6 files changed, 98 insertions, 280 deletions

diff --git a/src/common/doc/Gudhi_banner.jpg b/src/common/doc/Gudhi_banner.jpg
new file mode 100644
index 00000000..ebd3d8af
--- /dev/null
+++ b/src/common/doc/Gudhi_banner.jpg
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index 4e36066f..b640ea7b 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -1,20 +1,38 @@
 /**
 \mainpage 
 
+\image html "Gudhi_banner.jpg" "" width=20cm
+
 The Gudhi library (Geometric Understanding in Higher Dimensions) is a generic C++ library for 
-computational topology. Its goal is to provide robust, efficient, flexible and easy to use 
+topological analysis of high-dimensional data whose goal is to provide robust, efficient, flexible and easy to use 
 implementations of 
-state-of-the-art algorithms and data structures for computational topology. We refer to 
+state-of-the-art algorithms and data structures for computational topology. 
+
+The current release of the library allows to use several data-structures for simplicial complexes :
+simplex tree, Hasse diagram or skeleton-blocker. Several  operations can then be done on top of these
+representations such a spersistent homology computation or simplification. 
+
+All data-structures are generic and several of their aspects (such as stored elements, policies) 
+can be parametrized via template classes.
+
+We refer to 
 \cite gudhilibrary_ICMS14
 for a detailed description of the design of the library.
 
-The current release of the library allows the user to construct representations of simplicial complexes -- 
-simplex tree or Hasse diagram -- from a point 
-cloud (Rips complex) or 
-a list of simplices, and to compute their persistent homology with coefficients in a field 
-\f$\mathbb{Z}/p\mathbb{Z}\f$ (for an arbitrary prime \f$p\f$), or simultaneously with coefficients 
-in a family of fields (multi-field persistent homology).
 
+\section Compiling
+
+The library uses c++11 and requires Boost with version 1.48.0 or more recent :  http://www.boost.org/.
+Some packages require additional libraries :
+\li the multi-field persistent homology algorithm has an optional dependency with GMP
+\li Qt demos require CGAL, Qt4 and QGLViewer
+
+The procedure to install these packages according to your operating system is 
+detailled here http://doc.cgal.org/latest/Manual/installation.html
+
+The library compiles in Linux and Mac OSX. 
+
+\section d Demos and Examples
 
 To build the library, run the following in a terminal:
 
@@ -26,27 +44,13 @@ cmake -DCMAKE_BUILD_TYPE=Release ..
 make
 \endverbatim
 
-The library has dependencies with Boost 1.48.0 or more recent (required):  http://www.boost.org/
-and with GMP: https://gmplib.org/ The dependency with GMP is optional, and is used only for the 
-multi-field persistent homology algorithm.
-
-
-We provide example files: run these examples with -h for details on their use, and read the README file.
-
-\li <CODE>rips_persistence.cpp</CODE> computes the Rips complex of a point cloud and its persistence diagram.
 
-\li <CODE>rips_multifield_persistence.cpp</CODE> computes the Rips complex of a point cloud and its persistence diagram 
-with a family of field coefficients.
 
-\li <CODE>performance_rips_persistence.cpp</CODE> provides timings for the construction of the Rips complex on a set of 
-points sampling a Klein bottle in \f$\mathbb{R}^5\f$ with a simplex tree, its conversion to a 
-Hasse diagram and the computation of persistent homology and multi-field persistent homology for the 
-different representations.
 
 
 \details 
 
 \copyright GNU General Public License v3.                         
-\verbatim  Contact: Clément Maria,     clement.maria@inria.fr \endverbatim
+\verbatim  Contact: gudhi-devel@lists.gforge.inria.fr \endverbatim
 
 */
\ No newline at end of file
diff --git a/src/common/include/gudhi/Clock.h b/src/common/include/gudhi/Clock.h
index ea21659e..08096c05 100644
--- a/src/common/include/gudhi/Clock.h
+++ b/src/common/include/gudhi/Clock.h
@@ -1,9 +1,24 @@
-/*
- * Clock.h
- *
- *  Created on: Jun 17, 2014
- *      Author: dsalinas
- */
+ /*    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
+  *
+  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+  *
+  *    This program 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.
+  *
+  *    This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.
+  */
 
