[Insight-users] how to get the buffer data

Ali Habib ali.mahmoud.habib at gmail.com
Wed Dec 29 08:40:59 EST 2010


and how to get bytes per pixel

Best regards

On Wed, Dec 29, 2010 at 4:58 PM, Ali Habib <ali.mahmoud.habib at gmail.com>wrote:

> I got it ,
>
> but may I ask a question what's  the difference between  bitsPerComponent,
> and
> bitsPerPixel
> I just get confused
>
> Best regards
>
>
> On Wed, Dec 29, 2010 at 4:16 PM, Dan Mueller <dan.muel at gmail.com> wrote:
>
>> Hi Ali,
>>
>> Option 1:
>> ImageType::Pointer image_1 = reader->GetOutput();
>> unsigned int numComponents = image_1->GetNumberOfComponentsPerPixel();
>> // NOTE: Only really works for itk::Vector images eg. RGBPixel returns 1
>>
>> Option 2:
>> ImageType::Pointer image_1 = reader->GetOutput();
>> InputImageType::IndexType index;
>> index[0]=1;
>> index[1]=1;
>> ImageType::PixelType pixel_value= image_1->GetPixel( index );
>> unsigned int numComponents =
>>
>> itk::VectorPixelTraits<ImageType::PixelType>::GetNumberOfComponents(pixel_value);
>> // NOTE: This works for many image types. eg.
>> // unsigned char returns 1
>> // RGB returns 3
>> // FixedArray<float, 4> returns 4
>>
>> HTH
>>
>> Cheers, Dan
>>
>> On 29 December 2010 11:17, Ali Habib <ali.mahmoud.habib at gmail.com> wrote:
>> > Sorry for disturbance,
>> > but I have
>> > ImageType::Pointer image_1 = reader->GetOutput() ;
>> > I misunderstand how to get the pixel type of  image_1 , using the 2
>> options
>> > you gave me . could u give me more details
>> > Best regards
>> >
>> > On Tue, Dec 28, 2010 at 11:26 AM, Dan Mueller <dan.muel at gmail.com>
>> wrote:
>> >>
>> >> Hi Ali,
>> >>
>> >> Try the following to get the image buffer as a pointer:
>> >>    InputPixelType* buffer = image_1->GetBufferPointer();
>> >>
>> >> You can then treat the buffer as a simple pointer (e.g. cast to
>> >> unsigned char *, whatever).
>> >>
>> >> Determining if the pixel type is scalar or not is a little trickier.
>> >> At first glance the method
>> >> itk::ImageBase::GetNumberOfComponentsPerPixel() seems helpful, but it
>> >> does not work as you might expect (see documentation). I'm not sure if
>> >> there is a better way, but I use a specialized traits class to help
>> >> (see below). You use the class as follows:
>> >>    InputPixelType pixel;
>> >>    unsigned int numComponents =
>> >> itk::VectorPixelTraits<InputPixelType>::GetNumberOfComponents(pixel);
>> >>
>> >> HTH
>> >>
>> >> Cheers, Dan
>> >>
>> >>
>> >>
>> /*=========================================================================
>> >>
>> >>  Program:   Insight Segmentation & Registration Toolkit
>> >>  Module:    $RCSfile: itkVectorPixelTraits.h,v $
>> >>  Language:  C++
>> >>  Date:      $Date$
>> >>  Version:   $Revision$
>> >>
>> >>  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.
>> >>
>> >>
>> >>
>> =========================================================================*/
>> >> #ifndef __itkVectorPixelTraits_h
>> >> #define __itkVectorPixelTraits_h
>> >>
>> >> #include "itkMacro.h"
>> >> #include "itkArray.h"
>> >> #include "itkVector.h"
>> >> #include "itkFixedArray.h"
>> >> #include "itkRGBPixel.h"
>> >> #include "itkRGBAPixel.h"
>> >> #include "itkVariableLengthVector.h"
>> >> #include "itkNumericTraits.h"
>> >>
>> >> namespace itk
>> >> {
>> >>
>> >> /** \class VectorPixelTraits
>> >>  * \brief Define additional traits for vector pixels (eg. fixed array,
>> >> RGB).
