genericmap.cpp 31.5 KB
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/*******************************************************************************
* CGoGN: Combinatorial and Geometric modeling with Generic N-dimensional Maps  *
* version 0.1                                                                  *
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* Copyright (C) 2009-2012, IGG Team, LSIIT, University of Strasbourg           *
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*                                                                              *
* This library is free software; you can redistribute it and/or modify it      *
* under the terms of the GNU Lesser General Public License as published by the *
* Free Software Foundation; either version 2.1 of the License, or (at your     *
* option) any later version.                                                   *
*                                                                              *
* This library is distributed in the hope that it will be useful, but WITHOUT  *
* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or        *
* FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License  *
* for more details.                                                            *
*                                                                              *
* You should have received a copy of the GNU Lesser General Public License     *
* along with this library; if not, write to the Free Software Foundation,      *
* Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301 USA.           *
*                                                                              *
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* Web site: http://cgogn.unistra.fr/                                           *
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* Contact information: cgogn@unistra.fr                                        *
*                                                                              *
*******************************************************************************/

#include "Topology/generic/genericmap.h"
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#include "Topology/generic/attributeHandler.h"
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#include "Topology/generic/traversorCell.h"

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#include "Geometry/vector_gen.h"
#include "Geometry/matrix.h"
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#include "Container/registered.h"
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namespace CGoGN
{
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std::map<std::string, RegisteredBaseAttribute*>* GenericMap::m_attributes_registry_map = NULL;
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int GenericMap::m_nbInstances = 0;
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GenericMap::GenericMap() : m_nbThreads(1)
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{
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	if(m_attributes_registry_map == NULL)
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	{
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		m_attributes_registry_map = new std::map<std::string, RegisteredBaseAttribute*>;
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		// register all known types
		registerAttribute<Dart>("Dart");
		registerAttribute<Mark>("Mark");
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		registerAttribute<char>("char");
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		registerAttribute<short>("short");
		registerAttribute<int>("int");
		registerAttribute<long>("long");
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		registerAttribute<unsigned char>("unsigned char");
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		registerAttribute<unsigned short>("unsigned short");
		registerAttribute<unsigned int>("unsigned int");
		registerAttribute<unsigned long>("unsigned long");

		registerAttribute<float>("float");
		registerAttribute<double>("double");
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		registerAttribute<Geom::Vec2f>(Geom::Vec2f::CGoGNnameOfType());
		registerAttribute<Geom::Vec3f>(Geom::Vec3f::CGoGNnameOfType());
		registerAttribute<Geom::Vec4f>(Geom::Vec4f::CGoGNnameOfType());
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		registerAttribute<Geom::Vec2d>(Geom::Vec2d::CGoGNnameOfType());
		registerAttribute<Geom::Vec3d>(Geom::Vec3d::CGoGNnameOfType());
		registerAttribute<Geom::Vec4d>(Geom::Vec4d::CGoGNnameOfType());
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		registerAttribute<Geom::Matrix33f>(Geom::Matrix33f::CGoGNnameOfType());
		registerAttribute<Geom::Matrix44f>(Geom::Matrix44f::CGoGNnameOfType());
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		registerAttribute<Geom::Matrix33d>(Geom::Matrix33d::CGoGNnameOfType());
		registerAttribute<Geom::Matrix44d>(Geom::Matrix44d::CGoGNnameOfType());
	}

	m_nbInstances++;
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	for(unsigned int i = 0; i < NB_ORBITS; ++i)
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	{
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		m_attribs[i].setOrbit(i) ;
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		m_attribs[i].setRegistry(m_attributes_registry_map) ;
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		m_embeddings[i] = NULL ;
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		m_quickTraversal[i] = NULL ;
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		for(unsigned int j = 0; j < NB_THREAD; ++j)
		{
			m_marksets[i][j].clear() ;
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			m_markTables[i][j] = NULL ;
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		}
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		for(unsigned int j = 0; j < NB_ORBITS; ++j)
		{
			m_quickLocalIncidentTraversal[i][j] = NULL ;
			m_quickLocalAdjacentTraversal[i][j] = NULL ;
		}
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	}
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	for (unsigned int i=0; i<NB_THREAD; ++i)
	{
		dartMarkers[i].reserve(16) ;
		cellMarkers[i].reserve(16) ;
	}
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	// get & lock marker for boundary
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	m_boundaryMarkers[0] =  m_marksets[DART][0].getNewMark();
	m_boundaryMarkers[1] =  m_marksets[DART][0].getNewMark();
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	if (m_isMultiRes)
		initMR() ;
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	m_currentBrowser = NULL;
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}

GenericMap::~GenericMap()
{
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	// release marker for boundary
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	m_marksets[DART][0].releaseMark(m_boundaryMarkers[0]);
	m_marksets[DART][0].releaseMark(m_boundaryMarkers[1]);
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	for(unsigned int i = 0; i < NB_ORBITS; ++i)
	{
		if(isOrbitEmbedded(i))
			m_attribs[i].clear(true) ;
	}
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	for(std::multimap<AttributeMultiVectorGen*, AttributeHandlerGen*>::iterator it = attributeHandlers.begin(); it != attributeHandlers.end(); ++it)
		(*it).second->setInvalid() ;
	attributeHandlers.clear() ;

