-- 
cgit v1.2.3

From e7162cf121d5e1619ca4b7b54b9cef4d9ff1c9f7 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 16 May 2017 14:25:19 +0000
Subject: Add read_persistence_diagram_from_file

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2439 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 026fbb0528343a15a46935ded3aaf13297afeff5
---
 src/common/include/gudhi/reader_utils.h | 38 ++++++++++++++++++++++++++++++++-
 1 file changed, 37 insertions(+), 1 deletion(-)

diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 97a87edd..ceee8daf 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -2,7 +2,7 @@
  *    (Geometric Understanding in Higher Dimensions) is a generic C++ 
  *    library for computational topology.
  *
- *    Author(s):       Clement Maria, Pawel Dlotko
+ *    Author(s):       Clement Maria, Pawel Dlotko, Clement Jamin
  *
  *    Copyright (C) 2014  INRIA
  *
@@ -295,4 +295,40 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from
   return result;
 }  // read_lower_triangular_matrix_from_csv_file
 
+/**
+Reads a file containing persistance intervals.
+Each line might contain 2, 3 or 4 values: [field] [dimension] birth death
+**/
+
+std::vector< std::pair<double, double> > read_persistence_diagram_from_file(std::string const& filename) {
+
+  std::vector< std::pair<double, double> > result;
+
+  std::ifstream in;
+  in.open(filename);
+  if (!in.is_open()) {
+#ifdef DEBUG_TRACES
+    std::cerr << "File \"" << filename << "\" does not exist.\n";
+#endif  // DEBUG_TRACES
+    return result;
+  }
+
+  std::string line;
+  while (!in.eof()) {
+    getline(in, line);
+    if (line.length() != 0 && line[0] != '#') {
+      double numbers[4];
+      int n = sscanf(line.c_str(), "%lf %lf %lf %lf", &numbers[0], &numbers[1], &numbers[2], &numbers[3]);
+      result.push_back(std::make_pair(numbers[n - 2], numbers[n - 1]));
+#ifdef DEBUG_TRACES
+      std::cerr << numbers[n - 2] << " - " << numbers[n - 1] << "\n";
+#endif  // DEBUG_TRACES
+    }
+  }
+
+  in.close();
+  return result;
+}  // read_diagram_from_file
+
+
 #endif  // READER_UTILS_H_
-- 
cgit v1.2.3


From 884d91ed81876af1a3d986843253acaaff443834 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 16 May 2017 14:26:11 +0000
Subject: Use read_persistence_diagram_from_file in this example

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2440 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: cb5cbba3f968c6cd16025250076bbe1df4f2e11a
---
 .../example/bottleneck_read_file_example.cpp       | 31 +++-------------------
 1 file changed, 4 insertions(+), 27 deletions(-)

diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
index bde05825..e50a243d 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
@@ -21,8 +21,10 @@
  */
 
 #define CGAL_HAS_THREADS
+#define DEBUG_TRACES
 
 #include <gudhi/Bottleneck.h>
+#include <gudhi/reader_utils.h>
 #include <iostream>
 #include <vector>
 #include <utility>  // for pair
@@ -30,39 +32,14 @@
 #include <sstream>
 #include <string>
 
-std::vector< std::pair<double, double> > read_diagram_from_file(const char* filename) {
-  std::ifstream in;
-  in.open(filename);
-  std::vector< std::pair<double, double> > result;
-  if (!in.is_open()) {
-    std::cerr << "File : " << filename << " do not exist. The program will now terminate \n";
-    throw "File do not exist \n";
-  }
-
-  std::string line;
-  while (!in.eof()) {
-    getline(in, line);
-    if (line.length() != 0) {
-      std::stringstream lineSS;
-      lineSS << line;
-      double beginn, endd;
-      lineSS >> beginn;
-      lineSS >> endd;
-      result.push_back(std::make_pair(beginn, endd));
-    }
-  }
-  in.close();
-  return result;
-}  // read_diagram_from_file
-
 int main(int argc, char** argv) {
   if (argc < 3) {
     std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file " <<
         "should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" <<
         " distance (set by default to zero). The program will now terminate \n";
   }
-  std::vector< std::pair< double, double > > diag1 = read_diagram_from_file(argv[1]);
-  std::vector< std::pair< double, double > > diag2 = read_diagram_from_file(argv[2]);
+  std::vector< std::pair< double, double > > diag1 = read_persistence_diagram_from_file(argv[1]);
+  std::vector< std::pair< double, double > > diag2 = read_persistence_diagram_from_file(argv[2]);
   double tolerance = 0.;
   if (argc == 4) {
     tolerance = atof(argv[3]);
-- 
cgit v1.2.3


From f8992aa852dc1a5ef1392837581f55650cccaebf Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 19 May 2017 08:52:58 +0000
Subject: Remove DEBUG_TRACES

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2446 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 2290435a73db6bea9297fa79e10f7e36be10a43e
---
 src/Bottleneck_distance/example/bottleneck_read_file_example.cpp | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
index e50a243d..67bd27db 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
@@ -21,7 +21,6 @@
  */
 
 #define CGAL_HAS_THREADS
-#define DEBUG_TRACES
 
 #include <gudhi/Bottleneck.h>
 #include <gudhi/reader_utils.h>
-- 
cgit v1.2.3


From 269fa842c2eaeb7ddf8040abfd6c18d23ac767e9 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 23 May 2017 09:10:41 +0000
Subject: read_persistence_diagram_from_file now uses an output iterator

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2455 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 3969666dcde3581a75789c5a4b62817dea553f9f
---
 .../example/bottleneck_read_file_example.cpp            | 15 +++++++++++++--
 src/common/include/gudhi/reader_utils.h                 | 17 ++++++++---------
 2 files changed, 21 insertions(+), 11 deletions(-)

diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
index 67bd27db..74c8d1ab 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
@@ -31,14 +31,25 @@
 #include <sstream>
 #include <string>
 
