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IDProjectCategoryView StatusLast Update
0001534OpenFOAMBugpublic2015-02-16 22:12
Reporterwyldckat Assigned Tohenry  
PrioritylowSeveritytextReproducibilityN/A
Status resolvedResolutionfixed 
Summary0001534: surfaceCheck: option "-blockMesh" gives hard to see/parse output
DescriptionWhen using the "-blockMesh" option in "surfaceCheck", it's a bit hard to visually see where the output will end for the suggested "blockMeshDict" contents.
And it's harder to have automatic parsing... well, unless the detection is based on finding "patches\n();".

Attached is both the patch "surfaceCheck_block_format.patch" and the modified file "applications/utilities/surface/surfaceCheck/surfaceCheck.C".

I didn't suggest using "IOobject::writeDivider" and "writeEndDivider", because it made things a bit confusing.
TagsNo tags attached.

Activities

wyldckat

2015-02-16 19:40

updater  

surfaceCheck_block_format.patch (900 bytes)   
diff --git a/applications/utilities/surface/surfaceCheck/surfaceCheck.C b/applications/utilities/surface/surfaceCheck/surfaceCheck.C
index 8116ab0..756b56c 100644
--- a/applications/utilities/surface/surfaceCheck/surfaceCheck.C
+++ b/applications/utilities/surface/surfaceCheck/surfaceCheck.C
@@ -223,8 +223,9 @@ int main(int argc, char *argv[])
     {
         pointField cornerPts(boundBox(surf.points(), false).points());
 
-        Info<<"// blockMeshDict info" << nl
-            <<"vertices\n(" << nl;
+        Info<<"// blockMeshDict info" << nl << nl;
+
+        Info<<"vertices\n(" << nl;
         forAll(cornerPts, ptI)
         {
             Info << "    " << cornerPts[ptI] << nl;
@@ -239,6 +240,8 @@ int main(int argc, char *argv[])
 
         Info<<"edges\n();" << nl
             <<"patches\n();" << endl;
+
+        Info<< nl << "// end blockMeshDict info" << nl << endl;
     }
 
 

wyldckat

2015-02-16 19:40

updater  

surfaceCheck.C (21,519 bytes)   
/*---------------------------------------------------------------------------*\
  =========                 |
  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
   \\    /   O peration     |
    \\  /    A nd           | Copyright (C) 2011-2014 OpenFOAM Foundation
     \\/     M anipulation  |
-------------------------------------------------------------------------------
License
    This file is part of OpenFOAM.

    OpenFOAM is free software: you can redistribute it and/or modify it
    under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
    ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
    for more details.

    You should have received a copy of the GNU General Public License
    along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.

Application
    surfaceCheck

Description
    Checks geometric and topological quality of a surface.

\*---------------------------------------------------------------------------*/

#include "triangle.H"
#include "triSurface.H"
#include "triSurfaceSearch.H"
#include "argList.H"
#include "OFstream.H"
#include "OBJstream.H"
#include "SortableList.H"
#include "PatchTools.H"
#include "vtkSurfaceWriter.H"

using namespace Foam;

// Does face use valid vertices?
bool validTri
(
    const bool verbose,
    const triSurface& surf,
    const label faceI
)
{
    // Simple check on indices ok.

    const labelledTri& f = surf[faceI];

    forAll(f, fp)
    {
        if (f[fp] < 0 || f[fp] >= surf.points().size())
        {
            WarningIn("validTri(const triSurface&, const label)")
                << "triangle " << faceI << " vertices " << f
                << " uses point indices outside point range 0.."
                << surf.points().size()-1 << endl;
            return false;
        }
    }

    if ((f[0] == f[1]) || (f[0] == f[2]) || (f[1] == f[2]))
    {
        WarningIn("validTri(const triSurface&, const label)")
            << "triangle " << faceI
            << " uses non-unique vertices " << f
            << " coords:" << f.points(surf.points())
            << endl;
        return false;
    }

    // duplicate triangle check

    const labelList& fFaces = surf.faceFaces()[faceI];

