added unitary tests for kernels

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/kernels@3391 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: d383ed76f3cfd3724449cb7e8c24b895a7322d52
author: mcarrier <mcarrier@636b058d-ea47-450e-bf9e-a15bfbe3eedb> 2018-04-23 20:34:49 +0000
committer: mcarrier <mcarrier@636b058d-ea47-450e-bf9e-a15bfbe3eedb> 2018-04-23 20:34:49 +0000
commit: c11a8596bc7ee8705f99258886714da7757f2334 (patch)
tree: dd3787d1ee5c72eaef0e0215036ba5af2d9c5a81 /src/common
parent: ea11100d803c86a0fd5cfec1b9431110b48d87c9 (diff)
parent: dc1a4ce409292138cf1380ca673a72eaae67675a (diff)
11 files changed, 214 insertions, 32 deletions
diff --git a/src/common/doc/header.html b/src/common/doc/header.html
index d69b28fa..2f54e68d 100644
--- a/src/common/doc/header.html
+++ b/src/common/doc/header.html
@@ -9,7 +9,7 @@
 <!--BEGIN PROJECT_NAME--><title>$projectname: $title</title><!--END PROJECT_NAME-->
 <!--BEGIN !PROJECT_NAME--><title>$title</title><!--END !PROJECT_NAME-->
 <!-- GUDHI website css for header BEGIN -->
-<link rel="stylesheet" type="text/css" href="http://pages.saclay.inria.fr/vincent.rouvreau/gudhi/gudhi-doc-2.0.0/assets/css/styles_feeling_responsive.css" />
+<link rel="stylesheet" type="text/css" href="http://gudhi.gforge.inria.fr/assets/css/styles_feeling_responsive.css" />
 <!-- GUDHI website css for header END -->
 <link href="$relpath^tabs.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="$relpath^jquery.js"></script>
diff --git a/src/common/doc/offline_header.html b/src/common/doc/offline_header.html
new file mode 100644
index 00000000..6a02a895
--- /dev/null
+++ b/src/common/doc/offline_header.html
@@ -0,0 +1,41 @@
+<!-- HTML header for doxygen 1.8.6-->
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<!-- GUDHI website : class="no-js" lang="en" is necessary -->
+<html xmlns="http://www.w3.org/1999/xhtml" class="no-js" lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen $doxygenversion"/>
+<!--BEGIN PROJECT_NAME--><title>$projectname: $title</title><!--END PROJECT_NAME-->
+<!--BEGIN !PROJECT_NAME--><title>$title</title><!--END !PROJECT_NAME-->
+<!-- GUDHI website css for header END -->
+<link href="$relpath^tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="$relpath^jquery.js"></script>
+<script type="text/javascript" src="$relpath^dynsections.js"></script>
+$treeview
+$search
+$mathjax
+<link href="$relpath^$stylesheet" rel="stylesheet" type="text/css" />
+$extrastylesheet
+</head>
+<body>
+
+
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+
+<!--BEGIN TITLEAREA-->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 30px;">
+  <!--BEGIN DISABLE_INDEX-->
+   <!--BEGIN SEARCHENGINE-->
+   <td>$searchbox</td>
+   <!--END SEARCHENGINE-->
+  <!--END DISABLE_INDEX-->
+ </tr>
+ </tbody>
+</table>
+</div>
+<!--END TITLEAREA-->
+<!-- end header part -->
diff --git a/src/common/example/CMakeLists.txt b/src/common/example/CMakeLists.txt
index afe865d4..1273c699 100644
--- a/src/common/example/CMakeLists.txt
+++ b/src/common/example/CMakeLists.txt
@@ -3,11 +3,20 @@ project(Common_examples)
 
 add_executable ( vector_double_off_reader example_vector_double_points_off_reader.cpp )
 target_link_libraries(vector_double_off_reader ${CGAL_LIBRARY})
+file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 add_test(NAME Common_example_vector_double_off_reader COMMAND $<TARGET_FILE:vector_double_off_reader>
-    "${CMAKE_SOURCE_DIR}/data/points/SO3_10000.off")
+    "alphacomplexdoc.off")
 
 install(TARGETS vector_double_off_reader DESTINATION bin)
 