>> >>  *
>> >>  * VectorPixelTraits is used to extend the traits associated with
>> vector
>> >> pixel
>> >>  * types such as fixed array, RGBPixel, VariableLengthVector, and so
>> on.
>> >>  * These traits also support scalar types (such as unsigned char,
>> short)
>> >>  * so that both vector and scalar types can be treated in a unified
>> way.
>> >>  *
>> >>  * Note this default implementation defines traits for all scalar types
>> >>  * (eg. unsigned char, short, double, etc).
>> >>  *
>> >>  * \ingroup DataRepresentation
>> >>  */
>> >> template <class T>
>> >> class VectorPixelTraits {
>> >> public:
>> >>  /** Get the number of components for the given type.
>> >>    * An input is required for variable length types whose
>> >>    * length is defined at run-time rather than compile-time.
>> >>    * For other types the input is simply ignored. */
>> >>  static unsigned int GetNumberOfComponents( T input ) { return 1; }
>> >>
>> >>  /* Return the reference to the given indexed element in the vector. */
>> >>  static T *GetElement( unsigned int i, T *pixel ) { return pixel; }
>> >>
>> >>  /* Set the value of the left element with the value of the right. */
>> >>  static void SetElement( unsigned int i, T &left, T right ) { left =
>> >> right; }
>> >>
>> >>  /* Return the zero value. */
>> >>  static T ZeroValue( T input ) { return NumericTraits<T>::ZeroValue();
>> }
>> >>
>> >>  /* Convert the given double to the pixel type.
>> >>     NOTE: This is not implemented for VariableLengthVectors! */
>> >>  static T Convert( double input ) { return static_cast<T>(input); }
>> >> };
>> >>
>> >> /** Define a macro to be used for RGB types. */
>> >> #define RGBSTATICTRAITSMACRO( T, E ) \
>> >> template<> \
>> >> class VectorPixelTraits< T<E> > { \
>> >> public: \
>> >>  static unsigned int GetNumberOfComponents( T<E> input ) \
>> >>    { return 3; } \
>> >>  static E *GetElement( unsigned int i, T<E> *pixel ) \
>> >>    { return &((*pixel)[i]); } \
>> >>  static void SetElement( unsigned int i, T<E> &left, T<E> right ) \
>> >>    { left[i] = right[i]; } \
>> >>  static T<E> ZeroValue( T<E> input ) \
>> >>    { return NumericTraits<T<E>>::ZeroValue(); } \
>> >>  static T<E> Convert( double input ) \
>> >>    { T<E> value( static_cast<E>(input) ); return value; } \
>> >> }; \
>> >>
>> >> RGBSTATICTRAITSMACRO( RGBPixel, unsigned char );
>> >> RGBSTATICTRAITSMACRO( RGBPixel, signed char );
>> >> RGBSTATICTRAITSMACRO( RGBPixel, unsigned short );
>> >> RGBSTATICTRAITSMACRO( RGBPixel, signed short );
>> >> RGBSTATICTRAITSMACRO( RGBPixel, unsigned long );
>> >> RGBSTATICTRAITSMACRO( RGBPixel, signed long );
>> >> RGBSTATICTRAITSMACRO( RGBPixel, float );
>> >> RGBSTATICTRAITSMACRO( RGBPixel, double );
>> >>
>> >> /** Define a macro to be used for RGBA types. */
>> >> #define RGBASTATICTRAITSMACRO( T, E ) \
>> >> template<> \
>> >> class VectorPixelTraits< T<E> > { \
>> >> public: \
>> >>  static unsigned int GetNumberOfComponents( T<E> input ) { return 4; }
>> \
>> >>  static E *GetElement( unsigned int i, T<E> *pixel ) { return
>> >> &((*pixel)[i]); } \
>> >>  static void SetElement( unsigned int i, T<E> &left, T<E> right ) {
>> >> left[i] = right[i]; } \
>> >>  static T<E> ZeroValue( T<E> input ) { T<E> zero =
>> >> NumericTraits<T<E>>::ZeroValue(); zero.SetAlpha( 254 ); return zero; }
>> >> \
>> >>  static T<E> Convert( double input ) { T<E> value(
>> >> static_cast<E>(input) ); return value; } \
>> >> }; \
>> >>
>> >> RGBASTATICTRAITSMACRO( RGBAPixel, unsigned char );
>> >> RGBASTATICTRAITSMACRO( RGBAPixel, signed char );
>> >> RGBASTATICTRAITSMACRO( RGBAPixel, unsigned short );
>> >> RGBASTATICTRAITSMACRO( RGBAPixel, signed short );
>> >> RGBASTATICTRAITSMACRO( RGBAPixel, unsigned long );
>> >> RGBASTATICTRAITSMACRO( RGBAPixel, signed long );
>> >> RGBASTATICTRAITSMACRO( RGBAPixel, float );
>> >> RGBASTATICTRAITSMACRO( RGBAPixel, double );
>> >>
>> >> /** Define a macro to be used for all (fixed) array types. */
>> >> #define FIXEDARRAYSTATICTRAITSMACRO( T, E, N ) \
>> >> template<> \
>> >> class VectorPixelTraits< T<E,N> > { \
