Merging newest master branch in.

.gitignore

@@ -6,7 +6,7 @@ lib/local/LandmarkDetector/x64/
 exe/FaceLandmarkImg/x64/
 exe/FaceLandmarkVid/x64/
 exe/FeatureExtraction/x64/
-x64/Release/
+/x64/Release/
 OpenFace.VC.opendb
 OpenFace.sdf
 matlab_runners/Action Unit Experiments/AU_preds/
@@ -21,13 +21,14 @@ matlab_runners/Feature Point Experiments/yt_features_clm/
 matlab_runners/Gaze Experiments/mpii_out/
 build/
 Release/AU_predictors/
-Release/
+/Debug/
+/Release/
 exe/Recording/recording/
 ipch/
 exe/FeatureExtraction/out_bp4d/
 matlab_runners/Action Unit Experiments/out_bp4d/
 matlab_runners/Action Unit Experiments/out_SEMAINE/
-x64/Debug/
+/x64/Debug/
 matlab_runners/Action Unit Experiments/out_unbc/
 matlab_runners/Action Unit Experiments/out_bosph/
 matlab_runners/Action Unit Experiments/out_DISFA/
@@ -51,5 +52,22 @@ lib/local/LandmarkDetector/Debug/
 OpenFaceDemo/bin/
 OpenFaceDemo/obj/
 Debug/model/
-Debug/
 *.suo
+lib/3rdParty/dlib/Debug/
+lib/local/FaceAnalyser/Debug/
+lib/local/LandmarkDetector/Debug/
+matlab_runners/Head Pose Experiments/experiments/biwi_out/
+matlab_runners/Head Pose Experiments/experiments/bu_out/
+matlab_runners/Head Pose Experiments/experiments/ict_out/
+exe/FaceLandmarkImg/Release/
+exe/FaceLandmarkVid/Release/
+exe/FaceLandmarkVidMulti/Release/
+exe/FeatureExtraction/Release/
+exe/Recording/Release/
+gui/OpenFaceDemo/obj/
+lib/3rdParty/dlib/Release/
+lib/local/CamCom/Release/
+lib/local/CppInerop/Release/
+lib/local/CppInerop/x64/
+lib/local/FaceAnalyser/Release/
+lib/local/LandmarkDetector/Release/

.travis.yml

@@ -14,48 +14,55 @@ os:
   - linux  
   
 before_install:
+
+  # OpenCV dependencies and boost
+  - if [ ${TRAVIS_OS_NAME} = linux ]; then  
+      sudo apt-get install git libgtk2.0-dev pkg-config libavcodec-dev libavformat-dev libswscale-dev;      
+      sudo apt-get install python-dev python-numpy libtbb2 libtbb-dev libjpeg-dev libpng-dev libtiff-dev libjasper-dev libdc1394-22-dev checkinstall;
+      sudo add-apt-repository -y ppa:boost-latest/ppa;
+      sudo apt-get update;
+      sudo apt-get install libboost1.55-all-dev;
+      wget https://github.com/Itseez/opencv/archive/3.1.0.zip;
+      sudo unzip 3.1.0.zip;
+      cd opencv-3.1.0;
+      sudo mkdir build;
+      cd build;
+    fi
+
   # g++4.8.1
-  - if [ "$CXX" == "g++" ]; then
+  - if [ "$CXX" = "g++" ]; then
-      if [[ ${TRAVIS_OS_NAME} = linux ]]; then
+      if [ ${TRAVIS_OS_NAME} = linux ]; then
         sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test; 
+        sudo apt-get update -qq;
+        sudo apt-get install -qq g++-4.8; 
+        export CXX="g++-4.8";		
+        sudo cmake -D CMAKE_BUILD_TYPE=RELEASE -D WITH_V4L=ON -D WITH_OPENCL=OFF -D INSTALL_C_EXAMPLES=OFF -D BUILD_EXAMPLES=OFF -D BUILD_TESTS=OFF -D BUILD_PERF_TESTS=OFF -D BUILD_EXAMPLES=OFF -D INSTALL_PYTHON_EXAMPLES=OFF ..;
       fi 
     fi
 
   # clang 3.4
-  - if [ "$CXX" == "clang++" ]; then
+  - if [ "$CXX" = "clang++" ]; then
-      if [[ ${TRAVIS_OS_NAME} = linux ]]; then  
+      if [ ${TRAVIS_OS_NAME} = linux ]; then  
-        sudo add-apt-repository -y ppa:h-rayflood/llvm;
+        $CXX --version;
+        sudo sed -i -e 's/^Defaults\tsecure_path.*$//' /etc/sudoers;
+        sudo cmake -D CMAKE_BUILD_TYPE=RELEASE -D WITH_V4L=ON -D WITH_OPENCL=OFF -D INSTALL_C_EXAMPLES=OFF -D BUILD_EXAMPLES=OFF -D BUILD_TESTS=OFF -D BUILD_PERF_TESTS=OFF -D BUILD_EXAMPLES=OFF -D INSTALL_PYTHON_EXAMPLES=OFF ..;
       fi
     fi
 
-  - if [[ ${TRAVIS_OS_NAME} = linux ]]; then sudo apt-get update -qq; fi
+  - if [ ${TRAVIS_OS_NAME} = osx ]; then
-  
+      brew update;
-install:
+      brew install tbb;
-  - if [ "$CXX" == "g++" ]; then if [[ ${TRAVIS_OS_NAME} = linux ]]; then sudo apt-get install -qq g++-4.8; fi fi
+      wget https://github.com/Itseez/opencv/archive/3.1.0.zip;
-  - if [ "$CXX" == "g++" ]; then if [[ ${TRAVIS_OS_NAME} = linux ]]; then export CXX="g++-4.8"; fi fi 
+      sudo unzip 3.1.0.zip;
-  - if [ "$CXX" == "clang++" ]; then if [[ ${TRAVIS_OS_NAME} = linux ]]; then sudo apt-get install -qq clang-3.4; fi fi
+      cd opencv-3.1.0;
-  - if [ "$CXX" == "clang++" ]; then if [[ ${TRAVIS_OS_NAME} = linux ]]; then export CXX="clang++-3.4"; fi fi
+      sudo mkdir build;
-
+      cd build;
-  - if [[ ${TRAVIS_OS_NAME} = linux ]]; then sudo apt-get install git libgtk2.0-dev pkg-config libavcodec-dev libavformat-dev libswscale-dev; fi
+      sudo cmake -D CMAKE_BUILD_TYPE=RELEASE -D WITH_V4L=ON ..;
-  - if [[ ${TRAVIS_OS_NAME} = linux ]]; then sudo apt-get install python-dev python-numpy libtbb2 libtbb-dev libjpeg-dev libpng-dev libtiff-dev libjasper-dev libdc1394-22-dev checkinstall; fi
+    fi
-    
-   # Getting newest boost
-  - if [[ ${TRAVIS_OS_NAME} = linux ]]; then sudo add-apt-repository -y ppa:boost-latest/ppa; fi
-  - if [[ ${TRAVIS_OS_NAME} = linux ]]; then sudo apt-get update; fi
-  - if [[ ${TRAVIS_OS_NAME} = linux ]]; then sudo apt-get install libboost1.55-all-dev; fi
-  
-  - if [[ ${TRAVIS_OS_NAME} = osx ]]; then brew update; fi
-  - if [[ ${TRAVIS_OS_NAME} = osx ]]; then brew tap homebrew/science; fi
-  - if [[ ${TRAVIS_OS_NAME} = osx ]]; then brew install tbb opencv3; fi
 
 before_script:
-  - git clone https://github.com/Itseez/opencv.git
+  - sudo make -j4
-  - cd opencv
+  - sudo make install
-  - mkdir build
-  - cd build
-  - cmake ..
-  - make -j2
-  - sudo make -j2 install
   - cd ../.. 
   
 script:
@@ -68,4 +75,5 @@ script:
   - ../build/bin/FaceLandmarkImg -inroot ../videos -f Obama.jpg -outroot data -of obama.txt -op obama.3d -oi obama.bmp -multi_view 1 -wild -q
   - ../build/bin/FaceLandmarkVidMulti -inroot ../videos -f multi_face.avi -outroot output -ov multi_face.avi -q
   - ../build/bin/FeatureExtraction -f "../videos/1815_01_008_tony_blair.avi" -outroot output_features -ov blair.avi -of "1815_01_008_tony_blair.txt" -simalign aligned -ov feat_test.avi -hogalign hog_test.dat -q
+  - ../build/bin/FeatureExtraction -f "../videos/1815_01_008_tony_blair.avi" -outroot output_features -simsize 200 -simscale 0.5 -ov blair.avi -of "1815_01_008_tony_blair.txt" -simalign aligned -ov feat_test.avi -hogalign hog_test.dat -q
   - ../build/bin/FaceLandmarkVid -inroot ../videos -f 1815_01_008_tony_blair.avi -f 0188_03_021_al_pacino.avi -f 0217_03_006_alanis_morissette.avi -outroot output_data -ov 1.avi -ov 2.avi -ov 3.avi -q

CMakeLists.txt

@@ -5,7 +5,12 @@ set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin/)
 
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/modules/")
 
+set(CMAKE_CONFIG_DIR etc/OpenFace)
+set(CONFIG_DIR "${CMAKE_INSTALL_PREFIX}/${CMAKE_CONFIG_DIR}")
+add_definitions(-DCONFIG_DIR="${CONFIG_DIR}")
+
 find_package( OpenCV REQUIRED )
+
 MESSAGE("OpenCV information:") 
 MESSAGE("  OpenCV_INCLUDE_DIRS: ${OpenCV_INCLUDE_DIRS}") 
 MESSAGE("  OpenCV_LIBRARIES: ${OpenCV_LIBRARIES}") 
@@ -33,6 +38,8 @@ foreach(file ${files})
 	else(MSVC)
 		file(COPY ${file} DESTINATION ${CMAKE_BINARY_DIR}/bin/model)
 	endif(MSVC)
+
+	install(FILES ${file} DESTINATION ${CMAKE_CONFIG_DIR}/model)
 endforeach()
 
 # Move the hierarchical LandmarkDetector models
@@ -44,6 +51,8 @@ foreach(file ${files})
 	else(MSVC)
 		file(COPY ${file} DESTINATION ${CMAKE_BINARY_DIR}/bin/model)
 	endif(MSVC)
+
+	install(DIRECTORY ${file} DESTINATION ${CMAKE_CONFIG_DIR}/model)
 endforeach()
 
 file(GLOB files "lib/local/LandmarkDetector/model/detection_validation/*.txt")
@@ -54,6 +63,8 @@ foreach(file ${files})
 	else(MSVC)
 		file(COPY ${file} DESTINATION ${CMAKE_BINARY_DIR}/bin/model/detection_validation)
 	endif(MSVC)
+
+	install(FILES ${file} DESTINATION ${CMAKE_CONFIG_DIR}/model/detection_validation)
 endforeach()
 
 file(GLOB files "lib/local/LandmarkDetector/model/patch_experts/*.txt")
@@ -64,6 +75,8 @@ foreach(file ${files})
 	else(MSVC)
 		file(COPY ${file} DESTINATION ${CMAKE_BINARY_DIR}/bin/model/patch_experts)
 	endif(MSVC)
+
+	install(FILES ${file} DESTINATION ${CMAKE_CONFIG_DIR}/model/patch_experts)
 endforeach()
 
 file(GLOB files "lib/local/LandmarkDetector/model/pdms/*.txt")
@@ -74,6 +87,8 @@ foreach(file ${files})
 	else(MSVC)
 		file(COPY ${file} DESTINATION ${CMAKE_BINARY_DIR}/bin/model/pdms)
 	endif(MSVC)
+
+	install(FILES ${file} DESTINATION ${CMAKE_CONFIG_DIR}/model/pdms)
 endforeach()
 
 # Move OpenCV classifiers
@@ -85,6 +100,8 @@ foreach(file ${files})
 	else(MSVC)
 		file(COPY ${file} DESTINATION ${CMAKE_BINARY_DIR}/bin/classifiers)
 	endif(MSVC)
+
+	install(FILES ${file} DESTINATION ${CMAKE_CONFIG_DIR}/classifiers)
 endforeach()
 
 # Move AU prediction modules
@@ -96,6 +113,8 @@ foreach(file ${files})
 	else(MSVC)
 		file(COPY ${file} DESTINATION ${CMAKE_BINARY_DIR}/bin/AU_predictors)
 	endif(MSVC)
+
+	install(FILES ${file} DESTINATION ${CMAKE_CONFIG_DIR}/AU_predictors)
 endforeach()
 
 # Move AU prediction modules
@@ -107,6 +126,8 @@ foreach(file ${files})
 	else(MSVC)
 		file(COPY ${file} DESTINATION ${CMAKE_BINARY_DIR}/bin/AU_predictors)
 	endif(MSVC)
+
+	install(DIRECTORY ${file} DESTINATION ${CMAKE_CONFIG_DIR}/AU_predictors)
 endforeach()
 
 # Move AU prediction modules
@@ -118,6 +139,8 @@ foreach(file ${files})
 	else(MSVC)
 		file(COPY ${file} DESTINATION ${CMAKE_BINARY_DIR}/bin/AU_predictors)
 	endif(MSVC)
+
+	install(DIRECTORY ${file} DESTINATION ${CMAKE_CONFIG_DIR}/AU_predictors)
 endforeach()
 
 if (${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")

README.md

@@ -9,7 +9,8 @@ The code was written mainly by Tadas Baltrusaitis during his time at the Languag
 
 Special thanks goes to Louis-Philippe Morency and his MultiComp Lab at Institute for Creative Technologies for help in writing and testing the code, and Erroll Wood for the gaze estimation work.
 
-**For instructions of how to install/compile/use the project please see [wiki](https://github.com/TadasBaltrusaitis/OpenFace/wiki)**
+## WIKI
+**For instructions of how to install/compile/use the project please see [WIKI](https://github.com/TadasBaltrusaitis/OpenFace/wiki)**
 
 More details about the project - http://www.cl.cam.ac.uk/research/rainbow/projects/openface/
 

appveyor.yml

@@ -25,4 +25,5 @@ test_script:
   - cmd: if exist "../videos" (FaceLandmarkImg.exe -inroot ../videos -f obama.jpg -outroot out_data -of obama.pts -op obama.3d -oi obama.bmp -q) else (FaceLandmarkImg.exe -inroot ../../videos -f obama.jpg -outroot out_data -of obama.pts -op obama.3d -oi obama.bmp -q)
   - cmd: if exist "../videos" (FaceLandmarkVidMulti.exe -inroot ../videos -f multi_face.avi -ov multi_face.avi -q) else (FaceLandmarkVidMulti.exe -inroot ../../videos -f multi_face.avi -ov multi_face.avi -q)
   - cmd: if exist "../videos" (FeatureExtraction.exe -f "../videos/1815_01_008_tony_blair.avi" -outroot output_features -of "1815_01_008_tony_blair.txt" -simalign aligned -ov feat_track.avi -hogalign hog_test.dat -q) else (FeatureExtraction.exe -f "../../videos/1815_01_008_tony_blair.avi" -outroot output_features -of "1815_01_008_tony_blair.txt" -simalign aligned -ov feat_track.avi -hogalign hog_test.dat -q)
+  - cmd: if exist "../videos" (FeatureExtraction.exe -f "../videos/1815_01_008_tony_blair.avi" -outroot output_features -of "1815_01_008_tony_blair.txt" -simalign aligned -simsize 200 -simscale 0.5 -ov feat_track.avi -hogalign hog_test.dat -q) else (FeatureExtraction.exe -f "../../videos/1815_01_008_tony_blair.avi" -outroot output_features -of "1815_01_008_tony_blair.txt" -simalign aligned -simsize 200 -simscale 0.5 -ov feat_track.avi -hogalign hog_test.dat -q)
   - cmd: if exist "../videos" (FaceLandmarkVid.exe -f "../videos/1815_01_008_tony_blair.avi" -ov track.avi -q) else (FaceLandmarkVid.exe -f "../../videos/1815_01_008_tony_blair.avi" -ov track.avi -q)

exe/FaceLandmarkImg/FaceLandmarkImg.cpp

@@ -78,6 +78,10 @@
 #include <FaceAnalyser.h>
 #include <GazeEstimation.h>
 
+#ifndef CONFIG_DIR
+#define CONFIG_DIR "~"
+#endif
+
 using namespace std;
 
 vector<string> get_arguments(int argc, char **argv)
@@ -317,6 +321,10 @@ int main (int argc, char **argv)
 	//Convert arguments to more convenient vector form
 	vector<string> arguments = get_arguments(argc, argv);
 
+	// Search paths
+	boost::filesystem::path config_path = boost::filesystem::path(CONFIG_DIR);
+	boost::filesystem::path parent_path = boost::filesystem::path(arguments[0]).parent_path();
+
 	// Some initial parameters that can be overriden from command line
 	vector<string> files, depth_files, output_images, output_landmark_locations, output_pose_locations;
 
@@ -356,38 +364,44 @@ int main (int argc, char **argv)
 	// Loading the AU prediction models
 	string au_loc = "AU_predictors/AU_all_static.txt";
 
-	if (!boost::filesystem::exists(boost::filesystem::path(au_loc)))
+	boost::filesystem::path au_loc_path = boost::filesystem::path(au_loc);
+	if (boost::filesystem::exists(au_loc_path))
 	{
-		boost::filesystem::path loc = boost::filesystem::path(arguments[0]).parent_path() / au_loc;
+		au_loc = au_loc_path.string();
-
+	}
-		if (boost::filesystem::exists(loc))
+	else if (boost::filesystem::exists(parent_path/au_loc_path))
-		{
+	{
-			au_loc = loc.string();
+		au_loc = (parent_path/au_loc_path).string();
-		}
+	}
-		else
+	else if (boost::filesystem::exists(config_path/au_loc_path))
-		{
+	{
-			cout << "Can't find AU prediction files, exiting" << endl;
+		au_loc = (config_path/au_loc_path).string();
-			return 1;
+	}
-		}
+	else
+	{
+		cout << "Can't find AU prediction files, exiting" << endl;
+		return 1;
 	}
 
 	// Used for image masking for AUs
 	string tri_loc;
-	if (boost::filesystem::exists(boost::filesystem::path("model/tris_68_full.txt")))
+	boost::filesystem::path tri_loc_path = boost::filesystem::path("model/tris_68_full.txt");
+	if (boost::filesystem::exists(tri_loc_path))
 	{
-		std::ifstream triangulation_file("model/tris_68_full.txt");
+		tri_loc = tri_loc_path.string();
-		tri_loc = "model/tris_68_full.txt";
+	}
+	else if (boost::filesystem::exists(parent_path/tri_loc_path))
+	{
+		tri_loc = (parent_path/tri_loc_path).string();
+	}
+	else if (boost::filesystem::exists(config_path/tri_loc_path))
+	{
+		tri_loc = (config_path/tri_loc_path).string();
 	}
 	else
 	{
-		boost::filesystem::path loc = boost::filesystem::path(arguments[0]).parent_path() / "model/tris_68_full.txt";
+		cout << "Can't find triangulation files, exiting" << endl;
-		tri_loc = loc.string();
+		return 1;
-
-		if (!exists(loc))
-		{
-			cout << "Can't find triangulation files, exiting" << endl;
-			return 1;
-		}
 	}
 
 	FaceAnalysis::FaceAnalyser face_analyser(vector<cv::Vec3d>(), 0.7, 112, 112, au_loc, tri_loc);

exe/FeatureExtraction/CMakeLists.txt

@@ -14,3 +14,5 @@ target_link_libraries(FeatureExtraction FaceAnalyser)
 target_link_libraries(FeatureExtraction dlib)
 
 target_link_libraries(FeatureExtraction ${OpenCV_LIBS} ${Boost_LIBRARIES} ${TBB_LIBRARIES})
+
+install (TARGETS FeatureExtraction DESTINATION bin)

exe/FeatureExtraction/FeatureExtraction.cpp

@@ -2,7 +2,7 @@
 // Copyright (C) 2016, Carnegie Mellon University and University of Cambridge,
 // all rights reserved.
 //
-// THIS SOFTWARE IS PROVIDED “AS IS” FOR ACADEMIC USE ONLY AND ANY EXPRESS
+// THIS SOFTWARE IS PROVIDED “AS IS” FOR ACADEMIC USE ONLY AND ANY EXPRESS
 // OR IMPLIED WARRANTIES WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
 // THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
 // PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS
@@ -15,13 +15,13 @@
 // POSSIBILITY OF SUCH DAMAGE.
 //
 // Notwithstanding the license granted herein, Licensee acknowledges that certain components
-// of the Software may be covered by so-called “open source” software licenses (“Open Source
+// of the Software may be covered by so-called “open source” software licenses (“Open Source
-// Components”), which means any software licenses approved as open source licenses by the
+// Components”), which means any software licenses approved as open source licenses by the
 // Open Source Initiative or any substantially similar licenses, including without limitation any
 // license that, as a condition of distribution of the software licensed under such license,
 // requires that the distributor make the software available in source code format. Licensor shall
 // provide a list of Open Source Components for a particular version of the Software upon
-// Licensee’s request. Licensee will comply with the applicable terms of such licenses and to
+// Licensee’s request. Licensee will comply with the applicable terms of such licenses and to
 // the extent required by the licenses covering Open Source Components, the terms of such
 // licenses will apply in lieu of the terms of this Agreement. To the extent the terms of the
 // licenses applicable to Open Source Components prohibit any of the restrictions in this
@@ -38,20 +38,20 @@
 //       reports and manuals, must cite at least one of the following works:
 //
 //       OpenFace: an open source facial behavior analysis toolkit
-//       Tadas Baltrušaitis, Peter Robinson, and Louis-Philippe Morency
+//       Tadas Baltrušaitis, Peter Robinson, and Louis-Philippe Morency
 //       in IEEE Winter Conference on Applications of Computer Vision, 2016  
 //
 //       Rendering of Eyes for Eye-Shape Registration and Gaze Estimation
-//       Erroll Wood, Tadas Baltrušaitis, Xucong Zhang, Yusuke Sugano, Peter Robinson, and Andreas Bulling 
+//       Erroll Wood, Tadas Baltrušaitis, Xucong Zhang, Yusuke Sugano, Peter Robinson, and Andreas Bulling 
 //       in IEEE International. Conference on Computer Vision (ICCV),  2015 
 //
 //       Cross-dataset learning and person-speci?c normalisation for automatic Action Unit detection
-//       Tadas Baltrušaitis, Marwa Mahmoud, and Peter Robinson 
+//       Tadas Baltrušaitis, Marwa Mahmoud, and Peter Robinson 
 //       in Facial Expression Recognition and Analysis Challenge, 
 //       IEEE International Conference on Automatic Face and Gesture Recognition, 2015 
 //
 //       Constrained Local Neural Fields for robust facial landmark detection in the wild.
-//       Tadas Baltrušaitis, Peter Robinson, and Louis-Philippe Morency. 
+//       Tadas Baltrušaitis, Peter Robinson, and Louis-Philippe Morency. 
 //       in IEEE Int. Conference on Computer Vision Workshops, 300 Faces in-the-Wild Challenge, 2013.    
 //
 ///////////////////////////////////////////////////////////////////////////////
@@ -81,6 +81,9 @@
 #include <FaceAnalyser.h>
 #include <GazeEstimation.h>
 
+#ifndef CONFIG_DIR
+#define CONFIG_DIR "~"
+#endif
 
 #define INFO_STREAM( stream ) \
 std::cout << stream << std::endl
@@ -239,6 +242,10 @@ int main (int argc, char **argv)
 
 	vector<string> arguments = get_arguments(argc, argv);
 
+	// Search paths
+	boost::filesystem::path config_path = boost::filesystem::path(CONFIG_DIR);
+	boost::filesystem::path parent_path = boost::filesystem::path(arguments[0]).parent_path();
+
 	// Some initial parameters that can be overriden from command line	
 	vector<string> input_files, depth_directories, output_files, tracked_videos_output;
 	
@@ -317,24 +324,25 @@ int main (int argc, char **argv)
 	get_output_feature_params(output_similarity_align, output_hog_align_files, sim_scale, sim_size, grayscale, verbose, dynamic,
 		output_2D_landmarks, output_3D_landmarks, output_model_params, output_pose, output_AUs, output_gaze, arguments);
 
