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itk::BioRadImageIO Class Reference
Data Processing Objects » Filters » Input and Output FiltersGroup IO » | Module ITKIOBioRad

#include <itkBioRadImageIO.h>

Detailed Description

ImageIO class for reading Bio-Rad images. Bio-Rad file format are used by confocal microscopes like MRC 1024, MRC 600 https://www.bio-rad.com/.

The reader/writer was based on a scanned copy of the MRC-600 documentation https://forums.ni.com/attachments/ni/200/7567/1/file%20format.pdf

Definition at line 51 of file itkBioRadImageIO.h.

+ Inheritance diagram for itk::BioRadImageIO:
+ Collaboration diagram for itk::BioRadImageIO:

Public Types

using Pointer = SmartPointer< Self >
 
using Self = BioRadImageIO
 
using Superclass = ImageIOBase
 
- Public Types inherited from itk::ImageIOBase
using ArrayOfExtensionsType = std::vector< std::string >
 
using BufferSizeType = itk::OffsetValueType
 
using ConstPointer = SmartPointer< const Self >
 
using IndexValueType = itk::IndexValueType
 
using IOByteOrderEnum = itk::IOByteOrderEnum
 
using IOComponentEnum = itk::IOComponentEnum
 
using IOFileEnum = itk::IOFileEnum
 
using Pointer = SmartPointer< Self >
 
using Self = ImageIOBase
 
using SizeType = itk::intmax_t
 
using SizeValueType = itk::SizeValueType
 
using Superclass = LightProcessObject
 
- Public Types inherited from itk::LightProcessObject
using ConstPointer = SmartPointer< const Self >
 
using Pointer = SmartPointer< Self >
 
using Self = LightProcessObject
 
using Superclass = Object
 
- Public Types inherited from itk::Object
using ConstPointer = SmartPointer< const Self >
 
using Pointer = SmartPointer< Self >
 
using Self = Object
 
using Superclass = LightObject
 
- Public Types inherited from itk::LightObject
using ConstPointer = SmartPointer< const Self >
 
using Pointer = SmartPointer< Self >
 
using Self = LightObject
 

Public Member Functions

bool CanReadFile (const char *) override
 
bool CanWriteFile (const char *) override
 
const char * GetNameOfClass () const override
 
void Read (void *buffer) override
 
void ReadImageInformation () override
 
void Write (const void *buffer) override
 
void WriteImageInformation () override
 
- Public Member Functions inherited from itk::ImageIOBase
virtual bool CanStreamRead ()
 
virtual bool CanStreamWrite ()
 
virtual ImageIORegion GenerateStreamableReadRegionFromRequestedRegion (const ImageIORegion &requested) const
 
virtual unsigned int GetActualNumberOfSplitsForWriting (unsigned int numberOfRequestedSplits, const ImageIORegion &pasteRegion, const ImageIORegion &largestPossibleRegion)
 
std::string GetByteOrderAsString (IOByteOrderEnum) const
 
virtual unsigned int GetComponentSize () const
 
virtual IOComponentEnum GetComponentType () const
 
virtual const std::type_info & GetComponentTypeInfo () const
 
virtual int GetCompressionLevel () const
 
virtual const std::string & GetCompressor () const
 
virtual std::vector< double > GetDefaultDirection (unsigned int k) const
 
virtual SizeValueType GetDimensions (unsigned int i) const
 
virtual std::vector< double > GetDirection (unsigned int i) const
 
std::string GetFileTypeAsString (IOFileEnum) const
 
SizeType GetImageSizeInBytes () const
 
SizeType GetImageSizeInComponents () const
 
SizeType GetImageSizeInPixels () const
 
virtual bool GetIsReadAsScalarPlusPalette () const
 
virtual unsigned int GetNumberOfDimensions () const
 
virtual double GetOrigin (unsigned int i) const
 
virtual SizeType GetPixelStride () const
 
virtual double GetSpacing (unsigned int i) const
 
virtual ImageIORegion GetSplitRegionForWriting (unsigned int ithPiece, unsigned int numberOfActualSplits, const ImageIORegion &pasteRegion, const ImageIORegion &largestPossibleRegion)
 
const ArrayOfExtensionsType & GetSupportedReadExtensions () const
 
const ArrayOfExtensionsType & GetSupportedWriteExtensions () const
 
void SetByteOrderToLittleEndian ()
 
virtual void SetComponentType (const IOComponentEnum _arg)
 
virtual void SetCompressionLevel (int _arg)
 
virtual void SetCompressor (std::string _c)
 
virtual void SetDirection (unsigned int i, const std::vector< double > &direction)
 
virtual void SetDirection (unsigned int i, const vnl_vector< double > &direction)
 
