Merge modifications for simplex_tree automatic dimension set

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_automatic_dimension_set@2689 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: c18c6316d51f476a795b59c8b870db1aaf0b4591

20 files changed, 421 insertions, 316 deletions

diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h
index 1ff95c3d..5f7d7622 100644
--- a/src/Alpha_complex/include/gudhi/Alpha_complex.h
+++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h
@@ -268,8 +268,6 @@ class Alpha_complex {
       return false;  // ----- >>
     }
 
-    complex.set_dimension(triangulation_->maximal_dimension());
-
     // --------------------------------------------------------------------------------------------
     // Simplex_tree construction from loop on triangulation finite full cells list
     if (triangulation_->number_of_vertices() > 0) {
diff --git a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
index 7380547f..166373fe 100644
--- a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
+++ b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
@@ -159,7 +159,7 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) {
   BOOST_CHECK(simplex_tree.num_simplices() == 15);
 
   std::cout << "simplex_tree.dimension()=" << simplex_tree.dimension() << std::endl;
-  BOOST_CHECK(simplex_tree.dimension() == 4);
+  BOOST_CHECK(simplex_tree.dimension() == 3);
   std::cout << "simplex_tree.num_vertices()=" << simplex_tree.num_vertices() << std::endl;
   BOOST_CHECK(simplex_tree.num_vertices() == 4);
 
@@ -232,7 +232,7 @@ BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) {
   BOOST_CHECK(simplex_tree.num_simplices() == 10);
 
   std::cout << "simplex_tree.dimension()=" << simplex_tree.dimension() << std::endl;
-  BOOST_CHECK(simplex_tree.dimension() == 4);
+  BOOST_CHECK(simplex_tree.dimension() == 1);
   std::cout << "simplex_tree.num_vertices()=" << simplex_tree.num_vertices() << std::endl;
   BOOST_CHECK(simplex_tree.num_vertices() == 4);
 
diff --git a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
index fd227b82..40eb3576 100644
--- a/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
@@ -203,7 +203,6 @@ int main(int argc, char * const argv[]) {
       std::cout << "This shall not happen" << std::endl;
   }
   simplex_tree.set_filtration(filtration_max);
-  simplex_tree.set_dimension(dim_max);
 
 #ifdef DEBUG_TRACES
   std::cout << "vertices \t\t" << count_vertices << std::endl;
diff --git a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp
index 8a335075..9881debf 100644
--- a/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/exact_alpha_complex_3d_persistence.cpp
@@ -205,7 +205,6 @@ int main(int argc, char * const argv[]) {
       std::cout << "This shall not happen" << std::endl;
   }
   simplex_tree.set_filtration(filtration_max);
-  simplex_tree.set_dimension(dim_max);
 
 #ifdef DEBUG_TRACES
   std::cout << "vertices \t\t" << count_vertices << std::endl;
diff --git a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
index 8928cfc2..71faebd7 100644
--- a/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/periodic_alpha_complex_3d_persistence.cpp
@@ -222,7 +222,6 @@ int main(int argc, char * const argv[]) {
       std::cout << "This shall not happen" << std::endl;
   }
   simplex_tree.set_filtration(filtration_max);
-  simplex_tree.set_dimension(dim_max);
 
 #ifdef DEBUG_TRACES
   std::cout << "vertices \t\t" << count_vertices << std::endl;
diff --git a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
index 7ca9410a..7809d5ff 100644
--- a/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
+++ b/src/Persistent_cohomology/example/persistence_from_simple_simplex_tree.cpp
@@ -142,7 +142,6 @@ int main(int argc, char * const argv[]) {
   /*   An edge [11,6]         */
   /*   An edge [10,12,2]      */
 
-  st.set_dimension(2);
   st.set_filtration(0.4);
 
   std::cout << "The complex contains " << st.num_simplices() << " simplices - " << st.num_vertices() << " vertices "
diff --git a/src/Persistent_cohomology/example/plain_homology.cpp b/src/Persistent_cohomology/example/plain_homology.cpp
index 50f692f2..a5ae09c8 100644
--- a/src/Persistent_cohomology/example/plain_homology.cpp
+++ b/src/Persistent_cohomology/example/plain_homology.cpp
@@ -64,8 +64,6 @@ int main() {
   st.insert_simplex_and_subfaces(edge03);
   st.insert_simplex(edge13);
   st.insert_simplex(vertex4);
-  // FIXME: Remove this line
-  st.set_dimension(2);
 
   // Sort the simplices in the order of the filtration
   st.initialize_filtration();
diff --git a/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp
index 554eeba6..75580aac 100644
--- a/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence_step_by_step.cpp
@@ -88,6 +88,9 @@ int main(int argc, char * argv[]) {
   Simplex_tree st;
   // insert the proximity graph in the simplex tree
   st.insert_graph(prox_graph);
+  std::cout << "The complex contains " << st.num_simplices() << " simplices \n";
+  std::cout << "   and has dimension " << st.dimension() << " \n";
+/*
   // expand the graph until dimension dim_max
   st.expansion(dim_max);
 
@@ -112,7 +115,7 @@ int main(int argc, char * argv[]) {
     pcoh.output_diagram(out);
     out.close();
   }
-
+*/
   return 0;
 }
 
diff --git a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
index 34b90933..968db753 100644
--- a/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
+++ b/src/Persistent_cohomology/example/weighted_alpha_complex_3d_persistence.cpp
@@ -223,7 +223,6 @@ int main(int argc, char * const argv[]) {
       std::cout << "This shall not happen" << std::endl;
   }
   simplex_tree.set_filtration(filtration_max);
-  simplex_tree.set_dimension(dim_max);
 
