Rename library to Fast Methods, reorganize code, and update documentation.

Author: jvgomez

.gitignore

@@ -2,6 +2,7 @@ build/
 *.*~
 examples/build/
 doc/html/
+.vscode
 
 #QtCreator temps
 .idea

CMakeLists.txt

@@ -1,5 +1,5 @@
 cmake_minimum_required (VERSION 2.6) 
-project (FMM) 
+project (fast_methods) 
 
 # set a default build type for single-configuration
 # CMake generators if no build type is set.
@@ -9,7 +9,7 @@ endif(NOT CMAKE_CONFIGURATION_TYPES AND NOT CMAKE_BUILD_TYPE)
 
 set(BUILD_EXAMPLES true CACHE STRING "True (default) to build examples")
 if(BUILD_EXAMPLES)
-    message(STATUS "Examples are being built (NOT installed).")
+    message(STATUS "Examples are being built and installed.")
 endif(BUILD_EXAMPLES)
 
 # Select flags.
@@ -39,84 +39,61 @@ endif()
 include_directories (
     ${Boost_INCLUDE_DIRS}
     ${CImg_INCLUDE_DIRS}
-    console
-    ndgridmap
-    fmm
-    fmm/fmdata
-    fm2
-    io
-    gradientdescent
-    thirdparty
+    include
 )
 
 # Create main library
-add_library(fastmarching SHARED
-    console/console.cpp
-    ndgridmap/cell.cpp
-    fmm/fmdata/fmcell.cpp
+add_library(fast_methods SHARED
+    src/console/console.cpp
+    src/ndgridmap/cell.cpp
+    src/ndgridmap/fmcell.cpp
 )
 
 # Linking 
-target_link_libraries(fastmarching
+target_link_libraries(fast_methods
     ${Boost_LIBRARIES}
     ${CImg_SYSTEM_LIBS}
 )
 
 # Add benchmarking capabilities
-add_executable (fmmbenchmark benchmark/fmm_benchmark.cpp)  
+add_executable(fm_benchmark src/benchmark/fm_benchmark.cpp)  
 
-target_link_libraries (fmmbenchmark fastmarching)
+target_link_libraries(fm_benchmark fast_methods)
 
 # Create main example
 if(BUILD_EXAMPLES)
-    add_executable(fmm main.cpp)
-    target_link_libraries(fmm fastmarching)
     add_subdirectory(examples)
 endif(BUILD_EXAMPLES)
 
 # Install section
 # We are not using CMakePackageConfigHelpers because CIMG variables are lists
 # and those functions do not manage them properly.
 configure_file(
-    cmake/FMConfig.cmake.in
-    ${CMAKE_BINARY_DIR}/FMConfig.cmake
+    cmake/fast_methods-config.cmake.in
+    ${CMAKE_BINARY_DIR}/fast_methods-config.cmake
 )
 
-install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FMConfig.cmake
-    DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/cmake/FM
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/fast_methods-config.cmake
+    DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/cmake/fast_methods
 )
 
-install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FMConfig.cmake
-    DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/cmake/FM
-)
-
-install(TARGETS fastmarching
+install(TARGETS fast_methods
     DESTINATION ${CMAKE_INSTALL_PREFIX}/lib
 )
 
-install(TARGETS fmmbenchmark
+install(TARGETS fm_benchmark
     DESTINATION ${CMAKE_INSTALL_PREFIX}/bin
 )
 
-install(DIRECTORY scripts DESTINATION ${CMAKE_INSTALL_PREFIX}/share/FM)
+install(DIRECTORY scripts
+    DESTINATION ${CMAKE_INSTALL_PREFIX}/share/fast_methods)
 
-install(DIRECTORY benchmark/cfg DESTINATION ${CMAKE_INSTALL_PREFIX}/share/FM)
-
-install(DIRECTORY ${CMAKE_SOURCE_DIR} DESTINATION ${CMAKE_INSTALL_PREFIX}/include
+install(DIRECTORY include/ DESTINATION ${CMAKE_INSTALL_PREFIX}/include
     FILES_MATCHING
         PATTERN "*.hpp"
         PATTERN "*.h"
-    REGEX "/build$" EXCLUDE
-    REGEX ".git$" EXCLUDE
-    REGEX "/examples$" EXCLUDE
-    REGEX "/doc$" EXCLUDE
-    REGEX "/data$" EXCLUDE
-    REGEX "/cfg$" EXCLUDE
-    REGEX "/cmake$" EXCLUDE
-    REGEX "/scripts$" EXCLUDE
 )
 
-
 # Uninstall target
 configure_file(
     "${CMAKE_CURRENT_SOURCE_DIR}/cmake/cmake_uninstall.cmake.in"

