instrospect-> introspect, minor changes

.gitattributes

@@ -449,6 +449,8 @@ Jet_fitting_3/examples/Jet_fitting_3/data/bezierpb3-0.007812.off -text
 Jet_fitting_3/examples/Jet_fitting_3/data/ellipe0.003.off -text
 Jet_fitting_3/examples/Jet_fitting_3/data/venus.off -text
 Jet_fitting_3/examples/Jet_fitting_3/test.off -text
+Jet_fitting_3/test/Jet_fitting_3/blind_1pt.C -text
+Jet_fitting_3/test/Jet_fitting_3/makefile -text
 Kernel_23/doc_tex/Kernel_23_ref/fig/IsoCuboid.eps -text
 Kernel_23/doc_tex/Kernel_23_ref/fig/IsoCuboid.gif -text svneol=unset#unset
 Kernel_23/doc_tex/Kernel_23_ref/fig/IsoCuboid.pdf -text svneol=unset#unset

Jet_fitting_3/demo/Jet_fitting_3/makefile

@@ -46,7 +46,7 @@ QTLDFLAGS = \
           $(CGAL_QT_LDFLAGS) -lGL -lglut
 
 
-INTRO_LD_FLAGS=-L$(INTROSPEC_DIR) -lInstrospect
+INTRO_LD_FLAGS=-L$(INTROSPEC_DIR) -lIntrospect
 
 #---------------------------------------------------------------------#
 #                    target entries

Jet_fitting_3/doc_tex/Jet_fitting_3/main.tex

@@ -1,7 +1,7 @@
 \ccUserChapter{Estimation of local differential properties of sampled
 surfaces via polynomial fitting}
 \label{chap:Jet_fitting_3}
-\ccChapterAuthor{Marc Pouget and Frédéric Cazals}
+\ccChapterAuthor{Marc Pouget and Frederic Cazals}
 
 \minitoc
 

Jet_fitting_3/doc_tex/Jet_fitting_3_ref/LinAlgTraits.tex

@@ -35,8 +35,6 @@ the \ccc{LocalKernel} concept~: \ccc{LocalKernel::FT}.
 % +------------------------------------------------------------------
 \ccNestedType{FT}{The scalar type.}
 \ccGlue
-\ccNestedType{Vector}{The Vector type.}
-\ccGlue
 \ccNestedType{Matrix }{The Matrix type.}
 
 %\ccCreation
@@ -45,22 +43,28 @@ the \ccc{LocalKernel} concept~: \ccc{LocalKernel::FT}.
 %\ccConstructor{LinAlgTraits();}{default constructor.}
 
 \ccOperations
+The Matrix has classical access to its elements.
 
-Usual brackets operator for Vector and Matrix types.
+\ccMethod{void set_elt(size_t i, size_t j, const FT value)}{}
+\ccGlue
+\ccMethod{FT get_elt(size_t i, size_t j)}{}
 
-\ccMethod{void eigen_symm_algo(Matrix& S, Vector& eval, Matrix&
+The LinAlgTraits has an eigenanalysis and a singular value
+decomposition algorithm.
+
+\ccMethod{void eigen_symm_algo(Matrix& S, FT* eval, Matrix&
 evec);} {Performs an eigenanalysis of a real symmetric matrix.  Eigen
-values are sorted in descending order, eigen vectors are sorted in
+values are sorted in ascending order, eigen vectors are sorted in
 accordance. }
-\ccMethod{void solve_ls_svd_algo(Matrix& M, Vector& X, const Vector&
+\ccMethod{void solve_ls_svd_algo(Matrix& M, FT* B, FT* cond_nb);}
-B, double &cond_nb);}{ Solves the system MX=B (in the least square
+{ Solves the system MX=B (in the least square sense if M is not
-sense if M is not square) using a Singular Value Decomposition and
+square) using a Singular Value Decomposition and gives the condition
-gives the condition number of M.}
+number of M. The solution is stored in B.}
 
 \ccHasModels
 % +------------------------------------------------------------------
-\ccc{GSL}. See the implementation in the exemple directory
+\ccc{Lapack}. See the implementation in the exemple directory
-exemples/Jet\_fitting\_3/GSL.h .
+exemples/Jet\_fitting\_3/LinAlg\_lapack.h .
 
