4 files changed, 201 insertions, 201 deletions

diff --git a/src/Contraction/example/Rips_contraction.cpp b/src/Contraction/example/Rips_contraction.cpp
index acfb516d..59cdec97 100644
--- a/src/Contraction/example/Rips_contraction.cpp
+++ b/src/Contraction/example/Rips_contraction.cpp
@@ -48,25 +48,28 @@ void build_rips(ComplexType& complex, double offset){
 				complex.add_edge(*p,*q);
 }
 
+int main (int argc, char *argv[])
+{
+	if (argc!=3){
+		std::cerr << "Usage "<<argv[0]<<" GUDHIPATH/src/data/sphere3D.off 0.1 to load the file GUDHIPATH/src/data/sphere3D.off and contract the Rips complex built with paremeter 0.2.\n";
+		return -1;
+	}
 
-
-
-void test_contraction_rips(string name_file, double offset){
 	boost::timer::auto_cpu_timer t;
 	Complex complex;
 
 	// load the points
-	Skeleton_blocker_off_reader<Complex> off_reader(name_file,complex,true);
+	Skeleton_blocker_off_reader<Complex> off_reader(argv[1],complex,true);
 	if(!off_reader.is_valid()){
-		std::cerr << "Unable to read file:"<<name_file<<std::endl;
-		return;
+		std::cerr << "Unable to read file:"<<argv[1]<<std::endl;
+		return EXIT_FAILURE;
 	}
-	std::cerr << "build the Rips complex"<<std::endl;
+	std::cout << "build the Rips complex"<<std::endl;
 
-	build_rips(complex,offset);
+	build_rips(complex,atof(argv[2]));
 
 
-	std::cerr << "Initial complex has "<<
+	std::cout << "Initial complex has "<<
 			complex.num_vertices()<<" vertices, and "<<
 			complex.num_edges()<<" edges."<<std::endl;
 
@@ -77,24 +80,12 @@ void test_contraction_rips(string name_file, double offset){
 			contraction::make_remove_popable_blockers_visitor<Profile>());
 	contractor.contract_edges();
 
-	std::cerr << "Resulting complex has "<<
+	std::cout << "Resulting complex has "<<
 			complex.num_vertices()<<" vertices, "<<
 			complex.num_edges()<<"edges and "<<
 			complex.num_blockers()<<" blockers"<<std::endl;
 
-
-}
-
-
-int main (int argc, char *argv[])
-{
-	if (argc!=3){
-		std::cerr << "Usage "<<argv[0]<<" GUDHIPATH/src/data/sphere3D.off 0.1 to load the file GUDHIPATH/src/data/sphere3D.off and contract the Rips complex built with paremeter 0.2.\n";
-		return -1;
-	}
-
-	std::string name_file(argv[1]);
-	test_contraction_rips(name_file,atof(argv[2]));
+	return EXIT_SUCCESS;
 }
 
 
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h
index 924b653c..bcaa3d8c 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h
@@ -46,9 +46,10 @@ public:
 	/**
 	 * @brief Add a vertex to the complex with its associated point.
 	 */
-	void add_vertex(const Point& point){
+	Vertex_handle add_vertex(const Point& point){
 		Vertex_handle ad = SimplifiableSkeletonblocker::add_vertex();
 		(*this)[ad].point() = point;
+		return ad;
 	}
 
 
diff --git a/src/common/include/gudhi/Off_reader.h b/src/common/include/gudhi/Off_reader.h
index a9c64f97..1c99a90a 100644
--- a/src/common/include/gudhi/Off_reader.h
+++ b/src/common/include/gudhi/Off_reader.h
@@ -1,8 +1,8 @@
 /*
  * Off_reader.h
  *  Created on: Nov 28, 2014
- * This file is part of the Gudhi Library. The Gudhi library 
- *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
+ * This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
  *    library for computational topology.
  *
  *    Author(s):       David Salinas
@@ -21,7 +21,7 @@
  *
  *    You should have received a copy of the GNU General Public License
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- * 
+ *
  */
 
