From cb2d0752dff0548376f5a5b1345d59861bc21fed Mon Sep 17 00:00:00 2001
From: Paolo Cignoni cignoni <paolo.cignoni@isti.cnr.it>
Date: Tue, 25 Oct 2016 22:07:46 +0000
Subject: [PATCH] Cleaning messages and parameters

---
 .../filter_screened_poisson.cpp               | 107 ++++++++++--------
 .../filter_screened_poisson.xml               |  22 ++--
 2 files changed, 67 insertions(+), 62 deletions(-)

diff --git a/src/meshlabplugins/filter_screened_poisson/filter_screened_poisson.cpp b/src/meshlabplugins/filter_screened_poisson/filter_screened_poisson.cpp
index 40fa5dcd0..55a1f4ef6 100644
--- a/src/meshlabplugins/filter_screened_poisson/filter_screened_poisson.cpp
+++ b/src/meshlabplugins/filter_screened_poisson/filter_screened_poisson.cpp
@@ -149,7 +149,7 @@ public:
   Real SamplesPerNodeVal;
   Real ScaleVal;
   bool ConfidenceFlag;
-  bool NormalWeightsFlag;
+  bool CleanFlag;
   bool DensityFlag;
   Real PointWeightVal;
   int AdaptiveExponentVal;
@@ -177,7 +177,7 @@ public:
     SamplesPerNodeVal =1.5f;
     ScaleVal=1.1f;
     ConfidenceFlag=false;
-    NormalWeightsFlag=false;
+    CleanFlag=false;
     DensityFlag=false;
     PointWeightVal = 4.0f;
     AdaptiveExponentVal=1;
@@ -504,9 +504,9 @@ int _Execute(OrientedPointStream< Real > *pointStream, Box3m bb, CMeshO &pm, Poi
           Point3D<Real> pp = iXForm*pt->point;          
            vcg::tri::Allocator<CMeshO>::AddVertex(pm,Point3m(pp[0],pp[1],pp[2]));
            pm.vert.back().Q() = pt->value;
-           pm.vert.back().C()[0] = pt->color[0]*255.0;
-           pm.vert.back().C()[1] = pt->color[1]*255.0;
-           pm.vert.back().C()[2] = pt->color[2]*255.0;
+           pm.vert.back().C()[0] = pt->color[0];
+           pm.vert.back().C()[1] = pt->color[1];
+           pm.vert.back().C()[2] = pt->color[2];
         }
         for (int ii=0; ii < mesh.outOfCorePointCount(); ii++){
           Vertex pt; 
@@ -514,9 +514,9 @@ int _Execute(OrientedPointStream< Real > *pointStream, Box3m bb, CMeshO &pm, Poi
           Point3D<Real> pp = iXForm*pt.point;
           vcg::tri::Allocator<CMeshO>::AddVertex(pm,Point3m(pp[0],pp[1],pp[2]));
           pm.vert.back().Q() = pt.value;
-          pm.vert.back().C()[0] = pt.color[0]*1.0;
-          pm.vert.back().C()[1] = pt.color[1]*1.0;
-          pm.vert.back().C()[2] = pt.color[2]*1.0;
+          pm.vert.back().C()[0] = pt.color[0];
+          pm.vert.back().C()[1] = pt.color[1];
+          pm.vert.back().C()[2] = pt.color[2];
         }
       
         std::vector< CoredVertexIndex > polygon;      
@@ -545,16 +545,17 @@ int _Execute(OrientedPointStream< Real > *pointStream, Box3m bb, CMeshO &pm, Poi
 
 
 template <class MeshType>
-void PoissonClean(MeshType &m, bool scaleNormal)
+void PoissonClean(MeshType &m, bool scaleNormal, bool cleanFlag)
 {
-
-  if(m.face.size()>0)
-    vcg::tri::Clean<MeshType>::RemoveUnreferencedVertex(m);
+  if(cleanFlag) {
+    if(m.face.size()>0)
