[Insight-users] Segmentation of 3D image (itk)

[Luis Ibanez]

Hi Abder-Rahman,

Please find below the diffs that you have to apply to
this example in order to make it work for 3D images.


   Thanks


       Luis


diff --git a/Examples/Segmentation/ConnectedThresholdImageFilter.cxx
b/Examples/Segmentation/ConnectedThresholdImageFilter.cxx
index 5fdfb24..38ef54c 100644
--- a/Examples/Segmentation/ConnectedThresholdImageFilter.cxx
+++ b/Examples/Segmentation/ConnectedThresholdImageFilter.cxx
@@ -95,11 +95,11 @@

 int main( int argc, char *argv[])
 {
-  if( argc < 7 )
+  if( argc < 8 )
     {
     std::cerr << "Missing Parameters " << std::endl;
     std::cerr << "Usage: " << argv[0];
-    std::cerr << " inputImage  outputImage seedX seedY lowerThreshold
upperThreshold" << std::endl;
+    std::cerr << " inputImage  outputImage seedX seedY seedZ
lowerThreshold upperThreshold" << std::endl;
     return 1;
     }

@@ -114,7 +114,7 @@ int main( int argc, char *argv[])

   // Software Guide : BeginCodeSnippet
   typedef   float           InternalPixelType;
-  const     unsigned int    Dimension = 2;
+  const     unsigned int    Dimension = 3;
   typedef itk::Image< InternalPixelType, Dimension >  InternalImageType;
   // Software Guide : EndCodeSnippet

@@ -217,7 +217,7 @@ int main( int argc, char *argv[])

   // Software Guide : BeginCodeSnippet
   smoothing->SetNumberOfIterations( 5 );
-  smoothing->SetTimeStep( 0.125 );
+  smoothing->SetTimeStep( 0.025 );
   // Software Guide : EndCodeSnippet


@@ -235,8 +235,8 @@ int main( int argc, char *argv[])
   //
   //  Software Guide : EndLatex

-  const InternalPixelType lowerThreshold = atof( argv[5] );
-  const InternalPixelType upperThreshold = atof( argv[6] );
+  const InternalPixelType lowerThreshold = atof( argv[6] );
+  const InternalPixelType upperThreshold = atof( argv[7] );

   // Software Guide : BeginCodeSnippet
   connectedThreshold->SetLower(  lowerThreshold  );
@@ -275,6 +275,7 @@ int main( int argc, char *argv[])

   index[0] = atoi( argv[3] );
   index[1] = atoi( argv[4] );
+  index[2] = atoi( argv[5] );


   // Software Guide : BeginCodeSnippet



---------------------------------
On Sat, Mar 24, 2012 at 11:14 AM, Abder-Rahman Ali
<abder.rahman.ali at gmail.com> wrote:
> Hello,
>
> I just have a question and thought you may have an idea on it.
>
> Inside the `InsightToolkit` directory there is the
> `Examples/Segmentation/ConnectedThresholdImageFilter.xx` file.
>
> Now, I want to make it operate on a three dimensional image. In this case,
> will the changes that I have to do bee applied to those lines of code (lines
> 102-110):
>
>     int main( int argc, char *argv[])
>     {
>       if( argc < 7 )
>         {
>         std::cerr << "Missing Parameters " << std::endl;
>         std::cerr << "Usage: " << argv[0];
>         std::cerr << " inputImage  outputImage seedX seedY lowerThreshold
> upperThreshold" << std::endl;
>         return 1;
>         }
>
> And, in order to do that, should I add the following `seedZ` to:
>
>     std::cerr << " inputImage  outputImage seedX seedY lowerThreshold
> upperThreshold" << std::endl;
>
> And, what change should I perform to the arguments in this case?
>
> Thanks a lot and apologize for my disturbance.
>
> Abder-Rahman
>
-------------- next part --------------
diff --git a/Examples/Segmentation/ConnectedThresholdImageFilter.cxx b/Examples/Segmentation/ConnectedThresholdImageFilter.cxx
index 5fdfb24..38ef54c 100644
--- a/Examples/Segmentation/ConnectedThresholdImageFilter.cxx
+++ b/Examples/Segmentation/ConnectedThresholdImageFilter.cxx
@@ -95,11 +95,11 @@
 
 int main( int argc, char *argv[])
 {
-  if( argc < 7 )
+  if( argc < 8 )
     {
     std::cerr << "Missing Parameters " << std::endl;
     std::cerr << "Usage: " << argv[0];
-    std::cerr << " inputImage  outputImage seedX seedY lowerThreshold upperThreshold" << std::endl;
+    std::cerr << " inputImage  outputImage seedX seedY seedZ lowerThreshold upperThreshold" << std::endl;
     return 1;
     }
 
@@ -114,7 +114,7 @@ int main( int argc, char *argv[])
 
   // Software Guide : BeginCodeSnippet
   typedef   float           InternalPixelType;
-  const     unsigned int    Dimension = 2;
+  const     unsigned int    Dimension = 3;
   typedef itk::Image< InternalPixelType, Dimension >  InternalImageType;
   // Software Guide : EndCodeSnippet
 
@@ -217,7 +217,7 @@ int main( int argc, char *argv[])
 
   // Software Guide : BeginCodeSnippet
   smoothing->SetNumberOfIterations( 5 );
-  smoothing->SetTimeStep( 0.125 );
+  smoothing->SetTimeStep( 0.025 );
   // Software Guide : EndCodeSnippet
 
 
@@ -235,8 +235,8 @@ int main( int argc, char *argv[])
   //
   //  Software Guide : EndLatex
 
-  const InternalPixelType lowerThreshold = atof( argv[5] );
-  const InternalPixelType upperThreshold = atof( argv[6] );
+  const InternalPixelType lowerThreshold = atof( argv[6] );
+  const InternalPixelType upperThreshold = atof( argv[7] );
 
   // Software Guide : BeginCodeSnippet
   connectedThreshold->SetLower(  lowerThreshold  );
@@ -275,6 +275,7 @@ int main( int argc, char *argv[])
 
   index[0] = atoi( argv[3] );
   index[1] = atoi( argv[4] );
+  index[2] = atoi( argv[5] );
 
 
   // Software Guide : BeginCodeSnippet