>> >> public: \
>> >>  static unsigned int GetNumberOfComponents(T<E,N> input) { return N; }
>> \
>> >>  static E *GetElement( unsigned int i, T<E,N> *pixel) { return
>> >> &((*pixel)[i]); } \
>> >>  static void SetElement( unsigned int i, T<E,N> &left, T<E,N> right)
>> >> { left[i] = right[i]; } \
>> >>  static T<E,N> ZeroValue( T<E,N> input ) { T<E,N> zero; zero.Fill(
>> >> NumericTraits<E>::ZeroValue() ); return zero; } \
>> >>  static T<E,N> Convert( double input ) { T<E,N> value; value.Fill(
>> >> static_cast<E>(input) ); return value; } \
>> >> }; \
>> >>
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, unsigned char, 1 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, signed char, 1 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, unsigned short, 1 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, signed short, 1 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, unsigned long, 1 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, signed long, 1 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, float, 1 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, double, 1 );
>> >>
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, unsigned char, 2 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, signed char, 2 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, unsigned short, 2 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, signed short, 2 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, unsigned long, 2 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, signed long, 2 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, float, 2 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, double, 2 );
>> >>
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, unsigned char, 3 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, signed char, 3 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, unsigned short, 3 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, signed short, 3 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, unsigned long, 3 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, signed long, 3 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, float, 3 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, double, 3 );
>> >>
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, unsigned char, 4 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, signed char, 4 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, unsigned short, 4 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, signed short, 4 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, unsigned long, 4 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, signed long, 4 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, float, 4 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( FixedArray, double, 4 );
>> >>
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, unsigned char, 1 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, signed char, 1 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, unsigned short, 1 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, signed short, 1 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, unsigned long, 1 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, signed long, 1 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, float, 1 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, double, 1 );
>> >>
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, unsigned char, 2 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, signed char, 2 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, unsigned short, 2 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, signed short, 2 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, unsigned long, 2 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, signed long, 2 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, float, 2 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, double, 2 );
>> >>
