merge 'of-0.11.2' branch to 'master'

Signed-off-by: Miaofei <[email protected]>

CMakeLists.txt

@@ -1,71 +1,137 @@
-# ======================= ofxCMake Vers. 0.1 =============
-#  PUT THIS FILE INTO YOUR OPENFRAMEWORKS PROJECT FOLDER
-
 # ========================================================
 # ===================== CMake Settings ===================
 # ========================================================
-cmake_minimum_required( VERSION 3.3 )
-project( openframeworks )
+cmake_minimum_required(VERSION 3.3)
+
+include(ExternalProject)
+include(GNUInstallDirs)
+include(ProcessorCount)
+
+ProcessorCount(NUM_CPUS)
+if(NUM_CPUS EQUAL 0)
+    set(NUM_CPUS 1)
+endif()
 
 # ========================================================
 # ===================== User Settings ====================
 # ========================================================
-# ------------------------ OF Path -----------------------
-# --- If outside the OF structure, set an absolute OF path
-set( OF_DIRECTORY_BY_USER "${CMAKE_CURRENT_LIST_DIR}/openFrameworks-0.10.1" )
+
+project(mrg-cpp)
 
 # ---------------------- App name  -----------------------
-set( APP_NAME mrg_axon_model )
+set(APP_NAME mrg_axon_model)
 
 # --------------------- Source Files ---------------------
-set( ${APP_NAME}_SOURCE_FILES
-        src/MRG_main.cpp
-        src/MRG_init.cpp
-        src/MRG_ode.cpp
-        src/utils.cpp
-        src/ofApp.cpp
-        )
-
-# ------------------------ AddOns  -----------------------
-set( OFX_ADDONS_ACTIVE
-         ofxPoco
-         ofxVideoRecorder
-#        ofxXmlSettings
-#        ofxOsc
-#        ofxGui
-#        ofxNetwork
-#        ofxVectorGraphics
-#        ofxThreadedImageLoader
-#        ofxAssimpModelLoader
-#        ofxKinect
-#        ofxOpenCv
-#        ofxSvg
-#        ofxEmscripten (untested)
-        )
-
-# =========================================================================
-# ============================== OpenFrameworks ===========================
-# =========================================================================
-include( ${OF_DIRECTORY_BY_USER}/addons/ofxCMake/modules/main.cmake )
-# =========================================================================
-
-# =========================================================================
-# ============================== Armadillo ================================
-# =========================================================================
-target_include_directories(${APP_NAME} PRIVATE src/libs/armadillo-9.200.5)
-# =========================================================================
-
-# =========================================================================
-# ============================== SUNDIALS =================================
-# =========================================================================
-add_subdirectory(src/libs/sundials-4.0.0 "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/sundials")
-target_include_directories(${APP_NAME} PRIVATE ${sundials_SOURCE_DIR}/include)
+set(${APP_NAME}_SOURCE_FILES
+    src/MRG_main.cpp
+    src/MRG_init.cpp
+    src/MRG_ode.cpp
+    src/ofApp.cpp
+    src/utils/utils.cpp
+)
+
+# ========================================================
+
+
+# ===============================================================
+# ==================== External Dependencies ====================
+# ===============================================================
+
+find_package(PkgConfig) 
+pkg_check_modules(GLIB REQUIRED glib-2.0) 
+pkg_check_modules(GSTREAMER REQUIRED gstreamer-1.0)
+pkg_check_modules(GSTREAMER_APP REQUIRED gstreamer-app-1.0)
+pkg_check_modules(GSTREAMER_VIDEO REQUIRED gstreamer-video-1.0)
+pkg_check_modules(CAIRO REQUIRED cairo)
+
+add_definitions(-DBOOST_ERROR_CODE_HEADER_ONLY)
+
+ExternalProject_Add(armadillo
+    URL "${CMAKE_SOURCE_DIR}/external_libs/armadillo-9.200.5.tar.bz2"
+    CONFIGURE_COMMAND ""
+    BUILD_COMMAND ""
+    INSTALL_COMMAND ${CMAKE_COMMAND} -E copy_directory <SOURCE_DIR>
+                    "${CMAKE_BINARY_DIR}/${CMAKE_INSTALL_INCLUDEDIR}"
+)
+
+ExternalProject_Add(sundials
