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git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2884 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: c5e0a65a484a71d8a9fc1fc2b695dd20a367fd0c

5 files changed, 27 insertions, 9 deletions

diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt
index 120ca416..18699650 100644
--- a/src/Alpha_complex/utilities/CMakeLists.txt
+++ b/src/Alpha_complex/utilities/CMakeLists.txt
@@ -17,9 +17,9 @@ if(CGAL_FOUND)
   
   add_test(NAME Alpha_complex_utilities_alpha_complex_3d_persistence COMMAND $<TARGET_FILE:alpha_complex_3d_persistence>
       "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "2" "0.45")
-  add_test(NAME Persistent_cohomology_example_exact_alpha_complex_3d COMMAND $<TARGET_FILE:exact_alpha_complex_3d_persistence>
+  add_test(NAME Alpha_complex_utilities_exact_alpha_complex_3d COMMAND $<TARGET_FILE:exact_alpha_complex_3d_persistence>
       "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "2" "0.45")
-  add_test(NAME Persistent_cohomology_example_weighted_alpha_complex_3d COMMAND $<TARGET_FILE:weighted_alpha_complex_3d_persistence>
+  add_test(NAME Alpha_complex_utilities_weighted_alpha_complex_3d COMMAND $<TARGET_FILE:weighted_alpha_complex_3d_persistence>
       "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off" "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.weights" "2" "0.45")
 
   install(TARGETS alpha_complex_3d_persistence DESTINATION bin)
diff --git a/src/Alpha_complex/utilities/README b/src/Alpha_complex/utilities/README
index 67ea1875..6e7d16b7 100644
--- a/src/Alpha_complex/utilities/README
+++ b/src/Alpha_complex/utilities/README
@@ -39,6 +39,23 @@ N.B.:
 
 
 
+## `exact_alpha_complex_3d_persistence` ##
+Same as `alpha_complex_3d_persistence`, but using exact computation. It is slower, but it is necessary when points are on a grid for instance.
+
+
+
+## `weighted_alpha_complex_3d_persistence` ##
+Same as `alpha_complex_3d_persistence`, but using weighted points.
+
+**Usage**
+`weighted_alpha_complex_3d_persistence <input OFF file> <input weights file> <p> <min_persistence>` 
+where
+`<input OFF file>` is the path to the input point cloud in OFF format.
+`<input weights file>` is the path to the file containing the weights of the points (one value per line).
+`<p>` is the characteristic p of the coefficient field *Z/pZ* for computing homology. It must be a stricly positive integer.
+`<min_persistence>` is the minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.
+
+
 
 ## `periodic_alpha_complex_3d_persistence` ##
 This program computes the persistent homology with coefficient field Z/pZ of the 3D periodic alpha complex built from a 3D point cloud. The output diagram contains one bar per line, written with the convention:
diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt
index 9677f5c5..2ae45dc5 100644
--- a/src/Bottleneck_distance/example/CMakeLists.txt
+++ b/src/Bottleneck_distance/example/CMakeLists.txt
@@ -6,6 +6,10 @@ if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
   add_executable (alpha_rips_persistence_bottleneck_distance alpha_rips_persistence_bottleneck_distance.cpp)
   target_link_libraries(alpha_rips_persistence_bottleneck_distance ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
+  if (TBB_FOUND)
+    target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES})
+  endif(TBB_FOUND)
+  
   add_test(NAME Bottleneck_distance_example_basic COMMAND $<TARGET_FILE:bottleneck_basic_example>)
   add_test(NAME Bottleneck_distance_example_alpha_rips_persistence_bottleneck
       COMMAND $<TARGET_FILE:alpha_rips_persistence_bottleneck_distance>
diff --git a/src/Bottleneck_distance/utilities/CMakeLists.txt b/src/Bottleneck_distance/utilities/CMakeLists.txt
index decdc789..cdf76c85 100644
--- a/src/Bottleneck_distance/utilities/CMakeLists.txt
+++ b/src/Bottleneck_distance/utilities/CMakeLists.txt
@@ -2,15 +2,12 @@ cmake_minimum_required(VERSION 2.6)
 project(Bottleneck_distance_utilities)
 
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
-  add_executable (bottleneck_read_file_example bottleneck_read_file_example.cpp)
-  if (TBB_FOUND)
-    target_link_libraries(alpha_rips_persistence_bottleneck_distance ${TBB_LIBRARIES})
-  endif(TBB_FOUND)
+  add_executable (bottleneck_read_file bottleneck_read_file.cpp)
 
-  add_test(NAME Bottleneck_read_file_example
-      COMMAND $<TARGET_FILE:bottleneck_read_file_example>
+  add_test(NAME Bottleneck_distance_utilities_Bottleneck_read_file
+      COMMAND $<TARGET_FILE:bottleneck_read_file>
       "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/second.pers")
 
-  install(TARGETS bottleneck_read_file_example DESTINATION bin)
+  install(TARGETS bottleneck_read_file DESTINATION bin)
 
 endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Bottleneck_distance/utilities/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/utilities/bottleneck_read_file.cpp
index 9dd52b31..9dd52b31 100644
--- a/src/Bottleneck_distance/utilities/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/utilities/bottleneck_read_file.cpp