/*
# ---------------------------------------------------------------------
#
# Copyright (c) CREATIS (Centre de Recherche en Acquisition et Traitement de l'Image 
#                        pour la Santé)
# Authors : Eduardo Davila, Frederic Cervenansky, Claire Mouton
# Previous Authors : Laurent Guigues, Jean-Pierre Roux
# CreaTools website : www.creatis.insa-lyon.fr/site/fr/creatools_accueil
#
#  This software is governed by the CeCILL-B license under French law and 
#  abiding by the rules of distribution of free software. You can  use, 
#  modify and/ or redistribute the software under the terms of the CeCILL-B 
#  license as circulated by CEA, CNRS and INRIA at the following URL 
#  http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html 
#  or in the file LICENSE.txt.
#
#  As a counterpart to the access to the source code and  rights to copy,
#  modify and redistribute granted by the license, users are provided only
#  with a limited warranty  and the software's author,  the holder of the
#  economic rights,  and the successive licensors  have only  limited
#  liability. 
#
#  The fact that you are presently reading this means that you have had
#  knowledge of the CeCILL-B license and that you accept its terms.
# ------------------------------------------------------------------------
*/

#include "boost/filesystem/operations.hpp"
#include "boost/filesystem/fstream.hpp"

#include "creaImageIOSimpleView.h"
#include "creaImageIOUnMosaicVtkImageData.h"

namespace creaImageIO
{
	bool SimpleView::readFile(	std::vector<std::string> i_filenames,   								// in information names
										std::vector<std::string> i_attr,								// in information attributes names
										std::vector<std::map <std::string , std::string> > &i_imgAttr,	// out information attributes names-values
										std::vector<vtkImageData *> &i_img)     						// out information vtkImageData
	{
		  //Mosaic Attribute for Simens		
			i_attr.push_back("D0019_100a");  // Number of images in mosaic (Simens)
			i_attr.push_back("D0018_0088");  // Spacing Between Slices
			creaImageIOUnMosaicVtkImageData Mosaic;
			vtkImageData* tmpImg1;
			vtkImageData* tmpImg2;
			int numberOfImagesInMosaic;
			double spc[3];
			double spcZ;

			bool bresult, bfinal = true;
			ImageReader *mReader = new ImageReader();
			std::vector<std::string>::iterator it = i_filenames.begin();
			for (; it != i_filenames.end(); it++)
			{
				bresult = mReader->CanRead((*it).c_str());
				if(bresult)
				{
					std::map <std::string , std::string> mapAttr;
					mReader->getAttributes( (*it).c_str() , mapAttr, i_attr ); //  filename, outMapAttr-NameValue, inVectAttributeName
					i_imgAttr.push_back( mapAttr );

//EED borrame
//					i_img.push_back( mReader->ReadImage( (*it).c_str() ) );


					// EED 18 octt 2014
					std::map <std::string , std::string>::iterator itMapAttr;
					std::string numberOfImagesInMosaicStr="";
					std::string spaceBetweenSliceStr="";

					itMapAttr = mapAttr.find("D0019_100a");
					if ( itMapAttr!=mapAttr.end() ) numberOfImagesInMosaicStr = itMapAttr->second;

//					std::string numberOfImagesInMosaicStr = mapAttr.find("D0019_100a")->second;
					itMapAttr = mapAttr.find("D0018_0088");
					if ( itMapAttr!=mapAttr.end() ) spaceBetweenSliceStr = itMapAttr->second;

//					std::string spaceBetweenSliceStr = mapAttr.find("D0018_0088")->second;
					if (numberOfImagesInMosaicStr=="")
					{
						i_img.push_back( mReader->ReadImage( (*it).c_str() ) );
					} else {
						numberOfImagesInMosaic = atoi(numberOfImagesInMosaicStr.c_str());
						spcZ = atoi(spaceBetweenSliceStr.c_str());
						tmpImg1 = mReader->ReadImage( (*it).c_str() ) ;
						tmpImg1->GetSpacing( spc );	
						tmpImg2 = Mosaic.unMosaic( tmpImg1 , numberOfImagesInMosaic );
						tmpImg2->SetSpacing( spc[0], spc[1], spcZ );	
						i_img.push_back( tmpImg2 );
					}// elemet