+struct Persistence_interval
+  : std::pair<double, double>
+{
+  Persistence_interval(std::tuple<int, double, double> data)
+    : std::pair<double, double>(std::make_pair(std::get<1>(data), std::get<2>(data)))
+  {}
+};
+
 int main(int argc, char** argv) {
   if (argc < 3) {
     std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file " <<
         "should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" <<
         " distance (set by default to zero). The program will now terminate \n";
   }
-  std::vector< std::pair< double, double > > diag1 = read_persistence_diagram_from_file(argv[1]);
-  std::vector< std::pair< double, double > > diag2 = read_persistence_diagram_from_file(argv[2]);
+  std::vector<Persistence_interval> diag1;
+  std::vector<Persistence_interval> diag2;
+  read_persistence_diagram_from_file(argv[1], std::back_inserter(diag1));
+  read_persistence_diagram_from_file(argv[2], std::back_inserter(diag2));
+
   double tolerance = 0.;
   if (argc == 4) {
     tolerance = atof(argv[3]);
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index ceee8daf..019a3db2 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -298,11 +298,11 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from
 /**
 Reads a file containing persistance intervals.
 Each line might contain 2, 3 or 4 values: [field] [dimension] birth death
+The output iterator `out` is used this way: `*out++ = std::make_tuple(dim, birth, death);`
+where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
 **/
-
-std::vector< std::pair<double, double> > read_persistence_diagram_from_file(std::string const& filename) {
-
-  std::vector< std::pair<double, double> > result;
+template <typename OutputIterator>
+void read_persistence_diagram_from_file(std::string const& filename, OutputIterator out) {
 
   std::ifstream in;
   in.open(filename);
@@ -310,7 +310,6 @@ std::vector< std::pair<double, double> > read_persistence_diagram_from_file(std:
 #ifdef DEBUG_TRACES
     std::cerr << "File \"" << filename << "\" does not exist.\n";
 #endif  // DEBUG_TRACES
-    return result;
   }
 
   std::string line;
@@ -319,7 +318,9 @@ std::vector< std::pair<double, double> > read_persistence_diagram_from_file(std:
     if (line.length() != 0 && line[0] != '#') {
       double numbers[4];
       int n = sscanf(line.c_str(), "%lf %lf %lf %lf", &numbers[0], &numbers[1], &numbers[2], &numbers[3]);
-      result.push_back(std::make_pair(numbers[n - 2], numbers[n - 1]));
+      //int field = (n == 4 ? static_cast<int>(numbers[0]) : -1);
+      int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1);
+      *out++ = std::make_tuple(dim, numbers[n - 2], numbers[n - 1]);
 #ifdef DEBUG_TRACES
       std::cerr << numbers[n - 2] << " - " << numbers[n - 1] << "\n";
 #endif  // DEBUG_TRACES
@@ -327,8 +328,6 @@ std::vector< std::pair<double, double> > read_persistence_diagram_from_file(std:
   }
 
   in.close();
-  return result;
-}  // read_diagram_from_file
-
+} // read_persistence_diagram_from_file
 
 #endif  // READER_UTILS_H_
-- 
cgit v1.2.3


From 71527e6ff81a7ac657f8a797a050bbcf7a131cb9 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Mon, 29 May 2017 16:22:49 +0000
Subject: Add 2 new variants of read_persistence_diagram_from_file

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2463 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: bd0dd2c981856c8e1a51b2b97ac10d9edd59f694
---
 .../example/bottleneck_read_file_example.cpp       |  6 +-
 src/common/include/gudhi/reader_utils.h            | 85 ++++++++++++++++++++--
 2 files changed, 82 insertions(+), 9 deletions(-)

diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
index 74c8d1ab..e26edd26 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
@@ -45,10 +45,8 @@ int main(int argc, char** argv) {
         "should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" <<
         " distance (set by default to zero). The program will now terminate \n";
   }
-  std::vector<Persistence_interval> diag1;
-  std::vector<Persistence_interval> diag2;
-  read_persistence_diagram_from_file(argv[1], std::back_inserter(diag1));
-  read_persistence_diagram_from_file(argv[2], std::back_inserter(diag2));
+  std::vector<std::pair<double, double>> diag1 = read_persistence_diagram_from_file(argv[1], -1);
+  std::vector<std::pair<double, double>> diag2 = read_persistence_diagram_from_file(argv[2], -1);
 
   double tolerance = 0.;
   if (argc == 4) {
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 019a3db2..7b371afc 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -310,24 +310,99 @@ void read_persistence_diagram_from_file(std::string const& filename, OutputItera
 #ifdef DEBUG_TRACES
     std::cerr << "File \"" << filename << "\" does not exist.\n";
 #endif  // DEBUG_TRACES
+    return;
   }
 