-
 	// Used for image masking
-
 	string tri_loc;
-	if(boost::filesystem::exists(path("model/tris_68_full.txt")))
+	boost::filesystem::path tri_loc_path = boost::filesystem::path("model/tris_68_full.txt");
+	if (boost::filesystem::exists(tri_loc_path))
 	{
-		tri_loc = "model/tris_68_full.txt";
+		tri_loc = tri_loc_path.string();
+	}
+	else if (boost::filesystem::exists(parent_path/tri_loc_path))
+	{
+		tri_loc = (parent_path/tri_loc_path).string();
+	}
+	else if (boost::filesystem::exists(config_path/tri_loc_path))
+	{
+		tri_loc = (config_path/tri_loc_path).string();
 	}
 	else
 	{
-		path loc = path(arguments[0]).parent_path() / "model/tris_68_full.txt";
+		cout << "Can't find triangulation files, exiting" << endl;
-		tri_loc = loc.string();
+		return 1;
-
-		if(!exists(loc))
-		{
-			cout << "Can't find triangulation files, exiting" << endl;
-			return 1;
-		}
 	}
 
 	// If multiple video files are tracked, use this to indicate if we are done
@@ -354,23 +362,23 @@ int main (int argc, char **argv)
 		au_loc_local = "AU_predictors/AU_all_static.txt";
 	}
 
-	if(boost::filesystem::exists(path(au_loc_local)))
+	boost::filesystem::path au_loc_path = boost::filesystem::path(au_loc_local);
+	if (boost::filesystem::exists(au_loc_path))
 	{
-		au_loc = au_loc_local;
+		au_loc = au_loc_path.string();
+	}
+	else if (boost::filesystem::exists(parent_path/au_loc_path))
+	{
+		au_loc = (parent_path/au_loc_path).string();
+	}
+	else if (boost::filesystem::exists(config_path/au_loc_path))
+	{
+		au_loc = (config_path/au_loc_path).string();
 	}
 	else
 	{
-		path loc = path(arguments[0]).parent_path() / au_loc_local;
+		cout << "Can't find AU prediction files, exiting" << endl;
-
+		return 1;
-		if(exists(loc))
-		{
-			au_loc = loc.string();
-		}
-		else
-		{
-			cout << "Can't find AU prediction files, exiting" << endl;
-			return 1;
-		}
 	}
 
 	// Creating a  face analyser that will be used for AU extraction
@@ -597,13 +605,13 @@ int main (int argc, char **argv)
 			}
 
 
-			if(hog_output_file.is_open())
+			if (hog_output_file.is_open())
 			{
 				output_HOG_frame(&hog_output_file, detection_success, hog_descriptor, num_hog_rows, num_hog_cols);
 			}
 
 			// Write the similarity normalised output
-			if(!output_similarity_align.empty())
+			if (!output_similarity_align.empty())
 			{
 
 				if (sim_warped_img.channels() == 3 && grayscale)
@@ -662,18 +670,22 @@ int main (int argc, char **argv)
 					captured_image = cv::Mat();
 				}
 			}
-			// detect key presses
-			char character_press = cv::waitKey(1);
 			
-			// restart the tracker
+			if (!det_parameters.quiet_mode)
-			if(character_press == 'r')
 			{
-				face_model.Reset();
+				// detect key presses
-			}
+				char character_press = cv::waitKey(1);
-			// quit the application
+			
-			else if(character_press=='q')
+				// restart the tracker
-			{
+				if(character_press == 'r')
-				return(0);
+				{
+					face_model.Reset();
+				}
+				// quit the application
+				else if(character_press=='q')
+				{
+					return(0);
+				}
 			}
 			
 			// Update the frame count
@@ -692,7 +704,7 @@ int main (int argc, char **argv)
 		
 		output_file.close();
 
-		if(output_files.size() > 0 && output_AUs)
+		if (output_files.size() > 0 && output_AUs)
 		{
 			cout << "Postprocessing the Action Unit predictions" << endl;
 			face_analyser.PostprocessOutputFile(output_files[f_n], dynamic);
@@ -1113,6 +1125,7 @@ void get_output_feature_params(vector<string> &output_similarity_aligned, vector
 
 }
 
+
 // Can process images via directories creating a separate output file per directory
 void get_image_input_output_params_feats(vector<vector<string> > &input_image_files, bool& as_video, vector<string> &arguments)
 {

install.sh

@@ -0,0 +1,86 @@
+#!/bin/bash
+#==============================================================================
+# Title: install.sh
+# Description: Install everything necessary for OpenFace to compile.
+# Author: Daniyal Shahrokhian <daniyal@kth.se>
+# Date: 20170310
+# Version : 1.0
+# Usage: bash install.sh <directory in which you want the project to be installed>
+# NOTES: There are certain steps to be taken in the system before installing 
+#        via this script (refer to README): Run 
+#        `sudo gedit /etc/apt/sources.list` and change the line 
+#        `deb http://us.archive.ubuntu.com/ubuntu/ xenial main restricted` to 
+#        `deb http://us.archive.ubuntu.com/ubuntu/ xenial main universe`
+#==============================================================================
+
+# Exit script if any command fails
+set -e 
+set -o pipefail
+
+if [ $# -ne 1 ]
+  then
+    echo "Usage: install.sh <directory in which you want the project to be installed>"
+    exit 1
+fi
+
+DIRECTORY="$1"
+cd "$DIRECTORY"
+echo "Installation under ${DIRECTORY}"
+
+# Essential Dependencies
+echo "Installing Essential dependencies..."
+sudo apt-get update
+sudo apt-get install build-essential
+sudo apt-get install llvm
+
+sudo apt-get update
+sudo apt-get install clang-3.7 libc++-dev libc++abi-dev
+sudo apt-get install cmake
+sudo apt-get install libopenblas-dev liblapack-dev
+sudo apt-get install git libgtk2.0-dev pkg-config libavcodec-dev libavformat-dev libswscale-dev
+sudo apt-get install python-dev python-numpy libtbb2 libtbb-dev libjpeg-dev libpng-dev libtiff-dev libjasper-dev libdc1394-22-dev checkinstall
+echo "Essential dependencies installed."
+
+# OpenCV Dependency
+echo "Downloading OpenCV..."
+if [ -d "opencv-3.1.0" ]; then
+  sudo rm -r "opencv-3.1.0"
+fi
+
+wget https://github.com/Itseez/opencv/archive/3.1.0.zip
+unzip 3.1.0.zip
+rm 3.1.0.zip
+cd opencv-3.1.0
+mkdir build
+cd build
+echo "Installing OpenCV..."
+cmake -D CMAKE_BUILD_TYPE=RELEASE -D CMAKE_INSTALL_PREFIX=/usr/local -D WITH_TBB=ON -D BUILD_SHARED_LIBS=OFF ..
+make -j4
+sudo make install
+cd "../.."
+echo "OpenCV installed."
+
+# Boost C++ Dependency
+echo "Installing Boost..."
+sudo apt-get install libboost-all-dev
+echo "Boost installed."
+
+# OpenFace installation
+echo "Downloading OpenFace..."
+if [ -d "OpenFace" ]; then
+  sudo rm -r "OpenFace"
+fi
+
+git clone https://github.com/TadasBaltrusaitis/OpenFace.git
+cd OpenFace
+mkdir build
+cd build
+echo "Installing OpenFace..."
+cmake -D CMAKE_BUILD_TYPE=RELEASE ..
+make
+echo "OpenFace installed."
+
+# Installation test
+echo "Testing installation..."
+./bin/FaceLandmarkVid -f "../videos/changeLighting.wmv"
+echo "Installation tested."

lib/local/FaceAnalyser/CMakeLists.txt

@@ -29,5 +29,5 @@ include_directories(../LandmarkDetector/include)
 
 add_library( FaceAnalyser ${SOURCE} ${HEADERS})
 
-install (TARGETS FaceAnalyser DESTINATION bin)
+install (TARGETS FaceAnalyser DESTINATION lib)
-install (FILES ${HEADERS} DESTINATION include)
+install (FILES ${HEADERS} DESTINATION include/OpenFace)

lib/local/FaceAnalyser/src/Face_utils.cpp

@@ -221,19 +221,19 @@ namespace FaceAnalysis
 		destination_landmarks.col(1) = destination_landmarks.col(1) + warp_matrix(1,2);
 		
 		// Move the eyebrows up to include more of upper face
-		destination_landmarks.at<double>(0,1) -= 30; 
+		destination_landmarks.at<double>(0,1) -= (30/0.7)*sim_scale; 
-		destination_landmarks.at<double>(16,1) -= 30;
+		destination_landmarks.at<double>(16,1) -= (30 / 0.7)*sim_scale;
 
-		destination_landmarks.at<double>(17,1) -= 30;
+		destination_landmarks.at<double>(17,1) -= (30 / 0.7)*sim_scale;
-		destination_landmarks.at<double>(18,1) -= 30;
+		destination_landmarks.at<double>(18,1) -= (30 / 0.7)*sim_scale;
-		destination_landmarks.at<double>(19,1) -= 30;
+		destination_landmarks.at<double>(19,1) -= (30 / 0.7)*sim_scale;
-		destination_landmarks.at<double>(20,1) -= 30;
+		destination_landmarks.at<double>(20,1) -= (30 / 0.7)*sim_scale;
-		destination_landmarks.at<double>(21,1) -= 30;
+		destination_landmarks.at<double>(21,1) -= (30 / 0.7)*sim_scale;
-		destination_landmarks.at<double>(22,1) -= 30;
+		destination_landmarks.at<double>(22,1) -= (30 / 0.7)*sim_scale;
-		destination_landmarks.at<double>(23,1) -= 30;
+		destination_landmarks.at<double>(23,1) -= (30 / 0.7)*sim_scale;
-		destination_landmarks.at<double>(24,1) -= 30;
+		destination_landmarks.at<double>(24,1) -= (30 / 0.7)*sim_scale;
-		destination_landmarks.at<double>(25,1) -= 30;
+		destination_landmarks.at<double>(25,1) -= (30 / 0.7)*sim_scale;
-		destination_landmarks.at<double>(26,1) -= 30;
+		destination_landmarks.at<double>(26,1) -= (30 / 0.7)*sim_scale;
 
 		destination_landmarks = cv::Mat(destination_landmarks.t()).reshape(1, 1).t();
 

lib/local/LandmarkDetector/CMakeLists.txt

@@ -35,7 +35,7 @@ SET(HEADERS
 include_directories(./include)
 include_directories(${LandmarkDetector_SOURCE_DIR}/include)
 
-add_library( LandmarkDetector ${SOURCE} ${HEADERS})
+add_library( LandmarkDetector ${SOURCE} ${HEADERS} )
 
-install (TARGETS LandmarkDetector DESTINATION bin)
+install (TARGETS LandmarkDetector DESTINATION lib)
-install (FILES ${HEADERS} DESTINATION include)
+install (FILES ${HEADERS} DESTINATION include/OpenFace)

lib/local/LandmarkDetector/include/LandmarkDetectorModel.h

@@ -2,7 +2,7 @@
 // Copyright (C) 2016, Carnegie Mellon University and University of Cambridge,
 // all rights reserved.
 //
-// THIS SOFTWARE IS PROVIDED “AS IS” FOR ACADEMIC USE ONLY AND ANY EXPRESS
+// THIS SOFTWARE IS PROVIDED “AS IS” FOR ACADEMIC USE ONLY AND ANY EXPRESS
 // OR IMPLIED WARRANTIES WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
 // THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
 // PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS
@@ -15,13 +15,13 @@
 // POSSIBILITY OF SUCH DAMAGE.
 //
 // Notwithstanding the license granted herein, Licensee acknowledges that certain components
-// of the Software may be covered by so-called “open source” software licenses (“Open Source
+// of the Software may be covered by so-called “open source” software licenses (“Open Source
-// Components”), which means any software licenses approved as open source licenses by the
+// Components”), which means any software licenses approved as open source licenses by the
 // Open Source Initiative or any substantially similar licenses, including without limitation any
 // license that, as a condition of distribution of the software licensed under such license,
 // requires that the distributor make the software available in source code format. Licensor shall
 // provide a list of Open Source Components for a particular version of the Software upon
-// Licensee’s request. Licensee will comply with the applicable terms of such licenses and to
+// Licensee’s request. Licensee will comply with the applicable terms of such licenses and to
 // the extent required by the licenses covering Open Source Components, the terms of such
 // licenses will apply in lieu of the terms of this Agreement. To the extent the terms of the
 // licenses applicable to Open Source Components prohibit any of the restrictions in this
@@ -38,20 +38,20 @@
 //       reports and manuals, must cite at least one of the following works:
 //
 //       OpenFace: an open source facial behavior analysis toolkit
-//       Tadas Baltrušaitis, Peter Robinson, and Louis-Philippe Morency
+//       Tadas Baltrušaitis, Peter Robinson, and Louis-Philippe Morency
 //       in IEEE Winter Conference on Applications of Computer Vision, 2016  
 //
 //       Rendering of Eyes for Eye-Shape Registration and Gaze Estimation
-//       Erroll Wood, Tadas Baltrušaitis, Xucong Zhang, Yusuke Sugano, Peter Robinson, and Andreas Bulling 
+//       Erroll Wood, Tadas Baltrušaitis, Xucong Zhang, Yusuke Sugano, Peter Robinson, and Andreas Bulling 
 //       in IEEE International. Conference on Computer Vision (ICCV),  2015 
 //
 //       Cross-dataset learning and person-speci?c normalisation for automatic Action Unit detection
-//       Tadas Baltrušaitis, Marwa Mahmoud, and Peter Robinson 
+//       Tadas Baltrušaitis, Marwa Mahmoud, and Peter Robinson 
 //       in Facial Expression Recognition and Analysis Challenge, 
 //       IEEE International Conference on Automatic Face and Gesture Recognition, 2015 
 //
 //       Constrained Local Neural Fields for robust facial landmark detection in the wild.
-//       Tadas Baltrušaitis, Peter Robinson, and Louis-Philippe Morency. 
+//       Tadas Baltrušaitis, Peter Robinson, and Louis-Philippe Morency. 
 //       in IEEE Int. Conference on Computer Vision Workshops, 300 Faces in-the-Wild Challenge, 2013.    
 //
 ///////////////////////////////////////////////////////////////////////////////
@@ -130,7 +130,7 @@ public:
 	double				detection_certainty; 
 
 	// Indicator if eye model is there for eye detection
-	bool				eye_model = false;
+	bool				eye_model;
 
 	// the triangulation per each view (for drawing purposes only)
 	vector<cv::Mat_<int> >	triangulations;

lib/local/LandmarkDetector/src/LandmarkDetectorFunc.cpp

@@ -408,7 +408,7 @@ bool LandmarkDetector::DetectLandmarksInVideo(const cv::Mat_<uchar> &grayscale_i
 
 bool LandmarkDetector::DetectLandmarksInVideo(const cv::Mat_<uchar> &grayscale_image, const cv::Rect_<double> bounding_box, CLNF& clnf_model, FaceModelParameters& params)
 {
-	return DetectLandmarksInVideo(grayscale_image, cv::Mat_<float>(), clnf_model, params);
+	return DetectLandmarksInVideo(grayscale_image, cv::Mat_<float>(), bounding_box, clnf_model, params);
 }
 
 //================================================================================================================

lib/local/LandmarkDetector/src/LandmarkDetectorModel.cpp

@@ -2,7 +2,7 @@
 // Copyright (C) 2016, Carnegie Mellon University and University of Cambridge,
 // all rights reserved.
 //
-// THIS SOFTWARE IS PROVIDED “AS IS” FOR ACADEMIC USE ONLY AND ANY EXPRESS
+// THIS SOFTWARE IS PROVIDED “AS IS” FOR ACADEMIC USE ONLY AND ANY EXPRESS
 // OR IMPLIED WARRANTIES WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
 // THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
 // PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS
@@ -15,13 +15,13 @@
 // POSSIBILITY OF SUCH DAMAGE.
 //
 // Notwithstanding the license granted herein, Licensee acknowledges that certain components
-// of the Software may be covered by so-called “open source” software licenses (“Open Source
+// of the Software may be covered by so-called “open source” software licenses (“Open Source
-// Components”), which means any software licenses approved as open source licenses by the
+// Components”), which means any software licenses approved as open source licenses by the
 // Open Source Initiative or any substantially similar licenses, including without limitation any
 // license that, as a condition of distribution of the software licensed under such license,
 // requires that the distributor make the software available in source code format. Licensor shall
 // provide a list of Open Source Components for a particular version of the Software upon
-// Licensee’s request. Licensee will comply with the applicable terms of such licenses and to
+// Licensee’s request. Licensee will comply with the applicable terms of such licenses and to
 // the extent required by the licenses covering Open Source Components, the terms of such
 // licenses will apply in lieu of the terms of this Agreement. To the extent the terms of the
 // licenses applicable to Open Source Components prohibit any of the restrictions in this
@@ -38,20 +38,20 @@
 //       reports and manuals, must cite at least one of the following works:
 //
 //       OpenFace: an open source facial behavior analysis toolkit
-//       Tadas Baltrušaitis, Peter Robinson, and Louis-Philippe Morency
+//       Tadas Baltrušaitis, Peter Robinson, and Louis-Philippe Morency
 //       in IEEE Winter Conference on Applications of Computer Vision, 2016  
 //
 //       Rendering of Eyes for Eye-Shape Registration and Gaze Estimation
-//       Erroll Wood, Tadas Baltrušaitis, Xucong Zhang, Yusuke Sugano, Peter Robinson, and Andreas Bulling 
+//       Erroll Wood, Tadas Baltrušaitis, Xucong Zhang, Yusuke Sugano, Peter Robinson, and Andreas Bulling 
 //       in IEEE International. Conference on Computer Vision (ICCV),  2015 
 //
 //       Cross-dataset learning and person-speci?c normalisation for automatic Action Unit detection
-//       Tadas Baltrušaitis, Marwa Mahmoud, and Peter Robinson 
+//       Tadas Baltrušaitis, Marwa Mahmoud, and Peter Robinson 
 //       in Facial Expression Recognition and Analysis Challenge, 
 //       IEEE International Conference on Automatic Face and Gesture Recognition, 2015 
 //
 //       Constrained Local Neural Fields for robust facial landmark detection in the wild.
-//       Tadas Baltrušaitis, Peter Robinson, and Louis-Philippe Morency. 
+//       Tadas Baltrušaitis, Peter Robinson, and Louis-Philippe Morency. 
 //       in IEEE Int. Conference on Computer Vision Workshops, 300 Faces in-the-Wild Challenge, 2013.    
 //
 ///////////////////////////////////////////////////////////////////////////////
@@ -378,6 +378,9 @@ void CLNF::Read(string main_location)
 	detect_Z_max = -1;
 	detect_ROI = cv::Rect_<double>(0, 0, 1, 1);
 
+	// Assume no eye model, unless read-in
+	eye_model = false;
+
 	// The main file contains the references to other files
 	while (!locations.eof())
 	{ 
@@ -399,6 +402,7 @@ void CLNF::Read(string main_location)
 			location = location.substr(0, location.size()-1);
 		}
 
+
 		// append to root
 		location = (root / location).string();
 		if (module.compare("LandmarkDetector") == 0) 

lib/local/LandmarkDetector/src/LandmarkDetectorParameters.cpp

@@ -67,6 +67,11 @@
 // System includes
 #include <sstream>
 #include <iostream>
+#include <cstdlib>
+
+#ifndef CONFIG_DIR
+#define CONFIG_DIR "~"
+#endif
 
 using namespace std;
 
@@ -200,15 +205,25 @@ FaceModelParameters::FaceModelParameters(vector<string> &arguments)
 	}
 
 	// Make sure model_location is valid
-	if (!boost::filesystem::exists(boost::filesystem::path(model_location)))
+	// First check working directory, then the executable's directory, then the config path set by the build process.
+	boost::filesystem::path config_path = boost::filesystem::path(CONFIG_DIR);
+	boost::filesystem::path model_path = boost::filesystem::path(model_location);
+	if (boost::filesystem::exists(model_path))
 	{
-		model_location = (root / model_location).string();
+		model_location = model_path.string();
-		if (!boost::filesystem::exists(boost::filesystem::path(model_location)))
+	}
-		{
+	else if (boost::filesystem::exists(root/model_path))
-			std::cout << "Could not find the landmark detection model to load" << std::endl;
+	{
-		}
+		model_location = (root/model_path).string();
+	}
+	else if (boost::filesystem::exists(config_path/model_path))
+	{
+		model_location = (config_path/model_path).string();
+	}
+	else
+	{
+		std::cout << "Could not find the landmark detection model to load" << std::endl;
 	}
-
 }
 
 void FaceModelParameters::init()

matlab_runners/Action Unit Experiments/helpers/ParseSEMAINEAnnotations.m

@@ -0,0 +1,181 @@
+
+% Function ParseSEMAINEAnnotations is intended to demonstrate example usage
+% of SEMAINE Action Unit annotations made with ELAN annotation toolbox.
+% This function loads the XML structure from an ELAN annotation file with
+% ".eaf" extension, parses it and returns a numerical matrix called
+% "activations" of size NUMBER OF FRAMES X NUMBER OF ACTION UNITS. The
+% matrix holds binary activation status for each frame / AU combination.
+% The matrix also has a row header showing which AU corresponds to which
+% row as well as a column header displaying original frame indexes.
+
+% The function takes 1 compulsory and 2 optional arguments: 
+
+% - "filepath" (compulsory) - complete path to an annotation file to parse.
+% For example, "/matlab/annotation.eaf" or "C:\matlab\annotation.eaf" on
+% Windows.
+
+% - "startFrame" (optional) - ignore all annotations before "startFrame".
+% Default is 1.
+
+% - "endFrame" (optional) - ignore all annotations after "endFrame".
+% Default is the last frame of a video.
+
+% The function requires XML IO Toolbox
+% (http://www.mathworks.com/matlabcentral/fileexchange/12907-xml-io-tools)
+% to run properly (supplied).
+
+function activations = ParseSEMAINEAnnotations (filepath, startFrame, endFrame)
+    activations = [];
+
+    % Framerate value used to convert ELAN millisecond time slots to more
+    % usual frames. 50 is a valid framerate for all SEMAINE videos.
+    framerate = 50;
+
+    % A fixed set of 6 Action Units selected for the challenge from the
+    % SEMAINE annotations
+    aus = [2 12 17 25 28 45];
+    
+    % Total number of AUs.
+	naus = length(aus);
+    
+    % Load XML structure from the file, return in case of a problem.
+    [success, XML] = OpenXML(filepath);
+    if ~success
+		return
+    end
+    
+    % Parse annotation time slots
+    tslots = ParseTimeSlots(XML);
+    
+    % Init start and end frames with default values
+    if nargin < 2
+        startFrame = 1;
+    end
+    
+    if nargin < 3
+        % Get total number of time slots
+        ntslots = length(tslots);
+        % Get last slot ID        
+        lastID = strcat('ts', num2str(ntslots));
+        % Get last time slot value in ms
+        lastValue = tslots(lastID);
+        % Convert last time slot value in ms to frames
+        endFrame = floor((lastValue / 1000) * framerate);
+    end
+    
+    % Get total number of tiers. There are 65 of them, 1 for speech, 32 for
+    % activations (1 per AU) and 32 for intensities. We are going to ignore
+    % intensity tiers.
+    ntiers = length(XML.TIER);
+    
+    % Compose vector of frame indexes to extract annotations from
+	frames = (startFrame:endFrame);
+    
+    % Preallocate activations matrix
+    activations = zeros(length(frames), naus);
+    
+    indx = 1;
+    % Go through all tiers skipping the first one (speech) as well as every
+    % intensity tier. A single activation tier is processed at every
+    % iteration.
+    for k = 2:2:ntiers
+		tier = XML.TIER(k);
+        % Only extract annotations of selected AUs, skip the rest
+        au = strcat('AU', num2str(aus(indx)));
+        if strcmp(au, tier.ATTRIBUTE.TIER_ID)
+            % Read all activation periods from the current tier
+            activationTier = ParseActivationTier(tier, tslots);
+            % Convert of all activation periods into frame level numerical
+            % representation
+            activations(:, indx) = ParseOccurrences(activationTier, frames, framerate);
+
+            indx = indx + 1;
+        end
+        
+        if indx > naus
+            break
+        end
+    end
+    
+    activations = [frames' activations];
+    activations = [[0 aus]; activations];
+end
+
+function occurrences = ParseOccurrences (activations, frames, framerate)
+    % Preallocate activations vector
+    occurrences = zeros(length(frames), 1);
+    % Go through all activation periods, convert ms into frames and init
+    % corresponding values of activations vector with 1 leaving the rest be 0
+	for i = 1:length(activations)
+        % Convert ms into frames 
+		sframe = floor((activations(i).start / 1000) * framerate);
+		eframe = floor((activations(i).end / 1000) * framerate);
+
+        % Determine indexes of frames vector corresponding to the above
+        % time frame
+		sindx = find(frames == sframe);
+		eindx = find(frames == eframe);
+
+        % Mark active set of frames with 1
+		occurrences(sindx:eindx) = 1;
+	end
+end
+
+function activationTier = ParseActivationTier (tier, tslots)
+    % Get total number of activation periods
+    nactivations = length(tier.ANNOTATION);
+    % Preallocate activation tier structure holding start and end time
+    % stamps of all activation periods for the given AU
+	activationTier = repmat(struct('start', 0, 'end', 0), nactivations, 1);
+    % Go through all activation periods and init activation tier
+    % structure array
+    for i = 1:nactivations
+        % Read start time slot ID of the current activation period
+		t = tier.ANNOTATION(i).ALIGNABLE_ANNOTATION.ATTRIBUTE.TIME_SLOT_REF1;
+        % Read time in ms corresponding to the time slot ID
+        activationTier(i).start = tslots(t);
+        
+        % Read end time slot ID of the current activation period
+		t = tier.ANNOTATION(i).ALIGNABLE_ANNOTATION.ATTRIBUTE.TIME_SLOT_REF2;
+        % Read time in ms corresponding to the time slot ID
+		activationTier(i).end = tslots(t);
+    end
+end
+
+function tslots = ParseTimeSlots (xmlObject)
+    % Get total number of time slots
+	nslots = length(xmlObject.TIME_ORDER.TIME_SLOT);
+    % Preallocate cell arrays of time slot IDs and values
+	tids = cell(nslots, 1);
+	tvalues = zeros(nslots, 1);
+    % Read all time slot IDs and numerical values (in ms)
+	for i = 1:nslots
+		tids{i} = xmlObject.TIME_ORDER.TIME_SLOT(i).ATTRIBUTE.TIME_SLOT_ID;
+		tvalues(i) = xmlObject.TIME_ORDER.TIME_SLOT(i).ATTRIBUTE.TIME_VALUE;
+    end
+    % Map time slot IDs and values together so that values are accessible
+    % by their IDs
+	tslots = containers.Map(tids, tvalues);
+end
+
+function [success, xmlObject] = OpenXML (xmlPath)
+	fprintf(' *** Attempting to load \"%s\" ... ', xmlPath);
+	xmlObject = [];
+    success = false;
+    % Check if the specified file exists and return error otherwise
+	if exist(xmlPath, 'file')
+        % Load XML structure
+		xmlObject = xml_read(xmlPath);
+        % Check if XML object loaded correctly, return error otherwise
+		if isempty(xmlObject)
+			fprintf(' ERROR - unable to read xml tree *** \n');
+			return
+		else
+			success = true;
+		end
+	else
+		fprintf(' ERROR - specified path does not exist *** \n');
+		return
+	end
+	fprintf(' Done *** \n');
+end

matlab_runners/Action Unit Experiments/helpers/extract_SEMAINE_labels.m

@@ -26,14 +26,9 @@ function [ labels, valid_ids, vid_ids  ] = extract_SEMAINE_labels( SEMAINE_dir,
         
         xml_file = [SEMAINE_dir, recs{i}, '\' file.name];
         [root_xml, name_xml, ~] = fileparts(xml_file);
-        m_file = [root_xml, name_xml, '.mat'];
             
