Class that defines how to read Analyze file format. Analyze IMAGE FILE FORMAT - As much information as I can determine from the Medical image formats web site, and the Analyze75.pdf file provided from the Mayo clinic. A special note of thanks to Dennis P. Hanson (dph@mayo.edu) for his generous contributions in getting this information correct. More...

#include <itkAnalyzeImageIO.h>

Inheritance diagram for itk::AnalyzeImageIO:

Collaboration diagram for itk::AnalyzeImageIO:

List of all members.

Public Types
typedef SmartPointer< Self >	Pointer
typedef AnalyzeImageIO	Self
typedef ImageIOBase	Superclass
Public Member Functions
virtual bool	CanReadFile (const char *FileNameToRead)
virtual bool	CanWriteFile (const char *FileNameToWrite)
virtual ::itk::LightObject::Pointer	CreateAnother (void) const
virtual std::vector< double >	GetDefaultDirection (unsigned int i) const
virtual std::vector< double >	GetDirection (unsigned int i) const
virtual const char *	GetNameOfClass () const
virtual void	Read (void *buffer)
virtual void	ReadImageInformation ()
virtual void	Write (const void *buffer)
virtual void	WriteImageInformation ()
Static Public Member Functions
static Pointer	New ()
Protected Member Functions
	AnalyzeImageIO ()
void	PrintSelf (std::ostream &os, Indent indent) const
	~AnalyzeImageIO ()
Private Types
enum	ValidAnalyzeOrientationFlags
Private Member Functions
	AnalyzeImageIO (const Self &)
ImageIOBase::ByteOrder	CheckAnalyzeEndian (const struct dsr &temphdr)
void	DefineHeaderObjectDataType (void)
void	operator= (const Self &)
void	SwapBytesIfNecessary (void *buffer, SizeType numberOfPixels)
void	SwapHeaderBytesIfNecessary (struct dsr *const imageheader)
Private Attributes
struct dsr	m_Hdr
ImageIOBase::ByteOrder	m_MachineByteOrder

Detailed Description

Class that defines how to read Analyze file format. Analyze IMAGE FILE FORMAT - As much information as I can determine from the Medical image formats web site, and the Analyze75.pdf file provided from the Mayo clinic. A special note of thanks to Dennis P. Hanson (dph@mayo.edu) for his generous contributions in getting this information correct.

Author:

Hans J. Johnson Analyze image file sets consist of at least 2 files: REQUIRED:

an image file ([basename].img or [basename].img.gz or [basename].img.Z) This contains the binary represenation of the raw voxel values. If the file is uncompressed, it should be of of size (sizeof(storagetype)*NX*NY*NZ(*NT). The format of the image file is very simple; containing usually uncompressed voxel data for the images in one of the several possible voxel formats:
- 1 bit packed binary (slices begin on byte boundaries)
- 8 bit (unsigned char) gray scale unless .lkup file present
- 16 bit signed short
- 32 bit signed integers or float
- 24 bit RGB, 8 bits per channel
a header file ([basename].hdr) This a 348 byte file 99.99% of all images that contains a binary represenation of the C-struct defined in this file. The analyze 7.5 header structure may, however, be extended beyond this minimal defintion to encompase site specific information, and would have more than 348 bytes. Given that the ability to extend the header has rarely been used, this implementation of the Analyze 7.5 file will only read the first 348 bytes into the structure defined in this file, and all informaiton beyond the 348 bytes will be ignored. OPTIONAL:
a color lookup file ([basename].lkup) The .lkup file is a plain ASCII text file that contains 3 integer values between 0 and 255 on each line. Each line of the lkup file represents one color table entry for the Red, Green and Blue color components, respectively. The total dynamic range of the image is divided by the number of colors in color table to determine mapping of the image through these colors. For example, an 8-color 'rainbow colors' lookup table is represented as: =========================== 255 0 0 255 128 0 255 255 0 128 255 0 0 255 0 0 0 255 128 0 255 255 0 255 ===========================
an object file ([basename].obj) A specially formated file with a mapping between object name and image code used to associate image voxel locations with a label. This file is run length encoded to save disk storage.

Definition at line 92 of file itkAnalyzeImageIO.h.

Member Typedef Documentation

typedef SmartPointer< Self > itk::AnalyzeImageIO::Pointer

Reimplemented from itk::ImageIOBase.

Definition at line 98 of file itkAnalyzeImageIO.h.

typedef AnalyzeImageIO itk::AnalyzeImageIO::Self

Standard class typedefs.

Reimplemented from itk::ImageIOBase.

Definition at line 96 of file itkAnalyzeImageIO.h.

typedef ImageIOBase itk::AnalyzeImageIO::Superclass

Reimplemented from itk::ImageIOBase.

