Merge remote-tracking branch 'upstream/master' into optimal_matching_wasserstein

17 files changed, 192 insertions, 66 deletions

diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt
index b0337934..2eecd50c 100644
--- a/src/Alpha_complex/example/CMakeLists.txt
+++ b/src/Alpha_complex/example/CMakeLists.txt
@@ -32,14 +32,18 @@ if (DIFF_PATH)
 
     add_test(Alpha_complex_example_from_off_60_diff_files ${DIFF_PATH}
         ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_60.txt)
+    set_tests_properties(Alpha_complex_example_from_off_60_diff_files PROPERTIES DEPENDS Alpha_complex_example_from_off_60) 
     add_test(Alpha_complex_example_from_off_32_diff_files ${DIFF_PATH}
         ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt)
+    set_tests_properties(Alpha_complex_example_from_off_32_diff_files PROPERTIES DEPENDS Alpha_complex_example_from_off_32) 
 
     add_test(Alpha_complex_example_fast_from_off_60_diff_files ${DIFF_PATH}
         ${CMAKE_CURRENT_BINARY_DIR}/fastalphaoffreader_result_60.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_60.txt)
+    set_tests_properties(Alpha_complex_example_fast_from_off_60_diff_files PROPERTIES DEPENDS Alpha_complex_example_fast_from_off_60) 
     add_test(Alpha_complex_example_fast_from_off_32_diff_files ${DIFF_PATH}
         ${CMAKE_CURRENT_BINARY_DIR}/fastalphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt)
-  endif()
+    set_tests_properties(Alpha_complex_example_fast_from_off_32_diff_files PROPERTIES DEPENDS Alpha_complex_example_fast_from_off_32) 
+endif()
 
   add_executable ( Alpha_complex_example_weighted_3d_from_points Weighted_alpha_complex_3d_from_points.cpp )
   target_link_libraries(Alpha_complex_example_weighted_3d_from_points  ${CGAL_LIBRARY})
diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt
index a3b0cc24..2ffbdde0 100644
--- a/src/Alpha_complex/utilities/CMakeLists.txt
+++ b/src/Alpha_complex/utilities/CMakeLists.txt
@@ -16,8 +16,14 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
   if (DIFF_PATH)
     add_test(Alpha_complex_utilities_diff_exact_alpha_complex ${DIFF_PATH}
              "exact.pers" "safe.pers")
+    set_tests_properties(Alpha_complex_utilities_diff_exact_alpha_complex PROPERTIES DEPENDS
+             "Alpha_complex_utilities_exact_alpha_complex_persistence;Alpha_complex_utilities_safe_alpha_complex_persistence")
+             
     add_test(Alpha_complex_utilities_diff_fast_alpha_complex ${DIFF_PATH}
              "fast.pers" "safe.pers")
+    set_tests_properties(Alpha_complex_utilities_diff_fast_alpha_complex PROPERTIES DEPENDS
+             "Alpha_complex_utilities_fast_alpha_complex_persistence;Alpha_complex_utilities_safe_alpha_complex_persistence")
+
   endif()
   
   install(TARGETS alpha_complex_persistence DESTINATION bin)
@@ -36,15 +42,19 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
           "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off"
           "-p" "2" "-m" "0.45" "-o" "exact_3d.pers" "-e")
 
-  add_test(NAME Alpha_complex_utilities_safe_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence>
+  add_test(NAME Alpha_complex_utilities_fast_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence>
           "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off"
           "-p" "2" "-m" "0.45" "-o" "fast_3d.pers" "-f")
 
   if (DIFF_PATH)
     add_test(Alpha_complex_utilities_diff_exact_alpha_complex_3d ${DIFF_PATH}
             "exact_3d.pers" "safe_3d.pers")
+    set_tests_properties(Alpha_complex_utilities_diff_exact_alpha_complex_3d PROPERTIES DEPENDS
+            "Alpha_complex_utilities_exact_alpha_complex_3d;Alpha_complex_utilities_alpha_complex_3d")
     add_test(Alpha_complex_utilities_diff_fast_alpha_complex_3d ${DIFF_PATH}
             "fast_3d.pers" "safe_3d.pers")
+    set_tests_properties(Alpha_complex_utilities_diff_fast_alpha_complex_3d PROPERTIES DEPENDS
+            "Alpha_complex_utilities_fast_alpha_complex_3d;Alpha_complex_utilities_alpha_complex_3d")
   endif()
 