 #ifdef DEBUG_TRACES
   std::cout << "vertices \t\t" << count_vertices << std::endl;
diff --git a/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp b/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp
index da418034..0a08d200 100644
--- a/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp
+++ b/src/Persistent_cohomology/test/betti_numbers_unit_test.cpp
@@ -62,8 +62,6 @@ BOOST_AUTO_TEST_CASE( plain_homology_betti_numbers )
   st.insert_simplex_and_subfaces(edge04);
   st.insert_simplex(edge14);
   st.insert_simplex(vertex5);
-  // FIXME: Remove this line
-  st.set_dimension(3);
 
   // Sort the simplices in the order of the filtration
   st.initialize_filtration();
@@ -170,8 +168,6 @@ BOOST_AUTO_TEST_CASE( betti_numbers )
   st.insert_simplex_and_subfaces(edge04, 2.0);
   st.insert_simplex(edge14, 2.0);
   st.insert_simplex(vertex5, 1.0);
-  // FIXME: Remove this line
-  st.set_dimension(3);
 
   // Sort the simplices in the order of the filtration
   st.initialize_filtration();
diff --git a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
index f8174020..887aa25f 100644
--- a/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
+++ b/src/Persistent_cohomology/test/persistent_cohomology_unit_test.cpp
@@ -197,8 +197,6 @@ BOOST_AUTO_TEST_CASE( persistence_constructor_exception )
   // To make number of simplices = 255
   const short simplex_0[] = {0, 1, 2, 3, 4, 5, 6, 7};
   st.insert_simplex_and_subfaces(simplex_0);
-  // FIXME: Remove this line
-  st.set_dimension(8);
 
   // Sort the simplices in the order of the filtration
   st.initialize_filtration();
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index 317bce23..478ed80f 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -601,7 +601,11 @@ class Simplex_tree {
       // if filtration value unchanged
       return std::pair<Simplex_handle, bool>(null_simplex(), false);
     }
-    // otherwise the insertion has succeeded
+    // otherwise the insertion has succeeded - size is a size_type
+    if (static_cast<int>(simplex.size()) - 1 > dimension_) {
+      // Update dimension if needed
+      dimension_ = static_cast<int>(simplex.size()) - 1;
+    }
     return res_insert;
   }
 
@@ -1159,7 +1163,11 @@ class Simplex_tree {
    * complex has changed , please call `initialize_filtration()` to recompute it.
    */
   bool prune_above_filtration(Filtration_value filtration) {
-    return rec_prune_above_filtration(root(), filtration);
+    bool modified = rec_prune_above_filtration(root(), filtration);
+    if (modified) {
+      auto_dimension_set(dimension());
+    }
+    return modified;
   }
 
  private:
@@ -1187,6 +1195,33 @@ class Simplex_tree {
     return modified;
   }
 
+ private:
+  /** \brief Resets the Simplex_tree dimension.
+   * @param[in] old_dimension The former dimension value until the loop stopped when it is reached.
+   * @return The dimension modification information.
+   * \pre Please check the simplex has not a too low dimension value.
+   * This cannot happen if set_dimension has not been performed.
+   */
+  bool auto_dimension_set(int old_dimension) {
+    int new_dimension = -1;
+    for (Simplex_handle sh : skeleton_simplex_range(old_dimension)) {
+#ifdef DEBUG_TRACES
+      for (auto vertex : simplex_vertex_range(sh)) {
+        std::cout << " " << vertex;
+      }
+      std::cout << std::endl;
+#endif  // DEBUG_TRACES
+
+      int sh_dimension = dimension(sh);
+      if (sh_dimension >= old_dimension)
+        return false;
+      new_dimension = std::max<int>(new_dimension, sh_dimension);
+    }
+    set_dimension(new_dimension);
+    return true;
+  }
+
+
  public:
   /** \brief Remove a maximal simplex.
    * @param[in] sh Simplex handle on the maximal simplex to remove.
@@ -1207,9 +1242,17 @@ class Simplex_tree {
       // Special case when child is the root of the simplex tree, just remove it from members
       child->erase(sh);
     } else {
+      // Keep information before remove action
+      int sh_dim = dimension(sh);
+
       // Sibling is emptied : must be deleted, and its parent must point on his own Sibling
       child->oncles()->members().at(child->parent()).assign_children(child->oncles());
       delete child;
+
+      // No need to reset dimension in case maximal simplex is not the maximal dimension one
+      if (sh_dim >= dimension()) {
+        auto_dimension_set(sh_dim);
+      }
     }
   }
 
diff --git a/src/Simplex_tree/test/CMakeLists.txt b/src/Simplex_tree/test/CMakeLists.txt
index 81999de6..1c169ff7 100644
--- a/src/Simplex_tree/test/CMakeLists.txt
+++ b/src/Simplex_tree/test/CMakeLists.txt
@@ -3,13 +3,21 @@ project(Simplex_tree_tests)
 
 include(GUDHI_test_coverage)
 
+# Do not forget to copy test files in current binary dir
+file(COPY "simplex_tree_for_unit_test.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+
 add_executable ( Simplex_tree_test_unit simplex_tree_unit_test.cpp )
 target_link_libraries(Simplex_tree_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
 if (TBB_FOUND)
   target_link_libraries(Simplex_tree_test_unit ${TBB_LIBRARIES})
 endif()
 
