Merge cgogn:~thery/CGoGN

Apps/Examples/Tests/CMakeLists.txt

@@ -35,6 +35,10 @@ add_executable( Geom_intersectionD ./Geom_intersection.cpp)
 target_link_libraries( Geom_intersectionD
 	${CGoGN_LIBS_D} ${CGoGN_EXT_LIBS})
 	
+add_executable( test_compactD ./test_compact.cpp)
+target_link_libraries( test_compactD
+	${CGoGN_LIBS_D} ${CGoGN_EXT_LIBS})
+	
 	
 IF (WITH_QT)
 	QT4_WRAP_CPP(concave_rendering_moc concave_rendering.h)

Apps/Examples/clipping.cpp

@@ -793,11 +793,8 @@ void Clipping::importMesh(std::string& filename)
 {
 	std::vector<std::string> attrNames ;
 
-	std::string extension;
-	size_t pos;
-
-	pos = filename.rfind(".");    // position of "." in filename
-	 extension = filename.substr(pos);
+	size_t pos = filename.rfind(".");    // position of "." in filename
+	std::string extension = filename.substr(pos);
 
 	if(extension == std::string(".tet"))
 	{
@@ -819,6 +816,17 @@ void Clipping::importMesh(std::string& filename)
 		else
 			position = myMap.getAttribute<PFP::VEC3>(VERTEX , attrNames[0]) ;
 	}
+	if(extension == std::string(".map"))
+	{
+		if(!myMap.loadMapBin(filename))
+		{
+			CGoGNerr << "could not import " << filename << CGoGNendl ;
+			return;
+		}
+		else
+			position = myMap.getAttribute<PFP::VEC3>(VERTEX , "position") ;
+	}
+
 
 	updateVBOprimitives(Algo::Render::GL2::TRIANGLES | Algo::Render::GL2::LINES | Algo::Render::GL2::POINTS) ;
 

Apps/Examples/viewer.cpp

@@ -184,13 +184,25 @@ void Viewer::importMesh(std::string& filename)
 {
 	myMap.clear(true) ;
 
-	std::vector<std::string> attrNames ;
-	if(!Algo::Import::importMesh<PFP>(myMap, filename.c_str(), attrNames))
+	size_t pos = filename.rfind(".");    // position of "." in filename
+	std::string extension = filename.substr(pos);
+
+	if (extension == std::string(".map"))
+	{
+		myMap.loadMapBin(filename);
+		position = myMap.getAttribute<PFP::VEC3>(VERTEX, "position") ;
+	}
+	else
 	{
-		CGoGNerr << "could not import " << filename << CGoGNendl ;
-		return;
+		std::vector<std::string> attrNames ;
+		if(!Algo::Import::importMesh<PFP>(myMap, filename.c_str(), attrNames))
+		{
+			CGoGNerr << "could not import " << filename << CGoGNendl ;
+			return;
+		}
+		position = myMap.getAttribute<PFP::VEC3>(VERTEX, attrNames[0]) ;
 	}
-	position = myMap.getAttribute<PFP::VEC3>(VERTEX, attrNames[0]) ;
+
 
 	m_render->initPrimitives<PFP>(myMap, allDarts, Algo::Render::GL2::POINTS) ;
 	m_render->initPrimitives<PFP>(myMap, allDarts, Algo::Render::GL2::LINES) ;

README.TXT

@@ -24,7 +24,40 @@ Les applications (Examples et Tutos) sont dans le répertoire Apps
 Les binaires sont générés dans le repertoire bin
 
