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Maniphest T12682

PixelType initialization of an Image in mitkItkImageFileReader is wrong
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Description

The PixelType of the image to be read in is created upon the information provided by the itk::ImageIOBase. This does not provide a type_info for the whole pixeltype ( i.e. itk::RGBPixel< T1 > ) but only for the component type.

To have some type_info provided for the method, the ComponentTypeInfo() is used instead.

For this reason, simply enhancing the MITK_ACCESSBYITK_PIXEL_TYPES_SEQ by the composite type ( itk::RGBPixel< T1 > ) will not work, since while iterating through the sequence the PixelType stored in the mitk::Image does not match the composite pixel type.

So what will be needed is a method somewhere in mitk ( possible declared in mitk::PixelType directly in the mitk scope )

const type_info& GetPixelTypeFromITKImageIO( const itk::ImageIOBase::Pointer)

which will return the component type for scalar types and the correct type for composite types, i.e.

IN: itk::ImageIOBase::RGBA --> RETURN: typeid( itk::RGBAPixel< ComponentType > )

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Event Timeline

• hering added projects: MITK, Bugzilla.Jul 19 2012, 1:27 PM
• hering added a subscriber: • hering.Jul 19 2012, 1:37 PM

As a proof of concept I have tried following (minimal) changes:

  • enhance the MITK_ACCESSBYITK_PIXEL_TYPES_SEQ by (itk::RGBAPixel< unsigned char>)
  • implement prototype of the GetPixelTypeFromITKImageIO() and pass the return value to the creation of the pixel type in mitk::ItkImageFileReader::GenerateData()
  • use the new type in mitk::ImageWriter::WriteByITK

    // OLD: AccessByItk_1( image, _mitkItkPictureWrite, fileName ); AccessFixedPixelTypeByItk_1( image, _mitkItkPictureWrite, (itk::RGBAPixel<unsigned char>) )

and a 2D RGBA image in PNG format was stored successfully with correct format and also image data.

• hering added a comment.Aug 1 2012, 3:53 PM

Added ChangeRequest. Requesting Core_Modification flag.

• hering added a comment.Aug 2 2012, 11:57 AM

[30ab25]: Merge branch 'bug-12682-Fix-PixelType-for-RGB_A'

Merged commits:

2012-08-02 11:49:19 Jan Hering [f5feb4]
Fixed macro call

2012-08-01 17:38:45 Jan Hering [cd0e99]
Extended ImageWriter Tests

+ added new tests ( 2D PNG RGB and RGBA images )
+ added short CompareMacro to verify the MetaData of the image that was
written out

2012-08-01 17:37:37 Jan Hering [1796ac]
Adapted WriteByITK to the new macros

  • splitted execution for single-component and composite pixel types

2012-08-01 17:01:29 Jan Hering [a2f549]
Fixed pixeltype creation for ItkImageFileReader

2012-08-01 16:53:07 Jan Hering [23f94f]
Adapted _mitkItkPictureWrite to composite pixel types

+ added new mitkItkPictureWriteComposite method
+ extended the method's instantiation

2012-08-01 16:08:32 Jan Hering [73886a]
Added function transforming itk::ImageIOBase into type_info&

2012-08-01 15:47:57 Jan Hering [62d33c]
Enhancing default values for COMPOSITE list

  • added itk::RGB(A)Pixel types to the COMPOSITE_TYPE list
  • excluded the COMPOSITE_TYPE list from the

MITK_ACCESSBYITK_PIXEL_TYPE_SEQ

• hering added a comment.Aug 2 2012, 1:49 PM

[7dc57b]: Merge branch 'bug-12682-Fix-PixelType-CMakeConfig'

Merged commits:

2012-08-02 13:44:42 Jan Hering [4e8afe]
COMP: Enforce setting COMPOSITE_PIXEL_TYPES variable

• hering added a comment.Aug 6 2012, 1:37 PM

[adc916]: Merge branch 'bug-12682-Fix-PixelType-MissingTests'

Merged commits:

2012-08-06 13:32:17 Jan Hering [9d09aa]
Re-defining new ImageWriterTests

  • the lines were incidentally removed during merge conflict resolving
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