PROG: Merging CorrelationMatrix from ipce to trunk. (e973e3d0) · Commits · aflab / astrogeology / ISIS3

isis/src/control/objs/CorrelationMatrix/CorrelationMatrix.cpp

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		#include "CorrelationMatrix.h"

		#include <QDataStream>
		#include <QDebug>
		#include <QFile>
		#include <QList>
		#include <QString>
		#include <QStringList>
		#include <QtCore/qmath.h>

		#include "IException.h"
		#include "Pvl.h"
		#include "PvlObject.h"
		#include "SparseBlockMatrix.h"

		namespace Isis {
		/**
		* Default Constructor
		*/
		CorrelationMatrix::CorrelationMatrix() {
		m_covarianceFileName = new FileName("");
		m_correlationFileName = new FileName("");
		m_visibleBlocks = new QList<SparseBlockColumnMatrix>();
		m_imagesAndParameters = new QMap<QString, QStringList>();
		m_diagonals = new QList<double>();
		}


		/**
		* This constructor will create a CorrelationMatrix object given a pvl.
		*
		* Object = CorrelationMatrix
		*
		* CovarianceFileName = fileName.dat
		* CorrelationFileName = fileName.dat
		*
		* Group = ImagesAndParameters
		* Image1 = "Parameter1", "Parameter2", "..."
		* Image2 = "Parameter1", "Parameter2", "..."
		* Image3 = "Parameter1", "Parameter2", "..."
		* End_Group
		*
		* End_Object
		*
		* @param storedMatrixData A PvlObject containing data about the
		* covariance/correlation matrix.
		*
		* @throws IException::User "This Pvl Object does not have the correct correlation information.
		* The Object you are looking for is called CorrelationMatrixData"
		*
		* @throws IException::User "Could not find the Covariance Matrix .dat file name."
		*
		* @throws IException::User "Could not find the Correlation Matrix .dat file name."
		*
		* @throws IException::User "Could not get Images and Parameters from ImagesAndParameters group."
		*
		*/
		CorrelationMatrix::CorrelationMatrix(PvlObject storedMatrixData) {
		//m_imagesAndParameters = NULL;
		m_imagesAndParameters = new QMap<QString, QStringList>();
		m_covarianceFileName = new FileName("");
		m_correlationFileName = new FileName("");
		m_diagonals = NULL;
		m_visibleBlocks = NULL;

		if (storedMatrixData.name() != "CorrelationMatrixData") {
		QString msg = "This Pvl Object does not have the correct correlation information. The Object "
		"you are looking for is called CorrelationMatrixData.";
		throw IException(IException::User, msg, _FILEINFO_);
		}

		try {
		m_covarianceFileName =
		new FileName(storedMatrixData.findKeyword("CovarianceMatrixFileName")[0]);
		}
		catch (IException &e) {
		QString msg = "Could not find the Covariance Matrix .dat file name.";
		throw IException(e, IException::User, msg, _FILEINFO_);
		}

		try {
		QString corrFileName = storedMatrixData.findKeyword("CorrelationMatrixFileName")[0];
		if (corrFileName == "NULL") {
		m_correlationFileName = new FileName;
		}
		else {
		m_correlationFileName = new FileName(corrFileName);
		}
		}
		catch (IException &e) {
		QString msg = "Could not find the Correlation Matrix .dat file name.";
		throw IException(e, IException::User, msg, _FILEINFO_);
		}

		try {
		PvlObject::PvlKeywordIterator
		imgsIt = storedMatrixData.findGroup("ImagesAndParameters").begin();
		while ( imgsIt != storedMatrixData.findGroup("ImagesAndParameters").end() ) {
		QStringList params = (*imgsIt)[0].split(",");
		m_imagesAndParameters->insert(imgsIt->name(), params);
		imgsIt++;
		}
		}
		catch (IException &e) {
		QString msg = "Could not get Images and Parameters from ImagesAndParameters group.";
		throw IException(e, IException::User, msg, _FILEINFO_);
		}
		}