 Des exemples de données:
-- fichiers trianbgz
-- fichiers png (contenant des images voxel 3D)
+- fichiers trianbgz, off, etc
 sont accessible à l'adresse suivante: 
 https://iggservis.u-strasbg.fr/Data/data.zip
+
+=========================================================================================
+                                ENGLISH VERSION
+=========================================================================================
+
+Linux dependencies:
+install the following packages:
+ccmake libXi-dev libXmu-dev libglew-dev libxml2-dev libboost-all-dev zlib1g-dev qt4-designer qt4-dev-tools uuid-dev
+
+To compile CGoGN:
+- Go ThirdParty, cd build, type "cmake .." and then make (with -j x if you have x core on your machine)
+We can set some option to not compile everything (see the README.TXT in ThirdParty)
+You can also compile debug by creating a directory that ended Debug build instead
+
+- Go to build and type "cmake .." and then make
+	Options (Boolean) are also available here:
+	BUILD_SHARED_LIBS (F) experimental!
+	WITH_ASSIMP (T)
+	WITH_NUMERICAL (T)
+	WITH_ZINRI (T)
+	WITH_QT (T)
+	to minimize dependencies and compilation time /
+
+
+- the compilation of each sub-parts is done by going in the subdirectories of build
+
+Applications (examples and tutorials) are in the Apps directory
+
+The binaries are generated in the bin directory
+
+Examples of data:
+- Trianbgz files, off, etc.
+are accessible at the following address:
+https://iggservis.u-strasbg.fr/Data/data.zip

README_APPS.TXT

-Principe des applications dans CGoGN_Apps
+Principe des applications dans CGoGN_Apps (english version bellow
 
 
 
@@ -24,7 +24,6 @@ IF (NOT WIN32)
 ENDIF (NOT WIN32)
 
 
-
 Le CMakeLists (Release par exemple) doit ensuite contenir:
 
 SET(CMAKE_BUILD_TYPE Release)
@@ -66,3 +65,80 @@ ici WITH_QT, WITH_ASSIMP, WITH_NUMERICAL, WITH_ZINRI.
 Ceci ajoutera automatiquement tout ce qu'il faut aux variables COMMON_INCLUDES
 et COMMON_LIBS.
 On peut aussi utiliser cmake avec l'option -D (moins pratique).
+
+
+
+=========================================================================================
+                                ENGLISH VERSION
+=========================================================================================
+
+Create a directory CGoGN_Apps where you want. Inside create subdirectories, one for each application.
+
+The CMakeLists.txt to the root of the application must begin with
+
+cmake_minimum_required(VERSION 2.8)
+PROJECT(NOM_DE_L_APPLICATION)
+SET(CGoGN_ROOT_DIR ${CMAKE_SOURCE_DIR}/../../CGoGN CACHE STRING "CGoGN root dir")
+INCLUDE(${CGoGN_ROOT_DIR}/apps_cmake.txt)
+
+
+The .. / .. / CGoGN corresponds to the relative path to your version of CGoGN
+(here placed at the same level as CGoGN_Apps)
+
+
+If you want to do in release and debug directories:
+
+add_subdirectory(${CMAKE_SOURCE_DIR}/Release Release)
+IF (NOT WIN32)
+	add_subdirectory(${CMAKE_SOURCE_DIR}/Debug Debug)
+ENDIF (NOT WIN32)
+
+
+The CMakeLists (here in Release) must then contain:
+
+SET(CMAKE_BUILD_TYPE Release)
+
+IF(WIN32)
+	link_directories( ${CGoGN_ROOT_DIR}/lib/$(ConfigurationName) )
+ELSE (WIN32)
+	link_directories( ${CGoGN_ROOT_DIR}/lib/Release/ )
+ENDIF (WIN32)
+
+# Watch out for the debug version, two solutions:
+# Debug and Release to be if you want to use ThirdParty in release version
+# or Debug only, but you have to compile ThirdParty in debug
+
+include_directories(
+	${CGoGN_ROOT_DIR}/include		# for CGoGN
+	${COMMON_INCLUDES}				# for thirdparty & system
+	${CMAKE_CURRENT_SOURCE_DIR}		# for application
+	${CMAKE_CURRENT_BINARY_DIR}		# for qt (ui,moc,etc.) if necessary
+)
+
+# for a QT application
+QT4_WRAP_UI( source_ui ../source.ui )
+QT4_WRAP_CPP( source_moc ../source.h )
+
+add_executable( mon_exec
+	${CMAKE_SOURCE_DIR}/mon_source.cpp
+# for a QT application
+	${source_moc}
+	${source_ui}
+)
+
+target_link_libraries( mon_exec ${CGoGN_LIBS_R} ${COMMON_LIBS})
+
+
+
+
+To compile the cleanest way is to build a directory, to go inside and make ccmake .. (I have written "..")
+ccmake (or an equivalent type cmake-gui) is used to update the variables, WITH_QT here, WITH_ASSIMP,
+WITH_NUMERICAL, WITH_ZINRI.
+This will automatically add it all the variables COMMON_INCLUDES and COMMON_LIBS.
+You can also use cmake with -D option (less convenient).
+
+
+
+
+
+