-        if(~exist(m_file, 'file'))            
+        activations = ParseSEMAINEAnnotations([SEMAINE_dir, recs{i}, '/' file.name]);
-            activations = ParseSEMAINEAnnotations([SEMAINE_dir, recs{i}, '\' file.name]);
+            
-            save(m_file, 'activations');
-        else
-            load(m_file);
-        end
         if(size(activations,1) < vid_ids(i,2))
             vid_ids(i,2) = size(activations,1);
             if(vid_ids(i,2) > 2999)

matlab_runners/Action Unit Experiments/helpers/find_FERA2011.m

@@ -1,6 +1,7 @@
 if(exist('D:\Datasets\fera/au_training', 'file'))
     FERA2011_dir = 'D:\Datasets\fera/au_training/';   
-    hog_data_dir = 'D:\Datasets\face_datasets\hog_aligned_rigid/';
+elseif(exist('/multicomp/datasets/fera2011/', 'file'))
+    FERA2011_dir = '/multicomp/datasets/fera2011/au_training/';   
 else
     fprintf('FERA2011 location not found (or not defined)\n'); 
 end

matlab_runners/Action Unit Experiments/helpers/find_SEMAINE.m

@@ -10,8 +10,10 @@ elseif(exist('D:\Datasets\FERA_2015\semaine\SEMAINE-Sessions/', 'file'))
     SEMAINE_dir = 'D:\Datasets\FERA_2015\semaine\SEMAINE-Sessions/';    
 elseif(exist('D:/fera_2015/semaine/SEMAINE-Sessions/', 'file'))
     SEMAINE_dir = 'D:/fera_2015/semaine/SEMAINE-Sessions/';
+elseif(exist('/multicomp/datasets/face_datasets/FERA_2015/Semaine/SEMAINE-Sessions/', 'file'))
+    SEMAINE_dir = '/multicomp/datasets/face_datasets/FERA_2015/Semaine/SEMAINE-Sessions/';
 else
-    fprintf('DISFA location not found (or not defined)\n'); 
+    fprintf('SEMAINE location not found (or not defined)\n'); 
 end
 
 if(exist('SEMAINE_dir', 'var'))

matlab_runners/Action Unit Experiments/helpers/xml_io_tools_2010_11_05/base64decode.m

@@ -0,0 +1,117 @@
+function y = base64decode(x, outfname, alg)
+%BASE64DECODE Perform base64 decoding on a string.
+%
+% INPUT:
+%   x    - block of data to be decoded.  Can be a string or a numeric  
+%          vector containing integers in the range 0-255. Any character
+%          not part of the 65-character base64 subset set is silently
+%          ignored.  Characters occuring after a '=' padding character are 
+%          never decoded. If the length of the string to decode (after 
+%          ignoring non-base64 chars) is not a multiple of 4, then a 
+%          warning is generated.
+%
+%   outfname - if provided the binary date from decoded string will be
+%          saved into a file. Since Base64 coding is often used to embbed
+%          binary data in xml files, this option can be used to extract and
+%          save them.
+%
+%   alg  - Algorithm to use: can take values 'java' or 'matlab'. Optional
+%          variable defaulting to 'java' which is a little faster. If 
+%          'java' is chosen than core of the code is performed by a call to
+%          a java library. Optionally all operations can be performed using
+%          matleb code. 
+%
+% OUTPUT:
+%   y    - array of binary data returned as uint8 
+%
+%   This function is used to decode strings from the Base64 encoding specified
+%   in RFC 2045 - MIME (Multipurpose Internet Mail Extensions).  The Base64
+%   encoding is designed to represent arbitrary sequences of octets in a form
+%   that need not be humanly readable.  A 65-character subset ([A-Za-z0-9+/=])
+%   of US-ASCII is used, enabling 6 bits to be represented per printable
+%   character.
+%
+%   See also BASE64ENCODE.
+%
+%   Written by Jarek Tuszynski, SAIC, jaroslaw.w.tuszynski_at_saic.com
+%
+%   Matlab version based on 2004 code by Peter J. Acklam
+%   E-mail:      pjacklam@online.no
+%   URL:         http://home.online.no/~pjacklam
+%   http://home.online.no/~pjacklam/matlab/software/util/datautil/base64encode.m
+
+if nargin<3, alg='java';  end
+if nargin<2, outfname=''; end
+
+%% if x happen to be a filename than read the file
+if (numel(x)<256)
+  if (exist(x, 'file')==2)
+    fid = fopen(x,'rb');
+    x = fread(fid, 'uint8');   
+    fclose(fid);
+  end
+end
+x = uint8(x(:)); % unify format
+
+%% Perform conversion
+switch (alg)
+  case 'java' 
+    base64 = org.apache.commons.codec.binary.Base64;
+    y = base64.decode(x);
+    y = mod(int16(y),256); % convert from int8 to uint8
+  case 'matlab'
+    %%  Perform the mapping
+    %   A-Z  ->  0  - 25
+    %   a-z  ->  26 - 51
+    %   0-9  ->  52 - 61
+    %   + -  ->  62       '-' is URL_SAFE alternative
+    %   / _  ->  63       '_' is URL_SAFE alternative
+    map = uint8(zeros(1,256)+65);
+    map(uint8(['A':'Z', 'a':'z', '0':'9', '+/=']))= 0:64;
+    map(uint8('-_'))= 62:63;  % URL_SAFE alternatives
+    x = map(x);  % mapping
+    
+    x(x>64)=[]; % remove non-base64 chars
+    if rem(numel(x), 4)
+      warning('Length of base64 data not a multiple of 4; padding input.');
+    end
+    x(x==64)=[]; % remove padding characters
+    
+    %% add padding and reshape
+    nebytes = length(x);         % number of encoded bytes
+    nchunks = ceil(nebytes/4);   % number of chunks/groups
+    if rem(nebytes, 4)>0
+      x(end+1 : 4*nchunks) = 0;  % add padding
+    end
+    x = reshape(uint8(x), 4, nchunks);
+    y = repmat(uint8(0), 3, nchunks);            % for the decoded data
+    
+    %% Rearrange every 4 bytes into 3 bytes
+    %    00aaaaaa 00bbbbbb 00cccccc 00dddddd
+    % to form
+    %    aaaaaabb bbbbcccc ccdddddd
+    y(1,:) = bitshift(x(1,:), 2);                 % 6 highest bits of y(1,:)
+    y(1,:) = bitor(y(1,:), bitshift(x(2,:), -4)); % 2 lowest  bits of y(1,:)
+    y(2,:) = bitshift(x(2,:), 4);                 % 4 highest bits of y(2,:)
+    y(2,:) = bitor(y(2,:), bitshift(x(3,:), -2)); % 4 lowest  bits of y(2,:)
+    y(3,:) = bitshift(x(3,:), 6);                 % 2 highest bits of y(3,:)
+    y(3,:) = bitor(y(3,:), x(4,:));               % 6 lowest  bits of y(3,:)
+    
+    %% remove extra padding
+    switch rem(nebytes, 4)
+      case 2
+        y = y(1:end-2);
+      case 3
+        y = y(1:end-1);
+    end
+end
+
+%% reshape to a row vector and make it a character array
+y = uint8(reshape(y, 1, numel(y)));
+
+%% save to file if needed
+if ~isempty(outfname)
+  fid = fopen(outfname,'wb');
+  fwrite(fid, y, 'uint8');  
+  fclose(fid);
+end

matlab_runners/Action Unit Experiments/helpers/xml_io_tools_2010_11_05/base64encode.m

@@ -0,0 +1,138 @@
+function y = base64encode(x, alg, isChunked, url_safe)
+%BASE64ENCODE Perform base64 encoding on a string.
+% INPUT:
+%   x    - block of data to be encoded.  Can be a string or a numeric
+%          vector containing integers in the range 0-255.
+%   alg  - Algorithm to use: can take values 'java' or 'matlab'. Optional
+%          variable defaulting to 'java' which is a little faster. If
+%          'java' is chosen than core of the code is performed by a call to
+%          a java library. Optionally all operations can be performed using
+%          matleb code.
+%   isChunked - encode output into 76 character blocks. The returned 
+%          encoded string is broken into lines of no more than
+%          76 characters each, and each line will end with EOL. Notice that
+%          if resulting string is saved as part of an xml file, those EOL's
+%          are often stripped by xmlwrite funtrion prior to saving.      
+%   url_safe - use Modified Base64 for URL applications ('base64url'
+%   encoding) "Base64 alphabet" ([A-Za-z0-9-_=]). 
+%
+%
+% OUTPUT:
+%   y    - character array using only "Base64 alphabet" characters 
+%
+%   This function may be used to encode strings into the Base64 encoding
+%   specified in RFC 2045 - MIME (Multipurpose Internet Mail Extensions).  
+%   The Base64 encoding is designed to represent arbitrary sequences of 
+%   octets in a form that need not be humanly readable.  A 65-character 
+%   subset ([A-Za-z0-9+/=]) of US-ASCII is used, enabling 6 bits to be 
+%   represented per printable character.
+%
+%   See also BASE64DECODE.
+%
+%   Written by Jarek Tuszynski, SAIC, jaroslaw.w.tuszynski_at_saic.com
+%
+%   Matlab version based on 2004 code by Peter J. Acklam
+%   E-mail:      pjacklam@online.no
+%   URL:         http://home.online.no/~pjacklam
+%   http://home.online.no/~pjacklam/matlab/software/util/datautil/base64encode.m
+
+if nargin<2, alg='java';      end
+if nargin<3, isChunked=false; end
+if ~islogical(isChunked) 
+  if isnumeric(isChunked)
+    isChunked=(isChunked>0);
+  else
+    isChunked=false;
+  end 
+end
+if nargin<4, url_safe=false; end
+if ~islogical(url_safe) 
+  if isnumeric(url_safe)
+    url_safe=(url_safe>0);
+  else
+    url_safe=false;
+  end 
+end
+
+
+%% if x happen to be a filename than read the file
+if (numel(x)<256)
+  if (exist(x, 'file')==2)
+    fid = fopen(x,'rb');
+    x = fread(fid, 'uint8');             % read image file as a raw binary
+    fclose(fid);
+  end
+end
+
+%% Perform conversion
+switch (alg)
+  case 'java'
+    base64 = org.apache.commons.codec.binary.Base64;
+    y = base64.encodeBase64(x, isChunked); 
+    if url_safe
+      y = strrep(y,'=','-');
+      y = strrep(y,'/','_');
+    end
+    
+  case 'matlab'
+    
+    %% add padding if necessary, to make the length of x a multiple of 3
+    x   = uint8(x(:));
+    ndbytes = length(x);                 % number of decoded bytes
+    nchunks = ceil(ndbytes / 3);         % number of chunks/groups
+    if rem(ndbytes, 3)>0
+      x(end+1 : 3*nchunks) = 0;          % add padding
+    end
+    x = reshape(x, [3, nchunks]);        % reshape the data
+    y = repmat(uint8(0), 4, nchunks);    % for the encoded data
+    
+    %% Split up every 3 bytes into 4 pieces
+    %    aaaaaabb bbbbcccc ccdddddd
+    % to form
+    %    00aaaaaa 00bbbbbb 00cccccc 00dddddd
+    y(1,:) = bitshift(x(1,:), -2);                  % 6 highest bits of x(1,:)
+    y(2,:) = bitshift(bitand(x(1,:), 3), 4);        % 2 lowest  bits of x(1,:)
+    y(2,:) = bitor(y(2,:), bitshift(x(2,:), -4));   % 4 highest bits of x(2,:)
+    y(3,:) = bitshift(bitand(x(2,:), 15), 2);       % 4 lowest  bits of x(2,:)
+    y(3,:) = bitor(y(3,:), bitshift(x(3,:), -6));   % 2 highest bits of x(3,:)
+    y(4,:) = bitand(x(3,:), 63);                    % 6 lowest  bits of x(3,:)
+    
+    %% Perform the mapping
+    %   0  - 25  ->  A-Z
+    %   26 - 51  ->  a-z
+    %   52 - 61  ->  0-9
+    %   62       ->  +
+    %   63       ->  /
+    map = ['A':'Z', 'a':'z', '0':'9', '+/'];
+    if (url_safe), map(63:64)='-_'; end
+    y = map(y(:)+1);
+    
+    %% Add padding if necessary.
+    npbytes = 3 * nchunks - ndbytes;    % number of padding bytes
+    if npbytes>0
+      y(end-npbytes+1 : end) = '=';     % '=' is used for padding
+    end
+    
+    %% break into lines with length LineLength
+    if (isChunked)
+      eol = sprintf('\n');
+      nebytes = numel(y);
+      nlines  = ceil(nebytes / 76);     % number of lines
+      neolbytes = length(eol);          % number of bytes in eol string
+      
+      % pad data so it becomes a multiple of 76 elements
+      y(nebytes + 1 : 76 * nlines) = 0;
+      y = reshape(y, 76, nlines);
+      
+      % insert eol strings
+      y(end + 1 : end + neolbytes, :) = eol(:, ones(1, nlines));
+      
+      % remove padding, but keep the last eol string
+      m = nebytes + neolbytes * (nlines - 1);
+      n = (76+neolbytes)*nlines - neolbytes;
+      y(m+1 : n) = [];
+    end
+end
+
+%% reshape to a row vector and make it a character array
+y = char(reshape(y, 1, numel(y)));

matlab_runners/Action Unit Experiments/helpers/xml_io_tools_2010_11_05/gen_object_display.m

@@ -0,0 +1,143 @@
+function gen_object_display( obj_struct,indent )
+%
+% gen_object_display - general function to display an object's content
+%
+% format:   gen_object_display( obj_struct,indent )
+%
+% input:    obj_struct  - a copy of the object stored inside a structure
+%           indent      - amount of "indent" when printing to the screen
+%
+% output:   to the screen
+%
+% example:  gen_object_display( struct( my_object_handle) );
+%           gen_object_display( ny_structure );
+%
+% Correction History:
+%  2006-11-01 - Jarek Tuszynski - added support for struct arrays
+
+%% handle insufficient input
+if ( nargin == 0 )
+  help gen_object_display;
+  return;
+elseif (nargin == 1)
+  indent = 1;
+end
+
+%% check input for errors
+% if ~isstruct( obj_struct )
+%     fprintf( '\n\n\tMake sure that ''obj_struct'' is a struct type\n' );
+%     return
+% end
+
+% if (iscell( obj_struct ))
+%   for i =1:length(obj_struct)
+%     gen_object_display( obj_struct{i},indent + 2 );
+%   end
+%   return
+% end
+if ~isstruct( obj_struct )
+  space = sprintf( sprintf( '%%%ds',indent ),' ' );
+  fprintf( '   %s', space);
+  disp(obj_struct);
+  return
+end
+
+% find the longest name
+field_list      = fieldnames( obj_struct );
+max_strlen      = 0;
+for idx = 1:length( field_list )
+  max_strlen  = max( max_strlen,length(field_list{idx}) );
+end
+
+%% setup the display format (spacing)
+space       = sprintf( sprintf( '%%%ds',indent ),' ' );
+name_format = sprintf( '   %s%%%ds: ', space, max_strlen );
+name_format2= sprintf( '     %s%%%ds', space, max_strlen );
+max_displen = 110 - max_strlen - indent;
+
+%% display each field, if it is not too long
+for iItem = 1:length( obj_struct ) % loop added  by JT
+  for idx = 1:length( field_list )
+    
+    % prepare field name to be displayed
+    name = sprintf( name_format,field_list{idx} );
+    %temp = getfield( obj_struct,field_list{idx} ); % original by OG
+    temp = obj_struct(iItem).(field_list{idx});    % modification by JT
+    
+    % proceed according the variable's type
+    switch (1)
+      case islogical( temp ), % case added by JT
+        if isscalar(temp)
+          if (temp)
+            fprintf( '%strue\n',name );
+          else
+            fprintf( '%sfalse\n',name );
+          end
+        else
+          fprintf( '%s[%dx%d logical]\n',name,size(temp,1),size(temp,2) );
+        end
+      case ischar( temp ),
+        if (length(temp)<max_displen )
+          fprintf( '%s''%s''\n',name,temp' );
+        else
+          fprintf( '%s[%dx%d char]\n',name,size(temp,1),size(temp,2) );
+        end
+      case isnumeric( temp ),
+        if (size( temp,1 )==1 )
+          temp_b = num2str( temp );
+          if (length(temp_b)<max_displen )
+            fprintf( '%s[%s]\n',name,temp_b );
+          else
+            fprintf( '%s[%dx%d double]\n',name,size(temp,1),size(temp,2) );
+          end
+        else
+          fprintf( '%s[%dx%d double]\n',name,size(temp,1),size(temp,2) );
+        end
+      case iscell( temp ),
+        if (numel(temp)<10 && (isvector(temp) || isscalar(temp)))
+          fprintf( '%s[%dx%d cell] = \n',name,size(temp,1),size(temp,2) );
+          %disp(temp)
+          for r =1:numel(temp)
+            gen_object_display( temp{r},indent + max_strlen + 2 );
+            fprintf('\n');
+          end
+        elseif (numel(temp)<10)
+          fprintf( '%s[%dx%d cell] = \n',name,size(temp,1),size(temp,2) );
+          for r =1:size(temp,1)
+            gen_object_display( temp(r,:),indent + max_strlen + 2 );
+          end
+        else
+          fprintf( '%s[%dx%d cell]\n',name,size(temp,1),size(temp,2) );
+        end
+      case isstruct( temp ),  
+        fprintf( '%s[%dx%d struct]\n',name,size(temp,1),size(temp,2) );
+        if (indent<80)
+          if (numel(temp)<10 && (isvector(temp) || isscalar(temp))) 
+            gen_object_display( temp,indent + max_strlen + 2 );
+          elseif (numel(temp)<10)
+            name2 = sprintf( name_format2,field_list{idx} );
+            for r =1:size(temp,1)
+              for c =1:size(temp,2)
+                fprintf( '%s(%d,%d) =\n',name2,r,c );
+                gen_object_display( temp(r,c),indent + max_strlen + 3 );
+              end
+            end
+          end
+        end
+      case isobject( temp ),  fprintf( '%s[inherent object]\n',name );
+        if (indent<80)
+          cmd = sprintf( 'display( obj_struct.%s,%d );',field_list{idx},indent + max_strlen + 2 );
+          eval( cmd );
+        end
+      otherwise,
+        fprintf( '%s',name );
+        try
+          fprintf( temp );
+        catch %#ok<CTCH>
+          fprintf( '[No method to display type]' );
+        end
+        fprintf( '\n' );
+    end
+  end
+  if (length(obj_struct)>1), fprintf('\n'); end % added by JT
+end                                             % added by JT

matlab_runners/Action Unit Experiments/helpers/xml_io_tools_2010_11_05/html/test.html

@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="utf-8"?>
+<MyTree>
+   <table border="1">
+      <tr>
+         <td>Apples</td>
+         <td>44%</td>
+      </tr>
+      <tr>
+         <td>Bannanas</td>
+         <td>23%</td>
+      </tr>
+      <tr>
+         <td>Oranges</td>
+         <td>13%</td>
+      </tr>
+      <tr>
+         <td>Other</td>
+         <td>10%</td>
+      </tr>
+   </table>
+</MyTree>

matlab_runners/Action Unit Experiments/helpers/xml_io_tools_2010_11_05/license.txt

@@ -0,0 +1,24 @@
+Copyright (c) 2007, Jaroslaw Tuszynski
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+    * Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+    * Redistributions in binary form must reproduce the above copyright
+      notice, this list of conditions and the following disclaimer in
+      the documentation and/or other materials provided with the distribution
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.

matlab_runners/Action Unit Experiments/helpers/xml_io_tools_2010_11_05/test_file.xml

@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="utf-8" ?> 
+<?xml-stylesheet type="text/css" href="foo.css"?>
+<!-- This is a Global Comment -->
+<aaa xmlns:xsi="http://www.foo.org">
+  <?ProcInst type="local processing instruction"?>
+  <!-- local comment 1 -->
+  bbb
+  <!-- local comment 2 -->
+  ccc
+  <matrix bad-name='fff'>
+    5e3+2*i, Inf
+    NaN,     pi
+  </matrix>
+  <ee_e> ee_e </ee_e>
+  <ff-f> ff-f </ff-f>
+  <ggög> ggög </ggög>
+  <![CDATA[
+    Here <ddd>xml</ddd> tags are treated as ...
+    ... text
+	]]>
+</aaa>
+

matlab_runners/Action Unit Experiments/helpers/xml_io_tools_2010_11_05/xml_read.m