+    URL "${CMAKE_SOURCE_DIR}/external_libs/sundials-4.0.2.tar.gz"
+    CMAKE_ARGS "-DCMAKE_INSTALL_PREFIX=${CMAKE_BINARY_DIR}"
+)
+
+ExternalProject_Add(openframeworks
+    URL "${CMAKE_SOURCE_DIR}/external_libs/of_v0.11.2_linux64gcc6_release"
+    CONFIGURE_COMMAND ""
+    BUILD_COMMAND <SOURCE_DIR>/scripts/linux/compileOF.sh -j${NUM_CPUS}
+    BUILD_IN_SOURCE 1
+    INSTALL_COMMAND ${CMAKE_COMMAND}
+                    -DSRC_PREFIX=<SOURCE_DIR>
+                    -DDST_PREFIX=${CMAKE_BINARY_DIR}
+                    -P ${CMAKE_SOURCE_DIR}/external_libs/install_openframeworks.cmake
+)
+
+link_directories("${CMAKE_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR}")
+
+# ===============================================================
+
+
+# =======================================================
+# ==================== Build Project ====================
+# =======================================================
+
+add_executable(${APP_NAME}
+    ${${APP_NAME}_SOURCE_FILES}
+)
+
+target_include_directories(${APP_NAME} BEFORE
+    PRIVATE "${CMAKE_BINARY_DIR}/${CMAKE_INSTALL_INCLUDEDIR}"
+            ${GLIB_INCLUDE_DIRS}
+            ${GSTREAMER_INCLUDE_DIRS}
+            ${CAIRO_INCLUDE_DIRS}
+)
+
 target_link_libraries(${APP_NAME}
-                        ofxPoco
-                        sundials_cvode_static
-                        sundials_sunlinsoldense_static
-                        sundials_sunmatrixdense_static
-                        sundials_nvecserial_static
-                        ofxVideoRecorder
-                        )
-# =========================================================================
+    libsundials_cvode.a
+    libsundials_sunlinsoldense.a
+    libsundials_sunmatrixdense.a
+    libsundials_nvecserial.a
+    libopenFrameworks.a
+    GLEW
+    GLU
+    GL
+    glut
+    glfw
+    openal
+    sndfile
+    kiss
+    tess2
+    PocoUtil
+    PocoFoundation
+    fontconfig
+    freetype
+    freeimage
+    X11
+    ${GSTREAMER_LIBRARIES}
+    ${GSTREAMER_APP_LIBRARIES}
+    ${GSTREAMER_VIDEO_LIBRARIES}
+    ${CAIRO_LIBRARIES}
+    ${GLIB_LIBRARIES}
+    uriparser
+    curl
+    boost_filesystem
+    boost_system
+    pthread
+)
+
+add_dependencies(${APP_NAME} armadillo sundials openframeworks)
+
+set_target_properties(${APP_NAME}
+    PROPERTIES
+    ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib"
+    LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib"
+    RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin"
+)
+
+file(COPY reference/activateF.txt DESTINATION bin/)
+
+# =======================================================

README.md

@@ -9,49 +9,45 @@ Visualization (implemented using openFrameworks) is also addded.
 
 - Obtain the source:
 
-    ```bash
-    $ git clone https://github.com/mm318/mrg-cpp.git
-    $ cd mrg-cpp
-    ```
-
-- Setup openFrameworks 0.10.1 and its CMake build:
-
-    ```bash
-    $ wget https://github.com/openframeworks/openFrameworks/archive/0.10.1.tar.gz && tar xvzf 0.10.1.tar.gz && rm 0.10.1.tar.gz
+```bash
+git clone https://github.com/mm318/mrg-cpp.git
+cd mrg-cpp/
+```
 
-    # optional if dependencies are already installed
-    $ sudo openFrameworks-0.10.1/scripts/linux/ubuntu/install_dependencies.sh
+- Setup openFrameworks 0.11.2 and its CMake build:
 
-    $ openFrameworks-0.10.1/scripts/linux/download_libs.sh
-    $ rm -rf openFrameworks-0.10.1/addons/ofxPoco/libs/
-    $ tar xvjf libs/libPoco-1.9.0.tar.bz2 -C openFrameworks-0.10.1/addons/ofxPoco/
+```bash
+wget https://github.com/openframeworks/openFrameworks/releases/download/0.11.2/of_v0.11.2_linux64gcc6_release.tar.gz \
+    && tar xvzf of_v0.11.2_linux64gcc6_release.tar.gz -C external_libs/ \
+    && rm of_v0.11.2_linux64gcc6_release.tar.gz
 
-    $ git clone https://github.com/mm318/ofxCMake.git openFrameworks-0.10.1/addons/ofxCMake
-    $ git clone https://github.com/timscaffidi/ofxVideoRecorder.git openFrameworks-0.10.1/addons/ofxVideoRecorder
-    ```
+# optional if dependencies are already installed
+sudo external_libs/of_v0.11.2_linux64gcc6_release/scripts/linux/ubuntu/install_dependencies.sh
+```
 
