Updates cmake files and installation info.

Cleans and updates cmakelist files and updates installation info
accordingly in readme file. Also renames the main executable file to simul_atrophy.

CMakeLists.txt

@@ -1,47 +1,14 @@
 cmake_minimum_required(VERSION 2.8)
-project(ADDeformationModeling)
-
-# For cluster use argument: -DIS_CLUSTER:bool=true
-set(IS_CLUSTER false CACHE BOOL "cmake run in the cluster: true or false")
-
-# For new cluster also use argument: -DIS_NEW_CLUSTER:bool=true
-set(IS_NEW_CLUSTER false CACHE BOOL "cmake run in new cluster: true or false")
+project(simul@atrophy)
 
+# add cmake modules path to the default one:
 MESSAGE("The directory is: ${CMAKE_SOURCE_DIR}")
-#add cmake modules path to the default one:
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules")
 
-#Find the external library for Petsc
-find_package(PETSc COMPONENTS CXX REQUIRED)
-#find_package(PETSc COMPONENTS)
-set(CMAKE_CXX_COMPILER ${PETSC_COMPILER})
-
-#Home directory
-if(IS_CLUSTER)
-  if(IS_NEW_CLUSTER)
-    set(ITK_DIR /data/asclepios/user/bkhanal/softwares/ITK-build)
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
-    # This part taken from: http://stackoverflow.com/questions/10851247/how-to-activate-c-11-in-cmake
-    include(CheckCXXCompilerFlag)
-    CHECK_CXX_COMPILER_FLAG("-std=c++11" COMPILER_SUPPORTS_CXX11)
-    CHECK_CXX_COMPILER_FLAG("-std=c++0x" COMPILER_SUPPORTS_CXX0X)
-    if(COMPILER_SUPPORTS_CXX11)
-      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
-    elseif(COMPILER_SUPPORTS_CXX0X)
-      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++0x")
-    else()
-      message(STATUS "The compiler ${CMAKE_CXX_COMPILER} has no C++11 support. Please use a different C++ compiler.")
-    endif()
-    message("setting up for new cluster")
-
-  else(IS_NEW_CLUSTER)
-    set(ITK_DIR /epi/asclepios2/bkhanal/ITK-build)
-    message("setting up for legacy cluster")
-  endif(IS_NEW_CLUSTER)
+# Use cxx11 or not; If yes run cmake as: cmake -DUSE_CXX11:bool=true .. 
+set(USE_CXX11 false CACHE BOOL "use cxx11: true or false")
 
-else(IS_CLUSTER)
-  set(ITK_DIR /home/bkhanal/Documents/softwares/ITK-build)
-  set(CMAKE_EXPORT_COMPILE_COMMANDS on) #Will generate compile_commands.json file used by irony-mode in emacs code completion.
+if(USE_CXX11)
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
   # This part taken from: http://stackoverflow.com/questions/10851247/how-to-activate-c-11-in-cmake
   include(CheckCXXCompilerFlag)
@@ -54,9 +21,19 @@ else(IS_CLUSTER)
   else()
     message(STATUS "The compiler ${CMAKE_CXX_COMPILER} has no C++11 support. Please use a different C++ compiler.")
   endif()
-  message("setting up for delorme")
-endif(IS_CLUSTER)
+endif(USE_CXX11)
+
+
+# Find the external library for PETSc
+# PETSc must have been configured with --with-clanguage=cxx option!
+find_package(PETSc COMPONENTS CXX REQUIRED)
+set(CMAKE_CXX_COMPILER ${PETSC_COMPILER})
+
+# Generate compile_commands.json file used by irony-mode in emacs code completion.
+set(CMAKE_EXPORT_COMPILE_COMMANDS on)
+
 
+# Find ITK
 FIND_PACKAGE(ITK)
 IF(ITK_FOUND)
   INCLUDE(${ITK_USE_FILE})
@@ -65,7 +42,7 @@ ELSE(ITK_FOUND)
     "ITK not found. Please set ITK_DIR.")
 ENDIF(ITK_FOUND)
 
-#boost
+# Find boost
 find_package(Boost COMPONENTS program_options REQUIRED)
 
 add_subdirectory(src)

readme.md

@@ -4,18 +4,52 @@
 ### Requirements
 1. Cmake > 2.8
 2. [PETSc](https://www.mcs.anl.gov/petsc/index.html) version 3.6.3.1
+**Use `--with-clanguage=cxx` option** when configuring PETSc.
 3. [ITK](https://itk.org/) version 4.9
 
