Handles converting buffers to and from disk. More...

#include <CubeIoHandler.h>

Inheritance diagram for Isis::CubeIoHandler:

Collaboration diagram for Isis::CubeIoHandler:

Classes
class	BufferToChunkWriter
	This class is designed to handle write() asynchronously. More...

Public Member Functions
	CubeIoHandler (QFile dataFile, const QList< int > virtualBandList, const Pvl &label, bool alreadyOnDisk)
	Creates a new CubeIoHandler using a RegionalCachingAlgorithm.

virtual	~CubeIoHandler ()
	Cleans up all allocated memory.

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

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

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

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

BigInt	getDataSize () const

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

virtual void	updateLabels (Pvl &labels)=0
	Function to update the labels with a Pvl object.

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

Protected Member Functions
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.

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.

virtual void	readRaw (RawCubeChunk &chunkToFill)=0
	This needs to populate the chunkToFill with unswapped raw bytes from the disk.

virtual void	writeRaw (const RawCubeChunk &chunkToWrite)=0
	This needs to write the chunkToWrite directly to disk with no modifications to the data itself.

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

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

void	blockUntilThreadPoolEmpty () const
	This blocks (doesn't return) until the number of active runnables in the thread pool goes to 0.

QPair< QList< RawCubeChunk * >, QList< int > >	findCubeChunks (int startSample, int numSamples, int startLine, int numLines, int startBand, int numBands) const
	Get the cube chunks that correspond to the given cube area.

void	findIntersection (const RawCubeChunk &cube1, const Buffer &cube2, int &startX, int &startY, int &startZ, int &endX, int &endY, int &endZ) const
	Find the intersection between the buffer area and the cube chunk.

void	flushWriteCache (bool force=false) const
	This attempts to write the so-far-unwritten buffers from m_writeCache into the cube's RawCubeChunk cache.

void	freeChunk (RawCubeChunk *chunkToFree) const
	If the chunk is dirty, then we write it to disk.

RawCubeChunk *	getChunk (int chunkIndex, bool allocateIfNecessary) const
	Retrieve the cached chunk at the given chunk index, if there is one.

int	getChunkCount () const

void	getChunkPlacement (int chunkIndex, int &startSample, int &startLine, int &startBand, int &endSample, int &endLine, int &endBand) const
	Get the X/Y/Z (Sample,Line,Band) range of the chunk at the given index.

RawCubeChunk *	getNullChunk (int chunkIndex) const
	This creates a chunk filled with NULLs whose placement is at chunkIndex's position.

void	minimizeCache (const QList< RawCubeChunk * > &justUsed, const Buffer &justRequested) const
	Apply the caching algorithms and get rid of excess cube data in memory.

void	synchronousWrite (const Buffer &bufferToWrite)
	This method takes the given buffer and synchronously puts it into the Cube's cache.

void	writeIntoDouble (const RawCubeChunk &chunk, Buffer &output, int startIndex) const
	Write the intersecting area of the chunk into the buffer.

void	writeIntoRaw (const Buffer &buffer, RawCubeChunk &output, int index) const
	Write the intersecting area of the buffer into the chunk.

void	writeNullDataToDisk () const
	Write all NULL cube chunks that have not yet been accessed to disk.

Static Private Member Functions
static bool	bufferLessThan (Buffer const &lhs, Buffer const &rhs)
	This is used for sorting buffers into the most efficient write order.

Private Attributes
QFile *	m_dataFile
	The file containing cube data.

BigInt	m_startByte
	The start byte of the cube data.

PixelType	m_pixelType
	The format of each DN in the cube.

double	m_base
	The additive offset of the data on disk.

double	m_multiplier
	The multiplicative factor of the data on disk.

ByteOrder	m_byteOrder
	The byte order (endianness) of the data on disk.

EndianSwapper *	m_byteSwapper
	A helper that swaps byte order to and from file order.

int	m_numSamples
	The number of samples in the cube.

int	m_numLines
	The number of lines in the cube.

int	m_numBands
	The number of physical bands in the cube.

QList< CubeCachingAlgorithm * > *	m_cachingAlgorithms
	The caching algorithms to use, in order of priority.

QMap< int, RawCubeChunk * > *	m_rawData
	The map from chunk index to chunk for cached data.

QMap< int, bool > *	m_dataIsOnDiskMap
	The map from chunk index to on-disk status, all true if not allocated.

QList< int > *	m_virtualBands
	Converts from virtual band to physical band.

int	m_samplesInChunk
	The number of samples in a cube chunk.

int	m_linesInChunk
	The number of lines in a cube chunk.

int	m_bandsInChunk
	The number of physical bands in a cube chunk.

QList< RawCubeChunk * > *	m_lastProcessByLineChunks
	This is an optimization for process by line.

QByteArray *	m_nullChunkData
	A raw cube chunk's data when it was all NULL's. Used for speed.

QPair< QMutex , QList< Buffer > > *	m_writeCache
	These are the buffers we need to write to raw cube chunks.

QThreadPool *	m_ioThreadPool
	This contains threads for doing cube writes (and later maybe cube reads).

bool	m_lastOperationWasWrite
	If the last operation was a write then we need to flush the cache when reading.

bool	m_useOptimizedCubeWrite
	This is true if the Isis preference for the cube write thread is optimized.