README.md

@@ -1,150 +1,64 @@
-N-Dimensional Fast Marching Method V1.0
+N-Dimensional Fast Methods Library v0.7
 
 **Authors:**
  - [Javier V. Gomez](http://jvgomez.github.io) javvgomez _at_ gmail.com
  - Jose Pardeiro jose.pardeiro _at_ gmail.com
  - Pablo Gely
 
 ## ALGORITHMS
+All the theory and algorithms implemented in this library can be found in my [PhD thesis](doc/files/phd_thesis.pdf). In fact, all the benchmarking data in chapter 4 has been produced with this library and it is stored on the `experiments` branch.
+
+
 **Fast Marching Methods:**
-- [FMM](http://jvgomez.github.io/fastmarching/classFMM.html): Fast Marching Method with Binary Queue and Fibonacci Queue (binary by default).
-- [FMM*](http://jvgomez.github.io/fastmarching/classFMMStar.html): FMM with CostToGo heuristics.
-- [SFMM](http://jvgomez.github.io/fastmarching/classSFMM.html): Simplified Fast Marhching Method.
-- [SFMM*](http://jvgomez.github.io/fastmarching/classSFMMStar.html): SFMM with CostToGo heuristics..
+- [FMM](http://jvgomez.github.io/fast_methods/classFMM.html): Fast Marching Method with Binary Queue and Fibonacci Queue (binary by default).
+- [FMM*](http://jvgomez.github.io/fast_methods/classFMMStar.html): FMM with CostToGo heuristics.
+- [SFMM](http://jvgomez.github.io/fast_methods/classSFMM.html): Simplified Fast Marhching Method.
+- [SFMM*](http://jvgomez.github.io/fast_methods/classSFMMStar.html): SFMM with CostToGo heuristics..
 
 **O(n) Fast Marching Methods:**
-- [GMM](http://jvgomez.github.io/fastmarching/classGMM.html): Group Marching Method.
-- [UFMM](http://jvgomez.github.io/fastmarching/classUFMM.html): Untidy Fast Marching Method.
-- [FIM](http://jvgomez.github.io/fastmarching/classFIM.html): Fast Iterative Method.
+- [GMM](http://jvgomez.github.io/fast_methods/classGMM.html): Group Marching Method.
+- [UFMM](http://jvgomez.github.io/fast_methods/classUFMM.html): Untidy Fast Marching Method.
+- [FIM](http://jvgomez.github.io/fast_methods/classFIM.html): Fast Iterative Method.
 
 **Fast Sweeping Methods:**
-- [FSM](http://jvgomez.github.io/fastmarching/classFSM.html): Fast Sweeping Method.
-- [LSM](http://jvgomez.github.io/fastmarching/classLSM.html): Lock Sweeping Method.
-
-**Other methods:**
-- [DDQM](http://jvgomez.github.io/fastmarching/classDDQM.html): Dynamic Double Queue Method.
+- [FSM](http://jvgomez.github.io/fast_methods/classFSM.html): Fast Sweeping Method.
+- [LSM](http://jvgomez.github.io/fast_methods/classLSM.html): Lock Sweeping Method.
+- [DDQM](http://jvgomez.github.io/fast_methods/classDDQM.html): Dynamic Double Queue Method.
 
 **Fast Marching Square motion planning algorithms:**
-- [FM2](http://jvgomez.github.io/fastmarching/classFM2.html): Fast Marching Square Method.
-- [FM2*](http://jvgomez.github.io/fastmarching/classFM2Star.html): Fast Marching Square Star FM2 with CostToGo heuristics.
+- [FM2](http://jvgomez.github.io/fast_methods/classFM2.html): Fast Marching Square Method.
+- [FM2*](http://jvgomez.github.io/fast_methods/classFM2Star.html): Fast Marching Square Star FM2 with CostToGo heuristics.
 
 **ROS**
 
-ROS nodes using this code (tested in the TurtleBot) are provided in a separate repo:
-https://github.com/jpardeiro/fastmarching_node
+ROS nodes using this code (tested in the TurtleBot) are provided in a [separate repo](https://github.com/jpardeiro/fastmarching_node)
+
 
 ## DISCLAIMER and IMPORTANT NOTES
 
 - The code is not deeply tested. I've just tested it works for the cases I need. If you find any problem, have any question (or whatever), please write to: javvgomez _at_ gmail.com
 
-- The compilation time is highly increased due to CImg library. Please, omit it when possible.
+- The compilation time is highly increased due to CImg library. Please, omit it when possible as it is used only for visualization purposes.
 
