IO Handler for Isis Cubes using the BSQ format. More...

#include <CubeBsqHandler.h>

Inheritance diagram for Isis::CubeBsqHandler:

Collaboration diagram for Isis::CubeBsqHandler:

Public Member Functions
	CubeBsqHandler (QFile dataFile, const QList< int > virtualBandList, const Pvl &label, bool alreadyOnDisk)
	Construct a BSQ IO handler. More...

	~CubeBsqHandler ()
	The destructor writes all cached data to disk. More...

void	updateLabels (Pvl &labels)
	Function to update the labels with a Pvl object. More...

void	read (Buffer &bufferToFill) const
	Read cube data from disk into the buffer. More...

void	write (const Buffer &bufferToWrite)
	Write buffer data into the cube data on disk. More...

void	addCachingAlgorithm (CubeCachingAlgorithm *algorithm)
	This will add the given caching algorithm to the list of attempted caching algorithms. More...

void	clearCache (bool blockForWriteCache=true) const
	Free all cube chunks (cached cube data) from memory and write them to disk. More...

BigInt	getDataSize () const

void	setVirtualBands (const QList< int > *virtualBandList)
	This changes the virtual band list. More...

QMutex *	dataFileMutex ()
	Get the mutex that this IO handler is using around I/Os on the given data file. More...

Protected Member Functions
virtual void	readRaw (RawCubeChunk &chunkToFill)
	This needs to populate the chunkToFill with unswapped raw bytes from the disk. More...

virtual void	writeRaw (const RawCubeChunk &chunkToWrite)
	This needs to write the chunkToWrite directly to disk with no modifications to the data itself. More...

int	bandCount () const

int	getBandCountInChunk () const

BigInt	getBytesPerChunk () const

int	getChunkCountInBandDimension () const

int	getChunkCountInLineDimension () const

int	getChunkCountInSampleDimension () const

int	getChunkIndex (const RawCubeChunk &) const
	Given a chunk, what's its index in the file. More...

BigInt	getDataStartByte () const

QFile *	getDataFile ()

int	lineCount () const

int	getLineCountInChunk () const

PixelType	pixelType () const

int	sampleCount () const

int	getSampleCountInChunk () const

void	setChunkSizes (int numSamples, int numLines, int numBands)
	This should be called once from the child constructor. More...

Private Member Functions
	CubeBsqHandler (const CubeBsqHandler &other)
	Disallow copying of this object. More...

CubeBsqHandler &	operator= (const CubeBsqHandler &other)
	Disallow assignments of this object. More...

int	findGoodSize (int maxSize, int dimensionSize) const
	This method attempts to compute a good chunk line size. More...

BigInt	getChunkStartByte (const RawCubeChunk &chunk) const
	This is a helper method that goes from chunk to file position. More...

Detailed Description

IO Handler for Isis Cubes using the BSQ format.

This class is used to open, create, read, and write data from Isis cube files.

Author: 2003-02-14 Jeff Anderson

History:

2007-09-14 Stuart Sides - Fixed bug where pixels from a buffer outside the ns/nl were being transfered to the right most and bottom most tiles

2007-10-11 Stuart Sides - Fixed bug introduced with previous bug fix.

2008-09-03 Steven Lambright - Fixed MSB/LSB problem with the Move() method

2011-06-16 Jai Rideout and Steven Lambright - Refactored to work with the new parent.

2011-07-18 Jai Rideout and Steven Lambright - Added unimplemented copy constructor and assignment operator.

2014-09-16 Ian Humphrey - Increased size limit for determining chunk sizes. Added findGoodSize method to better calculate number of lines in chunks for bsq cubes. References #1689.

2017-09-22 Cole Neubauer - Fixed documentation. References #4807

Definition at line 57 of file CubeBsqHandler.h.

Constructor & Destructor Documentation

◆ CubeBsqHandler() [1/2]

Isis::CubeBsqHandler::CubeBsqHandler	(	QFile *	dataFile,
		const QList< int > *	virtualBandList,
		const Pvl &	labels,
		bool	alreadyOnDisk
	)

Construct a BSQ IO handler.

This will determine a good chunk size to use that does not result in the cube being enlarged or misordered.

Parameters

dataFile	The file with cube DN data in it
virtualBandList	The mapping from virtual band to physical band, see CubeIoHandler's description.
labels	The Pvl labels for the cube
alreadyOnDisk	True if the cube is allocated on the disk, false otherwise

Definition at line 50 of file CubeBsqHandler.cpp.