-# Do not forget to copy test files in current binary dir
-file(COPY "simplex_tree_for_unit_test.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
-
 gudhi_add_coverage_test(Simplex_tree_test_unit)
+
+add_executable ( Simplex_tree_remove_test_unit simplex_tree_remove_unit_test.cpp )
+target_link_libraries(Simplex_tree_remove_test_unit ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+if (TBB_FOUND)
+  target_link_libraries(Simplex_tree_remove_test_unit ${TBB_LIBRARIES})
+endif()
+
+gudhi_add_coverage_test(Simplex_tree_remove_test_unit)
diff --git a/src/Simplex_tree/test/README b/src/Simplex_tree/test/README
index 21c3d871..df2ab89a 100644
--- a/src/Simplex_tree/test/README
+++ b/src/Simplex_tree/test/README
@@ -9,6 +9,6 @@ make
 To launch with details:
 ***********************
 
-./SimplexTreeUT --report_level=detailed --log_level=all 
+./Simplex_tree_test_unit --report_level=detailed --log_level=all
 
    ==> echo $? returns 0 in case of success (non-zero otherwise)
diff --git a/src/Simplex_tree/test/simplex_tree_remove_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_remove_unit_test.cpp
new file mode 100644
index 00000000..ad71fed3
--- /dev/null
+++ b/src/Simplex_tree/test/simplex_tree_remove_unit_test.cpp
@@ -0,0 +1,346 @@
+#include <iostream>
+
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "simplex_tree_remove"
+#include <boost/test/unit_test.hpp>
+#include <boost/mpl/list.hpp>
+
+//  ^
+// /!\ Nothing else from Simplex_tree shall be included to test includes are well defined.
+#include "gudhi/Simplex_tree.h"
+
+using namespace Gudhi;
+
+struct MyOptions : Simplex_tree_options_full_featured {
+  // Not doing persistence, so we don't need those
+  static const bool store_key = false;
+  static const bool store_filtration = false;
+  // I have few vertices
+  typedef short Vertex_handle;
+};
+
+using Mini_stree = Simplex_tree<MyOptions>;
+using Stree = Simplex_tree<>;
+
+BOOST_AUTO_TEST_CASE(remove_maximal_simplex) {
+  std::cout << "********************************************************************" << std::endl;
+  std::cout << "REMOVE MAXIMAL SIMPLEX" << std::endl;
+
+  Mini_stree st;
+
+  st.insert_simplex_and_subfaces({0, 1, 6, 7});
+  st.insert_simplex_and_subfaces({3, 4, 5});
+
+  // Constructs a copy at this state for further test purpose
+  Mini_stree st_pruned = st;
+
+  st.insert_simplex_and_subfaces({3, 0});
+  st.insert_simplex_and_subfaces({2, 1, 0});
+
+  // Constructs a copy at this state for further test purpose
+  Mini_stree st_complete = st;
+  // st_complete and st:
+  //    1   6
+  //    o---o
+  //   /X\7/
+  //  o---o---o---o
+  //  2   0   3\X/4
+  //            o
+  //            5
+  // st_pruned:
+  //    1   6
+  //    o---o
+  //     \7/
+  //      o   o---o
+  //      0   3\X/4
+  //            o
+  //            5
+
+#ifdef GUDHI_DEBUG
+  std::cout << "Check exception throw in debug mode" << std::endl;
+  // throw excpt because sh has children
+  BOOST_CHECK_THROW (st.remove_maximal_simplex(st.find({0, 1, 6})), std::invalid_argument);
+  BOOST_CHECK_THROW (st.remove_maximal_simplex(st.find({3})), std::invalid_argument);
+  BOOST_CHECK(st == st_complete);
+#endif
+  std::cout << "st.remove_maximal_simplex({0, 2})" << std::endl;
+  st.remove_maximal_simplex(st.find({0, 2}));
+  std::cout << "st.remove_maximal_simplex({0, 1, 2})" << std::endl;
+  st.remove_maximal_simplex(st.find({0, 1, 2}));
+  std::cout << "st.remove_maximal_simplex({1, 2})" << std::endl;
+  st.remove_maximal_simplex(st.find({1, 2}));
+  std::cout << "st.remove_maximal_simplex({2})" << std::endl;
+  st.remove_maximal_simplex(st.find({2}));
+  std::cout << "st.remove_maximal_simplex({3})" << std::endl;
+  st.remove_maximal_simplex(st.find({0, 3}));
+  
+  BOOST_CHECK(st == st_pruned);
+  // Remove all, but as the simplex tree is not storing filtration, there is no modification
+  st.prune_above_filtration(0.0);
+  BOOST_CHECK(st == st_pruned);
+  
+  Mini_stree st_wo_seven;
+
+  st_wo_seven.insert_simplex_and_subfaces({0, 1, 6});
+  st_wo_seven.insert_simplex_and_subfaces({3, 4, 5});
+  // st_wo_seven:
+  //    1   6
+  //    o---o
+  //     \X/
+  //      o   o---o
+  //      0   3\X/4
+  //            o
+  //            5
+
+  // Remove all 7 to test the both remove_maximal_simplex cases (when _members is empty or not)
+  std::cout << "st.remove_maximal_simplex({0, 1, 6, 7})" << std::endl;
+  st.remove_maximal_simplex(st.find({0, 1, 6, 7}));
+  std::cout << "st.remove_maximal_simplex({0, 1, 7})" << std::endl;
+  st.remove_maximal_simplex(st.find({0, 1, 7}));
+  std::cout << "st.remove_maximal_simplex({0, 6, 7})" << std::endl;
+  st.remove_maximal_simplex(st.find({0, 6, 7}));
+  std::cout << "st.remove_maximal_simplex({0, 7})" << std::endl;
+  st.remove_maximal_simplex(st.find({0, 7}));
+  std::cout << "st.remove_maximal_simplex({1, 6, 7})" << std::endl;
+  st.remove_maximal_simplex(st.find({1, 6, 7}));
+  std::cout << "st.remove_maximal_simplex({1, 7})" << std::endl;
+  st.remove_maximal_simplex(st.find({1, 7}));
+  std::cout << "st.remove_maximal_simplex({6, 7})" << std::endl;
+  st.remove_maximal_simplex(st.find({6, 7}));
+  std::cout << "st.remove_maximal_simplex({7})" << std::endl;
+  st.remove_maximal_simplex(st.find({7}));
+  
+  std::cout << "st.dimension()=" << st.dimension() << " | st_wo_seven.dimension()=" << st_wo_seven.dimension() << std::endl;
+  BOOST_CHECK(st == st_wo_seven);
+}
+
+BOOST_AUTO_TEST_CASE(auto_dimension_set) {
+  std::cout << "********************************************************************" << std::endl;
+  std::cout << "DIMENSION ON REMOVE MAXIMAL SIMPLEX" << std::endl;
+
+  Mini_stree st;
+
+  st.insert_simplex_and_subfaces({0, 1, 2});
+  st.insert_simplex_and_subfaces({0, 1, 3});
+  st.insert_simplex_and_subfaces({1, 2, 3, 4});
+  st.insert_simplex_and_subfaces({1, 2, 3, 5});
+  st.insert_simplex_and_subfaces({6, 7, 8, 9});
+  st.insert_simplex_and_subfaces({6, 7, 8, 10});
+
+  BOOST_CHECK(st.dimension() == 3);
+
+  std::cout << "st.remove_maximal_simplex({6, 7, 8, 10})" << std::endl;
+  st.remove_maximal_simplex(st.find({6, 7, 8, 10}));
+  BOOST_CHECK(st.dimension() == 3);
+
+  std::cout << "st.remove_maximal_simplex({6, 7, 8, 9})" << std::endl;
+  st.remove_maximal_simplex(st.find({6, 7, 8, 9}));
+  BOOST_CHECK(st.dimension() == 3);
+
+  std::cout << "st.remove_maximal_simplex({1, 2, 3, 4})" << std::endl;
+  st.remove_maximal_simplex(st.find({1, 2, 3, 4}));
+  BOOST_CHECK(st.dimension() == 3);
+
+  std::cout << "st.remove_maximal_simplex({1, 2, 3, 5})" << std::endl;
+  st.remove_maximal_simplex(st.find({1, 2, 3, 5}));
+  BOOST_CHECK(st.dimension() == 2);
+
+  std::cout << "st.insert_simplex_and_subfaces({1, 2, 3, 5})" << std::endl;
+  st.insert_simplex_and_subfaces({1, 2, 3, 5});
+  BOOST_CHECK(st.dimension() == 3);
+
+  std::cout << "st.insert_simplex_and_subfaces({1, 2, 3, 4})" << std::endl;
