X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;ds=sidebyside;f=packages%2Fgdcmvtk%2Fsrc%2FbbgdcmvtkGetXCoherentInfoGdcmReader.cxx;h=77929b8207b5e345a353dd84f19ad965177965cb;hb=0589a26d1de5c18fed06165b035c0737bf1cf285;hp=e638f0ffa55f62b4d3b0e950319668ce83602f4e;hpb=b4f2f6f7aaea4344223882054b61faca214a1d99;p=bbtk.git

diff --git a/packages/gdcmvtk/src/bbgdcmvtkGetXCoherentInfoGdcmReader.cxx b/packages/gdcmvtk/src/bbgdcmvtkGetXCoherentInfoGdcmReader.cxx
index e638f0f..77929b8 100644
--- a/packages/gdcmvtk/src/bbgdcmvtkGetXCoherentInfoGdcmReader.cxx
+++ b/packages/gdcmvtk/src/bbgdcmvtkGetXCoherentInfoGdcmReader.cxx
@@ -2,16 +2,25 @@
 #include "bbgdcmvtkPackage.h"
 
 #include "gdcmFile.h"
-#include "gdcmFileHelper.h"
 #include "vtkImageData.h"
-#include "vtkGdcmReader.h"
 #include <vtkIndent.h>
+#if defined USE_GDCM
+#include "gdcmFileHelper.h"
+#endif
+#if defined USE_GDCM2
+	#include <gdcmReader.h>
+	#include <gdcmImageHelper.h>
+	#include <gdcmIPPSorter.h>
+	#include <vtkGDCMImageReader.h>
+	#include "vtkStringArray.h"
+#endif
 
 namespace bbgdcmvtk
 {
 
 BBTK_ADD_BLACK_BOX_TO_PACKAGE(gdcmvtk,GetXCoherentInfoGdcmReader)
 BBTK_BLACK_BOX_IMPLEMENTATION(GetXCoherentInfoGdcmReader,bbtk::AtomicBlackBox);
+#if defined USE_GDCM
 void GetXCoherentInfoGdcmReader::Process()
 {
  // Read the *first* image file (a SET of file names is given as input) 
@@ -29,6 +38,7 @@ void GetXCoherentInfoGdcmReader::Process()
    std::vector<double> v_iop;
    float iop[6];
    f->GetImageOrientationPatient(iop);
+   
    for(i=0; i< 6; i++)
       v_iop.push_back(iop[i]);
    bbSetOutputIOP(v_iop );
@@ -36,14 +46,15 @@ void GetXCoherentInfoGdcmReader::Process()
    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)
@@ -60,40 +71,117 @@ void GetXCoherentInfoGdcmReader::Process()
    int nbFiles;
    double zspacing = 0.;
    nbFiles = l->size() ;
-   sh->OrderFileList(l);
+   sh->OrderFileList(l); // this one should compute the *actual* Z Spacing!
    zspacing = sh->GetZSpacing();
+   std::vector<double> v_pixelspacing;
+   v_pixelspacing.push_back( f->GetXSpacing() );
+   v_pixelspacing.push_back( f->GetYSpacing() );
+   v_pixelspacing.push_back( zspacing );
+//   if (f->GetZSize() != 1) {
+//      v_pixelspacing.push_back(f->GetZSpacing());
+//   }
+   bbSetOutputPixelSpacing(v_pixelspacing);
+
+   if (reader!=NULL)
+   { 
+      reader->Delete();
+      reader=NULL;
+   }
+   reader = vtkGdcmReader::New();
+   //reader->SetFileName( bbGetInputIn().c_str() );
+   reader->SetCoherentFileList(l);
+   reader->Update();
+   reader->GetOutput();
+
+   bbSetOutputOut( reader->GetOutput() );
+}
+#endif
+// endif USE_GDCM
+
+#if defined USE_GDCM2
+void GetXCoherentInfoGdcmReader::Process()
+{
+ // 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());
+  
+	bool res = read->Read();  
+   if ( !res )
+   {
+      delete read;
+      bbSetOutputOut(0);
+      return;
+   }
+    
+ // Get info from the first image file
+   const gdcm::File &f = read->GetFile();
+   int i;
+   std::vector<double> v_iop;
+   const gdcm::DataElement &deIop = f.GetDataSet().GetDataElement(gdcm::Tag(0x0020, 0x0037));
+   std::stringstream ss;
+   deIop.GetValue().Print(ss);
+   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]));
+   bbSetOutputIOP(v_iop );
+ 
+  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++)
+		v_ipp.push_back((float)(ipp[i]));
+   bbSetOutputIPP(v_ipp );
 
