MRC file reader. More...

#include <VolumeViz/readers/SoVRMrcFileReader.h>

Inheritance diagram for SoVRMrcFileReader:

Public Member Functions
virtual SoType	getTypeId () const
	Returns the type identifier for this specific instance.

	SoVRMrcFileReader ()
	Constructor.

virtual int	setFilename (const SbString &filename) override
	Specifies the path of the file.

virtual ReadError	getDataChar (SbBox3f &size, SoDataSet::DataType &type, SbVec3i32 &dim) override
	Gets the characteristics (file header) of the data volume.

virtual void	getSubSlice (const SbBox2i32 &subSlice, int sliceNumber, void *data) override
	Must copy the rectangular part defined by subSlice of the XY slice sliceNumber to the memory referenced by data.

virtual void	getSubSlice (const SbBox2i32 &subSlice, int sliceNumber, SoBufferObject *dataBuffer) override
	Same as getSubSlice( const SbBox2i32& subSlice, int sliceNumber, void * data ) but using an SoBufferObject as the target of the data.

virtual SoVolumeReader::ReaderType	getReaderType () override
	Returns the reader type.

virtual SbBool	isThreadSafe () const override
	Return true as this reader is thread safe.

Public Member Functions inherited from SoVolumeReader
	SoVolumeReader ()
	Constructor.

virtual SbBool	setOutputDataType (SbBool doChange, SoDataSet::DataType outputType)
	Sets the output data type.

virtual SbBool	setInputDataRange (SbBool doChange, double min, double max)
	Requests that the input be converted from the specified range to the range depending on the output data type.

virtual int	getNumSignificantBits ()
	This method is optional.

SbVec3i32	getNumVoxels (const SbVec3i32 &realSize, const SbVec3i32 &subsamplingLevel)
	Utility function provided by SoVolumeReader for subclass readers to call.

SbVec3i32	getSizeToAllocate (const SbVec3i32 &realSize, const SbVec3i32 &subsamplingLevel)
	Utility function provided by SoVolumeReader for subclass readers to call.

SbString	getFilename () const
	Returns the path of the file.

virtual SbBool	isDataConverted () const
	Returns TRUE if the data is already organized in tiles for the LDM module.

virtual void	reloadTileMinMax ()

virtual SbBool	getTileSize (SbVec3i32 &size)
	Returns tile dimensions in voxels when using data stored in tiles.

virtual SoBufferObject *	readTile (int index, const SbBox3i32 &tilePosition)
	Given an index, reads a tile if the data is organized in tiles (for LDM).

virtual SbBool	readXTraceInTile (int index, unsigned char *&buffer, const SbBox3i32 &tilePosition, const SbVec2i32 &tracePosition)
	Read directly from the data source, a trace inside a tile.

virtual SbBool	readYSliceInTile (int index, unsigned char *&buffer, const SbBox3i32 &tilePosition, const uint32_t &slicePosition)
	Read directly from the data source, an orthoslice on the Y axis (Zaxis == 1) inside a tile.

virtual SbBool	readZSliceInTile (int index, unsigned char *&buffer, const SbBox3i32 &tilePosition, const uint32_t &slicePosition)
	Read directly from the data source, an orthoslice on the Z axis (Zaxis == 2) inside a tile.

virtual SbBool	readXSliceInTile (int index, unsigned char *&buffer, const SbBox3i32 &tilePosition, const uint32_t &slicePosition)
	Read directly from the data source, an orthoslice on the X axis (Zaxis == 0) inside a tile.

virtual SbBool	isIgnoredFile () const
	Should return TRUE if at least one file has been ignored during reading.

virtual SbString	getOriginalFilename () const
	Returns original file name from which the data has been converted to LDM format if stored in file.

virtual SbBool	getMinMax (int64_t &min, int64_t &max)
	Returns min and max for integer data type, if available.

virtual SbBool	getMinMax (double &min, double &max)
	Returns min max for float data type, if available.

virtual SbBool	getHistogram (std::vector< int64_t > &numVox)
	Returns histogram if available.

virtual SbBool	setDirectCoordSysAutoDetection (SbBool autoValue)
	Sets whether or not the reader should automatically try to detect if the coordinate system used is direct or not.

virtual SbBool	getDirectCoordSysAutoDetection ()
	Return automatic detection value.

virtual SbBool	setDirectCoorSys (SbBool directCoord)
	Specify if the coordinate system used is direct or not.

virtual SbBool	getDirectCoordSys ()
	Return whether the coordinate system used is direct or not.

virtual SbVec2d	getTileMinMax (int index) const
	Returns the minimum and maximum data values for the given tile.

virtual SoVolumeWriter *	getConfiguredWriter ()
	Returns a volume writer that corresponds to this reader (same format, parameters, etc).