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	for (unsigned int i=0; i<NB_THREAD; ++i)
	{
		for(std::vector<DartMarkerGen*>::iterator it = dartMarkers[i].begin(); it != dartMarkers[i].end(); ++it)
			(*it)->setReleaseOnDestruct(false) ;
		dartMarkers[i].clear() ;
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		for(std::vector<CellMarkerGen*>::iterator it = cellMarkers[i].begin(); it != cellMarkers[i].end(); ++it)
			(*it)->setReleaseOnDestruct(false) ;
		cellMarkers[i].clear() ;
	}
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	// clean type registry if necessary
	m_nbInstances--;
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	if (m_nbInstances <= 0)
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	{
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		for (std::map<std::string, RegisteredBaseAttribute*>::iterator it =  m_attributes_registry_map->begin(); it != m_attributes_registry_map->end(); ++it)
			delete it->second;

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		delete m_attributes_registry_map;
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		m_attributes_registry_map = NULL;
	}
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}

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void GenericMap::clear(bool removeAttrib)
{
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	if (removeAttrib)
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	{
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		for(unsigned int i = 0; i < NB_ORBITS; ++i)
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		{
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			m_attribs[i].clear(true) ;
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			m_embeddings[i] = NULL ;
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			m_quickTraversal[i] = NULL;
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		}
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		for(std::multimap<AttributeMultiVectorGen*, AttributeHandlerGen*>::iterator it = attributeHandlers.begin(); it != attributeHandlers.end(); ++it)
			(*it).second->setInvalid() ;
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		attributeHandlers.clear() ;
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	}
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	else
	{
		for(unsigned int i = 0; i < NB_ORBITS; ++i)
			m_attribs[i].clear(false) ;
	}
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	if (m_isMultiRes)
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		initMR() ;
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}

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/****************************************
 *           MULTIRES                   *
 ****************************************/

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void GenericMap::printMR()
{
	std::cout << std::endl ;

	for(unsigned int j = 0; j < m_mrNbDarts.size(); ++j)
		std::cout << m_mrNbDarts[j] << " / " ;
	std::cout << std::endl << "==========" << std::endl ;

	for(unsigned int i = m_mrattribs.begin(); i != m_mrattribs.end(); m_mrattribs.next(i))
	{
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		std::cout << i << " : " << (*m_mrLevels)[i] << " / " ;
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		for(unsigned int j = 0; j < m_mrDarts.size(); ++j)
			std::cout << (*m_mrDarts[j])[i] << " ; " ;
		std::cout << std::endl ;
	}
}

void GenericMap::initMR()
{
	m_mrattribs.clear(true) ;
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	m_mrattribs.setRegistry(m_attributes_registry_map) ;

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	m_mrDarts.clear() ;
	m_mrDarts.reserve(16) ;
	m_mrNbDarts.clear();
	m_mrNbDarts.reserve(16);
	m_mrLevelStack.clear() ;
	m_mrLevelStack.reserve(16) ;

	m_mrLevels = m_mrattribs.addAttribute<unsigned int>("MRLevel") ;
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	AttributeMultiVector<unsigned int>* newAttrib = m_mrattribs.addAttribute<unsigned int>("MRdart_0") ;
	m_mrDarts.push_back(newAttrib) ;
	m_mrNbDarts.push_back(0) ;

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	setCurrentLevel(0) ;
}

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//AttributeMultiVector<unsigned int>* GenericMap::addLevel()
//{
//	unsigned int newLevel = m_mrDarts.size() ;
//	std::stringstream ss ;
//	ss << "MRdart_"<< newLevel ;
//	AttributeMultiVector<unsigned int>* newAttrib = m_mrattribs.addAttribute<unsigned int>(ss.str()) ;
//	AttributeMultiVector<unsigned int>* prevAttrib = m_mrDarts[newLevel - 1];
//
//	// copy the indices of previous level into new level
//	m_mrattribs.copyAttribute(newAttrib->getIndex(), prevAttrib->getIndex()) ;
//
//	return newAttrib;
//}

void GenericMap::addLevelBack()
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{
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	//AttributeMultiVector<unsigned int>* newAttrib = addLevel();

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	unsigned int newLevel = m_mrDarts.size() ;
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	std::stringstream ss ;
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	ss << "MRdart_"<< newLevel ;
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	AttributeMultiVector<unsigned int>* newAttrib = m_mrattribs.addAttribute<unsigned int>(ss.str()) ;
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	AttributeMultiVector<unsigned int>* prevAttrib = m_mrDarts[newLevel - 1];
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	// copy the indices of previous level into new level
	m_mrattribs.copyAttribute(newAttrib->getIndex(), prevAttrib->getIndex()) ;
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	m_mrDarts.push_back(newAttrib) ;
	m_mrNbDarts.push_back(0) ;
}
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void GenericMap::addLevelFront()
{
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	//AttributeMultiVector<unsigned int>* newAttrib = addLevel();

	unsigned int newLevel = m_mrDarts.size() ;
	std::stringstream ss ;
	ss << "MRdart_"<< newLevel ;
	AttributeMultiVector<unsigned int>* newAttrib = m_mrattribs.addAttribute<unsigned int>(ss.str()) ;
	AttributeMultiVector<unsigned int>* prevAttrib = m_mrDarts[0];