QMutex *	m_writeThreadMutex
	This enables us to block while the write thread is working.

volatile int	m_idealFlushSize
	Ideal write cache flush size.

int	m_consecutiveOverflowCount
	How many times the write cache has overflown in a row.

Detailed Description

Handles converting buffers to and from disk.

This class handles converting buffers to and from disk. This class holds the cube chunks in memory and is capable of reading and writing them. It asks the caching algorithms to recommend cube chunks to not keep in memory. Children need to call setChunkSizes() in their constructor.

This class handles all of the virtual band conversions. This class also guarantees that unwritten cube data ends up read and written as NULLs. The default caching algorithm is a RegionalCachingAlgorithm.

Author: 2011-??-?? Jai Rideout and Steven Lambright

History

2011-06-27 Steven Lambright - Added addCachingAlgorithm()

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

2011-07-18 Jai Rideout and Steven Lambright - getDataFile() is no longer const, along with readRaw() and writeRaw().

2011-11-23 Jai Rideout - Added fix to findCubeChunks() and findIntersection() so that requested areas that are outside of the virtual bands of the cube will no longer fail, but instead will fill the buffer with nulls.

2012-02-17 Steven Lambright - The read() method is now const - the caching should be transparent to the API. It is still important to note that you cannot call read() and write() simultaneously - Cube is guaranteeing this. Backgrounded writes are now implemented and fully supported. Timing tests show results like this: Before: User: 358.71 Kernel: 38.29 Total Elapsed: 6:49.83 After: User: 380.01 Kernel: 44.97 Total Elapsed: 6:19.96 User- user-space CPU time consumed. Kernel- kernel-space CPU time consumed. The CPU consumption and kernel time consumption goes up, but the overall run time is lower. This makes the option perfectly viable for typical multi-core desktop solutions. Turning off the cube write optimization results in equivalent run times as before implementation. These time tests were run before the adaptive cache flush size was added, which improved performance further. References #727.

2012-06-06 Jeff Anderson - The read() method was modified to improve the speed for small buffer sizes as seen in ProcessByBoxcar and ProcessRubbersheet. The internal cache was always checked to be minimized which is slow for every read. Now the cache is only mimimized if it changed in size. Reference #894.

2014-04-07 Kimberly Oyama and Stuart Sides - Modified the findCubeChunks, writeIntoDouble, and writeIntoRaw methods to handle repeating virtual bands. Fixes #1927.

2014-09-30 Ian Humphrey - Modified read method to correctly access virtual bands when cube dimensions and buffer shape are same size. Fixes #1689.

2015-01-30 Ian Humphrey - Modified destructor to free m_writThreadMutex to prevent memory leaks upon destruction. Fixes #2082.

2016-04-21 Makayla Shepherd - Added UnsignedWord pixel type handling.

2016-06-21 Kris Becker - Properly forward declare QPair as struct not class

2016-08-28 Kelvin Rodriguez - updateLabels now a pure virtual, it had no implementation causing warnings in clang. Part of OS X 10.11 porting. QPair forward declaration now properly claims it as a struct.

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

2018-07-20 Tyler Wilson - Added support for unsigned integer special pixel values. in functions writeIntoRaw(...) and writeIntoDouble(...) References #971.

2018-08-13 Summer Stapleton - Fixed incoming buffer comparison values for unsigned int type in writeIntoRaw(...).

Definition at line 109 of file CubeIoHandler.h.

Constructor & Destructor Documentation

◆ CubeIoHandler() [1/2]

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

Creates a new CubeIoHandler using a RegionalCachingAlgorithm.

The chunk sizes must be set by a child in its constructor.

Parameters

dataFile	The file that contains cube data. This should be a valid, opened QFile and may not be NULL. The file should have at least read permissions.
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).
label	The label which contains the "Pixels" and "Core" groups.
alreadyOnDisk	True if the cube exists; false ensures all NULLs are initialized into the file before this object is destructed.

Definition at line 61 of file CubeIoHandler.cpp.

References Isis::PvlContainer::findKeyword(), Isis::PvlObject::findObject(), m_bandsInChunk, m_base, m_byteSwapper, m_cachingAlgorithms, m_consecutiveOverflowCount, m_dataFile, m_dataIsOnDiskMap, m_idealFlushSize, m_ioThreadPool, m_lastOperationWasWrite, m_lastProcessByLineChunks, m_linesInChunk, m_multiplier, m_nullChunkData, m_numBands, m_numLines, m_numSamples, m_pixelType, m_rawData, m_samplesInChunk, m_startByte, m_useOptimizedCubeWrite, m_virtualBands, m_writeCache, m_writeThreadMutex, Isis::PixelTypeEnumeration(), Isis::IException::Programmer, and setVirtualBands().

◆ ~CubeIoHandler()

Isis::CubeIoHandler::~CubeIoHandler ( )

virtual

Cleans up all allocated memory.

Child destructors must call clearCache() because we can no longer do IO by the time this destructor is called.

Definition at line 155 of file CubeIoHandler.cpp.

