[Insight-users] Reading bmp image with ITK

[Luis Ibanez]

Hi Jimmy,

When you read/write BMP images you should use
images defined over RGBPixels. Like in


typedef unsigned char ComponentType;
typedef itk::RGBPixel<ComponentType> PixelType;
const unsigned int Dimension = 2;
typedef itk::Image< PixelType, Dimension >	ImageType;

typedef itk::ImageFileReader< ImageType >	ReaderType;
typedef itk::ImageFileWriter< ImageType >	WriterType;

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

reader->SetFileName("Input.bmp");
reader->Update();


Please find attached the modified version of
your program. It is now using RGBPixels and
it is working fine for reading and writing BMP.


   Regards,


      Luis



-----------------------------
Jimmy Wong wrote:
> Thank you for these information.
> 
> Actually, I am using the data provided by Brainweb Database.
> 
> But if I want to use some synthetic images to test my algorithm, I have 
> no choice but use bmp. For this part, any suggestion.
> 
> For the program, I think it should be ok. But whenever I run it, it 
> poped a dialog with " The instruction at "0x77f58df" referenced memory 
> at "0x2a262430". The memory could not be "written"". I don't know why.
> 
> My synthetic image is 256 by 256 bmp image.
> 
> Zhimin
> 
> 
>> From: Luis Ibanez <luis.ibanez at kitware.com>
>> To: Jimmy Wong <good_piggy at msn.com>
>> CC: Insight-users at itk.org
>> Subject: Re: [Insight-users] Reading bmp image with ITK
>> Date: Mon, 01 Nov 2004 10:33:20 -0500
>>
>>
>> Hi Jimmy,
>>
>> If you want to rank these three file formats by
>> they suitability for storing Medical Images,
>> here is a tentative list:
>>
>>       BMP  is poor
>>       JPEG is poorer
>>       RAW  is the poorest
>>
>> All of them lack fields for patient information,
>> spacing (BMP has a bit of spacing in the form of
>> #pixels per centimeter), origin, orientation.
>>
>> JPEG is poorer because it uses lossy compression.
>> The JPEG compression algorithm was not designed
>> for medical images but for picture scenes, for
>> example the photos of a Birthday party or the
>> picture of a dog sitting in the backyard.  :-)
>>
>> JPEG is not what you want to use if your image
>> actually contain a tumor. It is particularly bad
>> for segmentation because the compression is done
>> in blocks of 8x8 pixels, therefore the consistency
>> of intensities across those blocks is compromised.
>>
>> RAW is plain *dangerous* it doesn't contain any
>> information about the pixel type being used, the
>> image dimensions, the endianess, the pixel spacing,
>> the origin.  In practice, RAW is useless if you don't
>> have an accompanying header that tells you the
>> characteristics of the image.
>>
>>
>> If you are storing real patient data you may want
>> to use Analyze, GIPL or MetaImage, or to stick to
>> the original DICOM files that are produced from
>> CT and MRI scanners.
>>
>>
>> -------------------
>>
>> About your code:
>>
>> It seems to be fine for reading a BMP image
>> and writing it down.
>>
>> Did you find any problem while running this code ?
>>
>>
>>
>>    Regards,
>>
>>
>>       Luis
>>
>>
>>
>> PS: Note that a bug was recently fixed in the BMP
>> reader/writer. This bug manifested in problems when
>> reading or writing images whose row size was not a
>> multiple of 4.  If you are using BMP images you may
>> want to use a recent CVS checkout of the toolkit.
>>
>>
>> --------------------
>> Jimmy Wong wrote:
>>
>>> Thank you for your reply.
>>>
>>> If bmp is poor, which one is better? raw or jpg?
>>>
>>> I've read the manual, but very confuse of it.
>>>
>>> Here is my main function
>>>
>>> **********************************************
>>> void main()
>>> {
>>>     // Definition of stuctures
>>>     typedef unsigned char    PixelType;
>>>     const    unsigned int    Dimension = 2;
>>>     typedef itk::Image< PixelType, Dimension >    ImageType;
>>>
>>>     typedef itk::ImageFileReader< ImageType >    ReaderType;