    // Check if faceNeighbours use same points as this face.
    // Note: discards normal information - sides of baffle are merged.
    forAll(fFaces, i)
    {
        label nbrFaceI = fFaces[i];

        if (nbrFaceI <= faceI)
        {
            // lower numbered faces already checked
            continue;
        }

        const labelledTri& nbrF = surf[nbrFaceI];

        if
        (
            ((f[0] == nbrF[0]) || (f[0] == nbrF[1]) || (f[0] == nbrF[2]))
         && ((f[1] == nbrF[0]) || (f[1] == nbrF[1]) || (f[1] == nbrF[2]))
         && ((f[2] == nbrF[0]) || (f[2] == nbrF[1]) || (f[2] == nbrF[2]))
        )
        {
            WarningIn("validTri(const triSurface&, const label)")
                << "triangle " << faceI << " vertices " << f
                << " has the same vertices as triangle " << nbrFaceI
                << " vertices " << nbrF
                << " coords:" << f.points(surf.points())
                << endl;

            return false;
        }
    }
    return true;
}


labelList countBins
(
    const scalar min,
    const scalar max,
    const label nBins,
    const scalarField& vals
)
{
    scalar dist = nBins/(max - min);

    labelList binCount(nBins, 0);

    forAll(vals, i)
    {
        scalar val = vals[i];

        label index = -1;

        if (Foam::mag(val - min) < SMALL)
        {
            index = 0;
        }
        else if (val >= max - SMALL)
        {
            index = nBins - 1;
        }
        else
        {
            index = label((val - min)*dist);

            if ((index < 0) || (index >= nBins))
            {
                WarningIn
                (
                    "countBins(const scalar, const scalar, const label"
                    ", const scalarField&)"
                )   << "value " << val << " at index " << i
                    << " outside range " << min << " .. " << max << endl;

                if (index < 0)
                {
                    index = 0;
                }
                else
                {
                    index = nBins - 1;
                }
            }
        }
        binCount[index]++;
    }

    return binCount;
}


// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

int main(int argc, char *argv[])
{
    argList::noParallel();
    argList::validArgs.append("surfaceFile");
    argList::addBoolOption
    (
        "checkSelfIntersection",
        "also check for self-intersection"
    );
    argList::addBoolOption
    (
        "splitNonManifold",
        "split surface along non-manifold edges"
        " (default split is fully disconnected)"
    );
    argList::addBoolOption
    (
        "verbose",
        "verbose operation"
    );
    argList::addBoolOption
    (
        "blockMesh",
        "write vertices/blocks for blockMeshDict"
    );

    argList args(argc, argv);

    const fileName surfFileName = args[1];
    const bool checkSelfIntersect = args.optionFound("checkSelfIntersection");
    const bool verbose = args.optionFound("verbose");
    const bool splitNonManifold = args.optionFound("splitNonManifold");

    Info<< "Reading surface from " << surfFileName << " ..." << nl << endl;


    // Read
    // ~~~~

    triSurface surf(surfFileName);


    Info<< "Statistics:" << endl;
    surf.writeStats(Info);
    Info<< endl;

    // write bounding box corners
    if (args.optionFound("blockMesh"))
    {
        pointField cornerPts(boundBox(surf.points(), false).points());

        Info<<"// blockMeshDict info" << nl << nl;

        Info<<"vertices\n(" << nl;
        forAll(cornerPts, ptI)
        {
            Info << "    " << cornerPts[ptI] << nl;
        }

        // number of divisions needs adjustment later
        Info<<");\n" << nl
            <<"blocks\n"
            <<"(\n"
            <<"    hex (0 1 2 3 4 5 6 7) (10 10 10) simpleGrading (1 1 1)\n"
            <<");\n" << nl;

        Info<<"edges\n();" << nl
            <<"patches\n();" << endl;

        Info<< nl << "// end blockMeshDict info" << nl << endl;
    }


    // Region sizes
    // ~~~~~~~~~~~~

    {
        labelList regionSize(surf.patches().size(), 0);

        forAll(surf, faceI)
        {
            label region = surf[faceI].region();

            if (region < 0 || region >= regionSize.size())
            {
                WarningIn(args.executable())
                    << "Triangle " << faceI << " vertices " << surf[faceI]
                    << " has region " << region << " which is outside the range"
                    << " of regions 0.." << surf.patches().size()-1
                    << endl;
            }
            else
            {
                regionSize[region]++;
            }
        }

        Info<< "Region\tSize" << nl
            << "------\t----" << nl;
        forAll(surf.patches(), patchI)
        {
            Info<< surf.patches()[patchI].name() << '\t'
                << regionSize[patchI] << nl;
        }
        Info<< nl << endl;
    }