CoordinateType	getCoordinateType ()
	Returns coordinate type used by the data set.

const float *	getRectilinearCoordinates (Axis axis) const
	Returns the coordinates for the specified axis.

void	setRectilinearCoordinates (const float x, const float y, const float *z)
	Sets rectilinear coordinates for the data set.

virtual SbBool	isRGBA () const
	Returns TRUE if the data set contains RGBA color values.

void	setRGBA (const SbBool flag)
	Specifies if data must be considered as RGBA.

virtual void	closeAllHandles ()
	Close all resources that are locked by the reader.

virtual void	restoreAllHandles ()
	Restore resources that were closed by closeAllHandles().

virtual SoDEPRECATED SbBool	readTile (int index, unsigned char *&buffer, const SbBox3i32 &tilePosition)
	Given an index, reads a tile if the data is organized in tiles (for LDM).

virtual SoDEPRECATED SbBool	readTile (int index, SoBufferObject *buffer, const SbBox3i32 &tilePosition)
	Same as readTile(int index, unsigned char*& buffer, const SbBox3i32& tilePosition) but using an SoBufferObject (allocated by LDM) as the target of the data.

virtual SoDEPRECATED int	getBorderFlag ()
	Returns border (overlap) value if stored in file.

virtual SoDEPRECATED SbBool	getMinMax (int &min, int &max)
	Returns min max if stored in file.

Public Member Functions inherited from SoFieldContainer
void	setToDefaults ()
	Sets all fields in this object to their default values.

SbBool	hasDefaultValues () const
	Returns TRUE if all of the object's fields have their default values.

SbBool	fieldsAreEqual (const SoFieldContainer *fc) const
	Returns TRUE if this object's fields are exactly equal to fc's fields.

void	copyFieldValues (const SoFieldContainer *fc, SbBool copyConnections=FALSE)
	Copies the contents of fc's fields into this object's fields.

SoNONUNICODE SbBool	set (const char *fieldDataString)
	Sets one or more fields in this object to the values specified in the given string, which should be a string in the Open Inventor file format.

SbBool	set (const SbString &fieldDataString)
	Sets one or more fields in this object to the values specified in the given string, which should be a string in the Open Inventor file format.

void	get (SbString &fieldDataString)
	Returns the values of the fields of this object in the Open Inventor ASCII file format in the given string.

virtual int	getFields (SoFieldList &list) const
	Appends references to all of this object's fields to resultList, and returns the number of fields appended.

virtual int	getAllFields (SoFieldList &list) const
	Returns a list of fields, including the eventIn's and eventOut's.

virtual SoField *	getField (const SbName &fieldName) const
	Returns a the field of this object whose name is fieldName.

virtual SoField *	getEventIn (const SbName &fieldName) const
	Returns a the eventIn with the given name.

virtual SoField *	getEventOut (const SbName &fieldName) const
	Returns the eventOut with the given name.

SbBool	getFieldName (const SoField *field, SbName &fieldName) const
	Returns the name of the given field in the fieldName argument.

SbBool	enableNotify (SbBool flag)
	Notification at this Field Container is enabled (if flag == TRUE) or disabled (if flag == FALSE).

SbBool	isNotifyEnabled () const
	Notification is the process of telling interested objects that this object has changed.

virtual void	setUserData (void *data)
	Sets application data.

void *	getUserData (void) const
	Gets user application data.

Public Member Functions inherited from SoBase
virtual void	touch ()
	Marks an instance as modified, simulating a change to it.

virtual SbName	getName () const
	Returns the name of an instance.

virtual void	setName (const SbName &name)
	Sets the name of an instance.

void	setSynchronizable (const bool b)
	Sets this to be a ScaleViz synchronizable object.

bool	isSynchronizable () const
	Gets the ScaleViz synchronizable state of this object.

