X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=packages%2Fgdcmvtk%2Fsrc%2FbbgdcmvtkGetXCoherentInfoGdcmReader.cxx;h=25700ecdd80ce3d34c415c07e44265ced2a230d2;hb=8ba18df584ba0a409fb042663be9fa76ccb0e0b0;hp=dd8e57a87b8bdd3eaf86387f8b98fad4b8308e03;hpb=cfad95b6e08e6e53846ffcda7fbc5932065f2c47;p=bbtk.git

diff --git a/packages/gdcmvtk/src/bbgdcmvtkGetXCoherentInfoGdcmReader.cxx b/packages/gdcmvtk/src/bbgdcmvtkGetXCoherentInfoGdcmReader.cxx
index dd8e57a..25700ec 100644
--- a/packages/gdcmvtk/src/bbgdcmvtkGetXCoherentInfoGdcmReader.cxx
+++ b/packages/gdcmvtk/src/bbgdcmvtkGetXCoherentInfoGdcmReader.cxx
@@ -1,3 +1,4 @@
+/*
 # ---------------------------------------------------------------------
 #
 # Copyright (c) CREATIS (Centre de Recherche en Acquisition et Traitement de l'Image
@@ -47,19 +48,91 @@ namespace bbgdcmvtk
 
 BBTK_ADD_BLACK_BOX_TO_PACKAGE(gdcmvtk,GetXCoherentInfoGdcmReader)
 BBTK_BLACK_BOX_IMPLEMENTATION(GetXCoherentInfoGdcmReader,bbtk::AtomicBlackBox);
+
+
+vtkImageData* GetXCoherentInfoGdcmReader::CreateDefaultImage()
+{
+	int i;
+	int sizeX, sizeY, sizeZ;
+	sizeX = 200;
+	sizeY = sizeX;
+	sizeZ = 1;
+	vtkImageData *newImage = vtkImageData::New();
+   	newImage->Initialize();
+   	newImage->SetSpacing( 1,1,1 );
+   	newImage->SetDimensions(  sizeX,sizeY,sizeZ );
+   	newImage->SetExtent(0,  sizeX-1,0,sizeY-1,0,sizeZ-1 );
+
+//EED 2017-01-01 Migration VTK7
+#if VTK_MAJOR_VERSION <= 5
+   	newImage->SetWholeExtent(0,  sizeX-1,0,sizeY-1,0,sizeZ-1 );
+   	newImage->SetScalarTypeToUnsignedChar();
+   	newImage->SetNumberOfScalarComponents(1);
+   	newImage->AllocateScalars();
+   	newImage->Update();
+#else
+   	newImage->AllocateScalars(VTK_UNSIGNED_CHAR,1);
+#endif
+
+	memset ( (void*)newImage->GetScalarPointer(), 0, sizeX*sizeY*1 );
+   	for (i=0; i<sizeX; i++)
+   	{
+		newImage->SetScalarComponentFromDouble(i,i,0, 0, 255 );
+		newImage->SetScalarComponentFromDouble(i,sizeY-1-i,0, 0, 255 );
+  	} // for i
+	return newImage;
+} 
+
+
 #if defined USE_GDCM
+
+void GetXCoherentInfoGdcmReader::Process2()
+{
+    printf("EED GetXCoherentInfoGdcmReader::Process >>>>>> \n" );
+    GDCM_NAME_SPACE::FileList   lstFiles;
+    int i,size=bbGetInputIn().size();
+    for (i=0;i<size;i++)
+    {
+        printf("a: %s\n",bbGetInputIn()[i].c_str() );
+        f = GDCM_NAME_SPACE::File::New();
+        f->SetFileName( bbGetInputIn()[i] );
+        bool res = f->Load();
+        if ( res==true )
+        {
+            lstFiles.push_back(f);
+        }
+    } // for
+    sh = GDCM_NAME_SPACE::SerieHelper::New();
+    sh->ImagePositionPatientOrdering( &lstFiles );
+    size=lstFiles.size();
+    for (i=0;i<size;i++)
+    {
+        printf("d:  %s\n", lstFiles[i]->GetFileName().c_str() );
+    } // for
+}
+
+
 void GetXCoherentInfoGdcmReader::Process()
 {
  // Read the *first* image file (a SET of file names is given as input) 
    f = GDCM_NAME_SPACE::File::New();
-   f->SetFileName( bbGetInputIn()[0] );
+
+	if ( bbGetInputIn().size()!=0 )
+	{
+		f->SetFileName( bbGetInputIn()[0] );
+	} else {
+		f->SetFileName( "" );
+	} // if
+
    bool res = f->Load();  
    if ( !res )
    {
-      f->Delete();
-      bbSetOutputOut(0);
-      return;
-   }
+		printf("EED GetXCoherentInfoGdcmReader::Process resultImage NULL\n");
+      	f->Delete();
+      	bbSetOutputOut( CreateDefaultImage() );
+      	return;
+   } // if res
+
  // Get info from the first image file
    int i;
    std::vector<double> v_iop;
@@ -67,39 +140,63 @@ void GetXCoherentInfoGdcmReader::Process()
    f->GetImageOrientationPatient(iop);
    