 - Build like an usual CMake project, for example:
 
-    ```bash
-    $ mkdir build
-    $ cd build
-    $ cmake ..
-    $ make -j4
-    ```
+```bash
+mkdir build
+cd build/
+cmake ..
+make -j4
+```
 
 
 ## Usage
 
 ```
-mrg_axon_model [--record-video=<video name>] <axon file> <V_fe (mV)> <V_applied (mV)> <duration (ms)> <stim start (ms)> <stim end (ms)>
+mrg_axon_model <axon file> <V_fe (mV)> <V_applied (mV)> <duration (ms)> <stim start (ms)> <stim end (ms)>
 ```
 
 The axon file is in the format (tab separated): `<x (m)> <y (m)> <z (m)> <Ve_pulse (V)>`
 
 ### Example
 
 ```bash
-mrg_axon_model reference/activateF.txt --record-video=replay 1 3 3 2 2.5
+cd build/bin/
+./mrg_axon_model activateF.txt 1 3 3 2 2.5
 ```
 
 ![Example visualization](reference/example_screenshot.png "Example visualization")

external_libs/install_openframeworks.cmake

@@ -0,0 +1,30 @@
+cmake_minimum_required(VERSION 3.6)
+
+include(GNUInstallDirs)
+
+file(GLOB_RECURSE of_libs
+     LIST_DIRECTORIES false
+     ${SRC_PREFIX}/*.a)
+
+list(FILTER of_libs EXCLUDE REGEX "/emscripten/")
+
+file(GLOB_RECURSE of_includes
+     LIST_DIRECTORIES false
+     ${SRC_PREFIX}/libs/openFrameworks/of*.h)
+
+file(GLOB_RECURSE of_inlines
+     LIST_DIRECTORIES false
+     ${SRC_PREFIX}/libs/openFrameworks/of*.inl)
+
+file(GLOB of_dep_include_dirs
+     LIST_DIRECTORIES true
+     ${SRC_PREFIX}/libs/*/${CMAKE_INSTALL_INCLUDEDIR})
+
+file(COPY ${of_libs}
+     DESTINATION ${DST_PREFIX}/${CMAKE_INSTALL_LIBDIR})
+
+file(COPY ${of_includes} ${of_inlines}
+     DESTINATION ${DST_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR})
+
+file(COPY ${of_dep_include_dirs}
+     DESTINATION ${DST_PREFIX})

src/MRG.h

@@ -8,7 +8,7 @@
 typedef realtype            MRG_REAL;
 typedef arma::Mat<MRG_REAL> MRG_MATRIX_REAL;
 
-#include "utils.h"
+#include "utils/utils.h"
 
 
 class MRG

src/MRG_init.cpp

@@ -3,7 +3,7 @@
 #include <fstream>
 
 #include "MRG.h"
-#include "utils.h"
+#include "utils/utils.h"
 
 #include <nvector/nvector_serial.h>
 #include <cvode/cvode.h>

src/MRG_ode.cpp

@@ -3,7 +3,7 @@
 #include <thread>
 
 #include "MRG.h"
-#include "utils.h"
+#include "utils/utils.h"
 
 #include <nvector/nvector_serial.h>
 #include <sunmatrix/sunmatrix_dense.h> /* access to dense SUNMatrix            */