 
 

Jet_fitting_3/examples/Jet_fitting_3/blind_1pt.C

@@ -81,65 +81,16 @@ int main(int argc, char *argv[])
   //OUTPUT on outFile
   CGAL::set_pretty_mode(outFile);
   outFile   << "vertex : " << in_points[0] << std::endl
-	    << "number of points used : " << in_points.size() << std::endl
+	    << "number of points used : " << in_points.size() << std::endl;
-	    << "origin : " << monge_rep.origin_pt() << std::endl
+  monge_rep.dump_verbose(outFile);
-	    << "d1 : " << monge_rep.d1() << std::endl 
+  monge_info.dump_verbose(outFile);
-	    << "d2 : " << monge_rep.d2() << std::endl
-	    << "n : " << monge_rep.n() << std::endl
-	    << "cond_nb : " << monge_info.cond_nb() << std::endl 
-	    << "pca_eigen_vals " << monge_info.pca_eigen_vals()[0] 
-	    << " " << monge_info.pca_eigen_vals()[2] 
-	    << " " << monge_info.pca_eigen_vals()[3]  << std::endl 
-	    << "pca_eigen_vecs : " << std::endl 
-	    << monge_info.pca_eigen_vecs()[0] << std::endl 
-	    << monge_info.pca_eigen_vecs()[1] << std::endl 
-	    << monge_info.pca_eigen_vecs()[2] << std::endl
-	    << std::endl ;
-  if ( d_monge >= 2) 
-    outFile   << "k1 : " << monge_rep.coefficients()[0] << std::endl 
-	      << "k2 : " << monge_rep.coefficients()[1] << std::endl;
-  if ( d_monge >= 3) 
-    outFile   << "b0 : " << monge_rep.coefficients()[2] << std::endl 
-	      << "b1 : " << monge_rep.coefficients()[3] << std::endl
-	      << "b2 : " << monge_rep.coefficients()[4] << std::endl 
-	      << "b3 : " << monge_rep.coefficients()[5] << std::endl; 
-  if ( d_monge >= 4) 
-    outFile   << "c0 : " << monge_rep.coefficients()[6] << std::endl 
-	      << "c1 : " << monge_rep.coefficients()[7] << std::endl
-	      << "c2 : " << monge_rep.coefficients()[8] << std::endl 
-	      << "c3 : " << monge_rep.coefficients()[9] << std::endl 
-	      << "c4 : " << monge_rep.coefficients()[10] << std::endl; 
   
-   //OUTPUT on std::cout
+  //OUTPUT on std::cout
   CGAL::set_pretty_mode(std::cout);
   std::cout << "vertex : " << in_points[0] << std::endl
-	    << "number of points used : " << in_points.size() << std::endl
+	    << "number of points used : " << in_points.size() << std::endl;
-	    << "origin : " << monge_rep.origin_pt() << std::endl
+  monge_rep.dump_verbose(std::cout);
-	    << "d1 : " << monge_rep.d1() << std::endl 
+  monge_info.dump_verbose(std::cout);
-	    << "d2 : " << monge_rep.d2() << std::endl
+
-	    << "n : " << monge_rep.n() << std::endl
-	    << "cond_nb : " << monge_info.cond_nb() << std::endl 
-	    << "pca_eigen_vals " << monge_info.pca_eigen_vals()[0] 
-	    << " " << monge_info.pca_eigen_vals()[2] 
-	    << " " << monge_info.pca_eigen_vals()[3]  << std::endl 
-	    << "pca_eigen_vecs : " << std::endl 
-	    << monge_info.pca_eigen_vecs()[0] << std::endl 
-	    << monge_info.pca_eigen_vecs()[1] << std::endl 
-	    << monge_info.pca_eigen_vecs()[2] << std::endl
-	    << std::endl ;
-  if ( d_monge >= 2) 
-    std::cout << "k1 : " << monge_rep.coefficients()[0] << std::endl 
-	      << "k2 : " << monge_rep.coefficients()[1] << std::endl;
-  if ( d_monge >= 3) 
-    std::cout << "b0 : " << monge_rep.coefficients()[2] << std::endl 
-	      << "b1 : " << monge_rep.coefficients()[3] << std::endl
-	      << "b2 : " << monge_rep.coefficients()[4] << std::endl 
-	      << "b3 : " << monge_rep.coefficients()[5] << std::endl; 
-  if ( d_monge >= 4) 
-    std::cout << "c0 : " << monge_rep.coefficients()[6] << std::endl 
-	      << "c1 : " << monge_rep.coefficients()[7] << std::endl
-	      << "c2 : " << monge_rep.coefficients()[8] << std::endl 
-	      << "c3 : " << monge_rep.coefficients()[9] << std::endl 
-	      << "c4 : " << monge_rep.coefficients()[10] << std::endl; 
   return 1;
 }

