Merge remote-tracking branch 'origin2/master' into documentation

Author: VibekeSkytt

compositemodel/src/SurfaceModelUtils.C

@@ -2390,7 +2390,12 @@ void SurfaceModelUtils::tesselateOneSrf(shared_ptr<ParamSurface> surf,
 	  else
 	  {
 	      ParametricSurfaceTesselator tesselator(*surf.get());
-	      tesselator.changeRes(n, m);
+	      int n2, m2;
+	      tesselator.getRes(n2, m2);
+	      if (n == n2 && m == m2)
+		tesselator.tesselate();
+	      else
+		tesselator.changeRes(n, m);
 	      mesh = tesselator.getMesh();
 	  }
       }

gotools-core/src/geometry/BoundedSurface.C

@@ -331,6 +331,7 @@ BoundedSurface(shared_ptr<ParamSurface> surf,
       loop_fixed_ = bd_sf->loop_fixed_;
       iso_trim_= bd_sf->iso_trim_;
       iso_trim_tol_ = bd_sf->iso_trim_tol_;
+      valid_state_ = bd_sf->valid_state_;
     }
   else
     {
@@ -346,10 +347,10 @@ BoundedSurface(shared_ptr<ParamSurface> surf,
 	}
       iso_trim_ = true;
       iso_trim_tol_ = space_epsilon;
+
+      // We then analyze the loops and set valid_state_.
+      analyzeLoops();
     }
-    
-  // We then analyze the loops and set valid_state_.
-  analyzeLoops();
 }
 
 //===========================================================================

gotools-core/src/geometry/SplineUtils.C

@@ -220,6 +220,10 @@ void SplineUtils::closest_on_rectgrid(const double* pt, const double* array,
     clo_v = best_v;
     int ii = min(int(floor(clo_u)), u_max - 1);
     int jj = min(int(floor(clo_v)), v_max - 1);
+    if (ii < 0)
+      ii = floor(0.5*u_max);
+    if (jj < 0)
+      jj = floor(0.5*v_max);
     p[0].setValue(array + (jj*nmb_coefs_u + ii)*3);
     p[1].setValue(array + (jj*nmb_coefs_u + ii+1)*3);
     p[2].setValue(array + ((jj+1)*nmb_coefs_u + ii+1)*3);

lrsplines2D/app/PointCloud2LR.C

@@ -102,6 +102,7 @@ void print_help_text()
   std::cout << "-toldoc: Documentation on file format for tolerance domains. \n";
   std::cout << "-featuredoc: Show feature documentation \n";
   std::cout << "-refstrat: Print parameter information to define refinement strategy. \n";
+  std::cout << "-AIC <filename>: Compute AIC at each iteration level and output to the given file. Time consuming. Default: No AIC computations \n";
   std::cout << "-h or --help : Write this text\n";
 }
 
@@ -231,6 +232,8 @@ int main(int argc, char *argv[])
   double minsize = -1.0;
   int feature_out = -1;
   int verbose = 0;
+  int AIC = 0;
+  char *AIC_file = 0;
 
   int initncoef = 10;
   int distribute_ncoef = 0;
@@ -514,7 +517,14 @@ int main(int argc, char *argv[])
 	  if (stat < 0)
 	    return 1;
 	}
-	
+      else if (arg == "-AIC")
+	{
+	  AIC = 1;
+	  int stat = fetchCharParameter(argc, argv, ki, AIC_file, 
+					nmb_par, par_read);
+	  if (stat < 0)
+	    return 1;
+	}
     }
 
   // Read remaining parameters
@@ -848,6 +858,10 @@ int main(int argc, char *argv[])
       approx->addUpperConstraint(extent[5] + zfac);
       approx->setLocalConstraint(zfac);
     }
+
+  if (AIC)
+    approx->setAIC(true);
+  
 #ifdef DEBUG
   std::cout << "Range: " << extent[1]-extent[0] << ", " << extent[3]-extent[2];
   std::cout << ", " << extent[5]-extent[4] << std::endl;
@@ -930,7 +944,25 @@ int main(int argc, char *argv[])
       regular_cloud.write(ofr);
     }
 