+  st.insert_simplex_and_subfaces({1, 2, 3, 4});
+  BOOST_CHECK(st.dimension() == 3);
+
+  std::cout << "st.remove_maximal_simplex({1, 2, 3, 5})" << std::endl;
+  st.remove_maximal_simplex(st.find({1, 2, 3, 5}));
+  BOOST_CHECK(st.dimension() == 3);
+
+  std::cout << "st.remove_maximal_simplex({1, 2, 3, 4})" << std::endl;
+  st.remove_maximal_simplex(st.find({1, 2, 3, 4}));
+  BOOST_CHECK(st.dimension() == 2);
+
+  std::cout << "st.insert_simplex_and_subfaces({0, 1, 3, 4})" << std::endl;
+  st.insert_simplex_and_subfaces({0, 1, 3, 4});
+  BOOST_CHECK(st.dimension() == 3);
+
+  std::cout << "st.remove_maximal_simplex({0, 1, 3, 4})" << std::endl;
+  st.remove_maximal_simplex(st.find({0, 1, 3, 4}));
+  BOOST_CHECK(st.dimension() == 2);
+
+  std::cout << "st.insert_simplex_and_subfaces({0, 1, 2, 3, 4, 5, 6})" << std::endl;
+  st.insert_simplex_and_subfaces({0, 1, 2, 3, 4, 5, 6});
+  BOOST_CHECK(st.dimension() == 6);
+
+  std::cout << "st.remove_maximal_simplex({0, 1, 2, 3, 4, 5, 6})" << std::endl;
+  st.remove_maximal_simplex(st.find({0, 1, 2, 3, 4, 5, 6}));
+  BOOST_CHECK(st.dimension() == 5);
+
+}
+
+BOOST_AUTO_TEST_CASE(prune_above_filtration) {
+  std::cout << "********************************************************************" << std::endl;
+  std::cout << "PRUNE ABOVE FILTRATION" << std::endl;
+
+  Stree st;
+
+  st.insert_simplex_and_subfaces({0, 1, 6, 7}, 1.0);
+  st.insert_simplex_and_subfaces({3, 4, 5}, 2.0);
+
+  // Constructs a copy at this state for further test purpose
+  Stree st_pruned = st;
+  st_pruned.initialize_filtration();  // reset
+
+  st.insert_simplex_and_subfaces({3, 0}, 3.0);
+  st.insert_simplex_and_subfaces({2, 1, 0}, 4.0);
+
+  // Constructs a copy at this state for further test purpose
+  Stree st_complete = st;
+  // st_complete and st:
+  //    1   6
+  //    o---o
+  //   /X\7/
+  //  o---o---o---o
+  //  2   0   3\X/4
+  //            o
+  //            5
+  // st_pruned:
+  //    1   6
+  //    o---o
+  //     \7/
+  //      o   o---o
+  //      0   3\X/4
+  //            o
+  //            5
+
+  bool simplex_is_changed = false;
+  // Check the no action cases
+  // greater than initial filtration value
+  simplex_is_changed = st.prune_above_filtration(10.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  BOOST_CHECK(st == st_complete);
+  BOOST_CHECK(!simplex_is_changed);
+  // equal to initial filtration value
+  simplex_is_changed = st.prune_above_filtration(6.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  BOOST_CHECK(st == st_complete);
+  BOOST_CHECK(!simplex_is_changed);
+  // lower than initial filtration value, but still greater than the maximum filtration value
+  simplex_is_changed = st.prune_above_filtration(5.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  BOOST_CHECK(st == st_complete);
+  BOOST_CHECK(!simplex_is_changed);
+
+  // Display the Simplex_tree
+  std::cout << "The complex contains " << st.num_simplices() << " simplices";
+  std::cout << " - dimension " << st.dimension() << std::endl;
+  std::cout << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
+  for (auto f_simplex : st.filtration_simplex_range()) {
+    std::cout << "   " << "[" << st.filtration(f_simplex) << "] ";
+    for (auto vertex : st.simplex_vertex_range(f_simplex)) {
+      std::cout << (int) vertex << " ";
+    }
+    std::cout << std::endl;
+  }
+
+  // Check the pruned cases
+  simplex_is_changed = st.prune_above_filtration(2.5);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  BOOST_CHECK(st == st_pruned);
+  BOOST_CHECK(simplex_is_changed);
+
+  // Display the Simplex_tree
+  std::cout << "The complex pruned at 2.5 contains " << st.num_simplices() << " simplices";
+  std::cout << " - dimension " << st.dimension() << std::endl;
+
+  simplex_is_changed = st.prune_above_filtration(2.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  
+  std::cout << "The complex pruned at 2.0 contains " << st.num_simplices() << " simplices";
+  std::cout << " - dimension " << st.dimension() << std::endl;
+
+  BOOST_CHECK(st == st_pruned);
+  BOOST_CHECK(!simplex_is_changed);
+
+  Stree st_empty;
+  simplex_is_changed = st.prune_above_filtration(0.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+
+  // Display the Simplex_tree
+  std::cout << "The complex pruned at 0.0 contains " << st.num_simplices() << " simplices";
+  std::cout << " - dimension " << st.dimension() << std::endl;
+
+  BOOST_CHECK(st == st_empty);
+  BOOST_CHECK(simplex_is_changed);
+
+  // Test case to the limit
+  simplex_is_changed = st.prune_above_filtration(-1.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  BOOST_CHECK(st == st_empty);
+  BOOST_CHECK(!simplex_is_changed);
+}
+
+BOOST_AUTO_TEST_CASE(mini_prune_above_filtration) {
+  std::cout << "********************************************************************" << std::endl;
+  std::cout << "MINI PRUNE ABOVE FILTRATION" << std::endl;
+
+  Mini_stree st;
+
+  st.insert_simplex_and_subfaces({0, 1, 6, 7});
+  st.insert_simplex_and_subfaces({3, 4, 5});
+  st.insert_simplex_and_subfaces({3, 0});
+  st.insert_simplex_and_subfaces({2, 1, 0});
+
+  // st:
+  //    1   6
+  //    o---o
+  //   /X\7/
+  //  o---o---o---o
+  //  2   0   3\X/4
+  //            o
+  //            5
+
+  st.initialize_filtration();
+  
+  // Display the Simplex_tree
+  std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl;
+  BOOST_CHECK(st.num_simplices() == 27);
+
+  // Test case to the limit - With these options, there is no filtration, which means filtration is 0
+  bool simplex_is_changed = st.prune_above_filtration(1.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  // Display the Simplex_tree
+  std::cout << "The complex pruned at 1.0 contains " << st.num_simplices() << " simplices" << std::endl;
+  BOOST_CHECK(!simplex_is_changed);
+  BOOST_CHECK(st.num_simplices() == 27);
+
+  simplex_is_changed = st.prune_above_filtration(0.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  // Display the Simplex_tree
+  std::cout << "The complex pruned at 0.0 contains " << st.num_simplices() << " simplices" << std::endl;
+  BOOST_CHECK(!simplex_is_changed);
+  BOOST_CHECK(st.num_simplices() == 27);
+
+  // Test case to the limit
+  simplex_is_changed = st.prune_above_filtration(-1.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  // Display the Simplex_tree
+  std::cout << "The complex pruned at -1.0 contains " << st.num_simplices() << " simplices" << std::endl;
+  BOOST_CHECK(simplex_is_changed);
+  BOOST_CHECK(st.num_simplices() == 0);
+
+  // Display the Simplex_tree
+  std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl;
+
+}
diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
index b06d7ec9..7323aa6c 100644
--- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp
+++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
@@ -148,16 +148,9 @@ void test_simplex_tree_insert_returns_true(const typePairSimplexBool& returnValu
 