@@ -0,0 +1,550 @@
+function [tree, RootName, DOMnode] = xml_read(xmlfile, Pref)
+%XML_READ reads xml files and converts them into Matlab's struct tree.
+%
+% DESCRIPTION
+% tree = xml_read(xmlfile) reads 'xmlfile' into data structure 'tree'
+%
+% tree = xml_read(xmlfile, Pref) reads 'xmlfile' into data structure 'tree'
+% according to your preferences
+%
+% [tree, RootName, DOMnode] = xml_read(xmlfile) get additional information
+% about XML file
+%
+% INPUT:
+%  xmlfile	URL or filename of xml file to read
+%  Pref     Preferences:
+%    Pref.ItemName - default 'item' - name of a special tag used to itemize
+%                    cell arrays
+%    Pref.ReadAttr - default true - allow reading attributes
+%    Pref.ReadSpec - default true - allow reading special nodes
+%    Pref.Str2Num  - default 'smart' - convert strings that look like numbers
+%                   to numbers. Options: "always", "never", and "smart"
+%    Pref.KeepNS   - default true - keep or strip namespace info
+%    Pref.NoCells  - default true - force output to have no cell arrays
+%    Pref.Debug    - default false - show mode specific error messages
+%    Pref.NumLevels- default infinity - how many recursive levels are
+%      allowed. Can be used to speed up the function by prunning the tree.
+%    Pref.RootOnly - default true - output variable 'tree' corresponds to
+%      xml file root element, otherwise it correspond to the whole file.
+%    Pref.CellItem - default 'true' - leave 'item' nodes in cell notation.
+% OUTPUT:
+%  tree         tree of structs and/or cell arrays corresponding to xml file
+%  RootName     XML tag name used for root (top level) node.
+%               Optionally it can be a string cell array storing: Name of
+%               root node, document "Processing Instructions" data and
+%               document "comment" string
+%  DOMnode      output of xmlread
+%
+% DETAILS:
+% Function xml_read first calls MATLAB's xmlread function and than
+% converts its output ('Document Object Model' tree of Java objects)
+% to tree of MATLAB struct's. The output is in format of nested structs
+% and cells. In the output data structure field names are based on
+% XML tags, except in cases when tags produce illegal variable names.
+%
+% Several special xml node types result in special tags for fields of
+% 'tree' nodes:
+%  - node.CONTENT - stores data section of the node if other fields are
+%    present. Usually data section is stored directly in 'node'.
+%  - node.ATTRIBUTE.name - stores node's attribute called 'name'.
+%  - node.COMMENT - stores node's comment section (string). For global
+%    comments see "RootName" output variable.
+%  - node.CDATA_SECTION - stores node's CDATA section (string).
+%  - node.PROCESSING_INSTRUCTIONS - stores "processing instruction" child
+%    node. For global "processing instructions" see "RootName" output variable.
+%  - other special node types like: document fragment nodes, document type
+%   nodes, entity nodes, notation nodes and processing instruction nodes
+%   will be treated like regular nodes
+%
+% EXAMPLES:
+%   MyTree=[];
+%   MyTree.MyNumber = 13;
+%   MyTree.MyString = 'Hello World';
+%   xml_write('test.xml', MyTree);
+%   [tree treeName] = xml_read ('test.xml');
+%   disp(treeName)
+%   gen_object_display()
+%   % See also xml_examples.m
+%
+% See also:
+%   xml_write, xmlread, xmlwrite
+%
+% Written by Jarek Tuszynski, SAIC, jaroslaw.w.tuszynski_at_saic.com
+% References:
+%  - Function inspired by Example 3 found in xmlread function.
+%  - Output data structures inspired by xml_toolbox structures.
+
+%% default preferences
+DPref.TableName  = {'tr','td'}; % name of a special tags used to itemize 2D cell arrays
+DPref.ItemName  = 'item'; % name of a special tag used to itemize 1D cell arrays
+DPref.CellItem  = false;  % leave 'item' nodes in cell notation
+DPref.ReadAttr  = true;   % allow reading attributes
+DPref.ReadSpec  = true;   % allow reading special nodes: comments, CData, etc.
+DPref.KeepNS    = true;   % Keep or strip namespace info
+DPref.Str2Num   = 'smart';% convert strings that look like numbers to numbers
+DPref.NoCells   = true;   % force output to have no cell arrays
+DPref.NumLevels = 1e10;   % number of recurence levels
+DPref.PreserveSpace = false; % Preserve or delete spaces at the beggining and the end of stings?
+RootOnly        = true;   % return root node  with no top level special nodes
+Debug           = false;  % show specific errors (true) or general (false)?
+tree            = [];
+RootName        = [];
+
+%% Check Matlab Version
+v = ver('MATLAB');
+version = str2double(regexp(v.Version, '\d.\d','match','once'));
+if (version<7.1)
+  error('Your MATLAB version is too old. You need version 7.1 or newer.');
+end
+
+%% read user preferences
+if (nargin>1)
+  if (isfield(Pref, 'TableName')), DPref.TableName = Pref.TableName; end
+  if (isfield(Pref, 'ItemName' )), DPref.ItemName  = Pref.ItemName;  end
+  if (isfield(Pref, 'CellItem' )), DPref.CellItem  = Pref.CellItem;  end
+  if (isfield(Pref, 'Str2Num'  )), DPref.Str2Num   = Pref.Str2Num ;  end
+  if (isfield(Pref, 'NoCells'  )), DPref.NoCells   = Pref.NoCells ;  end
+  if (isfield(Pref, 'NumLevels')), DPref.NumLevels = Pref.NumLevels; end
+  if (isfield(Pref, 'ReadAttr' )), DPref.ReadAttr  = Pref.ReadAttr;  end
+  if (isfield(Pref, 'ReadSpec' )), DPref.ReadSpec  = Pref.ReadSpec;  end
+  if (isfield(Pref, 'KeepNS'   )), DPref.KeepNS    = Pref.KeepNS;    end
+  if (isfield(Pref, 'RootOnly' )), RootOnly        = Pref.RootOnly;  end
+  if (isfield(Pref, 'Debug'    )), Debug           = Pref.Debug   ;  end
+  if (isfield(Pref, 'PreserveSpace')), DPref.PreserveSpace = Pref.PreserveSpace; end
+end
+if ischar(DPref.Str2Num), % convert from character description to numbers
+  DPref.Str2Num = find(strcmpi(DPref.Str2Num, {'never', 'smart', 'always'}))-1;
+  if isempty(DPref.Str2Num), DPref.Str2Num=1; end % 1-smart by default
+end
+
+%% read xml file using Matlab function
+if isa(xmlfile, 'org.apache.xerces.dom.DeferredDocumentImpl');
+  % if xmlfile is a DOMnode than skip the call to xmlread
+  try
+    try
+      DOMnode = xmlfile;
+    catch ME
+      error('Invalid DOM node: \n%s.', getReport(ME));
+    end
+  catch %#ok<CTCH> catch for mablab versions prior to 7.5
+    error('Invalid DOM node. \n');
+  end
+else         % we assume xmlfile is a filename
+  if (Debug) % in debuging mode crashes are allowed
+    DOMnode = xmlread(xmlfile);
+  else       % in normal mode crashes are not allowed
+    try
+      try
+        DOMnode = xmlread(xmlfile);
+      catch ME
+        error('Failed to read XML file %s: \n%s',xmlfile, getReport(ME));
+      end
+    catch %#ok<CTCH> catch for mablab versions prior to 7.5
+      error('Failed to read XML file %s\n',xmlfile);
+    end
+  end
+end
+Node = DOMnode.getFirstChild;
+
+%% Find the Root node. Also store data from Global Comment and Processing
+%  Instruction nodes, if any.
+GlobalTextNodes = cell(1,3);
+GlobalProcInst  = [];
+GlobalComment   = [];
+GlobalDocType   = [];
+while (~isempty(Node))
+  if (Node.getNodeType==Node.ELEMENT_NODE)
+    RootNode=Node;
+  elseif (Node.getNodeType==Node.PROCESSING_INSTRUCTION_NODE)
+    data   = strtrim(char(Node.getData));
+    target = strtrim(char(Node.getTarget));
+    GlobalProcInst = [target, ' ', data];
+    GlobalTextNodes{2} = GlobalProcInst;
+  elseif (Node.getNodeType==Node.COMMENT_NODE)
+    GlobalComment = strtrim(char(Node.getData));
+    GlobalTextNodes{3} = GlobalComment;
+    %   elseif (Node.getNodeType==Node.DOCUMENT_TYPE_NODE)
+    %     GlobalTextNodes{4} = GlobalDocType;
+  end
+  Node = Node.getNextSibling;
+end
+
+%% parse xml file through calls to recursive DOMnode2struct function
+if (Debug)   % in debuging mode crashes are allowed
+  [tree RootName] = DOMnode2struct(RootNode, DPref, 1);
+else         % in normal mode crashes are not allowed
+  try
+    try
+      [tree RootName] = DOMnode2struct(RootNode, DPref, 1);
+    catch ME
+      error('Unable to parse XML file %s: \n %s.',xmlfile, getReport(ME));
+    end
+  catch %#ok<CTCH> catch for mablab versions prior to 7.5
+    error('Unable to parse XML file %s.',xmlfile);
+  end
+end
+
+%% If there were any Global Text nodes than return them
+if (~RootOnly)
+  if (~isempty(GlobalProcInst) && DPref.ReadSpec)
+    t.PROCESSING_INSTRUCTION = GlobalProcInst;
+  end
+  if (~isempty(GlobalComment) && DPref.ReadSpec)
+    t.COMMENT = GlobalComment;
+  end
+  if (~isempty(GlobalDocType) && DPref.ReadSpec)
+    t.DOCUMENT_TYPE = GlobalDocType;
+  end
+  t.(RootName) = tree;
+  tree=t;
+end
+if (~isempty(GlobalTextNodes))
+  GlobalTextNodes{1} = RootName;
+  RootName = GlobalTextNodes;
+end
+
+
+%% =======================================================================
+%  === DOMnode2struct Function ===========================================
+%  =======================================================================
+function [s TagName LeafNode] = DOMnode2struct(node, Pref, level)
+
+%% === Step 1: Get node name and check if it is a leaf node ==============
+[TagName LeafNode] = NodeName(node, Pref.KeepNS);
+s = []; % initialize output structure
+
+%% === Step 2: Process Leaf Nodes (nodes with no children) ===============
+if (LeafNode)
+  if (LeafNode>1 && ~Pref.ReadSpec), LeafNode=-1; end % tags only so ignore special nodes
+  if (LeafNode>0) % supported leaf node types
+    try
+      try         % use try-catch: errors here are often due to VERY large fields (like images) that overflow java memory
+        s = char(node.getData);
+        if (isempty(s)), s = ' '; end                              % make it a string
+        % for some reason current xmlread 'creates' a lot of empty text
+        % fields with first chatacter=10 - those will be deleted.
+        if (~Pref.PreserveSpace || s(1)==10) 
+          if (isspace(s(1)) || isspace(s(end))), s = strtrim(s); end % trim speces is any
+        end
+        if (LeafNode==1), s=str2var(s, Pref.Str2Num, 0); end       % convert to number(s) if needed
+      catch ME    % catch for mablab versions 7.5 and higher
+        warning('xml_io_tools:read:LeafRead', ...
+          'This leaf node could not be read and was ignored. ');
+        getReport(ME)
+      end
+    catch         %#ok<CTCH> catch for mablab versions prior to 7.5
+      warning('xml_io_tools:read:LeafRead', ...
+        'This leaf node could not be read and was ignored. ');
+    end
+  end
+  if (LeafNode==3) % ProcessingInstructions need special treatment
+    target = strtrim(char(node.getTarget));
+    s = [target, ' ', s];
+  end
+  return % We are done the rest of the function deals with nodes with children
+end
+if (level>Pref.NumLevels+1), return; end % if Pref.NumLevels is reached than we are done
+
+%% === Step 3: Process nodes with children ===============================
+if (node.hasChildNodes)        % children present
+  Child  = node.getChildNodes; % create array of children nodes
+  nChild = Child.getLength;    % number of children
+  
+  % --- pass 1: how many children with each name -----------------------
+  f = [];
+  for iChild = 1:nChild        % read in each child
+    [cname cLeaf] = NodeName(Child.item(iChild-1), Pref.KeepNS);
+    if (cLeaf<0), continue; end % unsupported leaf node types
+    if (~isfield(f,cname)),
+      f.(cname)=0;           % initialize first time I see this name
+    end
+    f.(cname) = f.(cname)+1; % add to the counter
+  end                        % end for iChild
+  % text_nodes become CONTENT & for some reason current xmlread 'creates' a
+  % lot of empty text fields so f.CONTENT value should not be trusted
+  if (isfield(f,'CONTENT') && f.CONTENT>2), f.CONTENT=2; end
+  
+  % --- pass 2: store all the children as struct of cell arrays ----------
+  for iChild = 1:nChild        % read in each child
+    [c cname cLeaf] = DOMnode2struct(Child.item(iChild-1), Pref, level+1);
+    if (cLeaf && isempty(c))   % if empty leaf node than skip
+      continue;                % usually empty text node or one of unhandled node types
+    elseif (nChild==1 && cLeaf==1)
+      s=c;                     % shortcut for a common case
+    else                       % if normal node
+      if (level>Pref.NumLevels), continue; end
+      n = f.(cname);           % how many of them in the array so far?
+      if (~isfield(s,cname))   % encountered this name for the first time
+        if (n==1)              % if there will be only one of them ...
+          s.(cname) = c;       % than save it in format it came in
+        else                   % if there will be many of them ...
+          s.(cname) = cell(1,n);
+          s.(cname){1} = c;    % than save as cell array
+        end
+        f.(cname) = 1;         % initialize the counter
+      else                     % already have seen this name
+        s.(cname){n+1} = c;    % add to the array
+        f.(cname) = n+1;       % add to the array counter
+      end
+    end
+  end   % for iChild
+end % end if (node.hasChildNodes)
+
+%% === Step 4: Post-process struct's created for nodes with children =====
+if (isstruct(s))
+  fields = fieldnames(s);
+  nField = length(fields);
+  
+  % Detect structure that looks like Html table and store it in cell Matrix
+  if (nField==1 && strcmpi(fields{1},Pref.TableName{1}))
+    tr = s.(Pref.TableName{1});
+    fields2 = fieldnames(tr{1});
+    if (length(fields2)==1 && strcmpi(fields2{1},Pref.TableName{2}))
+      % This seems to be a special structure such that for 
+      % Pref.TableName = {'tr','td'} 's' corresponds to 
+      %    <tr> <td>M11</td> <td>M12</td> </tr>
+      %    <tr> <td>M12</td> <td>M22</td> </tr>
+      % Recognize it as encoding for 2D struct
+      nr = length(tr);
+      for r = 1:nr
+        row = tr{r}.(Pref.TableName{2});
+        Table(r,1:length(row)) = row; %#ok<AGROW>
+      end
+      s = Table;
+    end
+  end
+
+  % --- Post-processing: convert 'struct of cell-arrays' to 'array of structs'
+  % Example: let say s has 3 fields s.a, s.b & s.c  and each field is an
+  % cell-array with more than one cell-element and all 3 have the same length.
+  % Then change it to array of structs, each with single cell.
+  % This way element s.a{1} will be now accessed through s(1).a
+  vec = zeros(size(fields));
+  for i=1:nField, vec(i) = f.(fields{i}); end
+  if (numel(vec)>1 && vec(1)>1 && var(vec)==0)  % convert from struct of
+    s = cell2struct(struct2cell(s), fields, 1); % arrays to array of struct
+  end % if anyone knows better way to do above conversion please let me know.
+
+end
+
+%% === Step 5: Process nodes with attributes =============================
+if (node.hasAttributes && Pref.ReadAttr)
+  if (~isstruct(s)),              % make into struct if is not already
+    ss.CONTENT=s;
+    s=ss;
+  end
+  Attr  = node.getAttributes;     % list of all attributes
+  for iAttr = 1:Attr.getLength    % for each attribute
+    name  = char(Attr.item(iAttr-1).getName);  % attribute name
+    name  = str2varName(name, Pref.KeepNS);    % fix name if needed
+    value = char(Attr.item(iAttr-1).getValue); % attribute value
+    value = str2var(value, Pref.Str2Num, 1);   % convert to number if possible
+    s.ATTRIBUTE.(name) = value;   % save again
+  end                             % end iAttr loop
+end % done with attributes
+if (~isstruct(s)), return; end %The rest of the code deals with struct's
+
+%% === Post-processing: fields of "s"
+% convert  'cell-array of structs' to 'arrays of structs'
+fields = fieldnames(s);     % get field names
+nField = length(fields);
+for iItem=1:length(s)       % for each struct in the array - usually one
+  for iField=1:length(fields)
+    field = fields{iField}; % get field name
+    % if this is an 'item' field and user want to leave those as cells
+    % than skip this one
+    if (strcmpi(field, Pref.ItemName) && Pref.CellItem), continue; end
+    x = s(iItem).(field);
+    if (iscell(x) && all(cellfun(@isstruct,x(:))) && numel(x)>1) % it's cell-array of structs
+      % numel(x)>1 check is to keep 1 cell-arrays created when Pref.CellItem=1
+      try                           % this operation fails sometimes
+        % example: change s(1).a{1}.b='jack'; s(1).a{2}.b='john'; to
+        % more convinient s(1).a(1).b='jack'; s(1).a(2).b='john';
+        s(iItem).(field) = [x{:}]';  %#ok<AGROW> % converted to arrays of structs
+      catch %#ok<CTCH>
+        % above operation will fail if s(1).a{1} and s(1).a{2} have
+        % different fields. If desired, function forceCell2Struct can force
+        % them to the same field structure by adding empty fields.
+        if (Pref.NoCells)
+          s(iItem).(field) = forceCell2Struct(x); %#ok<AGROW>
+        end
+      end % end catch
+    end
+  end
+end
+
+%% === Step 4: Post-process struct's created for nodes with children =====
+
+% --- Post-processing: remove special 'item' tags ---------------------
+% many xml writes (including xml_write) use a special keyword to mark
+% arrays of nodes (see xml_write for examples). The code below converts
+% s.item to s.CONTENT
+ItemContent = false;
+if (isfield(s,Pref.ItemName))
+  s.CONTENT = s.(Pref.ItemName);
+  s = rmfield(s,Pref.ItemName);
+  ItemContent = Pref.CellItem; % if CellItem than keep s.CONTENT as cells
+end
+
+% --- Post-processing: clean up CONTENT tags ---------------------
+% if s.CONTENT is a cell-array with empty elements at the end than trim
+% the length of this cell-array. Also if s.CONTENT is the only field than
+% remove .CONTENT part and store it as s.
+if (isfield(s,'CONTENT'))
+  if (iscell(s.CONTENT) && isvector(s.CONTENT))
+    x = s.CONTENT;
+    for i=numel(x):-1:1, if ~isempty(x{i}), break; end; end
+    if (i==1 && ~ItemContent)
+      s.CONTENT = x{1};   % delete cell structure
+    else
+      s.CONTENT = x(1:i); % delete empty cells
+    end
+  end
+  if (nField==1)
+    if (ItemContent)
+      ss = s.CONTENT;       % only child: remove a level but ensure output is a cell-array
+      s=[]; s{1}=ss;
+    else
+      s = s.CONTENT;        % only child: remove a level
+    end
+  end
+end
+
+
+
+%% =======================================================================
+%  === forceCell2Struct Function =========================================
+%  =======================================================================
+function s = forceCell2Struct(x)
+% Convert cell-array of structs, where not all of structs have the same
+% fields, to a single array of structs
+
+%% Convert 1D cell array of structs to 2D cell array, where each row
+% represents item in original array and each column corresponds to a unique
+% field name. Array "AllFields" store fieldnames for each column
+AllFields = fieldnames(x{1});     % get field names of the first struct
+CellMat = cell(length(x), length(AllFields));
+for iItem=1:length(x)
+  fields = fieldnames(x{iItem});  % get field names of the next struct
+  for iField=1:length(fields)     % inspect all fieldnames and find those
+    field = fields{iField};       % get field name
+    col = find(strcmp(field,AllFields),1);
+    if isempty(col)               % no column for such fieldname yet
+      AllFields = [AllFields; field]; %#ok<AGROW>
+      col = length(AllFields);    % create a new column for it
+    end
+    CellMat{iItem,col} = x{iItem}.(field); % store rearanged data
+  end
+end
+%% Convert 2D cell array to array of structs
+s = cell2struct(CellMat, AllFields, 2);
+
+%% =======================================================================
+%  === str2var Function ==================================================
+%  =======================================================================
+function val=str2var(str, option, attribute)
+% Can this string 'str' be converted to a number? if so than do it.
+val = str;
+len = numel(str);
+if (len==0    || option==0), return; end % Str2Num="never" of empty string -> do not do enything
+if (len>10000 && option==1), return; end % Str2Num="smart" and string is very long -> probably base64 encoded binary
+digits = '(Inf)|(NaN)|(pi)|[\t\n\d\+\-\*\.ei EI\[\]\;\,]';
+s = regexprep(str, digits, ''); % remove all the digits and other allowed characters
+if (~all(~isempty(s)))          % if nothing left than this is probably a number
+  if (~isempty(strfind(str, ' '))), option=2; end %if str has white-spaces assume by default that it is not a date string
+  if (~isempty(strfind(str, '['))), option=2; end % same with brackets
+  str(strfind(str, '\n')) = ';';% parse data tables into 2D arrays, if any
+  if (option==1)                % the 'smart' option
+    try                         % try to convert to a date, like 2007-12-05
+      datenum(str);             % if successful than leave it as string
+    catch                       %#ok<CTCH> % if this is not a date than ...
+      option=2;                 % ... try converting to a number
+    end
+  end
+  if (option==2)
+    if (attribute)
+      num = str2double(str);      % try converting to a single number using sscanf function
+      if isnan(num), return; end  % So, it wasn't really a number after all    
+    else
+      num = str2num(str);         %#ok<ST2NM> % try converting to a single number or array using eval function
+    end
+    if(isnumeric(num) && numel(num)>0), val=num; end % if convertion to a single was succesful than save
+  end
+elseif ((str(1)=='[' && str(end)==']') || (str(1)=='{' && str(end)=='}')) % this looks like a (cell) array encoded as a string
+  try 
+    val = eval(str); 
+  catch              %#ok<CTCH>
+    val = str; 
+  end                     
+elseif (~attribute)   % see if it is a boolean array with no [] brackets
+  str1 = lower(str);
+  str1 = strrep(str1, 'false', '0');
+  str1 = strrep(str1, 'true' , '1');
+  s = regexprep(str1, '[01 \;\,]', ''); % remove all 0/1, spaces, commas and semicolons 
+  if (~all(~isempty(s)))          % if nothing left than this is probably a boolean array
+    num  = str2num(str1); %#ok<ST2NM>
+    if(isnumeric(num) && numel(num)>0), val = (num>0);  end % if convertion was succesful than save as logical
+  end
+end
+
+
+%% =======================================================================
+%  === str2varName Function ==============================================
+%  =======================================================================
+function str = str2varName(str, KeepNS)
+% convert a sting to a valid matlab variable name
+if(KeepNS)
+  str = regexprep(str,':','_COLON_', 'once', 'ignorecase');
+else
+  k = strfind(str,':');
+  if (~isempty(k))
+    str = str(k+1:end);
+  end
+end
+str = regexprep(str,'-','_DASH_'  ,'once', 'ignorecase');
+if (~isvarname(str)) && (~iskeyword(str))
+  str = genvarname(str);
+end
+
+%% =======================================================================
+%  === NodeName Function =================================================
+%  =======================================================================
+function [Name LeafNode] = NodeName(node, KeepNS)
+% get node name and make sure it is a valid variable name in Matlab.
+% also get node type:
+%   LeafNode=0 - normal element node,
+%   LeafNode=1 - text node
+%   LeafNode=2 - supported non-text leaf node,
+%   LeafNode=3 - supported processing instructions leaf node,
+%   LeafNode=-1 - unsupported non-text leaf node
+switch (node.getNodeType)
+  case node.ELEMENT_NODE
+    Name = char(node.getNodeName);% capture name of the node
+    Name = str2varName(Name, KeepNS);     % if Name is not a good variable name - fix it
+    LeafNode = 0;
+  case node.TEXT_NODE
+    Name = 'CONTENT';
+    LeafNode = 1;
+  case node.COMMENT_NODE
+    Name = 'COMMENT';
+    LeafNode = 2;
+  case node.CDATA_SECTION_NODE
+    Name = 'CDATA_SECTION';
+    LeafNode = 2;
+  case node.DOCUMENT_TYPE_NODE
+    Name = 'DOCUMENT_TYPE';
+    LeafNode = 2;
+  case node.PROCESSING_INSTRUCTION_NODE
+    Name = 'PROCESSING_INSTRUCTION';
+    LeafNode = 3;
+  otherwise
+    NodeType = {'ELEMENT','ATTRIBUTE','TEXT','CDATA_SECTION', ...
+      'ENTITY_REFERENCE', 'ENTITY', 'PROCESSING_INSTRUCTION', 'COMMENT',...
+      'DOCUMENT', 'DOCUMENT_TYPE', 'DOCUMENT_FRAGMENT', 'NOTATION'};
+    Name = char(node.getNodeName);% capture name of the node
+    warning('xml_io_tools:read:unkNode', ...
+      'Unknown node type encountered: %s_NODE (%s)', NodeType{node.getNodeType}, Name);
+    LeafNode = -1;
+end
+
+

matlab_runners/Action Unit Experiments/helpers/xml_io_tools_2010_11_05/xml_tutorial_script.m