	// copy the indices of previous level into new level
	m_mrattribs.copyAttribute(newAttrib->getIndex(), prevAttrib->getIndex()) ;

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	m_mrDarts.insert(m_mrDarts.begin(), newAttrib) ;
	m_mrNbDarts.insert(m_mrNbDarts.begin(), 0) ;
}

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void GenericMap::removeLevelBack()
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{
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	unsigned int maxL = getMaxLevel() ;
	if(maxL > 0)
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	{
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		AttributeMultiVector<unsigned int>* maxMR = m_mrDarts[maxL] ;
		AttributeMultiVector<unsigned int>* prevMR = m_mrDarts[maxL - 1] ;
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		for(unsigned int i = m_mrattribs.begin(); i != m_mrattribs.end(); m_mrattribs.next(i))
		{
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			unsigned int idx = (*maxMR)[i] ;
			if((*m_mrLevels)[i] == maxL)	// if the MRdart was introduced on the level we're removing
			{
				deleteDartLine(idx) ;		// delete the pointed dart line
				m_mrattribs.removeLine(i) ;	// delete the MRdart line
			}
			else							// if the dart was introduced on a previous level
			{
				if(idx != (*prevMR)[i])		// delete the pointed dart line only if
					deleteDartLine(idx) ;	// it is not shared with previous level
			}
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		}

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		m_mrattribs.removeAttribute<unsigned int>(maxMR->getIndex()) ;
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		m_mrDarts.pop_back() ;
		m_mrNbDarts.pop_back() ;

		if(m_mrCurrentLevel == maxL)
			--m_mrCurrentLevel ;
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	}
}

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void GenericMap::removeLevelFront()
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{
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	unsigned int maxL = getMaxLevel() ;
	if(maxL > 0) //must have at min 2 levels (0 and 1) to remove the front one
	{
		AttributeMultiVector<unsigned int>* minMR = m_mrDarts[0] ;
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//		AttributeMultiVector<unsigned int>* firstMR = m_mrDarts[1] ;
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		for(unsigned int i = m_mrattribs.begin(); i != m_mrattribs.end(); m_mrattribs.next(i))
		{
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//			unsigned int idx = (*minMR)[i] ;
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			if((*m_mrLevels)[i] != 0)	// if the MRdart was introduced after the level we're removing
			{
				--(*m_mrLevels)[i]; //decrement his level of insertion
			}
			else							// if the dart was introduced on a this level and not used after
			{
//				if(idx != (*firstMR)[i])		// delete the pointed dart line only if
//					deleteDartLine(idx) ;	// it is not shared with next level
			}
		}

		m_mrNbDarts[1] += m_mrNbDarts[0];

		m_mrattribs.removeAttribute<unsigned int>(minMR->getIndex()) ;
		m_mrDarts.erase(m_mrDarts.begin()) ;
		m_mrNbDarts.erase(m_mrNbDarts.begin()) ;

		--m_mrCurrentLevel ;
	}
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}

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void GenericMap::copyLevel(unsigned int level)
{
	AttributeMultiVector<unsigned int>* newAttrib = m_mrDarts[level] ;
	AttributeMultiVector<unsigned int>* prevAttrib = m_mrDarts[level - 1];

	// copy the indices of previous level into new level
	m_mrattribs.copyAttribute(newAttrib->getIndex(), prevAttrib->getIndex()) ;
}

void GenericMap::duplicateDarts(unsigned int level)
{
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	AttributeMultiVector<unsigned int>* attrib = m_mrDarts[level] ;
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	for(unsigned int i = m_mrattribs.begin(); i != m_mrattribs.end(); m_mrattribs.next(i))
	{
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		unsigned int oldi = (*attrib)[i] ;	// get the index of the dart in previous level
		(*attrib)[i] = copyDartLine(oldi) ;	// copy the dart and affect it to the new level
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	}
}

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/****************************************
 *        ATTRIBUTES MANAGEMENT         *
 ****************************************/

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void GenericMap::swapEmbeddingContainers(unsigned int orbit1, unsigned int orbit2)
{
	assert(orbit1 != orbit2 || !"Cannot swap a container with itself") ;
	assert((orbit1 != DART && orbit2 != DART) || !"Cannot swap the darts container") ;

	m_attribs[orbit1].swap(m_attribs[orbit2]) ;
	m_attribs[orbit1].setOrbit(orbit1) ;	// to update the orbit information
	m_attribs[orbit2].setOrbit(orbit2) ;	// in the contained AttributeMultiVectors

	m_embeddings[orbit1]->swap(m_embeddings[orbit2]) ;

	for(unsigned int t = 0; t < m_nbThreads; ++t)
	{
		AttributeMultiVector<Mark>* m = m_markTables[orbit1][t] ;
		m_markTables[orbit1][t] = m_markTables[orbit2][t] ;
		m_markTables[orbit2][t] = m ;

