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-rw-r--r--src/common/include/gudhi/Debug_utils.h (renamed from src/common/include/gudhi/Utils.h)41
-rw-r--r--src/common/include/gudhi/Off_reader.h49
-rw-r--r--src/common/include/gudhi/Points_off_io.h177
-rw-r--r--src/common/include/gudhi/distance_functions.h4
-rw-r--r--src/common/include/gudhi/reader_utils.h6
5 files changed, 231 insertions, 46 deletions
diff --git a/src/common/include/gudhi/Utils.h b/src/common/include/gudhi/Debug_utils.h
index 43916f11..7573a9db 100644
--- a/src/common/include/gudhi/Utils.h
+++ b/src/common/include/gudhi/Debug_utils.h
@@ -19,28 +19,37 @@
* 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 UTILS_H_
-#define UTILS_H_
+#ifndef DEBUG_UTILS_H_
+#define DEBUG_UTILS_H_
+#include <iostream>
+
+#ifndef NDEBUG
+ // GUDHI_DEBUG is the Gudhi official flag for debug mode.
+ #define GUDHI_DEBUG
+#endif
+
+// GUDHI_CHECK throw an exception if expression is false in debug mode, but does nothing in release mode
+// Could assert in release mode, but cmake sets NDEBUG (for "NO DEBUG") in this mode, means assert does nothing.
+#ifdef GUDHI_DEBUG
+ #define GUDHI_CHECK(expression, excpt) if ((expression) == 0) throw excpt
+#else
+ #define GUDHI_CHECK(expression, excpt) (void) 0
+#endif
#define PRINT(a) std::cerr << #a << ": " << (a) << " (DISP)" << std::endl
// #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
-#define DBGVALUE(a) std::cerr << "DBG: " << #a << ": " << a << std::endl
-#define DBGCONT(a) std::cerr << "DBG: container " << #a << " -> "; for (auto x : a) std::cerr << x << ","; std::cerr <<
-std::endl
+ #define DBG(a) std::cout << "DBG: " << (a) << std::endl
+ #define DBGMSG(a, b) std::cout << "DBG: " << a << b << std::endl
+ #define DBGVALUE(a) std::cout << "DBG: " << #a << ": " << a << std::endl
+ #define DBGCONT(a) std::cout << "DBG: container " << #a << " -> "; for (auto x : a) std::cout << x << ","; std::cout << std::endl
#else
-// #define DBG(a) a
-// #define DBGMSG(a,b) b
-// #define DBGVALUE(a) a
-// #define DBGCONT(a) a
-#define DBG(a)
-#define DBGMSG(a, b)
-#define DBGVALUE(a)
-#define DBGCONT(a)
+ #define DBG(a) (void) 0
+ #define DBGMSG(a, b) (void) 0
+ #define DBGVALUE(a) (void) 0
+ #define DBGCONT(a) (void) 0
#endif
-#endif // UTILS_H_
+#endif // DEBUG_UTILS_H_
diff --git a/src/common/include/gudhi/Off_reader.h b/src/common/include/gudhi/Off_reader.h
index 81b9e634..4fcd2af2 100644
--- a/src/common/include/gudhi/Off_reader.h
+++ b/src/common/include/gudhi/Off_reader.h
@@ -31,40 +31,35 @@
#include <iterator>
#include <string>
#include <vector>
+#include <fstream>
namespace Gudhi {
-/**
- * Read an off file and calls a visitor methods while reading it.
- * An off file must have its first/snd line in this format :
- * OFF
- * num_vert num_faces num_edges
- *
- * A noff file must have its first/snd line in this format :
- * nOFF
- * dim num_vert num_faces num_edges
- *
- * The number of edges num_edges is optional and can be left to zero.
+/** \brief OFF file reader top class visitor.
+ *
+ * OFF file must be conform to format described here :
+ * http://www.geomview.org/docs/html/OFF.html
*/
class Off_reader {
public:
Off_reader(std::ifstream& stream) : stream_(stream) { }
- // Off_reader(const std::string& name):stream_(name){
- // if(!stream_.is_open())
- // std::cerr <<"could not open file \n";
- // }
~Off_reader() {
stream_.close();
}
- /**
- * read an off file and calls the following methods :
- * void init(int dim,int num_vertices,int num_faces,int num_edges); //num_edges may not be set
- * void point(const std::vector<double>& point);
- * void maximal_face(const std::list<int>& face);
- * void done();
- * of the visitor when reading a point or a maximal face.