-  std::string line;
   while (!in.eof()) {
+    std::string line;
     getline(in, line);
     if (line.length() != 0 && line[0] != '#') {
       double numbers[4];
       int n = sscanf(line.c_str(), "%lf %lf %lf %lf", &numbers[0], &numbers[1], &numbers[2], &numbers[3]);
-      //int field = (n == 4 ? static_cast<int>(numbers[0]) : -1);
-      int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1);
-      *out++ = std::make_tuple(dim, numbers[n - 2], numbers[n - 1]);
+      if (n >= 2) {
+        //int field = (n == 4 ? static_cast<int>(numbers[0]) : -1);
+        int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1);
+        *out++ = std::make_tuple(dim, numbers[n - 2], numbers[n - 1]);
+      }
+    }
+  }
+
+  in.close();
+} // read_persistence_diagram_from_file
+
+/**
+Reads a file containing persistance intervals.
+Each line might contain 2, 3 or 4 values: [field] [dimension] birth death
+The return value is an `std::map[dim, std::vector[std::pair[birth, death]]]`
+where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
+**/
+std::map<int, std::vector<std::pair<double, double>>> read_persistence_diagram_from_file(std::string const& filename) {
+
+  std::map<int, std::vector<std::pair<double, double>>> ret;
+
+  std::ifstream in;
+  in.open(filename);
+  if (!in.is_open()) {
 #ifdef DEBUG_TRACES
-      std::cerr << numbers[n - 2] << " - " << numbers[n - 1] << "\n";
+    std::cerr << "File \"" << filename << "\" does not exist.\n";
 #endif  // DEBUG_TRACES
+    return ret;
+  }
+
+  while (!in.eof()) {
+    std::string line;
+    getline(in, line);
+    if (line.length() != 0 && line[0] != '#') {
+      double numbers[4];
+      int n = sscanf(line.c_str(), "%lf %lf %lf %lf", &numbers[0], &numbers[1], &numbers[2], &numbers[3]);
+      if (n >= 2) {
+        int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1);
+        ret[dim].push_back(std::make_pair(numbers[n - 2], numbers[n - 1]));
+      }
+    }
+  }
+
+  in.close();
+  return ret;
+} // read_persistence_diagram_from_file
+
+
+/**
+Reads a file containing persistance intervals.
+Each line might contain 2, 3 or 4 values: [field] [dimension] birth death
+If `only_this_dim` = -1, dimension is ignored and all lines are returned.
+If `only_this_dim` is >= 0, only the lines where dimension = `only_this_dim` 
+(or where dimension is not specified) are returned.
+The return value is an `std::vector[std::pair[birth, death]]`
+where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
+**/
+std::vector<std::pair<double, double>> read_persistence_diagram_from_file(std::string const& filename, int only_this_dim) {
+
+  std::vector<std::pair<double, double>> ret;
+
+  std::ifstream in;
+  in.open(filename);
+  if (!in.is_open()) {
+#ifdef DEBUG_TRACES
+    std::cerr << "File \"" << filename << "\" does not exist.\n";
+#endif  // DEBUG_TRACES
+    return ret;
+  }
+
+  while (!in.eof()) {
+    std::string line;
+    getline(in, line);
+    if (line.length() != 0 && line[0] != '#') {
+      double numbers[4];
+      int n = sscanf(line.c_str(), "%lf %lf %lf %lf", &numbers[0], &numbers[1], &numbers[2], &numbers[3]);
+      int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1);
+      if (n >= 2 && (only_this_dim == -1 || dim == only_this_dim))
+        ret.push_back(std::make_pair(numbers[n - 2], numbers[n - 1]));
     }
   }
 
   in.close();
+  return ret;
 } // read_persistence_diagram_from_file
 
 #endif  // READER_UTILS_H_
-- 
cgit v1.2.3


From 006516d2df5eaa6e38765158f72fa29fea8fb610 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 30 May 2017 12:50:12 +0000
Subject: Remove debug code

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2473 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 458dcfcf18b36f8dd0023dfe5af0d6083d1c7684
---
 src/Bottleneck_distance/example/bottleneck_read_file_example.cpp | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
index e26edd26..f6fd6501 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
@@ -20,8 +20,6 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-#define CGAL_HAS_THREADS
-
 #include <gudhi/Bottleneck.h>
 #include <gudhi/reader_utils.h>
 #include <iostream>
-- 
cgit v1.2.3


From 6d4b5ec65b863abb5b183635a0e64341c19e7b4b Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 30 May 2017 13:00:15 +0000
Subject: Clean-up

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2474 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 9586b4987dad745fa60bca1a433349a2f78fa9bd
---
 src/Bottleneck_distance/example/bottleneck_read_file_example.cpp | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
index f6fd6501..de8c7f9d 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
@@ -29,14 +29,6 @@
 #include <sstream>
 #include <string>
 
-struct Persistence_interval
-  : std::pair<double, double>
-{
-  Persistence_interval(std::tuple<int, double, double> data)
-    : std::pair<double, double>(std::make_pair(std::get<1>(data), std::get<2>(data)))
-  {}
-};
-
 int main(int argc, char** argv) {
   if (argc < 3) {
     std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file " <<
-- 
cgit v1.2.3


From 53abf1ac75eefcecc1391d140183a49588f0d2d2 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 31 May 2017 11:30:58 +0000
Subject: Fix doc and shorten code

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2485 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 97dcd51c0dc9cef00a655e5e0ad078de752eabe8
---
 src/common/include/gudhi/reader_utils.h | 19 ++++++-------------
 1 file changed, 6 insertions(+), 13 deletions(-)

diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 7b371afc..df10d5a5 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -297,15 +297,14 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from
 
 /**
 Reads a file containing persistance intervals.
-Each line might contain 2, 3 or 4 values: [field] [dimension] birth death
+Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
 The output iterator `out` is used this way: `*out++ = std::make_tuple(dim, birth, death);`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
 **/
 template <typename OutputIterator>
 void read_persistence_diagram_from_file(std::string const& filename, OutputIterator out) {
 
-  std::ifstream in;
-  in.open(filename);
+  std::ifstream in(filename);
   if (!in.is_open()) {
 #ifdef DEBUG_TRACES
     std::cerr << "File \"" << filename << "\" does not exist.\n";
@@ -326,13 +325,11 @@ void read_persistence_diagram_from_file(std::string const& filename, OutputItera
       }
     }
   }
-
-  in.close();
 } // read_persistence_diagram_from_file
 
 /**
 Reads a file containing persistance intervals.
-Each line might contain 2, 3 or 4 values: [field] [dimension] birth death
+Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
 The return value is an `std::map[dim, std::vector[std::pair[birth, death]]]`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
 **/
@@ -340,8 +337,7 @@ std::map<int, std::vector<std::pair<double, double>>> read_persistence_diagram_f
 
   std::map<int, std::vector<std::pair<double, double>>> ret;
 