-First install right versions of PETSc and ITK.
+## Installation
+First make sure that:
 
-## Quickstart
-Clone this repository and create a `build` directory inside it.
-Get into the `build` directory and run `cmake ..` followed by `make all`
+* You have **right versions** of PETSc and ITK.
+* That you configured PETSc with `--with-clanguage=cxx` option.
+* Set `PETSC_DIR`, `PETSC_ARCH` and `ITK_DIR`.
+For example, I have my `.bashrc` with:
+```
+ITK_DIR=/home/bkhanal/Documents/softwares/ITK-build
+export ITK_DIR
+PETSC_DIR=/home/bkhanal/Documents/softwares/petsc
+export PETSC_DIR
+PETSC_ARCH=arch-linux2-cxx-debug
+export PETSC_ARCH
+```
+
+Now, build `simul@trophy` with the following steps. *I assume that you are inside a `curr_dir`, replace `curr_dir` with a directory of your choice.*
+
+```bash
+curr_dir$ git clone https://github.com/Inria-Asclepios/simul-atrophy.git
+curr_dir$ cd simul-atrophy
+simul-atrophy$ mkdir build && cd build
+```
+Use `cmake` to build the files.
+```bash
+build$ cmake ..
+build$ make
+```
+
+If you have ITK installed with `c++11`, then use the following options with cmake:
 
-The main simulator executable is `build/src/AdLemMain`.
-Run with `-h` option to see the arguments that must be given.
+```bash
+build$ cmake -DUSE_CXX11:bool=true ..
+build$ make
+```
+
+This should install the software to your machine.
+
+## Quickstart
+The main simulator executable is `build/src/simul_atrophy`.
+Run with `-h` option to see in detail how to use it.
 
-If you have python, it might be easier to use `scripts/runAdLemModel.py` instead of the executable.
+Otherwise, there is also a python script at 'simul-atrophy/scripts/simul_atrophy.py' which you can use.
 Once again, use `-h` option to see the details.
 
 

scripts/bish_utils.py

@@ -3,7 +3,7 @@
 Copying a directory tree.
 """
 # Author: Bishesh Khanal <[email protected]>
-#
+# Asclepios INRIA Sophia Antipolis
 #
 
 import subprocess

scripts/create_atrophy_map.py

@@ -3,7 +3,7 @@
 or input images.
 """
 # Author: Bishesh Khanal <[email protected]>
-#
+# Asclepios INRIA Sophia Antipolis
 #
 
 import argparse as ag

scripts/extractSliceVideoFrom4d.py

@@ -1,4 +1,11 @@
 #!/usr/bin/env python
+""" Script to:
+    Extract 3D images from a 4D image and then extract one selected slice
+    from each of these 3D images and combine them as a gif.
+"""
+# Author: Bishesh Khanal <[email protected]>
+# Asclepios INRIA Sophia Antipolis
+
 import subprocess
 import sys
 import argparse as ag

scripts/runAdLemModel.py → scripts/simul_atrophy.py

@@ -1,4 +1,10 @@
 #!/usr/bin/env python
+""" Script to run simul@atrophy
+"""
+# Author: Bishesh Khanal <[email protected]>
+# Asclepios INRIA Sophia Antipolis
+#
+
 import os
 import os.path as op
 import argparse as ag

scripts/runAdLemModelMultipleImages.py → scripts/simul_atrophy_multiple_images.py

@@ -1,4 +1,10 @@
 #!/usr/bin/env python
+""" Script to run simul@atrophy for multiple images
+"""
+# Author: Bishesh Khanal <[email protected]>
+# Asclepios INRIA Sophia Antipolis
+#
+
 import os
 import os.path as op
 import argparse as ag

src/CMakeLists.txt

@@ -11,10 +11,10 @@ link_directories(${PETSC_LIBRARIES})
 #     PetscAdLemMain.cxx
 #     )
 
-add_executable(AdLemMain
+add_executable(simul_atrophy
   PetscAdLemMain.cxx
   )
-target_link_libraries(AdLemMain ${PETSC_LIBRARIES} ${ITK_LIBRARIES})
+target_link_libraries(simul_atrophy ${PETSC_LIBRARIES} ${ITK_LIBRARIES})
 
 
 add_executable(UpdateMaskAndAtrophy