   add_test(NAME Alpha_complex_utilities_periodic_alpha_complex_3d_persistence COMMAND $<TARGET_FILE:alpha_complex_3d_persistence>
diff --git a/src/Doxyfile.in b/src/Doxyfile.in
index ec551882..49e781bd 100644
--- a/src/Doxyfile.in
+++ b/src/Doxyfile.in
@@ -785,6 +785,7 @@ EXCLUDE                = data/                   \
 	                     GudhUI/                 \
                          cmake/                  \
                          python/                 \
+                         ext/                    \
                          README.md
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
diff --git a/src/Persistence_representations/utilities/CMakeLists.txt b/src/Persistence_representations/utilities/CMakeLists.txt
index fc51b1d6..85633b7b 100644
--- a/src/Persistence_representations/utilities/CMakeLists.txt
+++ b/src/Persistence_representations/utilities/CMakeLists.txt
@@ -14,7 +14,7 @@ function(add_persistence_representation_creation_utility creation_utility)
     install(TARGETS ${creation_utility} DESTINATION bin)
 endfunction(add_persistence_representation_creation_utility)
 
-function(add_persistence_representation_plot_utility plot_utility tool_extension)
+function(add_persistence_representation_plot_utility creation_utility plot_utility tool_extension)
     add_executable ( ${plot_utility} ${plot_utility}.cpp )
 
     # as the function is called in a subdirectory level, need to '../' to find persistence heat maps files
@@ -22,17 +22,21 @@ function(add_persistence_representation_plot_utility plot_utility tool_extension
         "${CMAKE_CURRENT_BINARY_DIR}/../first.pers${tool_extension}")
     #add_test(NAME Persistence_representation_utilities_${plot_utility}_second COMMAND $<TARGET_FILE:${plot_utility}>
     #    "${CMAKE_CURRENT_BINARY_DIR}/../second.pers${tool_extension}")
+    set_tests_properties(Persistence_representation_utilities_${plot_utility}_first PROPERTIES DEPENDS
+                         Persistence_representation_utilities_${creation_utility})
     if(GNUPLOT_PATH)
         add_test(NAME Persistence_representation_utilities_${plot_utility}_first_gnuplot COMMAND ${GNUPLOT_PATH}
             "-e" "load '${CMAKE_CURRENT_BINARY_DIR}/../first.pers${tool_extension}_GnuplotScript'")
         #add_test(NAME Persistence_representation_utilities_${plot_utility}_second_gnuplot COMMAND ${GNUPLOT_PATH}
         #    "-e" "load '${CMAKE_CURRENT_BINARY_DIR}/../second.pers${tool_extension}_GnuplotScript'")
+        set_tests_properties(Persistence_representation_utilities_${plot_utility}_first_gnuplot PROPERTIES DEPENDS
+                             Persistence_representation_utilities_${plot_utility}_first)
     endif()
 
     install(TARGETS ${plot_utility} DESTINATION bin)
 endfunction(add_persistence_representation_plot_utility)
 
-function(add_persistence_representation_function_utility function_utility tool_extension)
+function(add_persistence_representation_function_utility creation_utility function_utility tool_extension)
     add_executable ( ${function_utility} ${function_utility}.cpp )
 
     # ARGV2 is an optional argument
@@ -48,6 +52,8 @@ function(add_persistence_representation_function_utility function_utility tool_e
             "${CMAKE_CURRENT_BINARY_DIR}/../first.pers${tool_extension}"
             "${CMAKE_CURRENT_BINARY_DIR}/../second.pers${tool_extension}")
     endif()
+    set_tests_properties(Persistence_representation_utilities_${function_utility} PROPERTIES DEPENDS
+                         Persistence_representation_utilities_${creation_utility})
 
     install(TARGETS ${function_utility} DESTINATION bin)
 endfunction(add_persistence_representation_function_utility)
diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt
index 89ef232f..e4c471c2 100644
--- a/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt
+++ b/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt
@@ -2,13 +2,24 @@ project(Persistence_representations_heat_maps_utilities)
 
 add_persistence_representation_creation_utility(create_pssk  "10" "-1" "-1" "4" "-1")
 add_persistence_representation_creation_utility(create_p_h_m_weighted_by_arctan_of_their_persistence "10" "-1" "-1" "4" "-1")
+
 add_persistence_representation_creation_utility(create_p_h_m_weighted_by_distance_from_diagonal "10" "-1" "-1" "4" "-1")
+# Tests output the same file
+set_tests_properties(Persistence_representation_utilities_create_p_h_m_weighted_by_distance_from_diagonal PROPERTIES DEPENDS
+                     Persistence_representation_utilities_create_p_h_m_weighted_by_arctan_of_their_persistence)
+
 add_persistence_representation_creation_utility(create_p_h_m_weighted_by_squared_diag_distance "10" "-1" "-1" "4" "-1")
+# Tests output the same file
+set_tests_properties(Persistence_representation_utilities_create_p_h_m_weighted_by_squared_diag_distance PROPERTIES DEPENDS
+                     Persistence_representation_utilities_create_p_h_m_weighted_by_distance_from_diagonal)
+
 # Need to set grid min and max for further average, distance and scalar_product
 add_persistence_representation_creation_utility(create_persistence_heat_maps "10" "0" "35" "10" "-1")
+set_tests_properties(Persistence_representation_utilities_create_persistence_heat_maps PROPERTIES DEPENDS
+                     Persistence_representation_utilities_create_p_h_m_weighted_by_squared_diag_distance)
 