-  std::ifstream in;
-  in.open(filename);
+  std::ifstream in(filename);
   if (!in.is_open()) {
 #ifdef DEBUG_TRACES
     std::cerr << "File \"" << filename << "\" does not exist.\n";
@@ -362,14 +358,13 @@ std::map<int, std::vector<std::pair<double, double>>> read_persistence_diagram_f
     }
   }
 
-  in.close();
   return ret;
 } // read_persistence_diagram_from_file
 
 
 /**
 Reads a file containing persistance intervals.
-Each line might contain 2, 3 or 4 values: [field] [dimension] birth death
+Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
 If `only_this_dim` = -1, dimension is ignored and all lines are returned.
 If `only_this_dim` is >= 0, only the lines where dimension = `only_this_dim` 
 (or where dimension is not specified) are returned.
@@ -380,8 +375,7 @@ std::vector<std::pair<double, double>> read_persistence_diagram_from_file(std::s
 
   std::vector<std::pair<double, double>> ret;
 
-  std::ifstream in;
-  in.open(filename);
+  std::ifstream in(filename);
   if (!in.is_open()) {
 #ifdef DEBUG_TRACES
     std::cerr << "File \"" << filename << "\" does not exist.\n";
@@ -401,7 +395,6 @@ std::vector<std::pair<double, double>> read_persistence_diagram_from_file(std::s
     }
   }
 
-  in.close();
   return ret;
 } // read_persistence_diagram_from_file
 
-- 
cgit v1.2.3


From 8457da40a4af813d6368cd85d1f60d2b2de52191 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 31 May 2017 11:36:20 +0000
Subject: Typo

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2486 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: dcc6134d95dea816a3c54a2a796535f384ccfc54
---
 src/common/include/gudhi/reader_utils.h | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index df10d5a5..55a1e875 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -296,7 +296,7 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from
 }  // read_lower_triangular_matrix_from_csv_file
 
 /**
-Reads a file containing persistance intervals.
+Reads a file containing persistence intervals.
 Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
 The output iterator `out` is used this way: `*out++ = std::make_tuple(dim, birth, death);`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
@@ -328,7 +328,7 @@ void read_persistence_diagram_from_file(std::string const& filename, OutputItera
 } // read_persistence_diagram_from_file
 
 /**
-Reads a file containing persistance intervals.
+Reads a file containing persistence intervals.
 Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
 The return value is an `std::map[dim, std::vector[std::pair[birth, death]]]`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
@@ -363,7 +363,7 @@ std::map<int, std::vector<std::pair<double, double>>> read_persistence_diagram_f
 
 
 /**
-Reads a file containing persistance intervals.
+Reads a file containing persistence intervals.
 Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
 If `only_this_dim` = -1, dimension is ignored and all lines are returned.
 If `only_this_dim` is >= 0, only the lines where dimension = `only_this_dim` 
-- 
cgit v1.2.3


From cbcf098dbc2af8f385216d74d6ffbbe08deaff66 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 31 May 2017 11:44:16 +0000
Subject: Fix doc

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2487 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 7be9a5da2a64835ff7558373e7a754647bc5b663
---
 src/common/include/gudhi/reader_utils.h | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 55a1e875..bb744b1c 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -330,7 +330,7 @@ void read_persistence_diagram_from_file(std::string const& filename, OutputItera
 /**
 Reads a file containing persistence intervals.
 Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
-The return value is an `std::map[dim, std::vector[std::pair[birth, death]]]`
+The return value is an `std::map<dim, std::vector<std::pair<birth, death>>>`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
 **/
 std::map<int, std::vector<std::pair<double, double>>> read_persistence_diagram_from_file(std::string const& filename) {
@@ -368,7 +368,7 @@ Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
 If `only_this_dim` = -1, dimension is ignored and all lines are returned.
 If `only_this_dim` is >= 0, only the lines where dimension = `only_this_dim` 
 (or where dimension is not specified) are returned.
-The return value is an `std::vector[std::pair[birth, death]]`
+The return value is an `std::vector<std::pair<birth, death>>`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
 **/
 std::vector<std::pair<double, double>> read_persistence_diagram_from_file(std::string const& filename, int only_this_dim) {
-- 
cgit v1.2.3


From 66873d7ee6dd369dd3d8c1909d6376ed2bce4cc7 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 31 May 2017 11:54:55 +0000
Subject: Check if birth <= death

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2488 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: fc7aeca7ca7cd1ec2e9a9263849ec34d4dfa8414
---
 src/common/include/gudhi/reader_utils.h | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index bb744b1c..6a89ce90 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -24,6 +24,7 @@
 #define READER_UTILS_H_
 
 #include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/Debug_utils.h>
 
 #include <boost/graph/adjacency_list.hpp>
 
@@ -321,6 +322,7 @@ void read_persistence_diagram_from_file(std::string const& filename, OutputItera
       if (n >= 2) {
         //int field = (n == 4 ? static_cast<int>(numbers[0]) : -1);
         int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1);
+        GUDHI_CHECK(numbers[n - 2] <= numbers[n - 1], "Error: birth > death.");
         *out++ = std::make_tuple(dim, numbers[n - 2], numbers[n - 1]);
       }
     }
@@ -353,6 +355,7 @@ std::map<int, std::vector<std::pair<double, double>>> read_persistence_diagram_f
       int n = sscanf(line.c_str(), "%lf %lf %lf %lf", &numbers[0], &numbers[1], &numbers[2], &numbers[3]);
       if (n >= 2) {
         int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1);
+        GUDHI_CHECK(numbers[n - 2] <= numbers[n - 1], "Error: birth > death.");
         ret[dim].push_back(std::make_pair(numbers[n - 2], numbers[n - 1]));
       }
     }
@@ -391,7 +394,10 @@ std::vector<std::pair<double, double>> read_persistence_diagram_from_file(std::s
       int n = sscanf(line.c_str(), "%lf %lf %lf %lf", &numbers[0], &numbers[1], &numbers[2], &numbers[3]);
       int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1);
       if (n >= 2 && (only_this_dim == -1 || dim == only_this_dim))
+      {
+        GUDHI_CHECK(numbers[n - 2] <= numbers[n - 1], "Error: birth > death.");
         ret.push_back(std::make_pair(numbers[n - 2], numbers[n - 1]));
+      }
     }
   }
 