 #ifndef GUDHI_CLOCK_H_
 #define GUDHI_CLOCK_H_
diff --git a/src/common/include/gudhi/Off_reader.h b/src/common/include/gudhi/Off_reader.h
index a9c64f97..e29218d8 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] != '%');
 	}
 
@@ -171,6 +179,19 @@ private:
 };
 
 
+template<typename OFFVisitor>
+void read_off(const std::string& name_file_off,OFFVisitor& vis){
+	std::ifstream stream(name_file_off);
+	if(!stream.is_open())
+		std::cerr <<"could not open file \n";
+	else{
+		Off_reader off_reader(stream);
+		off_reader.read(vis);
+	}
+}
+
+
+
 }  // namespace Gudhi
 
 
diff --git a/src/common/include/gudhi/Utils.h b/src/common/include/gudhi/Utils.h
index cef361dc..1626a0bf 100644
--- a/src/common/include/gudhi/Utils.h
+++ b/src/common/include/gudhi/Utils.h
@@ -1,17 +1,31 @@
-/*
- * Utils.h
- *
- *  Created on: 13 juin 2013
- *      Author: salinasd
- */
-
+ /*    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
+  *
+  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+  *
+  *    This program 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.
+  *
+  *    This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.
+  */
 #ifndef GUDHI_UTILS_H_
 #define GUDHI_UTILS_H_
 
 
 #define PRINT(a) std::cerr << #a << ": " << (a) << " (DISP)"<<std::endl
 
-//#define DBG_VERBOSE
+#define DBG_VERBOSE
 #ifdef DBG_VERBOSE
 #define DBG(a) std::cerr << "DBG: " << (a)<<std::endl
 #define DBGMSG(a,b) std::cerr << "DBG: " << a<<b<<std::endl
diff --git a/src/common/include/gudhi/iofile.h b/src/common/include/gudhi/iofile.h
deleted file mode 100644
index b939d45b..00000000
--- a/src/common/include/gudhi/iofile.h
+++ /dev/null
@@ -1,236 +0,0 @@
-//todo remove and use off_reader instead
-
-#ifndef GUDHI_IOFILE_H_
-#define GUDHI_IOFILE_H_
-
-#include <iostream>
-#include <fstream>
-#include <sstream>
-#include <vector>
-#include <cstdio>
-#include <cstring>
-#include <list>
-#include <cassert>
-
-
-
-//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>
-class Geometric_flag_complex_wrapper{
-  Complex& complex_;
-  typedef typename Complex::Vertex_handle Vertex_handle;
-  typedef typename Complex::Point Point;
-
-  const bool load_only_points_;
-
-public:
-  Geometric_flag_complex_wrapper(Complex& complex,bool load_only_points = false):
-    complex_(complex),
-    load_only_points_(load_only_points)
-{}
-
-
-  void add_vertex(double* xyz,int dim){
-    Point p(dim);
-    for(int i=0;i<dim;++i)
-      p[i] = xyz[i];
-    complex_.add_vertex(p);
-  }
-
-  void add_face(int dimension ,int* vertices){
-    if (!load_only_points_){
-      for (int i = 0; i<dimension ; ++i)
-        for (int j = i+1; j<dimension ; ++j)
-          complex_.add_edge(Vertex_handle(vertices[i]),Vertex_handle(vertices[j]));
-    }
-  }
-};
-
-
-
-
-/**
- * @brief Read a mesh into a OFF file
- * load_only_points should be true if only the points have to be loaded.
- */
-template<typename Complex>
-bool read_off_file(std::string file_name,Complex &complex,bool load_only_points = false){
-  complex.clear();
-  Geometric_flag_complex_wrapper<Complex> complex_wrapper(complex,load_only_points);
-  return general_read_off_file(file_name,complex_wrapper);
-
-}
-
-
-#endif