-
+  if (AIC)
+    {
+      // Fetch Mahalanobis distance and log likelyhood
+      vector<double> AICinfo;
+      vector<int> ncoef;
+      approx->getAICInfo(AICinfo, ncoef);
+      std::ofstream ofAIC(AIC_file);
+      ofAIC.precision(10);
+      ofAIC << "For each iteration level the following is reported: " << std::endl;
+      ofAIC << "level, number of coefficients, Mahalanobix distance with students t-distribution, \n";
+      ofAIC << "AIC student t-distribution, Mahalanobix distance normal distribution, AIC normal distribution" << std::endl;
+      for (size_t ki=0; ki<ncoef.size(); ++ki)
+	{
+	  ofAIC << ki << "\t" << ncoef[ki];
+	  for (size_t kj=0; kj<4; ++kj)
+	    ofAIC << "\t" << AICinfo[4*ki+kj];
+	  ofAIC << std::endl;
+	}
+    }
 
   std::ofstream sfout(surffile);     // Surface output stream
 

lrsplines2D/app/getLRSfDomain.C

@@ -94,9 +94,15 @@ int main( int argc, char* argv[] )
   // Fetch domain
   RectDomain domain = sf->containingDomain();
 
+  // Fetch box
+  BoundingBox bb = sf->boundingBox();
+  
+
   // Output
+  int dim = sf->dimension();
   printf("Surface domain: %13.4f %13.4f %13.4f %13.4f \n", domain.umin(), 
 	 domain.umax(), domain.vmin(), domain.vmax());
+  printf("Bound z: %13.7f %13.7f \n", bb.low()[dim-1], bb.high()[dim-1]);
 
   shared_ptr<LRSplineSurface> lrsf = 
     dynamic_pointer_cast<LRSplineSurface, ParamSurface>(sf);

lrsplines2D/app/isoContours.C

@@ -299,6 +299,7 @@ namespace {
 
   const double minval = bbox.low()[0];
   const double maxval = bbox.high()[0];
+  std::cout << "Minval: " << minval << ", maxval: " << maxval << std::endl;
 
   vector<double> result(num_contours, 0);
   for (int i = 0; i != num_contours; ++i)

lrsplines2D/app/liftSurfTo3D.C

@@ -41,6 +41,7 @@
 
 #include "GoTools/geometry/ObjectHeader.h"
 #include "GoTools/geometry/BoundedSurface.h"
+#include "GoTools/geometry/SplineSurface.h"
 #include "GoTools/lrsplines2D/LRSplineSurface.h"
 #include "GoTools/geometry/GoTools.h"
 #include "GoTools/geometry/Factory.h"
@@ -105,6 +106,16 @@ int main(int argc, char *argv[])
 	  MESSAGE("Surface type " << header.classType() << " in the underlying surface is not supported.");
       }
   }
+  else if (header.classType() == Class_SplineSurface)
+    {
+      shared_ptr<SplineSurface> sf(new SplineSurface());
+      sf->read(filein);
+      shared_ptr<LRSplineSurface> lr_sf(new LRSplineSurface(sf.get(), 1.0e-8));
+      lr_sf->to3D();
+      shared_ptr<SplineSurface> splsf(lr_sf->asSplineSurface());
+      splsf->writeStandardHeader(fileout);
+      splsf->write(fileout);	  
+    }
   else
   {
       MESSAGE("Surface type " << header.classType() << " is not supported.");

