Document utilies in README files using Markdown + move/rename some utilities

Only missing doc for now: Garland_heckbert

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2752 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 7ba0113762b6622130835dc9e372acfae29c2db8

6 files changed, 95 insertions, 24 deletions

diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt
index f8527e0f..a8231392 100644
--- a/src/Witness_complex/example/CMakeLists.txt
+++ b/src/Witness_complex/example/CMakeLists.txt
@@ -14,25 +14,22 @@ install(TARGETS Witness_complex_example_nearest_landmark_table DESTINATION bin)
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
   add_executable( Witness_complex_example_off example_witness_complex_off.cpp )
   add_executable ( Witness_complex_example_sphere example_witness_complex_sphere.cpp )
-
-  add_executable ( Witness_complex_example_witness_persistence example_witness_complex_persistence.cpp )
-  target_link_libraries(Witness_complex_example_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
-
-  if (TBB_FOUND)
-    target_link_libraries(Witness_complex_example_witness_persistence ${TBB_LIBRARIES})
-  endif()
+  
+  add_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp )
+  target_link_libraries(Witness_complex_example_strong_off)
 
   add_test(NAME Witness_complex_example_off_test_torus
       COMMAND $<TARGET_FILE:Witness_complex_example_off>
       "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "20" "1.0" "3")
   add_test(NAME Witness_complex_example_test_sphere_10
       COMMAND $<TARGET_FILE:Witness_complex_example_sphere> "10")
-  add_test(NAME Witness_complex_example_test_torus_persistence
-      COMMAND $<TARGET_FILE:Witness_complex_example_witness_persistence>
-      "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5")
-
+  add_test(NAME Witness_complex_example_strong_off_test_torus
+      COMMAND $<TARGET_FILE:Witness_complex_example_strong_off>
+      "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "20" "1.0" "3")
+      
   install(TARGETS Witness_complex_example_off DESTINATION bin)
   install(TARGETS Witness_complex_example_sphere DESTINATION bin)
-  install(TARGETS Witness_complex_example_witness_persistence DESTINATION bin)
+  install(TARGETS Witness_complex_example_strong_off DESTINATION bin)
+
 
 endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
diff --git a/src/Witness_complex/utilities/example_strong_witness_complex_off.cpp b/src/Witness_complex/example/example_strong_witness_complex_off.cpp
index 0ee9ee90..0ee9ee90 100644
--- a/src/Witness_complex/utilities/example_strong_witness_complex_off.cpp
+++ b/src/Witness_complex/example/example_strong_witness_complex_off.cpp
diff --git a/src/Witness_complex/utilities/CMakeLists.txt b/src/Witness_complex/utilities/CMakeLists.txt
index 918ab864..125a41ff 100644
--- a/src/Witness_complex/utilities/CMakeLists.txt
+++ b/src/Witness_complex/utilities/CMakeLists.txt
@@ -3,24 +3,26 @@ project(Witness_complex_utilities)
 
 # CGAL and Eigen3 are required for Euclidean version of Witness
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
-  add_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp )
-  target_link_libraries(Witness_complex_example_strong_off)
+  
+  add_executable ( Witness_complex_strong_witness_persistence strong_witness_persistence.cpp )
+  target_link_libraries(Witness_complex_strong_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
-  add_executable ( Witness_complex_example_strong_witness_persistence example_strong_witness_persistence.cpp )
-  target_link_libraries(Witness_complex_example_strong_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
+  add_executable ( Witness_complex_weak_witness_persistence weak_witness_persistence.cpp )
+  target_link_libraries(Witness_complex_weak_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
   if (TBB_FOUND)
-    target_link_libraries(Witness_complex_example_strong_witness_persistence ${TBB_LIBRARIES})
+    target_link_libraries(Witness_complex_strong_witness_persistence ${TBB_LIBRARIES})
+    target_link_libraries(Witness_complex_weak_witness_persistence ${TBB_LIBRARIES})
   endif()
 