References findGoodSize(), Isis::CubeIoHandler::lineCount(), Isis::CubeIoHandler::pixelType(), Isis::CubeIoHandler::sampleCount(), Isis::CubeIoHandler::setChunkSizes(), and Isis::SizeOf().

◆ ~CubeBsqHandler()

Isis::CubeBsqHandler::~CubeBsqHandler ( )

The destructor writes all cached data to disk.

Definition at line 74 of file CubeBsqHandler.cpp.

References Isis::CubeIoHandler::clearCache().

◆ CubeBsqHandler() [2/2]

Isis::CubeBsqHandler::CubeBsqHandler ( const CubeBsqHandler & other )

private

Disallow copying of this object.

Parameters

other The object to copy.

Member Function Documentation

◆ addCachingAlgorithm()

void Isis::CubeIoHandler::addCachingAlgorithm ( CubeCachingAlgorithm * algorithm )

inherited

This will add the given caching algorithm to the list of attempted caching algorithms.

The algorithms are tried in the opposite order that they were added - the first algorithm added is the last algorithm tried.

This method takes ownership of algorithm.

Parameters

algorithm The caching algorithm to add to the Cube for I/O

Definition at line 384 of file CubeIoHandler.cpp.

◆ bandCount()

int Isis::CubeIoHandler::bandCount ( ) const

protectedinherited

Returns: the number of physical bands in the cube.

Definition at line 482 of file CubeIoHandler.cpp.

◆ clearCache()

void Isis::CubeIoHandler::clearCache ( bool blockForWriteCache = true ) const

inherited

Free all cube chunks (cached cube data) from memory and write them to disk.

Child destructors need to call this method.

This method should only be called otherwise when lots of cubes are in memory and the many caches cause problems with system RAM limitations.

Parameters

blockForWriteCache This should be true unless this method is called from the write thread.

Definition at line 399 of file CubeIoHandler.cpp.

Referenced by ~CubeBsqHandler(), and Isis::CubeTileHandler::~CubeTileHandler().

◆ dataFileMutex()

QMutex * Isis::CubeIoHandler::dataFileMutex ( )

inherited

Get the mutex that this IO handler is using around I/Os on the given data file.

A lock should be acquired before doing any reads/writes on the data file externally.

Returns: A mutex that can guarantee exclusive access to the data file

Definition at line 475 of file CubeIoHandler.cpp.

◆ findGoodSize()

int Isis::CubeBsqHandler::findGoodSize	(	int	maxSize,
		int	dimensionSize
	)		const

private

This method attempts to compute a good chunk line size.

Chunk band size is always 1 and chunk sample size is always number of samples in the cube for this format.

Parameters

maxSize	The largest allowed size of a chunk dimension
dimensionSize	The cube's size for the chunk size we are trying to calculate (number of lines)

Returns: The calculated chunk size for the dimension given

Definition at line 149 of file CubeBsqHandler.cpp.

Referenced by CubeBsqHandler().

◆ getBandCountInChunk()

int Isis::CubeIoHandler::getBandCountInChunk ( ) const

protectedinherited

Returns: the number of bands per chunk for this cube.

Definition at line 490 of file CubeIoHandler.cpp.

◆ getBytesPerChunk()

BigInt Isis::CubeIoHandler::getBytesPerChunk ( ) const

protectedinherited

Returns: the byte size of each chunk in the cube. Currently they must be constant size, but this is planned to be changed at some point in time.; Number of bytes in a cube chunk

Definition at line 502 of file CubeIoHandler.cpp.

References Isis::SizeOf().

Referenced by getChunkStartByte(), and Isis::CubeTileHandler::getTileStartByte().

◆ getChunkCountInBandDimension()

int Isis::CubeIoHandler::getChunkCountInBandDimension ( ) const

protectedinherited

Returns: the total number of chunks in the band (Z) dimension. This is always enough to contain every band in the cube.

Definition at line 512 of file CubeIoHandler.cpp.

◆ getChunkCountInLineDimension()

int Isis::CubeIoHandler::getChunkCountInLineDimension ( ) const

protectedinherited

Returns: the total number of chunks in the line (Y) dimension. This is always enough to contain every line in the cube.

Definition at line 521 of file CubeIoHandler.cpp.

◆ getChunkCountInSampleDimension()

int Isis::CubeIoHandler::getChunkCountInSampleDimension ( ) const

protectedinherited

Returns: the total number of chunks in the sample (X) dimension. This is always enough to contain every sample in the cube.

Definition at line 530 of file CubeIoHandler.cpp.

◆ getChunkIndex()

int Isis::CubeIoHandler::getChunkIndex ( const RawCubeChunk & chunk ) const

protectedinherited

Given a chunk, what's its index in the file.

