
///////////////////////////////////////////////////////////
//                                                       //
//                         SAGA                          //
//                                                       //
//      System for Automated Geoscientific Analyses      //
//                                                       //
//                     Tool Library                      //
//                   pointcloud_tools                    //
//                                                       //
//-------------------------------------------------------//
//                                                       //
//                 pc_cluster_analysis.h                 //
//                                                       //
//                 Copyright (C) 2010 by                 //
//                    Volker Wichmann                    //
//                                                       //
//   This tool is a port of the Grid_Cluster_Analysis    //
//   tool from the Grid_Discretisation module library,   //
//                 Copyright (C) 2003 by                 //
//                      Olaf Conrad                      //
//                                                       //
//-------------------------------------------------------//
//                                                       //
// This file is part of 'SAGA - System for Automated     //
// Geoscientific Analyses'. SAGA is free software; you   //
// can redistribute it and/or modify it under the terms  //
// of the GNU General Public License as published by the //
// Free Software Foundation, either version 2 of the     //
// License, or (at your option) any later version.       //
//                                                       //
// SAGA 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 General Public        //
// License for more details.                             //
//                                                       //
// You should have received a copy of the GNU General    //
// Public License along with this program; if not, see   //
// <http://www.gnu.org/licenses/>.                       //
//                                                       //
//-------------------------------------------------------//
//                                                       //
//    e-mail:     wichmann@laserdata                     //
//                                                       //
//    contact:    Volker Wichmann                        //
//                LASERDATA GmbH                         //
//                Management and analysis of             //
//                laserscanning data                     //
//                Innsbruck, Austria                     //
//                                                       //
///////////////////////////////////////////////////////////

//---------------------------------------------------------
#include "pc_cluster_analysis.h"


///////////////////////////////////////////////////////////
//														 //
//														 //
//														 //
///////////////////////////////////////////////////////////

//---------------------------------------------------------
CPC_Cluster_Analysis::CPC_Cluster_Analysis(void)
{
	Set_Name		(_TL("Cluster Analysis for Point Clouds"));

	Set_Author		("Volker Wichmann (c) 2010, LASERDATA GmbH");

	Set_Description	(_TW(		
		"Cluster analysis for point clouds.\n"
		"This tool is a port of the 'Cluster Analysis for Grids' "
		"tool from the 'Imagery - Classification' tool library. "
	));

	Add_Reference("Forgy, E.", "1965",
		"Cluster Analysis of multivariate data: efficiency vs. interpretability of classifications",
		"Biometrics 21:768."
	);

	Add_Reference("Rubin, J.", "1967",
		"Optimal Classification into Groups: An Approach for Solving the Taxonomy Problem",
		"J. Theoretical Biology, 15:103-144."
	);

	//-----------------------------------------------------
	Parameters.Add_PointCloud("",
		"PC_IN"			,_TL("Point Cloud"),
		_TL("Input"),
		PARAMETER_INPUT
	);

	Parameters.Add_Table_Fields("PC_IN",
		"FIELDS"		, _TL("Attributes"),
		_TL("The attribute fields to cluster")
	);

	Parameters.Add_PointCloud("",
		"PC_OUT"		,_TL("Result"),
		_TL("Output"),
		PARAMETER_OUTPUT_OPTIONAL
	);

	Parameters.Add_Table("",
		"STATISTICS"	, _TL("Statistics"),
		_TL(""),
		PARAMETER_OUTPUT
	);

	//-----------------------------------------------------
	Parameters.Add_Choice("",
		"METHOD"		, _TL("Method"),
		_TL(""),
		CSG_String::Format("%s|%s|%s",
			_TL("Iterative Minimum Distance (Forgy 1965)"),
			_TL("Hill-Climbing (Rubin 1967)"),
			_TL("Combined Minimum Distance / Hillclimbing") 
		), 1
	);

	Parameters.Add_Int("",
		"NCLUSTER"		, _TL("Clusters"),
		_TL("Number of clusters"),
		10, 2, true
	);