+if (DIFF_PATH)
+  # Do not forget to copy test results files in current binary dir
+  file(COPY "vectordoubleoffreader_result.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+
+  add_test(Common_example_vector_double_off_reader_diff_files ${DIFF_PATH}
+      ${CMAKE_CURRENT_BINARY_DIR}/vectordoubleoffreader_result.txt ${CMAKE_CURRENT_BINARY_DIR}/alphacomplexdoc.off.txt)
+endif()
+
 if(CGAL_FOUND)
   add_executable ( cgal_3D_off_reader example_CGAL_3D_points_off_reader.cpp )
   target_link_libraries(cgal_3D_off_reader ${CGAL_LIBRARY})
diff --git a/src/common/example/example_CGAL_3D_points_off_reader.cpp b/src/common/example/example_CGAL_3D_points_off_reader.cpp
index 665b7a29..4658d8d5 100644
--- a/src/common/example/example_CGAL_3D_points_off_reader.cpp
+++ b/src/common/example/example_CGAL_3D_points_off_reader.cpp
@@ -20,12 +20,12 @@ int main(int argc, char **argv) {
     usage(argv[0]);
   }
 
-  std::string offInputFile(argv[1]);
+  std::string off_input_file(argv[1]);
   // Read the OFF file (input file name given as parameter) and triangulate points
-  Gudhi::Points_3D_off_reader<Point_3> off_reader(offInputFile);
+  Gudhi::Points_3D_off_reader<Point_3> off_reader(off_input_file);
   // Check the read operation was correct
   if (!off_reader.is_valid()) {
-    std::cerr << "Unable to read file " << offInputFile << std::endl;
+    std::cerr << "Unable to read file " << off_input_file << std::endl;
     usage(argv[0]);
   }
 
diff --git a/src/common/example/example_CGAL_points_off_reader.cpp b/src/common/example/example_CGAL_points_off_reader.cpp
index 8c6a6b54..f45683a5 100644
--- a/src/common/example/example_CGAL_points_off_reader.cpp
+++ b/src/common/example/example_CGAL_points_off_reader.cpp
@@ -22,12 +22,12 @@ int main(int argc, char **argv) {
     usage(argv[0]);
   }
 
-  std::string offInputFile(argv[1]);
+  std::string off_input_file(argv[1]);
   // Read the OFF file (input file name given as parameter) and triangulate points
-  Gudhi::Points_off_reader<Point_d> off_reader(offInputFile);
+  Gudhi::Points_off_reader<Point_d> off_reader(off_input_file);
   // Check the read operation was correct
   if (!off_reader.is_valid()) {
-    std::cerr << "Unable to read file " << offInputFile << std::endl;
+    std::cerr << "Unable to read file " << off_input_file << std::endl;
     usage(argv[0]);
   }
 
diff --git a/src/common/example/example_vector_double_points_off_reader.cpp b/src/common/example/example_vector_double_points_off_reader.cpp
index 8aecb26e..5093da85 100644
--- a/src/common/example/example_vector_double_points_off_reader.cpp
+++ b/src/common/example/example_vector_double_points_off_reader.cpp
@@ -17,25 +17,27 @@ int main(int argc, char **argv) {
     usage(argv[0]);
   }
 
-  std::string offInputFile(argv[1]);
+  std::string off_input_file(argv[1]);
   // Read the OFF file (input file name given as parameter) and triangulate points
-  Gudhi::Points_off_reader<Point_d> off_reader(offInputFile);
+  Gudhi::Points_off_reader<Point_d> off_reader(off_input_file);
   // Check the read operation was correct
   if (!off_reader.is_valid()) {
-    std::cerr << "Unable to read file " << offInputFile << std::endl;
+    std::cerr << "Unable to read file " << off_input_file << std::endl;
     usage(argv[0]);
   }
 
   // Retrieve the triangulation
   std::vector<Point_d> point_cloud = off_reader.get_point_cloud();
 
