Merge add_utils_in_gudhi_v2 branch after 2nd round of review

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3041 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: ad134cc2b6756e20afc8d9db9e40c5af87d09f9d

5 files changed, 25 insertions, 72 deletions

diff --git a/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
index daba15a4..ee84e201 100644
--- a/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
+++ b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
@@ -63,7 +63,7 @@ namespace cubical_complex {
  * For further details and theory of cubical complexes, please consult \cite kaczynski2004computational as well as the
  * following paper \cite peikert2012topological .
  *
- * \section cubicalcomplexdatastructure Data structure.
+ * \section cubicalcomplexdatastructure Data structure
  *
  * The implementation of Cubical complex provides a representation of complexes that occupy a rectangular region in
  * \f$\mathbb{R}^n\f$. This extra assumption allows for a memory efficient way of storing cubical complexes in a form
@@ -85,37 +85,14 @@ namespace cubical_complex {
  * present in the product that gives the cube \f$C\f$. In a similar way, we can compute boundary and the coboundary of
  * each cube. Further details can be found in the literature.
  *
- * \section inputformat Input Format.
+ * \section inputformat Input Format
  *
  * In the current implantation, filtration is given at the maximal cubes, and it is then extended by the lower star
  * filtration to all cubes. There are a number of constructors that can be used to construct cubical complex by users
  * who want to use the code directly. They can be found in the \a Bitmap_cubical_complex class.
  * Currently one input from a text file is used. It uses a format used already in Perseus software
- * (http://www.sas.upenn.edu/~vnanda/perseus/) by Vidit Nanda.
- * Below we are providing a description of the format. The first line contains a number d begin the dimension of the
- * bitmap (2 in the example below). Next d lines are the numbers of top dimensional cubes in each dimensions (3 and 3
- * in the example below). Next, in lexicographical order, the filtration of top dimensional cubes is given (1 4 6 8
- * 20 4 7 6 5 in the example below).
- *
- *
- * \image html "exampleBitmap.png" "Example of a input data."
- *
- * The input file for the following complex is:
- * \verbatim
-2
-3
-3
-1
-4
-6
-8
-20
-4
-7
-6
-5
-\endverbatim
-
+ * (http://www.sas.upenn.edu/~vnanda/perseus/) by Vidit Nanda. The file format is described here: \ref FileFormatsPerseus.
+ *
  * \section PeriodicBoundaryConditions Periodic boundary conditions
  * Often one would like to impose periodic boundary conditions to the cubical complex. Let \f$ I_1\times ... \times
  * I_n \f$ be a box that is decomposed with a cubical complex \f$ \mathcal{K} \f$. Imposing periodic boundary
@@ -123,26 +100,8 @@ namespace cubical_complex {
  * considered the same. In particular, if for a bitmap \f$ \mathcal{K} \f$ periodic boundary conditions are imposed
  * in all directions, then complex \f$ \mathcal{K} \f$ became n-dimensional torus. One can use various constructors
  * from the file Bitmap_cubical_complex_periodic_boundary_conditions_base.h to construct cubical complex with periodic
- * boundary conditions. One can also use Perseus style input files. To indicate periodic boundary conditions in a
- * given direction, then number of top dimensional cells in this direction have to be multiplied by -1. For instance:
-
- *\verbatim
-2
--3
-3
-1
-4
-6
-8
-20
-4
-7
-6
-5
-\endverbatim
-
- * Indicate that we have imposed periodic boundary conditions in the direction x, but not in the direction y.
-
+ * boundary conditions. One can also use Perseus style input files (see \ref FileFormatsPerseus).
+ *
  * \section BitmapExamples Examples
  * End user programs are available in example/Bitmap_cubical_complex and utilities/Bitmap_cubical_complex folders.
  * 
diff --git a/src/Bitmap_cubical_complex/utilities/CMakeLists.txt b/src/Bitmap_cubical_complex/utilities/CMakeLists.txt
index f0f80059..676a730a 100644
--- a/src/Bitmap_cubical_complex/utilities/CMakeLists.txt
+++ b/src/Bitmap_cubical_complex/utilities/CMakeLists.txt
@@ -1,29 +1,29 @@
 cmake_minimum_required(VERSION 2.6)
 project(Bitmap_cubical_complex_utilities)
 
-add_executable ( Bitmap_cubical_complex Bitmap_cubical_complex.cpp )
+add_executable ( cubical_complex_persistence cubical_complex_persistence.cpp )
 if (TBB_FOUND)
-  target_link_libraries(Bitmap_cubical_complex ${TBB_LIBRARIES})
+  target_link_libraries(cubical_complex_persistence ${TBB_LIBRARIES})
 endif()
 
-add_test(NAME Bitmap_cubical_complex_utility_persistence_one_sphere COMMAND $<TARGET_FILE:Bitmap_cubical_complex>
+add_test(NAME Bitmap_cubical_complex_utility_persistence_one_sphere COMMAND $<TARGET_FILE:cubical_complex_persistence>
     "${CMAKE_SOURCE_DIR}/data/bitmap/CubicalOneSphere.txt")
 
-add_test(NAME Bitmap_cubical_complex_utility_persistence_two_sphere COMMAND $<TARGET_FILE:Bitmap_cubical_complex>
+add_test(NAME Bitmap_cubical_complex_utility_persistence_two_sphere COMMAND $<TARGET_FILE:cubical_complex_persistence>
     "${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt")
 