		/**
		* @brief Copy Constructor
		*
		* @param other The CorrelationMatrix to copy.
		*/
		CorrelationMatrix::CorrelationMatrix(const CorrelationMatrix &other) {
		m_imagesAndParameters = new QMap<QString, QStringList>(*other.m_imagesAndParameters);
		m_covarianceFileName = new FileName(*other.m_covarianceFileName);
		m_correlationFileName = new FileName(*other.m_correlationFileName);
		m_diagonals = new QList<double>(*other.m_diagonals);
		m_visibleBlocks = new QList<SparseBlockColumnMatrix>(*other.m_visibleBlocks);
		}


		/**
		* Destructor
		*/
		CorrelationMatrix::~CorrelationMatrix() {
		delete m_imagesAndParameters;
		m_imagesAndParameters = NULL;

		delete m_covarianceFileName;
		m_covarianceFileName = NULL;

		delete m_correlationFileName;
		m_correlationFileName = NULL;

		delete m_diagonals;
		m_diagonals = NULL;

		delete m_visibleBlocks;
		m_visibleBlocks = NULL;
		}


		/**
		* @brief Equal Operator
		*
		* Should this call the copy constructor???
		*
		* @param other The matrix to assign to this matrix.
		* @return @b CorrelationMatrix Returns the new matrix.
		*/
		CorrelationMatrix &CorrelationMatrix::operator=(const CorrelationMatrix &other) {

		if (&other != this) {

		delete m_imagesAndParameters;
		m_imagesAndParameters = NULL;
		m_imagesAndParameters = new QMap<QString, QStringList>(*other.m_imagesAndParameters);

		delete m_covarianceFileName;
		m_covarianceFileName = NULL;
		m_covarianceFileName = new FileName(*other.m_covarianceFileName);

		delete m_correlationFileName;
		m_correlationFileName = NULL;
		m_correlationFileName = new FileName(*other.m_correlationFileName);

		delete m_diagonals;
		m_diagonals = NULL;
		m_diagonals = new QList<double>(*other.m_diagonals);

		delete m_visibleBlocks;
		m_visibleBlocks = NULL;
		m_visibleBlocks = new QList<SparseBlockColumnMatrix>(*other.m_visibleBlocks);

		}

		return *this;
		}


		/**
		* @description This method reads the covariance matrix in from a file,
		* one SparseBlockColumnMatrix at a time. It then stores the diagonal values from that column
		* and computes the correlation values. The resulting SparseBlockMatrix is written to a
		* new file, one SparseBlockColumnMatrix at a time.
		*
		* @throws IException::Progammer "Cannot compute correlation matrix without a specified
		* file name. Use setCorrelationFileName(FileName) before calling computeCorrelationMatrix()."
		*/
		void CorrelationMatrix::computeCorrelationMatrix() {

		if ( !isValid() ) {
		QString msg = "Cannot compute correlation matrix without a specified file name. Use "
		"setCorrelationFileName(FileName) before calling computeCorrelationMatrix().";
		throw IException(IException::Programmer, msg, _FILEINFO_);
		}
		delete m_visibleBlocks;
		m_visibleBlocks = NULL;
		m_visibleBlocks = new QList<SparseBlockColumnMatrix>;

		// Create file handle
		QFile matrixInput( m_covarianceFileName->expanded() );
		QFile matrixOutput( m_correlationFileName->expanded() );

		// Open file to write to
		matrixInput.open(QIODevice::ReadOnly);
		matrixOutput.open(QIODevice::WriteOnly);

		// Open Stream
		QDataStream inStream(&matrixInput);
		QDataStream outStream(&matrixOutput);

		double firstParam1 = 0, //starting param for each iteration
		firstParam2 = 0;
		double param1 = 0, // current param for each iteration
		param2 = 0;
		// Read one column at a time
		SparseBlockColumnMatrix sbcm;
		while ( !inStream.atEnd() ) {
		inStream >> sbcm;