				} else {
					printf("ERROR. Impossible to read file %s\n", (*it).c_str() );
					bfinal = false;
				} // if
			} // for
			delete mReader;
			return bfinal;	
	}


	bool SimpleView::readDirectory(	const std::string i_pathname, 											// in information names
												std::vector<std::string> i_attr,											// in information attributes names
												std::vector<std::map <std::string , std::string> > &i_imgAttr,	// out information attributes names-values
												std::vector<vtkImageData *> &i_imgs)									// out information vtkImageData
	{
			bool bresult = true;
			ImageReader *mReader = new ImageReader();
                        std::vector<std::string> names;
			bresult = boost::filesystem::exists( i_pathname );
			if (bresult)
			{
				boost::filesystem::directory_iterator itr(i_pathname);
				boost::filesystem::directory_iterator end_itr; 
				for(;itr != end_itr; ++itr)
				{
					if (!boost::filesystem::is_directory(itr->status()))
					{
						if( mReader->CanRead(itr->path().string()) )
						{
							names.push_back(itr->path().string()); 
						}
					}
				}
				std::sort (names.begin(), names.end()); // make sure names are in lexicographical order
				int lgr = (int)names.size();
				
				for(int i=0; i<lgr; i++)
				{
               std::cout << names[i] << std::endl;

					std::map <std::string , std::string> mapAttr;
					mReader->getAttributes( names[i] , mapAttr, i_attr ); //  filename, outMapAttr-NameValue, inVectAttributeName
					i_imgAttr.push_back( mapAttr );

					//UnMosaic step..

				   i_imgs.push_back( mReader->ReadImage(names[i]) );  
				}			
			}
			return bresult;
	}

	
	vtkImageData* SimpleView::getVolumeSelected( std::vector<vtkImageData*> lstImages)
	{
		vtkImageData *result;

//        creaImageIO::WxSimpleDlg dlg(0,crea::std2wx(bbGetInputTitle()),"localdatabase_Descriptor.dscp","Local Database"); 
//		dlg.SetAttrDicomTags( bbGetInputDicomTags() );
//		dlg.ShowModal(); 
//		bbSetOutputDicomInfo( dlg.getDicomInfoImagesSelected() );

		if (lstImages.size()!=0)
		{ 
//		  bbSetOutputFileName( std::string( dlg.getInfoImage().mb_str() ) );
		  if(lstImages.size() ==1)
		  {
			result = lstImages[0] ;  
		  } else {
				// FCY: it will be a big problem if we have several kind of data in the same folder.
			  	// creation of a huge vtkImageData!!!!
			  	vtkImageData* first = lstImages[0];
			  	int dim[3];
			  	first->GetDimensions(dim);
			  	if (dim[2]==1)
				{
					vtkImageData *out = vtkImageData::New();
				  	int ext[6];
//EED 2017-01-01 Migration VTK7
#if VTK_MAJOR_VERSION <= 5
				  	first->GetWholeExtent(ext); 
#else
				  	first->GetExtent(ext); 
#endif
				  	if(ext[5] == 0)
				  	{
				 	   ext[5] = lstImages.size()-1;
				 	 } else {
						ext[5] = ext[5] * lstImages.size()-1; // to deal with multiframes 
				  	} // ext
				  	out->SetExtent(ext);
				  	double spac[3];
				  	first->GetDimensions(dim);
				  	first->GetSpacing(spac);
 				  	if (spac[0]==spac[1])
					{
						spac[2]=spac[0];  
		          	}
					out->SetSpacing(spac);
					out->SetDimensions(dim[0], dim[1], lstImages.size() );
//EED 2017-01-01 Migration VTK7
#if VTK_MAJOR_VERSION <= 5

				  	out->SetScalarType(first->GetScalarType());
				  	out->SetNumberOfScalarComponents(first->GetNumberOfScalarComponents());
					out->AllocateScalars();
					out->Update();
#else
					out->AllocateScalars(first->GetScalarType(),first->GetNumberOfScalarComponents());
#endif


					unsigned long imsize = dim[0] * dim[1];
					imsize = imsize * dim[2];  // deal with multiframes here
					// differents formats char , short, etc...
					// differents components 1..3  ex. jpg ->RGB 3
					imsize = imsize * first->GetScalarSize() * first->GetNumberOfScalarComponents();
  		        	int slice,sizeImageVector=lstImages.size();
					for (slice=0 ; slice<sizeImageVector ; slice++)
					{
						vtkImageData *img = lstImages[slice];
						memcpy(out->GetScalarPointer(0,0,slice), img->GetScalarPointer(0,0,0), imsize);
						//img->Delete();
				 	} // for slice	
					out->Modified();
//EED This is NOT working. The iteration over the pointer vtkImageData
//		    	  	int slice=0;
//		  	    	std::vector<vtkImageData*>::iterator it;
//		  	    	for (it=dlg.getImagesSelected().begin(); it!=dlg.getImagesSelected().end(); ++it) 
//					{
//						  memcpy(out->GetScalarPointer(0,0,slice), (*it)->GetScalarPointer(0,0,0), imsize);
//						  slice++;
//					}	
//		     	  	//for (it=dlg.getImagesSelected().begin(); it!=dlg.getImagesSelected().end(); ++it) 
//					//{
// 					//		(*it)->Delete();
//					//}

					result =out;

				} else {
					result = first;
				} // dim
			} // if getImagesSelected size
			result->Modified();
		} else { 
	    	result = NULL;  
		} // getImagesSelected().size()!=0
       	return result;
	}
	
	
} // NAMESPACE