git-svn-id: svn+ssh://orchestra.med.harvard.edu/svn/megason/Code/GoFi…

…gure2@1075 ef826fda-c0ae-4237-af8e-f8dcbcf7929c

trunk/Testing/Examples/vtkLSM/CMakeLists.txt

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+ADD_EXECUTABLE( lsm2jpg 
+   lsm2jpg.cxx
+   vtkLSMReader.cxx
+  )
+TARGET_LINK_LIBRARIES( lsm2jpg 
+  vtkIO
+  vtkImaging 
+  )
+
+ADD_EXECUTABLE( lsm2mha 
+   lsm2mha.cxx
+   vtkLSMReader.cxx
+  )
+TARGET_LINK_LIBRARIES( lsm2mha 
+  vtkIO
+  vtkImaging 
+  )
+
+ADD_EXECUTABLE( lsmColorVizu 
+  lsmColorVizu.cxx
+  vtkLSMReader.cxx
+  )
+TARGET_LINK_LIBRARIES( lsmColorVizu 
+  vtkIO
+  vtkImaging 
+  vtkRendering
+  vtkRenderingAddOn2
+  )
+

trunk/Testing/Examples/vtkLSM/lsm2jpg.cxx

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+#include "vtkLSMReader.h"
+#include <iostream>
+#include <sstream>
+#include "vtkJPEGWriter.h"
+#include "vtkImageAppendComponents.h"
+#include "vtkIndent.h"
+#include "vtkImageData.h"
+
+int main(int argc,char* argv[])
+{
+  if (argc<3 || argc>4)
+    {
+    std::cout << "Usage: ";
+    std::cout << "(exe) FileName IsChannelToBeBlended";
+    std::cout << std::endl;
+    return 0;
+    }  
+
+  if( !( atoi(argv[2]) == 0 || atoi(argv[2]) == 1 ) )
+    {
+    std::cout << "Second argument must be either 0 or 1." << std::endl;
+    return 0;
+    }
+
+  //read the LSM file:
+  vtkLSMReader* reader=vtkLSMReader::New();
+  reader->SetFileName(argv[1]);
+  reader->Update();
+
+  int NumberOfTimePoints = reader->GetNumberOfTimePoints();
+  int NumberOfChannels = reader->GetNumberOfChannels();
+
+  reader->PrintSelf(std::cout, vtkIndent(0));
+
+  vtkJPEGWriter * writer = vtkJPEGWriter::New();
+  writer->SetFileDimensionality( 2 );
+
+  for( int timePoint = 0;timePoint < NumberOfTimePoints; timePoint++)
+    {
+    if( atoi(argv[2]) == 0 || NumberOfChannels == 1 )
+      {
+      for( int channel = 0; channel < NumberOfChannels; channel++)
+        {
+        vtkLSMReader* treader=vtkLSMReader::New();
+        treader->SetFileName(argv[1]);
+        treader->SetUpdateTimePoint( timePoint );
+        treader->SetUpdateChannel( channel );
+        treader->Update();
+
+        std::stringstream namebuffer;
+        namebuffer << argv[1];
+        namebuffer << "_T_"  << timePoint;
+        namebuffer << "_Ch_" << channel;
+        std::cout << namebuffer.str();
+        namebuffer << "_Z_ ";
+        writer->SetFilePrefix(namebuffer.str().c_str()); 
+        writer->SetInputConnection( treader->GetOutputPort( ) );
+        writer->SetFilePattern( "%s%d.jpg");
+        writer->Write(); 
+        }
+      }
+    else
+      {
+      // read the first channel, then Append other channel as components
+      // of myImage. Finally, write it.
+      // note that jpgwriter only handles 1 or 3 comp images.
+      // if only one channel, no compositing
+      // if two channel, compose with a dummy (empty) third channel
+      // if three channels, no problem
+      // if more than three channel, we should blend (TBD)
+      if( NumberOfChannels < 4 )
+        {
+        vtkImageData* myImage_ch1;
+        vtkImageData* myImage_ch2;
+        vtkImageData* myImage_ch3;
+
+        {
+        vtkLSMReader* treader=vtkLSMReader::New();
+        treader->SetFileName(argv[1]);
+        treader->SetUpdateTimePoint( timePoint );
+        treader->SetUpdateChannel( 0 );
+        treader->Update();
+        myImage_ch1 = treader->GetOutput();
+        }
+
+        {
+        vtkLSMReader* treader=vtkLSMReader::New();
+        treader->SetFileName(argv[1]);
+        treader->SetUpdateTimePoint( timePoint );
+        treader->SetUpdateChannel( 1 );
+        treader->Update();
+        myImage_ch2 = treader->GetOutput();
+        }
+
+        {
+        vtkLSMReader* treader=vtkLSMReader::New();
+        treader->SetFileName(argv[1]);
+        treader->SetUpdateTimePoint( timePoint );
+        treader->SetUpdateChannel( 2 );
+        treader->Update();
+        std::cout << "Third reader done." << std::endl;
+        int * dimensions = treader->GetDimensions();
+        int  flatindex = dimensions[0] * dimensions[1] * dimensions[2];
+        myImage_ch3 = treader->GetOutput();
+        if( NumberOfChannels == 2 ) // dummy third channel 
+          {
+          // here we suppose the type to be char
+          // to be improved
+          char *ptr = (char*)( myImage_ch3->GetScalarPointer());
+          for( int k=0; k < flatindex; k++ )
+            {
+            *ptr++ = 0; 
+            }            
+          }
+        std::cout << "third channel ready." << std::endl;
+        }
+
+        vtkImageAppendComponents* appendFilter1 = vtkImageAppendComponents::New();
+        appendFilter1->AddInput( myImage_ch1 );
+        appendFilter1->AddInput( myImage_ch2 );
+        appendFilter1->Update();
+        std::cout << "Two first channel composed." << std::endl;
+
+        vtkImageAppendComponents* appendFilter2 = vtkImageAppendComponents::New();
+        appendFilter2->AddInput( appendFilter1->GetOutput() );
+        appendFilter2->AddInput( myImage_ch3 );
+        appendFilter2->Update(); 
+        std::cout << "Third channel composed." << std::endl;
+
+        std::stringstream namebuffer;
+        namebuffer << argv[1];
+        namebuffer << "_T_"  << timePoint;
+        std::cout << namebuffer.str();
+        namebuffer << "_Z_ ";
+        writer->SetFilePrefix(namebuffer.str().c_str()); 
+        writer->SetInput( appendFilter2->GetOutput( ) );
+        writer->SetFilePattern( "%s%d.jpg");
+        writer->Write(); 
+        }
+      else
+        {
+        // num of channel > 3
+        // TBD
+        }     
+      } 
+    } 
+  return 1;
+}