-add_persistence_representation_plot_utility(plot_persistence_heat_map ".mps")
+add_persistence_representation_plot_utility(create_persistence_heat_maps plot_persistence_heat_map ".mps")
 
-add_persistence_representation_function_utility(average_persistence_heat_maps ".mps")
-add_persistence_representation_function_utility(compute_distance_of_persistence_heat_maps ".mps" "1")
-add_persistence_representation_function_utility(compute_scalar_product_of_persistence_heat_maps ".mps")
+add_persistence_representation_function_utility(create_persistence_heat_maps average_persistence_heat_maps ".mps")
+add_persistence_representation_function_utility(create_persistence_heat_maps compute_distance_of_persistence_heat_maps ".mps" "1")
+add_persistence_representation_function_utility(create_persistence_heat_maps compute_scalar_product_of_persistence_heat_maps ".mps")
diff --git a/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt
index a025183e..118c1e9b 100644
--- a/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt
+++ b/src/Persistence_representations/utilities/persistence_intervals/CMakeLists.txt
@@ -3,17 +3,16 @@ project(Persistence_representations_intervals_utilities)
 
 add_executable ( plot_histogram_of_intervals_lengths plot_histogram_of_intervals_lengths.cpp )
 
-add_test(NAME plot_histogram_of_intervals_lengths COMMAND $<TARGET_FILE:plot_histogram_of_intervals_lengths>
+add_test(NAME Persistence_representation_utilities_plot_histogram_of_intervals_lengths COMMAND $<TARGET_FILE:plot_histogram_of_intervals_lengths>
     "${CMAKE_CURRENT_BINARY_DIR}/../first.pers" "-1")
 
 install(TARGETS plot_histogram_of_intervals_lengths DESTINATION bin)
 
-add_persistence_representation_plot_utility(plot_persistence_intervals "")
-add_persistence_representation_plot_utility(plot_persistence_Betti_numbers "")
+add_persistence_representation_plot_utility(plot_histogram_of_intervals_lengths plot_persistence_intervals "")
+add_persistence_representation_plot_utility(plot_histogram_of_intervals_lengths plot_persistence_Betti_numbers "")
 
 add_persistence_representation_creation_utility(compute_birth_death_range_in_persistence_diagram "-1")
 
-
 add_executable ( compute_number_of_dominant_intervals compute_number_of_dominant_intervals.cpp )
 add_test(NAME Persistence_representation_utilities_compute_number_of_dominant_intervals
     COMMAND $<TARGET_FILE:compute_number_of_dominant_intervals>
diff --git a/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt
index 6b24d032..4df84d36 100644
--- a/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt
+++ b/src/Persistence_representations/utilities/persistence_landscapes/CMakeLists.txt
@@ -2,8 +2,8 @@ project(Persistence_representations_landscapes_utilities)
 
 add_persistence_representation_creation_utility(create_landscapes "-1")
 
-add_persistence_representation_plot_utility(plot_landscapes ".land")
+add_persistence_representation_plot_utility(create_landscapes plot_landscapes ".land")
 
-add_persistence_representation_function_utility(average_landscapes ".land")
-add_persistence_representation_function_utility(compute_distance_of_landscapes ".land" "1")
-add_persistence_representation_function_utility(compute_scalar_product_of_landscapes ".land")
+add_persistence_representation_function_utility(create_landscapes average_landscapes ".land")
+add_persistence_representation_function_utility(create_landscapes compute_distance_of_landscapes ".land" "1")
+add_persistence_representation_function_utility(create_landscapes compute_scalar_product_of_landscapes ".land")
diff --git a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt
index 36f3196b..8cd965f1 100644
--- a/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt
+++ b/src/Persistence_representations/utilities/persistence_landscapes_on_grid/CMakeLists.txt
@@ -3,8 +3,8 @@ project(Persistence_representations_lanscapes_on_grid_utilities)
 # Need to set grid min and max for further average, distance and scalar_product
 add_persistence_representation_creation_utility(create_landscapes_on_grid "100" "0" "35" "-1")
 