Jet_fitting_3/test/Jet_fitting_3/blind_1pt.C

@@ -0,0 +1,65 @@
+#include <CGAL/basic.h>
+#include <CGAL/Cartesian.h>
+
+#include <stdio.h>
+#include <iostream>
+#include <fstream>
+#include <stdlib.h>
+
+#include <vector>
+#include "../../include/CGAL/Monge_via_jet_fitting.h" 
+#include "include/LinAlg_lapack.h" 
+
+typedef double                   DFT;
+typedef CGAL::Cartesian<DFT>     Data_Kernel;
+typedef Data_Kernel::Point_3     DPoint;
+typedef Data_Kernel::Vector_3     DVector;
+typedef CGAL::Monge_rep<Data_Kernel>   My_Monge_rep;
+
+typedef double                   LFT;
+typedef CGAL::Cartesian<LFT>     Local_Kernel;
+typedef CGAL::Monge_info<Local_Kernel> My_Monge_info;
+typedef CGAL::Monge_via_jet_fitting<Data_Kernel, Local_Kernel, Lapack> My_Monge_via_jet_fitting;
+
+       
+int main()
+{
+  //open the input file
+  std::ifstream inFile( "data/in_points_d4.txt", std::ios::in);
+  if ( !inFile ) 
+    {
+      std::cerr << "cannot open file for input\n";
+      exit(-1);
+    }
+  //initalize the in_points container
+  double x, y, z;
+  std::vector<DPoint> in_points;
+  char ch[40];
+  while (inFile >> ch) {
+    x = atof(ch);
+    inFile >> ch;
+    y = atof(ch); 
+    inFile >> ch;
+    z = atof(ch);
+    DPoint p(x,y,z);
+    in_points.push_back(p);
+  }
+  inFile.close();
+
+  // fct parameters
+  int d_fitting = 4;
+  int d_monge = 4;
+  My_Monge_rep monge_rep;
+  My_Monge_info monge_info;
+  //run the main fct
+  My_Monge_via_jet_fitting do_it(in_points.begin(), in_points.end(),
+				 d_fitting, d_monge, 
+				 monge_rep, monge_info);
+
+  monge_rep.comply_wrt_given_normal( -monge_rep.n() );
+  //OUTPUT on std::cout
+  monge_rep.dump_verbose( std::cout );
+  monge_rep.dump_4ogl( std::cout, 1 );
+  monge_info.dump_verbose( std::cout );
+  std::cout << "success\n";
+}

Jet_fitting_3/test/Jet_fitting_3/data/in_points_d4.txt

@@ -0,0 +1,17 @@
+0 0 0 
+0 1 .2
+0 -1 0.2
+1 0 0.1
+-1 0 0.1 
+1 1 0.3
+-1 1 .3
+-1 -1 .3
+1 -1 .3
+2 0 .4
+0 2 .8
+-2 0 .4
+0 -2 .8
+2 2 1.2
+-2 -2 1.2 
+2 -2 1.2
+-2 2 1.2