README_ECLIPSE.TXT

 Pour utiliser Eclipse (testé avec la version Helios, Galileo & Indigo)
+English version bellow
 
  * Configurer un projet dans Eclipse :
  - Faire un nouveau projet C++
@@ -57,3 +58,67 @@ Dans Preferences -> Shaders Preferences, on peut désormais configurer certaines
  - Installer CMakeEditor pour Eclipse en ajoutant l'URL dans Help -> Install New Software ... : http://cmakeed.sourceforge.net/eclipse/
  - Installer et redémarrer
  - Dans Preferences -> General -> Editors -> File Associations il est possible d'associer les CMakeLists.txt à ce logiciel d'édition
+ 
+=========================================================================================
+                                ENGLISH VERSION
+=========================================================================================
+
+To use Eclipse (tested with version Helios, Galileo & Indigo)
+
+ * Setting up a project in Eclipse:
+ - Make a new C + + project
+ - Select Makefile project -> Empty Project
+ - Choose As "Location": root CGoGN
+ - Select Toolchain: GCC Linux
+
+ * Compilation with the small hammer (icon)
+In the project properties:
+	-> C / C + + Build:
+	In the configuration Default | Active:
+	add to Build Directory path /build
+
+	you can then add configurations to compile what we want by just changing the Build directory:
+	CGoGNRelease: build / Release (compile the lib release)
+	CGoGNDebug: build / Debug (compiles in debug lib)
+	Apps: build / Apps (compile the examples and tutorials)
+	Tutorial: Build / Apps / Tutorial (compiles tutorials)
+	etc. ..
+
+This added to the directory of CGoGN a .project. and .cproject files.
+
+ * Inter-dependencies projects and autocompletion
+If the project X depends on another project, then:
+Project X -> Properties -> Project references: check the project which it depends.
+
+ * Qt dependencies:
+To avoid Eclipse rejects the Qt syntax (the Qt includes the Q_OBJECT, callbacks):
+ - Download the Qt plugin "eclipse-integration" http://qt.nokia.com/developer/eclipse-integration/
+ - Unzip the archive and copy its contents into the installation directory of Eclipse (plugins and features)
+ - Restart Eclipse at least once with the - clean (proofreading local directories)
+Normally in Window-> Preferences of Eclipse, Qt appears in the menu.
+ - Add the Qt directory (/ usr / bin on Debian / Ubuntu) and the directory include (/ usr/include/qt4).
+Then, for each project, add the following includes in Properties -> C / C + + general -> Paths and Symbols
+among the C + + includes:
+ - / Usr/include/qt4
+ - / Usr/include/qt4/Qt
+ - / Usr/include/qt4/QtCore
+ - / Usr/include/qt4/QtGui
+ - / Usr/include/qt4/QtOpenGL
+NOTE: at the bottom of this window, the button "Export Settings" allows you to export the configuration to XML
+import it into other projects.
+ - Finally, a small right-click the project -> Index -> Freshen all files and go.
+
+ * Syntax of shaders
+ - Download and unzip EclipseShaders: http://sourceforge.net/projects/glshaders/
+ - Copy the directories features and plugins in the eclipse installation directory
+ - Restart Eclipse at least once with the - clean (proofreading local directories)
+Eclipse will now recognize the files. And frag. Green.
+To assign other files in the program GLSLeditor:
+ - Preferences -> General -> Editors -> File Associations
+In Preferences -> Shaders Preferences, you can now configure some options related to the shader.
+
+ * Syntax highlighting for CMake files
+ - Install CMakeEditor for Eclipse by adding the URL in Help -> Install New Software ... : Http://cmakeed.sourceforge.net/eclipse/
+ - Install and restart
+ - In Preferences -> General -> Editors -> File Associations You can associate the CMakeLists.txt to editing software
+ 