		// Store diagonal
		int numOfBlocks = sbcm.size();
		int lastBlock = numOfBlocks - 1;
		int numDiagonals = sbcm[lastBlock]->size1();

		// Get Diagonals
		for (int i = 0; i < numDiagonals; i++) {
		double val = ( *(sbcm[lastBlock]) )(i, i);
		m_diagonals->append(val);
		}

		// compute correlations
		QMapIterator<int, boost::numeric::ublas::matrix<double>*> block(sbcm);

		while ( block.hasNext() ) { // each block in the column
		block.next();
		for (int row = 0; row < (int)block.value()->size1(); row++) { // each row in the block
		for (int column = 0; column < (int)block.value()->size2(); column++) { // each column
		// correlation = covariance / (variance1 * variance2)
		( block.value() )(row, column) = ( block.value() )(row, column) /
		sqrt( (m_diagonals)[param1]
		(*m_diagonals)[param2] );
		param2++;
		}
		param1++;
		param2 = firstParam2;
		}
		firstParam1 += block.value()->size1();
		param1 = firstParam1;
		}
		firstParam1 = 0; // start each column at first element of diagonal list
		param1 = firstParam1;
		firstParam2 += block.value()->size2();
		param2 = firstParam2;

		outStream << sbcm;
		m_visibleBlocks->append(sbcm);
		}

		// close file
		matrixInput.close();
		matrixOutput.close();
		}



		/**
		* @description This method will open the correlation matrix file and read in the blocks that
		* apply to the requested area. It will populate m_visibleElements.
		*
		* @param x first coordinate of the location in the matrix that the user wants to see.
		* @param y second coordinate of the location in the matrix that the user wants to see.
		*/
		void CorrelationMatrix::retrieveVisibleElements(int x, int y) {

		// if ( !correlationMatrixExists() ) {
		// call computeCorrelationMatrix
		// }
		// read the values we want from the correlation matrix file.

		// store values by column?
		// return list of values in m_visibleElements
		}



		/**
		* This is the public accessor for the list of elements that should be displayed in the current
		* view.
		*
		* @return QList<MatrixElement*> The list of currently visible elements.
		*
		*/
		// QList<MatrixElement*> CorrelationMatrix::visibleElements() {
		// return *m_visibleElements;
		// }



		/**
		* @brief See if the correlation matrix has already been calculated by checking to see if
		* the correlation matrix file has been created.
		*
		* @return @b bool Returns True if the correlation matrix has already been set.
		*/
		bool CorrelationMatrix::isValid() {

		return !(m_correlationFileName->name() == "" \|\| m_covarianceFileName->name() == "");
		}


		/**
		* @description This is used to make sure the covariance matrix exists.
		* If it doesn't this class is not valid. If this file exists, we can compute the
		* correlation matrix.
		*
		* @return @b bool Returns True if the covariance matrix exists, and False if it does not.
		*/
		bool CorrelationMatrix::hasCovMat() {
		return !(m_covarianceFileName->name() == "");
		}


		// Set Methods
		/**
		* @brief Set the qmap of images and parameters.
		* @param correlationFileName The FileName of the stored correlation matrix data.
		*/
		void CorrelationMatrix::setCorrelationFileName(FileName correlationFileName) {
		if (m_correlationFileName == NULL) {
		m_correlationFileName = new FileName(correlationFileName);
		}
		else {
		*m_correlationFileName = correlationFileName;
		}
		}


		/**
		* @brief Set the qmap of images and parameters.
		* @param covarianceFileName The FileName of the stored covariance matrix data.
		*/
		void CorrelationMatrix::setCovarianceFileName(FileName covarianceFileName) {
		if (m_covarianceFileName == NULL) {
		m_covarianceFileName = new FileName(covarianceFileName);
		}
		else {
		*m_covarianceFileName = covarianceFileName;
		}
		//Make the correlation matrix file name match the covariance matrix file name.
		if (!isValid()) {
		QString fName = covarianceFileName.expanded().replace( QString("inverse"),
		QString("correlation") );
		setCorrelationFileName( FileName(fName) );
		}
		}