Jet_fitting_3/test/Jet_fitting_3/include/LinAlg_lapack.h

@@ -0,0 +1,110 @@
+#ifndef _LAPACK_H_
+#define _LAPACK_H_
+
+#include <stdlib.h>
+#include "blaswrap.h"
+#include "f2c.h"
+extern "C" {
+#include "clapack.h"
+}
+
+////////////////////////class Lapack_matrix/////////////////////
+//in Lapack, matrices are one-dimensional arrays 
+// and elements are column-major ordered
+// this class is a wrapper defining set and get in the usual way
+class Lapack_matrix{
+protected:
+  double* m_matrix;
+public:
+  size_t nb_rows;
+  size_t nb_columns;
+  //contructor
+  // initializes all the elements of the matrix to zero.
+  Lapack_matrix(size_t n1, size_t n2) { 
+    m_matrix = (double*) calloc (n1*n2, sizeof(double)); 
+    nb_rows = n1;
+    nb_columns = n2;
+  }
+
+  //destructor
+  //  ~Lapack_matrix();// { free m_matrix; }
+  
+  //access
+  const double* matrix() const { return m_matrix; }
+  double* matrix() { return m_matrix; }
+
+  void set_elt(size_t i, size_t j, const double value) { m_matrix[j*nb_rows+i] = value; }
+  double get_elt(size_t i, size_t j) { return m_matrix[j*nb_rows+i]; }
+}; 
+
+//Lapack_matrix::~Lapack_matrix() {  free m_matrix; } bug!
+
+////////////////////////class Lapack/////////////////////
+class Lapack{
+public:
+  typedef Lapack_matrix Matrix;
+  // solve for eigenvalues and eigenvectors.
+  // eigen values are sorted in ascending order, 
+  // eigen vectors are sorted in accordance.
+  static
+    void eigen_symm_algo(Matrix& S, double* eval, Matrix& evec);
+  //solve MX=B using SVD and give the condition number of M
+  static
+    void solve_ls_svd_algo(Matrix& M, double* B, double &cond_nb);
+};
+
+void Lapack::eigen_symm_algo(Matrix& S, double* eval, Matrix& evec)
+{
+  char jobz = 'V';
+  char range = 'A';
+  char uplo = 'U';
+  integer n = S.nb_rows,
+    lda = S.nb_rows,
+    il = 0, iu = 0,
+    m = n, 
+    lwork = 26*n,
+    liwork = 10*n,
+    info;
+  double vl=0, vu=0, abstol = 0;
+
+  integer* isuppz = (integer*) malloc(2*n*sizeof(integer));
+  double* work = (double*) malloc(lwork*sizeof(double));
+  integer* iwork = (integer*) malloc(liwork*sizeof(integer));
+
+  dsyevr_(&jobz, &range, &uplo, &n, S.matrix(), &lda, &vl, &vu, &il, &iu, &abstol, &m,
+	  eval, evec.matrix(), &n, isuppz, work, &lwork, iwork, &liwork, &info);
+  
+  //clean up 
+  free(isuppz); 
+  free(work);
+  free(iwork);
+}
+
+void Lapack::solve_ls_svd_algo(Matrix& M, double* B, double &cond_nb)
+{
+  integer m = M.nb_rows,
+    n = M.nb_columns,
+    nrhs = 1,
+    lda = m,
+    ldb = m,
+    rank,
+    lwork = 5*m,
+    info;
+  //c style
+  double* sing_values = (double*) malloc(n*sizeof(double));
+  double* work = (double*) malloc(lwork*sizeof(double));
+
+  double rcond = -1;
+
+  dgelss_(&m, &n, &nrhs, M.matrix(), &lda, B, &ldb, sing_values, 
+	  &rcond, &rank, work, &lwork, &info);
+  assert(info==0);
+
+  cond_nb = sing_values[0]/sing_values[n-1];
+  
+  //clean up 
+  free(sing_values);
+  free(work);
+}
+
+#endif