 // Global variables
 double max_fil = 0.0;
-int dim_max = -1;
 
 template<class typeST, class Filtration_value>
 void set_and_test_simplex_tree_dim_fil(typeST& simplexTree, int vectorSize, const Filtration_value& fil) {
-  if (vectorSize > dim_max + 1) {
-    dim_max = vectorSize - 1;
-    simplexTree.set_dimension(dim_max);
-    std::cout << "   set_and_test_simplex_tree_dim_fil - dim_max=" << dim_max
-        << std::endl;
-  }
   if (fil > max_fil) {
     max_fil = fil;
     simplexTree.set_filtration(max_fil);
@@ -165,7 +158,7 @@ void set_and_test_simplex_tree_dim_fil(typeST& simplexTree, int vectorSize, cons
         << std::endl;
   }
 
-  BOOST_CHECK(simplexTree.dimension() == dim_max);
+  BOOST_CHECK(simplexTree.dimension() >= vectorSize - 1);
   BOOST_CHECK(AreAlmostTheSame(simplexTree.filtration(), max_fil));
 
   // Another way to count simplices:
@@ -189,7 +182,6 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_insertion, typeST, list_of_tested_var
   const Filtration_value THIRD_FILTRATION_VALUE = 0.3;
   const Filtration_value FOURTH_FILTRATION_VALUE = 0.4;
   // reset since we run the test several times
-  dim_max = -1;
   max_fil = 0.0;
 
   // TEST OF INSERTION
@@ -308,8 +300,8 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_insertion, typeST, list_of_tested_var
   // Simplex_handle = boost::container::flat_map< typeST::Vertex_handle, Node >::iterator
   typename typeST::Simplex_handle shReturned = returnValue.first;
   BOOST_CHECK(shReturned == typename typeST::Simplex_handle(nullptr));
+  std::cout << "st.num_vertices()=" << st.num_vertices() << std::endl;
   BOOST_CHECK(st.num_vertices() == (size_t) 4); // Not incremented !!
-  BOOST_CHECK(st.dimension() == dim_max);
   BOOST_CHECK(AreAlmostTheSame(st.filtration(), max_fil));
 
   // ++ ELEVENTH
@@ -324,7 +316,8 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_insertion, typeST, list_of_tested_var
   shReturned = returnValue.first;
   BOOST_CHECK(shReturned == typename typeST::Simplex_handle(nullptr));
   BOOST_CHECK(st.num_vertices() == (size_t) 4); // Not incremented !!
-  BOOST_CHECK(st.dimension() == dim_max);
+  std::cout << "   - INSERT (2,1,0) (already inserted)" << std::endl;
+  BOOST_CHECK(st.dimension() == 2);
   BOOST_CHECK(AreAlmostTheSame(st.filtration(), max_fil));
 
   /* Inserted simplex:        */
@@ -630,9 +623,6 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(coface_on_simplex_tree, typeST, list_of_tested_var
   /*            o             */
   /*            5             */
 
-  // FIXME
-  st.set_dimension(3);
-
   std::vector<typename typeST::Vertex_handle> simplex_result;
   std::vector<typename typeST::Simplex_handle> result;
   std::cout << "First test - Star of (3):" << std::endl;
@@ -729,9 +719,6 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(copy_move_on_simplex_tree, typeST, list_of_tested_
   /*            o             */
   /*            5             */
 
-  // FIXME
-  st.set_dimension(3);
-
   std::cout << "Printing st - address = " << &st << std::endl;
 
   // Copy constructor  
@@ -882,271 +869,3 @@ BOOST_AUTO_TEST_CASE(make_filtration_non_decreasing) {
   BOOST_CHECK(st == st_other_copy);
   