README_MAC.TXT

@@ -16,4 +16,22 @@ Pour compiler CGoGN sur MAC (testé sur OS X 10.6)
     export LIBRARY_PATH=/opt/local/lib:/usr/X11/lib
 
 
+=========================================================================================
+                                ENGLISH VERSION
+=========================================================================================
+To compile CGoGN on MAC (tested on OSX 10.6 and OSX 10.7.2)
 
+1) create a link from sys/malloc to malloc.h in usr/include:
+    cd /usr/include; sudo ln -s sys/malloc.h . 
+	This solve compilation problems of some linux codes on mac
+
+2) install with macports or homebrew
+    zlib,  glew, boost (sudo port install xxxx)
+
+3) install Qt (http://qt.nokia.com/downloads/)
+
+4) Add if not already done (by homebrew) in bash_profile:
+    export LD_LIBRARY_PATH=/opt/local/lib 
+    export C_INCLUDE_PATH=/opt/local/include:/usr/X11/include
+    export CPLUS_INCLUDE_PATH=/opt/local/include:/usr/X11/include
+    export LIBRARY_PATH=/opt/local/lib:/usr/X11/lib

README_VISUAL.TXT

+Compilation sous VisualExpress C++ (english version bellow)
+
 Prérequis:
 Visual Studio ou C++ Express (au moins 2005, si possible 2010)
 CMake (au moins 2.8)
@@ -62,3 +64,80 @@ Remarque: gain de performance non négligeable en 64 bits (20/25%)
 
 (Merci à Olivier Génevaux pour son expertise en compilation sous Windows !)
 
+
+
+=========================================================================================
+                                ENGLISH VERSION
+=========================================================================================
+
+Prerequisites:
+Visual Studio and C + + Express (at least 2005, possibly 2010)
+CMake (at least 2.8)
+
+Unzip the windows_dependencies.zip (http://iggservis.u-strasbg.fr/Data/) is the root of CGoGN
+Install boost and Qt
+
+
+Warning installing the binaries of Qt in a version of different compilers (VS2008/VS2010)
+allows you to run but not in debug mode!
+
+If you use BoostPro (http://www.boostpro.com) install all versions multithreaded dll
+to avoid the pb of compilation.
+
+The safest but longest is to compile Qt yourself and Boost (good luck)
+
+
+For the "ThirdParty libs"
+Run CMake (gui)
+Put the path to the root of CGoGN + / ThirdParty sources for
+Put the path to the root of CGoGN + / ThirdParty / build to build in release
+Put the path to the root of CGoGN + / ThirdParty / buildDebug to build in debug
+Under windows the two versions are needed.
+
+The following applies to two directories:
+Click on Configure
+Choosing the right compiler (your version of Visual C + +)
+Change the variables in functions that you want to compile (README.TXT for ThirdParty)
+Edit CMAKE_PREFIX_PATH if necessary (see note dependencies)
+Click again on Configure
+Click on Generate
+Go compile under visual (in release)
+
+
+
+For CGoGN:
+Restart CMake
+Put the path to the root of CGoGN for sources
+Put the path to the root of CGoGN + / build (for example) to build
+Click on Configure
+Choosing the right compiler (your version of Visual C + +)
+Change the variables as ThirdParty (and CMAKE_PREFIX_PATH if necessary)
+Click again on Configure
+Click on Generate
+Go to Visual and double-click on CGoGN.sln!
+
+
+For running executables you have to add the path to the dll dependencies in the variable
+path environment (or copy the dll in a directory already in the path)
+
+
+Note Dependencies:
+If you want to use your own versions of dependency (Zlib / glew / Boost / Qt)
+CMAKE_PREFIX_PATH change (see below)
+Attention to Boost the prefix path does not work (use BOOST_ROOT and others if necessary)
+
+
+
+Compiling 64-bit:
+
+
+The libraries and the examples are compiled in 64bit Windows.
+Tested with Visual Express C + + 2010 + Windows SDK 7.1
+Dependencies are accessible in http://iggservis.u-strasbg.fr/Data/dependencies64.zip
+
+
+Caution must be changed and select projects in Windows7.1SDK tools platform
+in Configuration / General, to use the correct compiler and lib related.
+Note: significant performance gain in 64-bit (20/25%)
+
+(Thanks to Olivier Génevaux for its expertise in compilation under Windows!)

