[Insight-users] Re : problem with discrete gaussian filter

Tue Jul 28 06:54:55 EDT 2009

Hi Luis,

Thank for the replay.
1. My plateform is windows xp
2. You have said :"You should familiarize yourself, first, with using a command
line interface. Then you will be comfortable running the examples." .  Can i find a document that explain to me how can i uses a command line interface? Did you mean that is the " debogue comand" in visual c++?
3. If i try to use the examples with my own images how can i  modify to do it?
4.>>Once you are familiar with the examples, you can run them as:

> executable  input1 input2  output 
 I don't understand this part please can you explain more to me.
About the itksoftwareguide i have the 2.4 version and i read most of it but in vain i still find many difficulties in programs.
I'm so sorry if i have many questions.thank you really.

BEST REGARDS
Syrine

________________________________
De : Luis Ibanez <luis.ibanez at kitware.com>
À : Syrine Sahmim <syrine.sahmim at yahoo.fr>
Cc : insight-users at itk.org
Envoyé le : Mardi, 28 Juillet 2009, 11h35mn 05s
Objet : Re: [Insight-users] problem with discrete gaussian filter

Hi Syrine,

As described in the ITK Software Guide

     http://www.itk.org/ItkSoftwareGuide.pdf

all the examples in the directory:

               Insight/Examples

are intended to be run as command line executables.

This means that you must run them from:

    A) a GNU/Linux shell (in a terminal)   or
    B) a MS-DOS command window on Windows or
    C) a Visual Studio command prompt window

What is your platform ?
(Windows?, Linux?, Mac? other ?).

You should familiarize yourself, first, with using a command
line interface. Then you will be comfortable running the examples.

Once you are familiar with the examples, you can run them as:

> executable  input1 input2  output 

for example, the Median filter example in 

       Insight/Examples/Filtering

will work as:

> MedianImageFilter   BrainProtonDensitySlice.png  median.png

You will find ALL the images used for the ITK Software Guide,
in the directory:

      Insight/Testing/Data

(including the BrainProtonDensitySlice.png mentioned above).

---

About your process for reading a DICOM image, the problem
is that you are using the ImageFileReader, while you should be
using the ImageSeriesReader.

In your current code, you are only reading one slice of the
DICOM series.

Please read the ITK Software Guide

     http://www.itk.org/ItkSoftwareGuide.pdf

in particular the chapter "Reading and Writing Images", it has
detailed explanations on how to read a series of DICOM images
from a directory.

You will find useful to look at the Example:

     Insight/Examples/IO/
         DicomSeriesReadImageWrite2.cxx

      Regards,

            Luis

----------------------------------------------------------------------------------------------------------------

On Tue, Jul 28, 2009 at 5:26 AM, Syrine Sahmim <syrine.sahmim at yahoo.fr> wrote:

Hello every body,
>Yesterday i sent an email to the group to know what is the problem with my code and i did not receive answer.
>I want to understand some things at the begining:
>1. when i try the examples programs, i must give to the program the images as input. the problem is that i can't do that , i don't know how and where i must gives the input image and the out put one. if someone can explain more this issue to me.
>>2. i send again my previous program to try to find errors.
>I try to apply the discrete gaussian filter on a 3D dicom image. So i
>tried the code below. there's no errors on building step but the
>problem is after debugging. i don't have result.so i want to know
>where's the error or even i must do or add some codes to succeed
>execution.
>the code is:
>#if defined(_MSC_VER)
>#pragma warning ( disable : 4786 )
>#endif
>
>#ifdef __BORLANDC__
>#define ITK_LEAN_AND_MEAN
>#endif
>
>#include "itkImage.h"
>#include "itkImageFileReader.h"
>>#include "itkImageFileWriter.h"
>#include "itkRescaleIntensityImageFilter.h"
>
>
>#include "itkDiscreteGaussianImageFilter.h"
>
>int main( int argc, char * argv[] )
>{argc = 2;
>>    argv[1] = "003F87DA.png";
>    argv[2] = "DA.png";
> 
>  /*if( argc < 3 ) 
>    { 
>    std::cerr << "Usage: " << std::endl;
>    std::cerr << argv[0] << "  inputImageFile  outputImageFile  variance  maxKernelWidth " << std::endl;
>>    return EXIT_FAILURE;
>    }*/
>
> 
>  typedef    float    InputPixelType;
>  typedef    float    OutputPixelType;
>
>  typedef itk::Image< InputPixelType,  3 >   InputImageType;
>  typedef itk::Image< OutputPixelType, 3 >   OutputImageType;
>>  
>  typedef itk::ImageFileReader< InputImageType >  ReaderType;
>
>
>  
>  typedef
> itk::DiscreteGaussianImageFilter<
>                 InputImageType, OutputImageType >  FilterType;
>
>  FilterType::Pointer filter = FilterType::New();
>  
>  ReaderType::Pointer reader = ReaderType::New();
>>  reader->SetFileName( argv[1] );
> 
>  filter->SetInput( reader->GetOutput() );
> 
>  const double gaussianVariance = atof( argv[3] );
>  const unsigned int maxKernelWidth = atoi( argv[4] );
>
>  filter->SetVariance( gaussianVariance );
>>  filter->SetMaximumKernelWidth( maxKernelWidth );
> 
>  
>  filter->Update();
>  
>  typedef unsigned char WritePixelType;
>  typedef itk::Image< WritePixelType, 2 > WriteImageType;
>  typedef itk::RescaleIntensityImageFilter<
> 
>               OutputImageType, WriteImageType > RescaleFilterType;
>  RescaleFilterType::Pointer rescaler = RescaleFilterType::New();
>
>  rescaler->SetOutputMinimum(   0 );
>  rescaler->SetOutputMaximum( 255 );
>
>  typedef itk::ImageFileWriter< WriteImageType >  WriterType;
>  WriterType::Pointer writer = WriterType::New();
>  writer->SetFileName( argv[2] );
> 
>  // Software Guide : BeginCodeSnippet
>  rescaler->SetInput( filter->GetOutput() );
>>  writer->SetInput( rescaler->GetOutput() );
>  writer->Update();
>  
>  return EXIT_SUCCESS;
>}
>
>BEST REGARDS
>
>
>
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