    // Check triangles
    // ~~~~~~~~~~~~~~~

    {
        DynamicList<label> illegalFaces(surf.size()/100 + 1);

        forAll(surf, faceI)
        {
            if (!validTri(verbose, surf, faceI))
            {
                illegalFaces.append(faceI);
            }
        }

        if (illegalFaces.size())
        {
            Info<< "Surface has " << illegalFaces.size()
                << " illegal triangles." << endl;

            OFstream str("illegalFaces");
            Info<< "Dumping conflicting face labels to " << str.name() << endl
                << "Paste this into the input for surfaceSubset" << endl;
            str << illegalFaces;
        }
        else
        {
            Info<< "Surface has no illegal triangles." << endl;
        }
        Info<< endl;
    }



    // Triangle quality
    // ~~~~~~~~~~~~~~~~

    {
        scalarField triQ(surf.size(), 0);
        forAll(surf, faceI)
        {
            const labelledTri& f = surf[faceI];

            if (f[0] == f[1] || f[0] == f[2] || f[1] == f[2])
            {
                //WarningIn(args.executable())
                //    << "Illegal triangle " << faceI << " vertices " << f
                //    << " coords " << f.points(surf.points()) << endl;
            }
            else
            {
                triQ[faceI] = triPointRef
                (
                    surf.points()[f[0]],
                    surf.points()[f[1]],
                    surf.points()[f[2]]
                ).quality();
            }
        }

        labelList binCount = countBins(0, 1, 20, triQ);

        Info<< "Triangle quality (equilateral=1, collapsed=0):"
            << endl;


        OSstream& os = Info;
        os.width(4);

        scalar dist = (1.0 - 0.0)/20.0;
        scalar min = 0;
        forAll(binCount, binI)
        {
            Info<< "    " << min << " .. " << min+dist << "  : "
                << 1.0/surf.size() * binCount[binI]
                << endl;
            min += dist;
        }
        Info<< endl;

        label minIndex = findMin(triQ);
        label maxIndex = findMax(triQ);

        Info<< "    min " << triQ[minIndex] << " for triangle " << minIndex
            << nl
            << "    max " << triQ[maxIndex] << " for triangle " << maxIndex
            << nl
            << endl;


        if (triQ[minIndex] < SMALL)
        {
            WarningIn(args.executable()) << "Minimum triangle quality is "
                << triQ[minIndex] << ". This might give problems in"
                << " self-intersection testing later on." << endl;
        }

        // Dump for subsetting
        {
            DynamicList<label> problemFaces(surf.size()/100+1);

            forAll(triQ, faceI)
            {
                if (triQ[faceI] < 1e-11)
                {
                    problemFaces.append(faceI);
                }
            }

            if (!problemFaces.empty())
            {
                OFstream str("badFaces");

                Info<< "Dumping bad quality faces to " << str.name() << endl
                    << "Paste this into the input for surfaceSubset" << nl
                    << nl << endl;

                str << problemFaces;
            }
        }
    }



    // Edges
    // ~~~~~
    {
        const edgeList& edges = surf.edges();
        const pointField& localPoints = surf.localPoints();

        scalarField edgeMag(edges.size());

        forAll(edges, edgeI)
        {
            edgeMag[edgeI] = edges[edgeI].mag(localPoints);
        }

        label minEdgeI = findMin(edgeMag);
        label maxEdgeI = findMax(edgeMag);

        const edge& minE = edges[minEdgeI];
        const edge& maxE = edges[maxEdgeI];


        Info<< "Edges:" << nl
            << "    min " << edgeMag[minEdgeI] << " for edge " << minEdgeI
            << " points " << localPoints[minE[0]] << localPoints[minE[1]]
            << nl
            << "    max " << edgeMag[maxEdgeI] << " for edge " << maxEdgeI
            << " points " << localPoints[maxE[0]] << localPoints[maxE[1]]
            << nl
            << endl;
    }



    // Close points
    // ~~~~~~~~~~~~
    {
        const edgeList& edges = surf.edges();
        const pointField& localPoints = surf.localPoints();

        const boundBox bb(localPoints);
        scalar smallDim = 1e-6 * bb.mag();

        Info<< "Checking for points less than 1e-6 of bounding box ("
            << bb.span() << " metre) apart."
            << endl;