Jet_fitting_3/test/Jet_fitting_3/makefile

@@ -0,0 +1,141 @@
+# Created by the script create_makefile
+# This is the makefile for compiling a CGAL application.
+
+#---------------------------------------------------------------------#
+#                    include platform specific settings
+#---------------------------------------------------------------------#
+# Choose the right include file from the <cgalroot>/make directory.
+
+include $(CGAL_MAKEFILE)
+
+PROFOPT= -g  
+CFLAGS=${PROFOPT} 
+#---------------------------------------------------------------------#
+#                    compiler flags
+#---------------------------------------------------------------------#
+LAPACK_INCDIRS = -I$(LAPACK_DIR)/SRC -I$(LAPACK_DIR)
+
+CXXFLAGS = \
+           -I../../include \
+           $(CGAL_CXXFLAGS) \
+           $(LONG_NAME_PROBLEM_CXXFLAGS) \
+           $(LAPACK_INCDIRS) \
+           ${CFLAGS} 
+
+#---------------------------------------------------------------------#
+#                    linker flags
+#---------------------------------------------------------------------#
+F2CDIR  = $(LAPACK_DIR)/F2CLIBS
+LAPACK_LDLIBS  = $(LAPACK_DIR)/lapack_LINUX.a \
+          $(LAPACK_DIR)/blas_LINUX.a $(LAPACK_DIR)/tmglib_LINUX.a \
+          $(F2CDIR)/libF77.a $(F2CDIR)/libI77.a -lm -lc
+
+LIBPATH = \
+          $(CGAL_LIBPATH)
+
+LDFLAGS = \
+          $(LONG_NAME_PROBLEM_LDFLAGS) \
+          ${LAPACK_LDLIBS} \
+	  $(CGAL_LDFLAGS) \
+       
+
+
+#---------------------------------------------------------------------#
+#                    target entries
+#---------------------------------------------------------------------#
+
+all:            \
+                blind_1pt 
+
+blind_1pt: blind_1pt.o
+	$(CGAL_CXX) $(LIBPATH) -o blind_1pt.exe blind_1pt.o \
+	$(LDFLAGS) 
+
+rmexe:
+	rm *.exe
+
+clean: \
+         blind_1pt.clean 
+	rmexe
+
+
+depend: 
+	makedepend *.[Ch]
+
+#---------------------------------------------------------------------#
+#                    suffix rules
+#---------------------------------------------------------------------#
+
+.C$(OBJ_EXT):
+	$(CGAL_CXX) $(CXXFLAGS) $(OBJ_OPT) $<
+
+# DO NOT DELETE
+
+blind_1pt.o: /usr/include/stdio.h /usr/include/features.h
+blind_1pt.o: /usr/include/sys/cdefs.h /usr/include/gnu/stubs.h
+blind_1pt.o: /usr/include/bits/types.h /usr/include/bits/wordsize.h
+blind_1pt.o: /usr/include/bits/typesizes.h /usr/include/libio.h
+blind_1pt.o: /usr/include/_G_config.h /usr/include/wchar.h
+blind_1pt.o: /usr/include/bits/wchar.h /usr/include/gconv.h
+blind_1pt.o: /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h
+blind_1pt.o: /usr/include/stdlib.h /usr/include/sys/types.h
+blind_1pt.o: /usr/include/time.h /usr/include/endian.h
+blind_1pt.o: /usr/include/bits/endian.h /usr/include/sys/select.h
+blind_1pt.o: /usr/include/bits/select.h /usr/include/bits/sigset.h
+blind_1pt.o: /usr/include/bits/time.h /usr/include/sys/sysmacros.h
+blind_1pt.o: /usr/include/bits/pthreadtypes.h /usr/include/bits/sched.h