References m_byteSwapper, m_cachingAlgorithms, m_dataIsOnDiskMap, m_ioThreadPool, m_lastProcessByLineChunks, m_nullChunkData, m_rawData, m_virtualBands, m_writeCache, and m_writeThreadMutex.

◆ CubeIoHandler() [2/2]

Isis::CubeIoHandler::CubeIoHandler ( const CubeIoHandler & other )

private

Disallow copying of this object.

Parameters

other The object to copy.

Member Function Documentation

◆ addCachingAlgorithm()

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

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 364 of file CubeIoHandler.cpp.

References m_cachingAlgorithms.

Referenced by Isis::Cube::addCachingAlgorithm().

◆ bandCount()

int Isis::CubeIoHandler::bandCount ( ) const

protected

Returns: the number of physical bands in the cube.

Definition at line 462 of file CubeIoHandler.cpp.

References m_numBands.

Referenced by findCubeChunks().

◆ blockUntilThreadPoolEmpty()

void Isis::CubeIoHandler::blockUntilThreadPoolEmpty ( ) const

private

This blocks (doesn't return) until the number of active runnables in the thread pool goes to 0.

This uses the m_writeThreadMutex, because the thread pool doesn't delete threads immediately, so runnables might actually still exist but are inconsequential/being deleted already.

Definition at line 667 of file CubeIoHandler.cpp.

References m_ioThreadPool, and m_writeThreadMutex.

Referenced by flushWriteCache().

◆ bufferLessThan()

bool Isis::CubeIoHandler::bufferLessThan	(	Buffer *const &	lhs,
		Buffer *const &	rhs )

staticprivate

This is used for sorting buffers into the most efficient write order.

Parameters

lhs	The left hand side of the '<' operator
rhs	The right hand side of the '<' operator

Returns: True if lhs is obviously earlier in a cube than rhs.

Definition at line 681 of file CubeIoHandler.cpp.

References Isis::Displacement::Pixels, and Isis::Distance::Pixels.

◆ clearCache()

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

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 379 of file CubeIoHandler.cpp.

References flushWriteCache(), m_dataIsOnDiskMap, m_lastProcessByLineChunks, m_rawData, and writeNullDataToDisk().

Referenced by Isis::Cube::clearIoCache(), Isis::Cube::copy(), minimizeCache(), Isis::CubeBsqHandler::~CubeBsqHandler(), and Isis::CubeTileHandler::~CubeTileHandler().

◆ dataFileMutex()

QMutex * Isis::CubeIoHandler::dataFileMutex ( )

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 455 of file CubeIoHandler.cpp.

References m_writeThreadMutex.

Referenced by Isis::Cube::read(), Isis::Cube::write(), and Isis::Cube::writeLabels().

◆ findCubeChunks()

QPair< QList< RawCubeChunk * >, QList< int > > Isis::CubeIoHandler::findCubeChunks	(	int	startSample,
		int	numSamples,
		int	startLine,
		int	numLines,
		int	startBand,
		int	numBands ) const

private

Get the cube chunks that correspond to the given cube area.

This will create and initialize the chunks if they are not already in memory.

Parameters

startSample	The starting sample of the cube data
numSamples	The number of samples of cube data
startLine	The starting line of the cube data
numLines	The number of lines of cube data
startBand	The starting band of the cube data
numBands	The number of bands of cube data

Returns: The cube chunks that correspond to the given cube area

The user has requested a slice of a cube (a rectangle):

Cube
-----—

| | | <---------— Requested Area | | | | | -----— |

| |

But our cube is split into "chunks" which may not line up to what was requested:

| | | || |------------------—|| | -----— | || |—|---—|-------—|| (User requested area intersected with | | | | | || cube chunks) |------------------—||

| | | ||

| 1 | 2 | 3 || |------------------—|| | 4 | 5 | 6 || |------------------—|| (User requested area intersected with | 7 | 8 | 9 || cube chunks) |------------------—||

| 10 | 11 | 12 ||

(In this case we want chunks 4, 5, 7, and 8)

So we want to find which cube chunks line up to the requested area. To do this, we find which chunk intersects the top left of the requested cube area. That chunk is a given that we need it. Then we search in the positive X direction for more chunks that intersect the user-requested area until we no longer do. Then we know all of the chunks that intersect a whole y-range of the requested area. We shrink the requested area (remove the found y-range) and repeat.

Definition at line 730 of file CubeIoHandler.cpp.

References bandCount(), getChunk(), getChunkCountInLineDimension(), getChunkCountInSampleDimension(), lineCount(), m_bandsInChunk, m_linesInChunk, m_samplesInChunk, m_virtualBands, and sampleCount().

Referenced by read(), and synchronousWrite().

◆ findIntersection()

void Isis::CubeIoHandler::findIntersection	(	const RawCubeChunk &	cube1,
		const Buffer &	cube2,
		int &	startX,
		int &	startY,
		int &	startZ,
		int &	endX,
		int &	endY,
		int &	endZ ) const

private

Find the intersection between the buffer area and the cube chunk.

This accounts for virtual bands when considering the buffer and may return an area where all of the bands don't actually intersect due to virtual bands. This is implemented the way it is for performance reasons - so much as returning an Area3D or a QList<int> caused undesirable slowdowns.