-add_persistence_representation_plot_utility(plot_landscapes_on_grid ".g_land")
+add_persistence_representation_plot_utility(create_landscapes_on_grid plot_landscapes_on_grid ".g_land")
 
-add_persistence_representation_function_utility(average_landscapes_on_grid ".g_land")
-add_persistence_representation_function_utility(compute_distance_of_landscapes_on_grid ".g_land" "1")
-add_persistence_representation_function_utility(compute_scalar_product_of_landscapes_on_grid ".g_land")
+add_persistence_representation_function_utility(create_landscapes_on_grid average_landscapes_on_grid ".g_land")
+add_persistence_representation_function_utility(create_landscapes_on_grid compute_distance_of_landscapes_on_grid ".g_land" "1")
+add_persistence_representation_function_utility(create_landscapes_on_grid compute_scalar_product_of_landscapes_on_grid ".g_land")
diff --git a/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt
index bc982094..5b22ca84 100644
--- a/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt
+++ b/src/Persistence_representations/utilities/persistence_vectors/CMakeLists.txt
@@ -2,8 +2,8 @@ project(Persistence_vectors_utilities)
 
 add_persistence_representation_creation_utility(create_persistence_vectors "-1")
 
-add_persistence_representation_plot_utility(plot_persistence_vectors ".vect")
+add_persistence_representation_plot_utility(create_persistence_vectors plot_persistence_vectors ".vect")
 
-add_persistence_representation_function_utility(average_persistence_vectors ".vect")
-add_persistence_representation_function_utility(compute_distance_of_persistence_vectors ".vect" "1")
-add_persistence_representation_function_utility(compute_scalar_product_of_persistence_vectors ".vect")
+add_persistence_representation_function_utility(create_persistence_vectors average_persistence_vectors ".vect")
+add_persistence_representation_function_utility(create_persistence_vectors compute_distance_of_persistence_vectors ".vect" "1")
+add_persistence_representation_function_utility(create_persistence_vectors compute_scalar_product_of_persistence_vectors ".vect")
diff --git a/src/Rips_complex/example/CMakeLists.txt b/src/Rips_complex/example/CMakeLists.txt
index e7772bdb..244a93ec 100644
--- a/src/Rips_complex/example/CMakeLists.txt
+++ b/src/Rips_complex/example/CMakeLists.txt
@@ -53,15 +53,23 @@ if (DIFF_PATH)
   add_test(Rips_complex_example_from_off_doc_12_1_diff_files ${DIFF_PATH}
       ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_1.txt
       ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_for_doc.txt)
+  set_tests_properties(Rips_complex_example_from_off_doc_12_1_diff_files PROPERTIES DEPENDS Rips_complex_example_from_off_doc_12_1) 
+
   add_test(Rips_complex_example_from_off_doc_12_3_diff_files ${DIFF_PATH}
       ${CMAKE_CURRENT_BINARY_DIR}/ripsoffreader_result_12_3.txt
       ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_for_doc.txt)
+  set_tests_properties(Rips_complex_example_from_off_doc_12_3_diff_files PROPERTIES DEPENDS Rips_complex_example_from_off_doc_12_3) 
+
   add_test(Rips_complex_example_from_csv_distance_matrix_doc_12_1_diff_files ${DIFF_PATH}
       ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_1.txt
       ${CMAKE_CURRENT_BINARY_DIR}/one_skeleton_rips_for_doc.txt)
+  set_tests_properties(Rips_complex_example_from_csv_distance_matrix_doc_12_1_diff_files PROPERTIES DEPENDS Rips_complex_example_from_csv_distance_matrix_doc_12_1) 
+
   add_test(Rips_complex_example_from_csv_distance_matrix_doc_12_3_diff_files ${DIFF_PATH}
       ${CMAKE_CURRENT_BINARY_DIR}/ripscsvreader_result_12_3.txt
       ${CMAKE_CURRENT_BINARY_DIR}/full_skeleton_rips_for_doc.txt)
+  set_tests_properties(Rips_complex_example_from_csv_distance_matrix_doc_12_3_diff_files PROPERTIES DEPENDS Rips_complex_example_from_csv_distance_matrix_doc_12_3) 
+
 endif()
 
 install(TARGETS Rips_complex_example_from_off DESTINATION bin)
diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index 6db2c76b..2d010483 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -68,7 +68,7 @@ if(CGAL_FOUND)
 endif()
 