lrsplines2D/app/loglikelyhood.C

@@ -0,0 +1,77 @@
+/*
+ * Copyright (C) 1998, 2000-2007, 2010, 2011, 2012, 2013 SINTEF ICT,
+ * Applied Mathematics, Norway.
+ *
+ * Contact information: E-mail: [email protected]                      
+ * SINTEF ICT, Department of Applied Mathematics,                         
+ * P.O. Box 124 Blindern,                                                 
+ * 0314 Oslo, Norway.                                                     
+ *
+ * This file is part of GoTools.
+ *
+ * GoTools is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version. 
+ *
+ * GoTools 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 Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public
+ * License along with GoTools. If not, see
+ * <http://www.gnu.org/licenses/>.
+ *
+ * In accordance with Section 7(b) of the GNU Affero General Public
+ * License, a covered work must retain the producer line in every data
+ * file that is created or manipulated using GoTools.
+ *
+ * Other Usage
+ * You can be released from the requirements of the license by purchasing
+ * a commercial license. Buying such a license is mandatory as soon as you
+ * develop commercial activities involving the GoTools library without
+ * disclosing the source code of your own applications.
+ *
+ * This file may be used in accordance with the terms contained in a
+ * written agreement between you and SINTEF ICT. 
+ */
+
+#include "GoTools/geometry/GoTools.h"
+#include "GoTools/geometry/FileUtils.h"
+#include "GoTools/lrsplines2D/LogLikelyhood.h"
+#include <iostream>
+#include <fstream>
+
+using std::vector;
+using namespace Go;
+
+int main(int argc, char *argv[])
+{
+
+  if (argc != 2)
+    {
+      std::cout << "Parameters: residuals (x,y,z,r)" << std::endl;
+      return 1;
+    }
+  
+  std::ifstream input(argv[1]);
+  double Tny = 10.0;  // Guess value
+
+  // Read point cloud with residuals
+  vector<double> data;
+  vector<double> extent(8);   // Limits for points in all coordinates
+  int nmb_pts = 0;
+  FileUtils::readTxtPointFile(input, 4, data, nmb_pts, extent);
+
+  std::cout << "Number of points: " << nmb_pts << std::endl;
+  // Extract residuals
+  vector<double> residuals(nmb_pts);
+  for (size_t ki=0; ki<nmb_pts; ++ki)
+    residuals[ki] = data[4*ki+3];
+  std::cout << "Min: " << extent[6] << ", max: " << extent[7] << std::endl;
+
+  double loglh2 = 0.0;
+  double loglh = LogLikelyhood::compute(residuals, Tny, true, loglh2);
+  printf("Loglikelyhood: %7.13f, %7.13f \n",loglh, loglh2);
+}

lrsplines2D/app/loglikelyhoodFixed.C

@@ -0,0 +1,77 @@
+/*
+ * Copyright (C) 1998, 2000-2007, 2010, 2011, 2012, 2013 SINTEF ICT,
+ * Applied Mathematics, Norway.
+ *
+ * Contact information: E-mail: [email protected]                      
+ * SINTEF ICT, Department of Applied Mathematics,                         
+ * P.O. Box 124 Blindern,                                                 
+ * 0314 Oslo, Norway.                                                     
+ *
+ * This file is part of GoTools.
+ *
+ * GoTools is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version. 
+ *
+ * GoTools 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 Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public
+ * License along with GoTools. If not, see
+ * <http://www.gnu.org/licenses/>.
+ *
+ * In accordance with Section 7(b) of the GNU Affero General Public
+ * License, a covered work must retain the producer line in every data
+ * file that is created or manipulated using GoTools.
+ *
+ * Other Usage
+ * You can be released from the requirements of the license by purchasing
+ * a commercial license. Buying such a license is mandatory as soon as you
+ * develop commercial activities involving the GoTools library without
+ * disclosing the source code of your own applications.
+ *
+ * This file may be used in accordance with the terms contained in a
+ * written agreement between you and SINTEF ICT. 
+ */
+
+#include "GoTools/geometry/GoTools.h"
+#include "GoTools/geometry/FileUtils.h"
+#include "GoTools/lrsplines2D/LogLikelyhood.h"
+#include <iostream>
+#include <fstream>
+
+using std::vector;
+using namespace Go;
+
+int main(int argc, char *argv[])
+{
+
+  if (argc != 3)
+    {
+      std::cout << "Parameters: residuals (x,y,z,r), degrees of freedom in T-distribution" << std::endl;
+      return 1;
+    }
+  
+  std::ifstream input(argv[1]);
+  double Tny = atof(argv[2]);
+
+  // Read point cloud with residuals
+  vector<double> data;
+  vector<double> extent(8);   // Limits for points in all coordinates
+  int nmb_pts = 0;
+  FileUtils::readTxtPointFile(input, 4, data, nmb_pts, extent);
+
+  std::cout << "Number of points: " << nmb_pts << std::endl;
+  // Extract residuals
+  vector<double> residuals(nmb_pts);
+  for (size_t ki=0; ki<nmb_pts; ++ki)
+    residuals[ki] = data[4*ki+3];
+  std::cout << "Min: " << extent[6] << ", max: " << extent[7] << std::endl;
+
+  double loglh2 = 0.0;
+  double loglh = LogLikelyhood::compute(residuals, Tny, false, loglh2);
+  printf("Loglikelyhood: %7.13f, %7.13f \n",loglh, loglh2);
+}