Parameters

cube1	The cube chunk to intersect
cube2	The buffer (in virtual band space) to intersect
startX	(output) The leftmost sample position (inclusive)
startY	(output) The topmost line position (inclusive)
startZ	(output) The frontmost band position (inclusive)
endX	(output) The rightmost sample position (inclusive)
endY	(output) The bottommost line position (inclusive)
endZ	(output) The backmost band position (inclusive)

Definition at line 875 of file CubeIoHandler.cpp.

References m_virtualBands.

Referenced by writeIntoDouble(), and writeIntoRaw().

◆ flushWriteCache()

void Isis::CubeIoHandler::flushWriteCache ( bool force = false ) const

private

This attempts to write the so-far-unwritten buffers from m_writeCache into the cube's RawCubeChunk cache.

This will not do anything if there is a runnable and will block if the write cache grows to be too large.

Parameters

force Set to true to force start a flush

Definition at line 940 of file CubeIoHandler.cpp.

References blockUntilThreadPoolEmpty(), m_consecutiveOverflowCount, m_idealFlushSize, m_ioThreadPool, m_lastOperationWasWrite, m_useOptimizedCubeWrite, m_writeCache, m_writeThreadMutex, and synchronousWrite().

Referenced by clearCache(), read(), and write().

◆ freeChunk()

void Isis::CubeIoHandler::freeChunk ( RawCubeChunk * chunkToFree ) const

private

If the chunk is dirty, then we write it to disk.

Regardless, we then free it from memory.

Parameters

chunkToFree The chunk we're removing from memory

Definition at line 1017 of file CubeIoHandler.cpp.

References getChunkIndex(), m_lastProcessByLineChunks, and m_rawData.

Referenced by minimizeCache().

◆ getBandCountInChunk()

int Isis::CubeIoHandler::getBandCountInChunk ( ) const

protected

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

Definition at line 470 of file CubeIoHandler.cpp.

References m_bandsInChunk.

Referenced by getChunkIndex(), getChunkPlacement(), read(), and synchronousWrite().

◆ getBytesPerChunk()

BigInt Isis::CubeIoHandler::getBytesPerChunk ( ) const

protected

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 482 of file CubeIoHandler.cpp.

References m_bandsInChunk, m_linesInChunk, m_pixelType, m_samplesInChunk, and Isis::SizeOf().

Referenced by getChunk(), Isis::CubeBsqHandler::getChunkStartByte(), getDataSize(), getNullChunk(), Isis::CubeTileHandler::getTileStartByte(), and minimizeCache().

◆ getChunk()

RawCubeChunk * Isis::CubeIoHandler::getChunk	(	int	chunkIndex,
		bool	allocateIfNecessary ) const

private

Retrieve the cached chunk at the given chunk index, if there is one.

Parameters

chunkIndex	The position of the chunk in the cube
allocateIfNecessary	If true, the chunk will be read into cache when necessary and this method will not return NULL.

Returns: NULL if data is not cached, otherwise the cube file data

Definition at line 1045 of file CubeIoHandler.cpp.

References getBytesPerChunk(), getChunkPlacement(), getNullChunk(), m_dataIsOnDiskMap, and m_rawData.

Referenced by findCubeChunks(), read(), and synchronousWrite().

◆ getChunkCount()

int Isis::CubeIoHandler::getChunkCount ( ) const

private

Returns: The number of chunks that are required to encapsulate all of the cube data

Definition at line 1086 of file CubeIoHandler.cpp.

References getChunkCountInBandDimension(), getChunkCountInLineDimension(), and getChunkCountInSampleDimension().

Referenced by writeNullDataToDisk().

◆ getChunkCountInBandDimension()

int Isis::CubeIoHandler::getChunkCountInBandDimension ( ) const

protected

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 492 of file CubeIoHandler.cpp.

References m_bandsInChunk, and m_numBands.

Referenced by getChunkCount(), and getDataSize().

◆ getChunkCountInLineDimension()

int Isis::CubeIoHandler::getChunkCountInLineDimension ( ) const

protected

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 501 of file CubeIoHandler.cpp.

References m_linesInChunk, and m_numLines.

Referenced by findCubeChunks(), getChunkCount(), getChunkIndex(), getChunkPlacement(), getDataSize(), read(), and synchronousWrite().

◆ getChunkCountInSampleDimension()

int Isis::CubeIoHandler::getChunkCountInSampleDimension ( ) const

protected

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 510 of file CubeIoHandler.cpp.

References m_numSamples, and m_samplesInChunk.

Referenced by findCubeChunks(), getChunkCount(), getChunkIndex(), getChunkPlacement(), getDataSize(), read(), and synchronousWrite().

◆ getChunkIndex()

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

protected

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 526 of file CubeIoHandler.cpp.

References getBandCountInChunk(), getChunkCountInLineDimension(), getChunkCountInSampleDimension(), getLineCountInChunk(), and getSampleCountInChunk().

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

◆ getChunkPlacement()

void Isis::CubeIoHandler::getChunkPlacement	(	int	chunkIndex,
		int &	startSample,
		int &	startLine,
		int &	startBand,
		int &	endSample,
		int &	endLine,
		int &	endBand ) const

private

Get the X/Y/Z (Sample,Line,Band) range of the chunk at the given index.