	Parameters.Add_Bool("",
		"NORMALISE"		, _TL("Normalise"),
		_TL("Automatically normalise attributes by standard deviation before clustering."),
		true
	);
}


///////////////////////////////////////////////////////////
//														 //
///////////////////////////////////////////////////////////

//---------------------------------------------------------
bool CPC_Cluster_Analysis::On_Execute(void)
{
	int				nCluster;
	sLong			nElements;
	double			SP;

	//-----------------------------------------------------
	nCluster	= Parameters("NCLUSTER")->asInt();
	pPC_in		= Parameters("PC_IN"   )->asPointCloud();
	pPC_out		= Parameters("PC_OUT"  )->asPointCloud();

	//-------------------------------------------------
	m_Features	= (int *)Parameters("FIELDS")->asPointer();
	m_nFeatures	=        Parameters("FIELDS")->asInt    ();

	if( !m_Features || m_nFeatures <= 0 )
	{
		Error_Set(_TL("no features in selection"));

		return( false );
	}


	//-----------------------------------------------------
	if (!pPC_out || pPC_out == pPC_in)
	{
		pPC_out = &PC_out;
	}

	pPC_out->Create(pPC_in);

	pPC_out->Add_Field("CLUSTER", SG_DATATYPE_Int);
	clustField	= pPC_out->Get_Field_Count() - 1;

	pPC_out->Set_NoData_Value(-1.0);
	

	//-----------------------------------------------------
	Process_Set_Text(_TL("Initializing ..."));

	for( int i=0; i<m_nFeatures; i++ )
		vValues.push_back( std::vector<double>() );

	for(sLong i=0; i<pPC_in->Get_Count() && SG_UI_Process_Set_Progress(i, pPC_in->Get_Count()); i++ )
	{
		pPC_out->Add_Point(pPC_in->Get_X(i), pPC_in->Get_Y(i), pPC_in->Get_Z(i));

		for (int j=0; j<pPC_in->Get_Attribute_Count(); j++)
		{
			switch (pPC_in->Get_Attribute_Type(j))
			{
			default:					pPC_out->Set_Attribute(i, j, pPC_in->Get_Attribute(i, j));		break;
			case SG_DATATYPE_Date:
			case SG_DATATYPE_String:	CSG_String sAttr; pPC_in->Get_Attribute(i, j, sAttr); pPC_out->Set_Attribute(i, j, sAttr);		break;
			}
		}

		pPC_out->Set_NoData(i, clustField);
		
		bool bNoData = false;

		for( int j=0; j<m_nFeatures; j++)
		{
			if( pPC_in->is_NoData(i, m_Features[j]) )
			{
				bNoData = true;
				break;
			}
		}

		if( !bNoData )
		{
			for( int j=0; j<m_nFeatures; j++ )
			{
				if( Parameters("NORMALISE")->asBool() )
					vValues.at(j).push_back( (pPC_in->Get_Value(i, m_Features[j]) - pPC_in->Get_Mean(m_Features[j])) / pPC_in->Get_StdDev(m_Features[j]) );
				else
					vValues.at(j).push_back(pPC_in->Get_Value(i, m_Features[j]));
			}
		}
		else
		{
			for( int j=0; j<m_nFeatures; j++ )
			{
				vValues.at(j).push_back(pPC_in->Get_NoData_Value());
			}
		}
	}


	nMembers	= (int     *)SG_Malloc(nCluster * sizeof(int));
	Variances	= (double  *)SG_Malloc(nCluster * sizeof(double));
	Centroids	= (double **)SG_Malloc(nCluster * sizeof(double *));

	for( int i=0; i<nCluster; i++ )
	{
		Centroids[i]	= (double  *)SG_Malloc(m_nFeatures * sizeof(double));
	}

	//-------------------------------------------------
	nElements	= pPC_in->Get_Count();

	switch( Parameters("METHOD")->asInt() )
	{
	case 0:
		SP	= MinimumDistance	(nElements, nCluster);
		break;

	case 1:
		SP	= HillClimbing		(nElements, nCluster);
		break;

	case 2:
		SP	= MinimumDistance	(nElements, nCluster);

		nElements	= pPC_in->Get_Count();	// may have been diminished because of no data values...