-add_executable ( Bitmap_cubical_complex_periodic_boundary_conditions Bitmap_cubical_complex_periodic_boundary_conditions.cpp )
+add_executable ( periodic_cubical_complex_persistence periodic_cubical_complex_persistence.cpp )
 if (TBB_FOUND)
-  target_link_libraries(Bitmap_cubical_complex_periodic_boundary_conditions ${TBB_LIBRARIES})
+  target_link_libraries(periodic_cubical_complex_persistence ${TBB_LIBRARIES})
 endif()
 
 add_test(NAME Bitmap_cubical_complex_utility_periodic_boundary_conditions_2d_torus
-    COMMAND $<TARGET_FILE:Bitmap_cubical_complex_periodic_boundary_conditions>
+    COMMAND $<TARGET_FILE:periodic_cubical_complex_persistence>
     "${CMAKE_SOURCE_DIR}/data/bitmap/2d_torus.txt")
 
 add_test(NAME Bitmap_cubical_complex_utility_periodic_boundary_conditions_3d_torus
-    COMMAND $<TARGET_FILE:Bitmap_cubical_complex_periodic_boundary_conditions>
+    COMMAND $<TARGET_FILE:periodic_cubical_complex_persistence>
     "${CMAKE_SOURCE_DIR}/data/bitmap/3d_torus.txt")
 
-install(TARGETS Bitmap_cubical_complex DESTINATION bin)
-install(TARGETS Bitmap_cubical_complex_periodic_boundary_conditions DESTINATION bin)
+install(TARGETS cubical_complex_persistence DESTINATION bin)
+install(TARGETS periodic_cubical_complex_persistence DESTINATION bin)
diff --git a/src/Bitmap_cubical_complex/utilities/README b/src/Bitmap_cubical_complex/utilities/README
index d9085635..ddff7034 100644
--- a/src/Bitmap_cubical_complex/utilities/README
+++ b/src/Bitmap_cubical_complex/utilities/README
@@ -1,24 +1,18 @@
 # Bitmap_cubical_complex #

 

-## `Bitmap_cubical_complex` ##

-This program computes persistent homology, by using the Bitmap_cubical_complex class, of cubical complexes provided in text files in Perseus style. The only number in the first line is a dimension D of a bitmap. In the lines I between 2 and D+1 there are numbers of top dimensional cells in the direction I. Let N denote product of the numbers in the lines between 2 and D. In the lines D+2 to D+2+N there are filtrations of top dimensional cells. We assume that the cells are in the lexicographical order.

+## `cubical_complex_persistence` ##

+This program computes persistent homology, by using the Bitmap_cubical_complex class, of cubical complexes provided in text files in Perseus style. See [here](http://gudhi.gforge.inria.fr/doc/latest/fileformats.html#FileFormatsPerseus) for a description of the file format.

 

-Examples:

+Example:

 

-* Create a Cubical Complex from the Perseus style file CubicalOneSphere.txt, computes Persistence cohomology from it and writes the results in a persistence file:

-`Bitmap_cubical_complex data/bitmap/CubicalOneSphere.txt`

+* Create a Cubical Complex from the Perseus style file `CubicalTwoSphere.txt`, computes Persistence cohomology from it and writes the results in a persistence file `CubicalTwoSphere.txt_persistence`:

+`cubical_complex_persistence data/bitmap/CubicalTwoSphere.txt`

 

-* Create a Cubical Complex from the Perseus style file CubicalTwoSphere.txt, computes Persistence cohomology from it and writes the results in a persistence file:

-`Bitmap_cubical_complex data/bitmap/CubicalTwoSphere.txt`

-

-## `Bitmap_cubical_complex_periodic_boundary_conditions` ##

+## `periodic_cubical_complex_persistence` ##

 

 Same as above, but with periodic boundary conditions.

 

-Examples:

-

-* Create a Periodical Cubical Complex from the Perseus style file 2d_torus.txt, computes Persistence cohomology from it and writes the results in a persistence file:

-`Bitmap_cubical_complex_periodic_boundary_conditions.exe data/bitmap/2d_torus.txt`

+Example:

 

-* Create a Periodical Cubical Complex from the Perseus style file 3d_torus.txt, computes Persistence cohomology from it and writes the results in a persistence file:

-`Bitmap_cubical_complex_periodic_boundary_conditions.exe data/bitmap/3d_torus.txt`

+* Create a Periodical Cubical Complex from the Perseus style file `3d_torus.txt`, computes Persistence cohomology from it and writes the results in a persistence file `3d_torus.txt_persistence`:

+`periodic_cubical_complex_persistence data/bitmap/3d_torus.txt`

diff --git a/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex.cpp b/src/Bitmap_cubical_complex/utilities/cubical_complex_persistence.cpp
index 9d1bc08c..9d1bc08c 100644
--- a/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex.cpp
+++ b/src/Bitmap_cubical_complex/utilities/cubical_complex_persistence.cpp
diff --git a/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex_periodic_boundary_conditions.cpp b/src/Bitmap_cubical_complex/utilities/periodic_cubical_complex_persistence.cpp
index c812cb3a..c812cb3a 100644
--- a/src/Bitmap_cubical_complex/utilities/Bitmap_cubical_complex_periodic_boundary_conditions.cpp
+++ b/src/Bitmap_cubical_complex/utilities/periodic_cubical_complex_persistence.cpp