Merge branch 'master' into kernels

4 files changed, 52 insertions, 14 deletions

diff --git a/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
index d1836ef0..5fa02a5e 100644
--- a/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
+++ b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
@@ -87,11 +87,16 @@ namespace cubical_complex {
  *
  * \section inputformat Input Format
  *
- * In the current implantation, filtration is given at the maximal cubes, and it is then extended by the lower star
+ * In the current implementation, filtration is given at the maximal cubes, and it is then extended by the lower star
  * filtration to all cubes. There are a number of constructors that can be used to construct cubical complex by users
  * who want to use the code directly. They can be found in the \a Bitmap_cubical_complex class.
- * Currently one input from a text file is used. It uses a format used already in Perseus software
- * (http://www.sas.upenn.edu/~vnanda/perseus/) by Vidit Nanda. The file format is described here: \ref FileFormatsPerseus.
+ * Currently one input from a text file is used. It uses a format inspired from the Perseus software
+ * (http://www.sas.upenn.edu/~vnanda/perseus/) by Vidit Nanda.
+ * \note While Perseus assume the filtration of all maximal cubes to be non-negative, over here we do not enforce this
+ * and we allow any filtration values. As a consequence one cannot use `-1`'s to indicate missing cubes. If you have
+ * missing cubes in your complex, please set their filtration to \f$+\infty\f$ (aka. `inf` in the file).
+ *
+ * The file format is described in details in \ref FileFormatsPerseus file format section.
  *
  * \section PeriodicBoundaryConditions Periodic boundary conditions
  * Often one would like to impose periodic boundary conditions to the cubical complex. Let \f$ I_1\times ... \times
diff --git a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h
index 9b74e267..f5e005b2 100644
--- a/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h
+++ b/src/Bitmap_cubical_complex/include/gudhi/Bitmap_cubical_complex_base.h
@@ -650,18 +650,33 @@ void Bitmap_cubical_complex_base<T>::read_perseus_style_file(const char* perseus
   Bitmap_cubical_complex_base<T>::Top_dimensional_cells_iterator it(*this);
   it = this->top_dimensional_cells_iterator_begin();
 
-  T filtrationLevel;
-  for (std::size_t i = 0; i < dimensions; ++i) {
-    if (!(inFiltration >> filtrationLevel) || (inFiltration.eof())) {
-      throw std::ios_base::failure("Bad Perseus file format.");
-    }
-    if (dbg) {
-      std::cerr << "Cell of an index : " << it.compute_index_in_bitmap()
-                << " and dimension: " << this->get_dimension_of_a_cell(it.compute_index_in_bitmap())
-                << " get the value : " << filtrationLevel << std::endl;
+  T filtrationLevel = 0.;
+  std::size_t filtration_counter = 0;
+  while (!inFiltration.eof()) {
+    std::string line;
+    getline(inFiltration, line);
+    if (line.length() != 0) {
+      int n = sscanf(line.c_str(), "%lf", &filtrationLevel);
+      if (n != 1) {
+        std::string perseus_error("Bad Perseus file format. This line is incorrect : " + line);
+        throw std::ios_base::failure(perseus_error.c_str());
+      }
+
+      if (dbg) {
+        std::cerr << "Cell of an index : " << it.compute_index_in_bitmap()
+                  << " and dimension: " << this->get_dimension_of_a_cell(it.compute_index_in_bitmap())
+                  << " get the value : " << filtrationLevel << std::endl;
+      }
+      this->get_cell_data(*it) = filtrationLevel;
+      ++it;
+      ++filtration_counter;
     }
-    this->get_cell_data(*it) = filtrationLevel;
-    ++it;
+  }
+
+  if (filtration_counter != dimensions) {
+    std::string perseus_error("Bad Perseus file format. Read " + std::to_string(filtration_counter) + " expected " + \
+      std::to_string(dimensions) + " values");
+    throw std::ios_base::failure(perseus_error.c_str());
   }
 
   inFiltration.close();
diff --git a/src/Bitmap_cubical_complex/test/Bitmap_test.cpp b/src/Bitmap_cubical_complex/test/Bitmap_test.cpp
index ca7bd986..6a917c25 100644
--- a/src/Bitmap_cubical_complex/test/Bitmap_test.cpp
+++ b/src/Bitmap_cubical_complex/test/Bitmap_test.cpp
@@ -32,6 +32,7 @@
 #include <iostream>
 #include <sstream>
 #include <vector>
+#include <limits>
 
 typedef Gudhi::cubical_complex::Bitmap_cubical_complex_base<double> Bitmap_cubical_complex_base;
 typedef Gudhi::cubical_complex::Bitmap_cubical_complex<Bitmap_cubical_complex_base> Bitmap_cubical_complex;
@@ -1576,3 +1577,17 @@ BOOST_AUTO_TEST_CASE(compute_incidence_between_cells_test_periodic_boundary_cond
     }
   }
 }
+
+BOOST_AUTO_TEST_CASE(perseus_file_read) {
+  Bitmap_cubical_complex increasing("sinusoid.txt");
+
+  auto it = increasing.top_dimensional_cells_iterator_begin();
+  double value = increasing.get_cell_data(*it);
+  std::cout << "First value of sinusoid.txt is " << value << std::endl;
+  BOOST_CHECK(value == 10.);
+  // Next value
+  ++it;
+  value = increasing.get_cell_data(*it);
+  std::cout << "Second value of sinusoid.txt is " << value << std::endl;
+  BOOST_CHECK(value == std::numeric_limits<double>::infinity());
+}
diff --git a/src/Bitmap_cubical_complex/test/CMakeLists.txt b/src/Bitmap_cubical_complex/test/CMakeLists.txt
index 8b43632a..d2f002a6 100644
--- a/src/Bitmap_cubical_complex/test/CMakeLists.txt
+++ b/src/Bitmap_cubical_complex/test/CMakeLists.txt
@@ -2,6 +2,9 @@ project(Bitmap_cubical_complex_tests)
 
 include(GUDHI_test_coverage)
 
+# Do not forget to copy test files in current binary dir
+file(COPY "${CMAKE_SOURCE_DIR}/data/bitmap/sinusoid.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+
 add_executable ( Bitmap_cubical_complex_test_unit Bitmap_test.cpp )
 target_link_libraries(Bitmap_cubical_complex_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 if (TBB_FOUND)