Preliminary hdf serialization for Bundle classes. (f7aea713) · Commits · aflab / astrogeology / ISIS3

isis/src/base/objs/Statistics/Statistics.cpp

+131 −63

Original line number	Diff line number	Diff line
		@@ -27,6 +27,10 @@

		#include <float.h>

		#include <H5Cpp.h>
		#include <hdf5_hl.h>
		#include <hdf5.h>

		#include "IException.h"
		#include "IString.h"
		#include "Project.h"
		@@ -37,27 +41,23 @@ using namespace std;
		namespace Isis {
		//! Constructs an IsisStats object with accumulators and counters set to zero.
		Statistics::Statistics(QObject *parent) : QObject(parent) {
		m_id = NULL;
		m_id = new QUuid(QUuid::createUuid());
		// m_id = NULL;
		// m_id = new QUuid(QUuid::createUuid());
		SetValidRange();
		Reset(); // initialize
		}



		Statistics::Statistics(Project project, XmlStackedHandlerReader xmlReader, QObject *parent) { // TODO: does xml stuff need project???
		m_id = NULL;
		// m_id = NULL;
		SetValidRange();
		Reset(); // initialize
		xmlReader->pushContentHandler(new XmlHandler(this, project)); // TODO: does xml stuff need project???
		}




		Statistics::Statistics(const Statistics &other)
		: m_id(new QUuid(other.m_id->toString())),
		m_sum(other.m_sum),
		: m_sum(other.m_sum),
		m_sumsum(other.m_sumsum),
		m_minimum(other.m_minimum),
		m_maximum(other.m_maximum),
		@@ -74,23 +74,22 @@ namespace Isis {
		m_overRangePixels(other.m_overRangePixels),
		m_removedData(other.m_removedData) {
		}

		// : m_id(new QUuid(other.m_id->toString())),


		//! Destroys the IsisStats object.
		Statistics::~Statistics() {
		delete m_id;
		m_id = NULL;
		// delete m_id;
		// m_id = NULL;
		}



		Statistics &Statistics::operator=(const Statistics &other) {

		if (&other != this) {
		delete m_id;
		m_id = NULL;
		m_id = new QUuid(other.m_id->toString());
		// delete m_id;
		// m_id = NULL;
		// m_id = new QUuid(other.m_id->toString());

		m_sum = other.m_sum;
		m_sumsum = other.m_sumsum;
		@@ -114,7 +113,6 @@ namespace Isis {
		}



		//! Reset all accumulators and counters to zero.
		void Statistics::Reset() {
		m_sum = 0.0;
		@@ -134,7 +132,6 @@ namespace Isis {
		}



		/**
		* Add an array of doubles to the accumulators and counters.
		* This method can be invoked multiple times (for example: once
		@@ -153,7 +150,6 @@ namespace Isis {
		}



		/**
		* Add a double to the accumulators and counters. This method
		* can be invoked multiple times (for example: once for each
		@@ -198,7 +194,6 @@ namespace Isis {
		}



		/**
		* Remove an array of doubles from the accumulators and counters.
		* Note that is invalidates the absolute minimum and maximum. They
		@@ -213,7 +208,6 @@ namespace Isis {
		* doesn't exist.
		*/
		void Statistics::RemoveData(const double *data, const unsigned int count) {
		m_removedData = true;

		for(unsigned int i = 0; i < count; i++) {
		double value = data[i];
		@@ -222,7 +216,9 @@ namespace Isis {

		}


		void Statistics::RemoveData(const double data) {
		m_removedData = true;
		m_totalPixels--;

		if (Isis::IsNullPixel(data)) {
		@@ -256,8 +252,10 @@ namespace Isis {
		QString msg = "You are removing non-existant data in [Statistics::RemoveData]";
		throw IException(IException::Programmer, msg, _FILEINFO_);
		}
		// what happens to saved off min/max???
		}


		void Statistics::SetValidRange(const double minimum, const double maximum) {
		m_validMinimum = minimum;
		m_validMaximum = maximum;
		@@ -268,40 +266,35 @@ namespace Isis {
		+ "] must be less than the Maximum [" + toString(maximum) + "].";
		throw IException(IException::Programmer, msg, _FILEINFO_);
		}
		//??? throw exception if data has already been added???
		}



		double Statistics::ValidMinimum() const {
		return m_validMinimum;
		}



		double Statistics::ValidMaximum() const {
		return m_validMaximum;
		}



		bool Statistics::InRange(const double value) {
		return (!BelowRange(value) && !AboveRange(value));
		}



		bool Statistics::AboveRange(const double value) {
		return (value > m_validMaximum);
		}



		bool Statistics::BelowRange(const double value) {
		return (value < m_validMinimum);
		}