void SetFileTypeToBinary ()
 
void SetNumberOfDimensions (unsigned int)
 
virtual void SetOrigin (unsigned int i, double origin)
 
virtual void SetSpacing (unsigned int i, double spacing)
 
template<typename TPixel >
void SetTypeInfo (const TPixel *)
 
virtual bool SupportsDimension (unsigned long dim)
 
virtual void SetFileName (const char *_arg)
 
virtual const char * GetFileName () const
 
virtual void SetDimensions (unsigned int i, SizeValueType dim)
 
virtual void SetIORegion (ImageIORegion _arg)
 
virtual const ImageIORegion & GetIORegion () const
 
virtual void SetPixelType (const itk::CommonEnums::IOPixel _arg)
 
virtual itk::CommonEnums::IOPixel GetPixelType () const
 
virtual void SetNumberOfComponents (unsigned int _arg)
 
virtual const unsigned int & GetNumberOfComponents () const
 
virtual void SetUseCompression (bool _arg)
 
virtual bool GetUseCompression () const
 
virtual void UseCompressionOn ()
 
virtual void SetUseStreamedReading (bool _arg)
 
virtual bool GetUseStreamedReading () const
 
virtual void UseStreamedReadingOn ()
 
virtual void SetUseStreamedWriting (bool _arg)
 
virtual bool GetUseStreamedWriting () const
 
virtual void UseStreamedWritingOn ()
 
virtual void SetExpandRGBPalette (bool _arg)
 
virtual bool GetExpandRGBPalette () const
 
virtual void ExpandRGBPaletteOn ()
 
virtual void SetWritePalette (bool _arg)
 
virtual bool GetWritePalette () const
 
virtual void WritePaletteOn ()
 
virtual void SetFileType (const IOFileEnum _arg)
 
virtual IOFileEnum GetFileType () const
 
void SetFileTypeToASCII ()
 
virtual void SetByteOrder (const IOByteOrderEnum _arg)
 
virtual IOByteOrderEnum GetByteOrder () const
 
void SetByteOrderToBigEndian ()
 
template<typename TPixel >
void SetPixelTypeInfo (const TPixel *)
 
template<typename TPixel >
void SetPixelTypeInfo (const RGBPixel< TPixel > *)
 
template<typename TPixel >
void SetPixelTypeInfo (const RGBAPixel< TPixel > *)
 
template<unsigned int VLength>
void SetPixelTypeInfo (const Offset< VLength > *)
 
template<typename TPixel , unsigned int VLength>
void SetPixelTypeInfo (const Vector< TPixel, VLength > *)
 
template<typename TCoordRep , unsigned int VPointDimension>
void SetPixelTypeInfo (const Point< TCoordRep, VPointDimension > *)
 
template<typename TPixel , unsigned int VLength>
void SetPixelTypeInfo (const CovariantVector< TPixel, VLength > *)
 
template<typename TPixel , unsigned int VLength>
void SetPixelTypeInfo (const SymmetricSecondRankTensor< TPixel, VLength > *)
 
template<typename TPixel >
void SetPixelTypeInfo (const DiffusionTensor3D< TPixel > *)
 
template<typename TPixel >
void SetPixelTypeInfo (const std::complex< TPixel > *)
 
template<typename TPixel , unsigned int VLength>
void SetPixelTypeInfo (const FixedArray< TPixel, VLength > *)
 
template<typename TPixel >
void SetPixelTypeInfo (const VariableLengthVector< TPixel > *)
 
template<typename TValue >
void SetPixelTypeInfo (const Array< TValue > *)
 
template<typename TPixel , unsigned int VLength>
void SetPixelTypeInfo (const Matrix< TPixel, VLength, VLength > *)
 
template<typename TValue >
void SetPixelTypeInfo (const VariableSizeMatrix< TValue > *)
 
- Public Member Functions inherited from itk::LightProcessObject
virtual void AbortGenerateDataOn ()
 
virtual const bool & GetAbortGenerateData () const
 
virtual void SetAbortGenerateData (bool _arg)
 
virtual void UpdateOutputData ()
 
void UpdateProgress (float amount)
 
virtual void SetProgress (float _arg)
 
virtual const float & GetProgress () const
 
- Public Member Functions inherited from itk::Object
unsigned long AddObserver (const EventObject &event, Command *cmd) const
 
unsigned long AddObserver (const EventObject &event, std::function< void(const EventObject &)> function) const
 
