GUIPlugPackage Script Fix

[bbtk.git] / packages / itk / src / bbitkImageSeriesReader.cxx

diff --git a/packages/itk/src/bbitkImageSeriesReader.cxx b/packages/itk/src/bbitkImageSeriesReader.cxx
index 1a18bcbb97138b1024ac4780cf6da16f7581165d..9300d07545d2c3ae4dd17304ba5de0c42ce87232 100644 (file)
--- a/packages/itk/src/bbitkImageSeriesReader.cxx
+++ b/packages/itk/src/bbitkImageSeriesReader.cxx
@@ -2,8 +2,8 @@
   Program:   bbtk
   Module:    $RCSfile: bbitkImageSeriesReader.cxx,v $
   Language:  C++
-  Date:      $Date: 2008/11/26 10:13:32 $
-  Version:   $Revision: 1.7 $
+  Date:      $Date: 2010/09/12 23:15:17 $
+  Version:   $Revision: 1.11 $
 =========================================================================*/
 
 /* ---------------------------------------------------------------------
@@ -44,8 +44,30 @@ namespace bbitk
   
   BBTK_ADD_BLACK_BOX_TO_PACKAGE(itk,ImageSeriesReader);
 
+    
+       //-----------------------------------------------------------------     
+       void ImageSeriesReader::bbUserSetDefaultValues()
+       {
+               bbSetInputXSpacing(-1.0);
+               bbSetInputYSpacing(-1.0);
+               bbSetInputZSpacing(-1.0);               
+       }
+       
+       //-----------------------------------------------------------------     
+       void ImageSeriesReader::bbUserInitializeProcessing()
+       {
+       }
+       
+       //-----------------------------------------------------------------     
+       void ImageSeriesReader::bbUserFinalizeProcessing()
+       {
+       }       
+       
+       
+       
   void ImageSeriesReader::Read()
   {
+std::cout << "--------------------------------------------------- ImageSeriesReader::Read( NO template)" << std::endl;
     const std::vector<std::string>& filenames = bbGetInputFileNames();
     if (!filenames.size()) 
       {
@@ -60,12 +82,16 @@ namespace bbitk
        p->Allocate();
        p->Register();
        bbSetOutputOut(p.GetPointer());
+std::cout << "--------------------------------------------------- ImageSeriesReader::Read( NO image found)" << std::endl;
        return;
        //bbtkError("Void vector passed to "<<bbGetFullName());
       }
 
     std::string filename = filenames[0];
-    
+    std::cout << "--------------------------------------------------- size " << filenames.size() << std::endl;
+std::cout << "--------------------------------------------------- filenames[0] : " << filenames[0]<< std::endl; 
+std::cout << "--------------------------------------------------- filename.c_str : " << filename.c_str()<< std::endl; 
+   
     itk::ImageIOBase::Pointer genericReader = 
       itk::ImageIOFactory::CreateImageIO(filename.c_str(), 
                                         itk::ImageIOFactory::ReadMode);
@@ -77,6 +103,7 @@ namespace bbitk
     genericReader->SetFileName(filename.c_str());
     genericReader->ReadImageInformation();
     
+    // a stack of 2D images will result as a 3D image // JPRx
     int plusUn;
     if (filenames.size()>1)
        plusUn = 1;
@@ -95,6 +122,7 @@ namespace bbitk
   template<class T>
   void ImageSeriesReader::Read()
   {
+std::cout << "--------------------------------------------------- ImageSeriesReader::Read()" << std::endl;
     bbtkDebugMessageInc("Core",9,"bbitk::ImageSeriesReader<"
                        <<bbtk::TypeName<T>()
                        <<">::Read()"<<std::endl);
@@ -104,13 +132,45 @@ namespace bbitk
 
     typename itkReaderType::Pointer reader = itkReaderType::New();
     const std::vector<std::string>& filenames = bbGetInputFileNames();
-    reader->SetFileNames(filenames);
+    
+std::cout << "--------------------------------------------------- size " << filenames.size() << std::endl;
+       for (int i = 0; i< (int)(filenames.size()); i++)
+       std::cout << "-- [" <<filenames[i] << "]" << std::endl;
+       
+    reader->SetFileNames(filenames);    
+
     try { reader->Update(); }
     catch( std::exception& e ) 
       {
        bbtkError("could not read image series : "<<e.what());
       }
 
+    // JPRx     
+    typename itkImageType::SpacingType spacingJPRx;
+        
+    bool spacingToBeSet = false;
+    if (bbGetInputXSpacing() > 0.)
+    {
+       spacingToBeSet = true;
+       spacingJPRx[0]= bbGetInputXSpacing();
+    }
+
+    if (bbGetInputYSpacing() > 0.)
+    {
+       spacingToBeSet = true;
+       spacingJPRx[1]= bbGetInputYSpacing();
+    }
+
+    if (bbGetInputZSpacing() > 0.)
+    {
+       spacingToBeSet = true;
+       spacingJPRx[2]= bbGetInputZSpacing();
+    }
+
+    if (spacingToBeSet)
+       reader->GetOutput()->SetSpacing(spacingJPRx);   
+    // JPRx 
+
     reader->GetOutput()->Register();
     //    if (bbGetOutputOut()) 
     bbSetOutputOut ( reader->GetOutput() );
@@ -118,7 +178,6 @@ namespace bbitk
     bbtkDebugDecTab("Core",9);
   }
 
-
 }
 // eo namespace bbtk