		/**
		* Computes and returns the average.
		* If there are no valid pixels, then NULL8 is returned.
		@@ -313,6 +306,7 @@ namespace Isis {
		return m_sum / m_validPixels;
		}


		/**
		* Computes and returns the standard deviation.
		* If there are no valid pixels, then NULL8 is returned.
		@@ -324,6 +318,7 @@ namespace Isis {
		return sqrt(Variance());
		}


		/**
		* Computes and returns the variance.
		* If there are no valid pixels, then NULL8 is returned.
		@@ -342,7 +337,6 @@ namespace Isis {
		}



		/**
		* Returns the sum of all the data
		*
		@@ -353,7 +347,6 @@ namespace Isis {
		}



		/**
		* Returns the sum of all the squared data
		*
		@@ -364,7 +357,6 @@ namespace Isis {
		}



		/**
		* Computes and returns the rms.
		* If there are no valid pixels, then NULL8 is returned.
		@@ -381,6 +373,7 @@ namespace Isis {
		return sqrt(temp);
		}


		/**
		* Returns the absolute minimum double found in all data passed through the
		* AddData method. If there are no valid pixels, then NULL8 is returned.
		@@ -400,6 +393,7 @@ namespace Isis {
		return m_minimum;
		}


		/**
		* Returns the absolute maximum double found in all
		* data passed through the AddData method. If there
		@@ -420,6 +414,7 @@ namespace Isis {
		return m_maximum;
		}


		/**
		* Returns the total number of pixels processed
		* (valid and invalid).
		@@ -430,6 +425,7 @@ namespace Isis {
		return m_totalPixels;
		}


		/**
		* Returns the total number of valid pixels processed.
		* Only valid pixels are utilized when computing the
		@@ -442,6 +438,7 @@ namespace Isis {
		return m_validPixels;
		}


		/**
		* Returns the total number of pixels over the valid range
		* encountered.
		@@ -452,6 +449,7 @@ namespace Isis {
		return m_overRangePixels;
		}


		/**
		* Returns the total number of pixels under the valid range
		* encountered.
		@@ -462,6 +460,7 @@ namespace Isis {
		return m_underRangePixels;
		}


		/**
		* Returns the total number of NULL pixels encountered.
		*
		@@ -471,6 +470,7 @@ namespace Isis {
		return m_nullPixels;
		}


		/**
		* Returns the total number of low instrument
		* saturation (LIS) pixels encountered.
		@@ -481,6 +481,7 @@ namespace Isis {
		return m_lisPixels;
		}


		/**
		* Returns the total number of low representation
		* saturation (LRS) pixels encountered.
		@@ -491,6 +492,7 @@ namespace Isis {
		return m_lrsPixels;
		}


		/**
		* Returns the total number of high instrument
		* saturation (HIS) pixels encountered.
		@@ -501,6 +503,7 @@ namespace Isis {
		return m_hisPixels;
		}


		/**
		* Returns the total number of high representation
		* saturation (HRS) pixels encountered.
		@@ -511,6 +514,7 @@ namespace Isis {
		return m_hrsPixels;
		}


		/**
		* Returns the total number of pixels outside of
		* the valid range encountered.
		@@ -521,9 +525,12 @@ namespace Isis {
		return m_overRangePixels + m_underRangePixels;
		}


		bool Statistics::RemovedData() const {
		return m_removedData;
		}


		/**
		* This method returns a minimum such that X percent
		* of the data will fall with K standard deviations
		@@ -550,6 +557,7 @@ namespace Isis {
		return Average() - k * StandardDeviation();
		}


		/**
		* This method returns a maximum such that
		* X percent of the data will fall with K
		@@ -576,6 +584,7 @@ namespace Isis {
		return Average() + k * StandardDeviation();
		}


		/**
		* This method returns the better of the absolute
		* minimum or the Chebyshev minimum. The better
		@@ -597,6 +606,7 @@ namespace Isis {
		return min;
		}


		/**
		*
		* This method returns the better of the absolute
		@@ -619,6 +629,7 @@ namespace Isis {
		return max;
		}


		/**
		*
		* This method returns the better of the z-score
		@@ -644,11 +655,10 @@ namespace Isis {
		}



		void Statistics::save(QXmlStreamWriter &stream, const Project *project) const { // TODO: does xml stuff need project???

		stream.writeStartElement("statistics");
		stream.writeTextElement("id", m_id->toString());
		// stream.writeTextElement("id", m_id->toString());

		stream.writeTextElement("sum", toString(m_sum));
		stream.writeTextElement("sumSquares", toString(m_sumsum));
		@@ -678,7 +688,6 @@ namespace Isis {
		}