-- License GNU/GPL V3: http://www.gnu.org/copyleft/gpl.html
+- License [GNU/GPL V3](http://www.gnu.org/copyleft/gpl.html)
 
 - This is a source code intended for my research. Although I want it to be useful for other people it is not intended to act as a library (there are many many points to improve). However, if you show interest or have feature request do not hesitate to contact me and I will try my best to improve the code for whoever needs it. I am also open to contributions and to create a formal library if necessary.
 
 
 ## Documentation
 
-- [API Reference](jvgomez.github.io/fastmarching/)
-- This README is important as well.
-
-
-To build latest the documentation:
-
-    $ cd doc
-    $ doxygen
-
-Go into the HTML folder and open index.html
-
-
-## Dependencies:
-
-This code uses C\++11 so a compiler g++ 4.8 or equivalent is required. With GCC 4.7 some runtime problems can occur.
-
-Additional dependencies: Boost, imagemafick and CImg.
+- [API Reference](jvgomez.github.io/fast_methods/)
 
-    $ sudo apt-get install imagemagick libboost-all-dev cimg-dev
 
 ## Building the code
-To build the code:
-
-    $ cd build
-    $ cmake .. -DCMAKE_BUILD_TYPE=Release (Release, RelWithDebInf or Debug, Release by default)
-    $ make -j8 (or the number of cores you want to use during compilation)
-    $ sudo make install (only if you want to install the library)
-    $ ./fmm -map1 ../data/testimg.png -map2 ../data/map.png -vel ../data/velocities.png
-
-This main shows most of the utilities implemented so far.
-
-To uninstall:
-
-    $ sudo make uninstall
-
-
-## Folder structure
-
-Although there are a lot of folders, they are quite simple. It is organized this way because I'm focusing on an upload to Biicode (www.biicode.com)
-
-+ build: where the code should be compiled.
-+ console: the console class.
-+ data: additional files and maps to test.
-  + alpha: contains code the be refactorized and included in the library in the future.
-+ doc: doxygen documentation.
-+ examples: easy examples to understand how to use the code.
-+ fm2: Fast Marching Square (FM2) algorithms.
-+ fmm: Fast Marching Algorithms.
-  + fmdata: classes related to the data types of the Fast Marching Method and other algorithms.
-+ gradientdescent: under development.
-+ io: input/output helper classes.
-+ ndgridmap: main container.
-+ scripts: matlab scripts to parse outputs and automatic benchmarking bash script.
-+ thirdparty: others' software included.
-
-### Installation
-Default installation folder is` /usr/local` for Linux distributions (or equivalent on other OS). Libraries are installed in subfolder `lib`, together with CMake modules. All the includes are installed under `include` subfolder. Additionally, in the `share` subfolder the helper scripts and some samples of benchmark configurations files are installed. Finally, the benchmark binary is installed in `bin`.
-
-In order to change the default installation folder you can do:
-
-	$ cmake ../.. -DCMAKE_INSTALL_PREFIX=<your folder>
+Check the [building section](http://jvgomez.github.io/fast_methods/md_markdown_building.html) of the documentation.
 
 
-In this case, you will have to adapt your environment variables so that the libraries and CMake modules are found.
+## Design and folder structure
+Check the [design section](http://jvgomez.github.io/fast_methods/md_markdown_design.html) of the documentation.
 
 
 ## KNOWN ISSUES
 
 - Gradient Descent for FM2* could fail if very narrow passages are in the way of the path.
-- It seems that UFMM can fail in maps with random (or similar) velocity changes.
-
-## TODO
-
-At the top of each file there are specific TODO comments. Here are some others.
-
-### Code TODOs
-- Remove relative file dependencies (#include "../../fmm", filename = "../../data", CMakeLists.txt deps, etc).
-- MapLoader, GridWriter... get a naming convention. MapReader or GridSaver for instance.
-- printRunInfo implementation missing for most of the solvers.
-- Unify GridWriter and GridPlotter functions parameter order: (grid, name)
-- Fix Doxygen warnings.
-- Convert all scripts to python (or similar) so that they keep completely open source.
-- Reimplement FM2Dir from scratch. Currently in data/alpha folder.
-- Substitute arg parsing with boost_options.
-- Implement a grid copy constructor and assignment operator, etc.
-- Most of the unsigned int should be replaced by size_t to be type-correct.
-- Use smart pointers (specially for grid).
-- Create a testing framework.
-- BenchmarkCFG::configure, parse ctorParams_ with a variadic templated function, something like:` parseParams<int, bool>(param1, param2)`, `parseParams<string,double,bool>(p1,p2,p3)`.
-- GridPlotter code can be refactorized so that the same code is not repeated many times.
-- Review template template parameters, perhaps it can be simplified (specially for benchmark): `template <grid_t>` to `template <nDGridMap <cell_t, ndims>>` so we can use cell_t without doing `template <grid_t, cell_t>` (redundant).
-- Unify names: one thing is Fast Methods, other Fast Marching, etc.
-
-### Algorithmic TODOs
-- Improve untidy queue implementation with hash maps (specially remove element in increase_priority()).
-- Mix SFMM and UFMM (researchy TODO).
-- Improve the way FM2 and its versions deal with the grid when running multiple times on the same grid. Concretely, avoid recomputation of velocities map.
-- For most methods, neighbors for same cell are computed many times. Store them like FMT to save some computation time.
-
-### Documentation TODOs
-- Review and update nDGridMap.pdf
-- Link thesis and papers.
+- It seems that UFMM can fail in maps with random (or similar) velocity changes.