Public Member Functions inherited from SoRefCounter
void	ref () const
	Adds a reference to an instance.

void	unref () const
	Removes a reference from an instance.

void	unrefNoDelete () const
	unrefNoDelete() should be called when it is desired to decrement the reference count, but not delete the instance if this brings the reference count to zero.

int	getRefCount () const
	Returns current reference count.

void	lock () const
	lock this instance.

void	unlock () const
	unlock this instance.

Public Member Functions inherited from SoTypedObject
SbBool	isOfType (const SoType &type) const
	Returns TRUE if this object is of the type specified in type or is derived from that type.

template<typename TypedObjectClass >
SbBool	isOfType () const
	Returns TRUE if this object is of the type of class TypedObjectClass or is derived from that class.

Static Public Member Functions
static SoType	getClassTypeId ()
	Returns the type identifier for this class.

Static Public Member Functions inherited from SoVolumeReader
static SoType	getClassTypeId ()
	Returns the type identifier for this class.

static SoVolumeReader *	getAppropriateReader (const SbString &filename)
	Returns a preconfigured SoVolumeReader instance that can be used to load the given file (based on the filename extension).

Static Public Member Functions inherited from SoFieldContainer
static SoType	getClassTypeId ()
	Returns the type of this class.

Static Public Member Functions inherited from SoBase
static SoType	getClassTypeId ()
	Returns type identifier for this class.

Static Public Member Functions inherited from SoTypedObject
static SoType	getClassTypeId ()
	Returns the type identifier for this class.

Additional Inherited Members
Public Types inherited from SoVolumeReader
enum	ReadError { RD_NO_ERROR , RD_FILE_NOT_FOUND_ERROR , RD_INVALID_DATA_ERROR , RD_UNSUPPORTED_DATA_TYPE_ERROR , RD_FILE_FORMAT_NOT_VALID_ERROR , RD_UNKNOWN_ERROR }
	Read error. More...

enum	Axis { X , Y , Z }
	Which axis to handle. More...

enum	ReaderType { NO_READER , AM , AVS , DICOM , GENERIC , LDM , MEMORY , RASTERSTACK , SEGY , VOL , VOX , TIFF , MRC }
	Available reader type. More...

enum	CoordinateType { COORDINATES_UNIFORM = 0 , COORDINATES_RECTILINEAR }
	Coordinate type used by this data set. More...

Protected Member Functions inherited from SoVolumeReader
virtual	~SoVolumeReader ()
	Destructor.

void *	getBuffer (int64_t offset, unsigned int size)
	Returns a pointer to a buffer of size bytes corresponding to a part of the file at offset bytes from the beginning of the file.

int64_t	fileSize ()
	Returns the size of the file when file I/O is handled by this class.

Static Protected Member Functions inherited from SoVolumeReader
static bool	registerVolumeReaderExtension (const SbString &fileExtension, const SoType &readerType)
	Register an SoVolumeReader class to handle a file extension.

static bool	unregisterVolumeReaderExtensions (const SoType &readerType)
	Unregister all filename extensions associated with the specified SoVolumeReader class.

static int	bytesToInt (const unsigned char *ptr, int sizeBytes)
	Utility method that returns an integer from sizeBytes bytes starting at address ptr.

static void	swapBytes (int *intPtr, int sizeBytes)
	Utility method to convert an integer into the correct architecture (little/big endian).

static void	swapBytesN (void *buffer, int numElements, int numBytesPerElement)
	Utility method to swap bytes of each element of an array of numElements elements.

static SbBool	isValidFloat (const float val)
	Utility method to check if value is a valid IEEE 754 floating point number.

static SbBox3f	adjustFlatExtent (const SbString &fileName, const SbBox3f &extent, const SbVec3i32 &dim)
	VolumeViz doesn't handles empty extent (for ex.

Protected Attributes inherited from SoVolumeReader
SoDEPRECATED SbBool	m_dataConverted

Detailed Description

MRC file reader.

Volume reader for the MRC file format.

MRC is a file format that has become industry standard in cryo-electron microscopy (cryoEM) and electron tomography (ET), where the result of the technique is a three-dimensional grid of voxels each with a value corresponding to electron density or electric potential. It was developed by the MRC (Medical Research Council, UK) Laboratory of Molecular Biology. In 2014, the format was standardised. The format specification is available on the CCP-EM website. For details see: http://www.ccpem.ac.uk/mrc_format/mrc2014.php

SoVolumeData automatically selects this reader if a filename is given and the file extension is ".mrc". The application can also explicitly create an instance of this reader and call the SoVolumeData method setReader().