Parameters

chunkIndex	The chunk number in the cube file
startSample	(output) The leftmost sample position (inclusive)
startLine	(output) The topmost line position (inclusive)
startBand	(output) The frontmost band position (inclusive)
endSample	(output) The rightmost sample position (inclusive)
endLine	(output) The bottommost line position (inclusive)
endBand	(output) The backmost band position (inclusive)

Definition at line 1104 of file CubeIoHandler.cpp.

References getBandCountInChunk(), getChunkCountInLineDimension(), getChunkCountInSampleDimension(), getLineCountInChunk(), and getSampleCountInChunk().

Referenced by getChunk(), getNullChunk(), read(), and synchronousWrite().

◆ getDataFile()

QFile * Isis::CubeIoHandler::getDataFile ( )

protected

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 555 of file CubeIoHandler.cpp.

References m_dataFile.

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

◆ getDataSize()

BigInt Isis::CubeIoHandler::getDataSize ( ) const

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 421 of file CubeIoHandler.cpp.

References getBytesPerChunk(), getChunkCountInBandDimension(), getChunkCountInLineDimension(), and getChunkCountInSampleDimension().

Referenced by setChunkSizes(), and Isis::Cube::write().

◆ getDataStartByte()

BigInt Isis::CubeIoHandler::getDataStartByte ( ) const

protected

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

Definition at line 544 of file CubeIoHandler.cpp.

References m_startByte.

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

◆ getLineCountInChunk()

int Isis::CubeIoHandler::getLineCountInChunk ( ) const

protected

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

Definition at line 572 of file CubeIoHandler.cpp.

References m_linesInChunk.

Referenced by getChunkIndex(), getChunkPlacement(), read(), synchronousWrite(), and Isis::CubeTileHandler::updateLabels().

◆ getNullChunk()

RawCubeChunk * Isis::CubeIoHandler::getNullChunk ( int chunkIndex ) const

private

This creates a chunk filled with NULLs whose placement is at chunkIndex's position.

This is used for getting NULL-filled chunks the first time the chunk is requested.

Ownership of the return value is given to the caller.

Parameters

chunkIndex The chunk's index which provides it's positioning.

Returns: A chunk filled with nulls at the chunkIndex position

Definition at line 1136 of file CubeIoHandler.cpp.

References Isis::RawCubeChunk::bandCount(), getBytesPerChunk(), getChunkPlacement(), Isis::RawCubeChunk::getRawData(), Isis::RawCubeChunk::getStartBand(), Isis::RawCubeChunk::getStartLine(), Isis::RawCubeChunk::getStartSample(), Isis::RawCubeChunk::lineCount(), m_nullChunkData, Isis::Null, Isis::RawCubeChunk::sampleCount(), Isis::RawCubeChunk::setDirty(), Isis::RawCubeChunk::setRawData(), and writeIntoRaw().

Referenced by getChunk(), and writeNullDataToDisk().

◆ getSampleCountInChunk()

int Isis::CubeIoHandler::getSampleCountInChunk ( ) const

protected

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

Definition at line 597 of file CubeIoHandler.cpp.

References m_samplesInChunk.

Referenced by getChunkIndex(), getChunkPlacement(), read(), synchronousWrite(), and Isis::CubeTileHandler::updateLabels().

◆ lineCount()

int Isis::CubeIoHandler::lineCount ( ) const

protected

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

Definition at line 564 of file CubeIoHandler.cpp.

References m_numLines.

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

◆ minimizeCache()

void Isis::CubeIoHandler::minimizeCache	(	const QList< RawCubeChunk * > &	justUsed,
		const Buffer &	justRequested ) const

private

Apply the caching algorithms and get rid of excess cube data in memory.

This is intended to be called after every IO operation.

Parameters

justUsed	The cube chunks that were used in the IO operation that is calling this method.
justRequested	The buffer that was used in the IO operation that is calling this method.

Definition at line 1188 of file CubeIoHandler.cpp.

References Isis::CubeCachingAlgorithm::CacheResult::algorithmUnderstoodData(), clearCache(), freeChunk(), getBytesPerChunk(), Isis::CubeCachingAlgorithm::CacheResult::getChunksToFree(), m_cachingAlgorithms, m_rawData, and Isis::CubeCachingAlgorithm::recommendChunksToFree().

Referenced by read(), and synchronousWrite().

◆ operator=()

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

private

Disallow assignments of this object.

Parameters

other The CubeIoHandler 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

protected

Returns: the physical cube DN format.

Definition at line 580 of file CubeIoHandler.cpp.

References m_pixelType.

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

◆ read()

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

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 226 of file CubeIoHandler.cpp.

References findCubeChunks(), flushWriteCache(), getBandCountInChunk(), getChunk(), getChunkCountInLineDimension(), getChunkCountInSampleDimension(), getChunkPlacement(), getLineCountInChunk(), getSampleCountInChunk(), m_bandsInChunk, m_ioThreadPool, m_lastOperationWasWrite, m_linesInChunk, m_rawData, m_samplesInChunk, m_useOptimizedCubeWrite, m_virtualBands, m_writeThreadMutex, minimizeCache(), Isis::Null, and writeIntoDouble().