@@ -0,0 +1,914 @@
+%% Tutorial for xml_io_tools Package
+% *By Jarek Tuszynski*
+%
+% Package xml_io_tools can read XML files into MATLAB struct and writes 
+% MATLAB data types to XML files with help of simple interface to 
+% MATLAB's xmlwrite and xmlread functions.
+% 
+% Two function to simplify reading and writing XML files from MATLAB:
+%
+% * Function xml_read first calls MATLAB's xmlread function and than 
+% converts its output ('Document Object Model' tree of Java objects) 
+% to tree of MATLAB struct's. The output is in the format of nested 
+% structs and cells. In the output data structure field names are based on
+% XML tags.
+%
+% * Function xml_write first convert input tree of MATLAB structs and cells 
+% and other types to tree of 'Document Object Model' nodes, and then writes 
+% resulting object to XML file using MATLAB's xmlwrite function. .
+%
+%% This package can:
+% * Read most XML files, created inside and outside of MATLAB environment, 
+%   and convert them to MATLAB data structures.
+% * Write any MATLAB's struct tree to XML file
+% * Handle XML attributes and special XML nodes like comments, processing  
+%   instructions and CDATA sections
+% * Supports base64 encoding and decoding to allow handling embeded binary
+%   data
+% * Be studied, modified, customized, rewritten and used in other packages 
+%   without any limitations. All code is included and documented. Software
+%   is distributed under BSD Licence (included).   
+%
+%% This package does not:
+% * Guarantee to recover the same Matlab objects that were saved. If you 
+% need to be able to recover carbon copy of the structure that was saved 
+% than you will have to use one of the packages that uses special set of 
+% tags saved as xml attributes that help to guide the parsing of XML code. 
+% This package does not use those tags.
+% * Guarantee to work with older versions of MATLAB. Functions do not work
+% with versions of MATLAB prior to 7.1 (26-Jul-2005). 
+%
+%% Change History
+% * 2006-11-06 - original version
+% * 2006-11-26 - corrected xml_write to handle writing Matlab's column
+%   arrays to xml files. Bug discovered and diagnosed by Kalyan Dutta.
+% * 2006-11-28 - made changes to handle special node types like: 
+%   COMMENTS and CDATA sections 
+% * 2007-03-12 - Writing CDATA sections still did not worked. The problem 
+%   was diagnosed and fixed by Alberto Amaro. The fix involved rewriting
+%   xmlwrite to use Apache Xerces java files directly instead of MATLAB's 
+%   XMLUtils java class.
+% * 2007-06-21 - Fixed problem reported by Anna Kelbert in Reviews about 
+%   not writing attributes of ROOT node. Also: added support for Processing
+%   Instructions, added support for global text nodes: Processing
+%   Instructions and comments, allowed writing tag names with special
+%   characters
+% * 2007-07-20 - Added tutorial script file. Extended support for global
+%   text nodes. Added more Preference fields.
+% * 2008-01-23 - Fixed problem reported by Anna Krewet of converting dates 
+%   in format '2007-01-01' to numbers. Improved and added warning messages.
+%   Added detection of old Matlab versions incompatible with the library.
+%   Expanded documentation.
+% * 2008-06-23 - Fixed problem with writing 1D array reported by Mark Neil. 
+%   Extended xml_read's Pref.Num2Str to 3 settings (never, smart and always) 
+%   for better control. Added parameter Pref.KeepNS for keeping or ignoring 
+%   namespace data when reading. Fixed a bug related to writing 2D cell
+%   arrays brought up by Andrej's Mosat review. 
+% * 2008-09-11 - Resubmitting last upload - zip file is still old
+% * 2009-02-26 - Small changes. More error handling. More robust in case of
+%   large binary objects. Added support for Base64 encoding/decoding of
+%   binary objects (using functions by Peter J. Acklam).
+% * 2009-06-26 - changes to xml_read: added CellItem parameter to allow
+%   better control of reading files with 'item' notation (see comment by
+%   Shlomi); changed try-catch statements so xml_read would work for mablab
+%   versions prior to 7.5 (see Thomas Pilutti comment)
+% * 2009-12-03 - added PreserveSpace parameter for contolling empty string
+%   handling as suggested by Sebastiaan. Fix suggested by Michael Murphy.
+%   Fixed number recognition code as suggested by Yuan Ren.  
+% * 2010-05-04 - implemented fixes suggested by Dylan Reynolds from Airbus.  
+% * 2010-07-28 - implemented support for 2D arrays of cells and structs 
+%   suggested by Rodney Behn from MIT Lincoln Laboratory. Also attempted
+%   large scale cleanup of xml_write function
+% * 2010-08-18 - minor extension to allow better handling of logical
+%   scalars and arrays and function handles suggested by Andreas Richter 
+%   and others
+% * 2010-09-20 - allow reading and writing of sparse matrices. Improve
+%   reading of 1D boolean arrays.
+% * 2010-11-05 - Fix problem with empty cells reported by Richard Cotton;
+%   fixed issues with reading boolean arrays reported by Zohar Bar-Yehuda;
+%   Improved speed of base64 coding and decoding by switching to java based 
+%   code.
+%% Licence
+% The package is distributed under BSD License
+format compact; % viewing preference
+clear variables;
+type('license.txt')
+
+%% Write XML file based on a Struct using "xml_write"
+% Any MATLAB data struct can be saved to XML file.
+MyTree=[];
+MyTree.MyNumber = 13;
+MyTree.MyString = 'Hello World';
+xml_write('test.xml', MyTree);
+type('test.xml')
+
+%% Read XML file producing a Struct using "xml_read"
+[tree treeName] = xml_read ('test.xml');
+disp([treeName{1} ' ='])
+gen_object_display(tree)
+
+%% "Pref.XmlEngine" flag in "xml_write"
+% Occasionaly some operations are performed better by Apache Xerces XML 
+% engine than default xmlread function. That is why xml_write provide an 
+% option for choosing the underlaying xml engine. Code below performs the 
+% same operation as the previous section but using Apache Xerces XML engine.
+% Notice that in this case name of root element 
+% was passed as variable and not extracted from the variable name.
+Pref=[]; Pref.XmlEngine = 'Xerces';  % use Xerces xml generator directly
+xml_write('test.xml', MyTree, 'TreeOfMine', Pref);
+type('test.xml')
+
+%% Writing Struct with different type MATLAB arrays
+MyTree=[];
+MyTree.Empty   = [];                   % Empty variable
+MyTree.Num_1x1 = 13;                   % simple scalar
+MyTree.Vec_1x3 = [1 2 3];              % horizontal vector
+MyTree.Vec_4x1 = [1; 2; 3; 4];         % vertical vector
+MyTree.Mat_2x2 = [1, 2; 3, 4];         % 2D matrix
+MyTree.Cube_3D = reshape(1:8,[2 2 2]); % 3D array
+MyTree.String1 = '[2003 10 30]';       % number string with    [] brackets
+MyTree.String2 = ' 2003 10 30 ';       % number string without [] brackets
+MyTree.Logical_1x1 = false;            % single logical
+MyTree.Logical_2x2 = [false, true; true, false]; % 2D matrix of logicals
+MyTree.Logical_Str = 'False False	True True';
+MyTree.Int_2x2 = uint8([1 2;3 4]);     % 2D matrix of uint8 integers
+MyTree.Complex_1x1 = complex(1, 7);    % complex scalar
+MyTree.Complex_2x2 = complex([1 2;3 4],[2 2;7 7]); % 2D matrix of complex numbers
+MyTree.Sparse_9x9 = sparse(1:9,1:9,1); % sparse 9x9 matrix
+MyTree.Function = @sum;                % function handle
+xml_write('test.xml', MyTree);
+type('test.xml')
+
+%% Read Struct with MATLAB arrays
+% Notice that 'Cube_3D' did not preserve original dimentions 
+[tree treeName] = xml_read ('test.xml');
+disp([treeName{1} ' ='])
+gen_object_display(tree)
+
+%% "Pref.StructItem" flag in "xml_write" (controls 1D arrays of structs)
+% *Create a simple structure with 1D array of struct's*
+MyTree = [];
+MyTree.a(1).b = 'jack';
+MyTree.a(2).b = 'john';
+gen_object_display(MyTree)
+%%
+% *Write XML with "StructItem = true" (default).  Notice single 'a' 
+% section and multiple 'item' sub-sections. Those subsections are used 
+% to store array elements*
+wPref.StructItem = true;
+xml_write('test.xml', MyTree, 'MyTree',wPref);
+type('test.xml')
+fprintf('\nxml_read output:\n')
+gen_object_display(xml_read ('test.xml'))
+%%
+% *Write XML with "StructItem = false". Notice multiple 'a' sections*
+wPref.StructItem = false;
+xml_write('test.xml', MyTree, 'MyTree',wPref);
+type('test.xml')
+fprintf('\nxml_read output:\n')
+gen_object_display(xml_read ('test.xml'))
+%%
+% *Notice that xml_read function produced the same struct when reading both files*
+%%
+% *Potential problems with "StructItem = true":*
+wPref.StructItem = true;
+MyTree1 = []; MyTree1.a.b    = 'jack';
+MyTree2 = []; MyTree2.a(1).b = 'jack';
+MyTree3 = []; MyTree3.a(2).b = 'jack';
+xml_write('test.xml', MyTree1, [], wPref); type('test.xml');
+xml_write('test.xml', MyTree2, [], wPref); type('test.xml');
+xml_write('test.xml', MyTree3, [], wPref); type('test.xml');
+%%
+% *Notice that MyTree1 and MyTree2 produce identical files with no 'items',
+% while MyTree2 and MyTree3 produce very different file structures. It was
+% pointed out to me that files produced from MyTree2 and MyTree3 can not 
+% belong to the same schema, which can be a problem. The solution is to use 
+% cells.* 
+wPref.CellItem = true;
+wPref.NoCells  = true;
+MyTree2 = []; MyTree2.a{1}.b = 'jack';
+MyTree3 = []; MyTree3.a{2}.b = 'jack';
+xml_write('test.xml', MyTree2, [], wPref); type('test.xml');
+xml_write('test.xml', MyTree3, [], wPref); type('test.xml');
+
+
+%% "Pref.CellItem" flag in "xml_write" (controls 1D arrays of cells)
+% *Create a simple structure with cell arrays*
+MyTree = [];
+MyTree.a = {'jack', 'john'};
+disp(MyTree)
+%%
+% *Write XML with "CellItem = true" (default).  Notice single 'a' 
+% section and multiple 'item' sections*
+Pref=[]; Pref.CellItem = true;
+xml_write('test.xml', MyTree, 'MyTree',Pref);
+type('test.xml')
+fprintf('\nxml_read output:\n');
+disp(xml_read ('test.xml'))
+%%
+% *Write XML with "CellItem = false". Notice multiple 'a' sections*
+Pref=[]; Pref.CellItem = false;
+xml_write('test.xml', MyTree, 'MyTree',Pref);
+type('test.xml')
+fprintf('\nxml_read output:\n');
+disp(xml_read ('test.xml'))
+%%
+% *Notice that xml_read function produced the same struct when reading both files*
+
+%% "Pref.NoCells" flag in "xml_read"
+% *Create a cell/struct mixture object*
+MyTree = [];
+MyTree.a{1}.b = 'jack';
+MyTree.a{2}.b = [];
+MyTree.a{2}.c = 'john';
+gen_object_display(MyTree);
+%%
+% *Save it to xml file*
+Pref=[]; Pref.CellItem = false;
+xml_write('test.xml', MyTree, 'MyTree',Pref);
+type('test.xml')
+%%
+% *Read above file with "Pref.NoCells=true" (default) - output is quite different then input*
+% By default program is trying to convert everything to struct's and arrays
+% of structs. In case arrays of structs all the structs in array need to have the
+% same fields, and if they are not than MATLAB creates empty fields.
+Pref=[]; Pref.NoCells=true;
+gen_object_display(xml_read('test.xml', Pref))
+%%
+% *Read above file with "Pref.NoCells=false" - now input and output are the same*
+% Cell arrays of structs allow structs in array to have different fields.
+Pref=[]; Pref.NoCells=false;
+gen_object_display(xml_read('test.xml', Pref))
+
+%% "Pref.ItemName" flag in "xml_write" (customize 1D arrays of structs and cells)
+% *Create a cell/struct mixture object*
+MyTree = [];
+MyTree.a{1}.b = 'jack';
+MyTree.a{2}.c = 'john';
+gen_object_display(MyTree);
+%%
+% *Save it to xml file, using 'item' notation but with different name*
+Pref=[]; 
+Pref.CellItem = true;
+Pref.ItemName = 'MyItem';
+xml_write('test.xml', MyTree, 'MyTree',Pref);
+type('test.xml')
+
+%% "Pref.ItemName" flag in "xml_read"
+% *Read above file with default settings ("Pref.ItemName = 'item'")*
+% The results do not match the original structure
+Pref=[]; Pref.NoCells  = false;
+gen_object_display(xml_read('test.xml', Pref))
+%%
+% *Read above file with "Pref.ItemName = 'MyItem'" - now saved and read 
+% MATLAB structures are the same*
+Pref=[]; 
+Pref.ItemName = 'MyItem';
+Pref.NoCells  = false;
+gen_object_display(xml_read('test.xml', Pref))
+
+%% "Pref.CellItem" flag in "xml_read"
+% "Pref.ItemName" is used to create xml files with clearly marked arrays
+% "Pref.CellItem" flag in "xml_read" ensures that they are always read as
+% arrays by forcing output to stay in cell format. In cell format s{1} is
+% different than s, while s(1) is indistinguishable from s.
+%%
+% *Create a test file*
+MyTree = [];
+MyTree.a1{1}.b = 'jack'; % a1 - single struct
+MyTree.a2{1}.b = 'jack'; % a2 - cell array of structs with the same fields
+MyTree.a2{2}.b = 'john';
+MyTree.a3{1}.b = 'jack'; % a3 - cell array of structs with the different fields
+MyTree.a3{2}.c = 'john';
+Pref=[]; 
+Pref.CellItem = true;
+Pref.Debug = true;
+xml_write('test.xml', MyTree, 'MyTree',Pref);
+type('test.xml')
+%%
+% *Read above file with "Pref.CellItem = true" (default)*
+% All outputs are in cell format
+Pref=[]; 
+Pref.NoCells  = false;  % allow cell output
+Pref.CellItem = true;   % keep 'item' arrays as cells 
+gen_object_display(xml_read('test.xml', Pref))
+%%
+% *Read above file with "Pref.CellItem = false"*
+% Outputs format is determined by content
+Pref=[]; 
+Pref.NoCells  = false; % allow cell output
+Pref.CellItem = false; % allow 'item' arrays to beheave like other fields 
+gen_object_display(xml_read('test.xml', Pref))
+%%
+% *Read above file with "Pref.CellItem = false" and "Pref.NoCells  = true"*
+% All outputs are in struct format
+Pref=[]; 
+Pref.NoCells  = true;  % don't allow cell output 
+Pref.CellItem = false; % allow 'item' arrays to beheave like other fields
+gen_object_display(xml_read('test.xml', Pref))
+
+%% "Pref.CellTable" flag in "xml_write" (controls 2D arrays of cells)
+% *Create a structure with 2D arrays of cells*
+MyTree = [];
+MyTree.M = {[1,2;3,4], 'M12'; struct('a','jack'), {11, 'N12'; 21, 'N22'}};
+gen_object_display(MyTree)
+%%
+% *Write XML with "CellTable = 'Html" (default). This option mimics use of  
+%  HTML "tr" and "td" tags to encode 2D tables. Tag names can  
+%  be changed using TableName parameter (see below)*
+wPref = [];
+wPref.CellTable = 'Html';
+xml_write('test.xml', MyTree, 'MyTree',wPref);
+type('test.xml')
+fprintf('\nxml_read output:\n')
+rPref=[]; rPref.NoCells=false;
+gen_object_display(xml_read('test.xml', rPref))
+%%
+% *Write XML with "CellTable = 'Vector'".*
+%  Converts 2D arrays to 1D array and item or regular notation. This option 
+%  is mostly provided for backward compatibility since this was the 
+%  behavior in prior verions of the code
+wPref = [];
+wPref.CellTable = 'Vector';
+xml_write('test.xml', MyTree, 'MyTree',wPref);
+type('test.xml')
+fprintf('\nxml_read output:\n')
+rPref=[]; rPref.NoCells=false;
+gen_object_display(xml_read('test.xml', rPref))
+%%
+% *Create a simpler structure without struct's*
+MyTree = [];
+MyTree.M = {[1,2;3,4], 'M12'; 'M21', {11, 'N12'; 21, 'N22'}};
+gen_object_display(MyTree)
+%%
+% *Write XML with "CellTable = 'Matlab". This option encodes tables
+% consisting of numbers, strings and other cell arrays as MATLAB command
+% string. Unlike 'Html' option it does not work if one of the cells is 
+% a struct*
+wPref = [];
+wPref.CellTable = 'Matlab';
+xml_write('test.xml', MyTree, 'MyTree',wPref);
+type('test.xml')
+fprintf('\nxml_read output:\n')
+rPref=[]; rPref.NoCells=false;
+gen_object_display(xml_read('test.xml', rPref))
+
+%% Write 2D cell array in HTML format
+MyTree = [];
+MyTree.table.ATTRIBUTE.border=1;
+MyTree.table.CONTENT = {'Apples', '44%'; 'Bannanas', '23%'; 'Oranges', '13%'; 'Other', '10%'};
+xml_write('html/test.html', MyTree);
+type('html/test.html')
+%%
+% Click on <test.html> to opened this file with a web brouwser
+
+%% "Pref.StructTable" flag in "xml_write" (controls 2D arrays of structs)
+% *Create a simple structure with arrays of struct's*
+MyTree = [];
+MyTree.a(1,1).b = 'jack';
+MyTree.a(1,2).b = 'john';
+MyTree.a(2,1).b = 'jim';
+MyTree.a(2,2).b = 'jill';
+gen_object_display(MyTree)
+%%
+% *Write XML with "StructTable = 'Html" (default). This option mimics use of  
+%  HTML "tr" and "td"  tags to encode 2D tables. Tag names can  
+%  be changed using TableName parameter (see below)*
+wPref = [];
+wPref.StructTable = 'Html';
+xml_write('test.xml', MyTree, 'MyTree',wPref);
+type('test.xml')
+fprintf('\nxml_read output:\n')
+gen_object_display(xml_read ('test.xml'))
+%%
+% *Write XML with "CellTable = 'Vector'".*
+%  Converts 2D arrays to 1D array and item or regular notation. This option 
+%  is mostly provided for backward compatibility since this was the 
+%  behavior in prior verions of the code
+wPref = [];
+wPref.StructTable = 'Vector';
+xml_write('test.xml', MyTree, 'MyTree',wPref);
+type('test.xml')
+fprintf('\nxml_read output:\n')
+gen_object_display(xml_read ('test.xml'))
+
+%% "Pref.TableName" flag in "xml_write" (controls encoding tags used for 2D arrays)
+% *Create a cell object*
+MyTree = [];
+MyTree.M = {[1,2;3,4], 'M12'; 21, {11, 'N12'; 21, 'N22'}};
+gen_object_display(MyTree);
+%%
+% *Save it to xml file, using 'Html' notation but with different names for 
+%  rows and cells*
+Pref=[]; Pref.TableName = {'row','cell'};
+xml_write('test.xml', MyTree, 'MyTree',Pref);
+type('test.xml')
+
+%% "Pref.TableName" flag in "xml_read"
+% *Read above file with default settings ("Pref.TableName = {'tr','td'}")*
+% The results do not match the original structure
+Pref=[]; Pref.NoCells  = false;
+gen_object_display(xml_read('test.xml', Pref))
+%%
+% *Read above file with "Pref.TableName = {'row','cell'}" - now saved and read 
+% MATLAB structures are the same*
+Pref=[]; 
+Pref.TableName = {'row','cell'};
+Pref.NoCells  = false;
+gen_object_display(xml_read('test.xml', Pref))
+
+%% "Pref.Str2Num" flag in xml_read (control conversion to numbers while reading)
+% *Create a cell/struct mixture object*
+MyTree = [];
+MyTree.str     = 'sphere';
+MyTree.num1    =  123;
+MyTree.num2    = '123';
+MyTree.num3    = '[Inf,NaN]';
+MyTree.calc    = '1+2+3+4';
+MyTree.func    = 'sin(pi)/2';
+MyTree.String1 = '[2003 10 30]'; 
+MyTree.String2 = '2003 10 30';   % array resembling date
+MyTree.ISO8601 = '2003-10-30';   % date in ISO 8601 format
+MyTree.US_date = '2003/10/30';   % US style date format
+MyTree.complex = '2003i-10e-30'; % complex number resembling a date
+gen_object_display(MyTree);
+%%
+% *Save it to xml file*
+xml_write('test.xml', MyTree);
+type('test.xml')
+%%
+% *Read above file with default settings*