		Statistics::XmlHandler::XmlHandler(Statistics statistics, Project project) { // TODO: does xml stuff need project???
		m_xmlHandlerStatistics = statistics;
		m_xmlHandlerProject = project; // TODO: does xml stuff need project???
		@@ -686,7 +695,6 @@ namespace Isis {
		}



		Statistics::XmlHandler::~XmlHandler() {
		// do not delete this pointer... we don't own it, do we??? passed into StatCumProbDistDynCalc constructor as pointer
		// delete m_xmlHandlerProject; // TODO: does xml stuff need project???
		@@ -694,7 +702,6 @@ namespace Isis {
		}



		bool Statistics::XmlHandler::startElement(const QString &namespaceURI,
		const QString &localName,
		const QString &qName,
		@@ -707,20 +714,18 @@ namespace Isis {
		}



		bool Statistics::XmlHandler::characters(const QString &ch) {
		m_xmlHandlerCharacters += ch;
		return XmlStackedHandler::characters(ch);
		}



		bool Statistics::XmlHandler::endElement(const QString &namespaceURI, const QString &localName,
		const QString &qName) {
		if (!m_xmlHandlerCharacters.isEmpty()) {
		if (localName == "id") {
		m_xmlHandlerStatistics->m_id = NULL;
		m_xmlHandlerStatistics->m_id = new QUuid(m_xmlHandlerCharacters);
		// m_xmlHandlerStatistics->m_id = NULL;
		// m_xmlHandlerStatistics->m_id = new QUuid(m_xmlHandlerCharacters);
		}
		if (localName == "sum") {
		m_xmlHandlerStatistics->m_sum = toDouble(m_xmlHandlerCharacters);
		@@ -776,38 +781,43 @@ namespace Isis {
		}



		/**
		* Order saved must match the offsets in the static compoundH5DataType()
		* method.
		*/
		QDataStream &Statistics::write(QDataStream &stream) const {
		stream << m_id->toString()
		<< m_sum
		stream.setByteOrder(QDataStream::LittleEndian);
		stream << m_sum
		<< m_sumsum
		<< m_minimum
		<< m_maximum
		<< m_validMinimum
		<< m_validMaximum
		<< (qint32)m_totalPixels
		<< (qint32)m_validPixels
		<< (qint32)m_nullPixels
		<< (qint32)m_lrsPixels
		<< (qint32)m_lisPixels
		<< (qint32)m_hrsPixels
		<< (qint32)m_hisPixels
		<< (qint32)m_underRangePixels
		<< (qint32)m_overRangePixels
		<< m_removedData;
		<< (qint64)m_totalPixels
		<< (qint64)m_validPixels
		<< (qint64)m_nullPixels
		<< (qint64)m_lrsPixels
		<< (qint64)m_lisPixels
		<< (qint64)m_hrsPixels
		<< (qint64)m_hisPixels
		<< (qint64)m_underRangePixels
		<< (qint64)m_overRangePixels
		<< (qint32)m_removedData;
		return stream;
		// stream << m_id->toString()
		}



		QDataStream &Statistics::read(QDataStream &stream) {

		QString id;
		qint32 totalPixels, validPixels, nullPixels, lrsPixels, lisPixels,
		// QString id;
		qint64 totalPixels, validPixels, nullPixels, lrsPixels, lisPixels,
		hrsPixels, hisPixels, underRangePixels, overRangePixels;
		qint32 removedData;

		stream >> id
		>> m_sum
		stream.setByteOrder(QDataStream::LittleEndian);
		// stream >> id
		stream >> m_sum
		>> m_sumsum
		>> m_minimum
		>> m_maximum
		@@ -822,11 +832,11 @@ namespace Isis {
		>> hisPixels
		>> underRangePixels
		>> overRangePixels
		>> m_removedData;
		>> removedData;

		delete m_id;
		m_id = NULL;
		m_id = new QUuid(id);
		// delete m_id;
		// m_id = NULL;
		// m_id = new QUuid(id);

		m_totalPixels = (BigInt)totalPixels;
		m_validPixels = (BigInt)validPixels;
		@@ -837,20 +847,78 @@ namespace Isis {
		m_hisPixels = (BigInt)hisPixels;
		m_underRangePixels = (BigInt)underRangePixels;
		m_overRangePixels = (BigInt)overRangePixels;

		m_removedData = (bool)removedData;

		return stream;
		}



		QDataStream &operator<<(QDataStream &stream, const Statistics &statistics) {
		return statistics.write(stream);
		}



		QDataStream &operator>>(QDataStream &stream, Statistics &statistics) {
		return statistics.read(stream);
		}


		/**
		* H5 compound data type uses the offesets from the QDataStream returned by
		* the write(QDataStream &stream) method.
		*/
		H5::CompType Statistics::compoundH5DataType() {