include/Algo/Render/GL2/topo3Render.hpp

@@ -52,9 +52,13 @@ void Topo3RenderMapD::updateData(typename PFP::MAP& map, const FunctorSelect& go
 
 	if (m_attIndex.map() != &map)
 	{
-		m_attIndex  = map.template addAttribute<unsigned int>(DART, "dart_index");
+		m_attIndex  = map.template getAttribute<unsigned int>(DART, "dart_index");
+		if (!m_attIndex.isValid())
+			m_attIndex  = map.template addAttribute<unsigned int>(DART, "dart_index");
 	}
 
+
+
 	m_nbDarts = 0;
 
 	// table of center of volume
@@ -320,7 +324,9 @@ void Topo3RenderGMap::updateData(typename PFP::MAP& map, const FunctorSelect& go
 
 	if (m_attIndex.map() != &map)
 	{
-		m_attIndex  = map.template addAttribute<unsigned int>(DART, "dart_index");
+		m_attIndex  = map.template getAttribute<unsigned int>(DART, "dart_index");
+		if (!m_attIndex.isValid())
+			m_attIndex  = map.template addAttribute<unsigned int>(DART, "dart_index");
 	}
 
 	m_nbDarts = 0;

include/Container/attributeContainer.h

@@ -251,12 +251,19 @@ public:
 	unsigned int getAttributeBlocksPointers(unsigned int attrIndex, std::vector<T*>& vect_ptr, unsigned int& byteBlockSize);
 
 	/**
-	 * fill a vector with attributes' names
-	 * @param vector of names
-	 * @return number of attribute
+	 * fill a vector with attributes names
+	 * @param names vector of names
+	 * @return number of attributes
 	 */
 	unsigned int getAttributesNames(std::vector<std::string>& names);
 
+	/**
+	 * fill a vector with attribute type names
+	 * @param types vector of type names
+	 * @return number of attributes
+	 */
+	unsigned int getAttributesTypes(std::vector<std::string>& types);
+
 	/**************************************
 	 *        CONTAINER MANAGEMENT        *
 	 **************************************/
@@ -470,17 +477,17 @@ protected:
 	/**
 	 * load xmlpart of container
 	 */
-	bool loadXmlBWF(xmlNodePtr node);
+//	bool loadXmlBWF(xmlNodePtr node);
 
 	/**
 	 * load xmlpart of container
 	 */
-	bool loadXmlAN(xmlNodePtr node, unsigned int nbb);
+//	bool loadXmlAN(xmlNodePtr node, unsigned int nbb);
 
 	/**
 	 * load xmlpart of container
 	 */
-	bool loadXmlDL(xmlNodePtr node);
+//	bool loadXmlDL(xmlNodePtr node);
 
 public:
 	/**
@@ -488,20 +495,20 @@ public:
 	* @param writer a xmlTextWriterPtr obj
 	* @param id the id to save
 	*/
-	void saveXml(xmlTextWriterPtr writer, unsigned int id);
+//	void saveXml(xmlTextWriterPtr writer, unsigned int id);
 
 	/**
 	* get id from xml node
 	* @param node the node of container node of xml tree
 	* @return the value of id of the node
 	*/
-	static unsigned int getIdXmlNode(xmlNodePtr node);
+//	static unsigned int getIdXmlNode(xmlNodePtr node);
 
 	/**
 	* load from xml node
 	* @param node the node of container node of xml tree
 	*/
-	bool loadXml(xmlNodePtr node);
+//	bool loadXml(xmlNodePtr node);
 
 	/**
 	* save binary file

include/Container/attributeMultiVector.hpp

@@ -407,7 +407,6 @@ void AttributeMultiVector<T>::saveBin(CGoGNostream& fs, unsigned int id)
 	memcpy(buffer+len1,s2,len2);
 	fs.write(reinterpret_cast<const char*>(buffer),(len1+len2)*sizeof(char));
 
-
 	nbs[0] = m_tableData.size();
 	nbs[1] = nbs[0] * _BLOCKSIZE_* sizeof(T);
 	fs.write(reinterpret_cast<const char*>(nbs),2*sizeof(unsigned int));

include/Container/registered.h

@@ -66,7 +66,12 @@ public:
 