-- 
cgit v1.2.3


From df15aa4e16c00a7dc3bca01e01db8608b50dd4b9 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 31 May 2017 11:58:05 +0000
Subject: Add persistence diagram samples

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2489 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: bcad955589cbfccdb5f887e409df17a07288c9e4
---
 data/persistence_diagram/first.pers  | 5 +++++
 data/persistence_diagram/second.pers | 3 +++
 2 files changed, 8 insertions(+)
 create mode 100644 data/persistence_diagram/first.pers
 create mode 100644 data/persistence_diagram/second.pers

diff --git a/data/persistence_diagram/first.pers b/data/persistence_diagram/first.pers
new file mode 100644
index 00000000..193c60ba
--- /dev/null
+++ b/data/persistence_diagram/first.pers
@@ -0,0 +1,5 @@
+# Simple persistence diagram
+2.7 3.7
+9.6 14.
+34.2 34.974
+3. inf
\ No newline at end of file
diff --git a/data/persistence_diagram/second.pers b/data/persistence_diagram/second.pers
new file mode 100644
index 00000000..6292fde6
--- /dev/null
+++ b/data/persistence_diagram/second.pers
@@ -0,0 +1,3 @@
+2.8 4.45
+9.5 14.1
+3.2 inf
\ No newline at end of file
-- 
cgit v1.2.3


From 267f55ba68cd3c7beee9cd8c7bd9e13d90217848 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 31 May 2017 12:03:13 +0000
Subject: Test bottleneck_read_file_example

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2490 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: dbbce2ac4862dfdd3c01a619bf68120112ab44d5
---
 src/Bottleneck_distance/example/CMakeLists.txt | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt
index 0534a2c4..508e57bf 100644
--- a/src/Bottleneck_distance/example/CMakeLists.txt
+++ b/src/Bottleneck_distance/example/CMakeLists.txt
@@ -19,6 +19,10 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
       COMMAND $<TARGET_FILE:alpha_rips_persistence_bottleneck_distance>
       "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.15" "-m" "0.12" "-d" "3" "-p" "3")
 
+  add_test(NAME Bottleneck_read_file_example
+      COMMAND $<TARGET_FILE:bottleneck_read_file_example>
+      "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/second.pers")
+
   install(TARGETS bottleneck_read_file_example DESTINATION bin)
   install(TARGETS bottleneck_basic_example DESTINATION bin)
   install(TARGETS alpha_rips_persistence_bottleneck_distance DESTINATION bin)
-- 
cgit v1.2.3


From 8493f7a38001930329ec6204e6b3e8dff1c67df1 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 1 Jun 2017 10:26:05 +0000
Subject: Use make_function_output_iterator to avoid code duplication

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2498 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 7d9a9d3f72ef4af17f4a9b8263526df69498090c
---
 src/common/include/gudhi/reader_utils.h | 54 +++++----------------------------
 1 file changed, 7 insertions(+), 47 deletions(-)

diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 6a89ce90..f0903acc 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -25,6 +25,7 @@
 
 #include <gudhi/graph_simplicial_complex.h>
 #include <gudhi/Debug_utils.h>
+#include <boost/function_output_iterator.hpp>
 
 #include <boost/graph/adjacency_list.hpp>
 
@@ -338,29 +339,9 @@ where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
 std::map<int, std::vector<std::pair<double, double>>> read_persistence_diagram_from_file(std::string const& filename) {
 
   std::map<int, std::vector<std::pair<double, double>>> ret;
-
-  std::ifstream in(filename);
-  if (!in.is_open()) {
-#ifdef DEBUG_TRACES
-    std::cerr << "File \"" << filename << "\" does not exist.\n";
-#endif  // DEBUG_TRACES
-    return ret;
-  }
-
-  while (!in.eof()) {
-    std::string line;
-    getline(in, line);
-    if (line.length() != 0 && line[0] != '#') {
-      double numbers[4];
-      int n = sscanf(line.c_str(), "%lf %lf %lf %lf", &numbers[0], &numbers[1], &numbers[2], &numbers[3]);
-      if (n >= 2) {
-        int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1);
-        GUDHI_CHECK(numbers[n - 2] <= numbers[n - 1], "Error: birth > death.");
-        ret[dim].push_back(std::make_pair(numbers[n - 2], numbers[n - 1]));
-      }
-    }
-  }
-
+  read_persistence_diagram_from_file(
+    filename,
+    boost::make_function_output_iterator([&ret](auto t) { ret[get<0>(t)].push_back(std::make_pair(get<1>(t), get<2>(t))); }));
   return ret;
 } // read_persistence_diagram_from_file
 
@@ -377,30 +358,9 @@ where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
 std::vector<std::pair<double, double>> read_persistence_diagram_from_file(std::string const& filename, int only_this_dim) {
 
   std::vector<std::pair<double, double>> ret;
-
-  std::ifstream in(filename);
-  if (!in.is_open()) {
-#ifdef DEBUG_TRACES
-    std::cerr << "File \"" << filename << "\" does not exist.\n";
-#endif  // DEBUG_TRACES
-    return ret;
-  }
-
-  while (!in.eof()) {
-    std::string line;
-    getline(in, line);
-    if (line.length() != 0 && line[0] != '#') {
-      double numbers[4];
-      int n = sscanf(line.c_str(), "%lf %lf %lf %lf", &numbers[0], &numbers[1], &numbers[2], &numbers[3]);
-      int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1);
-      if (n >= 2 && (only_this_dim == -1 || dim == only_this_dim))
-      {
-        GUDHI_CHECK(numbers[n - 2] <= numbers[n - 1], "Error: birth > death.");
-        ret.push_back(std::make_pair(numbers[n - 2], numbers[n - 1]));
-      }
-    }
-  }
-
+  read_persistence_diagram_from_file(
+    filename, 
+    boost::make_function_output_iterator([&ret](auto t) { ret.emplace_back(get<1>(t), get<2>(t)); }));
   return ret;
 } // read_persistence_diagram_from_file
 