+      vcg::tri::Clean<MeshType>::RemoveUnreferencedVertex(m);
+  }
   vcg::tri::Allocator<MeshType>::CompactEveryVector(m);
   vcg::tri::UpdateNormal<MeshType>::NormalizePerVertex(m);
   if(scaleNormal)
   {
-    for(typename MeshType::VertexIterator vi=m.vert.begin();vi!=m.vert.end();++vi)
+    for(auto vi=m.vert.begin();vi!=m.vert.end();++vi)
       vi->N() *= vi->Q();
   }
 }
@@ -562,7 +563,7 @@ void PoissonClean(MeshType &m, bool scaleNormal)
 bool HasGoodNormal(CMeshO &m)
 {
   for(auto vi=m.vert.begin();vi!=m.vert.end();++vi)
-    if(vcg::SquaredNorm(vi->N()) < std::numeric_limits<float>::min()) 
+    if(vcg::SquaredNorm(vi->N()) < std::numeric_limits<float>::min()*10.0) 
       return false; 
   
   return true;
@@ -572,36 +573,7 @@ bool FilterScreenedPoissonPlugin::applyFilter( const QString& filterName,MeshDoc
 {
   if (filterName == "Screened Poisson Surface Reconstruction")
   {
-    MeshModel *mm =md.mm();
     PoissonParam<Scalarm> pp;
-    bool goodNormal=true, goodColor=true;
-    if(env.evalBool("visibleLayer") == false) {
-      goodNormal=HasGoodNormal(md.mm()->cm);
-      goodColor = md.mm()->hasDataMask(MeshModel::MM_VERTCOLOR);
-    } else{
-      MeshModel *_mm=0;
-      while(_mm=md.nextVisibleMesh(_mm)) {
-        goodNormal &= HasGoodNormal(_mm->cm);
-        goodColor  &= _mm->hasDataMask(MeshModel::MM_VERTCOLOR);
-        
-      }
-    }
-    
-    if(!goodNormal)
-    {
-      this->errorMessage = "Filter requires correct per vertex normals\n that your point could has a proper, not-null, normal for each sample";
-      return false;
-    }
-    
-    MeshModel *pm =md.addNewMesh("","Poisson mesh",false);
-    md.setVisible(pm->id(),false);
-    pm->updateDataMask(MeshModel::MM_VERTQUALITY);    
-    if(goodColor) pm->updateDataMask(MeshModel::MM_VERTCOLOR);
-    
-    
-    MeshModelPointStream<Scalarm> meshStream(mm->cm);
-    MeshDocumentPointStream<Scalarm> documentStream(md);
-
     pp.MaxDepthVal = env.evalInt("depth");
     pp.FullDepthVal = env.evalInt("fullDepth");
     pp.CGDepthVal= env.evalInt("cgDepth");
@@ -610,20 +582,55 @@ bool FilterScreenedPoissonPlugin::applyFilter( const QString& filterName,MeshDoc
     pp.PointWeightVal = env.evalFloat("pointWeight");
     pp.ItersVal = env.evalInt("iters");
     pp.ConfidenceFlag = env.evalBool("confidence");
-    pp.NormalWeightsFlag = env.evalBool("nWeights");
     pp.DensityFlag = true;
+    pp.CleanFlag = env.evalBool("preClean");
+    
+    bool goodNormal=true, goodColor=true;
+    if(env.evalBool("visibleLayer") == false) 
+    {
+      PoissonClean(md.mm()->cm, pp.ConfidenceFlag, pp.CleanFlag);
+      goodNormal=HasGoodNormal(md.mm()->cm);
+      goodColor = md.mm()->hasDataMask(MeshModel::MM_VERTCOLOR);
+    } 
+    else
+    {
+      MeshModel *_mm=0;
+      while(_mm=md.nextVisibleMesh(_mm)) {        
+        PoissonClean(_mm->cm,  pp.ConfidenceFlag, pp.CleanFlag);        
+        goodNormal &= HasGoodNormal(_mm->cm);