		/**
		* @brief Set the qmap of images and parameters.
		*
		* @param imagesAndParameters a QMap structure indexed by image keys, with an arbitrary set of
		* parameters for each image.
		*/
		void CorrelationMatrix::setImagesAndParameters(QMap<QString, QStringList> imagesAndParameters) {
		if (m_imagesAndParameters == NULL) {
		m_imagesAndParameters = new QMap<QString, QStringList>(imagesAndParameters);
		}
		else {
		*m_imagesAndParameters = imagesAndParameters;
		}
		}


		/**
		* @brief Public access for the correlation matrix file name.
		*
		* @return @b FileName The FileName of the correlation matrix data file.
		*/
		FileName CorrelationMatrix::correlationFileName() {
		return *m_correlationFileName;
		}


		/**
		* @brief Public access for the covariance matrix file name.
		*
		* @return @b FileName The FileName of the covariance data file.
		*/
		FileName CorrelationMatrix::covarianceFileName() {
		return *m_covarianceFileName;
		}


		/**
		* @brief Public access for the qmap of images and parameters.
		*
		* @return @b *QMap<QString,QStringList> A pointer to the QMap structure containing a list
		* of images (the keys) and their associated parameter values.
		*/
		QMap<QString, QStringList> *CorrelationMatrix::imagesAndParameters() {
		return m_imagesAndParameters;
		}


		/**
		* @description This method will read the matrix in from the file and hold on to the whole thing.
		* This will only be used when the matrix is small enough that this will be useful.
		*
		*/
		void CorrelationMatrix::getWholeMatrix() {
		// SparseBlockColumnMatrix sbcm;
		// QFile matrixInput( m_correlationFileName->expanded() );
		// matrixInput.open(QIODevice::ReadOnly);
		// QDataStream inStream(&matrixInput);
		//
		// while( !inStream.atEnd() ) {
		// inStream >> sbcm;
		// m_visibleBlocks->append(&sbcm);
		// }
		}


		/**
		* @description This method will be used when the matrix is too big to display the whole thing.
		* It will read in the block we want to see and the two blocks for the diagonals that belong to
		* the right images.
		*/
		void CorrelationMatrix::getThreeVisibleBlocks() {
		}


		/**
		* @brief Get the visible part of the matrix.
		* @return @b QList Returns a list of the non-empty diagonal blocks of the correlation matrix.
		*/
		QList<SparseBlockColumnMatrix> *CorrelationMatrix::visibleBlocks() {
		return m_visibleBlocks;
		}


		/**
		* @description This method creates a Pvl group with the information necessary to recreate
		* this correlation matrix.
		*
		* Object = CorrelationMatrixData
		* CovarianceMatrixFileName = /location/covarianceTmpFileName.dat
		* CorrelationMatrixFileName = /location/correlationTmpFileName.dat
		*
		* Group = ImagesAndParameters
		* Image1Name = "Param1, Param2, ..., ParamN"
		* ...
		* ImageNName = "..."
		* End_Group
		* End_Object
		*
		* @return @b PvlGroup Returns the information needed to recreate this correlation matrix.
		*/
		PvlObject CorrelationMatrix::pvlObject() {
		PvlObject corrMatInfo("CorrelationMatrixData");

		corrMatInfo += PvlKeyword( "CovarianceMatrixFileName", m_covarianceFileName->expanded() );
		corrMatInfo += PvlKeyword( "CorrelationMatrixFileName", m_correlationFileName->expanded() );

		PvlGroup imgsAndParams("ImagesAndParameters");
		QMapIterator<QString, QStringList> imgParamIt(*m_imagesAndParameters);
		while ( imgParamIt.hasNext() ) {
		imgParamIt.next();
		imgsAndParams += PvlKeyword( imgParamIt.key(), imgParamIt.value().join(",") );
		}
		corrMatInfo += imgsAndParams;

		return corrMatInfo;
		}


		/**
		* @brief Writes CorrelationMatrix data to the output stream and returns this stream
		* to the user.
		* @param stream The input stream containing the data.
		* @return @b QDataStream Returns the output stream.
		*/