 
@@ -113,18 +113,26 @@ private:
 		bool is_off_file = (line.find("OFF") != std::string::npos);
 		bool is_noff_file = (line.find("nOFF") != std::string::npos);
 
-    	if(!is_off_file && !is_noff_file) return false;
+    	if(!is_off_file && !is_noff_file) {
+    		std::cerr << line<<std::endl;
+    		std::cerr << "missing off header\n";
+    		return false;
+    	}
 
     	if(!goto_next_uncomment_line(line)) return false;
     	std::istringstream iss(line);
    		if(is_off_file){
 	  		off_info_.dim = 3;
-	  		if(!(iss >> off_info_.num_vertices >> off_info_.num_faces >> off_info_.num_edges))
+	  		if(!(iss >> off_info_.num_vertices >> off_info_.num_faces >> off_info_.num_edges)){
+	  			std::cerr << "incorrect number of vertices/faces/edges\n";
 	  			return false;
+	  		}
 		}
 		else
-			if(!(iss >> off_info_.dim >> off_info_.num_vertices >> off_info_.num_faces >> off_info_.num_edges))
+			if(!(iss >> off_info_.dim >> off_info_.num_vertices >> off_info_.num_faces >> off_info_.num_edges)){
+				std::cerr << "incorrect number of vertices/faces/edges\n";
 				return false;
+			}
    		off_visitor.init(off_info_.dim,off_info_.num_vertices,off_info_.num_faces,off_info_.num_edges);
 
    		return true;
@@ -134,7 +142,7 @@ private:
 		uncomment_line.clear();
 		do
 			std::getline(stream_, uncomment_line);
-    	while(uncomment_line[0] == '%');
+    	while(uncomment_line[0] == '%');// || uncomment_line.empty());
 		return (uncomment_line.size()>0 && uncomment_line[0] != '%');
 	}
 
diff --git a/src/common/include/gudhi/iofile.h b/src/common/include/gudhi/iofile.h
index b939d45b..9139a3cd 100644
--- a/src/common/include/gudhi/iofile.h
+++ b/src/common/include/gudhi/iofile.h
@@ -14,176 +14,176 @@
 
 
 