Referenced by Isis::Cube::read().

◆ readRaw()

virtual void Isis::CubeIoHandler::readRaw ( RawCubeChunk & chunkToFill )

protectedpure virtual

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.

Implemented in Isis::CubeBsqHandler, and Isis::CubeTileHandler.

◆ sampleCount()

int Isis::CubeIoHandler::sampleCount ( ) const

protected

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

Definition at line 589 of file CubeIoHandler.cpp.

References m_numSamples.

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

◆ setChunkSizes()

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

protected

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 614 of file CubeIoHandler.cpp.

References getDataSize(), getDataStartByte(), m_bandsInChunk, m_dataFile, m_dataIsOnDiskMap, m_linesInChunk, m_samplesInChunk, and Isis::IException::Programmer.

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

◆ setVirtualBands()

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

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 438 of file CubeIoHandler.cpp.

References m_virtualBands.

Referenced by CubeIoHandler(), and Isis::Cube::setVirtualBands().

◆ synchronousWrite()

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

private

This method takes the given buffer and synchronously puts it into the Cube's cache.

This includes reading missing cache areas and freeing extra cache areas. This is what the non-threaded CubeIoHandler::write used to do.

Parameters

bufferToWrite The buffer we're writing into this cube, synchronously

Definition at line 1237 of file CubeIoHandler.cpp.

References findCubeChunks(), getBandCountInChunk(), getChunk(), getChunkCountInLineDimension(), getChunkCountInSampleDimension(), getChunkPlacement(), getLineCountInChunk(), getSampleCountInChunk(), m_bandsInChunk, m_lastProcessByLineChunks, m_linesInChunk, m_samplesInChunk, minimizeCache(), sampleCount(), and writeIntoRaw().

Referenced by flushWriteCache(), and write().

◆ updateLabels()

virtual void Isis::CubeIoHandler::updateLabels ( Pvl & labels )

pure virtual

Function to update the labels with a Pvl object.

Parameters

labels Pvl object to update with

Implemented in Isis::CubeTileHandler, and Isis::CubeBsqHandler.

Referenced by Isis::Cube::create().

◆ write()

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

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 334 of file CubeIoHandler.cpp.

References flushWriteCache(), m_ioThreadPool, m_lastOperationWasWrite, m_writeCache, m_writeThreadMutex, and synchronousWrite().

Referenced by Isis::Cube::write().

◆ writeIntoDouble()

void Isis::CubeIoHandler::writeIntoDouble	(	const RawCubeChunk &	chunk,
		Buffer &	output,
		int	index ) const

private

Write the intersecting area of the chunk into the buffer.

Parameters

chunk	The data source
output	The data destination
index	int

Definition at line 1352 of file CubeIoHandler.cpp.

References findIntersection(), Isis::EndianSwapper::Float(), m_base, m_byteSwapper, m_multiplier, m_pixelType, Isis::EndianSwapper::ShortInt(), Isis::EndianSwapper::Uint32_t(), and Isis::EndianSwapper::UnsignedShortInt().

Referenced by read().

◆ writeIntoRaw()

void Isis::CubeIoHandler::writeIntoRaw	(	const Buffer &	buffer,
		RawCubeChunk &	output,
		int	index ) const

private

Write the intersecting area of the buffer into the chunk.

Parameters

buffer	The data source
output	The data destination
index	int

Definition at line 1552 of file CubeIoHandler.cpp.

References Isis::Buffer::Band(), Isis::Buffer::BandDimension(), Isis::Buffer::DoubleBuffer(), findIntersection(), Isis::EndianSwapper::Float(), Isis::Buffer::Index(), m_base, m_byteSwapper, m_multiplier, m_pixelType, m_virtualBands, Isis::EndianSwapper::ShortInt(), Isis::EndianSwapper::Uint32_t(), and Isis::EndianSwapper::UnsignedShortInt().

Referenced by getNullChunk(), and synchronousWrite().

◆ writeNullDataToDisk()

void Isis::CubeIoHandler::writeNullDataToDisk ( ) const

private

Write all NULL cube chunks that have not yet been accessed to disk.

Definition at line 1831 of file CubeIoHandler.cpp.

References getChunkCount(), getNullChunk(), m_dataIsOnDiskMap, and Isis::IException::Programmer.

Referenced by clearCache().

◆ writeRaw()

virtual void Isis::CubeIoHandler::writeRaw ( const RawCubeChunk & chunkToWrite )

protectedpure virtual

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.

Implemented in Isis::CubeBsqHandler, and Isis::CubeTileHandler.

Member Data Documentation

◆ m_bandsInChunk

int Isis::CubeIoHandler::m_bandsInChunk

private

The number of physical bands in a cube chunk.

Definition at line 323 of file CubeIoHandler.h.

Referenced by CubeIoHandler(), findCubeChunks(), getBandCountInChunk(), getBytesPerChunk(), getChunkCountInBandDimension(), read(), setChunkSizes(), and synchronousWrite().

◆ m_base

double Isis::CubeIoHandler::m_base

private

The additive offset of the data on disk.

Definition at line 284 of file CubeIoHandler.h.

Referenced by CubeIoHandler(), writeIntoDouble(), and writeIntoRaw().

◆ m_byteOrder

ByteOrder Isis::CubeIoHandler::m_byteOrder

private

The byte order (endianness) of the data on disk.

Definition at line 290 of file CubeIoHandler.h.

◆ m_byteSwapper

EndianSwapper* Isis::CubeIoHandler::m_byteSwapper

private

A helper that swaps byte order to and from file order.

Definition at line 293 of file CubeIoHandler.h.

Referenced by CubeIoHandler(), writeIntoDouble(), writeIntoRaw(), and ~CubeIoHandler().

◆ m_cachingAlgorithms

QList<CubeCachingAlgorithm *>* Isis::CubeIoHandler::m_cachingAlgorithms

private

The caching algorithms to use, in order of priority.

Definition at line 305 of file CubeIoHandler.h.

Referenced by addCachingAlgorithm(), CubeIoHandler(), minimizeCache(), and ~CubeIoHandler().

◆ m_consecutiveOverflowCount

int Isis::CubeIoHandler::m_consecutiveOverflowCount

mutableprivate

How many times the write cache has overflown in a row.

Definition at line 362 of file CubeIoHandler.h.

Referenced by CubeIoHandler(), and flushWriteCache().

◆ m_dataFile

QFile* Isis::CubeIoHandler::m_dataFile

private

The file containing cube data.

Definition at line 271 of file CubeIoHandler.h.

Referenced by CubeIoHandler(), getDataFile(), and setChunkSizes().

◆ m_dataIsOnDiskMap

QMap<int, bool>* Isis::CubeIoHandler::m_dataIsOnDiskMap

mutableprivate

The map from chunk index to on-disk status, all true if not allocated.

Definition at line 311 of file CubeIoHandler.h.

Referenced by clearCache(), CubeIoHandler(), getChunk(), setChunkSizes(), writeNullDataToDisk(), and ~CubeIoHandler().

◆ m_idealFlushSize

volatile int Isis::CubeIoHandler::m_idealFlushSize

mutableprivate

Ideal write cache flush size.

Definition at line 359 of file CubeIoHandler.h.

Referenced by CubeIoHandler(), and flushWriteCache().

◆ m_ioThreadPool

QThreadPool* Isis::CubeIoHandler::m_ioThreadPool

mutableprivate

This contains threads for doing cube writes (and later maybe cube reads).

We're using a thread pool so that the same QThread is reused for performance reasons.

Definition at line 342 of file CubeIoHandler.h.

Referenced by blockUntilThreadPoolEmpty(), CubeIoHandler(), flushWriteCache(), read(), write(), and ~CubeIoHandler().

◆ m_lastOperationWasWrite

bool Isis::CubeIoHandler::m_lastOperationWasWrite

mutableprivate

If the last operation was a write then we need to flush the cache when reading.

Keep track of this.

Definition at line 348 of file CubeIoHandler.h.

Referenced by CubeIoHandler(), flushWriteCache(), read(), and write().

◆ m_lastProcessByLineChunks

QList<RawCubeChunk *>* Isis::CubeIoHandler::m_lastProcessByLineChunks

mutableprivate

This is an optimization for process by line.

It relies on chunks found often being the exact same between multiple reads or multiple writes.

Definition at line 329 of file CubeIoHandler.h.

Referenced by clearCache(), CubeIoHandler(), freeChunk(), synchronousWrite(), and ~CubeIoHandler().

◆ m_linesInChunk

int Isis::CubeIoHandler::m_linesInChunk

private

The number of lines in a cube chunk.

Definition at line 320 of file CubeIoHandler.h.

Referenced by CubeIoHandler(), findCubeChunks(), getBytesPerChunk(), getChunkCountInLineDimension(), getLineCountInChunk(), read(), setChunkSizes(), and synchronousWrite().

◆ m_multiplier

double Isis::CubeIoHandler::m_multiplier

private

The multiplicative factor of the data on disk.

Definition at line 287 of file CubeIoHandler.h.

Referenced by CubeIoHandler(), writeIntoDouble(), and writeIntoRaw().

◆ m_nullChunkData

QByteArray* Isis::CubeIoHandler::m_nullChunkData

mutableprivate

A raw cube chunk's data when it was all NULL's. Used for speed.

Definition at line 332 of file CubeIoHandler.h.

Referenced by CubeIoHandler(), getNullChunk(), and ~CubeIoHandler().

◆ m_numBands

int Isis::CubeIoHandler::m_numBands

private

The number of physical bands in the cube.

Definition at line 302 of file CubeIoHandler.h.

Referenced by bandCount(), CubeIoHandler(), and getChunkCountInBandDimension().

◆ m_numLines

int Isis::CubeIoHandler::m_numLines

private

The number of lines in the cube.

Definition at line 299 of file CubeIoHandler.h.

Referenced by CubeIoHandler(), getChunkCountInLineDimension(), and lineCount().

◆ m_numSamples

int Isis::CubeIoHandler::m_numSamples

private

The number of samples in the cube.

Definition at line 296 of file CubeIoHandler.h.

Referenced by CubeIoHandler(), getChunkCountInSampleDimension(), and sampleCount().

◆ m_pixelType

PixelType Isis::CubeIoHandler::m_pixelType

private

The format of each DN in the cube.

Definition at line 281 of file CubeIoHandler.h.

Referenced by CubeIoHandler(), getBytesPerChunk(), pixelType(), writeIntoDouble(), and writeIntoRaw().

◆ m_rawData

QMap<int, RawCubeChunk *>* Isis::CubeIoHandler::m_rawData

mutableprivate

The map from chunk index to chunk for cached data.

Definition at line 308 of file CubeIoHandler.h.

Referenced by clearCache(), CubeIoHandler(), freeChunk(), getChunk(), minimizeCache(), read(), and ~CubeIoHandler().

◆ m_samplesInChunk

int Isis::CubeIoHandler::m_samplesInChunk

private

The number of samples in a cube chunk.

Definition at line 317 of file CubeIoHandler.h.

Referenced by CubeIoHandler(), findCubeChunks(), getBytesPerChunk(), getChunkCountInSampleDimension(), getSampleCountInChunk(), read(), setChunkSizes(), and synchronousWrite().

◆ m_startByte

BigInt Isis::CubeIoHandler::m_startByte

private

The start byte of the cube data.

This is 0-based (i.e. a value of 0 means write data into the first byte of the file). Usually the label is between 0 and m_startByte.

Definition at line 278 of file CubeIoHandler.h.

Referenced by CubeIoHandler(), and getDataStartByte().

◆ m_useOptimizedCubeWrite

bool Isis::CubeIoHandler::m_useOptimizedCubeWrite

private

This is true if the Isis preference for the cube write thread is optimized.

Definition at line 353 of file CubeIoHandler.h.

Referenced by CubeIoHandler(), flushWriteCache(), and read().

◆ m_virtualBands

QList<int>* Isis::CubeIoHandler::m_virtualBands

private

Converts from virtual band to physical band.

Definition at line 314 of file CubeIoHandler.h.

Referenced by CubeIoHandler(), findCubeChunks(), findIntersection(), read(), setVirtualBands(), writeIntoRaw(), and ~CubeIoHandler().

◆ m_writeCache

QPair< QMutex *, QList<Buffer *> >* Isis::CubeIoHandler::m_writeCache

private

These are the buffers we need to write to raw cube chunks.

Definition at line 335 of file CubeIoHandler.h.

Referenced by CubeIoHandler(), flushWriteCache(), write(), and ~CubeIoHandler().

◆ m_writeThreadMutex

QMutex* Isis::CubeIoHandler::m_writeThreadMutex

private

This enables us to block while the write thread is working.

Definition at line 356 of file CubeIoHandler.h.

Referenced by blockUntilThreadPoolEmpty(), Isis::CubeIoHandler::BufferToChunkWriter::BufferToChunkWriter(), CubeIoHandler(), dataFileMutex(), flushWriteCache(), read(), write(), and ~CubeIoHandler().

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

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

Classes

Public Member Functions

Protected Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ CubeIoHandler() [1/2]

◆ ~CubeIoHandler()

◆ CubeIoHandler() [2/2]

Member Function Documentation

◆ addCachingAlgorithm()

◆ bandCount()

◆ blockUntilThreadPoolEmpty()

◆ bufferLessThan()

◆ clearCache()

◆ dataFileMutex()

◆ findCubeChunks()

The user has requested a slice of a cube (a rectangle):

| |

| | | ||

| 10 | 11 | 12 ||

◆ findIntersection()

◆ flushWriteCache()

◆ freeChunk()

◆ getBandCountInChunk()

◆ getBytesPerChunk()

◆ getChunk()

◆ getChunkCount()

◆ getChunkCountInBandDimension()

◆ getChunkCountInLineDimension()

◆ getChunkCountInSampleDimension()

◆ getChunkIndex()

◆ getChunkPlacement()

◆ getDataFile()

◆ getDataSize()

◆ getDataStartByte()

◆ getLineCountInChunk()

◆ getNullChunk()

◆ getSampleCountInChunk()

◆ lineCount()

◆ minimizeCache()

◆ operator=()

◆ pixelType()

◆ read()

◆ readRaw()

◆ sampleCount()

◆ setChunkSizes()

◆ setVirtualBands()

◆ synchronousWrite()

◆ updateLabels()

◆ write()

◆ writeIntoDouble()

◆ writeIntoRaw()

◆ writeNullDataToDisk()

◆ writeRaw()

Member Data Documentation

◆ m_bandsInChunk

◆ m_base

◆ m_byteOrder

◆ m_byteSwapper

◆ m_cachingAlgorithms

◆ m_consecutiveOverflowCount

◆ m_dataFile

◆ m_dataIsOnDiskMap

◆ m_idealFlushSize

◆ m_ioThreadPool

◆ m_lastOperationWasWrite

◆ m_lastProcessByLineChunks

◆ m_linesInChunk

◆ m_multiplier

◆ m_nullChunkData

◆ m_numBands

◆ m_numLines

◆ m_numSamples

◆ m_pixelType

◆ m_rawData

◆ m_samplesInChunk

◆ m_startByte