[Insight-users] Using ImageReadCastWrite Example

[Luis Ibanez]

Hi Misha,


Thanks for posting the images, they help a lot.


There are two separate issues here:


1) Your GE image looks like a CT scan. Is it a CT scan ?

    If so, the reason why you see a color image in MRICro
    is because your are enabling artificial coloring of the
    dataset.

     You probably visited in MRICro the menu option:

              Overlay ---->>> Color Scheme

    which will simply enable a color map into your
    data set.

    This is a visualization issue, not something related
    to image analysis per se. If you *really* want to reproduce
    such coloring effect you should incorporate VTK visualization
    filter into your application and get familiar with the use
    of color maps for visualization.

    You could also implement a colormap in ITK by using the
    FunctorImageFilter.


2) The second image that you posted, just shows the
    known bug in the JPEG writer when you feed it with
    16 bits images.  Please use another file format.
    Probably Analyze is the best option since you will
    be able to read it in other programs including VolView,
    and MRICro.


Please let us know if you have further questions,


    Thanks


       Luis


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

Misha Nizker wrote:

> Hello, 
> 
> Thanks for the help, the .jpg conversions work now.  However, there is still
> a problem when using the GE5ImageIO filter.  For some reason, the GE images
> still get rendered into black and white.  They are also slightly shifted to
> the side.  
> 
> I am currently using RGBPixel< unsigned char > which seems to be working
> fine for .jpg.  I tried unsigned short to increase the bit depth (to
> 16-bit), but the fileReader complained that it wasn't configured to use that
> variable.  
> 
> Any idea on why the image is refusing to be rendered as colour?  I have
> hosted the input (as seen by MRIcro) at http://24.83.47.77/MRI/input.jpg and
> the output (converted into .png and took a screenshot, same result when
> converting to .jpg) at http://24.83.47.77/MRI/output.jpg.  
> 
> 
> Thank you,
> 
> Misha
> 
> -----Original Message-----
> From: Luis Ibanez [mailto:luis.ibanez at kitware.com] 
> Sent: Monday, June 28, 2004 8:35 PM
> To: EUGINE NIZKER
> Cc: insight-users at itk.org
> Subject: Re: [Insight-users] Using ImageReadCastWrite Example
> 
> 
> Hi Eugine,
> 
> If you want the image to be read and written in color
> you must use a RGBPixel<> type as the image pixel type.
> 
> Please look at the examples:
> 
>     Insight/Examples/IO/
>                RGBImageReadWrite.cxx
>                RGBImageSeriesReadWrite.cxx
> 
> 
> Regards,
> 
> 
>     Luis
> 
> 
> -----------------------
> EUGINE NIZKER wrote:
> 
> 
>>Hello,
>>
>>I have recently downloaded and installed ITK version 1.6 and am trying to
> 
> use it for doing a GE5 -> PNG conversion.  I gather that the
> ImageReadCastWrite code contains the proper info for that, and can actually
> get the image to show, but the problem is that it's in greyscale (almost
> black and white) instead of being in full color like the original image
> (seen by MRIcro).  
> 
>>I tested this with other conversions like .bmp to .jpg or even .jpg to
> 
> .jpg and the output always appears black and white for whatever reason...  I
> am currently using the RescaleIntensityImageFilter between the input and
> output since this is the one that was used in the example.  Could this be
> the problem?  I tried changing the maximum and minimum intensity settings on
> the filter, but that didn't seem to affect the output image at all.  
> 
>>Can anyone please help?  
>>
>>
>>
>>Here is my code just in case it's helpful:
>>
>>
> 
> /*=========================================================================
> 
>>  Program:   Insight Segmentation & Registration Toolkit
>>  Module:    $RCSfile: ImageReadCastWrite.cxx,v $
>>  Language:  C++
>>  Date:      $Date: 2003/12/17 12:55:28 $
>>  Version:   $Revision: 1.7 $
>>
>>  Copyright (c) Insight Software Consortium. All rights reserved.
>>  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for
> 
> details.
> 
>>     This software is distributed WITHOUT ANY WARRANTY; without even 
>>     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
>>     PURPOSE.  See the above copyright notices for more information.
>>
>>
> 
> =========================================================================*/
> 
>>#include "itkImageFileReader.h"
>>#include "itkImageFileWriter.h"
>>#include "itkRescaleIntensityImageFilter.h"
>>
>>#include "itkCropImageFilter.h"
>>
>>
>>#include "itkImage.h"
>>
>>
>>int main( int argc, char ** argv )
>>{
>>  if( argc < 3 )
>>    {
>>    std::cerr << "Usage: " << std::endl;
>>    std::cerr << argv[0] << " inputImageFile  outputImageFile " <<
> 
> std::endl;
> 
>>    return -1;
>>    }
>>
>>
>>  typedef unsigned char       InputPixelType;
>>  typedef unsigned char       OutputPixelType;
>>  const   unsigned int        Dimension = 2;
>>
>>  typedef itk::Image< InputPixelType,  Dimension >    InputImageType;
>>  typedef itk::Image< OutputPixelType, Dimension >    OutputImageType;
>>
>>  typedef itk::ImageFileReader< InputImageType  >  ReaderType;
>>  typedef itk::ImageFileWriter< OutputImageType >  WriterType;
>>
>>
>>  typedef itk::RescaleIntensityImageFilter< 
>>                                  InputImageType, 
>>                                  OutputImageType >    FilterType;
>> 
>>  FilterType::Pointer filter = FilterType::New();
>>  filter->SetOutputMinimum(   0 );
>>  filter->SetOutputMaximum( 255 );
>>
>>  ReaderType::Pointer reader = ReaderType::New();
>>  WriterType::Pointer writer = WriterType::New();
>>
>>  filter->SetInput( reader->GetOutput() );
>>  writer->SetInput( filter->GetOutput() );
>>
>>
>>  const char * inputFilename  = argv[1];
>>  const char * outputFilename = argv[2];
>>
>>  reader->SetFileName( inputFilename  );
>>  writer->SetFileName( outputFilename );
>>
>>
>>  try 
>>    { 
>>    writer->Update(); 
>>    } 
>>  catch( itk::ExceptionObject & err ) 
>>    { 
>>    std::cout << "ExceptionObject caught !" << std::endl; 
>>    std::cout << err << std::endl; 
>>    return -1;
>>    } 
>>
>>
>>  return 0;
>>}
>>
>>_______________________________________________
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>>Insight-users at itk.org
>>http://www.itk.org/mailman/listinfo/insight-users
>>
> 
> 
> 
> 
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