		MarkSet ms = m_marksets[orbit1][t] ;
		m_marksets[orbit1][t] = m_marksets[orbit2][t] ;
		m_marksets[orbit2][t] = ms ;
	}

	for (unsigned int i=0; i<NB_THREAD; ++i)
	{
		for(std::vector<CellMarkerGen*>::iterator it = cellMarkers[i].begin(); it != cellMarkers[i].end(); ++it)
		{
			if((*it)->m_cell == orbit1)
				(*it)->m_cell = orbit2 ;
			else if((*it)->m_cell == orbit2)
				(*it)->m_cell = orbit1 ;
		}
	}
}
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void GenericMap::viewAttributesTables()
{
	std::cout << "======================="<< std::endl ;
	for (unsigned int i = 0; i < NB_ORBITS; ++i)
	{
		std::cout << "ATTRIBUTE_CONTAINER " << i << std::endl ;
		AttributeContainer& cont = m_attribs[i] ;

		// get the list of attributes
		std::vector<std::string> listeNames ;
		cont.getAttributesNames(listeNames) ;
		for (std::vector<std::string>::iterator it = listeNames.begin(); it != listeNames.end(); ++it)
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		{
			unsigned int id = cont.getAttributeIndex(*it);
			std::cout << "    " << *it << " ("<<id<<")"<<std::endl ;
		}

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		std::cout << "-------------------------" << std::endl ;
	}
	std::cout << "m_embeddings: " << std::hex ;
	for (unsigned int i = 0; i < NB_ORBITS; ++i)
		std::cout << (long)(m_embeddings[i]) << " / " ;
	std::cout << std::endl << "-------------------------" << std::endl ;

	std::cout << "m_markTables: " ;
	for (unsigned int i = 0; i < NB_ORBITS; ++i)
		std::cout << (long)(m_markTables[i][0]) << " / " ;
	std::cout << std::endl << "-------------------------" << std::endl << std::dec ;
}

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void GenericMap::printDartsTable()
{
	std::cout << "======================="<< std::endl ;

	//m_attribs[DART]
}

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/****************************************
 *          THREAD MANAGEMENT           *
 ****************************************/

void GenericMap::addThreadMarker(unsigned int nb)
{
	unsigned int th ;

	for (unsigned int j = 0; j < nb; ++j)
	{
		th = m_nbThreads ;
		m_nbThreads++ ;

		for (unsigned int i = 0; i < NB_ORBITS; ++i)
		{
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			std::stringstream ss ;
			ss << "Mark_"<< th ;
			AttributeContainer& cellCont = m_attribs[i] ;
			AttributeMultiVector<Mark>* amvMark = cellCont.addAttribute<Mark>(ss.str()) ;
			m_markTables[i][th] = amvMark ;
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		}
	}
}

unsigned int GenericMap::getNbThreadMarkers()
{
	return m_nbThreads;
}

void GenericMap::removeThreadMarker(unsigned int nb)
{
	unsigned int th = 0;
	while ((m_nbThreads > 1) && (nb > 0))
	{
		th = --m_nbThreads ;
		--nb;
		for (unsigned int i = 0; i < NB_ORBITS; ++i)
		{
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			std::stringstream ss ;
			ss << "Mark_"<< th ;
			AttributeContainer& cellCont = m_attribs[i] ;
			cellCont.removeAttribute<Mark>(ss.str()) ;
			m_markTables[i][th] = NULL ;
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		}
	}
}
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/****************************************
 *             SAVE & LOAD              *
 ****************************************/

bool GenericMap::saveMapBin(const std::string& filename)
{
	CGoGNostream fs(filename.c_str(), std::ios::out|std::ios::binary);
	if (!fs)
	{
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		CGoGNerr << "Unable to open file for writing: " << filename << CGoGNendl;
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		return false;
	}

	// Entete
	char* buff = new char[256];
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	for (int i = 0; i < 256; ++i)
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		buff[i] = char(255);
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	if (m_isMultiRes)
	{
		const char* cgogn = "CGoGN_MRMap";
		memcpy(buff, cgogn, 12);
	}
	else
	{
		const char* cgogn = "CGoGN_Map";
		memcpy(buff, cgogn, 10);
	}
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	std::string mt = mapTypeName();
	const char* mtc = mt.c_str();
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	memcpy(buff+32, mtc, mt.size()+1);
	unsigned int *buffi = reinterpret_cast<unsigned int*>(buff + 64);
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	*buffi = NB_ORBITS;
	fs.write(reinterpret_cast<const char*>(buff), 256);
	delete buff;

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	// save all attribs
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	for (unsigned int i = 0; i < NB_ORBITS; ++i)
		m_attribs[i].saveBin(fs, i);
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	if (m_isMultiRes)
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	{
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		m_mrattribs.saveBin(fs, 00);

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		fs.write(reinterpret_cast<const char*>(&m_mrCurrentLevel), sizeof(unsigned int));

		unsigned int nb = m_mrNbDarts.size();
		fs.write(reinterpret_cast<const char*>(&nb), sizeof(unsigned int));
		fs.write(reinterpret_cast<const char*>(&(m_mrNbDarts[0])), nb *sizeof(unsigned int));
	}