 # For those who dislike bundled dependencies, this indicates where to find a preinstalled Hera.
-set(HERA_WASSERSTEIN_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/hera/geom_matching/wasserstein/include CACHE PATH "Directory where one can find Hera's wasserstein.h")
+set(HERA_WASSERSTEIN_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/hera/wasserstein/include CACHE PATH "Directory where one can find Hera's wasserstein.h")
 
 option(WITH_GUDHI_USE_TBB "Build with Intel TBB parallelization" ON)
 
diff --git a/src/cmake/modules/GUDHI_user_version_target.cmake b/src/cmake/modules/GUDHI_user_version_target.cmake
index 5047252f..257d1939 100644
--- a/src/cmake/modules/GUDHI_user_version_target.cmake
+++ b/src/cmake/modules/GUDHI_user_version_target.cmake
@@ -55,7 +55,7 @@ add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                    copy_directory ${CMAKE_SOURCE_DIR}/src/GudhUI ${GUDHI_USER_VERSION_DIR}/GudhUI)
 
 add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                   copy_directory ${CMAKE_SOURCE_DIR}/ext/hera/geom_matching/wasserstein/include ${GUDHI_USER_VERSION_DIR}/ext/hera/geom_matching/wasserstein/include)
+                   copy_directory ${CMAKE_SOURCE_DIR}/ext/hera/wasserstein/include ${GUDHI_USER_VERSION_DIR}/ext/hera/wasserstein/include)
 
 set(GUDHI_DIRECTORIES "doc;example;concept;utilities")
 
diff --git a/src/common/example/CMakeLists.txt b/src/common/example/CMakeLists.txt
index 583a0027..fa8eb98c 100644
--- a/src/common/example/CMakeLists.txt
+++ b/src/common/example/CMakeLists.txt
@@ -12,6 +12,7 @@ if (DIFF_PATH)
 
   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)
+  set_tests_properties(Common_example_vector_double_off_reader_diff_files PROPERTIES DEPENDS Common_example_vector_double_off_reader) 
 endif()
 
 if(NOT CGAL_VERSION VERSION_LESS 4.11.0)
diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 090a7446..20e72a5f 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -181,7 +181,7 @@ if(PYTHONINTERP_FOUND)
         set(GUDHI_PYTHON_LIBRARY_DIRS "${GUDHI_PYTHON_LIBRARY_DIRS}'${MPFR_LIBRARIES_DIR}', ")
         message("** Add mpfr ${MPFR_LIBRARIES}")
       endif(MPFR_FOUND)
-endif(CGAL_FOUND)
+    endif(CGAL_FOUND)
 
     # Specific for Mac
     if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
diff --git a/src/python/doc/persistence_graphical_tools_sum.inc b/src/python/doc/persistence_graphical_tools_sum.inc
index 0cdf8072..ef376802 100644
--- a/src/python/doc/persistence_graphical_tools_sum.inc
+++ b/src/python/doc/persistence_graphical_tools_sum.inc
@@ -2,11 +2,11 @@
    :widths: 30 50 20
 
    +-----------------------------------------------------------------+-----------------------------------------------------------------------+-----------------------------------------------+
-   | .. figure::                                                     | These graphical tools comes on top of persistence results and allows  | :Author: Vincent Rouvreau                     |
-   |      img/graphical_tools_representation.png                     | the user to build easily persistence barcode, diagram or density.     |                                               |
+   | .. figure::                                                     | These graphical tools comes on top of persistence results and allows  | :Author: Vincent Rouvreau, Theo Lacombe       |
+   |      img/graphical_tools_representation.png                     | the user to display easily persistence barcode, diagram or density.   |                                               |
    |                                                                 |                                                                       | :Introduced in: GUDHI 2.0.0                   |
-   |                                                                 |                                                                       |                                               |
-   |                                                                 |                                                                       | :Copyright: MIT                               |
+   |                                                                 | Note that these functions return the matplotlib axis, allowing        |                                               |
+   |                                                                 | for further modifications (title, aspect, etc.)                       | :Copyright: MIT                               |
    |                                                                 |                                                                       |                                               |
    |                                                                 |                                                                       | :Requires: matplotlib, numpy and scipy        |
    +-----------------------------------------------------------------+-----------------------------------------------------------------------+-----------------------------------------------+
diff --git a/src/python/doc/persistence_graphical_tools_user.rst b/src/python/doc/persistence_graphical_tools_user.rst
index 80002db6..91e52703 100644
--- a/src/python/doc/persistence_graphical_tools_user.rst
+++ b/src/python/doc/persistence_graphical_tools_user.rst
@@ -20,7 +20,7 @@ This function can display the persistence result as a barcode:
 .. plot::
    :include-source:
 