		SP	= HillClimbing		(nElements, nCluster);
		break;
	}

	//-------------------------------------------------
	if( Parameters("NORMALISE")->asBool() )
	{
		int		iv = 0;

		for( int i=0; i<m_nFeatures; i++ )
		{
			for( int j=0; j<nCluster; j++ )
			{
				Centroids[j][iv]	= sqrt(pPC_in->Get_Variance(m_Features[i])) * Centroids[j][iv] + pPC_in->Get_Mean(m_Features[i]);
			}

			iv++;
		}
	}

	Write_Result(Parameters("STATISTICS")->asTable(), nElements, nCluster, SP);

	//-------------------------------------------------
	for( int i=0; i<nCluster; i++ )
	{
		SG_Free(Centroids[i]);
	}

	SG_Free(Centroids);
	SG_Free(Variances);
	SG_Free(nMembers);

	vValues.clear();

	//-----------------------------------------------------
	if (pPC_out == &PC_out)
	{
		CSG_MetaData	History	= pPC_in->Get_History();
		CSG_String		sName	= pPC_in->Get_Name();

		pPC_in->Assign(pPC_out);

		pPC_in->Get_History() = History;
		pPC_in->Set_Name(sName);

		Parameters("PC_OUT")->Set_Value(pPC_in);
	}
	else
	{
		pPC_out->Fmt_Name("%s (%s)", _TL("Cluster"), pPC_in->Get_Name());
	}
	

	return( true );
}


///////////////////////////////////////////////////////////
//														 //
///////////////////////////////////////////////////////////

//---------------------------------------------------------
void CPC_Cluster_Analysis::Write_Result(CSG_Table *pTable, sLong nElements, int nCluster, double SP)
{
	CSG_String			s;
	CSG_Table_Record	*pRecord;

	pTable->Destroy();
	pTable->Fmt_Name("%s_%s", _TL("Cluster Analysis PC"), pPC_in->Get_Name());

	pTable->Add_Field(_TL("ClusterID"), SG_DATATYPE_Int);
	pTable->Add_Field(_TL("Elements" ), SG_DATATYPE_Int);
	pTable->Add_Field(_TL("Variance" ), SG_DATATYPE_Double);

	Message_Fmt("\n%s:\t%lld \n%s:\t%d \n%s:\t%d \n%s:\t%f",
		_TL("Number of Elements"      ), nElements,
		_TL("Number of Variables"     ), m_nFeatures,
		_TL("Number of Clusters"      ), nCluster,
		_TL("Value of Target Function"), SP
	);

	Message_Fmt("\n%s\t%s\t%s", _TL("Cluster"), _TL("Elements"), _TL("Variance"));

	for(int j=0; j<m_nFeatures; j++)
	{
		Message_Fmt("\t%02d_%s", j + 1, pPC_in->Get_Field_Name(m_Features[j]));

		pTable->Add_Field(pPC_in->Get_Field_Name(m_Features[j]), SG_DATATYPE_Double);
	}

	for(int i=0; i<nCluster; i++)
	{
		s.Printf("\n%d\t%d\t%f", i, nMembers[i], Variances[i]);

		pRecord	= pTable->Add_Record();
		pRecord->Set_Value(0, i);
		pRecord->Set_Value(1, nMembers[i]);
		pRecord->Set_Value(2, Variances[i]);

		for(int j=0; j<m_nFeatures; j++)
		{
			s.Append(CSG_String::Format("\t%f", Centroids[i][j]));

			pRecord->Set_Value(j + 3, Centroids[i][j]);
		}

		Message_Add(s, false);
	}
}


///////////////////////////////////////////////////////////
//														 //
//					Minimum Distance					 //
//														 //
///////////////////////////////////////////////////////////