-- 
cgit v1.2.3


From 03f7d661f8b5d34320a075a826c0bfeafa16633f Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Thu, 1 Jun 2017 14:55:10 +0000
Subject: Doc for "pers" file format

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2500 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 2da948fefffcb1961961e3111c89f400f23b65d3
---
 src/common/doc/main_page.h | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index bd4615f5..fba0a858 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -152,6 +152,27 @@
 </table>
  
  \section Toolbox Toolbox
+ \subsection FileFormats File Formats
+ \subsubsection FileFormatsPers Persistence Diagram
+
+ Such a file, whose extension is usually `.pers`, contains a list of persistence intervals.<br>
+ Lines starting with `#` are ignored (comments).<br>
+ Other lines might contain 2, 3 or 4 values (the number of values on each line must be the same for all lines):
+ \code{.unparsed}
+   [[field] dimension] birth death
+ \endcode
+
+ Here is a simple sample file:
+ \code{.unparsed}
+   # Beautiful persistence diagram
+   2 2.7 3.7
+   2 9.6 14.
+   3 34.2 34.974
+   4 3. inf
+ \endcode
+
+ Other sample files can be found in the `data/persistence_diagram`.
+
  \subsection BottleneckDistanceToolbox Bottleneck distance
  \image html "perturb_pd.png" "Bottleneck distance is the length of the longest edge"
 <table border="0">
-- 
cgit v1.2.3


From 3a7ffc0bfec712cb586d5c7ea154a4fd20be1a39 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 9 Jun 2017 10:32:48 +0000
Subject: Change names and adapt example

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2531 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 833a51dd03ddccca38c6011834bb58667d63ccbf
---
 .../example/bottleneck_read_file_example.cpp                   |  4 ++--
 src/common/include/gudhi/reader_utils.h                        | 10 +++++-----
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
index de8c7f9d..94d9a148 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
@@ -35,8 +35,8 @@ int main(int argc, char** argv) {
         "should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" <<
         " distance (set by default to zero). The program will now terminate \n";
   }
-  std::vector<std::pair<double, double>> diag1 = read_persistence_diagram_from_file(argv[1], -1);
-  std::vector<std::pair<double, double>> diag2 = read_persistence_diagram_from_file(argv[2], -1);
+  std::vector<std::pair<double, double>> diag1 = read_persistence_intervals_in_dimension(argv[1]);
+  std::vector<std::pair<double, double>> diag2 = read_persistence_intervals_in_dimension(argv[2]);
 
   double tolerance = 0.;
   if (argc == 4) {
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index f0903acc..62b479ac 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -304,7 +304,7 @@ The output iterator `out` is used this way: `*out++ = std::make_tuple(dim, birth
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
 **/
 template <typename OutputIterator>
-void read_persistence_diagram_from_file(std::string const& filename, OutputIterator out) {
+void read_persistence_intervals_and_dimension(std::string const& filename, OutputIterator out) {
 
   std::ifstream in(filename);
   if (!in.is_open()) {
@@ -336,10 +336,10 @@ Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
 The return value is an `std::map<dim, std::vector<std::pair<birth, death>>>`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
 **/
-std::map<int, std::vector<std::pair<double, double>>> read_persistence_diagram_from_file(std::string const& filename) {
+std::map<int, std::vector<std::pair<double, double>>> read_persistence_intervals_grouped_by_dimension(std::string const& filename) {
 
   std::map<int, std::vector<std::pair<double, double>>> ret;
-  read_persistence_diagram_from_file(
+  read_persistence_intervals_and_dimension(
     filename,
     boost::make_function_output_iterator([&ret](auto t) { ret[get<0>(t)].push_back(std::make_pair(get<1>(t), get<2>(t))); }));
   return ret;
@@ -355,10 +355,10 @@ If `only_this_dim` is >= 0, only the lines where dimension = `only_this_dim`
 The return value is an `std::vector<std::pair<birth, death>>`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
 **/
-std::vector<std::pair<double, double>> read_persistence_diagram_from_file(std::string const& filename, int only_this_dim) {
+std::vector<std::pair<double, double>> read_persistence_intervals_in_dimension(std::string const& filename, int only_this_dim = -1) {
 
   std::vector<std::pair<double, double>> ret;
-  read_persistence_diagram_from_file(
+  read_persistence_intervals_and_dimension(
     filename, 
     boost::make_function_output_iterator([&ret](auto t) { ret.emplace_back(get<1>(t), get<2>(t)); }));
   return ret;
-- 
cgit v1.2.3


From 2ceede5cd9f226e66bb1ecbe1798330c349c2aa0 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 9 Jun 2017 10:39:31 +0000
Subject: Missing "return"

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2532 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 8905e0d3406cbe26615b83ab7056e7fd5bd8ed0e
---
 src/Bottleneck_distance/example/bottleneck_read_file_example.cpp | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
index 94d9a148..6cfbeafa 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
@@ -34,6 +34,7 @@ int main(int argc, char** argv) {
     std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file " <<
         "should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" <<
         " distance (set by default to zero). The program will now terminate \n";
+    //return -1;
   }
   std::vector<std::pair<double, double>> diag1 = read_persistence_intervals_in_dimension(argv[1]);
   std::vector<std::pair<double, double>> diag2 = read_persistence_intervals_in_dimension(argv[2]);
@@ -44,4 +45,6 @@ int main(int argc, char** argv) {
   }
   double b = Gudhi::persistence_diagram::bottleneck_distance(diag1, diag2, tolerance);
   std::cout << "The distance between the diagrams is : " << b << ". The tolerance is : " << tolerance << std::endl;
+
+  return 0;
 }
-- 
cgit v1.2.3


