X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=tools%2FclitkProfileImageGenericFilter.cxx;h=6c81756fbcf7adf9a3f51bfa0ad7fd753a73431f;hb=f48c960aef6e0a5a4edea516b062197db009e25f;hp=1eb58c28ffd93f95775ff3a5d2b8d9eb3fb14923;hpb=e502d745ac4c73037ef615931db2dcbf36a94341;p=clitk.git

diff --git a/tools/clitkProfileImageGenericFilter.cxx b/tools/clitkProfileImageGenericFilter.cxx
index 1eb58c2..6c81756 100644
--- a/tools/clitkProfileImageGenericFilter.cxx
+++ b/tools/clitkProfileImageGenericFilter.cxx
@@ -31,6 +31,7 @@
 
 // itk include
 #include <itkLineIterator.h>
+#include <itkPoint.h>
 
 #include <clitkCommon.h>
 
@@ -119,6 +120,16 @@ ProfileImageGenericFilter::UpdateWithInputImageType()
   mArrayY = vtkSmartPointer<vtkFloatArray>::New();
   mCoord = vtkSmartPointer<vtkFloatArray>::New();
   mCoord->SetNumberOfComponents(InputImageType::ImageDimension);
+  mCoordmm = vtkSmartPointer<vtkFloatArray>::New();
+  mCoordmm->SetNumberOfComponents(InputImageType::ImageDimension);
+  mDimension = InputImageType::ImageDimension;
+  
+  /*typename InputImageType::Pointer outputImage;
+  outputImage = InputImageType::New();
+ 
+  outputImage->SetRegions(input->GetLargestPossibleRegion());
+  outputImage->Allocate();
+  outputImage->FillBuffer(0); */
   
   //Iterator
   IndexType pointBegin, pointEnd;
@@ -132,28 +143,111 @@ ProfileImageGenericFilter::UpdateWithInputImageType()
   itProfile.GoToBegin();
   int lineNumber(1);
   double *tuple;
+  double distance;
   tuple = new double[InputImageType::ImageDimension];
+  itk::Point<double, InputImageType::ImageDimension> transformedFirstPoint;
+  itk::Point<double, InputImageType::ImageDimension> transformedCurrentPoint;
+  
+  input->TransformIndexToPhysicalPoint(itProfile.GetIndex(), transformedFirstPoint);
   
   while (!itProfile.IsAtEnd())
   {    
-    // Fill in the table
-    mArrayX->InsertNextTuple1(lineNumber);
+    // Fill in the table the intensity value
     mArrayY->InsertNextTuple1(itProfile.Get());
         
     for (int i=0; i<InputImageType::ImageDimension; ++i) {
         tuple[i] = itProfile.GetIndex()[i];
     }
+
+    input->TransformIndexToPhysicalPoint(itProfile.GetIndex(), transformedCurrentPoint);
+    distance = transformedFirstPoint.EuclideanDistanceTo(transformedCurrentPoint);
+
+    // Fill in the table the distance value
+    mArrayX->InsertNextTuple1(distance);
     
-    mCoord->InsertNextTuple(tuple);
+    // Fill in the table the voxel coordinate value
+    mCoord->InsertNextTuple(tuple); //index
+    for (int i=0; i<InputImageType::ImageDimension; ++i) {
+        tuple[i] = transformedCurrentPoint[i];
+    }
+    mCoordmm->InsertNextTuple(tuple); //mm
     ++lineNumber;
     ++itProfile;
   }
+
+  if (mArgsInfo.output_given) {
+    std::string str(mArgsInfo.output_arg);
+    this->WriteOutput(str);
+  }
+  
+  /*
+  itk::LineIterator<InputImageType> otProfile(outputImage, pointBegin, pointEnd);
+  otProfile.GoToBegin();  
+  while (!otProfile.IsAtEnd())
+  {    
+    otProfile.Set(1.0);
+    ++otProfile;
+  }
+  
+  this->template SetNextOutput<InputImageType>(outputImage): */
   
   delete [] tuple;
 }
 //--------------------------------------------------------------------
 
 
+//--------------------------------------------------------------------
+void ProfileImageGenericFilter::WriteOutput(std::string outputFilename)
+{
+  ofstream fileOpen(outputFilename.c_str(), std::ofstream::trunc);
+
+  if(!fileOpen) {
+      cerr << "Error during saving" << endl;
+      return;
+  }
+
+  double *tuple;
+  tuple = new double[mDimension];
+  int i(0);
+  fileOpen << "The Bresenham algorithm is used to travel along the line. Values represent the center of each crossed voxel (in voxel and mm)" << endl;
+  fileOpen << "Id" << "\t" << "Value" << "\t" ;
+  fileOpen << "x(vox)" << "\t" << "y(vox)" << "\t";
+  if (mDimension >=3)
+      fileOpen << "z(vox)" << "\t";
+  if (mDimension >=4)
+      fileOpen << "t" << "\t";
+  fileOpen << "x(mm)" << "\t" << "y(mm)" << "\t";
+  if (mDimension >=3)
+      fileOpen << "z(mm)" << "\t";
+  if (mDimension >=4)
+      fileOpen << "t" << "\t";
+  fileOpen << endl;
+
+  while (i<mArrayX->GetNumberOfTuples()) {
+      fileOpen << i << "\t" << mArrayY->GetTuple(i)[0] << "\t" ;
+
+      mCoord->GetTuple(i, tuple);
+      for (int j=0; j<mDimension ; ++j) {
+          fileOpen << tuple[j] << "\t" ;
+      }
+      mCoordmm->GetTuple(i, tuple);
+      for (int j=0; j<mDimension ; ++j) {
+          fileOpen << tuple[j] << "\t" ;
+      }
+      if (mDimension == 4) {
+          fileOpen << tuple[3] << "\t" ;
+      }
+      fileOpen << endl;
+      ++i;
+  }
+
+  delete [] tuple;
+
+  fileOpen.close();
+}
+//--------------------------------------------------------------------
+
+
 }//end clitk
 
 #endif  //#define clitkProfileImageGenericFilter_cxx