SoVRMrcFileReader loads slices from a single multi-image MRC file. To load a volume from multiple MRC files, see the SoVRRasterStackReader class.

All the images contained in the file should have the same size. If it is not the case, the reader will find the largest image and take all images with the same size.

Supported:

Color index volume, or
RGBA volume with unsigned byte components (not RGBA).

For more information about volume readers see SoVolumeReader.

NOTE: Class available since Open Inventor 10.4.

Constructor & Destructor Documentation

◆ SoVRMrcFileReader()

SoVRMrcFileReader::SoVRMrcFileReader ( )

Constructor.

Member Function Documentation

◆ getClassTypeId()

static SoType SoVRMrcFileReader::getClassTypeId ( )

static

Returns the type identifier for this class.

◆ getDataChar()

virtual ReadError SoVRMrcFileReader::getDataChar	(	SbBox3f &	size,
		SoDataSet::DataType &	type,
		SbVec3i32 &	dim
	)

overridevirtual

Gets the characteristics (file header) of the data volume.

See SoDataSet::setVolumeData().
You can use the convenience method setFilename() to specify the file location, in which case you will not have to open the file yourself. Then you can use the convenience method getBuffer() to read the header in order to get the requested information.

NOTE: We strongly recommend that readers implement this version of getDataChar, introduced in VolumeViz 5.1, because it uses SbVec3i32 for the volume dimension.

Implements SoVolumeReader.

◆ getReaderType()

virtual SoVolumeReader::ReaderType SoVRMrcFileReader::getReaderType ( )

inlineoverridevirtual

Returns the reader type.

Reimplemented from SoVolumeReader.

Definition at line 102 of file SoVRMrcFileReader.h.

◆ getSubSlice() [1/2]

virtual void SoVRMrcFileReader::getSubSlice	(	const SbBox2i32 &	subSlice,
		int	sliceNumber,
		SoBufferObject *	dataBuffer
	)

overridevirtual

Same as getSubSlice( const SbBox2i32& subSlice, int sliceNumber, void * data ) but using an SoBufferObject as the target of the data.

If not reimplemented then the version with "unsigned char*" parameter is called

Parameters

subSlice	2D region of the slice to return.
sliceNumber	Slice number on the volume Z axis (first slice is 0).
dataBuffer	The target buffer to be filled.

Reimplemented from SoVolumeReader.

◆ getSubSlice() [2/2]

virtual void SoVRMrcFileReader::getSubSlice	(	const SbBox2i32 &	subSlice,
		int	sliceNumber,
		void *	data
	)

overridevirtual

Must copy the rectangular part defined by subSlice of the XY slice sliceNumber to the memory referenced by data.

Slices will not always be read sequentially.

Parameters

subSlice	2D region of the slice to return.
sliceNumber	Slice number on the volume Z axis (first slice is 0).
data	Copy the data into this buffer.

You can use the convenience method getBuffer() to read data from file. Note: setFilename() must have been called previously.

Reimplemented from SoVolumeReader.

◆ getTypeId()

virtual SoType SoVRMrcFileReader::getTypeId ( ) const

virtual

Returns the type identifier for this specific instance.

Reimplemented from SoVolumeReader.

◆ isThreadSafe()

virtual SbBool SoVRMrcFileReader::isThreadSafe ( ) const

overridevirtual

Return true as this reader is thread safe.

Reimplemented from SoVolumeReader.

◆ setFilename()

virtual int SoVRMrcFileReader::setFilename ( const SbString & filename )

overridevirtual

Specifies the path of the file.

Returns 0 for success. Any other return value indicates failure.

Reimplemented from SoVolumeReader.

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

VolumeViz/readers/SoVRMrcFileReader.h

Open Inventor Release 2023.2.3

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

SEE ALSO

Constructor & Destructor Documentation

◆ SoVRMrcFileReader()

Member Function Documentation

◆ getClassTypeId()

◆ getDataChar()

◆ getReaderType()

◆ getSubSlice() [1/2]

◆ getSubSlice() [2/2]

◆ getTypeId()

◆ isThreadSafe()

◆ setFilename()