From 4918b9c752a2d269678791dc4772ae9276539051 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 9 Jun 2017 10:42:12 +0000
Subject: Throw exceptions if file not found

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2533 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: b412f432aeac6aef07ac2d9d65d50dc8f508c2e6
---
 src/common/include/gudhi/reader_utils.h | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 62b479ac..35af09bd 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -94,7 +94,10 @@ template< typename Graph_t, typename Filtration_value, typename Vertex_handle >
 Graph_t read_graph(std::string file_name) {
   std::ifstream in_(file_name.c_str(), std::ios::in);
   if (!in_.is_open()) {
-    std::cerr << "Unable to open file " << file_name << std::endl;
+    std::string error_str("read_graph - Unable to open file ");
+    error_str.append(file_name);
+    std::cerr << error_str << std::endl;
+    throw std::invalid_argument(error_str);
   }
 
   typedef std::pair< Vertex_handle, Vertex_handle > Edge_t;
@@ -308,10 +311,10 @@ void read_persistence_intervals_and_dimension(std::string const& filename, Outpu
 
   std::ifstream in(filename);
   if (!in.is_open()) {
-#ifdef DEBUG_TRACES
-    std::cerr << "File \"" << filename << "\" does not exist.\n";
-#endif  // DEBUG_TRACES
-    return;
+    std::string error_str("read_persistence_intervals_and_dimension - Unable to open file ");
+    error_str.append(filename);
+    std::cerr << error_str << std::endl;
+    throw std::invalid_argument(error_str);
   }
 
   while (!in.eof()) {
-- 
cgit v1.2.3


From 93c97a9a93b930a2f3c1c119d9e4d2567c54dacc Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 9 Jun 2017 11:20:13 +0000
Subject: Create a new page for file formats

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2534 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: dc0d836b9df68a3f339dcbc6b8ff51577faf3d7b
---
 src/common/doc/file_formats.h | 25 +++++++++++++++++++++++++
 src/common/doc/main_page.h    | 23 ++---------------------
 2 files changed, 27 insertions(+), 21 deletions(-)
 create mode 100644 src/common/doc/file_formats.h

diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h
new file mode 100644
index 00000000..1f7ba201
--- /dev/null
+++ b/src/common/doc/file_formats.h
@@ -0,0 +1,25 @@
+/*! \page fileformats File formats
+ 
+ \tableofcontents
+
+ \section FileFormatsPers Persistence Diagram
+
+ Such a file, whose extension is usually `.pers`, contains a list of persistence intervals.<br>
+ Lines starting with `#` are ignored (comments).<br>
+ Other lines might contain 2, 3 or 4 values (the number of values on each line must be the same for all lines):
+ \code{.unparsed}
+   [[field] dimension] birth death
+ \endcode
+
+ Here is a simple sample file:
+ \code{.unparsed}
+   # Beautiful persistence diagram
+   2 2.7 3.7
+   2 9.6 14.
+   3 34.2 34.974
+   4 3. inf
+ \endcode
+
+ Other sample files can be found in the `data/persistence_diagram` folder.
+ 
+*/
\ No newline at end of file
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index fba0a858..b7f93ed2 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -152,27 +152,7 @@
 </table>
  
  \section Toolbox Toolbox
- \subsection FileFormats File Formats
- \subsubsection FileFormatsPers Persistence Diagram
-
- Such a file, whose extension is usually `.pers`, contains a list of persistence intervals.<br>
- Lines starting with `#` are ignored (comments).<br>
- Other lines might contain 2, 3 or 4 values (the number of values on each line must be the same for all lines):
- \code{.unparsed}
-   [[field] dimension] birth death
- \endcode
-
- Here is a simple sample file:
- \code{.unparsed}
-   # Beautiful persistence diagram
-   2 2.7 3.7
-   2 9.6 14.
-   3 34.2 34.974
-   4 3. inf
- \endcode
-
- Other sample files can be found in the `data/persistence_diagram`.
-
+ 
  \subsection BottleneckDistanceToolbox Bottleneck distance
  \image html "perturb_pd.png" "Bottleneck distance is the length of the longest edge"
 <table border="0">
@@ -489,3 +469,4 @@ make doxygen
  * @example Witness_complex/example_witness_complex_sphere.cpp
  */
 
+#include "file_formats.h"
\ No newline at end of file
-- 
cgit v1.2.3


From 8b8689e9dc0c9970eee7c75cb8ea08433ce28196 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 13 Jun 2017 13:37:48 +0000
Subject: Add header and namespace + remove unnecessary include

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2537 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: fc2da43c18649c606ac4760a923684f9eef0c95e
---
 src/common/doc/file_formats.h | 33 +++++++++++++++++++++++++++++++--
 src/common/doc/main_page.h    |  3 +--
 2 files changed, 32 insertions(+), 4 deletions(-)

diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h
index 1f7ba201..c145b271 100644
--- a/src/common/doc/file_formats.h
+++ b/src/common/doc/file_formats.h
@@ -1,3 +1,30 @@
+/*    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):       Clément Jamin
+*
+*    Copyright (C) 2017  INRIA
+*
+*    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 DOC_COMMON_FILE_FORMAT_H_
+#define DOC_COMMON_FILE_FORMAT_H_
+
+namespace Gudhi {
+
 /*! \page fileformats File formats
  
  \tableofcontents
@@ -21,5 +48,7 @@
  \endcode
 
  Other sample files can be found in the `data/persistence_diagram` folder.
- 
-*/
\ No newline at end of file
+*/
+}  // namespace Gudhi
+
+#endif  // DOC_COMMON_FILE_FORMAT_H_
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index b7f93ed2..12012ecb 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -468,5 +468,4 @@ make doxygen
  * @example Witness_complex/example_witness_complex_persistence.cpp
  * @example Witness_complex/example_witness_complex_sphere.cpp
  */
-
-#include "file_formats.h"
\ No newline at end of file
+ 
\ No newline at end of file
-- 
cgit v1.2.3