		QDataStream &CorrelationMatrix::write(QDataStream &stream) const {
		// QMaps
		stream << *m_imagesAndParameters;
		// FileNames
		stream << m_covarianceFileName->expanded() << m_correlationFileName->expanded();
		// QLists
		stream << m_diagonals << m_visibleBlocks;
		return stream;
		}


		/**
		* @brief Reads CorrelationMatrix data from the input stream and places the data
		* in member variables.
		* @param stream The input input stream containing the data.
		* @return @b QDataStream Returns the output data stream.
		*/
		QDataStream &CorrelationMatrix::read(QDataStream &stream) {
		// QMaps
		QMap<QString, QStringList> imagesAndParameters;
		stream >> imagesAndParameters;
		delete m_imagesAndParameters;
		m_imagesAndParameters = NULL;
		m_imagesAndParameters = new QMap<QString, QStringList>(imagesAndParameters);

		// FileNames
		QString covarianceFileName;
		stream >> covarianceFileName;
		delete m_covarianceFileName;
		m_covarianceFileName = NULL;
		m_covarianceFileName = new FileName(covarianceFileName);

		QString correlationFileName;
		stream >> correlationFileName;
		delete m_correlationFileName;
		m_correlationFileName = NULL;
		m_correlationFileName = new FileName(correlationFileName);

		// QLists
		QList<double> diagonals;
		stream >> diagonals;
		delete m_diagonals;
		m_diagonals = NULL;
		m_diagonals = new QList<double>(diagonals);

		QList<SparseBlockColumnMatrix> visibleBlocks;
		stream >> visibleBlocks;
		delete m_visibleBlocks;
		m_visibleBlocks = NULL;
		m_visibleBlocks = new QList<SparseBlockColumnMatrix>(visibleBlocks);

		return stream;
		}


		/**
		* @brief The operator << writes matrix data to a QDataStream.
		* @param stream The output stream upon which the matrix data is written.
		* @param matrix The CorrelationMatrix containing the data.
		* @return @b QDataStream Returns the output stream containing the matrix data.
		*/
		QDataStream &operator<<(QDataStream &stream, const CorrelationMatrix &matrix) {
		return matrix.write(stream);
		}


		/**
		* @brief The operator >> reads matrix data from a QDataStream.
		* @param stream The input stream containing the CorrelationMatrix data.
		* @param matrix The matrix which is going to be overwritten by the input stream.
		* @return @b QDataStream Returns the output stream containing the matrix data.
		*/
		QDataStream &operator>>(QDataStream &stream, CorrelationMatrix &matrix) {
		return matrix.read(stream);
		}
		}

isis/src/control/objs/CorrelationMatrix/CorrelationMatrix.h

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		#ifndef CorrelationMatrix_h
		#define CorrelationMatrix_h

		/**
		* @file
		* Unless noted otherwise, the portions of Isis written by the USGS are public
		* domain. See individual third-party library and package descriptions for
		* intellectual property information,user agreements, and related information.
		*
		* Although Isis has been used by the USGS, no warranty, expressed or implied,
		* is made by the USGS as to the accuracy and functioning of such software
		* and related material nor shall the fact of distribution constitute any such
		* warranty, and no responsibility is assumed by the USGS in connection
		* therewith.
		*
		* For additional information, launch
		* $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see
		* the Privacy & Disclaimers page on the Isis website,
		* http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on
		* http://www.usgs.gov/privacy.html.
		*/

		#include "FileName.h"

		#include <QDebug>
		#include <QList>
		#include <QMap>
		#include <QString>
		#include <QStringList>

		#include <boost/numeric/ublas/matrix_sparse.hpp>

		template <typename A, typename B> class QMap;
		template <typename A> class QList;

		namespace Isis {
		class FileName;
		class MosaicSceneWidget;
		class PvlObject;
		class SparseBlockColumnMatrix;


