[Insight-users] get the maximum pixel value using GetPixel() for 3D image

Tue Jun 7 10:10:19 EDT 2011

Can you post the exception please?

From: john smith [mailto:mkitkinsightuser at gmail.com] 
Sent: dinsdag 7 juni 2011 15:50
To: Brecht Heyde; insight-users at itk.org
Subject: Re: [Insight-users] get the maximum pixel value using GetPixel()
for 3D image

I have added this

  size = inputRegion.GetSize();
  // get the size of the hole 3D image
  size_x = size[0];
  size_y = size[1];
  size_z = size[2];

I am getting into the loop, but now I am getting an exception.Do you know
what I am doing wrong? I have declared the size_x,size_y,size_z in an other
function as it seems bellow, and declare them as global variable.Is it this
declaration responcible for the exception?

Thanks

2011/6/7 Brecht Heyde <Brecht.Heyde at med.kuleuven.be>

Sorry, it should have been:

size = inputRegion.GetSize();

Regards,

Brecht Heyde

From: insight-users-bounces at itk.org [mailto:insight-users-bounces at itk.org]
On Behalf Of Brecht Heyde
Sent: dinsdag 7 juni 2011 15:34
To: 'john smith'; 'robert tamburo'; insight-users at itk.org

Subject: Re: [Insight-users] get the maximum pixel value using GetPixel()
for 3D image

Hi,

Your size_x, size_y and size_z are not representing the actual  size of the
image.

Add:

size = inputRegion->GetSize();

Before 

size_x = .

size_y = .

size_z = .

I would however also suggest to use an imageIterator.

Regards,

Brecht Heyde

From: insight-users-bounces at itk.org [mailto:insight-users-bounces at itk.org]
On Behalf Of john smith
Sent: dinsdag 7 juni 2011 15:27
To: robert tamburo; insight-users at itk.org
Subject: Re: [Insight-users] get the maximum pixel value using GetPixel()
for 3D image

Thanks for your reply.I have used the MinimumMaximumImageCalculator, but
know I want to take the result playing with the raw data.But I am trying to
do that without using iterators, just with using for loop. I have added the
largest possible area from reader, but when I am debuging my code, it seems
that I cannot get inside the loop. Do you know why? Here is my code:

 ReaderType::Pointer reader = ReaderType::New();

     reader->SetFileName( fileName.toStdString()  );
     reader->Update();

      InputImageType::RegionType inputRegion =
           reader->GetOutput()->GetLargestPossibleRegion();

    //typedef itk::Image< short, 3 > InputImageType;

     InputImageType::Pointer image = reader->GetOutput();

  InputImageType::IndexType start;
  InputImageType::SizeType  size;

  // get the size of the hole 3D image
  size_x = size[0];
  size_y = size[1];
  size_z = size[2];

  start[0] =   0;  // first index on X
  start[1] =   0;  // first index on Y
  start[2] =   0;  // first index on Z

  InputImageType::RegionType region;
  region.SetSize( size );
  region.SetIndex( start );

  // Pixel data is allocated
  image->SetRegions( region );
  image->Allocate();

   int i,j,k;
 int max_value=0;

  for ( i=0;i<size_x;i++) {
      for ( j=0;i<size_y;j++){
          for ( k=0;i<size_z;k++){

              InputImageType::IndexType pixelIndex;
                pixelIndex[0] = i; // x position
                pixelIndex[1] = j; // y position
                pixelIndex[2] = k; // z position

                InputImageType::PixelType pixelValue = image->GetPixel(
pixelIndex );

                if(pixelValue>max_value){max_value=pixelValue;}

          }
      }
  }

   ui->label_22->setText(QString("maximum_value_raw%1").arg(max_value));

2011/6/7 robert tamburo <robert.tamburo at gmail.com>

GetPixel() belongs to itkImage, not the reader. Try
reader->GetOutput()->GetPixel(index).  

Two other things: 1) You may want to consider using an ImageRegionIterator
instead of for loops, and 2) You can use the MinimumMaximumImageCalculator
to get the maximum intensity in an image.

There are examples on how to use each class at
http://www.itk.org/Wiki/ITK/Examples

On Tue, Jun 7, 2011 at 8:36 AM, john smith <mkitkinsightuser at gmail.com>
wrote:

Hello,

I am trying to find the maximum pixel value of a 3D  image, and I am using
the GetPixel method with 3 loops.I want to load my image from a file so I
created a reader pointer.Does this pointer include the raw data of my image?
I have created the following code but I get an error: GetPixel() method is
not a member of reader. Could somebody tell me what I am doing wrong? How I
could find the maximum pixel value of a loaded image with the method of
GetPixel()?

Thanks

  typedef short               InputPixelType;
  const   unsigned int        Dimension = 3;

  typedef itk::Image< InputPixelType,  Dimension >    InputImageType;
  typedef itk::ImageFileReader< InputImageType  >  ReaderType;

  ReaderType::Pointer reader = ReaderType::New();

     reader->SetFileName( fileName.toStdString()  );
     reader->Update();

       InputImageType::RegionType inputRegion =
           reader->GetOutput()->GetLargestPossibleRegion();

  InputImageType::SizeType size = inputRegion.GetSize();

  // get the size of the hole 3D image
  size_x = size[0];
  size_y = size[1];
  size_z = size[2];

   InputImageType::IndexType start = inputRegion.GetIndex();
  start[0] =   0;  // first index on X
  start[1] =   0;  // first index on Y
  start[2] =   0;  // first index on Z

 int i,j,k;
 int max_value=0;
  for ( i=0;i<size_x;i++) {
      for ( j=0;i<size_y;j++){
          for ( k=0;i<size_z;k++){

              InputImageType::IndexType pixelIndex;
                pixelIndex[0] = i; // x position
                pixelIndex[1] = j; // y position
                pixelIndex[2] = k; // z position

                InputImageType::PixelType pixelValue = reader->GetPixel(
pixelIndex );

                if(pixelValue>max_value){max_value=pixelValue;}

          }
      }
  }

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