        // Sort points
        SortableList<scalar> sortedMag(mag(localPoints));

        label nClose = 0;

        for (label i = 1; i < sortedMag.size(); i++)
        {
            label ptI = sortedMag.indices()[i];

            label prevPtI = sortedMag.indices()[i-1];

            if (mag(localPoints[ptI] - localPoints[prevPtI]) < smallDim)
            {
                // Check if neighbours.
                const labelList& pEdges = surf.pointEdges()[ptI];

                label edgeI = -1;

                forAll(pEdges, i)
                {
                    const edge& e = edges[pEdges[i]];

                    if (e[0] == prevPtI || e[1] == prevPtI)
                    {
                        // point1 and point0 are connected through edge.
                        edgeI = pEdges[i];

                        break;
                    }
                }

                nClose++;

                if (edgeI == -1)
                {
                    Info<< "    close unconnected points "
                        << ptI << ' ' << localPoints[ptI]
                        << " and " << prevPtI << ' '
                        << localPoints[prevPtI]
                        << " distance:"
                        << mag(localPoints[ptI] - localPoints[prevPtI])
                        << endl;
                }
                else
                {
                    Info<< "    small edge between points "
                        << ptI << ' ' << localPoints[ptI]
                        << " and " << prevPtI << ' '
                        << localPoints[prevPtI]
                        << " distance:"
                        << mag(localPoints[ptI] - localPoints[prevPtI])
                        << endl;
                }
            }
        }

        Info<< "Found " << nClose << " nearby points." << nl
            << endl;
    }



    // Check manifold
    // ~~~~~~~~~~~~~~

    DynamicList<label> problemFaces(surf.size()/100 + 1);

    const labelListList& eFaces = surf.edgeFaces();

    label nSingleEdges = 0;
    forAll(eFaces, edgeI)
    {
        const labelList& myFaces = eFaces[edgeI];

        if (myFaces.size() == 1)
        {
            problemFaces.append(myFaces[0]);

            nSingleEdges++;
        }
    }

    label nMultEdges = 0;
    forAll(eFaces, edgeI)
    {
        const labelList& myFaces = eFaces[edgeI];

        if (myFaces.size() > 2)
        {
            forAll(myFaces, myFaceI)
            {
                problemFaces.append(myFaces[myFaceI]);
            }

            nMultEdges++;
        }
    }
    problemFaces.shrink();

    if ((nSingleEdges != 0) || (nMultEdges != 0))
    {
        Info<< "Surface is not closed since not all edges connected to "
            << "two faces:" << endl
            << "    connected to one face : " << nSingleEdges << endl
            << "    connected to >2 faces : " << nMultEdges << endl;

        Info<< "Conflicting face labels:" << problemFaces.size() << endl;

        OFstream str("problemFaces");

        Info<< "Dumping conflicting face labels to " << str.name() << endl
            << "Paste this into the input for surfaceSubset" << endl;

        str << problemFaces;
    }
    else
    {
        Info<< "Surface is closed. All edges connected to two faces." << endl;
    }
    Info<< endl;



    // Check singly connected domain
    // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

    {
        boolList borderEdge(surf.nEdges(), false);
        if (splitNonManifold)
        {
            const labelListList& eFaces = surf.edgeFaces();
            forAll(eFaces, edgeI)
            {
                if (eFaces[edgeI].size() > 2)
                {
                    borderEdge[edgeI] = true;
                }
            }
        }

        labelList faceZone;
        label numZones = surf.markZones(borderEdge, faceZone);

        Info<< "Number of unconnected parts : " << numZones << endl;

        if (numZones > 1)
        {
            Info<< "Splitting surface into parts ..." << endl << endl;

            fileName surfFileNameBase(surfFileName.name());
            const word fileType = surfFileNameBase.ext();
            // Strip extension
            surfFileNameBase = surfFileNameBase.lessExt();
            // If extension was .gz strip original extension
            if (fileType == "gz")
            {
                surfFileNameBase = surfFileNameBase.lessExt();
            }


            {
                Info<< "Writing zoning to "
                    <<  fileName
                        (
                            "zone_"
                          + surfFileNameBase
                          + '.'
                          + vtkSurfaceWriter::typeName
                        )
                    << "..." << endl << endl;

