[Insight-users] Reading bmp image with ITK
Luis Ibanez
luis.ibanez at kitware.com
Mon Nov 8 20:20:42 EST 2004
Hi Jimmy,
Please point us to the BMP version of Lena that you are trying to read.
The reason why this class is predispossed to RGB pixels is that this
is the generic form of BMP files.
You may want to log into the bug tracking database and add
this as a Feature Request. Somehting like "Extending BMP reader/writer
for supporting grayscale (non-RGB) images"
You can create your account in the bug tracker by simply using your
email address in the following link
http://www.itk.org/Bug/
Please let us know if you find any problem with the bug database,
Thanks
Luis
---------------------
Jimmy Wong wrote:
> Hi, Luis,
>
> Thank you for your code and revision. But still canno't read Lena.bmp,
> the most popular image. I don't know why. However, I try it on jpeg
> image, it works.
>
> Can you tell me why we need RGB pixels?
>
> Regards,
>
> 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: Tue, 02 Nov 2004 13:28:17 -0500
>>
>> 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);
>>> }
>>> }
>>>
>>>
>>
>> ================================================================
>>
>>
>>
>>
>>
>> #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;
>> }
>>
>>
>
>
>
>
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