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, unsigned char, 3 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, signed char, 3 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, unsigned short, 3 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, signed short, 3 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, unsigned long, 3 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, signed long, 3 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, float, 3 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, double, 3 );
>> >>
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, unsigned char, 4 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, signed char, 4 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, unsigned short, 4 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, signed short, 4 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, unsigned long, 4 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, signed long, 4 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, float, 4 );
>> >> FIXEDARRAYSTATICTRAITSMACRO( Vector, double, 4 );
>> >>
>> >> /** Define a macro to be used for all (variable) array types. */
>> >> #define VARIABLEARRAYSTATICTRAITSMACRO( T, E ) \
>> >> template<> \
>> >> class VectorPixelTraits< T<E> > { \
>> >> public: \
>> >>  static unsigned int GetNumberOfComponents(T<E> input) { return
>> >> input.Size(); } \
>> >>  static E *GetElement( unsigned int i, T<E> *pixel) { return
>> >> &((*pixel)[i]); } \
>> >>  static void SetElement( unsigned int i, T<E> &left, T<E> right) {
>> >> left[i] = right[i]; } \
>> >>  static T<E> ZeroValue( T<E> input ) { return
>> >> NumericTraits<T<E>>::Zero(input); } \
>> >>  static T<E> Convert( double input ) { T<E> value; /* NOT IMPLEMENTED
>> >> */ return value; } \
>> >> }; \
>> >>
>> >> VARIABLEARRAYSTATICTRAITSMACRO( VariableLengthVector, unsigned char );
>> >> VARIABLEARRAYSTATICTRAITSMACRO( VariableLengthVector, signed char );
>> >> VARIABLEARRAYSTATICTRAITSMACRO( VariableLengthVector, unsigned short );
>> >> VARIABLEARRAYSTATICTRAITSMACRO( VariableLengthVector, signed short );
>> >> VARIABLEARRAYSTATICTRAITSMACRO( VariableLengthVector, unsigned long );
>> >> VARIABLEARRAYSTATICTRAITSMACRO( VariableLengthVector, signed long );
>> >> VARIABLEARRAYSTATICTRAITSMACRO( VariableLengthVector, float );
>> >> VARIABLEARRAYSTATICTRAITSMACRO( VariableLengthVector, double );
>> >>
>> >> } // end namespace itk
>> >>
>> >> #endif
>> >>
>> >>
>> >> On 28 December 2010 09:52, Ali Habib <ali.mahmoud.habib at gmail.com>
>> wrote:
>> >> > Dear All,
>> >> > I need the pixel data as unsigned char* , I created my pipeline but I
>> >> > stuck
>> >> > on how to get the buffer data , also I need to know does the
>> pixel_value
>> >> > will show me if the input is scaler or not
>> >> > the code I use is :
>> >> > typedef signed short InputPixelType;
>> >> > const unsigned int   InputDimension = 2;
>> >> > typedef itk::Image< InputPixelType, InputDimension > InputImageType;
>> >> > typedef itk::ImageFileReader< InputImageType > ReaderType;
>> >> > typedef InputImageType::SizeType         SizeType;
>> >> > ReaderType::Pointer reader = ReaderType::New();
>> >> > reader->SetFileName( "4.dcm" );
>> >> > typedef itk::GDCMImageIO           ImageIOType;
>> >> > ImageIOType::Pointer gdcmImageIO = ImageIOType::New();
>> >> > reader->SetImageIO( gdcmImageIO );
>> >> > try
>> >> >     {
>> >> > reader->Update();
>> >> >     }
>> >> > catch (itk::ExceptionObject & e)
>> >> >     {
>> >> > std::cerr << "exception in file reader " << std::endl;
>> >> > std::cerr << e << std::endl;
>> >> > //          return EXIT_FAILURE;
>> >> >     }
>> >> > InputImageType::Pointer image_1 = reader->GetOutput() ;
>> >> > // the image parameters
>> >> > unsigned long lwidth =
>> image_1->GetLargestPossibleRegion().GetSize()[0]
>> >> > ;
>> >> > unsigned long lheight =
>> image_1->GetLargestPossibleRegion().GetSize()[1]
>> >> > ;
>> >> > InputImageType::IndexType index;
>> >> > index[0]=1;
>> >> > index[1]=1;
>> >> > signed short pixel_value;
>> >> > pixel_value= image_1->GetPixel( index );
>> >
>> >
>>
>
>
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