+        goodColor  &= _mm->hasDataMask(MeshModel::MM_VERTCOLOR);        
+      }
+    }
+    
+    if(!goodNormal)
+    {
+      this->errorMessage = "Filter requires correct per vertex normals.<br>"
+                           "E.g. it is necessary that your <b>ALL</b> the input vertices have a proper, not-null normal.<br> "
+                           "If you enconuter this error on a triangulated mesh try to use the <i>Remove Unreferenced Vertices</i> "
+                           "filter (usually unreferenced vertices on surfaces have null normals).<br>"
+                           "Enabling the Cleaning option also works.";
+      return false;
+    }
+    
+    MeshModel *pm =md.addNewMesh("","Poisson mesh",false);
+    md.setVisible(pm->id(),false);
+    pm->updateDataMask(MeshModel::MM_VERTQUALITY);    
+    if(goodColor) pm->updateDataMask(MeshModel::MM_VERTCOLOR);
+    
     if(env.evalBool("visibleLayer"))
     {
-      MeshModel *m=0;
-      while((m=md.nextVisibleMesh(m)))
-        PoissonClean(m->cm, (pp.ConfidenceFlag || pp.NormalWeightsFlag));
-      Box3m bb = md.bbox();
+      Box3m bb;
+      MeshModel *_mm=0;
+      while(_mm=md.nextVisibleMesh(_mm)) 
+        bb.Add(_mm->cm.Tr,_mm->cm.bbox);
+
+      MeshDocumentPointStream<Scalarm> documentStream(md);      
       _Execute<Scalarm,2,BOUNDARY_NEUMANN,PlyColorAndValueVertex<Scalarm> >(&documentStream,bb,pm->cm,pp,cb);
     }
     else
     {
-      PoissonClean(mm->cm, (pp.ConfidenceFlag || pp.NormalWeightsFlag));
-      _Execute<Scalarm,2,BOUNDARY_NEUMANN,PlyColorAndValueVertex<Scalarm> >(&meshStream,mm->cm.bbox,pm->cm,pp,cb);
+      MeshModelPointStream<Scalarm> meshStream(md.mm()->cm);      
+      _Execute<Scalarm,2,BOUNDARY_NEUMANN,PlyColorAndValueVertex<Scalarm> >(&meshStream,md.mm()->cm.bbox,pm->cm,pp,cb);
     }
     pm->UpdateBoxAndNormals();
     md.setVisible(pm->id(),true);
diff --git a/src/meshlabplugins/filter_screened_poisson/filter_screened_poisson.xml b/src/meshlabplugins/filter_screened_poisson/filter_screened_poisson.xml
index e0752a2f6..f4c5862ae 100644
--- a/src/meshlabplugins/filter_screened_poisson/filter_screened_poisson.xml
+++ b/src/meshlabplugins/filter_screened_poisson/filter_screened_poisson.xml
@@ -2,8 +2,7 @@
 <PLUGIN pluginName="FilterScreenedPoissonPlugin" pluginAuthor="Paolo Cignoni" pluginEmail="paolo.cignoni@isti.cnr.it">
 <FILTER filterFunction="screenedPoissonSurfaceReconstruction" filterName="Screened Poisson Surface Reconstruction" filterPre="MM_NONE" filterRasterArity="SingleRaster" filterClass="Remeshing" filterPost="MM_VERTNUMBER | MM_FACENUMBER" filterArity="Variable" filterIsInterruptible="true">
 <FILTER_HELP><![CDATA[This surface reconstruction algorithm
-creates watertight surfaces from oriented point sets. In this work we extend the technique to explicitly
-incorporate the points as interpolation constraints.
+creates watertight surfaces from oriented point sets.
