Clipping plane by using stencil buffer for mesh objects with unclosed tubes

[michael_ca]

:doh:
I have a project, which requires to intersect anatomical mesh objects along specified axis (e.g. from head to foot) into a series of 2D gray-level slices. I used OpenGL stencil buffer with defined clipping plane to generate 2D slices.
For most of mesh objects, I can obtain good 2D intersected slices. But some mesh objects, like heart and trachea, with more tubes not-enclosed (airways, arteries, veins), this clipping algorithm did not work well. After stacking 2D slices to a volume, it looks to be extended along the end of tube to the bottom. Fig. 1 is the mesh object with texturing, Fig.2 shows each slice and Fig. 3 the stacked volume.

Please help find possible reasons for this issue, and any helpful suggestions are welcome.

[ATTACH=CONFIG]1531[/ATTACH] [ATTACH=CONFIG]1534[/ATTACH] [ATTACH=CONFIG]1532[/ATTACH]

The following is my code snippets,

    GLdouble eq[] = {A, B, C, D};
    glClipPlane(GL_CLIP_PLANE0, eq);

    glDisable(GL_DEPTH_TEST);
    glEnable(GL_CLIP_PLANE0);
    glEnable(GL_STENCIL_TEST);
    
    glClear(GL_STENCIL_BUFFER_BIT);
    glColorMask(GL_FALSE, GL_FALSE, GL_FALSE, GL_FALSE);

    // first pass: back face increment
    glStencilFunc(GL_ALWAYS, 0, 0);
    glStencilOp(GL_KEEP, GL_KEEP, GL_INCR);
    glCullFace(GL_FRONT);
    glEnable(GL_CULL_FACE);

    DrawCore(false, false, false, false); // draw mesh objects

    // second pass: front face increment
    glStencilOp(GL_KEEP, GL_KEEP, GL_DECR);
    glCullFace(GL_BACK);
    glEnable(GL_CULL_FACE);

    DrawCore(false, false, false, false); // draw mesh objects

    // drawing clip planes masked by stencil buffer content
    glColorMask(GL_TRUE, GL_TRUE, GL_TRUE, GL_TRUE);
    glEnable(GL_DEPTH_TEST);
    glDisable(GL_CLIP_PLANE0);

    glStencilFunc(GL_NOTEQUAL, 0, ~0);

    // rendering clip edges to frame buffer
    glPushMatrix();
    glLoadMatrixf(view_mat);    // Clip plane had been set up after view_mat space, thus we need to load
                        // view_mat matrix before rendering clip plane
    glBegin(GL_QUADS);
            CVector nrml = cross(CVector(verts[m_nEquationSelection][2] - verts[m_nEquationSelection][1]), CVector(verts[m_nEquationSelection][1] - verts[m_nEquationSelection][0]));
            nrml.normalize();
            glNormal3f(nrml(0), nrml(1), nrml(2)); //We want plane to be lit properly, thus we need to specify it's normal.

            glVertex3f(verts[m_nEquationSelection][0](0) * 100.0, verts[m_nEquationSelection][0](1) - eq[3], verts[m_nEquationSelection][0](2) * 100.0);
            glVertex3f(verts[m_nEquationSelection][1](0) * 100.0, verts[m_nEquationSelection][1](1) - eq[3], verts[m_nEquationSelection][1](2) * 100.0);
            glVertex3f(verts[m_nEquationSelection][2](0) * 100.0, verts[m_nEquationSelection][2](1) - eq[3], verts[m_nEquationSelection][2](2) * 100.0);
            glVertex3f(verts[m_nEquationSelection][3](0) * 100.0, verts[m_nEquationSelection][3](1) - eq[3], verts[m_nEquationSelection][3](2) * 100.0);

    glEnd();

    glPopMatrix();

    saveStencilBufferToExtraMemory(…, …);    // using "glReadPixels()" to read the stencil buffer and save to memory and then to a file

    glDisable(GL_DEPTH_TEST);

    glDisable(GL_STENCIL_TEST);
    glClear(GL_STENCIL_BUFFER_BIT);