//---------------------------------------------------------
// (nElements)-Array -> Bei Eingabe Startgruppierung oder 0.
// Bei Ausgabe Gruppierung: >Das ite Element ist im Cluster Cluster(i).

double CPC_Cluster_Analysis::MinimumDistance(sLong &nElements, int nCluster)
{
	//-----------------------------------------------------
	// Variablen...

	bool	bContinue;
	int		iField, iCluster, nClusterElements = 0, nShifts, minCluster, nPasses;
	double	d, Variance, minVariance, SP, SP_Last	= -1;


	//-----------------------------------------------------
	// Anfangspartition (Standard falls nicht vorgegeben

	for(sLong iElement=0; iElement<nElements; iElement++ )
	{
		if( pPC_out->Get_Value(iElement, clustField) < 0 || pPC_out->Get_Value(iElement, clustField) >= nCluster )
		{
			pPC_out->Set_Value(iElement, clustField, iElement % nCluster);
		}

		nClusterElements++;
	}


	//-----------------------------------------------------
	// Hauptschleife der Iteration

	for( nPasses=1, bContinue=true; bContinue && Process_Get_Okay(false); nPasses++ )
	{
		//-------------------------------------------------
		for( iCluster=0; iCluster<nCluster; iCluster++ )
		{
			Variances[iCluster]	= 0;
			nMembers [iCluster]	= 0;

			for( iField=0; iField<m_nFeatures; iField++ )
			{
				Centroids[iCluster][iField]	= 0;
			}
		}

		//-------------------------------------------------
		for(sLong iElement=0; iElement<nElements; iElement++ )
		{
			if( pPC_out->Get_Value(iElement, clustField) >= 0 )
			{
				iCluster	= (int)pPC_out->Get_Value(iElement, clustField);
				nMembers[iCluster]++;

				for( iField=0; iField<m_nFeatures; iField++ )
				{
					Centroids[iCluster][iField]	+= vValues.at(iField).at(iElement);
				}
			}
		}

		//-------------------------------------------------
		for( iCluster=0; iCluster<nCluster; iCluster++ )
		{
			d		= nMembers[iCluster] > 0 ? 1.0 / (double)nMembers[iCluster] : 0;

			for( iField=0; iField<m_nFeatures; iField++ )
			{
				Centroids[iCluster][iField]	*= d;
			}
		}


		//-------------------------------------------------
		// Sift and Shift..

		SP		= 0;
		nShifts	= 0;

		for(sLong iElement=0; iElement<nElements && bContinue; iElement++ )
		{
			if( !(iElement % (nElements / 100)) && !Set_Progress(iElement, nElements) )
			{
				bContinue	= false;
			}

			if( pPC_out->Get_Value(iElement, clustField) >= 0 )
			{
				minVariance	= -1;

				for( iCluster=0; iCluster<nCluster; iCluster++ )
				{
					Variance	= 0;

					for( iField=0; iField<m_nFeatures; iField++ )
					{
						d			= Centroids[iCluster][iField] - vValues.at(iField).at(iElement);
						Variance	+= d * d;
					}

					if( minVariance<0 || Variance<minVariance )
					{
						minVariance	= Variance;
						minCluster	= iCluster;
					}
				}

				if( pPC_out->Get_Value(iElement, clustField) != minCluster )
				{
					pPC_out->Set_Value(iElement, clustField, minCluster);
					nShifts++;
				}

				SP						+= minVariance;
				Variances[minCluster]	+= minVariance;
			}
		}


		//-------------------------------------------------

		if( nShifts == 0 || (SP_Last >= 0 && SP >= SP_Last) )
		{
			bContinue	= false;
		}

		Process_Set_Text("%s: %d >> %s %f", _TL("pass"), nPasses, _TL("change"), SP_Last < 0.0 ? SP : SP_Last - SP);