-//todo use my new visitor based off instead
-/**
- * @brief OFF reader, save the content of the file (vertices and maximal faces) in 'complex'.
- * The class Complex has to handle the following operations:
- * - void add_vertex(double[dim],int dim)
- * - void add_face(int dimension ,int[dimension] vertices)
- * Source from : http://www.holmes3d.net/graphics/offfiles/OFFLoading.txt
- *
- * @todo todo ignore comments in the file -> # comment
- */
-template<typename Complex> inline
-bool general_read_off_file(const std::string & file_name, Complex& complex){
-  // Declare temporary variables to read data into.
-  // If the read goes well, we'll copy these into
-  // our class variables, overwriting what used to
-  // be there. If it doesn't, we won't have messed up
-  // our previous data structures.
-  int tempNumPoints   = 0;  // Number of x,y,z coordinate triples
-  int tempNumFaces    = 0;  // Number of polygon sets
-  int tempNumEdges    = 0;  // Unused, except for reading.
-  int tempDimPoints   = 0;
-  double** tempPoints = NULL;  // An array of x,y,z coordinates.
-  int** tempFaces = NULL;    // An array of arrays of point
-  // pointers. Each entry in this
-  // is an array of integers. Each
-  // integer in that array is the
-  // index of the x, y, and z
-  // coordinates in the corresponding
-  // arrays.
-  int*  tempFaceSizes = NULL;  // An array of polygon point counts.
-  // Each of the arrays in the tempFaces
-  // array may be of different lengths.
-  // This array corresponds to that
-  // array, and gives their lengths.
-  int i;        // Generic loop variable.
-  bool goodLoad = true;    // Set to false if the file appears
-  // not to be a valid OFF file.
-  char tempBuf[128];    // A buffer for reading strings
-  // from the file.
-
-  // Create an input file stream for the file the CArchive
-  // is connected to. This allows use of the overloaded
-  // extraction operator for conversion from string
-  // data to doubles and ints.
-  std::ifstream ifs (file_name.c_str(), std::ios::in);
-  if(!ifs.is_open()) {
-    std::cerr << "Unable to open file " << file_name << std::endl;
-    return false;
-  }
-
-  // Grab the first string. If it's "OFF", we think this
-  // is an OFF file and continue. Otherwise we give up.
-  ifs >> tempBuf;
-  if (strcmp(tempBuf, "OFF") != 0) {
-    goodLoad = false;
-    std::cerr << "No OFF preambule\n";
-  }
-
-  // Read the sizes for our two arrays, and the third
-  // int on the line. If the important two are zero
-  // sized, this is a messed up OFF file. Otherwise,
-  // we setup our temporary arrays.
-  if (goodLoad) {
-    ifs >> tempNumPoints >> tempNumFaces >> tempNumEdges;
-    if (tempNumPoints < 1 || tempNumFaces < 0) {
-      // If either of these were negative, we make
-      // sure that both are set to zero. This is
-      // important for later deleting our temporary
-      // storage.
-      goodLoad      = false;
-      std::cerr << "tempNumPoints < 1 || tempNumFaces < 0\n";
-      tempNumPoints = 0;
-      tempNumFaces  = 0;
-    } else {
-      tempPoints = new double*[tempNumPoints];
-      tempFaces = new int*[tempNumFaces];
-      tempFaceSizes = new int[tempNumFaces];
-    }
-  }
-
-  if (goodLoad) {
-    // Load all of the points.
-
-    // we start by loading the first one
-    // the case is difference because then we dont know the dimension by advance
-    // we discover the point dimension by reading the first line
-    std::string lineFirstPoint;
-	std::getline(ifs, lineFirstPoint);
-    while(lineFirstPoint.size()<3){
-    	std::getline(ifs, lineFirstPoint);
-    }
-
-    // we store the first point in a temporary list
-    std::istringstream lineFirstPointStream(lineFirstPoint);
-    std::list<double> firstTempPoint;
-    double coord;
-    while(lineFirstPointStream>>coord){
-      firstTempPoint.push_back(coord);
-      ++tempDimPoints;
-    }
-    // we store the point in our points array
-    tempPoints[0]=new double[tempDimPoints];
-    for( int j = 0 ; j<tempDimPoints; ++j){
-      tempPoints[0][j] = firstTempPoint.front();
-      firstTempPoint.pop_front();
-    }
-