 }
-
-struct MyOptions : Simplex_tree_options_full_featured {
-  // Not doing persistence, so we don't need those
-  static const bool store_key = false;
-  static const bool store_filtration = false;
-  // I have few vertices
-  typedef short Vertex_handle;
-};
-
-BOOST_AUTO_TEST_CASE(remove_maximal_simplex) {
-  std::cout << "********************************************************************" << std::endl;
-  std::cout << "REMOVE MAXIMAL SIMPLEX" << std::endl;
-
-
-  typedef Simplex_tree<MyOptions> miniST;
-  miniST st;
-
-  // FIXME
-  st.set_dimension(3);
-
-  st.insert_simplex_and_subfaces({0, 1, 6, 7});
-  st.insert_simplex_and_subfaces({3, 4, 5});
-
-  // Constructs a copy at this state for further test purpose
-  miniST st_pruned = st;
-
-  st.insert_simplex_and_subfaces({3, 0});
-  st.insert_simplex_and_subfaces({2, 1, 0});
-
-  // Constructs a copy at this state for further test purpose
-  miniST st_complete = st;
-  // st_complete and st:
-  //    1   6
-  //    o---o
-  //   /X\7/
-  //  o---o---o---o
-  //  2   0   3\X/4
-  //            o
-  //            5
-  // st_pruned:
-  //    1   6
-  //    o---o
-  //     \7/
-  //      o   o---o
-  //      0   3\X/4
-  //            o
-  //            5
-
-#ifdef GUDHI_DEBUG
-  std::cout << "Check exception throw in debug mode" << std::endl;
-  // throw excpt because sh has children
-  BOOST_CHECK_THROW (st.remove_maximal_simplex(st.find({0, 1, 6})), std::invalid_argument);
-  BOOST_CHECK_THROW (st.remove_maximal_simplex(st.find({3})), std::invalid_argument);
-  BOOST_CHECK(st == st_complete);
-#endif
-  
-  st.remove_maximal_simplex(st.find({0, 2}));
-  st.remove_maximal_simplex(st.find({0, 1, 2}));
-  st.remove_maximal_simplex(st.find({1, 2}));
-  st.remove_maximal_simplex(st.find({2}));
-  st.remove_maximal_simplex(st.find({0, 3}));
-  
-  BOOST_CHECK(st == st_pruned);
-  // Remove all, but as the simplex tree is not storing filtration, there is no modification
-  st.prune_above_filtration(0.0);
-  BOOST_CHECK(st == st_pruned);
-  
-  miniST st_wo_seven;
-  // FIXME
-  st_wo_seven.set_dimension(3);
-
-  st_wo_seven.insert_simplex_and_subfaces({0, 1, 6});
-  st_wo_seven.insert_simplex_and_subfaces({3, 4, 5});
-  // st_wo_seven:
-  //    1   6
-  //    o---o
-  //     \X/
-  //      o   o---o
-  //      0   3\X/4
-  //            o
-  //            5
-
-  // Remove all 7 to test the both remove_maximal_simplex cases (when _members is empty or not)
-  st.remove_maximal_simplex(st.find({0, 1, 6, 7}));
-  st.remove_maximal_simplex(st.find({0, 1, 7}));
-  st.remove_maximal_simplex(st.find({0, 6, 7}));
-  st.remove_maximal_simplex(st.find({0, 7}));
-  st.remove_maximal_simplex(st.find({1, 6, 7}));
-  st.remove_maximal_simplex(st.find({1, 7}));
-  st.remove_maximal_simplex(st.find({6, 7}));
-  st.remove_maximal_simplex(st.find({7}));
-  
-  BOOST_CHECK(st == st_wo_seven);
-}
-
-BOOST_AUTO_TEST_CASE(prune_above_filtration) {
-  std::cout << "********************************************************************" << std::endl;
-  std::cout << "PRUNE ABOVE FILTRATION" << std::endl;
-  typedef Simplex_tree<> typeST;
-  typeST st;
-
-  // FIXME
-  st.set_dimension(3);
-
-  st.insert_simplex_and_subfaces({0, 1, 6, 7}, 1.0);
-  st.insert_simplex_and_subfaces({3, 4, 5}, 2.0);
-
-  // Constructs a copy at this state for further test purpose
-  typeST st_pruned = st;
-  st_pruned.initialize_filtration();  // reset
-
-  st.insert_simplex_and_subfaces({3, 0}, 3.0);
-  st.insert_simplex_and_subfaces({2, 1, 0}, 4.0);
-
-  // Constructs a copy at this state for further test purpose
-  typeST st_complete = st;
-  // st_complete and st:
-  //    1   6
-  //    o---o
-  //   /X\7/
-  //  o---o---o---o
-  //  2   0   3\X/4
-  //            o
-  //            5
-  // st_pruned:
-  //    1   6
-  //    o---o
-  //     \7/
-  //      o   o---o
-  //      0   3\X/4
-  //            o
-  //            5
-
-  bool simplex_is_changed = false;
-  // Check the no action cases
-  // greater than initial filtration value
-  simplex_is_changed = st.prune_above_filtration(10.0);
-  if (simplex_is_changed)
-    st.initialize_filtration();
-  BOOST_CHECK(st == st_complete);
-  BOOST_CHECK(!simplex_is_changed);
-  // equal to initial filtration value
-  simplex_is_changed = st.prune_above_filtration(6.0);
-  if (simplex_is_changed)
-    st.initialize_filtration();
-  BOOST_CHECK(st == st_complete);
-  BOOST_CHECK(!simplex_is_changed);
-  // lower than initial filtration value, but still greater than the maximum filtration value
-  simplex_is_changed = st.prune_above_filtration(5.0);
-  if (simplex_is_changed)