trunk/Testing/Examples/vtkLSM/lsm2mha.cxx

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+#include "vtkLSMReader.h"
+#include <iostream>
+#include <sstream>
+#include "vtkMetaImageWriter.h"
+#include "vtkImageAppendComponents.h"
+#include "vtkIndent.h"
+#include "vtkImageData.h"
+
+int main(int argc,char* argv[])
+{
+  if (argc != 2)
+    {
+    std::cout << "Usage: ";
+    std::cout << "(exe) FileName";
+    std::cout << std::endl;
+    return 0;
+    }
+
+  //read the LSM file:
+  vtkLSMReader* reader=vtkLSMReader::New();
+  reader->SetFileName(argv[1]);
+  reader->Update();
+
+  int NumberOfTimePoints = reader->GetNumberOfTimePoints();
+  int NumberOfChannels = reader->GetNumberOfChannels();
+
+  vtkMetaImageWriter * writer = vtkMetaImageWriter::New();
+  writer->SetFileDimensionality( 3 );
+
+  for( int timePoint = 0;timePoint < NumberOfTimePoints; timePoint++)
+    {
+    for( int channel = 0; channel < NumberOfChannels; channel++)
+      {
+      vtkLSMReader* treader=vtkLSMReader::New();
+      treader->SetFileName(argv[1]);
+      treader->SetUpdateTimePoint( timePoint );
+      treader->SetUpdateChannel( channel );
+      treader->Update();
+
+      std::stringstream namebuffer;
+      namebuffer << argv[1];
+      namebuffer << "_T_"  << timePoint;
+      namebuffer << "_Ch_" << channel;
+      namebuffer << ".mha";
+
+      std::cout << namebuffer.str() << std::endl;;
+
+      writer->SetFileName( namebuffer.str().c_str() );
+      writer->SetInputConnection( treader->GetOutputPort( ) );
+      writer->Write();
+      }
+    }
+  return EXIT_SUCCESS;
+}