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	return true;
}

bool GenericMap::loadMapBin(const std::string& filename)
{
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	CGoGNistream fs(filename.c_str(), std::ios::in|std::ios::binary);
	if (!fs)
	{
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		CGoGNerr << "Unable to open file for loading" << CGoGNendl;
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		return false;
	}

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	GenericMap::clear(true);

	// read info
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	char* buff = new char[256];
	fs.read(reinterpret_cast<char*>(buff), 256);

	std::string buff_str(buff);
	// Check file type
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	if (m_isMultiRes)
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	{
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		if (buff_str == "CGoGN_Map")
		{
			CGoGNerr<< "Wrong binary file format, file is not a MR-Map"<< CGoGNendl;
			return false;
		}
		if (buff_str != "CGoGN_MRMap")
		{
			CGoGNerr<< "Wrong binary file format"<< CGoGNendl;
			return false;
		}
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	}
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	else
	{
		if (buff_str == "CGoGN_MRMap")
		{
			CGoGNerr<< "Wrong binary file format, file is a MR-Map"<< CGoGNendl;
			return false;
		}
		if (buff_str != "CGoGN_Map")
		{
			CGoGNerr<< "Wrong binary file format"<< CGoGNendl;
			return false;
		}
	}

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	// Check map type
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	buff_str = std::string(buff + 32);
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	std::string localType = this->mapTypeName();
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	std::string fileType = buff_str;
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	if (fileType != localType)
	{
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		CGoGNerr << "Not possible to load "<< fileType << " into " << localType << " object" << CGoGNendl;
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		return false;
	}

	// Check max nb orbit
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	unsigned int *ptr_nbo = reinterpret_cast<unsigned int*>(buff + 64);
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	unsigned int nbo = *ptr_nbo;
	if (nbo != NB_ORBITS)
	{
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		CGoGNerr << "Wrond max orbit number in file" << CGoGNendl;
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		return  false;
	}

	// load attrib container
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	for (unsigned int i = 0; i < NB_ORBITS; ++i)
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	{
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		unsigned int id = AttributeContainer::loadBinId(fs);
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		m_attribs[id].loadBin(fs);
	}

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	if (m_isMultiRes)
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	{
		AttributeContainer::loadBinId(fs); // not used but need to read to skip
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		m_mrattribs.loadBin(fs);

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		fs.read(reinterpret_cast<char*>(&m_mrCurrentLevel), sizeof(unsigned int));
		unsigned int nb;
		fs.read(reinterpret_cast<char*>(&nb), sizeof(unsigned int));
		m_mrNbDarts.resize(nb);
		fs.read(reinterpret_cast<char*>(&(m_mrNbDarts[0])), nb *sizeof(unsigned int));
	}

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	// retrieve m_embeddings (from m_attribs)
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	update_m_emb_afterLoad();
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	// recursive call from real type of map (for topo relation attributes pointers) down to GenericMap (for Marker_cleaning & pointers)
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	update_topo_shortcuts();
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	// restore nbThreads
	std::vector<std::string> typeMark;
	unsigned int nbatt0 = m_attribs[0].getAttributesTypes(typeMark);
	m_nbThreads = 0;
	for (unsigned int i = 0; i < nbatt0; ++i)
	{
		if (typeMark[i] == "Mark")
			++m_nbThreads;
	}

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	// restore quick traversals pointers if necessary (containers  already ok)
	for (unsigned int orb=0; orb<NB_ORBITS; ++orb)
	{
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		m_quickTraversal[orb] = m_attribs[orb].getDataVector<Dart>("quick_traversal") ;
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	}
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	return true;
}

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bool GenericMap::copyFrom(const GenericMap& map)
{
	if (mapTypeName() != map.mapTypeName())
	{
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		CGoGNerr << "try to copy from incompatible type map" << CGoGNendl;
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		return false;
	}

	GenericMap::clear(true);

	// load attrib container
	for (unsigned int i = 0; i < NB_ORBITS; ++i)
		m_attribs[i].copyFrom(map.m_attribs[i]);

	if (m_isMultiRes)
	{
		m_mrattribs.copyFrom(map.m_mrattribs);
		m_mrCurrentLevel = map.m_mrCurrentLevel;

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		unsigned int nb = map.m_mrNbDarts.size();
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		m_mrNbDarts.resize(nb);
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		for (unsigned int i = 0; i < nb; ++i)
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			m_mrNbDarts[i] = map.m_mrNbDarts[i];
	}

	// retrieve m_embeddings (from m_attribs)
	update_m_emb_afterLoad();

	// recursive call from real type of map (for topo relation attributes pointers) down to GenericMap (for Marker_cleaning & pointers)
	update_topo_shortcuts();

	return true;
}

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void GenericMap::update_m_emb_afterLoad()
{
	// get container of dart orbit
	AttributeContainer& cont = m_attribs[DART] ;

	// get the list of attributes
	std::vector<std::string> listeNames;
	cont.getAttributesNames(listeNames);