		SP_Last		= SP;
	}

	nElements	= nClusterElements;

	return( SP );
}


///////////////////////////////////////////////////////////
//														 //
//					Hill-Climbing						 //
//														 //
///////////////////////////////////////////////////////////

//---------------------------------------------------------
double CPC_Cluster_Analysis::HillClimbing(sLong &nElements, int nCluster)
{
	//-----------------------------------------------------
	// Variablen...

	bool	bContinue;
	int		iField, iCluster, jCluster, kCluster, nClusterElements = 0, noShift, nPasses;
	double	d, e, n_iK, n_jK, V, VMin, V1, V2, SP, SP_Last	= -1;


	//-----------------------------------------------------

	for( iCluster=0; iCluster<nCluster; iCluster++ )
	{
		Variances[iCluster]	= 0;
		nMembers [iCluster]	= 0;

		for( iField=0; iField<m_nFeatures; iField++)
		{
			Centroids[iCluster][iField]	= 0;
		}
	}


	//-----------------------------------------------------
	// Anfangspartition (Standard falls nicht vorgegeben)

	for(sLong iElement=0; iElement<nElements; iElement++ )
	{
		if( pPC_out->Get_Value(iElement, clustField) < 0 || pPC_out->Get_Value(iElement, clustField) >= nCluster )
		{
			pPC_out->Set_Value(iElement, clustField, iElement % nCluster);
		}

		nClusterElements++;
		
		iCluster	= (int)pPC_out->Get_Value(iElement, clustField);

		nMembers[iCluster]++;

		V			= 0.0;

		for( iField=0; iField<m_nFeatures; iField++)
		{
			d							 = vValues.at(iField).at(iElement);
			Centroids[iCluster][iField]	+= d;
			V							+= d * d;
		}

		Variances[iCluster]	+= V;
	}


	//-----------------------------------------------------

	SP	= 0.0;

	for( iCluster=0; iCluster<nCluster; iCluster++ )
	{
		d	= nMembers[iCluster] != 0 ? 1.0 / (double)nMembers[iCluster] : 0;
		V	= 0.0;

		for( iField=0; iField<m_nFeatures; iField++)
		{
			Centroids[iCluster][iField]	*= d;
			e							 = Centroids[iCluster][iField];
			V							+= e * e;
		}

		Variances[iCluster]	-= nMembers [iCluster] * V;
		SP					+= Variances[iCluster];
	}


	//-----------------------------------------------------
	// Hauptschleife der Iteration

	noShift		= 0;

	for( nPasses=1, bContinue=true; bContinue && Process_Get_Okay(false); nPasses++ )
	{
		//-------------------------------------------------
		for(sLong iElement=0; iElement<nElements && bContinue; iElement++ )
		{
			if( !(iElement % (nElements / 100)) && !Set_Progress(iElement, nElements) )
			{
				bContinue	= false;
			}

			if( pPC_out->Get_Value(iElement, clustField) >= 0 )
			{
				if( noShift++ >= nElements )
				{
					bContinue	= false;
				}
				else
				{

					//---------------------------------------------
					iCluster	= (int)pPC_out->Get_Value(iElement, clustField);

					if( nMembers[iCluster] > 1 )
					{
						V	= 0.0;

						for( iField=0; iField<m_nFeatures; iField++)
						{
							d	= Centroids[iCluster][iField] - vValues.at(iField).at(iElement);
							V	+= d * d;
						}

						n_iK	= nMembers[iCluster];
						V1		= V * n_iK / (n_iK - 1.0);
						VMin	= -1.0;

						//-----------------------------------------
						// Bestimme Gruppe iCluster mit evtl. groesster Verbesserung...