+ /** \brief
+ * Read an OFF file and calls the following methods :
+ *
+ * <CODE>void init(int dim,int num_vertices,int num_faces,int num_edges); // from file header - num_edges may not be set
+ *
+ * void point(const std::vector<double>& point); // for each point read
+ *
+ * void maximal_face(const std::list<int>& face); // for each face read
+ *
+ * void done(); // upon file read is finished</CODE>
+ *
+ * of the visitor when reading a point or a maximal face. Edges are not taken into account.
*/
template<typename OffVisitor>
bool read(OffVisitor& off_visitor) {
@@ -118,7 +113,7 @@ class Off_reader {
if (!goto_next_uncomment_line(line)) return false;
std::istringstream iss(line);
- if (is_off_file) {
+ 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";
@@ -126,8 +121,8 @@ class Off_reader {
}
} else {
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;
+ 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);
@@ -138,7 +133,7 @@ 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] == '%'); // || uncomment_line.empty());
+ std::getline(stream_, uncomment_line); while (uncomment_line[0] == '%');
return (uncomment_line.size() > 0 && uncomment_line[0] != '%');
}
@@ -166,7 +161,7 @@ class Off_reader {
iss >> num_face_vertices;
std::vector<int> face;
face.assign(std::istream_iterator<int>(iss), std::istream_iterator<int>());
- if (face.size() != off_info_.dim) return false;
+ // if (face.size() != (off_info_.dim + 1)) return false;
visitor.maximal_face(face);
}
return true;
diff --git a/src/common/include/gudhi/Points_off_io.h b/src/common/include/gudhi/Points_off_io.h
new file mode 100644
index 00000000..77f36be2
--- /dev/null
+++ b/src/common/include/gudhi/Points_off_io.h
@@ -0,0 +1,177 @@
+/* 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): Vincent Rouvreau
+ *
+ * Copyright (C) 2015 INRIA Saclay (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 POINTS_OFF_IO_H_
+#define POINTS_OFF_IO_H_
+
+#include <gudhi/Off_reader.h>
+
+#include <string>
+#include <vector>
+#include <fstream>
+#include <map>
+
+namespace Gudhi {
+
+/**
+ * \brief OFF file visitor implementation according to Off_reader in order to read points from an OFF file.
+ */
+template<typename Point_d>
+class Points_off_visitor_reader {
+ private:
+ std::vector<Point_d> point_cloud;
+
+ public:
+ /** \brief Off_reader visitor init implementation.
+ *
+ * The init parameters are set from OFF file header.
+ * Dimension value is required in order to construct Alpha complex.
+ *
+ * @param[in] dim space dimension of vertices.
+ * @param[in] num_vertices number of vertices in the OFF file (not used).
+ * @param[in] num_faces number of faces in the OFF file (not used).
+ * @param[in] num_edges number of edges in the OFF file (not used).
+ */
+ void init(int dim, int num_vertices, int num_faces, int num_edges) {
+#ifdef DEBUG_TRACES
+ std::cout << "Points_off_visitor_reader::init - dim=" << dim << " - num_vertices=" <<
+ num_vertices << " - num_faces=" << num_faces << " - num_edges=" << num_edges << std::endl;
+#endif // DEBUG_TRACES
+ if (num_faces > 0) {
+ std::cerr << "Points_off_visitor_reader::init faces are not taken into account from OFF file for Points.\n";
+ }
+ if (num_edges > 0) {
+ std::cerr << "Points_off_visitor_reader::init edges are not taken into account from OFF file for Points.\n";
+ }
+ }
+
+ /** \brief Off_reader visitor point implementation.
+ *
+ * The point function is called on each vertex line from OFF file.
+ * This function inserts the vertex in the Alpha complex.
+ *
+ * @param[in] point vector of vertex coordinates.
+ */
+ void point(const std::vector<double>& point) {
+#ifdef DEBUG_TRACES
+ std::cout << "Points_off_visitor_reader::point ";
+ for (auto coordinate : point) {
+ std::cout << coordinate << " | ";
+ }
+ std::cout << std::endl;
+#endif // DEBUG_TRACES
+ // Fill the point cloud
+ point_cloud.push_back(Point_d(point.size(), point.begin(), point.end()));
+ }
+
+ // Off_reader visitor maximal_face implementation - Only points are read
+ void maximal_face(const std::vector<int>& face) { }
+
+ // Off_reader visitor done implementation - Only points are read
+ void done() { }
+
+ /** \brief Point cloud getter.