-    import matplotlib.pyplot as plot
+    import matplotlib.pyplot as plt
     import gudhi
 
     off_file = gudhi.__root_source_dir__ + '/data/points/tore3D_300.off'
@@ -31,7 +31,7 @@ This function can display the persistence result as a barcode:
     diag = simplex_tree.persistence(min_persistence=0.4)
 
     gudhi.plot_persistence_barcode(diag)
-    plot.show()
+    plt.show()
 
 Show persistence as a diagram
 -----------------------------
@@ -44,15 +44,31 @@ This function can display the persistence result as a diagram:
 .. plot::
    :include-source:
 
-    import matplotlib.pyplot as plot
+    import matplotlib.pyplot as plt
     import gudhi
 
     # rips_on_tore3D_1307.pers obtained from write_persistence_diagram method
     persistence_file=gudhi.__root_source_dir__ + \
         '/data/persistence_diagram/rips_on_tore3D_1307.pers'
-    gudhi.plot_persistence_diagram(persistence_file=persistence_file,
+    ax = gudhi.plot_persistence_diagram(persistence_file=persistence_file,
         legend=True)
-    plot.show()
+    # We can modify the title, aspect, etc.
+    ax.set_title("Persistence diagram of a torus")
+    ax.set_aspect("equal")  # forces to be square shaped
+    plt.show()
+
+Note that (as barcode and density) it can also take a simple `np.array` 
+of shape (N x 2) encoding a persistence diagram (in a given dimension).
+
+.. plot::
+    :include-source:
+    
+    import matplotlib.pyplot as plt
+    import gudhi
+    import numpy as np
+    d = np.array([[0, 1], [1, 2], [1, np.inf]])
+    gudhi.plot_persistence_diagram(d)
+    plt.show()
 
 Persistence density
 -------------------
@@ -65,7 +81,7 @@ If you want more information on a specific dimension, for instance:
 .. plot::
    :include-source:
 
-    import matplotlib.pyplot as plot
+    import matplotlib.pyplot as plt
     import gudhi
     # rips_on_tore3D_1307.pers obtained from write_persistence_diagram method
     persistence_file=gudhi.__root_source_dir__ + \
@@ -75,9 +91,9 @@ If you want more information on a specific dimension, for instance:
         only_this_dim=1)
     pers_diag = [(1, elt) for elt in birth_death]
     # Use subplots to display diagram and density side by side
-    fig, axes = plot.subplots(nrows=1, ncols=2, figsize=(12, 5))
+    fig, axes = plt.subplots(nrows=1, ncols=2, figsize=(12, 5))
     gudhi.plot_persistence_diagram(persistence=pers_diag,
         axes=axes[0])
     gudhi.plot_persistence_density(persistence=pers_diag,
         dimension=1, legend=True, axes=axes[1])
-    plot.show()
+    plt.show()
diff --git a/src/python/gudhi/persistence_graphical_tools.py b/src/python/gudhi/persistence_graphical_tools.py
index 246280de..cc3db467 100644
--- a/src/python/gudhi/persistence_graphical_tools.py
+++ b/src/python/gudhi/persistence_graphical_tools.py
@@ -5,6 +5,7 @@
 # Copyright (C) 2016 Inria
 #
 # Modification(s):
+#   - 2020/02 Theo Lacombe: Added more options for improved rendering and more flexibility.
 #   - YYYY/MM Author: Description of the modification
 
 from os import path
@@ -14,7 +15,7 @@ import numpy as np
 from gudhi.reader_utils import read_persistence_intervals_in_dimension
 from gudhi.reader_utils import read_persistence_intervals_grouped_by_dimension
 
-__author__ = "Vincent Rouvreau, Bertrand Michel"
+__author__ = "Vincent Rouvreau, Bertrand Michel, Theo Lacombe"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "MIT"
 
@@ -43,6 +44,19 @@ def __min_birth_max_death(persistence, band=0.0):
         max_death += band
     return (min_birth, max_death)
 
+
+def _array_handler(a):
+    '''
+    :param a: if array, assumes it is a (n x 2) np.array and return a
+                persistence-compatible list (padding with 0), so that the
+                plot can be performed seamlessly.
+    '''
+    if isinstance(a[0][1], np.float64) or isinstance(a[0][1], float):
+        return [[0, x] for x in a]
+    else:
+        return a
+
+
 def plot_persistence_barcode(
     persistence=[],
     persistence_file="",
@@ -52,13 +66,16 @@ def plot_persistence_barcode(
     inf_delta=0.1,
     legend=False,
     colormap=None,
-    axes=None
+    axes=None,
+    fontsize=16,
 ):
     """This function plots the persistence bar code from persistence values list
+    , a np.array of shape (N x 2) (representing a diagram 
+    in a single homology dimension), 
     or from a :doc:`persistence file <fileformats>`.
 