+% ("Pref.Str2Num = true" or "Pref.Str2Num = 'smart'"). Under this setting all
+% strings that look like numbers are converted to numbers, except for 
+% strings that are recognized by MATLAB 'datenum' function as dates
+gen_object_display(xml_read('test.xml'))
+%%
+% *Note that all the fields of 'MyTree' can be converted to numbers (even 
+% 'sphere') but by default the function is trying to 'judge' if a string  
+% should be converted to a number or not*
+MyCell = {'sphere','1+2+3+4','sin(pi)/2','2003 10 30','2003-10-30','2003/10/30','2003i-10e-30'};
+cellfun(@str2num, MyCell, 'UniformOutput', false)
+%%
+% *Read above file with "Pref.Str2Num = false" or "Pref.Str2Num = 'never'" 
+% to keep all the fields in string format*
+Pref=[]; Pref.Str2Num = false;
+gen_object_display(xml_read('test.xml', Pref))
+%%
+% *Read above file with "Pref.Str2Num = always"  
+% to convert all strings that look like numbers to numbers* note the likelly 
+% unintendet conversion of 'ISO8601'
+Pref=[]; Pref.Str2Num   = 'always';
+gen_object_display(xml_read('test.xml', Pref))
+%%
+% *Notice that all three settings will produce the same output for "num1" and
+% "num2" and there is no way to reproduce the original "MyTree" structure.*
+
+%% "Pref.PreserveSpace" flag in xml_write (control handling of strings with leading/trailing spaces)
+% *Create a struct with strings*
+MyTree=[];
+MyTree.Empty     = '';
+MyTree.OneSpace  = ' ';
+MyTree.TwoSpaces = '  '; 
+MyTree.String1   = ' Hello      World ';
+%%
+% *Write XML with "PreserveSpace = false" (default).*
+Pref=[]; Pref.PreserveSpace = false; % (default setting)
+xml_write('test.xml', MyTree, [], Pref);
+type('test.xml')
+%%
+% *Write XML with "PreserveSpace = true".*
+Pref=[]; Pref.PreserveSpace = true; 
+xml_write('test.xml', MyTree, [], Pref);
+type('test.xml')
+
+%% "Pref.PreserveSpace" flag in xml_read
+% *Read file while using "PreserveSpace = false" (default).*
+Pref=[]; Pref.PreserveSpace = false; % (default setting)
+gen_object_display(xml_read('test.xml',Pref))
+%%
+% *Read file while using "PreserveSpace = true".*
+Pref=[]; Pref.PreserveSpace = true; 
+gen_object_display(xml_read('test.xml',Pref))
+
+
+%% Write XML files with ATTRIBUTEs 
+% In order to add node attributes a special ATTRIBUTE field is used. 
+% ATTRIBUTEs have to be of simple types like numbers or strings (not
+% struct or cells). Attributes are easy to attach to structs nodes like 
+% MyTree below. 
+MyTree=[];
+MyTree.MyNumber = 13;
+MyTree.MyString = 'Hello World'; % simple case
+MyTree.ATTRIBUTE.Num = 2;
+xml_write('test.xml', MyTree);
+type('test.xml')
+
+%%  
+% In case when one needs to attach attributes to nodes which are not
+% structs (for example strings, numbers or calls) then special CONTENT 
+% field needs to be used to make the node a struct node.
+MyTree=[];
+MyTree.MyNumber = 13;
+MyTree.MyString.CONTENT = 'Hello World'; % simple case
+MyTree.MyString.ATTRIBUTE.Num = 2;
+xml_write('test.xml', MyTree);
+type('test.xml')
+
+%% "Pref.Str2Num" flag in file with ATTRIBUTEs
+% *Create a cell/struct mixture object*
+MyTree = [];
+MyTree.X.ATTRIBUTE.str     = 'sphere';
+MyTree.X.ATTRIBUTE.num1    =  123;
+MyTree.X.ATTRIBUTE.num2    = '123';
+MyTree.X.ATTRIBUTE.num3    = '[Inf,NaN]';
+MyTree.X.ATTRIBUTE.calc    = '1+2+3+4';
+MyTree.X.ATTRIBUTE.func    = 'sin(pi)/2';
+MyTree.X.ATTRIBUTE.String1 = '[2003 10 30]'; 
+MyTree.X.ATTRIBUTE.String2 = '2003 10 30';   % array resembling date
+MyTree.X.ATTRIBUTE.ISO8601 = '2003-10-30';   % date in ISO 8601 format
+MyTree.X.ATTRIBUTE.US_date = '2003/10/30';   % US style date format
+MyTree.X.ATTRIBUTE.complex = '2003i-10e-30'; % complex number resembling a date
+gen_object_display(MyTree);
+%%
+% *Save it to xml file*
+xml_write('test.xml', MyTree);
+type('test.xml')
+%%
+% *Read above file with default settings*
+% ("Pref.Str2Num = true" or "Pref.Str2Num = 'smart'"). Under this setting all
+% strings that look like numbers are converted to numbers, except for 
+% strings that are recognized by MATLAB 'datenum' function as dates
+gen_object_display(xml_read('test.xml'))
+
+%%
+% *Read above file with "Pref.Str2Num = false" or "Pref.Str2Num = 'never'" 
+% to keep all the fields in string format*
+Pref=[]; Pref.Str2Num = false;
+gen_object_display(xml_read('test.xml', Pref))
+%%
+% *Read above file with "Pref.Str2Num = always"  
+% to convert all strings that look like numbers to numbers* 
+Pref=[]; Pref.Str2Num   = 'always';
+gen_object_display(xml_read('test.xml', Pref))
+%%
+% *Notice that all three settings will produce the same output for "num1" and
+% "num2" and there is no way to reproduce the original "MyTree" structure.*
+
+
+%% Write XML files with COMMENTs
+% Insertion of Comments is done with help of special COMMENT field.
+% Note that MATLAB's xmlwrite is less readable due to lack of end-of-line 
+% characters around comment section. 
+MyTree=[];
+MyTree.COMMENT = 'This is a comment';
+MyTree.MyNumber = 13;
+MyTree.MyString.CONTENT = 'Hello World';
+xml_write('test.xml', MyTree);
+type('test.xml')
+
+%%
+% *Same operation using Apache Xerces XML engine*
+% gives the same result
+Pref=[]; Pref.XmlEngine = 'Xerces';  % use Xerces xml generator directly
+xml_write('test.xml', MyTree, 'MyTree', Pref);
+type('test.xml')
+
+%%
+% *Comments in XML top level (method #1)*
+% This method uses cell array 
+MyTree=[];
+MyTree.MyNumber = 13;
+MyTree.MyString = 'Hello World';
+xml_write('test.xml', MyTree, {'MyTree', [], 'This is a global comment'});
+type('test.xml')
+%%
+% *Same operation using Apache Xerces XML engine* 
+% gives even nicer results.
+Pref=[]; Pref.XmlEngine = 'Xerces';  % use Xerces xml generator directly
+xml_write('test.xml', MyTree, {'MyTree', [], 'This is a global comment'}, Pref);
+type('test.xml')
+
+%%
+% *Comments in XML top level (method #2)*
+% This method adds an extra top layer to the struct 'tree' and sets
+% "Pref.RootOnly = false", which informs the function about the extra 
+% layer. Notice that RootName is also saved as a part of
+% the 'tree', and does not have to be passed in separately.
+MyTree=[];
+MyTree.COMMENT = 'This is a global comment';
+MyTree.MyTest.MyNumber = 13;
+MyTree.MyTest.MyString = 'Hello World';
+Pref=[]; Pref.RootOnly = false;
+xml_write('test.xml', MyTree, [], Pref);
+type('test.xml')
+%%
+% *Same operation using Apache Xerces XML engine*
+Pref=[]; Pref.XmlEngine = 'Xerces';  % use Xerces xml generator directly
+Pref.RootOnly  = false;
+xml_write('test.xml', MyTree, [], Pref);
+type('test.xml')
+
+%% Write XML files with PROCESSING_INSTRUCTIONs 
+% Insertion of Processing Instructions is done through use of special 
+% PROCESSING_INSTRUCTION field, which stores the instruction string. The
+% string has to be in 'target data' format separated by space.
+MyTree=[];
+MyTree.PROCESSING_INSTRUCTION = 'xml-stylesheet type="a" href="foo"';
+MyTree.MyNumber = 13;
+MyTree.MyString = 'Hello World';
+xml_write('test.xml', MyTree);
+type('test.xml')
+
+%%
+% *Same operation using Apache Xerces XML engine*
+Pref=[]; Pref.XmlEngine = 'Xerces';  % use Xerces xml generator directly
+xml_write('test.xml', MyTree, 'MyTree', Pref);
+type('test.xml')
+
+%%
+% *PROCESSING_INSTRUCTIONs in XML top level (method #1)*
+% This method uses cell array 
+MyTree=[];
+MyTree.MyNumber = 13;
+MyTree.MyString = 'Hello World';
+xml_write('test.xml', MyTree, {'MyTree', 'xml-stylesheet type="a" href="foo"'});
+type('test.xml')
+%%
+% *Same operation using Apache Xerces XML engine*
+Pref=[]; Pref.XmlEngine = 'Xerces';  % use Xerces xml generator directly
+xml_write('test.xml', MyTree, {'MyTree', 'xml-stylesheet type="a" href="foo"'}, Pref);
+type('test.xml')
+
+%%
+% *PROCESSING_INSTRUCTIONs in XML top level (method #2)*
+% This method adds an extra top layer to the struct 'tree' and sets
+% pref.RootOnly=false, which informs the function about the extra 
+% layer. Notice that RootName is also saved as a part of
+% the 'tree', and does not have to be passed in separately.
+MyTree=[];
+MyTree.PROCESSING_INSTRUCTION =  'xml-stylesheet type="a" href="foo"';
+MyTree.MyTest.MyNumber = 13;
+MyTree.MyTest.MyString = 'Hello World';
+Pref=[]; Pref.RootOnly = false;
+xml_write('test.xml', MyTree, [], Pref);
+type('test.xml')
+%%
+% *Same operation using Apache Xerces XML engine*
+Pref=[]; Pref.XmlEngine = 'Xerces';  % use Xerces xml generator directly
+Pref.RootOnly  = false;
+xml_write('test.xml', MyTree, 'MyTree', Pref);
+type('test.xml')
+
+%% Write XML files with CDATA Sections 
+% "In an XML document a CDATA (Character DATA) section is a section of 
+%  element content that is marked for the parser to interpret as only 
+%  character data, not markup." (from Wikipedia) 
+% To insert CDATA Sections one use special CDATA_SECTION field,
+%  which stores the instruction string. Note that MATLAB's xmlwrite created
+%  wrong xml code for CDATA section
+MyTree=[];
+MyTree.CDATA_SECTION = '<A>txt</A>';
+MyTree.MyNumber = 13;
+MyTree.MyString = 'Hello World';
+xml_write('test.xml', MyTree);
+type('test.xml')
+%%
+% *Same operation using Apache Xerces XML engine produces correct results*
+Pref=[]; Pref.XmlEngine = 'Xerces';  % use Xerces xml generator directly
+xml_write('test.xml', MyTree, 'MyTree', Pref);
+type('test.xml')
+
+%% Write XML files with special characters in TAG names
+% The input to xml_write requires that all tags one wants in XML document 
+% have to be encoded as field names of MATLAB's struct's. Matlab has a lot
+% of restrictions on variable names. This section is about XML tags with
+% names not allowed as MATLAB variables, or more specifically with
+% characters allowed as xml tag names but not allowed as MATLAB variable
+% names. Characters like that can be replaced by their hexadecimal
+% representation just as it is done by genvarname function. Alternative way
+% of writing the first example is:
+MyTree=[];
+MyTree.('MyNumber') = 13;               % same as MyTree.MyNumber = 13;
+MyTree.MyString.CONTENT = 'Hello World';
+MyTree.MyString.ATTRIBUTE.('Num') = 2;  % same as MyTree.MyString.ATTRIBUTE.Num = 2;
+xml_write('test.xml', MyTree);
+type('test.xml')
+
+%%
+% *This approach fails for some characters like dash '-', colon ':', and
+% international characters.*
+MyTree=[];
+try
+  MyTree.('My-Number') = 13;
+  MyTree.MyString.CONTENT = 'Hello World';
+  MyTree.MyString.ATTRIBUTE.('Num_ö') = 2;
+catch  %#ok<CTCH>
+  err = lasterror; %#ok<LERR>
+  disp(err.message);
+end
+
+%%
+% It can be overcome by replacing offending characters with their 
+% hexadecimal representation. That can be done manually or with use of 
+% genvarname function. Note that MATLAB 'type' function does not show
+% correctly 'ö' letter in xml file, but opening the file in editor shows 
+% that it is correct.
+MyTree=[];
+MyTree.(genvarname('My-Number')) = 13;
+MyTree.MyString.CONTENT = 'Hello World';
+MyTree.MyString.ATTRIBUTE.Num_0xF6 = 2;
+gen_object_display(MyTree);
+xml_write('test.xml', MyTree);
+type('test.xml')
+
+%%
+% *Also two of the characters '-' and ':' can be encoded by a special strings:
+% '_DASH_' and '_COLON_' respectively*
+MyTree=[];
+MyTree.My_DASH_Number = 13;
+MyTree.MyString.CONTENT = 'Hello World';
+MyTree.MyString.ATTRIBUTE.Num0xF6 = 2;
+xml_write('test.xml', MyTree);
+type('test.xml')
+
+%% Write XML files with Namespaces
+% No extra special fields are needed to define XML namespaces, only colon 
+% character written using '0x3A' or '_COLON_'. Below is an
+% example of a namespace definition
+MyTree=[];
+MyTree.f_COLON_child.ATTRIBUTE.xmlns_COLON_f = 'http://www.foo.com';
+MyTree.f_COLON_child.f_COLON_MyNumber = 13;
+MyTree.f_COLON_child.f_COLON_MyString = 'Hello World';
+xml_write('test.xml', MyTree, 'MyTree');
+type('test.xml')
+%%
+% *Same operation using Apache Xerces XML engine*
+Pref=[]; Pref.XmlEngine = 'Xerces';  % use Xerces xml generator directly
+xml_write('test.xml', MyTree, 'f_COLON_MyTree', Pref);
+type('test.xml')
+
+%% "Pref.KeepNS" flag in "xml_read"
+% Thise option allow keeping  or exclusion of namespaces in tag names. 
+% By default the namespace data is kept but it produces much longer field
+% names in the output structure. Ignoring namespace will produce more
+% readible output.
+% Perform default read of file with namespace
+tree = xml_read('test.xml');
+gen_object_display(tree);
+
+%%
+% Now the same operation with KeepNS = false. 
+Pref=[]; Pref.KeepNS = false; % do not read attributes
+tree = xml_read('test.xml', Pref);
+gen_object_display(tree);
+
+%% Read XML files with special node types
+% Display and read the file, then show the data structure. Note that 
+% MATLAB 'type' function shows 'ö' letter incorrectly as 'A¶' in xml file, 
+% but opening the file in editor shows that it is correct.
+fprintf('Test xml file:\n');
+type('test_file.xml')
+%%
+% Read only the Root Element (default) 
+[tree GlobalTextNodes] = xml_read('test_file.xml');
+fprintf('Global Data (Root name, Global Processing Instructions and Global Comments):\n');
+disp(GlobalTextNodes')
+fprintf('\nStructure read from the file (uncludes COMMENT and CDATA sections):\n');
+gen_object_display(tree);
+%%
+% Read the whole tree including global Comments and Processing Instructions
+Pref=[]; Pref.RootOnly = false;
+[tree GlobalTextNodes] = xml_read('test_file.xml', Pref);
+fprintf('Global Data (Root name, Global Processing Instructions and Global Comments):\n');
+disp(GlobalTextNodes')
+fprintf('\nStructure read from the file (uncludes COMMENT and CDATA sections):\n');
+gen_object_display(tree);
+
+%% "Pref.ReadAttr" flag in "xml_read" (control handling of nodes with attributes)
+% Those option allow exclusion of attributes 
+Pref=[]; Pref.ReadAttr = false; % do not read attributes
+tree = xml_read('test_file.xml', Pref);
+gen_object_display(tree);
+
+%% "Pref.ReadSpec" flag in "xml_read"
+% Those option allow exclusion of special nodes, like
+% comments, processing instructions, CData sections, etc.
+Pref=[]; Pref.ReadSpec = false; % do not read special node types
+tree = xml_read('test_file.xml', Pref);
+gen_object_display(tree);
+
+%% "Pref.RootOnly" flag in "xml_read"
+% As it was shown in previous examples RootOnly parameter can be used to
+% capture global (top level) special nodes (like COMMENTs and
+% PROCESSING_INSTRUCTIONs) which are ignored by default
+Pref=[]; Pref.RootOnly = false; % do not read special node types
+tree = xml_read('test_file.xml', Pref);
+gen_object_display(tree);
+
+%% "Pref.RootOnly" flag in "xml_write"
+% Writing previously read tree with default "Pref.RootOnly = true" gives
+% wrong output file
+Pref=[]; Pref.RootOnly = true; % do not read special node types
+xml_write('test.xml', tree, [], Pref);
+fprintf('Test xml file:\n');
+type('test.xml')
+%%
+% Writing the same tree with "Pref.RootOnly = false" gives correct output
+Pref=[]; Pref.RootOnly = false; % do not read special node types
+xml_write('test.xml', tree, [], Pref);
+fprintf('Test xml file:\n');
+type('test.xml')
+
+%% "Pref.NumLevels" flag in "xml_read"
+% This parameter allows user to skip parts of the tree in order to save
+% time and memory. Usefull only in a rare case when a small portion of
+% large XML file is needed.
+%
+% Create test tile
+MyTree = [];
+MyTree.Level1 = 1;
+MyTree.Level1_.Level2 = 2;
+MyTree.Level1_.Level2_.Level3 = 3;
+MyTree.Level1_.Level2_.Level3_.Level4 = 4;
+xml_write('test.xml', MyTree);
+fprintf('Test xml file:\n');
+type('test.xml')
+%%
+% *Use Default ("Pref.NumLevels = infinity") setting*
+tree = xml_read('test.xml');
+gen_object_display(tree);
+%%
+% *Limit the read to only 2 levels*
+Pref=[]; Pref.NumLevels = 2; 
+tree = xml_read('test.xml', Pref);
+gen_object_display(tree);
+
+
+
+
+%% Create DOM object based on a Struct using "xml_write"
+% *Create Struct tree*
+MyTree=[];
+MyTree.MyNumber = 13;
+MyTree.MyString = 'Hello World';
+%%
+% *Convert Struct to DOM object using xml_write*
+DOM = xml_write([], MyTree); 
+xmlwrite('test.xml', DOM);   % Save DOM object using MATLAB function 
+type('test.xml')
+
+%% Convert DOM object to Struct using "xml_read"
+DOM = xmlread('test.xml');       % Read DOM object using MATLAB function
+[tree treeName] = xml_read(DOM); % Convert DOM object to Struct
+disp([treeName{1} ' ='])
+gen_object_display(tree)
+
+%% Write XML file based on a DOM using "xml_write_xerces"
+xmlwrite_xerces('test.xml', DOM); % Save DOM object using Xerces library 
+type('test.xml')
+
+%% Write XML to string instead of a file
+DOM = xml_write([], MyTree);
+str = xmlwrite(DOM);
+disp(str)
+
+%% Write XML file with embedded binary data encoded as Base64 (using java version)
+fid = fopen('football.jpg', 'rb');       
+raw1 = uint8(fread(fid, 'uint8'));                % read image file as a raw binary
+fclose(fid);
+
+MyTree=[];
+MyTree.Size = 13;
+MyTree.MyString = 'Hello World'; % simple case
+MyTree.MyImage.ATTRIBUTE.EncodingMIMEType = 'base64';
+MyTree.MyImage.CONTENT = base64encode(raw1,'java');% perform base64 encoding of the binary data
+xml_write('test.xml', MyTree);             % write xml file
+
+%% Read XML file with embedded binary data encoded as Base64 (using java version)
+tree = xml_read('test.xml', Pref);         % read xml file
+raw  = base64decode(tree.MyImage.CONTENT, '', 'java');   % convert xml image to raw binary
+fid = fopen('MyFootball.jpg', 'wb');  
+fwrite(fid, raw, 'uint8');                 % dumb the raw binary to the hard disk 
+fclose(fid);
+I = imread('MyFootball.jpg');              % read it as an image
+imshow(I);
+
+%% Write XML file with embedded binary data encoded as Base64 (simpler version using only matlab code
+% Notice that process of writing to xml stripped all end-of-lie characters
+% from base64 code.
+isChunked = true; % break into chunks 76 characters long
+url_safe  = true; % 'base64url' encoding
+code = base64encode('license.txt', 'matlab', isChunked, url_safe);
+disp(code)
+MyTree=[];
+MyTree.Size = 13;
+MyTree.MyString = 'Hello World'; 
+MyTree.MyImage.ATTRIBUTE.EncodingMIMEType = 'base64';
+MyTree.MyImage.CONTENT = code;   % perform base64 encoding of the binary data
+xml_write('test.xml', MyTree);   % write xml file
+type('test.xml')
+
+%% Read XML file with embedded binary data encoded as Base64 (simpler version using only matlab code
+tree = xml_read('test.xml', Pref);         % read xml file
+base64decode(tree.MyImage.CONTENT, 'license2.txt', 'matlab'); % save xml image as raw binary
+type('license2.txt')