                // Convert data
                scalarField scalarFaceZone(faceZone.size());
                forAll(faceZone, i)
                {
                    scalarFaceZone[i] = faceZone[i];
                }
                faceList faces(surf.size());
                forAll(surf, i)
                {
                    faces[i] = surf[i].triFaceFace();
                }

                vtkSurfaceWriter().write
                (
                    surfFileName.path(),
                    surfFileNameBase,
                    surf.points(),
                    faces,
                    "zone",
                    scalarFaceZone,
                    false               // face based data
                );
            }


            for (label zone = 0; zone < numZones; zone++)
            {
                boolList includeMap(surf.size(), false);

                forAll(faceZone, faceI)
                {
                    if (faceZone[faceI] == zone)
                    {
                        includeMap[faceI] = true;
                    }
                }

                labelList pointMap;
                labelList faceMap;

                triSurface subSurf
                (
                    surf.subsetMesh
                    (
                        includeMap,
                        pointMap,
                        faceMap
                    )
                );

                fileName subName(surfFileNameBase + "_" + name(zone) + ".obj");

                Info<< "writing part " << zone << " size " << subSurf.size()
                    << " to " << subName << endl;

                subSurf.write(subName);
            }
        }
    }



    // Check orientation
    // ~~~~~~~~~~~~~~~~~

    labelHashSet borderEdge(surf.size()/1000);
    PatchTools::checkOrientation(surf, false, &borderEdge);

    //
    // Colour all faces into zones using borderEdge
    //
    labelList normalZone;
    label numNormalZones = PatchTools::markZones(surf, borderEdge, normalZone);

    Info<< endl
        << "Number of zones (connected area with consistent normal) : "
        << numNormalZones << endl;

    if (numNormalZones > 1)
    {
        Info<< "More than one normal orientation." << endl;
    }
    Info<< endl;



    // Check self-intersection
    // ~~~~~~~~~~~~~~~~~~~~~~~

    if (checkSelfIntersect)
    {
        Info<< "Checking self-intersection." << endl;

        triSurfaceSearch querySurf(surf);

        const indexedOctree<treeDataTriSurface>& tree = querySurf.tree();

        OBJstream intStream("selfInterPoints.obj");

        label nInt = 0;

        forAll(surf.edges(), edgeI)
        {
            const edge& e = surf.edges()[edgeI];

            pointIndexHit hitInfo
            (
                tree.findLine
                (
                    surf.points()[surf.meshPoints()[e[0]]],
                    surf.points()[surf.meshPoints()[e[1]]],
                    treeDataTriSurface::findSelfIntersectOp
                    (
                        tree,
                        edgeI
                    )
                )
            );

            if (hitInfo.hit())
            {
                intStream.write(hitInfo.hitPoint());
                nInt++;
            }
        }

        if (nInt == 0)
        {
            Info<< "Surface is not self-intersecting" << endl;
        }
        else
        {
            Info<< "Surface is self-intersecting at " << nInt
                << " locations." << endl;
            Info<< "Writing intersection points to " << intStream.name()
                << endl;
        }

        //surfaceIntersection inter(querySurf);
        //
        //if (inter.cutEdges().empty() && inter.cutPoints().empty())
        //{
        //    Info<< "Surface is not self-intersecting" << endl;
        //}
        //else
        //{
        //    Info<< "Surface is self-intersecting" << endl;
        //    Info<< "Writing edges of intersection to selfInter.obj" << endl;
        //
        //    OFstream intStream("selfInter.obj");
        //    forAll(inter.cutPoints(), cutPointI)
        //    {
        //        const point& pt = inter.cutPoints()[cutPointI];
        //
        //        intStream << "v " << pt.x() << ' ' << pt.y() << ' ' << pt.z()
        //            << endl;
        //    }
        //    forAll(inter.cutEdges(), cutEdgeI)
        //    {
        //        const edge& e = inter.cutEdges()[cutEdgeI];
        //
        //        intStream << "l " << e.start()+1 << ' ' << e.end()+1 << endl;
        //    }
        //}
        Info<< endl;
    }


    Info<< "\nEnd\n" << endl;

    return 0;
}


// ************************************************************************* //
surfaceCheck.C (21,519 bytes)   

henry

2015-02-16 22:12

manager   ~0003807

Thanks for the update
Resolved by commit 8d28dc8ad4596b048ca6c0d9803c0cc517acbf0b

Issue History

Date Modified Username Field Change
2015-02-16 19:40 wyldckat New Issue
2015-02-16 19:40 wyldckat File Added: surfaceCheck_block_format.patch
2015-02-16 19:40 wyldckat File Added: surfaceCheck.C
2015-02-16 22:12 henry Note Added: 0003807
2015-02-16 22:12 henry Status new => resolved
2015-02-16 22:12 henry Resolution open => fixed
2015-02-16 22:12 henry Assigned To => henry