Reorganized repo files

CMakeLists.txt

@@ -8,10 +8,10 @@ if(POLICY CMP0053)
 endif()
 
 if( CMAKE_SIZEOF_VOID_P EQUAL 8 )
-  message( STATUS "64 bits compiler detected" )    
+  message( STATUS "64 bits compiler detected" )
   set( EX_CONFIG "" )
   set(FIND_LIBRARY_USE_LIB64_PATHS ON)
-else( CMAKE_SIZEOF_VOID_P EQUAL 8 ) 
+else( CMAKE_SIZEOF_VOID_P EQUAL 8 )
   message( STATUS "32 bits compiler detected" )
   set( EX_CONFIG "32" )
   set(FIND_LIBRARY_USE_LIB64_PATHS OFF)
@@ -33,7 +33,7 @@ endif()
 string(TOLOWER ${CONFIGURATION} CONFIGURATION)
 
 set(CMAKE_CONFIGURATION_TYPES Debug Release RelWithDebInfo CACHE TYPE INTERNAL FORCE )
-if(MSVC)  
+if(MSVC)
   set(CMAKE_CXX_FLAGS_DEBUG "/D_DEBUG /MDd /Zi /Ob2 /Oi /Od /RTC1" CACHE TYPE INTERNAL FORCE)
 endif()
 
@@ -51,4 +51,4 @@ if(UNIX)
   set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_RPATH}:\$ORIGIN")
 endif()
 
-include(cmdsim.cmake)
+include(clasim.cmake)

README.md

-# CLASim
+# CLAsim
 The closed-loop assistant (CLA) simulation framework (CLASim) enables simulation of the interaction between closed-loop medical systems consisting of patient monitors, closed-loop physiology management algorithms, and infusion pumps, and patient physiology. It is writtne in C++ and relies on the <a href="https://physiology.kitware.com/">Pulse Physiology Engine</a> for simulating patient physiology.
 
 ## Getting Started
 
-### Installing Pulse and CLASim
-CLASim is has only been tested on Ubuntu 16.04. This is the recommended platform. We hope to support other platforms soon.
+### Installing Pulse and CLAsim
+CLAsim is has only been tested on Ubuntu 16.04. This is the recommended platform. We hope to support other platforms soon.
 
 #### Pulse
 To install <a href="https://gitlab.kitware.com/physiology/engine">Pulse repository</a> and follow the instructions there. Be sure to follow the instructions for Ubuntu. *For Java, be sure to use the openjdk version.*
 
 #### CLASim
-1. Check out the CLAsim repository into a folder of your choice
-2. Install libconfig++
-
+1. Check out the CLAsim repository into a folder of your choice.
+2. Install libconfig++  
    ~~~bash
    # update packages
-   sudo apt-get update
+   $ sudo apt-get update
    # install libconfig++
-   sudo apt-get install libconfig++-dev
+   $ sudo apt-get install libconfig++-dev
+   ~~~
+
+3. Use `$ dpkg -L libconfig++-dev` to find the location of `libconfig.h++` and `libconfig++.a`.
+4. Fill in lines 5 and 6 of `clasim.cmake` with the information for the locations for `libconfig.h++` and `libconfig++.a`.
+5. Install CLASim with CMake
+   ~~~bash
+   # make sure you are in the CLAsim folder
+   $ cd <PathToCLAsim>
+   # create a builds directory
+   $ mkdir builds
+   # enter builds folder
+   $ cd builds
+   # connect Pulse and CLASim for CMake Install
+   $ cmake .. -DCMAKE_PREFIX_PATH= <PathToPulse>/builds/install/
+   # create CLASim add_executable
+   $ make
+   $ make Install
+   ~~~
+
+6. Test that the CLASim executable installed properly.
+   ~~~bash
+   # go to Pulse bin directory
+   # (CLAsim executable installs there)
+   $ cd <PathToPulse>/builds/install/bin
+   # copy CLAsim config file to Pulse config folder
+   $ cp <PathToCLAsim>/resources/scenario.cfg config/
+   # run CLAsim
+   $ ./clasim
    ~~~
 
 ### Running Demo Examples

cmdsim.cmake → clasim.cmake

@@ -2,16 +2,17 @@ cmake_minimum_required(VERSION 3.9.4)
 
 project(cmd)
 
-# use ddpkg -L libconfig++-dev to find the location of libconfig.h++ and libconfig++.so
-find_path(CONFIG++_INCLUDE_DIR libconfig.h++ /usr/include /usr/local/include)
-find_library(CONFIG++_LIBRARY NAMES libconfig++.a PATH /usr/lib/x86_64-linux-gnu/)
+# use dpkg -L libconfig++-dev to find the location of libconfig.h++ and libconfig++.a
+find_path(CONFIG++_INCLUDE_DIR libconfig.h++ <libconfig.h++ location>)
+find_library(CONFIG++_LIBRARY NAMES libconfig++.a PATH <libconfig++.a location>)
 
 
-# source files directory -> To handle multiple controllers switch between different
-# source directories
-set(CMD_SRC_DIR src_ctrl2)
+# set your simulation source directory
+set(SIM_SRC_DIR simsrc/mcps2018/algo2)
 
-# source files
+
+# *** include your source files
+# list each file individually
 set(MY_SOURCE_FILES
 
     ${CMD_SRC_DIR}/SimEngine.cpp
@@ -25,14 +26,17 @@ set(MY_SOURCE_FILES
 
 add_executable(cmd ${MY_SOURCE_FILES})
 
-#cmd depends on pulse this will call will give you access to pulse directories  
+#cmd depends on pulse this will call will give you access to pulse directories
 #needed by cmd
-find_package(Pulse REQUIRED NO_MODULE) 
+find_package(Pulse REQUIRED NO_MODULE)
 
 #include directories
 target_include_directories(cmd PRIVATE ${Pulse_INCLUDE_DIRS})
 target_include_directories(cmd PRIVATE ${CONFIG++_INCLUDE_DIR})
-target_include_directories(cmd PRIVATE include/)
+
+# *** include your simulation include directories here
+target_include_directories(cmd PRIVATE simsrc/mcps2018/include/)
+
 #libraries
 target_link_libraries(cmd debug "${Pulse_DEBUG_LIBS}")
 target_link_libraries(cmd optimized "${Pulse_LIBS}")

docs/ReadMe.txt

-This "config file" goes inside pulse's "../install/bin/config/" directory