-    st.initialize_filtration();
-  BOOST_CHECK(st == st_complete);
-  BOOST_CHECK(!simplex_is_changed);
-
-  // Display the Simplex_tree
-  std::cout << "The complex contains " << st.num_simplices() << " simplices";
-  std::cout << " - dimension " << st.dimension() << std::endl;
-  std::cout << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
-  for (auto f_simplex : st.filtration_simplex_range()) {
-    std::cout << "   " << "[" << st.filtration(f_simplex) << "] ";
-    for (auto vertex : st.simplex_vertex_range(f_simplex)) {
-      std::cout << (int) vertex << " ";
-    }
-    std::cout << std::endl;
-  }
-
-  // Check the pruned cases
-  simplex_is_changed = st.prune_above_filtration(2.5);
-  if (simplex_is_changed)
-    st.initialize_filtration();
-  BOOST_CHECK(st == st_pruned);
-  BOOST_CHECK(simplex_is_changed);
-
-  // Display the Simplex_tree
-  std::cout << "The complex pruned at 2.5 contains " << st.num_simplices() << " simplices";
-  std::cout << " - dimension " << st.dimension() << std::endl;
-
-  simplex_is_changed = st.prune_above_filtration(2.0);
-  if (simplex_is_changed)
-    st.initialize_filtration();
-  
-  std::cout << "The complex pruned at 2.0 contains " << st.num_simplices() << " simplices";
-  std::cout << " - dimension " << st.dimension() << std::endl;
-
-  BOOST_CHECK(st == st_pruned);
-  BOOST_CHECK(!simplex_is_changed);
-
-  typeST st_empty;
-  // FIXME
-  st_empty.set_dimension(3);
-  simplex_is_changed = st.prune_above_filtration(0.0);
-  if (simplex_is_changed)
-    st.initialize_filtration();
-
-  // Display the Simplex_tree
-  std::cout << "The complex pruned at 0.0 contains " << st.num_simplices() << " simplices";
-  std::cout << " - dimension " << st.dimension() << std::endl;
-
-  BOOST_CHECK(st == st_empty);
-  BOOST_CHECK(simplex_is_changed);
-
-  // Test case to the limit
-  simplex_is_changed = st.prune_above_filtration(-1.0);
-  if (simplex_is_changed)
-    st.initialize_filtration();
-  BOOST_CHECK(st == st_empty);
-  BOOST_CHECK(!simplex_is_changed);
-}
-
-BOOST_AUTO_TEST_CASE(mini_prune_above_filtration) {
-  std::cout << "********************************************************************" << std::endl;
-  std::cout << "MINI PRUNE ABOVE FILTRATION" << std::endl;
-  typedef Simplex_tree<MyOptions> typeST;
-  typeST st;
-
-  // FIXME
-  st.set_dimension(3);
-
-  st.insert_simplex_and_subfaces({0, 1, 6, 7});
-  st.insert_simplex_and_subfaces({3, 4, 5});
-  st.insert_simplex_and_subfaces({3, 0});
-  st.insert_simplex_and_subfaces({2, 1, 0});
-
-  // st:
-  //    1   6
-  //    o---o
-  //   /X\7/
-  //  o---o---o---o
-  //  2   0   3\X/4
-  //            o
-  //            5
-
-  st.initialize_filtration();
-  
-  // Display the Simplex_tree
-  std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl;
-  BOOST_CHECK(st.num_simplices() == 27);
-
-  // Test case to the limit - With these options, there is no filtration, which means filtration is 0
-  bool simplex_is_changed = st.prune_above_filtration(1.0);
-  if (simplex_is_changed)
-    st.initialize_filtration();
-  // Display the Simplex_tree
-  std::cout << "The complex pruned at 1.0 contains " << st.num_simplices() << " simplices" << std::endl;
-  BOOST_CHECK(!simplex_is_changed);
-  BOOST_CHECK(st.num_simplices() == 27);
-
-  simplex_is_changed = st.prune_above_filtration(0.0);
-  if (simplex_is_changed)
-    st.initialize_filtration();
-  // Display the Simplex_tree
-  std::cout << "The complex pruned at 0.0 contains " << st.num_simplices() << " simplices" << std::endl;
-  BOOST_CHECK(!simplex_is_changed);
-  BOOST_CHECK(st.num_simplices() == 27);
-
-  // Test case to the limit
-  simplex_is_changed = st.prune_above_filtration(-1.0);
-  if (simplex_is_changed)
-    st.initialize_filtration();
-  // Display the Simplex_tree
-  std::cout << "The complex pruned at -1.0 contains " << st.num_simplices() << " simplices" << std::endl;
-  BOOST_CHECK(simplex_is_changed);
-  BOOST_CHECK(st.num_simplices() == 0);
-
-  // Display the Simplex_tree
-  std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl;
-
-}
\ No newline at end of file
diff --git a/src/Witness_complex/include/gudhi/Strong_witness_complex.h b/src/Witness_complex/include/gudhi/Strong_witness_complex.h
index 6f4bcf60..c18335d3 100644
--- a/src/Witness_complex/include/gudhi/Strong_witness_complex.h
+++ b/src/Witness_complex/include/gudhi/Strong_witness_complex.h
@@ -127,7 +127,6 @@ class Strong_witness_complex {
       if ((Landmark_id)simplex.size() - 1 > complex_dim)
         complex_dim = simplex.size() - 1;
     }
-    complex.set_dimension(complex_dim);
     return true;
   }
 
diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h
index bcfe8484..53c38520 100644
--- a/src/Witness_complex/include/gudhi/Witness_complex.h
+++ b/src/Witness_complex/include/gudhi/Witness_complex.h
@@ -130,7 +130,6 @@ class Witness_complex {
       }
       k++;
     }
-    complex.set_dimension(k-1);
     return true;
   }
 
diff --git a/src/cython/include/Tangential_complex_interface.h b/src/cython/include/Tangential_complex_interface.h
index 5e9dc0e4..ecf014b3 100644
--- a/src/cython/include/Tangential_complex_interface.h
+++ b/src/cython/include/Tangential_complex_interface.h
@@ -106,8 +106,6 @@ class Tangential_complex_interface {
 
   void create_simplex_tree(Simplex_tree<>* simplex_tree) {
     int max_dim = tangential_complex_->create_complex<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>(*simplex_tree);
-    // FIXME
-    simplex_tree->set_dimension(max_dim);
     simplex_tree->initialize_filtration();
   }
 
diff --git a/src/cython/test/test_simplex_tree.py b/src/cython/test/test_simplex_tree.py
index 3ae537e3..a6d6a9f3 100755
--- a/src/cython/test/test_simplex_tree.py
+++ b/src/cython/test/test_simplex_tree.py
@@ -34,9 +34,13 @@ def test_insertion():
 
     # insert test
     assert st.insert([0, 1]) == True
+
+    assert st.dimension() == 1
+
     assert st.insert([0, 1, 2], filtration=4.0) == True
-    # FIXME: Remove this line
-    st.set_dimension(2)
+
+    assert st.dimension() == 2
+
     assert st.num_simplices() == 7
     assert st.num_vertices() == 3
 
@@ -87,8 +91,9 @@ def test_insertion():
     assert st.find([2]) == True
 
     st.initialize_filtration()
-    assert st.persistence() == [(1, (4.0, float('inf'))), (0, (0.0, float('inf')))]
+    assert st.persistence(persistence_dim_max = True) == [(1, (4.0, float('inf'))), (0, (0.0, float('inf')))]
     assert st.__is_persistence_defined() == True
+
     assert st.betti_numbers() == [1, 1]
     assert st.persistent_betti_numbers(-0.1, 10000.0) == [0, 0]
     assert st.persistent_betti_numbers(0.0, 10000.0) == [1, 0]