Raster stack reader. More...

#include <VolumeViz/readers/SoVRRasterStackReader.h>

Inheritance diagram for SoVRRasterStackReader:

Public Types
enum	ChannelSelection { MAX_CHANNEL = 0 , LUMINANCE = 1 , RED_CHANNEL = 2 , GREEN_CHANNEL = 3 , BLUE_CHANNEL = 4 , ALPHA_CHANNEL = 5 , ALL_CHANNELS = 11 }
	Channel selection. More...

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...

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

	SoVRRasterStackReader ()
	Constructor.

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

SbBool	setFilenameList (const SbStringList &filenameList)
	Specify a list of files to load.

SbBool	setDirectory (const SbString &directory)
	Specify a directory containing image files to load (jpg, png, tif,...).

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

void	setSize (SbBox3f &size)
	Defines the bounding box size in physical units of the data set.

void	setChannelSelection (ChannelSelection cs)
	Selects channels to be used for data rendering.

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

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

virtual SbBool	isThreadSafe () const
	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.

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

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.

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
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

Raster stack reader.

Reader for a volume defined by a "stack" of images.

A raster stack is a list of raster images (that is, containing pixels, not vector graphics) of the same size so as to create a voxel volume. This reader uses a descriptive file (.lst) including a header and a list of all the raster image filenames. The file is structured as follows:

 Parameters {
   Raw 0
   Dims 2048 2048 100
   Size 10.000000 10.000000 10.000000 1250.000000 1250.000000 500.000000
   Channel 2
 }

 C:/tmp/tiff/img00000.tiff
 C:/tmp/tiff/img00001.tiff
 C:/tmp/tiff/img00002.tiff
 C:/tmp/tiff/img00003.tiff
 C:/tmp/tiff/img00004.tiff
 ....

OR

 Parameters {
   Raw 1
   Endianess 1
   HeaderLength 256
   PrimType 0
   Binary 0
   Dims 1024 1024 300
   Size 50.000000 50.000000 50.000000 1050.000000 1050.000000 250.000000
   Channel 1
 }

 img00000.raw
 img00001.raw
 img00002.raw
 img00003.raw
 img00004.raw
 ....

Header Description

Raw: 0 (formatted data file), 1 (raw data file).
Endianess: 0 (little endian), 1 (big endian) (for raw data only).
HeaderLength: length of header in characters/bytes (for raw data only).
PrimType: See SoDataSet::DataType (for raw data only).
Binary: 0 (ASCII), 1 (binary) (for raw data only).
Dims: height, width, depth in pixels of the stack.
Size: Xmin Ymin Zmin Xmax Ymax Zmax, bounding box of the data set.
Channel: See SoVRRasterStackReader::ChannelSelection.

Images in the list can be of different formats (uses all files formats supported by Open Inventor). VolumeViz can load image data in most common image formats including BMP, DDS, GIF, JPEG, JPEG2000, PNG and TIFF.

If images are different sizes, RD_UNSUPPORTED_DATA_TYPE_ERROR is returned by getDataChar.

The file path can be relative or absolute.

It is mandatory to have a line break after each property and/or filename otherwise VolumeViz could be unable to read the file properly.

Definition at line 114 of file SoVRRasterStackReader.h.

Member Enumeration Documentation

◆ ChannelSelection

enum SoVRRasterStackReader::ChannelSelection

Channel selection.

Enumerator
MAX_CHANNEL	Maximum of all channels.
LUMINANCE	Luminance.
RED_CHANNEL	Red channel.
GREEN_CHANNEL	Green channel.
BLUE_CHANNEL	Blue channel.
ALPHA_CHANNEL	Alpha channel.
ALL_CHANNELS	All channels combined.

Definition at line 121 of file SoVRRasterStackReader.h.

Constructor & Destructor Documentation

◆ SoVRRasterStackReader()

SoVRRasterStackReader::SoVRRasterStackReader ( )

Constructor.

Member Function Documentation

◆ getClassTypeId()

static SoType SoVRRasterStackReader::getClassTypeId ( )

static

Returns the type identifier for this class.

◆ getDataChar()

virtual ReadError SoVRRasterStackReader::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 SoVRRasterStackReader::getReaderType ( )

inlinevirtual

Returns the reader type.

Reimplemented from SoVolumeReader.

Definition at line 211 of file SoVRRasterStackReader.h.

◆ getSubSlice()

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

virtual

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 SoVRRasterStackReader::getTypeId ( ) const

virtual

Returns the type identifier for this specific instance.

Reimplemented from SoVolumeReader.

◆ isRGBA()

virtual SbBool SoVRRasterStackReader::isRGBA ( ) const

virtual

Returns TRUE if the data set contains RGBA color values.

Reimplemented from SoVolumeReader.

◆ isThreadSafe()

virtual SbBool SoVRRasterStackReader::isThreadSafe ( ) const

virtual

Return true as this reader is thread safe.

Reimplemented from SoVolumeReader.

◆ setChannelSelection()

void SoVRRasterStackReader::setChannelSelection ( ChannelSelection cs )

inline

Selects channels to be used for data rendering.

Definition at line 206 of file SoVRRasterStackReader.h.

◆ setDirectory()

SbBool SoVRRasterStackReader::setDirectory ( const SbString & directory )

Specify a directory containing image files to load (jpg, png, tif,...).

Each image file in this folder with the exact same dimension and the exact same number of components will be loaded.

Notes:

The directory should contain only valid image files.
The file format is automatically detected.
If the images are RGB or RGBA, the volume is loaded as RGBA data. (It is not possible to load a single component using this method.)

Parameters

directory The directory from which to load files.

Returns: true if successful.

Since Open Inventor 9.5.0

◆ setFilename()

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

virtual

Specifies the path of the descriptive (.lst) file.

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

Reimplemented from SoVolumeReader.

◆ setFilenameList()

SbBool SoVRRasterStackReader::setFilenameList ( const SbStringList & filenameList )

Specify a list of files to load.

All the specified files should be part of the same volume data set.

Returns: true if successful.

Since Open Inventor 9.7

◆ setSize()

void SoVRRasterStackReader::setSize ( SbBox3f & size )

inline

Defines the bounding box size in physical units of the data set.

Definition at line 201 of file SoVRRasterStackReader.h.

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

VolumeViz/readers/SoVRRasterStackReader.h

Open Inventor Release 2023.2.3

Public Types

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ ChannelSelection

Constructor & Destructor Documentation

◆ SoVRRasterStackReader()

Member Function Documentation

◆ getClassTypeId()

◆ getDataChar()

◆ getReaderType()

◆ getSubSlice()

◆ getTypeId()

◆ isRGBA()

◆ isThreadSafe()

◆ setChannelSelection()

◆ setDirectory()

◆ setFilename()

◆ setFilenameList()

◆ setSize()