Issue of extracting isosurfaces from voxel data using the MC algorithm.

[gecpgecp]

Thanks for your help:
Why do the iso extracted using the MC algorithm have some small holes（As shown in the figure below）?
I suspect these holes are due to missing faces or reversed normal vectors. Mesh.topology.isClosed() also shows that it's not closed.

data as follow:
t.zip
code as follow:

#include "MRMesh/MRMesh.h"
#include "MRMesh/MRMeshSave.h"
#include "MRMesh/MRMeshLoad.h"
#include <MRVoxels/MRVoxelsSave.h>
#include <MRVoxels/MRVoxelsLoad.h>
#include <MRMarchingCubes.h>
#include <iostream>
using namespace MR;
using namespace MR::VoxelsSave;
int main()
{

    MR::VoxelsLoad::LoadingTiffSettings loadTiffSetting = { .dir = "d:/t",.voxelSize = {0.0333333,0.0333333,0.03333333},
    .cb = [](float pro)->bool {
        std::cout << "load pro:" << pro * 100 << std::endl;
        return true;
        }
    };

    auto voxelLoadRes = MR::VoxelsLoad::loadTiffDir(loadTiffSetting);
    if (voxelLoadRes.has_value() == false) {
        std::cerr << voxelLoadRes.error() << std::endl;
        system("pause");
    }
    VdbVolume& volum = *voxelLoadRes;
    MR::MarchingCubesParams mcParam = { .iso = 20000};
    mcParam.cb = [](float pro)->bool {
        std::cout << "mc pro:" << pro * 100 << std::endl;
        return true;
        };
    auto mcRes = MR::marchingCubes(volum, mcParam);
    Mesh& meshMC = mcRes.value();
    
    printf("closed:%d\n", meshMC.topology.isClosed());
    MeshSave::toAnySupportedFormat(meshMC, "d:/t.ply");
    system("pause");
    return 0;
}

[Grantim]

Hello!

The reason behind this holes are zero values being marked as inactive and are not participating in marching cubes algorithm

To solve this you can either convert VdbVolume to SimpleVolume (vdbVolumeToSimpleVolume function) before using marching cubes, or mark all voxels in desired dimensions as active with opnvdb functions, somehow like this:

MeshLib/source/MRVoxels/MRObjectVoxels.cpp

Lines 345 to 368 in c30f894

	openvdb::CoordBBox activeVdbBox;
	activeVdbBox.min() = openvdb::Coord( activeBox.min.x, activeBox.min.y, activeBox.min.z );
	activeVdbBox.max() = openvdb::Coord( activeBox.max.x - 1, activeBox.max.y - 1, activeBox.max.z - 1 );
	// create active mask tree
	openvdb::TopologyTree topologyTree;
	reportProgress( cb, cbModifier * 0.25f );
	// update topology tree with new active box
	topologyTree.sparseFill( activeVdbBox, true );
	reportProgress( cb, cbModifier * 0.5f );
	// deactivate all of current grid
	openvdb::tools::foreach( vdbVolume_.data->tree().beginValueOn(), [] ( const openvdb::FloatTree::ValueOnIter& iter )
	{
	iter.setActiveState( false );
	}, false ); // looks like this operation is not safe to do in threaded mode
	reportProgress( cb, cbModifier * 0.75f );
	// copy valid topology to our tree part
	vdbVolume_.data->tree().topologyUnion( topologyTree );

You can also use gridToMesh function which is openvdb based, and might better process inactive values in this case but the result mesh will actually be dual to marching cubes mesh

[gecpgecp]

Okay, I understand. Thank you for your answer. I have another small question. In the official documentation, when I look up a certain interface function, I often don't know which header file to include. I often have to try several times to find it. Is it because I haven't found the right place?

[Grantim]

It seems that there is no clear way to find include file in documentation right now, thanks for reporting, we will try to improve it for next release.

For now you can use search on github to find required header file.

[gecpgecp]

thanks for your reply。