+  std::ofstream output_file(off_input_file + ".txt");
   int n {0};
   for (auto point : point_cloud) {
-    std::cout << "Point[" << n << "] = ";
+    output_file << "Point[" << n << "] = ";
     for (std::size_t i {0}; i < point.size(); i++)
-      std::cout << point[i] << " ";
-    std::cout << "\n";
+      output_file << point[i] << " ";
+    output_file << "\n";
     ++n;
   }
+  output_file.close();
   return 0;
 }
diff --git a/src/common/example/cgaloffreader_result.txt b/src/common/example/vectordoubleoffreader_result.txt
index 1deb8dbd..1deb8dbd 100644
--- a/src/common/example/cgaloffreader_result.txt
+++ b/src/common/example/vectordoubleoffreader_result.txt
diff --git a/src/common/include/gudhi/Off_reader.h b/src/common/include/gudhi/Off_reader.h
index 4fcd2af2..32320e4d 100644
--- a/src/common/include/gudhi/Off_reader.h
+++ b/src/common/include/gudhi/Off_reader.h
@@ -105,25 +105,26 @@ class Off_reader {
     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) {
       std::cerr << line << std::endl;
       std::cerr << "missing off header\n";
       return false;
     }
 
+    if (is_noff_file) {
+      // Should be on a separate line, but we accept it on the same line as the number of vertices
+      stream_ >> off_info_.dim;
+    } else {
+      off_info_.dim = 3;
+    }
+
     if (!goto_next_uncomment_line(line)) return false;
     std::istringstream iss(line);
-    if ((is_off_file) && (!is_noff_file)) {
-      off_info_.dim = 3;
-      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_.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);
 
@@ -131,10 +132,12 @@ class Off_reader {
   }
 
   bool goto_next_uncomment_line(std::string& uncomment_line) {
-    uncomment_line.clear();
-    do
-      std::getline(stream_, uncomment_line); while (uncomment_line[0] == '%');
-    return (uncomment_line.size() > 0 && uncomment_line[0] != '%');
+    do {
+      // skip whitespace, including empty lines
+      if (!std::ifstream::sentry(stream_)) return false;
+      std::getline(stream_, uncomment_line);
+    } while (uncomment_line[0] == '#');
+    return (bool)stream_;
   }
 