matlab_runners/Action Unit Experiments/helpers/xml_io_tools_2010_11_05/xml_write.m

@@ -0,0 +1,447 @@
+function DOMnode = xml_write(filename, tree, RootName, Pref)
+%XML_WRITE  Writes Matlab data structures to XML file
+%
+% DESCRIPTION
+% xml_write( filename, tree) Converts Matlab data structure 'tree' containing
+% cells, structs, numbers and strings to Document Object Model (DOM) node
+% tree, then saves it to XML file 'filename' using Matlab's xmlwrite
+% function. Optionally one can also use alternative version of xmlwrite
+% function which directly calls JAVA functions for XML writing without
+% MATLAB middleware. This function is provided as a patch to existing
+% bugs in xmlwrite (in R2006b).
+%
+% xml_write(filename, tree, RootName, Pref) allows you to specify
+% additional preferences about file format
+%
+% DOMnode = xml_write([], tree) same as above except that DOM node is
+% not saved to the file but returned.
+%
+% INPUT
+%   filename     file name
+%   tree         Matlab structure tree to store in xml file.
+%   RootName     String with XML tag name used for root (top level) node
+%                Optionally it can be a string cell array storing: Name of
+%                root node, document "Processing Instructions" data and
+%                document "comment" string
+%   Pref         Other preferences:
+%     Pref.ItemName - default 'item' -  name of a special tag used to
+%                     itemize cell or struct arrays
+%     Pref.XmlEngine - let you choose the XML engine. Currently default is
+%       'Xerces', which is using directly the apache xerces java file.
+%       Other option is 'Matlab' which uses MATLAB's xmlwrite and its
+%       XMLUtils java file. Both options create identical results except in
+%       case of CDATA sections where xmlwrite fails.
+%     Pref.CellItem - default 'true' - allow cell arrays to use 'item'
+%       notation. See below.
+%    Pref.RootOnly - default true - output variable 'tree' corresponds to
+%       xml file root element, otherwise it correspond to the whole file.
+%     Pref.StructItem - default 'true' - allow arrays of structs to use
+%       'item' notation. For example "Pref.StructItem = true" gives:
+%         <a>
+%           <b>
+%             <item> ... <\item>
+%             <item> ... <\item>
+%           <\b>
+%         <\a>
+%       while "Pref.StructItem = false" gives:
+%         <a>
+%           <b> ... <\b>
+%           <b> ... <\b>
+%         <\a>
+%
+%
+% Several special xml node types can be created if special tags are used
+% for field names of 'tree' nodes:
+%  - node.CONTENT - stores data section of the node if other fields
+%    (usually ATTRIBUTE are present. Usually data section is stored
+%    directly in 'node'.
+%  - node.ATTRIBUTE.name - stores node's attribute called 'name'.
+%  - node.COMMENT - create comment child node from the string. For global
+%    comments see "RootName" input variable.
+%  - node.PROCESSING_INSTRUCTIONS - create "processing instruction" child
+%    node from the string. For global "processing instructions" see
+%    "RootName" input variable.
+%  - node.CDATA_SECTION - stores node's CDATA section (string). Only works
+%    if Pref.XmlEngine='Xerces'. For more info, see comments of F_xmlwrite.
+%  - other special node types like: document fragment nodes, document type
+%    nodes, entity nodes and notation nodes are not being handled by
+%    'xml_write' at the moment.
+%
+% OUTPUT
+%   DOMnode      Document Object Model (DOM) node tree in the format
+%                required as input to xmlwrite. (optional)
+%
+% EXAMPLES:
+%   MyTree=[];
+%   MyTree.MyNumber = 13;
+%   MyTree.MyString = 'Hello World';
+%   xml_write('test.xml', MyTree);
+%   type('test.xml')
+%   %See also xml_tutorial.m
+%
+% See also
+%   xml_read, xmlread, xmlwrite
+%
+% Written by Jarek Tuszynski, SAIC, jaroslaw.w.tuszynski_at_saic.com
+
+%% Check Matlab Version
+v = ver('MATLAB');
+v = str2double(regexp(v.Version, '\d.\d','match','once'));
+if (v<7)
+  error('Your MATLAB version is too old. You need version 7.0 or newer.');
+end
+
+%% default preferences
+DPref.TableName  = {'tr','td'}; % name of a special tags used to itemize 2D cell arrays
+DPref.ItemName   = 'item'; % name of a special tag used to itemize 1D cell arrays
+DPref.StructItem = true;  % allow arrays of structs to use 'item' notation
+DPref.CellItem   = true;  % allow cell arrays to use 'item' notation
+DPref.StructTable= 'Html';
+DPref.CellTable  = 'Html';
+DPref.XmlEngine  = 'Matlab';  % use matlab provided XMLUtils
+%DPref.XmlEngine  = 'Xerces';  % use Xerces xml generator directly
+DPref.PreserveSpace = false; % Preserve or delete spaces at the beggining and the end of stings?
+RootOnly         = true;  % Input is root node only
+GlobalProcInst = [];
+GlobalComment  = [];
+GlobalDocType  = [];
+
+%% read user preferences
+if (nargin>3)
+  if (isfield(Pref, 'TableName' )),  DPref.TableName  = Pref.TableName; end
+  if (isfield(Pref, 'ItemName'  )), DPref.ItemName   = Pref.ItemName;   end
+  if (isfield(Pref, 'StructItem')), DPref.StructItem = Pref.StructItem; end
+  if (isfield(Pref, 'CellItem'  )), DPref.CellItem   = Pref.CellItem;   end
+  if (isfield(Pref, 'CellTable')),   DPref.CellTable  = Pref.CellTable; end
+  if (isfield(Pref, 'StructTable')), DPref.StructTable= Pref.StructTable; end
+  if (isfield(Pref, 'XmlEngine' )), DPref.XmlEngine  = Pref.XmlEngine;  end
+  if (isfield(Pref, 'RootOnly'  )), RootOnly         = Pref.RootOnly;   end
+  if (isfield(Pref, 'PreserveSpace')), DPref.PreserveSpace = Pref.PreserveSpace; end
+end
+if (nargin<3 || isempty(RootName)), RootName=inputname(2); end
+if (isempty(RootName)), RootName='ROOT'; end
+if (iscell(RootName)) % RootName also stores global text node data
+  rName = RootName;
+  RootName = char(rName{1});
+  if (length(rName)>1), GlobalProcInst = char(rName{2}); end
+  if (length(rName)>2), GlobalComment  = char(rName{3}); end
+  if (length(rName)>3), GlobalDocType  = char(rName{4}); end
+end
+if(~RootOnly && isstruct(tree))  % if struct than deal with each field separatly
+  fields = fieldnames(tree);
+  for i=1:length(fields)
+    field = fields{i};
+    x = tree(1).(field);
+    if (strcmp(field, 'COMMENT'))
+      GlobalComment = x;
+    elseif (strcmp(field, 'PROCESSING_INSTRUCTION'))
+      GlobalProcInst = x;
+    elseif (strcmp(field, 'DOCUMENT_TYPE'))
+      GlobalDocType = x;
+    else
+      RootName = field;
+      t = x;
+    end
+  end
+  tree = t;
+end
+
+%% Initialize jave object that will store xml data structure
+RootName = varName2str(RootName);
+if (~isempty(GlobalDocType))
+  %   n = strfind(GlobalDocType, ' ');
+  %   if (~isempty(n))
+  %     dtype = com.mathworks.xml.XMLUtils.createDocumentType(GlobalDocType);
+  %   end
+  %   DOMnode = com.mathworks.xml.XMLUtils.createDocument(RootName, dtype);
+  warning('xml_io_tools:write:docType', ...
+    'DOCUMENT_TYPE node was encountered which is not supported yet. Ignoring.');
+end
+DOMnode = com.mathworks.xml.XMLUtils.createDocument(RootName);
+
+
+%% Use recursive function to convert matlab data structure to XML
+root = DOMnode.getDocumentElement;
+struct2DOMnode(DOMnode, root, tree, DPref.ItemName, DPref);
+
+%% Remove the only child of the root node
+root   = DOMnode.getDocumentElement;
+Child  = root.getChildNodes; % create array of children nodes
+nChild = Child.getLength;    % number of children
+if (nChild==1)
+  node = root.removeChild(root.getFirstChild);
+  while(node.hasChildNodes)
+    root.appendChild(node.removeChild(node.getFirstChild));
+  end
+  while(node.hasAttributes)            % copy all attributes
+    root.setAttributeNode(node.removeAttributeNode(node.getAttributes.item(0)));
+  end
+end
+
+%% Save exotic Global nodes
+if (~isempty(GlobalComment))
+  DOMnode.insertBefore(DOMnode.createComment(GlobalComment), DOMnode.getFirstChild());
+end
+if (~isempty(GlobalProcInst))
+  n = strfind(GlobalProcInst, ' ');
+  if (~isempty(n))
+    proc = DOMnode.createProcessingInstruction(GlobalProcInst(1:(n(1)-1)),...
+      GlobalProcInst((n(1)+1):end));
+    DOMnode.insertBefore(proc, DOMnode.getFirstChild());
+  end
+end
+% Not supported yet as the code below does not work
+% if (~isempty(GlobalDocType))
+%   n = strfind(GlobalDocType, ' ');
+%   if (~isempty(n))
+%     dtype = DOMnode.createDocumentType(GlobalDocType);
+%     DOMnode.insertBefore(dtype, DOMnode.getFirstChild());
+%   end
+% end
+
+%% save java DOM tree to XML file
+if (~isempty(filename))
+  if (strcmpi(DPref.XmlEngine, 'Xerces'))
+    xmlwrite_xerces(filename, DOMnode);
+  else
+    xmlwrite(filename, DOMnode);
+  end
+end
+
+
+%% =======================================================================
+%  === struct2DOMnode Function ===========================================
+%  =======================================================================
+function [] = struct2DOMnode(xml, parent, s, TagName, Pref)
+% struct2DOMnode is a recursive function that converts matlab's structs to
+% DOM nodes.
+% INPUTS:
+%  xml - jave object that will store xml data structure
+%  parent - parent DOM Element
+%  s - Matlab data structure to save
+%  TagName - name to be used in xml tags describing 's'
+%  Pref - preferenced
+% OUTPUT:
+%  parent - modified 'parent'
+
+% perform some conversions
+if (ischar(s) && min(size(s))>1) % if 2D array of characters
+  s=cellstr(s);                  % than convert to cell array
+end
+% if (strcmp(TagName, 'CONTENT'))
+%   while (iscell(s) && length(s)==1), s = s{1}; end % unwrap cell arrays of length 1
+% end
+TagName  = varName2str(TagName);
+
+%% == node is a 2D cell array ==
+% convert to some other format prior to further processing
+nDim = nnz(size(s)>1);  % is it a scalar, vector, 2D array, 3D cube, etc?
+if (iscell(s) && nDim==2 && strcmpi(Pref.CellTable, 'Matlab'))
+  s = var2str(s, Pref.PreserveSpace);
+end
+if (nDim==2 && (iscell  (s) && strcmpi(Pref.CellTable,   'Vector')) || ...
+               (isstruct(s) && strcmpi(Pref.StructTable, 'Vector')))
+  s = s(:);
+end
+if (nDim>2), s = s(:); end % can not handle this case well
+nItem = numel(s);
+nDim  = nnz(size(s)>1);  % is it a scalar, vector, 2D array, 3D cube, etc?
+
+%% == node is a cell ==
+if (iscell(s)) % if this is a cell or cell array
+  if ((nDim==2 && strcmpi(Pref.CellTable,'Html')) || (nDim< 2 && Pref.CellItem))
+    % if 2D array of cells than can use HTML-like notation or if 1D array
+    % than can use item notation
+    if (strcmp(TagName, 'CONTENT')) % CONTENT nodes already have <TagName> ... </TagName>
+      array2DOMnode(xml, parent, s, Pref.ItemName, Pref ); % recursive call
+    else
+      node = xml.createElement(TagName);   % <TagName> ... </TagName>
+      array2DOMnode(xml, node, s, Pref.ItemName, Pref ); % recursive call
+      parent.appendChild(node);
+    end
+  else % use  <TagName>...<\TagName> <TagName>...<\TagName> notation
+    array2DOMnode(xml, parent, s, TagName, Pref ); % recursive call
+  end
+%% == node is a struct ==
+elseif (isstruct(s))  % if struct than deal with each field separatly
+  if ((nDim==2 && strcmpi(Pref.StructTable,'Html')) || (nItem>1 && Pref.StructItem))
+    % if 2D array of structs than can use HTML-like notation or
+    % if 1D array of structs than can use 'items' notation
+    node = xml.createElement(TagName);
+    array2DOMnode(xml, node, s, Pref.ItemName, Pref ); % recursive call
+    parent.appendChild(node);
+  elseif (nItem>1) % use  <TagName>...<\TagName> <TagName>...<\TagName> notation
+    array2DOMnode(xml, parent, s, TagName, Pref ); % recursive call
+  else % otherwise save each struct separatelly
+    fields = fieldnames(s);
+    node = xml.createElement(TagName);
+    for i=1:length(fields) % add field by field to the node
+      field = fields{i};
+      x = s.(field);
+      switch field
+        case {'COMMENT', 'CDATA_SECTION', 'PROCESSING_INSTRUCTION'}
+          if iscellstr(x)  % cell array of strings -> add them one by one
+            array2DOMnode(xml, node, x(:), field, Pref ); % recursive call will modify 'node'
+          elseif ischar(x) % single string -> add it
+            struct2DOMnode(xml, node, x, field, Pref ); % recursive call will modify 'node'
+          else % not a string - Ignore
+            warning('xml_io_tools:write:badSpecialNode', ...
+             ['Struct field named ',field,' encountered which was not a string. Ignoring.']);
+          end
+        case 'ATTRIBUTE' % set attributes of the node
+          if (isempty(x)), continue; end
+          if (isstruct(x))
+            attName = fieldnames(x);       % get names of all the attributes
+            for k=1:length(attName)        % attach them to the node
+              att = xml.createAttribute(varName2str(attName(k)));
+              att.setValue(var2str(x.(attName{k}),Pref.PreserveSpace));
+              node.setAttributeNode(att);
+            end
+          else
+            warning('xml_io_tools:write:badAttribute', ...
+              'Struct field named ATTRIBUTE encountered which was not a struct. Ignoring.');
+          end
+        otherwise                            % set children of the node
+          struct2DOMnode(xml, node, x, field, Pref ); % recursive call will modify 'node'
+      end
+    end  % end for i=1:nFields
+    parent.appendChild(node);
+  end
+%% == node is a leaf node ==
+else  % if not a struct and not a cell than it is a leaf node
+  switch TagName % different processing depending on desired type of the node
+    case 'COMMENT'   % create comment node
+      com = xml.createComment(s);
+      parent.appendChild(com);
+    case 'CDATA_SECTION' % create CDATA Section
+      cdt = xml.createCDATASection(s);
+      parent.appendChild(cdt);
+    case 'PROCESSING_INSTRUCTION' % set attributes of the node
+      OK = false;
+      if (ischar(s))
+        n = strfind(s, ' ');
+        if (~isempty(n))
+          proc = xml.createProcessingInstruction(s(1:(n(1)-1)),s((n(1)+1):end));
+          parent.insertBefore(proc, parent.getFirstChild());
+          OK = true;
+        end
+      end
+      if (~OK)
+        warning('xml_io_tools:write:badProcInst', ...
+          ['Struct field named PROCESSING_INSTRUCTION need to be',...
+          ' a string, for example: xml-stylesheet type="text/css" ', ...
+          'href="myStyleSheet.css". Ignoring.']);
+      end
+    case 'CONTENT' % this is text part of already existing node
+      txt  = xml.createTextNode(var2str(s, Pref.PreserveSpace)); % convert to text
+      parent.appendChild(txt);
+    otherwise      % I guess it is a regular text leaf node
+      txt  = xml.createTextNode(var2str(s, Pref.PreserveSpace));
+      node = xml.createElement(TagName);
+      node.appendChild(txt);
+      parent.appendChild(node);
+  end
+end % of struct2DOMnode function
+
+%% =======================================================================
+%  === array2DOMnode Function ============================================
+%  =======================================================================
+function [] = array2DOMnode(xml, parent, s, TagName, Pref)
+% Deal with 1D and 2D arrays of cell or struct. Will modify 'parent'.
+nDim = nnz(size(s)>1);  % is it a scalar, vector, 2D array, 3D cube, etc?
+switch nDim
+  case 2 % 2D array
+    for r=1:size(s,1)
+      subnode = xml.createElement(Pref.TableName{1});
+      for c=1:size(s,2)
+        v = s(r,c);
+        if iscell(v), v = v{1}; end
+        struct2DOMnode(xml, subnode, v, Pref.TableName{2}, Pref ); % recursive call
+      end
+      parent.appendChild(subnode);
+    end
+  case 1 %1D array
+    for iItem=1:numel(s)
+      v = s(iItem);
+      if iscell(v), v = v{1}; end
+      struct2DOMnode(xml, parent, v, TagName, Pref ); % recursive call
+    end
+  case 0 % scalar -> this case should never be called
+    if ~isempty(s) 
+      if iscell(s), s = s{1}; end
+      struct2DOMnode(xml, parent, s, TagName, Pref );
+    end
+end
+
+%% =======================================================================
+%  === var2str Function ==================================================
+%  =======================================================================
+function str = var2str(object, PreserveSpace)
+% convert matlab variables to a string
+switch (1)
+  case isempty(object)
+    str = '';
+  case (isnumeric(object) || islogical(object))
+    if ndims(object)>2, object=object(:); end  % can't handle arrays with dimention > 2
+    str=mat2str(object);           % convert matrix to a string
+    % mark logical scalars with [] (logical arrays already have them) so the xml_read
+    % recognizes them as MATLAB objects instead of strings. Same with sparse
+    % matrices
+    if ((islogical(object) && isscalar(object)) || issparse(object)),
+      str = ['[' str ']'];
+    end
+    if (isinteger(object)),
+      str = ['[', class(object), '(', str ')]'];
+    end
+  case iscell(object)
+    if ndims(object)>2, object=object(:); end  % can't handle cell arrays with dimention > 2
+    [nr nc] = size(object);
+    obj2 = object;
+    for i=1:length(object(:))
+      str = var2str(object{i}, PreserveSpace);
+      if (ischar(object{i})), object{i} = ['''' object{i} '''']; else object{i}=str; end
+      obj2{i} = [object{i} ','];
+    end
+    for r = 1:nr, obj2{r,nc} = [object{r,nc} ';']; end
+    obj2 = obj2.';
+    str = ['{' obj2{:} '}'];
+  case isstruct(object)
+    str='';
+    warning('xml_io_tools:write:var2str', ...
+      'Struct was encountered where string was expected. Ignoring.');
+  case isa(object, 'function_handle')
+    str = ['[@' char(object) ']'];
+  case ischar(object)
+    str = object;
+  otherwise
+    str = char(object);
+end
+
+%% string clean-up
+str=str(:); str=str.';            % make sure this is a row vector of char's
+if (~isempty(str))
+  str(str<32|str==127)=' ';       % convert no-printable characters to spaces
+  if (~PreserveSpace)
+    str = strtrim(str);             % remove spaces from begining and the end
+    str = regexprep(str,'\s+',' '); % remove multiple spaces
+  end
+end
+
+%% =======================================================================
+%  === var2Namestr Function ==============================================
+%  =======================================================================
+function str = varName2str(str)
+% convert matlab variable names to a sting
+str = char(str);
+p   = strfind(str,'0x');
+if (~isempty(p))
+  for i=1:length(p)
+    before = str( p(i)+(0:3) );          % string to replace
+    after  = char(hex2dec(before(3:4))); % string to replace with
+    str = regexprep(str,before,after, 'once', 'ignorecase');
+    p=p-3; % since 4 characters were replaced with one - compensate
+  end
+end
+str = regexprep(str,'_COLON_',':', 'once', 'ignorecase');
+str = regexprep(str,'_DASH_' ,'-', 'once', 'ignorecase');
+

matlab_runners/Action Unit Experiments/helpers/xml_io_tools_2010_11_05/xmlwrite_xerces.m

@@ -0,0 +1,109 @@
+function varargout=xmlwrite_xerces(varargin)
+%XMLWRITE_XERCES Serialize an XML Document Object Model node using Xerces parser. 
+%  xmlwrite_xerces(FILENAME,DOMNODE) serializes the DOMNODE to file FILENAME.
+%
+% The function xmlwrite_xerces is very similar the Matlab function xmlwrite 
+% but works directly with the XERCES java classes (written by Apache XML 
+% Project) instead of the XMLUtils class created by Mathworks. Xerces files
+% are provided in standard MATLAB instalation and live in root\java\jarext
+% directory. 
+%
+% Written by A.Amaro (02-22-2007) and generously donated to xml_io_tools. 
+% This function is needed as a work-around for a bug in XMLUtils library
+% which can not write CDATA SECTION nodes correctly. Also Xerces and 
+% XMLUtils libraries handle namespaces differently.  
+%
+% Examples:
+%   % See xmlwrite examples this function have almost identical behavior.
+%  
+% Advanced use:
+%  FILENAME can also be a URN, java.io.OutputStream or java.io.Writer object
+%  SOURCE can also be a SAX InputSource, JAXP Source, InputStream, or 
+%    Reader object
+
+returnString = false;
+if length(varargin)==1
+    returnString = true;
+    result = java.io.StringWriter;
+    source = varargin{1};
+else
+    result = varargin{1};
+    if ischar(result)
+      % Using the XERCES classes directly, is not needed to modify the
+      % filename string. So I have commented this next line
+      %  result = F_xmlstringinput(result,false);
+    end
+    
+    source = varargin{2};
+    if ischar(source)
+        source = F_xmlstringinput(source,true);
+    end
+end
+
+% SERIALIZATION OF THE DOM DOCUMENT USING XERCES CLASSES DIRECTLY
+
+% 1) create the output format according to the document definitions
+% and type
+objOutputFormat = org.apache.xml.serialize.OutputFormat(source);
+set(objOutputFormat,'Indenting','on');
+
+% 2) create the output stream. In this case: an XML file
+objFile = java.io.File(result);
+objOutputStream = java.io.FileOutputStream(objFile);
+
+% 3) Create the Xerces Serializer object
+objSerializer= org.apache.xml.serialize.XMLSerializer(objOutputStream,objOutputFormat);
+
+% 4) Serialize to the XML files
+javaMethod('serialize',objSerializer,source);
+
+% 5) IMPORTANT! Delete the objects to liberate the XML file created
+objOutputStream.close;
+
+if returnString
+    varargout{1}=char(result.toString);
+end
+
+%% ========================================================================
+ function out = F_xmlstringinput(xString,isFullSearch,varargin)
+% The function F_xmlstringinput is a copy of the private function:
+% 'xmlstringinput' that the original xmlwrite function uses.
+
+if isempty(xString)
+    error('Filename is empty');
+elseif ~isempty(findstr(xString,'://'))
+    %xString is already a URL, most likely prefaced by file:// or http://
+    out = xString;
+    return;
+end
+
+xPath=fileparts(xString);
+if isempty(xPath)
+    if nargin<2 || isFullSearch
+        out = which(xString);
+        if isempty(out)
+            error('xml:FileNotFound','File %s not found',xString);
+        end
+    else
+        out = fullfile(pwd,xString);
+    end
+else
+    out = xString;
+    if (nargin<2 || isFullSearch) && ~exist(xString,'file')
+        %search to see if xString exists when isFullSearch
+        error('xml:FileNotFound','File %s not found',xString);
+    end
+end
+
+%Return as a URN
+if strncmp(out,'\\',2)
+    % SAXON UNC filepaths need to look like file:///\\\server-name\
+    out = ['file:///\',out];
+elseif strncmp(out,'/',1)
+    % SAXON UNIX filepaths need to look like file:///root/dir/dir
+    out = ['file://',out];
+else
+    % DOS filepaths need to look like file:///d:/foo/bar
+    out = ['file:///',strrep(out,'\','/')];
+end
+

matlab_runners/Action Unit Experiments/run_AU_prediction_DISFA.m

@@ -1,6 +1,17 @@
 clear
-DISFA_dir = 'D:/Datasets/DISFA/Videos_LeftCamera/';
+
-executable = '"../../x64/Release/FeatureExtraction.exe"';
+if(isunix)
+    executable = '"../../build/bin/FeatureExtraction"';
+else
+    executable = '"../../x64/Release/FeatureExtraction.exe"';
+end
+
+if(exist('D:/Datasets/DISFA/Videos_LeftCamera/', 'file'))   
+    DISFA_dir = 'D:/Datasets/DISFA/Videos_LeftCamera/';  
+else
+    DISFA_dir = '/multicomp/datasets/face_datasets/DISFA/Videos_LeftCamera/';
+end
+
 
 videos = dir([DISFA_dir, '*.avi']);
 
@@ -22,7 +33,11 @@ parfor v = 1:numel(videos)
     output_file = [output name '_au.txt'];
     command = [executable ' -f "' vid_file '" -of "' output_file '" -q -no2Dfp -no3Dfp -noMparams -noPose -noGaze'];
         
-    dos(command);
+    if(isunix)
+        unix(command, '-echo');
+    else
+        dos(command);
+    end
     
 end
 
@@ -31,8 +46,7 @@ end
 % Note that DISFA was used in training, this is not meant for experimental
 % results but rather to show how to do AU prediction and how to interpret
 % the results
-
+Label_dir = [DISFA_dir, '/../ActionUnit_Labels/'];
-Label_dir = 'D:/Datasets/DISFA/ActionUnit_Labels/';
 prediction_dir = 'out_DISFA/';
 
 label_folders = dir([Label_dir, 'SN*']);

matlab_runners/Action Unit Experiments/run_AU_prediction_FERA2011.m

@@ -1,6 +1,7 @@
 clear
 
-fera_loc = 'D:\Datasets\fera\';
+addpath(genpath('helpers/'));
+find_FERA2011;
 
 out_loc = './out_fera/';
 
@@ -9,41 +10,38 @@ if(~exist(out_loc, 'dir'))
 end
 
 %%
-executable = '"../../x64/Release/FeatureExtraction.exe"';
+if(isunix)
+    executable = '"../../build/bin/FeatureExtraction"';
+else
+    executable = '"../../x64/Release/FeatureExtraction.exe"';
+end
 
-fera_dirs = dir([fera_loc, 'au_train*']);
+fera_dirs = dir([FERA2011_dir, 'train*']);
 
-for f1=1:numel(fera_dirs)
+parfor f1=1:numel(fera_dirs)
 
-    fera_dirs_level_2 = dir([fera_loc, fera_dirs(f1).name]);
+    vid_files = dir([FERA2011_dir, fera_dirs(f1).name, '/*.avi']);
-    fera_dirs_level_2 = fera_dirs_level_2(3:end);
 
-    parfor f2=1:numel(fera_dirs_level_2)
+    for v=1:numel(vid_files)
 
-        vid_files = dir([fera_loc, fera_dirs(f1).name, '/', fera_dirs_level_2(f2).name, '/*.avi']);
+        command = [executable ' -asvid -q -no2Dfp -no3Dfp -noMparams -noPose -noGaze -au_static '];
 
-        for v=1:numel(vid_files)
+        curr_vid = [FERA2011_dir, fera_dirs(f1).name, '/', vid_files(v).name];
 
-            command = [executable ' -asvid -q -no2Dfp -no3Dfp -noMparams -noPose -noGaze -au_static '];
+        [~,name,~] = fileparts(curr_vid);
-
+        output_file = [out_loc name '.au.txt'];
-            curr_vid = [fera_loc, fera_dirs(f1).name, '/', fera_dirs_level_2(f2).name, '/', vid_files(v).name];
-
-            [~,name,~] = fileparts(curr_vid);
-            output_file = [out_loc name '.au.txt'];
-
-            command = cat(2, command, [' -f "' curr_vid '" -of "' output_file '"']);
 
+        command = cat(2, command, [' -f "' curr_vid '" -of "' output_file '"']);
 
+        if(isunix)
+            unix(command, '-echo');
+        else
             dos(command);
         end
     end
 end
 
 %%
-addpath('./helpers/');
-
-find_FERA2011;
-
 [ labels_gt, valid_ids, filenames] = extract_FERA2011_labels(FERA2011_dir, all_recs, all_aus);
 labels_gt = cat(1, labels_gt{:});
 

matlab_runners/Action Unit Experiments/run_AU_prediction_SEMAINE.m

@@ -9,7 +9,11 @@ if(~exist(out_loc, 'dir'))
     mkdir(out_loc);
 end
 
-executable = '"../../x64/Release/FeatureExtraction.exe"';
+if(isunix)
+    executable = '"../../build/bin/FeatureExtraction"';
+else
+    executable = '"../../x64/Release/FeatureExtraction.exe"';
+end
 %%
 parfor f1=1:numel(devel_recs)
 
@@ -27,8 +31,13 @@ parfor f1=1:numel(devel_recs)
         name = f1_dir;
         output_aus = [out_loc name '.au.txt'];
 
-        command = cat(2, command, [' -f "' curr_vid '" -of "' output_aus]);
+        command = cat(2, command, [' -f "' curr_vid '" -of "' output_aus, '"']);
-        dos(command);
+        
+        if(isunix)
+            unix(command, '-echo');
+        else
+            dos(command);
+        end
 
     end
 end

matlab_runners/Demos/feature_extraction_demo_img_seq.m

@@ -1,4 +1,10 @@
-executable = '"../../x64/Release/FeatureExtraction.exe"';
+clear
+
+if(isunix)
+    executable = '"../../build/bin/FeatureExtraction"';
+else
+    executable = '"../../x64/Release/FeatureExtraction.exe"';
+end
 
 output = './output_features_seq/';
 
@@ -29,11 +35,15 @@ for i=1:numel(in_dirs)
     
     command = cat(2, command, ['-asvid -fdir "' in_dirs{i} '" -of "' outputFile '" ']);
         
-    command = cat(2, command, [' -simalign "' outputDir_aligned '" -hogalign "' outputHOG_aligned '"']);    
+    command = cat(2, command, [' -simalign "' outputDir_aligned '" -simsize 200 -hogalign "' outputHOG_aligned '"']);    
                  
 end
 
-dos(command);
+if(isunix)
+    unix(command);
+else
+    dos(command);
+end
 
 %% Demonstrating reading the output files
 

matlab_runners/Demos/feature_extraction_demo_vid.m

@@ -1,5 +1,10 @@
 clear
-executable = '"../../x64/Release/FeatureExtraction.exe"';
+
+if(isunix)
+    executable = '"../../build/bin/FeatureExtraction"';
+else
+    executable = '"../../x64/Release/FeatureExtraction.exe"';
+end
 
 output = './output_features_vid/';
 