    for(i=0; i< 6; i++)
+	{
       v_iop.push_back(iop[i]);
+	} // for i
    bbSetOutputIOP(v_iop );
- 
-   std::vector<double> v_ipp;
-   float ipp[3];
-   f->GetImagePositionPatient(ipp);
-   
-   for(i=0; i< 3; i++)
-      v_ipp.push_back(ipp[i]);
-   bbSetOutputIPP(v_ipp );
-
-// Add *all the files* to the SerieHelper
-   sh = GDCM_NAME_SPACE::SerieHelper::New();
-   std::vector<std::string> gii = bbGetInputIn();
-   
-   for(std::vector<std::string>::iterator it = gii.begin();
-                                          it != gii.end();
-                                        ++it)
-   {
-      sh->AddFileName(*it);
-   }
-
-   GDCM_NAME_SPACE::FileList::const_iterator it;
-   GDCM_NAME_SPACE::FileList *l;
+    
+// EED 2022-12-15
+//   std::vector<double> v_ipp;
+//   float ipp[3];
+//   f->GetImagePositionPatient(ipp);
+//   for(i=0; i< 3; i++)
+//	{
+//      v_ipp.push_back(ipp[i]);
+//	} // for i
+//   bbSetOutputIPP(v_ipp );
 
-   // Should only contain one!
-   l = sh->GetFirstSingleSerieUIDFileSet();
+// EED 2023-01-13
+    GDCM_NAME_SPACE::FileList   lstFiles;
+    GDCM_NAME_SPACE::FileList   *l;
 
-   int nbFiles;
+    if (bbGetInputRespectSerieUID()==false)
+    {
+        int i,size=bbGetInputIn().size();
+        for (i=0;i<size;i++)
+        {
+            f = GDCM_NAME_SPACE::File::New();
+            f->SetFileName( bbGetInputIn()[i] );
+            bool res = f->Load();
+            if ( res==true )
+            {
+                lstFiles.push_back(f);
+            }
+        } // for i
+        sh = GDCM_NAME_SPACE::SerieHelper::New();
+        l = &lstFiles;
+        sh->ImagePositionPatientOrdering( l );
+    } else{
+    // Add *all the files* to the SerieHelper
+       sh = GDCM_NAME_SPACE::SerieHelper::New();
+       std::vector<std::string> gii = bbGetInputIn();
+       for(std::vector<std::string>::iterator it = gii.begin();
+                                              it != gii.end();
+                                            ++it)
+       {
+          sh->AddFileName(*it);
+       } //for vector
+       GDCM_NAME_SPACE::FileList::const_iterator it;
+       // Should only contain one!
+       l = sh->GetFirstSingleSerieUIDFileSet();
+        if (l==NULL)
+        {
+            return;
+        }
+    } // if  bbGetInputForceRead
+    
    double zspacing = 0.;
-   nbFiles = l->size() ;
    sh->OrderFileList(l); // this one should compute the *actual* Z Spacing!
-   zspacing = sh->GetZSpacing();
+   zspacing 		= sh->GetZSpacing();
    std::vector<double> v_pixelspacing;
    v_pixelspacing.push_back( f->GetXSpacing() );
    v_pixelspacing.push_back( f->GetYSpacing() );
@@ -109,41 +206,88 @@ void GetXCoherentInfoGdcmReader::Process()
 //   }
    bbSetOutputPixelSpacing(v_pixelspacing);
 
-   if (reader!=NULL)
-   { 
-      reader->Delete();
-      reader=NULL;
-   }
-   reader = vtkGdcmReader::New();
-	
-	//EED 21 mars 2012  FLIP probleme  ..PLOP..
-	reader->SetFlipY(false);
-
-	
-   //reader->SetFileName( bbGetInputIn().c_str() );
-   reader->SetCoherentFileList(l);
-   reader->Update();
-   reader->GetOutput();
+	VectorMapInfoDicom vectormapinfodicom;
+	uint16_t group;
+	uint16_t elem;
+	std::string key;
+	std::string strTagValue;  // read on disc
+	int iTag,sizeDicomTagsVector=bbGetInputDicomTags().size();
+   	GDCM_NAME_SPACE::FileList::const_iterator iitt = l->begin();
+    float px,py,pz;
+    
+    std::vector<std::string> lstFileNames;
+    
+    for ( ; iitt != l->end(); ++iitt)
+   	{
+        lstFileNames.push_back( (*iitt)->GetFileName() );
+        // EED 2022-12-15
+        if ( iitt == l->begin() )   // The first ordered element IPP
+        {
+            group       = 0;
+            elem        = 0;
+            strTagValue = std::string("void");
+            sscanf("D0020_0032","D%04hx_%04hx",&group,&elem);
+            strTagValue = (*iitt)->GetEntryString(group,elem);
+            sscanf(strTagValue.c_str(),"%f\\%f\\%f\\%f", &px , &py , &pz);
+            std::vector<double> v_ipp;
+            v_ipp.push_back( (double)px );
+            v_ipp.push_back( (double)py );
+            v_ipp.push_back( (double)pz );
+            bbSetOutputIPP(v_ipp );
+        } // if first elemetn  get IPP
+     
+		MapInfoDicom mapinfodicom;
+	  	for (iTag=0; iTag<sizeDicomTagsVector; iTag++)
+		{
+			key = bbGetInputDicomTags()[iTag];
+			group = elem = 0;
+			if ( (key.size()==10) && (key[0] == 'D') && (key[5] == '_') )
+			{
+			 	sscanf(key.c_str(),"D%04hx_%04hx ",&group,&elem);  
+			}// if key
+		  	strTagValue = (*iitt)->GetEntryString(group,elem);
+			mapinfodicom.insert ( std::pair<std::string,std::string>(key,strTagValue) );
+		} // for iTag
+		vectormapinfodicom.push_back( mapinfodicom );
+   } // for iitt
+   bbSetOutputDicomInfo( vectormapinfodicom );
+   bbSetOutputOutFileNames( lstFileNames );
 