   template<typename OffVisitor>
diff --git a/src/common/include/gudhi/Points_off_io.h b/src/common/include/gudhi/Points_off_io.h
index 29af8a8a..08f324c6 100644
--- a/src/common/include/gudhi/Points_off_io.h
+++ b/src/common/include/gudhi/Points_off_io.h
@@ -126,9 +126,9 @@ class Points_off_visitor_reader {
  * \code $> ./vector_double_off_reader ../../data/points/alphacomplexdoc.off
  * \endcode
  *
- * the program output is:
+ * the program outputs a file ../../data/points/alphacomplexdoc.off.txt:
  * 
- * \include common/cgaloffreader_result.txt
+ * \include common/vectordoubleoffreader_result.txt
  */
 template<typename Point_d>
 class Points_off_reader {
diff --git a/src/common/include/gudhi/writing_persistence_to_file.h b/src/common/include/gudhi/writing_persistence_to_file.h
new file mode 100644
index 00000000..4c5ce918
--- /dev/null
+++ b/src/common/include/gudhi/writing_persistence_to_file.h
@@ -0,0 +1,117 @@
+/*    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):       Pawel Dlotko
+ *
+ *    Copyright (C) 2017  Swansea University, UK
+ *
+ *    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 WRITING_PERSISTENCE_TO_FILE_H
+#define WRITING_PERSISTENCE_TO_FILE_H
+
+#include <iostream>
+#include <string>
+#include <limits>
+
+namespace Gudhi {
+
+/**
+* This is a class to store persistence intervals. Its main purpose is to
+* exchange data in between different packages and provide unified way
+* of writing a collection of persistence intervals to file.
+**/
+template <typename Filtration_type, typename Coefficient_field>
+class Persistence_interval_common {
+ public:
+  /**
+   * Constructor taking as an input birth and death of the pair.
+  **/
+  Persistence_interval_common(Filtration_type birth, Filtration_type death)
+      : birth_(birth),
+        death_(death),
+        dimension_(std::numeric_limits<unsigned>::max()),
+        arith_element_(std::numeric_limits<Coefficient_field>::max()) {}
+
+  /**
+   * Constructor taking as an input birth, death and dimension of the pair.
+  **/
+  Persistence_interval_common(Filtration_type birth, Filtration_type death, unsigned dim)
+      : birth_(birth), death_(death), dimension_(dim), arith_element_(std::numeric_limits<Coefficient_field>::max()) {}
+
+  /**
+* Constructor taking as an input birth, death, dimension of the pair as well
+* as the number p such that this interval is present over Z_p field.
+**/
+  Persistence_interval_common(Filtration_type birth, Filtration_type death, unsigned dim, Coefficient_field field)
+      : birth_(birth), death_(death), dimension_(dim), arith_element_(field) {}
+
+  /**
+   * Operator to compare two persistence pairs. During the comparision all the
+   * fields: birth, death, dimensiona and arith_element_ are taken into account
+   * and they all have to be equal for two pairs to be equal.
+  **/
+  bool operator==(const Persistence_interval_common& i2) const {
+    return ((this->birth_ == i2.birth_) && (this->death_ == i2.death_) && (this->dimension_ == i2.dimension_) &&
+            (this->arith_element_ == i2.arith_element_));
+  }
+
+  /**
+   * Check if two persistence paris are not equal.
+  **/
+  bool operator!=(const Persistence_interval_common& i2) const { return (!((*this) == i2)); }
+
+  /**
+   * Operator to compare objects of a type Persistence_interval_common.
+   * One intervals is smaller than the other if it has lower persistence.
+   * Note that this operator do not take Arith_element into account when doing comparisions.
+  **/
+  bool operator<(const Persistence_interval_common& i2) const {
+    return fabs(this->death_ - this->birth_) < fabs(i2.death_ - i2.birth_);
+  }
+
+  friend std::ostream& operator<<(std::ostream& out, const Persistence_interval_common& it) {
+    if (it.arith_element_ != std::numeric_limits<Coefficient_field>::max()) {
+      out << it.arith_element_ << "  ";
+    }
+    if (it.dimension_ != std::numeric_limits<unsigned>::max()) {
+      out << it.dimension_ << " ";
+    }
+    out << it.birth_ << " " << it.death_ << " ";
+    return out;
+  }
+
+ private:
+  Filtration_type birth_;
+  Filtration_type death_;
+  unsigned dimension_;
+  Coefficient_field arith_element_;
+};
+
+/**
+ * This function write a vector<Persistence_interval_common> to a stream
+**/
+template <typename Persistence_interval_range>
+void write_persistence_intervals_to_stream(const Persistence_interval_range& intervals,
+                                           std::ostream& out = std::cout) {
+  for (auto interval : intervals) {
+    out << interval << "\n";
+  }
+}
+
+}
+
+#endif  // WRITING_PERSISTENCE_TO_FILE_H
diff --git a/src/common/utilities/pointsetgenerator.md b/src/common/utilities/pointsetgenerator.md
index 284715d4..3b23e668 100644
--- a/src/common/utilities/pointsetgenerator.md
+++ b/src/common/utilities/pointsetgenerator.md
@@ -1,6 +1,16 @@
-
-
-# common #
+---
+layout: page
+title: "OFF point set generator"
+meta_title: "OFF point set generator"
+teaser: ""
+permalink: /pointsetgenerator/
+---
+{::comment}
+Leave the lines above as it is required by the web site generator 'Jekyll'
+{:/comment}
+
+
+# Miscellaneous #
 
 ## off_file_from_shape_generator ##
author	mcarrier <mcarrier@636b058d-ea47-450e-bf9e-a15bfbe3eedb>	2018-04-23 20:34:49 +0000
committer	mcarrier <mcarrier@636b058d-ea47-450e-bf9e-a15bfbe3eedb>	2018-04-23 20:34:49 +0000
commit	c11a8596bc7ee8705f99258886714da7757f2334 (patch)
tree	dd3787d1ee5c72eaef0e0215036ba5af2d9c5a81 /src/common
parent	ea11100d803c86a0fd5cfec1b9431110b48d87c9 (diff)
parent	dc1a4ce409292138cf1380ca673a72eaae67675a (diff)