-    :param persistence: Persistence intervals values list grouped by dimension.
-    :type persistence: list of tuples(dimension, tuple(birth, death)).
+    :param persistence: Persistence intervals values list. Can be grouped by dimension or not.
+    :type persistence: an array of (dimension, array of (birth, death)) or an array of (birth, death).
     :param persistence_file: A :doc:`persistence file <fileformats>` style name
         (reset persistence if both are set).
     :type persistence_file: string
@@ -81,11 +98,19 @@ def plot_persistence_barcode(
     :param axes: A matplotlib-like subplot axes. If None, the plot is drawn on
         a new set of axes.
     :type axes: `matplotlib.axes.Axes`
+    :param fontsize: Fontsize to use in axis.
+    :type fontsize: int
     :returns: (`matplotlib.axes.Axes`): The axes on which the plot was drawn.
     """
     try:
         import matplotlib.pyplot as plt
         import matplotlib.patches as mpatches
+        from matplotlib import rc
+        plt.rc('text', usetex=True)
+        plt.rc('font', family='serif')
+
+
+        persistence = _array_handler(persistence)
 
         if persistence_file != "":
             if path.isfile(persistence_file):
@@ -163,7 +188,7 @@ def plot_persistence_barcode(
                 loc="lower right",
             )
 
-        axes.set_title("Persistence barcode")
+        axes.set_title("Persistence barcode", fontsize=fontsize)
 
         # Ends plot on infinity value and starts a little bit before min_birth
         axes.axis([axis_start, infinity, 0, ind])
@@ -183,13 +208,16 @@ def plot_persistence_diagram(
     inf_delta=0.1,
     legend=False,
     colormap=None,
-    axes=None
+    axes=None,
+    fontsize=16,
+    greyblock=True
 ):
     """This function plots the persistence diagram from persistence values
-    list or from a :doc:`persistence file <fileformats>`.
+    list, a np.array of shape (N x 2) representing a diagram in a single
+    homology dimension, or from a :doc:`persistence file <fileformats>`.
 
-    :param persistence: Persistence intervals values list grouped by dimension.
-    :type persistence: list of tuples(dimension, tuple(birth, death)).
+    :param persistence: Persistence intervals values list. Can be grouped by dimension or not.
+    :type persistence: an array of (dimension, array of (birth, death)) or an array of (birth, death).
     :param persistence_file: A :doc:`persistence file <fileformats>` style name
         (reset persistence if both are set).
     :type persistence_file: string
@@ -214,11 +242,20 @@ def plot_persistence_diagram(
     :param axes: A matplotlib-like subplot axes. If None, the plot is drawn on
         a new set of axes.
     :type axes: `matplotlib.axes.Axes`
+    :param fontsize: Fontsize to use in axis.
+    :type fontsize: int
+    :param greyblock: if we want to plot a grey patch on the lower half plane for nicer rendering. Default True.
+    :type greyblock: boolean
     :returns: (`matplotlib.axes.Axes`): The axes on which the plot was drawn.
     """
     try:
         import matplotlib.pyplot as plt
         import matplotlib.patches as mpatches
+        from matplotlib import rc
+        plt.rc('text', usetex=True)
+        plt.rc('font', family='serif')
+
+        persistence = _array_handler(persistence)
 
         if persistence_file != "":
             if path.isfile(persistence_file):
@@ -256,19 +293,18 @@ def plot_persistence_diagram(
         # Replace infinity values with max_death + delta for diagram to be more
         # readable
         infinity = max_death + delta
+        axis_end = max_death + delta / 2
         axis_start = min_birth - delta
 