Definition at line 97 of file itkAnalyzeImageIO.h.

Member Enumeration Documentation

enum itk::AnalyzeImageIO::ValidAnalyzeOrientationFlags [private]

Valid Orientation values for objects

Key Description Origin dims[1] dims[2] dims[3]
=================================================================
0 transverse-unflipped IRP R->L P->A I->S
1 coronal-unflipped IRP R->L I->S P->A
2 sagittal-unflipped IRP P->A I->S R->L
3 transverse-flipped IRA R->L A->P I->S
4 coronal-flipped SRP R->L S->I P->A
5 sagittal-flipped ILP P->A I->S L->R
Where the Origin disignators are with respect to the patient
[(I)nferior|(S)uperior] [(L}eft|(R)ight] [(A)nterior|(P)osterior]
Note:
Key's 0-5 correspond to the Analyze v7.5 orientations, and should not be changed.

Definition at line 167 of file itkAnalyzeImageIO.h.

Constructor & Destructor Documentation

itk::AnalyzeImageIO::AnalyzeImageIO ( ) [protected]

itk::AnalyzeImageIO::~AnalyzeImageIO ( ) [protected]

itk::AnalyzeImageIO::AnalyzeImageIO ( const Self & ) [private]

Member Function Documentation

virtual bool itk::AnalyzeImageIO::CanReadFile ( const char * FileNameToRead ) [virtual]

Determine if the file can be read with this ImageIO implementation.

Author:: Hans J Johnson

Parameters:

FileNameToRead The name of the file to test for reading.

Postcondition:: Sets classes ImageIOBase::m_FileName variable to be FileNameToWrite

Returns:: Returns true if this ImageIO can read the file specified.

Implements itk::ImageIOBase.

virtual bool itk::AnalyzeImageIO::CanWriteFile ( const char * FileNameToWrite ) [virtual]

Determine if the file can be written with this ImageIO implementation.

Parameters:

FileNameToWrite The name of the file to test for writing.

Author:: Hans J. Johnson

Postcondition:: Sets classes ImageIOBase::m_FileName variable to be FileNameToWrite

Returns:: Returns true if this ImageIO can write the file specified.

Implements itk::ImageIOBase.

ImageIOBase::ByteOrder itk::AnalyzeImageIO::CheckAnalyzeEndian ( const struct dsr & temphdr ) [private]

Author:: Hans J. Johnson Check the endedness of the header file.

Parameters:

temphdr - a reference to the header structure

Returns:: The endedness of the file

virtual::itk::LightObject::Pointer itk::AnalyzeImageIO::CreateAnother ( void ) const [virtual]

Create an object from an instance, potentially deferring to a factory. This method allows you to create an instance of an object that is exactly the same type as the referring object. This is useful in cases where an object has been cast back to a base class.

Reimplemented from itk::LightProcessObject.

void itk::AnalyzeImageIO::DefineHeaderObjectDataType ( void ) [private]

Author:: Hans J. Johnson Defines the header object data type feilds according to Analyze v7.5 specifications

Returns:: nothing

virtual std::vector< double > itk::AnalyzeImageIO::GetDefaultDirection ( unsigned int i ) const [virtual]

Return the directions to be assigned by default to recipient images whose dimension is smaller than the image dimension in file.

Reimplemented from itk::ImageIOBase.

virtual std::vector< double > itk::AnalyzeImageIO::GetDirection ( unsigned int i ) const [virtual]

Return the directions with a correction for the 2D case.

Reimplemented from itk::ImageIOBase.

virtual const char* itk::AnalyzeImageIO::GetNameOfClass ( ) const [virtual]

Run-time type information (and related methods).

Reimplemented from itk::ImageIOBase.

static Pointer itk::AnalyzeImageIO::New ( ) [static]

Method for creation through the object factory.

Reimplemented from itk::LightProcessObject.

void itk::AnalyzeImageIO::operator= ( const Self & ) [private]

This method causes the filter to generate its output.

Reimplemented from itk::ImageIOBase.

void itk::AnalyzeImageIO::PrintSelf	(	std::ostream &	os,
		Indent	indent
	)		const `[protected, virtual]`

Methods invoked by Print() to print information about the object including superclasses. Typically not called by the user (use Print() instead) but used in the hierarchical print process to combine the output of several classes.

Reimplemented from itk::ImageIOBase.

virtual void itk::AnalyzeImageIO::Read ( void * buffer ) [virtual]

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

virtual void itk::AnalyzeImageIO::ReadImageInformation ( ) [virtual]

Set the spacing and dimension information for the set filename.

Implements itk::ImageIOBase.