Chunks are ordered from left to right, then top to bottom, then front to back (BSQ). The first chunk is at the top left of band 1 and is index 0, for example. In other words, this is going from the value of m_rawData to the key.

Chunks which sit outside of the cube entirely must not be passed into this method; the results will be wrong.

Returns: The chunk's index into the file

Definition at line 546 of file CubeIoHandler.cpp.

References Isis::RawCubeChunk::getStartBand(), Isis::RawCubeChunk::getStartLine(), and Isis::RawCubeChunk::getStartSample().

Referenced by getChunkStartByte(), and Isis::CubeTileHandler::getTileStartByte().

◆ getChunkStartByte()

BigInt Isis::CubeBsqHandler::getChunkStartByte ( const RawCubeChunk & chunk ) const

private

This is a helper method that goes from chunk to file position.

Parameters

chunk The chunk to locate in the file.

Returns: The file position to start reading or writing at

Definition at line 173 of file CubeBsqHandler.cpp.

References Isis::CubeIoHandler::getBytesPerChunk(), Isis::CubeIoHandler::getChunkIndex(), and Isis::CubeIoHandler::getDataStartByte().

Referenced by readRaw(), and writeRaw().

◆ getDataFile()

QFile * Isis::CubeIoHandler::getDataFile ( )

protectedinherited

Returns: the QFile containing cube data. This is what should be read from and written to.; The data file for I/O

Definition at line 578 of file CubeIoHandler.cpp.

Referenced by Isis::CubeTileHandler::readRaw(), readRaw(), Isis::CubeTileHandler::writeRaw(), and writeRaw().

◆ getDataSize()

BigInt Isis::CubeIoHandler::getDataSize ( ) const

inherited

Returns: the number of bytes that the cube DNs will take up. This includes padding caused by the cube chunks not aligning with the cube dimensions.

Definition at line 441 of file CubeIoHandler.cpp.

◆ getDataStartByte()

BigInt Isis::CubeIoHandler::getDataStartByte ( ) const

protectedinherited

Returns: the byte offset to the beginning of the cube data.

Definition at line 567 of file CubeIoHandler.cpp.

Referenced by getChunkStartByte(), and Isis::CubeTileHandler::getTileStartByte().

◆ getLineCountInChunk()

int Isis::CubeIoHandler::getLineCountInChunk ( ) const

protectedinherited

Returns: the number of lines in each chunk of the cube.

Definition at line 595 of file CubeIoHandler.cpp.

Referenced by Isis::CubeTileHandler::updateLabels().

◆ getSampleCountInChunk()

int Isis::CubeIoHandler::getSampleCountInChunk ( ) const

protectedinherited

Returns: the number of samples in each chunk of the cube.

Definition at line 620 of file CubeIoHandler.cpp.

Referenced by Isis::CubeTileHandler::updateLabels().

◆ lineCount()

int Isis::CubeIoHandler::lineCount ( ) const

protectedinherited

Returns: the number of lines in the cube. This does not include lines created by the chunk overflowing the line dimension.

Definition at line 587 of file CubeIoHandler.cpp.

Referenced by CubeBsqHandler(), and Isis::CubeTileHandler::CubeTileHandler().

◆ operator=()

CubeBsqHandler& Isis::CubeBsqHandler::operator= ( const CubeBsqHandler & other )

private

Disallow assignments of this object.

Parameters

other The CubeBsqHandler on the right-hand side of the assignment that we are copying into *this.

Returns: A reference to *this.

◆ pixelType()

PixelType Isis::CubeIoHandler::pixelType ( ) const

protectedinherited

Returns: the physical cube DN format.

Definition at line 603 of file CubeIoHandler.cpp.

Referenced by CubeBsqHandler(), and Isis::CubeTileHandler::CubeTileHandler().

◆ read()

void Isis::CubeIoHandler::read ( Buffer & bufferToFill ) const

inherited

Read cube data from disk into the buffer.

This is not const because it caches the read cube chunks from the disk.

Parameters

bufferToFill The buffer to populate with cube data.

Definition at line 246 of file CubeIoHandler.cpp.

References Isis::Buffer::Band(), Isis::Buffer::BandDimension(), Isis::Buffer::Line(), Isis::Buffer::LineDimension(), Isis::Null, Isis::Buffer::Sample(), Isis::Buffer::SampleDimension(), and Isis::Buffer::size().

◆ readRaw()

void Isis::CubeBsqHandler::readRaw ( RawCubeChunk & chunkToFill )

protectedvirtual

This needs to populate the chunkToFill with unswapped raw bytes from the disk.