						for( jCluster=0; jCluster<nCluster; jCluster++ )
						{
							if( jCluster != iCluster )
							{
								V	= 0.0;

								for( iField=0; iField<m_nFeatures; iField++)
								{
									d	= Centroids[jCluster][iField] - vValues.at(iField).at(iElement);
									V	+= d * d;
								}

								n_jK	= nMembers[jCluster];
								V2		= V * n_jK / (n_jK + 1.0);

								if( VMin < 0 || V2 < VMin )
								{
									VMin		= V2;
									kCluster	= jCluster;
								}
							}
						}


						//-----------------------------------------
						// Gruppenwechsel und Neuberechnung der Gruppencentroide...

						if( VMin >= 0 && VMin < V1 )
						{
							noShift				= 0;
							Variances[iCluster]	-= V1;
							Variances[kCluster]	+= VMin;
							SP					= SP - V1 + VMin;
							V1					= 1.0 / (n_iK - 1.0);
							n_jK				= nMembers[kCluster];
							V2					= 1.0 / (n_jK + 1.0);

							for( iField=0; iField<m_nFeatures; iField++)
							{
								d							= vValues.at(iField).at(iElement);
								Centroids[iCluster][iField]	= (n_iK * Centroids[iCluster][iField] - d) * V1;
								Centroids[kCluster][iField]	= (n_jK * Centroids[kCluster][iField] + d) * V2;
							}

							pPC_out->Set_Value(iElement, clustField, kCluster);

							nMembers[iCluster]--;
							nMembers[kCluster]++;
						}
					}
				}
			}
		}

		Process_Set_Text("%s: %d >> %s %f", _TL("pass"), nPasses, _TL("change")	, SP_Last < 0.0 ? SP : SP_Last - SP);

		SP_Last		= SP;
	}

	nElements	= nClusterElements;

	return( SP );
}

//---------------------------------------------------------
bool CPC_Cluster_Analysis::On_After_Execution(void)
{
	CSG_PointCloud	*pPC_out	= Parameters("PC_OUT")->asPointCloud();

	if (pPC_out == NULL)
	{
		pPC_out = Parameters("PC_IN")->asPointCloud();
	}

	if( m_Features && m_nFeatures > 0 )
	{
		CSG_Parameters	Parms;

		if( DataObject_Get_Parameters(pPC_out, Parms) && Parms("COLORS_TYPE") && Parms("LUT") && Parms("LUT_ATTRIB") )
		{
			CSG_Table_Record	*pClass;
			CSG_Table			*pLUT	= Parms("LUT")->asTable();

			for( int i=0; i<=pPC_out->Get_Maximum(pPC_out->Get_Field_Count()-1); i++ )
			{
				if( (pClass = pLUT->Get_Record(i)) == NULL )
				{
					pClass	= pLUT->Add_Record();
					pClass->Set_Value(0, SG_GET_RGB(rand() * 255.0 / RAND_MAX, rand() * 255.0 / RAND_MAX, rand() * 255.0 / RAND_MAX));
				}

				pClass->Set_Value(1, CSG_String::Format("%s %d", _TL("Class"), i));
				pClass->Set_Value(2, CSG_String::Format("%s %d", _TL("Class"), i));
				pClass->Set_Value(3, i);
				pClass->Set_Value(4, i);
			}

			while( pLUT->Get_Count() > (pPC_out->Get_Maximum(pPC_out->Get_Field_Count()-1) + 1) )
			{
				pLUT->Del_Record(pLUT->Get_Count() - 1);
			}

			Parms("COLORS_TYPE")	->Set_Value(1);	// Color Classification Type: Lookup Table
			Parms("LUT_ATTRIB")		->Set_Value(clustField);

			DataObject_Set_Parameters(pPC_out, Parms);
		}
	}

	if (pPC_out == Parameters("PC_IN")->asPointCloud())
	{
		Parameters("PC_OUT")->Set_Value(DATAOBJECT_NOTSET);
	}

	return (true);
}

///////////////////////////////////////////////////////////
//														 //
//														 //
//														 //
///////////////////////////////////////////////////////////

//---------------------------------------------------------