trunk/Testing/Examples/vtkLSM/lsmColorVizu.cxx

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+#include "vtkLSMReader.h"
+#include "vtkImageAppendComponents.h"
+#include "vtkImageViewer2.h"
+#include "vtkIndent.h"
+#include "vtkImageData.h"
+#include "vtkViewImage.h"
+#include "vtkViewColorImage.h"
+
+int main(int argc,char* argv[])
+{
+  if (argc != 2)
+    {
+    std::cout << "Usage: ";
+    std::cout << "(exe) FileName";
+    std::cout << std::endl;
+    return 0;
+    }  
+
+  //read the LSM file:
+  vtkLSMReader* reader=vtkLSMReader::New();
+  reader->SetFileName(argv[1]);
+  reader->Update();
+
+  int NumberOfTimePoints = reader->GetNumberOfTimePoints();
+  int NumberOfChannels = reader->GetNumberOfChannels();
+
+  for( int timePoint = 0;timePoint < NumberOfTimePoints; timePoint++)
+    {
+      {
+        {
+        vtkImageData* myImage_ch1;
+        vtkImageData* myImage_ch2;
+        vtkImageData* myImage_ch3;
+
+        myImage_ch1 = reader->GetOutput();
+
+        {
+        vtkLSMReader* treader=vtkLSMReader::New();
+        treader->SetFileName(argv[1]);
+        treader->SetUpdateTimePoint( timePoint );
+        treader->SetUpdateChannel( 1 );
+        treader->Update();
+        int * dimensions = treader->GetDimensions();
+        int  flatindex = dimensions[0] * dimensions[1] * dimensions[2];
+        myImage_ch2 = treader->GetOutput();
+        if( NumberOfChannels == 1 ) 
+          {
+          char *ptr = (char*)( myImage_ch2->GetScalarPointer());
+          for( int k=0; k < flatindex; k++ )
+            {
+            *ptr++ = 0; 
+            }            
+          }
+        }
+
+        {
+        vtkLSMReader* treader=vtkLSMReader::New();
+        treader->SetFileName(argv[1]);
+        treader->SetUpdateTimePoint( timePoint );
+        treader->SetUpdateChannel( 2 );
+        treader->Update();
+        int * dimensions = treader->GetDimensions();
+        int  flatindex = dimensions[0] * dimensions[1] * dimensions[2];
+        myImage_ch3 = treader->GetOutput();
+        if( NumberOfChannels == 2 ) // dummy third channel 
+          {
+          char *ptr = (char*)( myImage_ch3->GetScalarPointer());
+          for( int k=0; k < flatindex; k++ )
+            {
+            *ptr++ = 0; 
+            }            
+          }
+        }
+
+        vtkImageAppendComponents* appendFilter1 = vtkImageAppendComponents::New();
+        appendFilter1->AddInput( myImage_ch1 );
+        appendFilter1->AddInput( myImage_ch2 );
+        appendFilter1->Update();
+
+        vtkImageAppendComponents* appendFilter2 = vtkImageAppendComponents::New();
+        appendFilter2->AddInput( appendFilter1->GetOutput() );
+        appendFilter2->AddInput( myImage_ch3 );
+        appendFilter2->Update(); 
+
+        {
+        std::cout << "vtkImageViewer2.: << std::endl;
+        vtkImageViewer2 * viewer = vtkImageViewer2::New();
+        viewer->SetInput( appendFilter2->GetOutput() );
+        viewer->Render();
+        char buffer;
+        cin >> buffer;
+        }
+        {
+        std::cout << "vtkViewImage.: << std::endl;
+        vtkViewImage * viewer = vtkViewImage::New();
+        viewer->SetInput( appendFilter2->GetOutput() );
+        viewer->Render();
+        char buffer;
+        cin >> buffer;
+        }
+        {
+        std::cout << "vtkViewColorImage.: << std::endl;
+        vtkViewColorImage * viewer = vtkViewColorImage::New();
+        viewer->SetInput( appendFilter2->GetOutput() );
+        viewer->Render();
+        char buffer;
+        cin >> buffer;
+        }
+        }
+      } 
+    } 
+  return 1;
+}