TODO.md

@@ -0,0 +1,33 @@
+# TODO
+
+At the top of each file there are specific TODO comments. (List [here](http://jvgomez.github.io/fast_methods/todo.html)). Here are some others.
+
+## Code TODOs
+- MapLoader, GridWriter... get a naming convention. MapReader or GridSaver for instance.
+- printRunInfo implementation missing for most of the solvers.
+- Unify GridWriter and GridPlotter functions parameter order: (grid, name)
+- Fix Doxygen warnings.
+- Convert all scripts to python (or similar) so that they keep completely open source.
+- Reimplement FM2Dir from scratch. Currently in data/alpha folder.
+- Substitute arg parsing with boost_options.
+- Implement a grid copy constructor and assignment operator, etc.
+- Most of the unsigned int should be replaced by size_t to be type-correct.
+- Use smart pointers (specially for grid).
+- Create a testing framework.
+- BenchmarkCFG::configure, parse ctorParams_ with a variadic templated function, something like:` parseParams<int, bool>(param1, param2)`, `parseParams<string,double,bool>(p1,p2,p3)`.
+- GridPlotter code can be refactorized so that the same code is not repeated many times.
+- Review template template parameters, perhaps it can be simplified (specially for benchmark): `template <grid_t>` to `template <nDGridMap <cell_t, ndims>>` so we can use cell_t without doing `template <grid_t, cell_t>` (redundant).
+- Add proper versioning in CMake.
+- use Git LFS for big files (and clean the experiments branch).
+
+## Algorithmic TODOs
+- Improve untidy queue implementation with hash maps (specially remove element in increase_priority()).
+- Mix SFMM and UFMM (researchy TODO).
+- Improve the way FM2 and its versions deal with the grid when running multiple times on the same grid. Concretely, avoid recomputation of velocities map.
+- For most methods, neighbors for same cell are computed many times. Store them like FMT to save some computation time.
+
+## Documentation TODOs
+- Review and update nDGridMap.pdf
+- Link thesis and papers.
+- Review and update: naming, folder structure, build instructions.
+- Add a make doc target.

changelog.md

@@ -2,6 +2,8 @@
 - Benchmarking can save only a grid per solver or grid for all runs with option savegrid=1 or `savegrid=2`
 - Benchmarking CFG files now accept .grid textfiles under the option `text=<path_to_text_grid>`
 - Added install and uninstall CMake targets.
+- Renamed library to Fast Methods.
+- Changed directory structure and includes.
 
 #### v0.6 ChangeLog
 - solveEikonal made more stable, but a bit less efficient.

cmake/FMConfig.cmake.in cmake/fast_methods-config.cmake.incmake/FMConfig.cmake.in renamed to cmake/fast_methods-config.cmake.in

@@ -1,13 +1,13 @@
-set(FM_FOUND 1)
+set(fast_methods_FOUND 1)
 
-set(FM_INCLUDE_DIRS
+set(fast_methods_INCLUDE_DIRS
     @Boost_INCLUDE_DIRS@
     @CImg_INCLUDE_DIRS@
     @CMAKE_INSTALL_PREFIX@/include
 )
 
-set(FM_LIBRARIES
-    @CMAKE_INSTALL_PREFIX@/lib/${CMAKE_SHARED_LIBRARY_PREFIX}fastmarching${CMAKE_SHARED_LIBRARY_SUFFIX}
+set(fast_methods_LIBRARIES
+    @CMAKE_INSTALL_PREFIX@/lib/${CMAKE_SHARED_LIBRARY_PREFIX}fast_methods${CMAKE_SHARED_LIBRARY_SUFFIX}
     @CImg_SYSTEM_LIBS@
     @Boost_LIBRARIES@
 )