LightObject::Pointer CreateAnother () const override
 
virtual void DebugOff () const
 
virtual void DebugOn () const
 
Command * GetCommand (unsigned long tag)
 
bool GetDebug () const
 
MetaDataDictionary & GetMetaDataDictionary ()
 
const MetaDataDictionary & GetMetaDataDictionary () const
 
virtual ModifiedTimeType GetMTime () const
 
virtual const TimeStamp & GetTimeStamp () const
 
bool HasObserver (const EventObject &event) const
 
void InvokeEvent (const EventObject &)
 
void InvokeEvent (const EventObject &) const
 
virtual void Modified () const
 
void Register () const override
 
void RemoveAllObservers ()
 
void RemoveObserver (unsigned long tag) const
 
void SetDebug (bool debugFlag) const
 
void SetReferenceCount (int) override
 
void UnRegister () const noexcept override
 
void SetMetaDataDictionary (const MetaDataDictionary &rhs)
 
void SetMetaDataDictionary (MetaDataDictionary &&rrhs)
 
virtual void SetObjectName (std::string _arg)
 
virtual const std::string & GetObjectName () const
 
- Public Member Functions inherited from itk::LightObject
Pointer Clone () const
 
virtual void Delete ()
 
virtual int GetReferenceCount () const
 
void Print (std::ostream &os, Indent indent=0) const
 

Static Public Member Functions

static Pointer New ()
 
- Static Public Member Functions inherited from itk::ImageIOBase
static std::string GetComponentTypeAsString (IOComponentEnum)
 
static IOComponentEnum GetComponentTypeFromString (const std::string &typeString)
 
static std::string GetPixelTypeAsString (IOPixelEnum)
 
static IOPixelEnum GetPixelTypeFromString (const std::string &pixelString)
 
- Static Public Member Functions inherited from itk::LightProcessObject
static Pointer New ()
 
- Static Public Member Functions inherited from itk::Object
static bool GetGlobalWarningDisplay ()
 
static void GlobalWarningDisplayOff ()
 
static void GlobalWarningDisplayOn ()
 
static Pointer New ()
 
static void SetGlobalWarningDisplay (bool val)
 
- Static Public Member Functions inherited from itk::LightObject
static void BreakOnError ()
 
static Pointer New ()
 

Protected Member Functions

 BioRadImageIO ()
 
void InternalReadImageInformation (std::ifstream &file)
 
void PrintSelf (std::ostream &os, Indent indent) const override
 
 ~BioRadImageIO () override
 
- Protected Member Functions inherited from itk::ImageIOBase
void AddSupportedReadExtension (const char *extension)
 
void AddSupportedWriteExtension (const char *extension)
 
void ComputeStrides ()
 
virtual unsigned int GetActualNumberOfSplitsForWritingCanStreamWrite (unsigned int numberOfRequestedSplits, const ImageIORegion &pasteRegion) const
 
SizeType GetComponentStride () const
 
virtual const ImageRegionSplitterBase * GetImageRegionSplitter () const
 
virtual unsigned int GetPixelSize () const
 
SizeType GetRowStride () const
 
SizeType GetSliceStride () const
 
virtual ImageIORegion GetSplitRegionForWritingCanStreamWrite (unsigned int ithPiece, unsigned int numberOfActualSplits, const ImageIORegion &pasteRegion) const
 
 ImageIOBase ()
 
virtual void InternalSetCompressor (const std::string &_compressor)
 
virtual void OpenFileForReading (std::ifstream &inputStream, const std::string &filename, bool ascii=false)
 
virtual void OpenFileForWriting (std::ofstream &outputStream, const std::string &filename, bool truncate=true, bool ascii=false)
 
virtual void ReadBufferAsASCII (std::istream &is, void *buffer, IOComponentEnum ctype, SizeType numComp)
 
bool ReadBufferAsBinary (std::istream &is, void *buffer, SizeType num)
 
virtual void Reset (const bool freeDynamic=true)
 
void Resize (const unsigned int numDimensions, const unsigned int *dimensions)
 
void SetSupportedReadExtensions (const ArrayOfExtensionsType &)
 
void SetSupportedWriteExtensions (const ArrayOfExtensionsType &)
 
virtual void WriteBufferAsASCII (std::ostream &os, const void *buffer, IOComponentEnum ctype, SizeType numComp)
 
 ~ImageIOBase () override
 
virtual bool HasSupportedReadExtension (const char *fileName, bool ignoreCase=true)
 
virtual bool HasSupportedWriteExtension (const char *fileName, bool ignoreCase=true)
 
virtual void SetMaximumCompressionLevel (int)
 
virtual int GetMaximumCompressionLevel () const
 
- Protected Member Functions inherited from itk::LightProcessObject
virtual void GenerateData ()
 
 LightProcessObject ()
 
 ~LightProcessObject () override
 
- Protected Member Functions inherited from itk::Object
 Object ()
 
bool PrintObservers (std::ostream &os, Indent indent) const
 
virtual void SetTimeStamp (const TimeStamp &timeStamp)
 