From e6b1730fd0832fad2a9103863428465155f70986 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Tue, 13 Jun 2017 15:29:35 +0000
Subject: This should never have been commented out

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2540 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 5e5fc971986908e5b9383130704536686e1b66ea
---
 src/Bottleneck_distance/example/bottleneck_read_file_example.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
index 6cfbeafa..238d99ad 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
@@ -34,7 +34,7 @@ int main(int argc, char** argv) {
     std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file " <<
         "should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" <<
         " distance (set by default to zero). The program will now terminate \n";
-    //return -1;
+    return -1;
   }
   std::vector<std::pair<double, double>> diag1 = read_persistence_intervals_in_dimension(argv[1]);
   std::vector<std::pair<double, double>> diag2 = read_persistence_intervals_in_dimension(argv[2]);
-- 
cgit v1.2.3


From a6b6f91bfd5a86ee88297b27f18c2bc7d38f6db4 Mon Sep 17 00:00:00 2001
From: cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Wed, 14 Jun 2017 07:45:09 +0000
Subject: Remove birth<=death check (should be done by the caller if necessary)

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2544 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: ce50159f4bf779a2a42d357cf1c2aa290feaf9b9
---
 src/common/include/gudhi/reader_utils.h | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 35af09bd..8df20dcc 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -305,6 +305,7 @@ Reads a file containing persistence intervals.
 Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
 The output iterator `out` is used this way: `*out++ = std::make_tuple(dim, birth, death);`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
+Note: the function does not check that birth <= death.
 **/
 template <typename OutputIterator>
 void read_persistence_intervals_and_dimension(std::string const& filename, OutputIterator out) {
@@ -326,7 +327,6 @@ void read_persistence_intervals_and_dimension(std::string const& filename, Outpu
       if (n >= 2) {
         //int field = (n == 4 ? static_cast<int>(numbers[0]) : -1);
         int dim = (n >= 3 ? static_cast<int>(numbers[n - 3]) : -1);
-        GUDHI_CHECK(numbers[n - 2] <= numbers[n - 1], "Error: birth > death.");
         *out++ = std::make_tuple(dim, numbers[n - 2], numbers[n - 1]);
       }
     }
@@ -338,6 +338,7 @@ Reads a file containing persistence intervals.
 Each line might contain 2, 3 or 4 values: [[field] dimension] birth death
 The return value is an `std::map<dim, std::vector<std::pair<birth, death>>>`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
+Note: the function does not check that birth <= death.
 **/
 std::map<int, std::vector<std::pair<double, double>>> read_persistence_intervals_grouped_by_dimension(std::string const& filename) {
 
@@ -357,6 +358,7 @@ If `only_this_dim` is >= 0, only the lines where dimension = `only_this_dim`
 (or where dimension is not specified) are returned.
 The return value is an `std::vector<std::pair<birth, death>>`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
+Note: the function does not check that birth <= death.
 **/
 std::vector<std::pair<double, double>> read_persistence_intervals_in_dimension(std::string const& filename, int only_this_dim = -1) {
 
-- 
cgit v1.2.3


From cdb39c39a60fe06009168c1ecb1d4ce5de0bed8c Mon Sep 17 00:00:00 2001
From: vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb>
Date: Fri, 16 Jun 2017 09:31:43 +0000
Subject: Fix auto lambda (requires C++14) compilation issue

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2550 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: df64cfdde77500b06f00432a1d1532518cd4dd37
---
 src/common/include/gudhi/reader_utils.h | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 8df20dcc..f1684d78 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -25,8 +25,8 @@
 
 #include <gudhi/graph_simplicial_complex.h>
 #include <gudhi/Debug_utils.h>
-#include <boost/function_output_iterator.hpp>
 
+#include <boost/function_output_iterator.hpp>
 #include <boost/graph/adjacency_list.hpp>
 
 #include <iostream>
@@ -340,12 +340,12 @@ The return value is an `std::map<dim, std::vector<std::pair<birth, death>>>`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
 Note: the function does not check that birth <= death.
 **/
-std::map<int, std::vector<std::pair<double, double>>> read_persistence_intervals_grouped_by_dimension(std::string const& filename) {
+inline std::map<int, std::vector<std::pair<double, double>>> read_persistence_intervals_grouped_by_dimension(std::string const& filename) {
 
   std::map<int, std::vector<std::pair<double, double>>> ret;
   read_persistence_intervals_and_dimension(
     filename,
-    boost::make_function_output_iterator([&ret](auto t) { ret[get<0>(t)].push_back(std::make_pair(get<1>(t), get<2>(t))); }));
+    boost::make_function_output_iterator([&ret](std::tuple<int, double, double> t) { ret[get<0>(t)].push_back(std::make_pair(get<1>(t), get<2>(t))); }));
   return ret;
 } // read_persistence_diagram_from_file
 
@@ -360,12 +360,12 @@ The return value is an `std::vector<std::pair<birth, death>>`
 where `dim` is an `int`, `birth` a `double`, and `death` a `double`.
 Note: the function does not check that birth <= death.
 **/
-std::vector<std::pair<double, double>> read_persistence_intervals_in_dimension(std::string const& filename, int only_this_dim = -1) {
+inline std::vector<std::pair<double, double>> read_persistence_intervals_in_dimension(std::string const& filename, int only_this_dim = -1) {
 
   std::vector<std::pair<double, double>> ret;
   read_persistence_intervals_and_dimension(
     filename, 
-    boost::make_function_output_iterator([&ret](auto t) { ret.emplace_back(get<1>(t), get<2>(t)); }));
+    boost::make_function_output_iterator([&ret](std::tuple<int, double, double> t) { ret.emplace_back(get<1>(t), get<2>(t)); }));
   return ret;
 } // read_persistence_diagram_from_file
 
-- 
cgit v1.2.3