-  add_test(NAME Witness_complex_example_strong_off_test_torus
-      COMMAND $<TARGET_FILE:Witness_complex_example_strong_off>
-      "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "20" "1.0" "3")
-  add_test(NAME Witness_complex_example_strong_test_torus_persistence
-      COMMAND $<TARGET_FILE:Witness_complex_example_strong_witness_persistence>
+  add_test(NAME Witness_complex_strong_test_torus_persistence
+      COMMAND $<TARGET_FILE:Witness_complex_strong_witness_persistence>
+      "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5")
+  add_test(NAME Witness_complex_weak_test_torus_persistence
+      COMMAND $<TARGET_FILE:Witness_complex_weak_witness_persistence>
       "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5")
 
-  install(TARGETS Witness_complex_example_strong_off DESTINATION bin)
-  install(TARGETS Witness_complex_example_strong_witness_persistence DESTINATION bin)
+  install(TARGETS Witness_complex_strong_witness_persistence DESTINATION bin)
+  install(TARGETS Witness_complex_weak_witness_persistence DESTINATION bin)
 
 endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
diff --git a/src/Witness_complex/utilities/README b/src/Witness_complex/utilities/README
new file mode 100644
index 00000000..d8dc9ca7
--- /dev/null
+++ b/src/Witness_complex/utilities/README
@@ -0,0 +1,72 @@
+# Witness_complex #

+

+## `weak_witness_persistence` ##

+This program computes the persistent homology with coefficient field *Z/pZ* of a Weak witness 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*

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

+

+*Allowed options*

+

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

+* `-l [ --landmarks ]` Number of landmarks to choose from the point cloud.

+* `-o [ --output-file ]` Name of file in which the persistence diagram is written. By default, print in std::cout.

+* `-a [ --max-sq-alpha ]` (default = inf) Maximal squared relaxation parameter.

+* `-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.

+* `-d [ --cpx-dimension ]` (default = 2147483647) Maximal dimension of the weak witness complex we want to compute.

+

+*Example*

+`weak_witness_persistence data/points/tore3D_1307.off -l 20 -a 0.5 -m 0.006`

+

+outputs:

+```

+Successfully read 1307 points.

+Ambient dimension is 3.

+The complex contains 732 simplices and has dimension 8 

+11  0 0 inf 

+11  1 0 inf 

+11  2 0.0275251 0.0534586 

+11  1 0 0.0239952 

+```

+

+N.B.: output is random as the 20 landmarks are chosen randomly.

+

+## `strong_witness_persistence` ##

+This program computes the persistent homology with coefficient field *Z/pZ* of a Strong witness 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*

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

+

+*Allowed options*

+

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

+* `-l [ --landmarks ]` Number of landmarks to choose from the point cloud.

+* `-o [ --output-file ]` Name of file in which the persistence diagram is written. By default, print in std::cout.

+* `-a [ --max-sq-alpha ]` (default = inf) Maximal squared relaxation parameter.

+* `-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.

+* `-d [ --cpx-dimension ]` (default = 2147483647) Maximal dimension of the weak witness complex we want to compute.

+

+*Example*

+`strong_witness_persistence data/points/tore3D_1307.off -l 20 -a 0.5 -m 0.06`

+

+outputs:

+```

+Successfully read 1307 points.

+Ambient dimension is 3.

+The complex contains 1836 simplices and has dimension 8 

+11  0 0 inf 

+11  1 0.00674748 inf 

+11  2 0.0937751 0.235354 

+```

+

+N.B.: output is random as the 20 landmarks are chosen randomly.

diff --git a/src/Witness_complex/utilities/example_strong_witness_persistence.cpp b/src/Witness_complex/utilities/strong_witness_persistence.cpp
index f786fe7b..f786fe7b 100644
--- a/src/Witness_complex/utilities/example_strong_witness_persistence.cpp
+++ b/src/Witness_complex/utilities/strong_witness_persistence.cpp
diff --git a/src/Witness_complex/example/example_witness_complex_persistence.cpp b/src/Witness_complex/utilities/weak_witness_persistence.cpp
index a1146922..a1146922 100644
--- a/src/Witness_complex/example/example_witness_complex_persistence.cpp
+++ b/src/Witness_complex/utilities/weak_witness_persistence.cpp