	// check if there are EMB_X attributes
	for (unsigned int i = 0;  i < listeNames.size(); ++i)
	{
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		std::string sub = listeNames[i].substr(0, listeNames[i].size() - 1);
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		if (sub == "EMB_")
		{
			unsigned int orb = listeNames[i][4]-'0'; // easy atoi computation for one char;
			AttributeMultiVector<unsigned int>* amv = cont.getDataVector<unsigned int>(i);
			m_embeddings[orb] = amv ;
		}
	}
}

void GenericMap::update_topo_shortcuts()
{
	for(unsigned int orbit = 0; orbit < NB_ORBITS; ++orbit)
	{
		AttributeContainer& cont = m_attribs[orbit];

		// get the list of attributes of orbit container
		std::vector<std::string> listeNames;
		cont.getAttributesNames(listeNames);

		for (unsigned int i = 0;  i < listeNames.size(); ++i)
		{
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			std::string sub = listeNames[i].substr(0, 5);
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			if (sub == "Mark_")
			{
				// get thread number
				unsigned int thread = listeNames[i][5]-'0';
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				if (listeNames[i].size() > 6) 					// thread number is >9
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					thread = 10*thread + (listeNames[i][6]-'0');
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				AttributeMultiVector<Mark>* amvMark = cont.getDataVector<Mark>(i);
				m_markTables[orbit][thread] = amvMark ;

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				if ((orbit == DART) && (thread == 0))	// for Marker of dart of thread O keep the boundary marker
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				{
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			// TODO Verifier ce qu fait exactement ce unsetMark sur m.invert ??
//					Mark m(m_boundaryMarker);
					Mark m(m_boundaryMarkers[0]+m_boundaryMarkers[1]);
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					m.invert();
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					for (unsigned int i = cont.begin(); i != cont.end(); cont.next(i))
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						amvMark->operator[](i).unsetMark(m);
				}
				else								// for others clear all
				{
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					for (unsigned int i = cont.begin(); i != cont.end(); cont.next(i))
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						amvMark->operator[](i).clear();
				}
			}
		}
	}
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	if (m_isMultiRes)
	{
		std::vector<std::string> names;
		m_mrattribs.getAttributesNames(names);
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		m_mrDarts.resize(names.size() - 1);
		for (unsigned int i = 0; i < m_mrDarts.size(); ++i)
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			m_mrDarts[i] = NULL;

		for (unsigned int i = 0;  i < names.size(); ++i)
		{
			std::string sub = names[i].substr(0, 7);

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			if (sub == "MRLevel")
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				m_mrLevels = m_mrattribs.getDataVector<unsigned int>(i);
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			if (sub == "MRdart_")
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			{
				sub = names[i].substr(7);	// compute number following MT_Dart_
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				unsigned int idx = 0;
				for (unsigned int j = 0; j < sub.length(); j++)
					idx = 10*idx + (sub[j]-'0');
				if (idx < names.size() - 1)
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					m_mrDarts[idx] = m_mrattribs.getDataVector<unsigned int>(i);
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				else
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					CGoGNerr << "Warning problem updating MR_DARTS" << CGoGNendl;
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			}
		}
		// check if all pointers are != NULL
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		for (unsigned int i = 0; i < m_mrDarts.size(); ++i)
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		{
			if (m_mrDarts[i] == NULL)
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				CGoGNerr << "Warning problem MR_DARTS = NULL" << CGoGNendl;
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		}
	}
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}

void GenericMap::dumpAttributesAndMarkers()
{
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	for (unsigned int i = 0; i < NB_ORBITS; ++i)
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	{
		std::vector<std::string> names;
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		names.reserve(32); 				//just to limit reallocation
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		m_attribs[i].getAttributesNames(names);
		unsigned int nb = names.size();
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		if (nb > 0)
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		{
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			CGoGNout << "ORBIT "<< i << CGoGNendl;
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			std::vector<std::string> types;
			types.reserve(nb);
			m_attribs[i].getAttributesTypes(types);
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			for (unsigned int j = 0; j < nb; ++j)
				CGoGNout << "    " << j << " : " << types[j] << " " << names[j] << CGoGNendl;
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		}
	}
	CGoGNout << "RESERVED MARKERS "<< CGoGNendl;
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	for (unsigned int i = 0; i < NB_ORBITS; ++i)
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	{
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		for (unsigned int j = 0; j < NB_THREAD; ++j)
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		{
			MarkSet ms = m_marksets[i][j];
			if (!ms.isClear())
			{
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				CGoGNout << "Orbit " << i << "  thread " << j << " : ";
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				Mark m(1);
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				for (unsigned i = 0; i < Mark::getNbMarks(); ++i)
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				{
					if (ms.testMark(m))
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						CGoGNout << m.getMarkVal() << ", ";
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					m.setMarkVal(m.getMarkVal()<<1);
				}
				CGoGNout << CGoGNendl;
			}
		}
	}
}