-    // now, we know the dimension and can read safely other points
-    for (i = 1; i < tempNumPoints; i++) {
-      tempPoints[i] = new double[tempDimPoints];
-      for (int j = 0 ; j<tempDimPoints ; ++j){
-        ifs>>tempPoints[i][j];
-      }
-    }
-
-    // Load all of the faces.
-    for (i = 0; i < tempNumFaces; i++) {
-      // This tells us how many points make up
-      // this face.
-      ifs >> tempFaceSizes[i];
-      // So we declare a new array of that size
-      tempFaces[i] = new int[tempFaceSizes[i]];
-      // And load its elements with the vertex indices.
-      for (int j = 0; j < tempFaceSizes[i]; j++) {
-        ifs >> tempFaces[i][j];
-      }
-      // Clear out any face color data by reading up to
-      // the newline. 128 is probably considerably more
-      // space than necessary, but better safe than
-      // sorry.
-      ifs.getline(tempBuf, 128);
-    }
-  }
-
-  // Here is where we copy the data from the temp
-  // structures into our permanent structures. We
-  // probably will do some more processing on the
-  // data at the same time. This code you must fill
-  // in on your own.
-  if (goodLoad) {
-    // we save vertices first in the complex
-    for (i = 0; i < tempNumPoints; i++)
-      complex.add_vertex(tempPoints[i],tempDimPoints);
-
-    // we save faces
-    for (i = 0; i < tempNumFaces; i++) {
-      for (int j = 0; j < tempFaceSizes[i]; j++)
-        complex.add_face(tempFaceSizes[i],tempFaces[i]);
-    }
-  }
-
-  // Now that we're done, we have to make sure we
-  // free our dynamic memory.
-  for (i = 0; i < tempNumPoints; i++) {
-    delete []tempPoints[i];
-  }
-  delete []tempPoints;
-
-  for (i = 0; i < tempNumFaces; i++) {
-    delete tempFaces[i];
-  }
-  delete []tempFaces;
-  delete []tempFaceSizes;
-
-  // Clean up our ifstream. The MFC framework will
-  // take care of the CArchive.
-  ifs.close();
-
-  return goodLoad;
-}
+////todo use my new visitor based off instead
+///**
+// * @brief OFF reader, save the content of the file (vertices and maximal faces) in 'complex'.
+// * The class Complex has to handle the following operations:
+// * - void add_vertex(double[dim],int dim)
+// * - void add_face(int dimension ,int[dimension] vertices)
+// * Source from : http://www.holmes3d.net/graphics/offfiles/OFFLoading.txt
+// *
+// * @todo todo ignore comments in the file -> # comment
+// */
+//template<typename Complex> inline
+//bool general_read_off_file(const std::string & file_name, Complex& complex){
+//  // Declare temporary variables to read data into.
+//  // If the read goes well, we'll copy these into
+//  // our class variables, overwriting what used to
+//  // be there. If it doesn't, we won't have messed up
+//  // our previous data structures.
+//  int tempNumPoints   = 0;  // Number of x,y,z coordinate triples
+//  int tempNumFaces    = 0;  // Number of polygon sets
+//  int tempNumEdges    = 0;  // Unused, except for reading.
+//  int tempDimPoints   = 0;
+//  double** tempPoints = NULL;  // An array of x,y,z coordinates.
+//  int** tempFaces = NULL;    // An array of arrays of point
+//  // pointers. Each entry in this
+//  // is an array of integers. Each
+//  // integer in that array is the
+//  // index of the x, y, and z
+//  // coordinates in the corresponding
+//  // arrays.
+//  int*  tempFaceSizes = NULL;  // An array of polygon point counts.
+//  // Each of the arrays in the tempFaces
+//  // array may be of different lengths.
+//  // This array corresponds to that
+//  // array, and gives their lengths.
+//  int i;        // Generic loop variable.
+//  bool goodLoad = true;    // Set to false if the file appears
+//  // not to be a valid OFF file.
+//  char tempBuf[128];    // A buffer for reading strings
+//  // from the file.
+//
+//  // Create an input file stream for the file the CArchive
+//  // is connected to. This allows use of the overloaded
+//  // extraction operator for conversion from string
+//  // data to doubles and ints.
+//  std::ifstream ifs (file_name.c_str(), std::ios::in);
+//  if(!ifs.is_open()) {
+//    std::cerr << "Unable to open file " << file_name << std::endl;
+//    return false;
+//  }
+//