+ *
+ * @return point_cloud.
+ */
+ const std::vector<Point_d>& get_point_cloud() const {
+ return point_cloud;
+ }
+};
+
+/**
+ * \brief OFF file reader implementation in order to read points from an OFF file.
+ *
+ * This class is using the Points_off_visitor_reader to visit the OFF file according to Off_reader.
+ *
+ * Point_d must have a constructor with the following form:
+ *
+ * \code template<class InputIterator > Point_d::Point_d(int d, InputIterator first, InputIterator last) \endcode
+ *
+ * where d is the point dimension.
+ *
+ * \section Example
+ *
+ * This example loads points from an OFF file and builds a vector of CGAL points in dimension d.
+ * Then, it is asked to display the points.
+ *
+ * \include common/CGAL_points_off_reader.cpp
+ *
+ * When launching:
+ *
+ * \code $> ./cgaloffreader ../../data/points/alphacomplexdoc.off
+ * \endcode
+ *
+ * the program output is:
+ *
+ * \include common/cgaloffreader_result.txt
+ */
+template<typename Point_d>
+class Points_off_reader {
+ public:
+ /** \brief Reads the OFF file and constructs the Alpha complex from the points
+ * that are in the OFF file.
+ *
+ * @param[in] name_file OFF file to read.
+ *
+ * \post Check with is_valid() function to see if read operation was successful.
+ */
+ Points_off_reader(const std::string& name_file)
+ : valid_(false) {
+ std::ifstream stream(name_file);
+ if (stream.is_open()) {
+ Off_reader off_reader(stream);
+ Points_off_visitor_reader<Point_d> off_visitor;
+ valid_ = off_reader.read(off_visitor);
+ if (valid_) {
+ point_cloud = off_visitor.get_point_cloud();
+ }
+ } else {
+ std::cerr << "Points_off_reader::Points_off_reader could not open file " << name_file << "\n";
+ }
+ }
+
+ /** \brief Returns if the OFF file read operation was successful or not.
+ *
+ * @return OFF file read status.
+ */
+ bool is_valid() const {
+ return valid_;
+ }
+
+ /** \brief Point cloud getter.
+ *
+ * @return point_cloud.
+ */
+ const std::vector<Point_d>& get_point_cloud() const {
+ return point_cloud;
+ }
+
+ private:
+ /** \brief point_cloud.*/
+ std::vector<Point_d> point_cloud;
+ /** \brief OFF file read status.*/
+ bool valid_;
+};
+
+} // namespace Gudhi
+
+#endif // POINTS_OFF_IO_H_
diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h
index e5c79ded..cd518581 100644
--- a/src/common/include/gudhi/distance_functions.h
+++ b/src/common/include/gudhi/distance_functions.h
@@ -23,6 +23,8 @@
#ifndef DISTANCE_FUNCTIONS_H_
#define DISTANCE_FUNCTIONS_H_
+#include <cmath> // for std::sqrt
+
/* Compute the Euclidean distance between two Points given
* by a range of coordinates. The points are assumed to have
* the same dimension. */
@@ -35,7 +37,7 @@ double euclidean_distance(Point &p1, Point &p2) {
double tmp = *it1 - *it2;
dist += tmp*tmp;
}
- return sqrt(dist);
+ return std::sqrt(dist);
}
#endif // DISTANCE_FUNCTIONS_H_
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index e05714c7..899f9df6 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -58,7 +58,9 @@ inline void read_points(std::string file_name, std::vector< std::vector< double
while (iss >> x) {
point.push_back(x);
}
- points.push_back(point);
+ // Check for empty lines
+ if (!point.empty())
+ points.push_back(point);
}
in_file.close();
}
@@ -159,7 +161,7 @@ bool read_simplex(std::istream & in_, std::vector< Vertex_handle > & simplex, Fi
simplex.push_back(v);
}
in_ >> fil;
- in_.ignore((std::numeric_limits<std::streamsize>::max)(), '\n'); // ignore until the carriage return
+ in_.ignore((std::numeric_limits<std::streamsize>::max)(), '\n'); // ignore until the carriage return
return true;
}
generated by cgit v1.2.3 (git 2.39.1) at 2024-06-28 19:39:22 +0000