

hadjiszs added 2 commits September 29, 2016 03:46

basic voxelization

3103dbb

minor change

eb27240

dcoeurjo self-assigned this Sep 30, 2016

dcoeurjo added Geometry FeatureRequest waiting author feedbacks and removed FeatureRequest labels Sep 30, 2016

hadjiszs added 3 commits September 30, 2016 19:14

Update MeshVoxelizer.h

4e9663c

minor change

fix debug warn

67c1b67

Merge branch 'voxelization' of https://github.com/hadjiszs/DGtal into…

6215672

… voxelization

hadjiszs and others added 4 commits October 6, 2016 06:00

fix doxygen warn

bbc3cca

Refactoring the code

d2edf68

Refactoring again

1d9e75a

minor rename and fix doxygen warn

cc50654

minor edits

db41176

Changing interface

9326508

dcoeurjo added 2 commits October 19, 2016 09:35

fixing BBOX computation

5c46393

Merge branch 'masterDGTal' into voxelization

0fcb6c9

dcoeurjo added 3 commits November 16, 2017 10:30

changelog

f05777a

Fixing build issue

15379e7

Fixing build issue

3cb479f

dcoeurjo added 2 commits November 18, 2017 14:06

merge

371a927

Merge branch 'voxelization' of github.com:hadjiszs/DGtal into voxeliz…

8bb1d2d

…ation

kerautret self-requested a review November 18, 2017 22:46

kerautret reviewed Nov 19, 2017

View reviewed changes

kerautret requested changes Nov 19, 2017

View reviewed changes

kerautret added waiting author feedbacks and removed ready for review 👍 labels Nov 19, 2017

dcoeurjo added 2 commits November 20, 2017 09:33

Fixing issues

da49226

Merge branch 'voxelization' of github.com:hadjiszs/DGtal into voxeliz…

7f2c4ff

…ation

kerautret approved these changes Nov 23, 2017

View reviewed changes

Figs

b8bdc0a

dcoeurjo added ready for review 👍 and removed waiting author feedbacks labels Nov 24, 2017

kerautret approved these changes Dec 2, 2017

View reviewed changes

dcoeurjo and others added 2 commits December 2, 2017 11:38

typo

adba706

Minor typo on README.md

5b1b71d

dcoeurjo merged commit 8c2c800 into DGtal-team:master Dec 4, 2017

hadjiszs mentioned this pull request Dec 6, 2017

add mesh voxelizer DGtal-team/DGtalTools#279

Merged

6 tasks


		\section sectVoxelization2 Basic Usage

		Given a Mesh @a aMesh, the MeshVoxelizer class is template by a


		@snippet examples/shapes/exampleMeshVoxelizer.cpp MeshVoxelizerDig

		Once exported


		we obtain the following voxel set:

		@image html resultCube.png "Resulting voxelSet (quad faces triangulated by the viewer)"


		We then create a voxelization of a scaled version of the cube onto a
		@f$ 128^3@f$ domain:

Voxelization #1209

Voxelization #1209

Conversation

hadjiszs commented Sep 30, 2016 • edited by dcoeurjo Loading

PR Description

Algorithm

6-separated

26-separated

Checklist

kerautret commented Sep 30, 2016

copyme commented Sep 30, 2016

dcoeurjo commented Sep 30, 2016 • edited Loading

kerautret commented Sep 30, 2016

dcoeurjo commented Oct 3, 2016

hadjiszs commented Oct 3, 2016

dcoeurjo commented Oct 12, 2016

hadjiszs commented Oct 16, 2016 • edited Loading

dcoeurjo commented Oct 16, 2016

dcoeurjo commented Oct 16, 2016

hadjiszs commented Oct 17, 2016

dcoeurjo commented Oct 19, 2016

dcoeurjo commented Nov 18, 2017

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dcoeurjo commented Nov 20, 2017

dcoeurjo commented Nov 20, 2017

kerautret commented Nov 20, 2017

dcoeurjo commented Nov 23, 2017

dcoeurjo commented Nov 24, 2017

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kerautret commented Dec 2, 2017

dcoeurjo commented Dec 4, 2017

hadjiszs commented Sep 30, 2016 •

edited by dcoeurjo

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dcoeurjo commented Sep 30, 2016 •

edited

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hadjiszs commented Oct 16, 2016 •

edited

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