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void GenericMap::compact()
{
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	// if MR compact the MR attrib container
	std::vector<unsigned int> oldnewMR;
	if (m_isMultiRes)
		m_mrattribs.compact(oldnewMR);
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	// compacting the orbits attributes
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//	for (unsigned int orbit = 0; orbit < NB_ORBITS; ++orbit)
//	{
//		if ((orbit != DART) && (isOrbitEmbedded(orbit)))
//		{
//			m_attribs[orbit].compact(oldnew);
//
//			for (unsigned int i = m_attribs[DART].begin(); i != m_attribs[DART].end(); m_attribs[DART].next(i))
//			{
//				unsigned int& idx = m_embeddings[orbit]->operator [](i);
//				unsigned int jdx = oldnew[idx];
//				if ((jdx != 0xffffffff) && (jdx != idx))
//					idx = jdx;
//			}
//		}
//	}

	// compact embedding attribs
	std::vector< std::vector<unsigned int>* > oldnews;
	oldnews.resize(NB_ORBITS);
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	for (unsigned int orbit = 0; orbit < NB_ORBITS; ++orbit)
	{
		if ((orbit != DART) && (isOrbitEmbedded(orbit)))
		{
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			oldnews[orbit] = new std::vector<unsigned int>;
			m_attribs[orbit].compact(*(oldnews[orbit]));
		}
	}
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	// update embedding indices of topo
	for (unsigned int i = m_attribs[DART].begin(); i != m_attribs[DART].end(); m_attribs[DART].next(i))
	{
		for (unsigned int orbit = 0; orbit < NB_ORBITS; ++orbit)
		{
			if ((orbit != DART) && (isOrbitEmbedded(orbit)))
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			{
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				unsigned int& idx = m_embeddings[orbit]->operator[](i);
				unsigned int jdx = oldnews[orbit]->operator[](idx);
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				if ((jdx != 0xffffffff) && (jdx != idx))
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					idx = jdx;
			}
		}
	}
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	// delete allocated vectors
	for (unsigned int orbit = 0; orbit < NB_ORBITS; ++orbit)
		if ((orbit != DART) && (isOrbitEmbedded(orbit)))
			delete[] oldnews[orbit];

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	std::vector<unsigned int> oldnew;
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	m_attribs[DART].compact(oldnew);

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	// update MR indices to attribs[DART]
	if (m_isMultiRes)
	{
		unsigned int nbl = m_mrDarts.size();
		for (unsigned int i = m_mrattribs.begin(); i != m_mrattribs.end(); m_mrattribs.next(i))
		{
			for (unsigned int j=0; j<nbl; ++j)
			{
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				unsigned int d_index = m_mrDarts[j]->operator[](i);
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				if (d_index != oldnew[d_index])
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					m_mrDarts[j]->operator[](i) = oldnew[d_index];
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			}
		}
	}

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	// update topo relations from real map
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	compactTopoRelations(oldnewMR);
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//	dumpAttributesAndMarkers();
}

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/****************************************
 *           DARTS TRAVERSALS           *
 ****************************************/

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bool GenericMap::foreach_dart(FunctorType& f)
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{
	for (Dart d = begin(); d != end(); next(d))
	{
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		if (f(d))
			return true;
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	}
	return false;
}