-   bbSetOutputOut( reader->GetOutput() );
+	if (bbGetInputReadRaw()==true)
+	{
+	   if (reader!=NULL)
+	   { 
+		  reader->Delete();
+		  reader = NULL;
+	   }
+	   reader = vtkGdcmReader::New();
+		//EED 21 mars 2012  FLIP probleme  ..PLOP..
+		reader->SetFlipY(false);
+	   //reader->SetFileName( bbGetInputIn().c_str() );
+	   reader->SetCoherentFileList(l);
+	   reader->Update();
+	   reader->GetOutput();
+	   bbSetOutputOut( reader->GetOutput() );
+	} // if bGetInputReadRaw
 }
 #endif
 // endif USE_GDCM
 
+
 #if defined USE_GDCM2
 void GetXCoherentInfoGdcmReader::Process()
 {
+//	printf("GetXCoherentInfoGdcmReader   %d files.\n", bbGetInputIn().size() );
  // Read the *first* image file (a SET of file names is given as input) 
 	gdcm::Reader *read = new gdcm::Reader();
-	reader->SetFileName( bbGetInputIn()[0].c_str());
-  
+	reader->SetFileName( bbGetInputIn()[0].c_str() );
 	bool res = read->Read();  
-   if ( !res )
-   {
-      delete read;
-      bbSetOutputOut(0);
-      return;
-   }
+  	if ( !res )
+   	{
+     	delete read;
+      	bbSetOutputOut(NULL);
+      	return;
+   	}
     
  // Get info from the first image file
    const gdcm::File &f = read->GetFile();
@@ -155,16 +299,20 @@ void GetXCoherentInfoGdcmReader::Process()
    gdcm::Element<gdcm::VR::DS,gdcm::VM::VM6> iop;
    iop.Read( ss );
    for(i=0; i< 6; i++)
-      v_iop.push_back((float)(iop[i]));
+   {
+      	v_iop.push_back((float)(iop[i]));
+   }
    bbSetOutputIOP(v_iop );
  
-  std::vector<double> v_ipp;
+   std::vector<double> v_ipp;
    const gdcm::DataElement &deIpp = f.GetDataSet().GetDataElement(gdcm::Tag((0x0020,0x0032)));
    deIpp.GetValue().Print(ss);
    gdcm::Element<gdcm::VR::DS,gdcm::VM::VM3> ipp;
    ipp.Read( ss );
-	  for(i=0; i< 3; i++)
+   for(i=0; i< 3; i++)
+	{
 		v_ipp.push_back((float)(ipp[i]));
+	} // for 3
    bbSetOutputIPP(v_ipp );
 
 // Add *all the files* to the IPPsorter
@@ -202,7 +350,6 @@ void GetXCoherentInfoGdcmReader::Process()
    }
    reader->SetFileNames(files);
    reader->Update();
-   reader->GetOutput();
    bbSetOutputOut( reader->GetOutput() );
 }
 #endif
@@ -210,26 +357,34 @@ void GetXCoherentInfoGdcmReader::Process()
 
 void GetXCoherentInfoGdcmReader::bbUserSetDefaultValues()
 {
+   reader=NULL;
    std::vector<std::string> init;
    init.push_back("");
    bbSetInputIn(init);  
+   bbSetInputReadRaw(true);  
+   bbSetInputRespectSerieUID(true);
    //reader=NULL;   /// \TODO fixme JPR
 }
 
 void GetXCoherentInfoGdcmReader::bbUserInitializeProcessing()
 {
-	
 }
 
 #if defined USE_GDCM
 void GetXCoherentInfoGdcmReader::bbUserFinalizeProcessing()
 {
    if(reader)
+	{
       reader->Delete();
+	} // if reader
    if(f)
+	{
       f->Delete();
+	} // if f
    if(sh)
+	{
       sh->Delete();      
+	} // if sh
 }
 #endif
 
@@ -237,7 +392,9 @@ void GetXCoherentInfoGdcmReader::bbUserFinalizeProcessing()
 void GetXCoherentInfoGdcmReader::bbUserFinalizeProcessing()
 {
    if(reader)
+	{
       reader->Delete();
+	}
 }
 #endif