Merge of the branch read_persistence_from_file

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2564 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: b534b8866e25cf86db1483d141ac217c82b36384

4 files changed, 141 insertions, 31 deletions

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)
diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
index bde05825..238d99ad 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
@@ -20,9 +20,8 @@
  *    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>
 #include <vector>
 #include <utility>  // for pair
@@ -30,43 +29,22 @@
 #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";
+    return -1;
   }
-  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_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) {
     tolerance = atof(argv[3]);
   }
   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;
 }
diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h
new file mode 100644
index 00000000..c145b271
--- /dev/null
+++ b/src/common/doc/file_formats.h
@@ -0,0 +1,54 @@
+/*    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
+
+ \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.
+*/
+}  // namespace Gudhi
+
+#endif  // DOC_COMMON_FILE_FORMAT_H_
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index 97a87edd..f1684d78 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
  *
@@ -24,7 +24,9 @@
 #define READER_UTILS_H_
 
 #include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/Debug_utils.h>
 
+#include <boost/function_output_iterator.hpp>
 #include <boost/graph/adjacency_list.hpp>
 
 #include <iostream>
@@ -92,7 +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;
@@ -295,4 +300,73 @@ std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from
   return result;
 }  // read_lower_triangular_matrix_from_csv_file
 
+/**
+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) {
+
+  std::ifstream in(filename);
+  if (!in.is_open()) {
+    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()) {
+    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 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]);
+      }
+    }
+  }
+} // read_persistence_diagram_from_file
+
+/**
+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.
+**/
+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](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
+
+
+/**
+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` 
+(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.
+**/
+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](std::tuple<int, double, double> t) { ret.emplace_back(get<1>(t), get<2>(t)); }));
+  return ret;
+} // read_persistence_diagram_from_file
+
 #endif  // READER_UTILS_H_