 ~Object () override
 
- Protected Member Functions inherited from itk::LightObject
virtual LightObject::Pointer InternalClone () const
 
 LightObject ()
 
virtual void PrintHeader (std::ostream &os, Indent indent) const
 
virtual void PrintTrailer (std::ostream &os, Indent indent) const
 
virtual ~LightObject ()
 

Additional Inherited Members

- Protected Attributes inherited from itk::ImageIOBase
IOByteOrderEnum m_ByteOrder { IOByteOrderEnum::OrderNotApplicable }
 
IOComponentEnum m_ComponentType { IOComponentEnum::UNKNOWNCOMPONENTTYPE }
 
int m_CompressionLevel { 30 }
 
std::string m_Compressor { "uninitialized" }
 
std::vector< SizeValueType > m_Dimensions {}
 
std::vector< std::vector< double > > m_Direction {}
 
bool m_ExpandRGBPalette {}
 
std::string m_FileName {}
 
IOFileEnum m_FileType { IOFileEnum::TypeNotApplicable }
 
bool m_Initialized {}
 
ImageIORegion m_IORegion {}
 
bool m_IsReadAsScalarPlusPalette {}
 
int m_MaximumCompressionLevel { 100 }
 
unsigned int m_NumberOfComponents {}
 
unsigned int m_NumberOfDimensions { 0 }
 
std::vector< double > m_Origin {}
 
IOPixelEnum m_PixelType { IOPixelEnum::SCALAR }
 
std::vector< double > m_Spacing {}
 
std::vector< SizeType > m_Strides {}
 
bool m_UseCompression { false }
 
bool m_UseStreamedReading {}
 
bool m_UseStreamedWriting {}
 
bool m_WritePalette {}
 
- Protected Attributes inherited from itk::LightObject
std::atomic< int > m_ReferenceCount {}
 

Member Typedef Documentation

◆ Pointer

using itk::BioRadImageIO::Pointer = SmartPointer<Self>

Definition at line 59 of file itkBioRadImageIO.h.

◆ Self

using itk::BioRadImageIO::Self = BioRadImageIO

Standard class type aliases.

Definition at line 57 of file itkBioRadImageIO.h.

◆ Superclass

using itk::BioRadImageIO::Superclass = ImageIOBase

Definition at line 58 of file itkBioRadImageIO.h.

Constructor & Destructor Documentation

◆ BioRadImageIO()

itk::BioRadImageIO::BioRadImageIO ( )
protected

◆ ~BioRadImageIO()

itk::BioRadImageIO::~BioRadImageIO ( )
overrideprotected

Member Function Documentation

◆ CanReadFile()

bool itk::BioRadImageIO::CanReadFile ( const char *  )
overridevirtual

Determine the file type. Returns true if this ImageIO can read the file specified.

Implements itk::ImageIOBase.

◆ CanWriteFile()

bool itk::BioRadImageIO::CanWriteFile ( const char *  )
overridevirtual

Determine the file type. Returns true if this ImageIO can read the file specified.

Implements itk::ImageIOBase.

◆ GetNameOfClass()

const char* itk::BioRadImageIO::GetNameOfClass ( ) const
overridevirtual
See also
LightObject::GetNameOfClass()

Reimplemented from itk::ImageIOBase.

◆ InternalReadImageInformation()

void itk::BioRadImageIO::InternalReadImageInformation ( std::ifstream &  file)
protected

◆ New()

static Pointer itk::BioRadImageIO::New ( )
static

Method for creation through the object factory.

◆ PrintSelf()

void itk::BioRadImageIO::PrintSelf ( std::ostream &  os,
Indent  indent 
) const
overrideprotectedvirtual

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.

◆ Read()

void itk::BioRadImageIO::Read ( void *  buffer)
overridevirtual

Reads the data from disk into the memory buffer provided.

Implements itk::ImageIOBase.

◆ ReadImageInformation()

void itk::BioRadImageIO::ReadImageInformation ( )
overridevirtual

Set the spacing and dimension information for the current filename.

Implements itk::ImageIOBase.

◆ Write()

void itk::BioRadImageIO::Write ( const void *  buffer)
overridevirtual

Writes the data to disk from the memory buffer provided. Make sure that the IORegion has been set properly.

Implements itk::ImageIOBase.

◆ WriteImageInformation()

void itk::BioRadImageIO::WriteImageInformation ( )
inlineoverridevirtual

Writes the spacing and dimensions of the image. Assumes SetFileName has been called with a valid file name.

Implements itk::ImageIOBase.

Definition at line 92 of file itkBioRadImageIO.h.

The documentation for this class was generated from the following file:
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