+//  // Grab the first string. If it's "OFF", we think this
+//  // is an OFF file and continue. Otherwise we give up.
+//  ifs >> tempBuf;
+//  if (strcmp(tempBuf, "OFF") != 0) {
+//    goodLoad = false;
+//    std::cerr << "No OFF preambule\n";
+//  }
+//
+//  // Read the sizes for our two arrays, and the third
+//  // int on the line. If the important two are zero
+//  // sized, this is a messed up OFF file. Otherwise,
+//  // we setup our temporary arrays.
+//  if (goodLoad) {
+//    ifs >> tempNumPoints >> tempNumFaces >> tempNumEdges;
+//    if (tempNumPoints < 1 || tempNumFaces < 0) {
+//      // If either of these were negative, we make
+//      // sure that both are set to zero. This is
+//      // important for later deleting our temporary
+//      // storage.
+//      goodLoad      = false;
+//      std::cerr << "tempNumPoints < 1 || tempNumFaces < 0\n";
+//      tempNumPoints = 0;
+//      tempNumFaces  = 0;
+//    } else {
+//      tempPoints = new double*[tempNumPoints];
+//      tempFaces = new int*[tempNumFaces];
+//      tempFaceSizes = new int[tempNumFaces];
+//    }
+//  }
+//
+//  if (goodLoad) {
+//    // Load all of the points.
+//
+//    // we start by loading the first one
+//    // the case is difference because then we dont know the dimension by advance
+//    // we discover the point dimension by reading the first line
+//    std::string lineFirstPoint;
+//	std::getline(ifs, lineFirstPoint);
+//    while(lineFirstPoint.size()<3){
+//    	std::getline(ifs, lineFirstPoint);
+//    }
+//
+//    // we store the first point in a temporary list
+//    std::istringstream lineFirstPointStream(lineFirstPoint);
+//    std::list<double> firstTempPoint;
+//    double coord;
+//    while(lineFirstPointStream>>coord){
+//      firstTempPoint.push_back(coord);
+//      ++tempDimPoints;
+//    }
+//    // we store the point in our points array
+//    tempPoints[0]=new double[tempDimPoints];
+//    for( int j = 0 ; j<tempDimPoints; ++j){
+//      tempPoints[0][j] = firstTempPoint.front();
+//      firstTempPoint.pop_front();
+//    }
+//
+//    // now, we know the dimension and can read safely other points
+//    for (i = 1; i < tempNumPoints; i++) {
+//      tempPoints[i] = new double[tempDimPoints];
+//      for (int j = 0 ; j<tempDimPoints ; ++j){
+//        ifs>>tempPoints[i][j];
+//      }
+//    }
+//
+//    // Load all of the faces.
+//    for (i = 0; i < tempNumFaces; i++) {
+//      // This tells us how many points make up
+//      // this face.
+//      ifs >> tempFaceSizes[i];
+//      // So we declare a new array of that size
+//      tempFaces[i] = new int[tempFaceSizes[i]];
+//      // And load its elements with the vertex indices.
+//      for (int j = 0; j < tempFaceSizes[i]; j++) {
+//        ifs >> tempFaces[i][j];
+//      }
+//      // Clear out any face color data by reading up to
+//      // the newline. 128 is probably considerably more
+//      // space than necessary, but better safe than
+//      // sorry.
+//      ifs.getline(tempBuf, 128);
+//    }
+//  }
+//
+//  // Here is where we copy the data from the temp
+//  // structures into our permanent structures. We
+//  // probably will do some more processing on the
+//  // data at the same time. This code you must fill
+//  // in on your own.
+//  if (goodLoad) {
+//    // we save vertices first in the complex
+//    for (i = 0; i < tempNumPoints; i++)
+//      complex.add_vertex(tempPoints[i],tempDimPoints);
+//
+//    // we save faces
+//    for (i = 0; i < tempNumFaces; i++) {
+//      for (int j = 0; j < tempFaceSizes[i]; j++)
+//        complex.add_face(tempFaceSizes[i],tempFaces[i]);
+//    }
+//  }
+//
+//  // Now that we're done, we have to make sure we
+//  // free our dynamic memory.
+//  for (i = 0; i < tempNumPoints; i++) {
+//    delete []tempPoints[i];
+//  }
+//  delete []tempPoints;
+//
+//  for (i = 0; i < tempNumFaces; i++) {
+//    delete tempFaces[i];
+//  }
+//  delete []tempFaces;
+//  delete []tempFaceSizes;
+//
+//  // Clean up our ifstream. The MFC framework will
+//  // take care of the CArchive.
+//  ifs.close();
+//
+//  return goodLoad;
+//}
 
 
 template<typename Complex>