 <br> The filter uses the original code of Michael Kazhdan and Matthew Bolitho implementing the algorithm described in the following paper:<br>
 <i>Michael Kazhdan, Hugues Hoppe</i>,<br>
 <b>"Screened Poisson surface reconstruction"</b><br>
@@ -34,18 +33,18 @@ ACM Trans. Graphics, 32(3), 2013<br>
    The default value for this parameter is 0.]]></PARAM_HELP>
    <EDIT_GUI guiLabel="Conjugate Gradients Depth"/>
    </PARAM>
-   <PARAM parName="scale" parIsImportant="true" parType="Real" parDefault="1.1">
+   <PARAM parName="scale" parIsImportant="false" parType="Real" parDefault="1.1">
    <PARAM_HELP><![CDATA[This floating point value specifies the ratio between the diameter of the cube used for
    reconstruction and the diameter of the samples' bounding cube.
    The default value is 1.1.]]></PARAM_HELP>
    <EDIT_GUI guiLabel="Scale Factor" />
    </PARAM>
-   <PARAM parName="samplesPerNode" parType="Real" parIsImportant="true" parDefault="1">
+   <PARAM parName="samplesPerNode" parType="Real" parIsImportant="true" parDefault="1.5">
    <PARAM_HELP><![CDATA[This floating point value specifies the minimum number of sample points that should fall
    within an octree node as the octree construction is adapted to sampling density. For noise-free samples, small values
    in the range [1.0 - 5.0] can be used. For more noisy samples, larger values in the range [15.0 - 20.0] may be needed
    to provide a smoother, noise-reduced, reconstruction.
-   The default value is 1.0.]]></PARAM_HELP>
+   The default value is 1.5.]]></PARAM_HELP>
    <EDIT_GUI guiLabel="Minimum Number of Samples"/>
    </PARAM>
    <PARAM parName="pointWeight" parType="Real" parIsImportant="true" parDefault="4">
@@ -55,22 +54,21 @@ ACM Trans. Graphics, 32(3), 2013<br>
       The default value for this parameter is 4.]]></PARAM_HELP>
       <EDIT_GUI guiLabel="Interpolation Weight"/>
    </PARAM>
-   <PARAM parName="iters" parType="Int" parIsImportant="true" parDefault="8">
+   <PARAM parName="iters" parType="Int" parIsImportant="false" parDefault="8">
      <PARAM_HELP><![CDATA[This integer value specifies the number of Gauss-Seidel relaxations to be performed at each
      level of the hiearchy.
      The default value for this parameter is 8.]]></PARAM_HELP>
    <EDIT_GUI guiLabel="Gauss-Seidel Relaxations"/>
    </PARAM>
    <PARAM parName="confidence" parIsImportant="true" parType="Boolean" parDefault="false">
-   <PARAM_HELP><![CDATA[Enabling this flag tells the reconstructor to use the size of the normals as confidence
-   information. When the flag is not enabled, all normals are normalized to have unit-length prior
+   <PARAM_HELP><![CDATA[Enabling this flag tells the reconstructor to use the quality as confidence
+   information; this is done by scaling the unit normals with the quality values. When the flag is not enabled, all normals are normalized to have unit-length prior
    to reconstruction.]]></PARAM_HELP>
    <CHECKBOX_GUI guiLabel="Confidence Flag"/>
    </PARAM>
-   <PARAM parName="nWeights" parIsImportant="true" parType="Boolean" parDefault="false">
-   <PARAM_HELP><![CDATA[Enabling this flag tells the reconstructor to use the size of the normals to modulate the
-   interpolation weights. When the flag is not enabled, all points are given the same weight.]]></PARAM_HELP>
-   <CHECKBOX_GUI guiLabel="Weight Flag"/>
+   <PARAM parName="preClean" parIsImportant="true" parType="Boolean" parDefault="false">
+   <PARAM_HELP><![CDATA[Enabling this flag force a cleaning pre-pass on the data removing all unreferenced vertices or vertices with null normals.]]></PARAM_HELP>
+   <CHECKBOX_GUI guiLabel="Pre-Clean"/>
    </PARAM>
   </FILTER>
   </PLUGIN>