See also: CubeTileHandler::readRaw()

Parameters

chunkToFill The container that needs to be filled with cube data.

Implements Isis::CubeIoHandler.

Definition at line 91 of file CubeBsqHandler.cpp.

References _FILEINFO_, Isis::RawCubeChunk::getByteCount(), getChunkStartByte(), Isis::CubeIoHandler::getDataFile(), Isis::IException::Io, and Isis::RawCubeChunk::setRawData().

◆ sampleCount()

int Isis::CubeIoHandler::sampleCount ( ) const

protectedinherited

Returns: the number of samples in the cube. This does not include samples created by the chunk overflowing the sample dimension.

Definition at line 612 of file CubeIoHandler.cpp.

Referenced by CubeBsqHandler(), and Isis::CubeTileHandler::CubeTileHandler().

◆ setChunkSizes()

void Isis::CubeIoHandler::setChunkSizes	(	int	numSamples,
		int	numLines,
		int	numBands
	)

protectedinherited

This should be called once from the child constructor.

This determines the chunk sizes used for the cube and often should remain constant for a particular cube (BSQ, for example, doesn't need it to be constant but Tile does). These being large can cause excessive use of disk space that stores no cube data. These being large can also drastically increase the amount of RAM consumed.

Parameters

numSamples	The chunk size in the sample dimension
numLines	The chunk size in the line dimension
numBands	The chunk size in the band dimension

Definition at line 637 of file CubeIoHandler.cpp.

References _FILEINFO_.

Referenced by CubeBsqHandler(), and Isis::CubeTileHandler::CubeTileHandler().

◆ setVirtualBands()

void Isis::CubeIoHandler::setVirtualBands ( const QList< int > * virtualBandList )

inherited

This changes the virtual band list.

Parameters

virtualBandList A list where the indices are the vbands and the values are the physical bands. The values are 1-based. This can be specified as NULL, in which case the vbands are the physical bands. The virtual band list is copied (the pointer provided isn't remembered).

Definition at line 458 of file CubeIoHandler.cpp.

◆ updateLabels()

void Isis::CubeBsqHandler::updateLabels ( Pvl & label )

virtual

Function to update the labels with a Pvl object.

Parameters

label Pvl object to update with

Implements Isis::CubeIoHandler.

Definition at line 84 of file CubeBsqHandler.cpp.

References Isis::PvlContainer::addKeyword(), and Isis::PvlObject::findObject().

◆ write()

void Isis::CubeIoHandler::write ( const Buffer & bufferToWrite )

inherited

Write buffer data into the cube data on disk.

This could do no IO if the cube chunks required are already in memory and our caching algorithms say to not free any of the cube chunks afterwards.

Parameters

bufferToWrite The buffer to get cube data from.

Definition at line 354 of file CubeIoHandler.cpp.

◆ writeRaw()

void Isis::CubeBsqHandler::writeRaw ( const RawCubeChunk & chunkToWrite )

protectedvirtual

This needs to write the chunkToWrite directly to disk with no modifications to the data itself.

See also: CubeTileHandler::writeRaw()

Parameters

chunkToWrite The container that needs to be put on disk.

Implements Isis::CubeIoHandler.

Definition at line 116 of file CubeBsqHandler.cpp.

References _FILEINFO_, Isis::RawCubeChunk::getByteCount(), getChunkStartByte(), Isis::CubeIoHandler::getDataFile(), Isis::RawCubeChunk::getRawData(), and Isis::IException::Io.

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

src/base/objs/Cube/CubeBsqHandler.h
src/base/objs/Cube/CubeBsqHandler.cpp

Public Member Functions

Protected Member Functions

Private Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ CubeBsqHandler() [1/2]

◆ ~CubeBsqHandler()

◆ CubeBsqHandler() [2/2]

Member Function Documentation

◆ addCachingAlgorithm()

◆ bandCount()

◆ clearCache()

◆ dataFileMutex()

◆ findGoodSize()

◆ getBandCountInChunk()

◆ getBytesPerChunk()

◆ getChunkCountInBandDimension()

◆ getChunkCountInLineDimension()

◆ getChunkCountInSampleDimension()

◆ getChunkIndex()

◆ getChunkStartByte()

◆ getDataFile()

◆ getDataSize()

◆ getDataStartByte()

◆ getLineCountInChunk()

◆ getSampleCountInChunk()

◆ lineCount()

◆ operator=()

◆ pixelType()

◆ read()

◆ readRaw()

◆ sampleCount()

◆ setChunkSizes()

◆ setVirtualBands()

◆ updateLabels()

◆ write()

◆ writeRaw()