 	AttributeMultiVectorGen* addAttribute(AttributeContainer& container, const std::string& attribName)
 	{
-		return container.addAttribute<T>(attribName);
+		unsigned int id = container.getAttributeIndex(attribName);
+		// new attribute
+		if (id == AttributeContainer::UNKNOWN)
+			return container.addAttribute<T>(attribName);
+		// or existing one
+		return container.getDataVector<T>(id);
 	}
 };
 

include/Topology/generic/attribmap.h

@@ -45,6 +45,7 @@ public:
 
 	virtual void clear(bool removeAttrib) ;
 
+
 	/****************************************
 	 *        ATTRIBUTES MANAGEMENT         *
 	 ****************************************/

include/Topology/generic/genericmap.h

@@ -300,6 +300,13 @@ protected:
 	 */
 	AttributeMultiVector<Dart>* addRelation(const std::string& name) ;
 
+	/**
+	 * Get attributeMultivector pointer of a relation attribute
+	 * @param anem name of relation
+	 * @return the attribute multi-vector pointer
+	 */
+	AttributeMultiVector<Dart>* getRelation(const std::string& name);
+
 	/****************************************
 	 *          THREAD MANAGEMENT           *
 	 ****************************************/
@@ -333,26 +340,31 @@ public:
 	 * @param name the name
 	 * @ return true if node has the good name
 	 */
-	bool chechXmlNode(xmlNodePtr node, const std::string& name) ;
+//	bool chechXmlNode(xmlNodePtr node, const std::string& name) ;
 
 	/**
 	 * update the pointer of embedding vector after loading
 	 */
 	void update_m_emb_afterLoad();
 
+	/**
+	 * update the markTables and recursively from real type the topo shortcut pointers
+	 */
+	virtual void update_topo_shortcuts();
+
 	/**
 	 * Save map in a XML file
 	 * @param filename the file name
 	 * @return true if OK
 	 */
-	bool saveMapXml(const std::string& filename, bool compress = false) ;
+//	bool saveMapXml(const std::string& filename, bool compress = false) ;
 
 	 /**
 	 * Load map from a XML file
 	 * @param filename the file name
 	 * @return true if OK
 	 */
-	bool loadMapXml(const std::string& filename, bool compress = false) ;
+//	bool loadMapXml(const std::string& filename, bool compress = false) ;
 
 	/**
 	 * Save map in a binary file
@@ -368,6 +380,21 @@ public:
 	 */
 	bool loadMapBin(const std::string& filename) ;
 
+	/**
+	 * Dump attributes types and names per orbit
+	 */
+	void dumpAttributesAndMarkers();
+
+	/**
+	 * update topo relation after compacting the container:
+	 */
+	virtual void compactTopoRelations(const std::vector<unsigned int>& oldnew)=0;
+
+	/**
+	 * compact the map
+	 */
+	void compact();
+
 	/****************************************
 	 *           DARTS TRAVERSALS           *
 	 ****************************************/

include/Topology/generic/genericmap.hpp

@@ -25,10 +25,10 @@
 namespace CGoGN
 {
 
-inline bool GenericMap::chechXmlNode(xmlNodePtr node, const std::string& name)
-{
-	return (strcmp((char*)(node->name),(char*)(name.c_str())) == 0);
-}
+//inline bool GenericMap::chechXmlNode(xmlNodePtr node, const std::string& name)
+//{
+//	return (strcmp((char*)(node->name),(char*)(name.c_str())) == 0);
+//}
 
 /****************************************
  *           DARTS MANAGEMENT           *
@@ -211,5 +211,13 @@ inline AttributeMultiVector<Dart>* GenericMap::addRelation(const std::string& na
 	return amv ;
 }
 
+inline AttributeMultiVector<Dart>* GenericMap::getRelation(const std::string& name)
+{
+	AttributeContainer& cont = m_attribs[DART] ;
+	AttributeMultiVector<Dart>* amv = cont.getDataVector<Dart>(cont.getAttributeIndex(name)) ;
+	return amv ;
+}
+
+
 
 } //namespace CGoGN

include/Topology/gmap/gmap0.h

@@ -52,6 +52,10 @@ public: