BSQ cubes are now read correctly with virtual bands considered for all sizes.... (c08fb790) · Commits · aflab / astrogeology / ISIS3

isis/src/base/objs/Cube/Cube.h

+4 −0

Original line number	Diff line number	Diff line
		@@ -142,6 +142,10 @@ namespace Isis {
		* @history 2012-12-31 Steven Lambright - Removed 'get' prefix from accessors. Fixes #1356.
		* @history 2014-06-20 Ian Humphrey - Added checks to statistics() and histogram() to throw
		* an error if the cube is unopened. Fixes #2085.
		* @history 2014-10-06 Ian Humphrey - Added case to unittest when chunk dimensions are the same
		* as the buffer shape to ensure virtual bands accessed correctly.
		* Added cases to test creating bsq and large bsq cubes.
		* References #1689.
		*/
		class Cube {
		public:

isis/src/base/objs/Cube/Cube.truth

+61 −0

Original line number	Diff line number	Diff line
		@@ -211,6 +211,67 @@ Reading completely outside virtual band boundaries ...
		Reading partially within virtual band boundaries ...
		Comparing results ...

		Testing one line BSQ cube (where chunk dimensions == buffer shape) ...
		Constructing cube ...

		File = IsisCube_bsqOneLine.cub
		Samps = 3
		Lines = 1
		Bands = 3
		Base = 0
		Mult = 1
		Type = 7
		Atchd = 1
		Format = 0
		Open = 1
		R/O = 0
		R/W = 1
		Lbytes = 65536

		Testing reading ascending repeating virtual bands (1, 2, 2, 3)...

		Testing reading skipped ascending virtual bands (1, 3, 3)...

		Testing reading outside of cube boundaries with virtual bands (1, 5)...

		Testing reading descending virtual bands (3, 1, 3)...

		Testing creating large BSQ where samples exceed 1GB chunk size limit ...
		Constructing cube ...

		File = IsisCube_largebsq.cub
		Samps = 268435457
		Lines = 2
		Bands = 1
		Base = 0
		Mult = 1
		Type = 7
		Atchd = 1
		Format = 0
		Open = 1
		R/O = 0
		R/W = 1
		Lbytes = 65536


		Testing creating BSQ cube where size of sample pixels exceeds cube's lineCount ...
		Constructing cube ...

		File = IsisCube_bsq.cub
		Samps = 15000
		Lines = 18000
		Bands = 1
		Base = 0
		Mult = 1
		Type = 7
		Atchd = 1
		Format = 0
		Open = 1
		R/O = 0
		R/W = 1
		Lbytes = 65536


		Testing errors ...
		PROGRAMMER ERROR You already have a cube opened.
		PROGRAMMER ERROR You already have a cube opened.

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

+36 −12

Original line number	Diff line number	Diff line
		@@ -52,20 +52,17 @@ namespace Isis {
		: CubeIoHandler(dataFile, virtualBandList, labels, alreadyOnDisk) {
		int numSamplesInChunk = sampleCount();
		int numLinesInChunk = 1;
		QList<int> primeFactors;

		// The chunk size must evenly divide into the cube size...
		if(lineCount() < 1024)
		numLinesInChunk = lineCount();
		else {
		int attemptedSize = 1024;
		// we want our chunk sizes to be less than 1GB
		int sizeLimit = 1024 * 1024 * 1024;
		int maxNumLines = (sizeLimit) / (SizeOf(pixelType()) * numSamplesInChunk);

		while(numLinesInChunk == 1 && attemptedSize > 1) {
		if(lineCount() % attemptedSize == 0)
		numLinesInChunk = attemptedSize;
		else
		attemptedSize /= 2;
		}
		}
		// we've exceed our sizeLimit; increase our limit so we can process an entire line
		if (maxNumLines == 0)
		maxNumLines = 1;

		numLinesInChunk = findGoodSize(maxNumLines, lineCount());

		setChunkSizes(numSamplesInChunk, numLinesInChunk, 1);
		}
		@@ -135,6 +132,33 @@ namespace Isis {
		}


		/**
		* 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.
		*
		* @param maxSize The largest allowed size of a chunk dimension
		* @param dimensionSize The cube's size for the chunk size we are trying to calculate
		* (number of lines)
		* @return The calculated chunk size for the dimension given
		*/
		int CubeBsqHandler::findGoodSize(int maxSize, int dimensionSize) const {
		int chunkDimensionSize;

		if (dimensionSize <= maxSize) {
		chunkDimensionSize = dimensionSize;
		}
		else {
		// find largest divisor of dimension size so chunks fit into cube uniformly
		int greatestDivisor = maxSize;
		while (dimensionSize % greatestDivisor > 0) {
		greatestDivisor--;
		}
		chunkDimensionSize = greatestDivisor;
		}
		return chunkDimensionSize;
		}


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

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

+4 −0

Original line number	Diff line number	Diff line
		@@ -49,6 +49,9 @@ namespace Isis {
		* @history 2011-07-18 Jai Rideout and Steven Lambright - Added
		* unimplemented copy constructor and assignment
		* operator.
		* @history 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.
		*/
		class CubeBsqHandler : public CubeIoHandler {
		public:
		@@ -79,6 +82,7 @@ namespace Isis {
		*/
		CubeBsqHandler &operator=(const CubeBsqHandler &other);

		int findGoodSize(int maxSize, int dimensionSize) const;
		BigInt getChunkStartByte(const RawCubeChunk &chunk) const;
		};
		}

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

+7 −1

Original line number	Diff line number	Diff line
		@@ -271,6 +271,7 @@ namespace Isis {
		int bufferLineCount = bufferToFill.LineDimension();
		int bufferBandCount = bufferToFill.BandDimension();

		// our chunk dimensions are same as buffer shape dimensions
		if (bufferSampleCount == m_samplesInChunk &&
		bufferLineCount == m_linesInChunk &&
		bufferBandCount == m_bandsInChunk) {
		@@ -282,11 +283,16 @@ namespace Isis {
		int bufferEndLine = bufferStartLine + bufferLineCount - 1;
		int bufferEndBand = bufferStartBand + bufferBandCount - 1;

		// make sure we access the correct band
		int startBand = bufferStartBand - 1;
		if (m_virtualBands)
		startBand = m_virtualBands->at(bufferStartBand - 1);

		int expectedChunkIndex =
		((bufferStartSample - 1) / getSampleCountInChunk()) +
		((bufferStartLine - 1) / getLineCountInChunk()) *
		getChunkCountInSampleDimension() +
		((bufferStartBand - 1) / getBandCountInChunk()) *
		((startBand - 1) / getBandCountInChunk()) *
		getChunkCountInSampleDimension() *
		getChunkCountInLineDimension();