-        # line display of equation : birth = death
-        x = np.linspace(axis_start, infinity, 1000)
-        # infinity line and text
-        axes.plot(x, x, color="k", linewidth=1.0)
-        axes.plot(x, [infinity] * len(x), linewidth=1.0, color="k", alpha=alpha)
-        axes.text(axis_start, infinity, r"$\infty$", color="k", alpha=alpha)
         # bootstrap band
         if band > 0.0:
+            x = np.linspace(axis_start, infinity, 1000)
             axes.fill_between(x, x, x + band, alpha=alpha, facecolor="red")
-
+        # lower diag patch
+        if greyblock:
+            axes.add_patch(mpatches.Polygon([[axis_start, axis_start], [axis_end, axis_start], [axis_end, axis_end]], fill=True, color='lightgrey'))
         # Draw points in loop
+        pts_at_infty = False  # Records presence of pts at infty
         for interval in reversed(persistence):
             if float(interval[1][1]) != float("inf"):
                 # Finite death case
@@ -279,10 +315,23 @@ def plot_persistence_diagram(
                     color=colormap[interval[0]],
                 )
             else:
+                pts_at_infty = True
                 # Infinite death case for diagram to be nicer
                 axes.scatter(
                     interval[1][0], infinity, alpha=alpha, color=colormap[interval[0]]
                 )
+        if pts_at_infty:
+            # infinity line and text
+            axes.plot([axis_start, axis_end], [axis_start, axis_end], linewidth=1.0, color="k")
+            axes.plot([axis_start, axis_end], [infinity, infinity], linewidth=1.0, color="k", alpha=alpha)
+            # Infinity label
+            yt = axes.get_yticks()
+            yt = yt[np.where(yt < axis_end)] # to avoid ploting ticklabel higher than infinity
+            yt = np.append(yt, infinity)
+            ytl = ["%.3f" % e for e in yt]  # to avoid float precision error
+            ytl[-1] = r'$+\infty$'
+            axes.set_yticks(yt)
+            axes.set_yticklabels(ytl)
 
         if legend:
             dimensions = list(set(item[0] for item in persistence))
@@ -293,11 +342,11 @@ def plot_persistence_diagram(
                 ]
             )
 
-        axes.set_xlabel("Birth")
-        axes.set_ylabel("Death")
+        axes.set_xlabel("Birth", fontsize=fontsize)
+        axes.set_ylabel("Death", fontsize=fontsize)
+        axes.set_title("Persistence diagram", fontsize=fontsize)
         # Ends plot on infinity value and starts a little bit before min_birth
-        axes.axis([axis_start, infinity, axis_start, infinity + delta])
-        axes.set_title("Persistence diagram")
+        axes.axis([axis_start, axis_end, axis_start, infinity + delta/2])
         return axes
 
     except ImportError:
@@ -313,16 +362,22 @@ def plot_persistence_density(
     dimension=None,
     cmap=None,
     legend=False,
-    axes=None
+    axes=None,
+    fontsize=16,
+    greyblock=False
 ):
     """This function plots the persistence density from persistence
-    values list or from a :doc:`persistence file <fileformats>`. Be
+    values list, np.array of shape (N x 2) representing a diagram
+    in a single homology dimension,
+    or from a :doc:`persistence file <fileformats>`. Be
     aware that this function does not distinguish the dimension, it is
     up to you to select the required one. This function also does not handle
     degenerate data set (scipy correlation matrix inversion can fail).
 
-    :param persistence: Persistence intervals values list grouped by dimension.
-    :type persistence: list of tuples(dimension, tuple(birth, death)).
+    :param persistence: Persistence intervals values list. 
+                        Can be grouped by dimension or not.
+    :type persistence: an array of (dimension, array of (birth, death)) 
+                        or an array of (birth, death).
     :param persistence_file: A :doc:`persistence file <fileformats>`
         style name (reset persistence if both are set).
     :type persistence_file: string
@@ -355,11 +410,22 @@ def plot_persistence_density(
     :param axes: A matplotlib-like subplot axes. If None, the plot is drawn on
         a new set of axes.
     :type axes: `matplotlib.axes.Axes`
+    :param fontsize: Fontsize to use in axis.
+    :type fontsize: int
+    :param greyblock: if we want to plot a grey patch on the lower half plane 
+                         for nicer rendering. Default False.
+    :type greyblock: boolean
     :returns: (`matplotlib.axes.Axes`): The axes on which the plot was drawn.
     """
     try:
         import matplotlib.pyplot as plt
+        import matplotlib.patches as mpatches
         from scipy.stats import kde
+        from matplotlib import rc
+        plt.rc('text', usetex=True)
+        plt.rc('font', family='serif')
+
+        persistence = _array_handler(persistence)
 
         if persistence_file != "":
             if dimension is None:
@@ -418,12 +484,16 @@ def plot_persistence_density(
         # Make the plot
         img = axes.pcolormesh(xi, yi, zi.reshape(xi.shape), cmap=cmap)
 
+        if greyblock:
+            axes.add_patch(mpatches.Polygon([[birth.min(), birth.min()], [death.max(), birth.min()], [death.max(), death.max()]], fill=True, color='lightgrey'))
+
         if legend:
             plt.colorbar(img, ax=axes)
 
-        axes.set_xlabel("Birth")
-        axes.set_ylabel("Death")
-        axes.set_title("Persistence density")
+        axes.set_xlabel("Birth", fontsize=fontsize)
+        axes.set_ylabel("Death", fontsize=fontsize)
+        axes.set_title("Persistence density", fontsize=fontsize)
+
         return axes
 
     except ImportError: