[Insight-users] Using ImageReadCastWrite Example
Misha Nizker
mishaniz at shaw.ca
Tue Jun 29 21:45:15 EDT 2004
Ah ha! Thank you very much.
Yup the image is a CT scan and I did use the color scheme feature. I was
suspecting that it was an internal color-changing feature, but had to be
sure. Since this particular scheme was called "GE_Color", I figured that it
was possible that that was the way it was supposed to come out. I'll look
into VTK.
As for the second image, it actually does the shift when using the PNG
format too. Is there another one I could try that wouldn't suffer from
these side-effects?
Thank you,
Misha
-----Original Message-----
From: Luis Ibanez [mailto:luis.ibanez at kitware.com]
Sent: Tuesday, June 29, 2004 5:54 PM
To: Misha Nizker
Cc: insight-users at itk.org
Subject: Re: [Insight-users] Using ImageReadCastWrite Example
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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>>
>
>
>
>
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