-	std::vector<double> v_pixelspacing;
-	v_pixelspacing.push_back( f->GetXSpacing() );
-	v_pixelspacing.push_back( f->GetYSpacing() );
+// Add *all the files* to the IPPsorter
+     gdcm::IPPSorter s;
+	 s.SetComputeZSpacing( true );
+     s.SetZSpacingTolerance( 1e-3 );
+     std::vector<std::string> gii = bbGetInputIn();
+     s.Sort(gii);
+
+	 //l = sh->GetFirstSingleSerieUIDFileSet();
+	 // no Test if we have multiple series
+	 //s.GetFilenames();
+  	 //int nbFiles;
+
+	double zspacing = 0.;
+	zspacing = s.GetZSpacing();
+	std::vector<double> v_pixelspacing = gdcm::ImageHelper::GetSpacingValue(f);
+	v_pixelspacing.push_back( v_pixelspacing[0] );
+	v_pixelspacing.push_back( v_pixelspacing[1] );
 	v_pixelspacing.push_back( zspacing );
-//	if (f->GetZSize() != 1) {
-//		v_pixelspacing.push_back(f->GetZSpacing());
-//	}
 	bbSetOutputPixelSpacing(v_pixelspacing);
-	
-	
 
-	if (reader!=NULL)
-	{ 
-		reader->Delete();
-		reader=NULL;
-	}
-	reader = vtkGdcmReader::New();
-   //reader->SetFileName( bbGetInputIn().c_str() );
-   reader->SetCoherentFileList(l);
+   if (reader!=NULL)
+   { 
+      reader->Delete();
+      reader=NULL;
+   }
+   reader = vtkGDCMImageReader::New();
+   vtkStringArray *files = vtkStringArray::New();
+   std::vector< std::string >::const_iterator it = s.GetFilenames().begin();
+   for( ; it != s.GetFilenames().end(); ++it)
+   {
+	  const std::string &f = *it;
+      files->InsertNextValue( f.c_str() );
+    }
+   reader->SetFileNames(files);
    reader->Update();
    reader->GetOutput();
-
    bbSetOutputOut( reader->GetOutput() );
 }
+#endif
+// endif USE_GDCM2
 
 void GetXCoherentInfoGdcmReader::bbUserSetDefaultValues()
 {
-    std::vector<std::string> init;
-    init.push_back("");
-    bbSetInputIn(init);  
-	reader=NULL;
+   std::vector<std::string> init;
+   init.push_back("");
+   bbSetInputIn(init);  
+   reader=NULL;
 }
 
 void GetXCoherentInfoGdcmReader::bbUserInitializeProcessing()
@@ -101,6 +189,7 @@ void GetXCoherentInfoGdcmReader::bbUserInitializeProcessing()
 	
 }
 
+#if defined USE_GDCM
 void GetXCoherentInfoGdcmReader::bbUserFinalizeProcessing()
 {
    if(reader)
@@ -110,8 +199,15 @@ void GetXCoherentInfoGdcmReader::bbUserFinalizeProcessing()
    if(sh)
       sh->Delete();      
 }
+#endif
 
+#if defined USE_GDCM2
+void GetXCoherentInfoGdcmReader::bbUserFinalizeProcessing()
+{
+   if(reader)
+      reader->Delete();
 }
-// EO namespace bbgdcmvtk
-
+#endif
 
+}
+// EO namespace bbgdcmvtk