Fixes according to Marc's review

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2881 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 84870193cb05cabd8c756a3bbc49083e4d739525

6 files changed, 36 insertions, 27 deletions

diff --git a/src/Bottleneck_distance/example/CMakeLists.txt b/src/Bottleneck_distance/example/CMakeLists.txt
index 6a602dbb..9677f5c5 100644
--- a/src/Bottleneck_distance/example/CMakeLists.txt
+++ b/src/Bottleneck_distance/example/CMakeLists.txt
@@ -3,15 +3,15 @@ project(Bottleneck_distance_examples)
 
 if (NOT CGAL_VERSION VERSION_LESS 4.8.1)
   add_executable (bottleneck_basic_example bottleneck_basic_example.cpp)
-  add_executable (bottleneck_read_file_example bottleneck_read_file_example.cpp)
+  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})
 
   add_test(NAME Bottleneck_distance_example_basic COMMAND $<TARGET_FILE:bottleneck_basic_example>)
+  add_test(NAME Bottleneck_distance_example_alpha_rips_persistence_bottleneck
+      COMMAND $<TARGET_FILE:alpha_rips_persistence_bottleneck_distance>
+      "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.15" "-m" "0.12" "-d" "3" "-p" "3")
 
-  add_test(NAME Bottleneck_read_file_example
-      COMMAND $<TARGET_FILE:bottleneck_read_file_example>
-      "${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_basic_example DESTINATION bin)
+  install(TARGETS alpha_rips_persistence_bottleneck_distance DESTINATION bin)
   
 endif (NOT CGAL_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Bottleneck_distance/example/README b/src/Bottleneck_distance/example/README
new file mode 100644
index 00000000..0e314608
--- /dev/null
+++ b/src/Bottleneck_distance/example/README
@@ -0,0 +1,19 @@
+# Bottleneck_distance #

+

+## `alpha_rips_persistence_bottleneck_distance` ##

+This program computes the persistent homology with coefficient field Z/pZ of a Rips complex defined on a set of input points. The output diagram contains one bar per line, written with the convention:

+

+`p dim b d`

+

+where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients.

+

+Usage:

+`alpha_rips_persistence_bottleneck_distance [options] <OFF input file>`

+

+Allowed options:

+

+* `-h [ --help ]` Produce help message

+* `-r [ --max-edge-length ]` (default = inf) Maximal length of an edge for the Rips complex construction.`

+* `-d [ --cpx-dimension ]` (default = 1) Maximal dimension of the Rips complex we want to compute.`

+* `-p [ --field-charac ]` (default = 11)     Characteristic p of the coefficient field Z/pZ for computing homology.

+* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.

diff --git a/src/Bottleneck_distance/utilities/alpha_rips_persistence_bottleneck_distance.cpp b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp
index fd164b22..fd164b22 100644
--- a/src/Bottleneck_distance/utilities/alpha_rips_persistence_bottleneck_distance.cpp
+++ b/src/Bottleneck_distance/example/alpha_rips_persistence_bottleneck_distance.cpp
diff --git a/src/Bottleneck_distance/utilities/CMakeLists.txt b/src/Bottleneck_distance/utilities/CMakeLists.txt
index 634b2479..decdc789 100644
--- a/src/Bottleneck_distance/utilities/CMakeLists.txt
+++ b/src/Bottleneck_distance/utilities/CMakeLists.txt
@@ -2,16 +2,15 @@ cmake_minimum_required(VERSION 2.6)
 project(Bottleneck_distance_utilities)
 
 if (NOT CGAL_WITH_EIGEN3_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})
+  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_test(NAME Bottleneck_distance_example_alpha_rips_persistence_bottleneck
-      COMMAND $<TARGET_FILE:alpha_rips_persistence_bottleneck_distance>
-      "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-r" "0.15" "-m" "0.12" "-d" "3" "-p" "3")
+  add_test(NAME Bottleneck_read_file_example
+      COMMAND $<TARGET_FILE:bottleneck_read_file_example>
+      "${CMAKE_SOURCE_DIR}/data/persistence_diagram/first.pers" "${CMAKE_SOURCE_DIR}/data/persistence_diagram/second.pers")
 
-  install(TARGETS alpha_rips_persistence_bottleneck_distance DESTINATION bin)
+  install(TARGETS bottleneck_read_file_example DESTINATION bin)
 
 endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
diff --git a/src/Bottleneck_distance/utilities/README b/src/Bottleneck_distance/utilities/README
index 4c9b0735..cfdccf0b 100644
--- a/src/Bottleneck_distance/utilities/README
+++ b/src/Bottleneck_distance/utilities/README
@@ -1,19 +1,10 @@
 # Bottleneck_distance #

 

-## `alpha_rips_persistence_bottleneck_distance` ##

-This program computes the persistent homology with coefficient field Z/pZ of a Rips complex defined on a set of input points. The output diagram contains one bar per line, written with the convention:

-

-`p dim b d`

-

-where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients.

+## `bottleneck_read_file_example` ##

+This program computes the Bottleneck distance between two persistence diagram files.

 

 Usage:

-`alpha_rips_persistence_bottleneck_distance [options] <OFF input file>`

-

-Allowed options:

+`bottleneck_read_file_example <file_1.pers> <file_2.pers> [<tolerance>]`

 

-* `-h [ --help ]` Produce help message

-* `-r [ --max-edge-length ]` (default = inf) Maximal length of an edge for the Rips complex construction.`

-* `-d [ --cpx-dimension ]` (default = 1) Maximal dimension of the Rips complex we want to compute.`

-* `-p [ --field-charac ]` (default = 11)     Characteristic p of the coefficient field Z/pZ for computing homology.

-* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.
\ No newline at end of file
+<file_1.pers> and <file_2.pers> must be in the format described [here](http://gudhi.gforge.inria.fr/doc/latest/fileformats.html#FileFormatsPers).

+<tolerance> is an error bound on the bottleneck distance (set by default to the smallest positive double value).

diff --git a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp b/src/Bottleneck_distance/utilities/bottleneck_read_file_example.cpp
index 24d73c57..9dd52b31 100644
--- a/src/Bottleneck_distance/example/bottleneck_read_file_example.cpp
+++ b/src/Bottleneck_distance/utilities/bottleneck_read_file_example.cpp
@@ -31,7 +31,7 @@
 int main(int argc, char** argv) {
   if (argc < 3) {
     std::cout << "To run this program please provide as an input two files with persistence diagrams. Each file" <<
-        " should contain a birth-death pair per line. Third, optional parameter is an error bound on a bottleneck" <<
+        " should contain a birth-death pair per line. Third, optional parameter is an error bound on the bottleneck" <<
         " distance (set by default to the smallest positive double value). If you set the error bound to 0, be" <<
         " aware this version is exact but expensive. The program will now terminate \n";
     return -1;