		/**
		* @brief This is a container for the correlation matrix that comes from a bundle adjust
		*
		* The bundle adjust will output the covariance matrix to a file. This class will read that file
		* in and compute the correlation matrix. The entire correlation matrix will be written to a file
		* and values will be read/displayed on an as-needed basis.
		*
		* @ingroup Visualization Tools
		*
		* @author 2014-05-02 Kimberly Oyama
		*
		* @internal
		* @history 2014-05-02 Kimberly Oyama - Original version.
		* @history 2014-07-23 Jeannie Backer - Added QDataStream >> and << operators and read/write
		* methods. Created unitTest. Added new operators to assignments in
		* copy constructor and operator= methods.
		* @history 2015-10-14 Jeffrey Covington - Declared CorrelationMatrix as a
		* Qt metatype for use with QVariant.
		* @history 2016-06-06 Tyler Wilson - Fixed a problem with a PvlKeywordIterator not
		* being incremented in the constructor which accepts a PvlObject.
		* There was also an issue with a QMap data structure not being
		* initialized, resulting in a segmentation fault. Also added
		* testing for exceptions being thrown in this constructor,
		* as well as the function computeCorrelationMatrix. Fixes #3997,3999.
		*/
		class CorrelationMatrix {
		public:
		CorrelationMatrix();
		CorrelationMatrix(PvlObject storedMatrixData);
		CorrelationMatrix(const CorrelationMatrix &other);
		~CorrelationMatrix();

		CorrelationMatrix &operator=(const CorrelationMatrix &other);

		void computeCorrelationMatrix();
		void retrieveVisibleElements(int x, int y);

		bool isValid();
		bool hasCovMat();
		//const bool hasCovMat() const;

		void setCorrelationFileName(FileName correlationFileName);
		void setCovarianceFileName(FileName covarianceFileName);
		void setImagesAndParameters(QMap<QString, QStringList> imagesAndParameters);

		SparseBlockColumnMatrix correlationMatrixFromFile(QDataStream inStream);
		//might need something called deleteLater(), called from MatrixTreeWidgetItem constructor.

		//if cov filename is null we need to ask the user to find it.

		FileName correlationFileName();
		FileName covarianceFileName();
		QMap<QString, QStringList> *imagesAndParameters();

		void getWholeMatrix();
		void getThreeVisibleBlocks();

		// Need these for range used to pick colors....
		QList<SparseBlockColumnMatrix> *visibleBlocks();

		PvlObject pvlObject();

		QDataStream &write(QDataStream &stream) const;
		QDataStream &read(QDataStream &stream);

		private:
		//! This map holds the images used to create this matrix and their associated parameters.
		QMap<QString, QStringList> *m_imagesAndParameters;

		//! FileName of the covariance matrix calculated when the bundle was run.
		FileName *m_covarianceFileName;

		//! FileName of the correlation matrix
		FileName *m_correlationFileName;

		/**
		* List of the parameter values. Stored so we don't need to store all the SBCMs when
		* calculating the correlation values.
		*/
		QList<double> *m_diagonals;

		/**
		* This will be the three blocks (or whole matrix depending on size) that apply to
		* the given area.
		*/
		QList<SparseBlockColumnMatrix> *m_visibleBlocks;
		};
		// operators to read/write CorrelationMatrix to/from binary disk file
		QDataStream &operator<<(QDataStream &stream, const CorrelationMatrix &matrix);
		QDataStream &operator>>(QDataStream &stream, CorrelationMatrix &matrix);
		};

		Q_DECLARE_METATYPE(Isis::CorrelationMatrix);

		#endif

isis/src/control/objs/CorrelationMatrix/CorrelationMatrix.truth

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isis/src/control/objs/CorrelationMatrix/Makefile

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		ifeq ($(ISISROOT), $(BLANK))
		.SILENT:
		error:
		echo "Please set ISISROOT";
		else
		include $(ISISROOT)/make/isismake.objs
		endif
		No newline at end of file

isis/src/control/objs/CorrelationMatrix/unitTest.cpp

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