@@ -40,7 +45,11 @@ for i=1:numel(in_files)
                  
 end
 
-dos(command);
+if(isunix)
+    unix(command);
+else
+    dos(command);
+end
 
 %% Demonstrating reading the output files
 

matlab_runners/Demos/gaze_extraction_demo_vid.m

@@ -1,4 +1,10 @@
-exe = '"../../x64/Release/FeatureExtraction.exe"';
+clear
+
+if(isunix)
+    executable = '"../../build/bin/FeatureExtraction"';
+else
+    executable = '"../../x64/Release/FeatureExtraction.exe"';
+end
 
 output = './output_features_vid/';
 
@@ -10,7 +16,7 @@ in_files = dir('../../videos/2015-10-15-15-14.avi');
 % some parameters
 verbose = true;
 
-command = exe;
+command = executable;
 command = cat(2, command, ' -verbose  -no2Dfp -no3Dfp -noMparams -noPose -noAUs ');
 
 % add all videos to single argument list (so as not to load the model anew
@@ -31,7 +37,11 @@ for i=1:numel(in_files)
                
 end
 
-dos(command);
+if(isunix)
+    unix(command);
+else
+    dos(command);
+end
 
 %% Demonstrating reading the output files
 filename = [output name];

matlab_runners/Demos/run_demo_images.m

@@ -1,6 +1,9 @@
 clear
-
+if(isunix)
-executable = '"../../x64/Release/FaceLandmarkImg.exe"';
+    executable = '"../../build/bin/FaceLandmarkImg"';
+else
+    executable = '"../../x64/Release/FaceLandmarkImg.exe"';
+end
     
 in_dir  = '../../videos/';
 out_dir = './demo_img/';
@@ -38,4 +41,8 @@ command = cat(2, command, [' -mloc "', model, '"']);
 % Comment to skip this functionality
 command = cat(2, command, ' -wild ');
 
-dos(command);
+if(isunix)
+    unix(command);
+else
+    dos(command);
+end

matlab_runners/Demos/run_demo_video_multi.m

@@ -1,4 +1,10 @@
-executable = '"../../x64/Release/FaceLandmarkVidMulti.exe"';
+clear;
+
+if(isunix)
+    executable = '"../../build/bin/FaceLandmarkVidMulti"';
+else
+    executable = '"../../x64/Release/FaceLandmarkVidMulti.exe"';
+end
 
 output = './demo_vid/';
 
@@ -38,4 +44,8 @@ for i=1:numel(in_files)
                  
 end
 
-dos(command);
+if(isunix)
+    unix(command);
+else
+    dos(command);
+end

matlab_runners/Demos/run_demo_videos.m

@@ -1,4 +1,10 @@
-executable = '"../../x64/Release/FaceLandmarkVid.exe"';
+clear
+
+if(isunix)
+    executable = '"../../build/bin/FaceLandmarkVid"';
+else
+    executable = '"../../x64/Release/FaceLandmarkVid.exe"';
+end
 
 output = './demo_vid/';
 
@@ -39,4 +45,8 @@ for i=1:numel(in_files)
                  
 end
 
-dos(command);
+if(isunix)
+    unix(command);
+else
+    dos(command);
+end

matlab_runners/Feature Point Experiments/Run_OF_on_images.m

@@ -1,6 +1,4 @@
-function [ err_outline, err_no_outline ] = Run_CLM_fitting_on_images(output_loc, database_root, varargin)
+function [ err_outline, err_no_outline ] = Run_OF_on_images(output_loc, database_root, varargin)
-%RUN_CLM_FITTING_ON_IMAGES Summary of this function goes here
-%   Detailed explanation goes here
 
 dataset_dirs = {};
 
@@ -27,7 +25,11 @@ else
     verbose = false;
 end
       
-command = '"../../x64/Release/FaceLandmarkImg.exe" ';
+if(isunix)
+    command = '"../../build/bin/FaceLandmarkImg"';
+else
+    command = '"../../x64/Release/FaceLandmarkImg.exe"';
+end
     
 if(any(strcmp(varargin, 'model')))
     model = varargin{find(strcmp(varargin, 'model')) + 1};
@@ -61,7 +63,11 @@ parfor i=1:numel(dataset_dirs)
     
     command_c = cat(2, command_c, ' -wild ');
     
-    dos(command_c);
+    if(isunix)
+        unix(command_c, '-echo');
+    else
+        dos(command_c);
+    end
 
 end
 toc

matlab_runners/Feature Point Experiments/run_OpenFace_feature_point_tests_300W.m

@@ -5,8 +5,10 @@ curr_dir = cd('.');
 % Replace this with your downloaded 300-W train data
 if(exist([getenv('USERPROFILE') '/Dropbox/AAM/test data/'], 'file'))
     database_root = [getenv('USERPROFILE') '/Dropbox/AAM/test data/'];    
-else
+elseif(exist('D:/Dropbox/Dropbox/AAM/test data/', 'file'))
     database_root = 'D:/Dropbox/Dropbox/AAM/test data/';
+else
+    database_root = '/multicomp/datasets/300-W/';
 end
 
 %% Run using CLNF in the wild model
@@ -15,7 +17,7 @@ if(~exist(out_clnf, 'file'))
    mkdir(out_clnf); 
 end
 
-[err_clnf_wild, err_no_out_clnf_wild] = Run_CLM_fitting_on_images(out_clnf, database_root, 'use_afw', 'use_lfpw', 'use_ibug', 'use_helen', 'verbose', 'model', 'model/main_clnf_wild.txt', 'multi_view', 1);
+[err_clnf_wild, err_no_out_clnf_wild] = Run_OF_on_images(out_clnf, database_root, 'use_afw', 'use_lfpw', 'use_ibug', 'use_helen', 'verbose', 'model', 'model/main_clnf_wild.txt', 'multi_view', 1);
 
 %% Run using SVR model
 out_svr = [curr_dir '/out_wild_svr_wild/'];
@@ -23,7 +25,7 @@ if(~exist(out_svr, 'file'))
    mkdir(out_svr); 
 end
 
-[err_svr_wild, err_no_out_svr_wild] = Run_CLM_fitting_on_images(out_svr, database_root, 'use_afw', 'use_lfpw', 'use_ibug', 'use_helen', 'verbose', 'model', 'model/main_clm_wild.txt', 'multi_view', 1);                
+[err_svr_wild, err_no_out_svr_wild] = Run_OF_on_images(out_svr, database_root, 'use_afw', 'use_lfpw', 'use_ibug', 'use_helen', 'verbose', 'model', 'model/main_clm_wild.txt', 'multi_view', 1);                
 
 %% Run using general CLNF model
 out_clnf = [curr_dir '/out_wild_clnf/'];
@@ -31,7 +33,7 @@ if(~exist(out_clnf, 'file'))
    mkdir(out_clnf); 
 end
 
-[err_clnf, err_no_out_clnf] = Run_CLM_fitting_on_images(out_clnf, database_root, 'use_afw', 'use_lfpw', 'use_ibug', 'use_helen', 'verbose', 'model', 'model/main_clnf_general.txt', 'multi_view', 1);
+[err_clnf, err_no_out_clnf] = Run_OF_on_images(out_clnf, database_root, 'use_afw', 'use_lfpw', 'use_ibug', 'use_helen', 'verbose', 'model', 'model/main_clnf_general.txt', 'multi_view', 1);
 
 %% Run using SVR model
 out_svr = [curr_dir '/out_wild_svr/'];
@@ -39,7 +41,7 @@ if(~exist(out_svr, 'file'))
    mkdir(out_svr); 
 end
 
-[err_svr, err_no_out_svr] = Run_CLM_fitting_on_images(out_svr, database_root, 'use_afw', 'use_lfpw', 'use_ibug', 'use_helen', 'verbose', 'model', 'model/main_clm_general.txt', 'multi_view', 1);                
+[err_svr, err_no_out_svr] = Run_OF_on_images(out_svr, database_root, 'use_afw', 'use_lfpw', 'use_ibug', 'use_helen', 'verbose', 'model', 'model/main_clm_general.txt', 'multi_view', 1);                
 
 %%
 save('results/landmark_detections.mat');

matlab_runners/Feature Point Experiments/run_yt_dataset.m

@@ -1,6 +1,10 @@
 clear
 
-executable = '"../../x64/Release/FeatureExtraction.exe"';
+if(isunix)
+    executable = '"../../build/bin/FeatureExtraction"';
+else
+    executable = '"../../x64/Release/FeatureExtraction.exe"';
+end
 
 output = 'yt_features/';
 
@@ -10,8 +14,10 @@ end
     
 if(exist([getenv('USERPROFILE') '/Dropbox/AAM/test data/'], 'file'))
     database_root = [getenv('USERPROFILE') '/Dropbox/AAM/test data/'];    
-else
+elseif(exist('D:/Dropbox/Dropbox/AAM/test data/', 'file'))
     database_root = 'D:/Dropbox/Dropbox/AAM/test data/';
+else
+    database_root = '/multicomp/datasets/';
 end
 
 database_root = [database_root, '/ytceleb/'];
@@ -33,7 +39,11 @@ for i=1:numel(in_vids)
     command = cat(2, command, [' -f "' in_file_name '" -of "' outputFile_fp '"']);                     
 end
 
-dos(command);
+if(isunix)
+    unix(command, '-echo')
+else
+    dos(command);
+end
 
 %%
 output = 'yt_features_clm/';
@@ -59,7 +69,11 @@ for i=1:numel(in_vids)
     command = cat(2, command, [' -f "' in_file_name '" -of "' outputFile_fp '"']);                     
 end
 
-dos(command);
+if(isunix)
+    unix(command, '-echo')
+else
+    dos(command);
+end
 %% evaluating yt datasets
 d_loc = 'yt_features/';
 d_loc_clm = 'yt_features_clm/';

matlab_runners/Full_test_suite.m

@@ -1,6 +1,6 @@
 % This is sort of the unit test for the whole module (needs datasets)
-% Will take over an hour to run all
+% Will take several hours to run all
-
+clear
 tic
 %% Head pose
 cd('Head Pose Experiments');
@@ -12,7 +12,7 @@ cd('../');
 
 %% Features
 cd('Feature Point Experiments');
-run_clm_feature_point_tests_wild;
+run_OpenFace_feature_point_tests_300W;
 assert(median(err_clnf) < 0.041);
 assert(median(err_clnf_wild) < 0.041);
 run_yt_dataset;

matlab_runners/Gaze Experiments/extract_mpii_gaze_test.m

@@ -7,9 +7,12 @@ if(exist([getenv('USERPROFILE') '/Dropbox/AAM/eye_clm/mpii_data/'], 'file'))
     database_root = [getenv('USERPROFILE') '/Dropbox/AAM/eye_clm/mpii_data/'];    
 elseif(exist('D:\Dropbox/Dropbox/AAM/eye_clm/mpii_data/', 'file'))
     database_root = 'D:\Dropbox/Dropbox/AAM/eye_clm/mpii_data/';    
+elseif(exist('/multicomp/datasets/mpii_gaze/mpii_data/', 'file'))
+    database_root = '/multicomp/datasets/mpii_gaze/mpii_data/';    
 else
     fprintf('MPII gaze dataset not found\n');
 end
+
 output_loc = './gaze_estimates_MPII/';
 if(~exist(output_loc, 'dir'))
     mkdir(output_loc);
@@ -18,7 +21,13 @@ end
 output = './mpii_out/';
 
 %% Perform actual gaze predictions
-command = sprintf('"../../x64/Release/FaceLandmarkImg.exe" -fx 1028 -fy 1028 -gaze ');
+if(isunix)
+    executable = '"../../build/bin/FaceLandmarkImg"';
+else
+    executable = '"../../x64/Release/FaceLandmarkImg.exe"';
+end
+
+command = sprintf('%s -fx 1028 -fy 1028 -gaze ', executable);
 p_dirs = dir([database_root, 'p*']);
 
 parfor p=1:numel(p_dirs)
@@ -30,7 +39,11 @@ parfor p=1:numel(p_dirs)
     command_c = cat(2, command, input_loc, out_img_loc, out_p_loc);
 
     command_c = cat(2, command_c, ' -wild');
-    dos(command_c);
+    if(isunix)
+        unix(command_c, '-echo');
+    else
+        dos(command_c);
+    end;
 
 end
 %%

matlab_runners/Head Pose Experiments/results/Pose_OF.txt

@@ -1,4 +1,4 @@
 Dataset and model,        pitch,  yaw,  roll,  mean,  median
-biwi error:  7.955,   5.583, 4.403,  5.980,  2.624
+biwi error:  7.955,   5.583, 4.402,  5.980,  2.624
-bu error:    2.734,   3.350, 2.459,  2.848,  1.974
+bu error:    2.762,   4.103, 2.568,  3.145,  2.118
-ict error:   3.610,   3.959, 3.369,  3.646,  1.967
+ict error:   3.620,   3.608, 3.626,  3.618,  2.028

matlab_runners/Head Pose Experiments/run_biwi_experiment.m

@@ -1,31 +1,26 @@
-function [fps, resDir] = run_biwi_experiment(rootDir, biwiDir, outputDir, verbose, depth, version, varargin)
+function [output_dir] = run_biwi_experiment(rootDir, biwiDir, verbose, depth, varargin)
 % Biwi dataset experiment
 
-executable = '"../../x64/Release/FeatureExtraction.exe"';
+if(isunix)
+    executable = '"../../build/bin/FeatureExtraction"';
+else
+    executable = '"../../x64/Release/FeatureExtraction.exe"';
+end
 
-output = 'Tracker_';
+output_dir = 'experiments/biwi_out';    
 
 dbSeqDir = dir([rootDir biwiDir]);
    
-% listing the output based on the current revision
-output = [output 'r' num2str(version)];
-   
 if(depth)
-    output = cat(2, output, '_depth');
+    output_dir = cat(2, output_dir, '_depth');
 end
 
-outputDir = cat(2, outputDir, ['/' output '/']);
+output_dir = cat(2, output_dir, '/');
-
-if(~exist([outputDir], 'dir'))
-    mkdir([outputDir]);    
-end
 
 offset = 0;
 
 r = 1 + offset;
     
-tic;
-    
 numTogether = 25;
 
 
@@ -34,7 +29,7 @@ for i=3 + offset:numTogether:numel(dbSeqDir)
        
     command = executable;
            
-    command = cat(2, command, [' -root ' '"' rootDir '"']);
+    command = cat(2, command, [' -inroot ' '"' rootDir '"']);
      
     % deal with edge cases
     if(numTogether + i > numel(dbSeqDir))
@@ -44,7 +39,7 @@ for i=3 + offset:numTogether:numel(dbSeqDir)
     for n=0:numTogether-1
         
         inputFile = [biwiDir dbSeqDir(i+n).name '/colour.avi'];
-        outputFile = [outputDir dbSeqDir(i+n).name '.txt'];
+        outputFile = [output_dir dbSeqDir(i+n).name '.txt'];
 
         command = cat(2, command, [' -f "' inputFile '" -of "' outputFile  '"']);
 
@@ -54,7 +49,7 @@ for i=3 + offset:numTogether:numel(dbSeqDir)
         end
 
         if(verbose)
-            outputVideo = [outputDir dbSeqDir(i).name '.avi'];
+            outputVideo = [output_dir dbSeqDir(i).name '.avi'];
             command = cat(2, command, [' -ov "' outputVideo '"']);    
         end
     end    
@@ -65,9 +60,9 @@ for i=3 + offset:numTogether:numel(dbSeqDir)
     end
             
     r = r+1;    
-    dos(command);
+    if(isunix)
+        unix(command, '-echo')
+    else
+        dos(command);
+    end
 end
-
-timeTaken = toc;
-fps = 15678 / timeTaken;
-resDir = outputDir;

matlab_runners/Head Pose Experiments/run_bu_experiment.m

@@ -1,27 +1,21 @@
-function [fps, resDir] = run_bu_experiment(bu_dir, verbose, version, varargin)
+function [output_dir] = run_bu_experiment(bu_dir, verbose, varargin)
    
-    executable = '"../../x64/Release/FeatureExtraction.exe"';
+    if(isunix)
-
+        executable = '"../../build/bin/FeatureExtraction"';
-    output = 'Tracker_';
+    else
-    
+        executable = '"../../x64/Release/FeatureExtraction.exe"';
-    % listing the output based on the current revision
-    output = [output 'r' num2str(version)];
-    
-    output = cat(2, output, '/');
-      
-    if(~exist([bu_dir output], 'dir'))
-        mkdir([bu_dir output]);    
     end
 
+    output_dir = 'experiments/bu_out/';        
+
     buFiles = dir([bu_dir '*.avi']);
     
     numTogether = 25;
     
-    tic;
     for i=1:numTogether:numel(buFiles)
         
         command = executable;
-        command = cat(2, command, [' -root ' '"' bu_dir '/"']);
+        command = cat(2, command, [' -inroot ' '"' bu_dir '/"']);
         
         % BU dataset orientation is in terms of camera plane, instruct the
         % tracker to output it in that format
@@ -37,12 +31,12 @@ function [fps, resDir] = run_bu_experiment(bu_dir, verbose, version, varargin)
             [~, name, ~] = fileparts(inputFile);   
 
             % where to output results
-            outputFile = [output name '.txt'];
+            outputFile = [output_dir name '.txt'];
             
             command = cat(2, command, [' -f "' inputFile '" -of "' outputFile '"']);
 
             if(verbose)
-                outputVideo = ['"' output name '.avi' '"'];
+                outputVideo = ['"' output_dir name '.avi' '"'];
                 command = cat(2, command, [' -ov ' outputVideo]);
             end
         end
@@ -53,13 +47,11 @@ function [fps, resDir] = run_bu_experiment(bu_dir, verbose, version, varargin)
             command = cat(2, command, [' -mloc "', varargin{find(strcmp('model', varargin))+1}, '"']);
         end  
         
-        dos(command);
+        if(isunix)
+            unix(command, '-echo')
+        else
+            dos(command);
+        end
     end
             
-    timeTaken = toc;
-    fps = 9000 / timeTaken;
-    
-    % tell the caller where the output was written
-    resDir = [bu_dir output];
-    
 end

matlab_runners/Head Pose Experiments/run_head_pose_tests_OpenFace.m

@@ -8,38 +8,34 @@ if exist('D:/Datasets/HeadPose', 'file')
     database_root = 'D:/Datasets/HeadPose/';    
 elseif(exist([getenv('USERPROFILE') '/Dropbox/AAM/test data/'], 'file'))
     database_root = [getenv('USERPROFILE') '/Dropbox/AAM/test data/'];    
-else
+elseif(exist([getenv('USERPROFILE') 'F:/Dropbox/Dropbox/AAM/test data/'], 'file'))
     database_root = 'F:/Dropbox/Dropbox/AAM/test data/';
+else
+    database_root = '/multicomp/datasets/head_pose_dbs/';
 end
 
 buDir = [database_root, '/bu/uniform-light/'];
 
 % The fast and accurate clnf
 %%
-v = 3;
+[resFolderBU_OF] = run_bu_experiment(buDir, false, 'model', 'model/main_clnf_general.txt');
-[fps_bu_OF, resFolderBU_OF] = run_bu_experiment(buDir, false, v, 'model', 'model/main_clnf_general.txt');
 [bu_error_OF, pred_hp_bu, gt_hp_bu, all_errors_bu_OF, rels_bu] = calcBUerror(resFolderBU_OF, buDir);
 
 %%
 % Run the Biwi test
 biwi_dir = '/biwi pose/';
-biwi_results_root = '/biwi pose results/';
 
-% Intensity
+[res_folder_biwi_OF] = run_biwi_experiment(database_root, biwi_dir, false, false, 'model', 'model/main_clnf_general.txt');
-v = 4;
-[fps_biwi_OF, res_folder_OF] = run_biwi_experiment(database_root, biwi_dir, biwi_results_root, false, false, v, 'model', 'model/main_clnf_general.txt');
 % Calculate the resulting errors
-[biwi_error_OF, pred_hp_biwi, gt_hp_biwi, ~, all_errors_biwi_OF, rels_biwi] = calcBiwiError([database_root res_folder_OF], [database_root biwi_dir]);
+[biwi_error_OF, pred_hp_biwi, gt_hp_biwi, ~, all_errors_biwi_OF, rels_biwi] = calcBiwiError(res_folder_biwi_OF, [database_root biwi_dir]);
 
 %% Run the ICT test
-ict_dir = ['ict/'];
+ict_dir = ['/ict/'];
-ict_results_root = ['ict results/'];
 
-v = 4;
 % Intensity
-[fps_ict_OF, res_folder_ict_OF] = run_ict_experiment(database_root, ict_dir, ict_results_root, false, false, v, 'model', 'model/main_clnf_general.txt');
+[res_folder_ict_OF] = run_ict_experiment(database_root, ict_dir, false, false, 'model', 'model/main_clnf_general.txt');
 % Calculate the resulting errors
-[ict_error_OF, pred_hp_ict, gt_hp_ict, ~, all_errors_ict_OF, rel_ict] = calcIctError([database_root res_folder_ict_OF], [database_root ict_dir]);
+[ict_error_OF, pred_hp_ict, gt_hp_ict, ~, all_errors_ict_OF, rel_ict] = calcIctError(res_folder_ict_OF, [database_root ict_dir]);
 
 %% Save the results
 filename = 'results/Pose_OF';

matlab_runners/Head Pose Experiments/run_ict_experiment.m

@@ -1,27 +1,22 @@
-function [fps, resDir] = run_ict_experiment(rootDir, ictDir, outputRoot, verbose, depth, version, varargin)
+function [output_dir] = run_ict_experiment(rootDir, ictDir, verbose, depth, varargin)
 %EVALUATEICTDATABASE Summary of this function goes here
 %   Detailed explanation goes here
 
-executable = '"../../x64/Release/FeatureExtraction.exe"';
+if(isunix)
+    executable = '"../../build/bin/FeatureExtraction"';
+else
+    executable = '"../../x64/Release/FeatureExtraction.exe"';
+end
 
-output = 'Tracker_';
+output_dir = 'experiments/ict_out';    
 
 dbSeqDir = dir([rootDir ictDir]);
    
-% listing the output based on the current revision
-output = [output 'r' num2str(version)];
-   
 if(depth)
-    output = cat(2, output, '_depth');
+    output_dir = cat(2, output_dir, '_depth');
 end
 
-outputDir = cat(2, outputRoot, ['/' output '/']);
+output_dir = cat(2, output_dir, '/');
-
-if(~exist([rootDir outputDir], 'dir'))
-    mkdir([rootDir outputDir]);    
-end
-
-tic;
 
 numTogether = 10;
 
@@ -29,7 +24,7 @@ for i=3:numTogether:numel(dbSeqDir)
         
     command = [executable  ' -fx 535 -fy 536 -cx 327 -cy 241 -no2Dfp -no3Dfp -noMparams -noAUs -noGaze '];
 
-    command = cat(2, command, [' -root ' '"' rootDir '/"']);
+    command = cat(2, command, [' -inroot ' '"' rootDir '/"']);
 
     % deal with edge cases
     if(numTogether + i > numel(dbSeqDir))
@@ -39,7 +34,7 @@ for i=3:numTogether:numel(dbSeqDir)
     for n=0:numTogether-1
         
         inputFile = [ictDir dbSeqDir(i+n).name '/colour undist.avi'];
-        outputFile = [outputDir dbSeqDir(i+n).name '.txt'];
+        outputFile = [output_dir dbSeqDir(i+n).name '.txt'];
         
         command = cat(2, command,  [' -f "' inputFile '" -of "' outputFile  '" ']);
         
@@ -49,7 +44,7 @@ for i=3:numTogether:numel(dbSeqDir)
         end
         
         if(verbose)
-            outputVideo = [outputDir dbSeqDir(i+n).name '.avi'];
+            outputVideo = [output_dir dbSeqDir(i+n).name '.avi'];
             command = cat(2, command, [' -ov "' outputVideo '"']);
         end
     end
@@ -58,12 +53,13 @@ for i=3:numTogether:numel(dbSeqDir)
         command = cat(2, command, [' -mloc "', varargin{find(strcmp('model', varargin))+1}, '"']);
     end    
         
-    dos(command);
+    if(isunix)
+        unix(command, '-echo')
+    else
+        dos(command);
+    end
 end
 
-timeTaken = toc;
-fps = 10661 / timeTaken;
-resDir = outputDir;
 
 end
 

matlab_runners/Readme.txt

@@ -1,6 +1,6 @@
 --------------------------------------- OpenFace Matlab runners -----------------------------------------------------------------------------	
 
-These are provided for recreation of some of the experiments described in the publications and to demonstrate the command line interface by calling the C++ executables from matlab. This is intended to test the Windows version of the code.
+These are provided for recreation of some of the experiments described in the publications and to demonstrate the command line interface by calling the C++ executables from Matlab.
 
 ======================== Demos ==================================