} // namespace CGoGN
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//
//bool GenericMap::saveMapXml(const std::string& filename, bool compress)
//{
//	xmlTextWriterPtr writer = xmlNewTextWriterFilename(filename.c_str(), 0);
//	xmlTextWriterStartDocument(writer,NULL,NULL,NULL);
//
//	// Entete
//	int rc = xmlTextWriterStartElement(writer, BAD_CAST "CGoGN_Map");
//	rc = xmlTextWriterWriteAttribute(writer,  BAD_CAST "type", BAD_CAST this->mapTypeName().c_str());
//	rc = xmlTextWriterWriteFormatAttribute(writer,  BAD_CAST "nb_max_orbits","%u",NB_ORBITS);
//
//	// save m_attribs
//	for (unsigned int i=0; i<NB_ORBITS; ++i)
//	{
//		m_attribs[i].saveXml(writer,i);
//	}
//
//	// save m_orbMarker
//	rc = xmlTextWriterStartElement(writer, BAD_CAST "Orbit_MarkerSet");
//	for (unsigned int i=0; i<NB_ORBITS; ++i)
//	{
//		int rc = xmlTextWriterStartElement(writer, BAD_CAST "MarkerSet");
//		rc = xmlTextWriterWriteFormatAttribute(writer,  BAD_CAST "orbit", "%u", i);
//		rc = xmlTextWriterWriteFormatAttribute(writer,  BAD_CAST "val", "%u", m_marksets[i][0].getMarkVal());
////		rc = xmlTextWriterWriteAttribute(writer,  BAD_CAST "bin", BAD_CAST m_marksets[i][0].getMarkerAsBinaryString().c_str());
////		m_marksets[i] ;
//		rc = xmlTextWriterEndElement(writer);
//	}
//	rc = xmlTextWriterEndElement(writer);
//
//	// save m_BoundaryMarkerVal
////	rc = xmlTextWriterStartElement(writer, BAD_CAST "Boundary_Marker");
////	rc = xmlTextWriterWriteFormatAttribute(writer,  BAD_CAST "val", "%u", m_BoundaryMarkerVal.getMarkVal());
////	rc = xmlTextWriterEndElement(writer);
//
//	rc = xmlTextWriterEndElement(writer); // of map
//
//	xmlTextWriterEndDocument(writer);
//	xmlFreeTextWriter(writer);
//
//	return true;
//}
//
//
//bool GenericMap::loadMapXml(const std::string& filename, bool compress)
//{
//
//	xmlDocPtr doc = xmlReadFile(filename.c_str(), NULL, 0);
//	xmlNodePtr map_node = xmlDocGetRootElement(doc);
//
//	// Check if it is a CGoGN_Map file
////	if (strcmp((char*)(map_node->name),(char*)"CGoGN_Map")!=0)
//	if (!chechXmlNode(map_node,"CGoGN_Map"))
//	{
//		CGoGNerr << "Wrong xml format: Root node != CGoGN_Map"<< CGoGNendl;
//		return false;
//	}
//
//	// check the file type
//	xmlChar *prop = xmlGetProp(map_node, BAD_CAST "type");
//	CGoGNout << "Loading "<< prop <<" xml file"<< CGoGNendl;
//
//	// check the nb max orbits
//	prop = xmlGetProp(map_node, BAD_CAST "nb_max_orbits");
//	unsigned int nbo = atoi((char*)prop);
//	if (nbo != NB_ORBITS)
//	{
//		CGoGNerr << "Wrong nb max orbits in xml map"<< CGoGNendl;
//		return false;
//	}
//
//	/***********************************************
//	*	 			 load attributs
//	************************************************/
//	for (xmlNode* cur_node = map_node->children; cur_node; cur_node = cur_node->next)
//	{
//		// for each attribute
////		if (strcmp((char*)(cur_node->name),(char*)"Attributes_Container")==0)
//		if (chechXmlNode(cur_node, "Attributes_Container"))
//		{
//			CGoGNout << "LOAD ATTRIBUT"<< CGoGNendl;
//			// get the orbit id
//			unsigned int id = AttributeContainer::getIdXmlNode(cur_node);
//			// and load container
//			unsigned int nba = m_attribs[id].getNbAttributes();
//
//
//			CGoGNout << "attribut "<<id<<" size="<< m_attribs[id].size()<< "  nbatt="<< nba<< CGoGNendl;
//
//			m_attribs[id].loadXml(cur_node);
//		}
//	}
//
//	/***********************************************
//	*   creation of the m_embeddings pointers table
//	************************************************/
////	// get attribute names of dart orbit
////	AttributeContainer& contDart = m_attribs[DART] ;
////	std::vector< std::string > tableNames;
////	contDart.getAttributesStrings(tableNames);
////
////	// find orbit frome name and store pointer in right place
////	for (unsigned int i = 0; i< tableNames.size(); ++i)
////	{
//////		CGoGNout << i <<" : "<< tableNames[i]<<CGoGNendl;
////
////		std::string& name = tableNames[i];
////		std::string is_an_emb = name.substr(0,4);
////		if (is_an_emb == "EMB_")
////		{
////			AttributeMultiVector<unsigned int>& amv = contDart.getDataVector<unsigned int>(i) ;
////
////			std::string orbitname = name.substr(4, name.size()-4);
////			std::istringstream iss(orbitname);
////			unsigned int orbit;
////			iss >> orbit;
////
////			m_embeddings[orbit] = &amv ;
////		}
////	}
////
////
//	update_m_emb_afterLoad();
//
//	/***********************************************
//	*	 load Orbit_MarkerSet & BoundaryMarker
//	************************************************/
//	xmlNode* cur_node = map_node->children;
//	bool read1=false;
//	bool read2=false;
//	while (!(read1 || read2) && cur_node)// scan nodes to find the one with right name
//	{
////		if (strcmp((char*)(cur_node->name),(char*)"Orbit_MarkerSet") == 0)
//		if (chechXmlNode(cur_node, "Orbit_MarkerSet"))
//		{
//			for (xmlNode* mark_node = cur_node->children; mark_node; mark_node = mark_node->next)
//			{
//				xmlChar* prop = xmlGetProp(mark_node, BAD_CAST "orbit");
//				unsigned int orb = atoi((char*)prop);
//				prop = xmlGetProp(mark_node, BAD_CAST "val");
//				unsigned int val = atoi((char*)prop);
//				m_marksets[orb][0].setMarkVal(val);
//			}
//			read1 =true;
//		}
//		else
//		{
////			if (strcmp((char*)(cur_node->name),(char*)"Boundary_Marker") == 0)
//			CGoGNout << "Orbit_MarkerSet"<<CGoGNendl;
////			if (chechXmlNode(cur_node, "Boundary_Marker"))
////			{
////				xmlChar* prop = xmlGetProp(cur_node, BAD_CAST "val");
////				unsigned int val = atoi((char*)prop);
////				m_BoundaryMarkerVal.setMarkVal(val);
////				read2 =true;
////			}
//		}
//		// next node
//		cur_node = cur_node->next;
//	}
//
//	if (!(read1 && read2))
//	{
//		CGoGNerr <<"Error reading Marker in xml node"<<CGoGNendl;
//		return false;
//	}
//
//	xmlFreeDoc(doc);
//
//	update_m_emb_afterLoad();
//
//	return true ;
//}