>>>     typedef itk::ImageFileWriter< ImageType >    WriterType;
>>>
>>>     // Create a object of reader and read the image
>>>     ReaderType::Pointer reader = ReaderType::New();
>>>     WriterType::Pointer writer = WriterType::New();
>>>
>>>     const char pInputfileName[] = "Input.bmp";
>>>     const char pOutputfileName[] = "Output.bmp";
>>>
>>>     reader->SetFileName( pInputfileName );
>>>     reader->Update();
>>>
>>>     ImageType::Pointer image = reader->GetOutput();
>>>
>>>
>>>     writer->SetFileName( pOutputfileName );
>>>
>>>     writer->SetInput( reader->GetOutput() );
>>>
>>>     try
>>>    {
>>>         writer->Update();
>>>    }
>>>
>>>     catch( itk::ExceptionObject & err )
>>>    {
>>>         std::cout << "ExceptionObject caught !" << std::endl;
>>>         std::cout << err << std::endl;
>>>         exit(-1);
>>>    }
>>> }
>>> ******************************************************
>>>
>>> Is it correct for reading image?
>>>
>>> Thank you again.
>>>
>>> Zhimin
>>>
>>>
>>>
>>>
>>
>>
>>
>>
> 
> # This project is designed to be built outside the Insight source tree.
> PROJECT(ReadWriteImage)
> 
> # Find ITK.
> FIND_PACKAGE(ITK)
> IF(ITK_FOUND)
>  INCLUDE(${ITK_USE_FILE})
> ENDIF(ITK_FOUND)
> 
> # Find VTK.
> FIND_PACKAGE ( VTK)
> IF ( VTK_FOUND)
>  INCLUDE( ${USE_VTK_FILE} )
> ENDIF( VTK_FOUND)
> 
> INCLUDE_DIRECTORIES(${myProject_SOURCE_DIR})
> 
> ADD_EXECUTABLE(ReadWriteImage ReadWriteImage.cxx )
> 
> TARGET_LINK_LIBRARIES(ReadWriteImage
> ITKBasicFilters ITKCommon ITKIO
> vtkRendering vtkGraphics vtkHybrid
> vtkImaging vtkIO vtkFiltering vtkCommon)
> 
> #include "itkImageFileReader.h"
> #include "itkImageFileWriter.h"
> #include "itkImage.h"
> 
> void main()
> {
>     // Definition of stuctures
>     typedef unsigned char    PixelType;
>     const    unsigned int    Dimension = 2;
>     typedef itk::Image< PixelType, Dimension >    ImageType;
> 
>     typedef itk::ImageFileReader< ImageType >    ReaderType;
>     typedef itk::ImageFileWriter< ImageType >    WriterType;
> 
>     // Create a object of reader and read the image
>     ReaderType::Pointer reader = ReaderType::New();
>     WriterType::Pointer writer = WriterType::New();
> 
>     const char pInputfileName[] = "Input.bmp";
>     const char pOutputfileName[] = "Output.bmp";
> 
>     reader->SetFileName( pInputfileName );
>     reader->Update();
> 
>     ImageType::Pointer image = reader->GetOutput();
> 
> 
>     writer->SetFileName( pOutputfileName );
> 
>     writer->SetInput( reader->GetOutput() );
> 
>     try
>    {
>         writer->Update();
>    }
> 
>     catch( itk::ExceptionObject & err )
>    {
>         std::cout << "ExceptionObject caught !" << std::endl;
>         std::cout << err << std::endl;
>         exit(-1);
>    }
> }
> 
> 

================================================================




-------------- next part --------------

#include "itkImageFileWriter.h"
#include "itkImageFileReader.h"
#include "itkImage.h"
#include "itkRGBPixel.h"

int main()
{
	// Definition of stuctures
	typedef unsigned char ComponentType;
	typedef itk::RGBPixel<ComponentType> PixelType;
	const	unsigned int	Dimension = 2;
	typedef itk::Image< PixelType, Dimension >	ImageType;

	typedef itk::ImageFileReader< ImageType >	ReaderType;
	typedef itk::ImageFileWriter< ImageType >	WriterType;

	// Create a object of reader and read the image
	ReaderType::Pointer reader = ReaderType::New();
	WriterType::Pointer writer = WriterType::New();

	const char * pInputfileName = "Input.bmp";
	const char * pOutputfileName = "Output.bmp";

	reader->SetFileName( pInputfileName );
	reader->Update();

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


	writer->SetFileName( pOutputfileName );

	writer->SetInput( reader->GetOutput() );

	try
    {
		writer->Update();
    }

	catch( itk::ExceptionObject & err )
    {
		std::cout << "ExceptionObject caught !" << std::endl;
		std::cout << err << std::endl;
		exit(-1);
    }
  return 0;
}