+blind_1pt.o: /usr/include/alloca.h ../../include/CGAL/Monge_via_jet_fitting.h
+blind_1pt.o: ../../include/CGAL/jet_fitting_3_assertions.h
+blind_1pt.o: /usr/include/math.h /usr/include/bits/huge_val.h
+blind_1pt.o: /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h
+blind_1pt.o: include/GSL.h /usr/include/gsl/gsl_linalg.h
+blind_1pt.o: /usr/include/gsl/gsl_mode.h /usr/include/gsl/gsl_permutation.h
+blind_1pt.o: /usr/include/gsl/gsl_types.h /usr/include/gsl/gsl_errno.h
+blind_1pt.o: /usr/include/errno.h /usr/include/bits/errno.h
+blind_1pt.o: /usr/include/linux/errno.h /usr/include/asm/errno.h
+blind_1pt.o: /usr/include/asm-i386/errno.h /usr/include/gsl/gsl_check_range.h
+blind_1pt.o: /usr/include/gsl/gsl_vector.h
+blind_1pt.o: /usr/include/gsl/gsl_vector_complex_long_double.h
+blind_1pt.o: /usr/include/gsl/gsl_complex.h
+blind_1pt.o: /usr/include/gsl/gsl_vector_long_double.h
+blind_1pt.o: /usr/include/gsl/gsl_block_long_double.h
+blind_1pt.o: /usr/include/gsl/gsl_vector_complex.h
+blind_1pt.o: /usr/include/gsl/gsl_block_complex_long_double.h
+blind_1pt.o: /usr/include/gsl/gsl_vector_complex_double.h
+blind_1pt.o: /usr/include/gsl/gsl_vector_double.h
+blind_1pt.o: /usr/include/gsl/gsl_block_double.h
+blind_1pt.o: /usr/include/gsl/gsl_block_complex_double.h
+blind_1pt.o: /usr/include/gsl/gsl_vector_complex_float.h
+blind_1pt.o: /usr/include/gsl/gsl_vector_float.h
+blind_1pt.o: /usr/include/gsl/gsl_block_float.h
+blind_1pt.o: /usr/include/gsl/gsl_block_complex_float.h
+blind_1pt.o: /usr/include/gsl/gsl_vector_ulong.h
+blind_1pt.o: /usr/include/gsl/gsl_block_ulong.h
+blind_1pt.o: /usr/include/gsl/gsl_vector_long.h
+blind_1pt.o: /usr/include/gsl/gsl_block_long.h
+blind_1pt.o: /usr/include/gsl/gsl_vector_uint.h
+blind_1pt.o: /usr/include/gsl/gsl_block_uint.h
+blind_1pt.o: /usr/include/gsl/gsl_vector_int.h
+blind_1pt.o: /usr/include/gsl/gsl_block_int.h
+blind_1pt.o: /usr/include/gsl/gsl_vector_ushort.h
+blind_1pt.o: /usr/include/gsl/gsl_block_ushort.h
+blind_1pt.o: /usr/include/gsl/gsl_vector_short.h
+blind_1pt.o: /usr/include/gsl/gsl_block_short.h
+blind_1pt.o: /usr/include/gsl/gsl_vector_uchar.h
+blind_1pt.o: /usr/include/gsl/gsl_block_uchar.h
+blind_1pt.o: /usr/include/gsl/gsl_vector_char.h
+blind_1pt.o: /usr/include/gsl/gsl_block_char.h /usr/include/gsl/gsl_matrix.h
+blind_1pt.o: /usr/include/gsl/gsl_matrix_complex_long_double.h
+blind_1pt.o: /usr/include/gsl/gsl_matrix_complex_double.h
+blind_1pt.o: /usr/include/gsl/gsl_matrix_complex_float.h
+blind_1pt.o: /usr/include/gsl/gsl_matrix_long_double.h
+blind_1pt.o: /usr/include/gsl/gsl_matrix_double.h
+blind_1pt.o: /usr/include/gsl/gsl_matrix_float.h
+blind_1pt.o: /usr/include/gsl/gsl_matrix_ulong.h
+blind_1pt.o: /usr/include/gsl/gsl_matrix_long.h
+blind_1pt.o: /usr/include/gsl/gsl_matrix_uint.h
+blind_1pt.o: /usr/include/gsl/gsl_matrix_int.h
+blind_1pt.o: /usr/include/gsl/gsl_matrix_ushort.h
+blind_1pt.o: /usr/include/gsl/gsl_matrix_short.h
+blind_1pt.o: /usr/include/gsl/gsl_matrix_uchar.h
+blind_1pt.o: /usr/include/gsl/gsl_matrix_char.h /usr/include/gsl/gsl_eigen.h