		H5::CompType compoundDataType((size_t)124);

		size_t offset = 0;
		compoundDataType.insertMember("Sum", offset, H5::PredType::NATIVE_DOUBLE);

		offset += sizeof(m_sum);
		compoundDataType.insertMember("SumSquared", offset, H5::PredType::NATIVE_DOUBLE);

		offset += sizeof(m_sumsum);
		compoundDataType.insertMember("Minimum", offset, H5::PredType::NATIVE_DOUBLE);

		offset += sizeof(m_minimum);
		compoundDataType.insertMember("Maximum", offset, H5::PredType::NATIVE_DOUBLE);

		offset += sizeof(m_maximum);
		compoundDataType.insertMember("ValidMinimum", offset, H5::PredType::NATIVE_DOUBLE);

		offset += sizeof(m_validMinimum);
		compoundDataType.insertMember("ValidMaximum", offset, H5::PredType::NATIVE_DOUBLE);

		offset += sizeof(m_validMaximum);
		compoundDataType.insertMember("TotalPixels", offset, H5::PredType::NATIVE_INT64);

		offset += sizeof(m_totalPixels);
		compoundDataType.insertMember("ValidPixels", offset, H5::PredType::NATIVE_INT64);

		offset += sizeof(m_validPixels);
		compoundDataType.insertMember("NullPixels", offset, H5::PredType::NATIVE_INT64);

		offset += sizeof(m_nullPixels);
		compoundDataType.insertMember("LRSPixels", offset, H5::PredType::NATIVE_INT64);

		offset += sizeof(m_lrsPixels);
		compoundDataType.insertMember("LISPixels", offset, H5::PredType::NATIVE_INT64);

		offset += sizeof(m_lisPixels);
		compoundDataType.insertMember("HRSPixels", offset, H5::PredType::NATIVE_INT64);

		offset += sizeof(m_hrsPixels);
		compoundDataType.insertMember("HISPixels", offset, H5::PredType::NATIVE_INT64);

		offset += sizeof(m_hisPixels);
		compoundDataType.insertMember("UnderRangePixels", offset, H5::PredType::NATIVE_INT64);

		offset += sizeof(m_underRangePixels);
		compoundDataType.insertMember("OverRangePixels", offset, H5::PredType::NATIVE_INT64);

		offset += sizeof(m_overRangePixels);
		compoundDataType.insertMember("RemovedData", offset, H5::PredType::NATIVE_HBOOL);

		return compoundDataType;
		}
		} // end namespace isis

isis/src/base/objs/Statistics/Statistics.h

+17 −5

Original line number	Diff line number	Diff line
		@@ -22,6 +22,10 @@

		#include <QObject>

		#include <H5Cpp.h>
		#include <hdf5_hl.h>
		#include <hdf5.h>

		#include "Constants.h"
		#include "SpecialPixel.h"
		#include "XmlStackedHandler.h"
		@@ -74,15 +78,20 @@ namespace Isis {
		* @history 2006-03-10 Jacob Danton - Added Z-score method
		* @history 2007-01-18 Robert Sucharski - Added AddData method for a single double value
		* @history 2008-05-06 Steven Lambright - Added AboveRange, BelowRange methods
		* @history 2010-03-18 Sharmila Prasad - Error message more meaningful for SetValidRange function
		* @history 2010-03-18 Sharmila Prasad - Error message more meaningful for SetValidRange
		* function
		* @history 2011-06-13 Ken Edmundson - Added Rms method.
		* @history 2011-06-23 Jeannie Backer - Added QDataStream read(), write() methods and added
		* QDataStream >> and << operators. Replaced std strings with QStrings.
		* @history 2014-09-05 Jeannie Backer - Added xml read/write capabilities. Moved method
		* implementation to cpp file. Improved coverage of unitTest. Brought
		* code closer to standards.
		* @history 2015-09-03 Jeannie Backer - Added hdf5 read/write capabilities by adding
		* compoundH5DataType() static method.
		*
		* @todo 2005-02-07 Deborah Lee Soltesz - add example using cube data to the class documentation
		* @todo 2015-08-13 Jeannie Backer - Clean up header and implementation files once
		* serialization is implemented. (Remove xml, data stream, hdf, etc)
		*
		*/
		class Statistics : public QObject {
		@@ -145,6 +154,8 @@ namespace Isis {
		QDataStream &write(QDataStream &stream) const;
		QDataStream &read(QDataStream &stream);

		static H5::CompType compoundH5DataType();

		private:
		/**
		*
		@@ -173,10 +184,11 @@ namespace Isis {
		QString m_xmlHandlerCharacters;
		};

		QUuid m_id; /*< A unique ID for this object (useful for others to reference
		this object when saving to disk).*/
		double m_sum; //!< Sum accumulator.
		double m_sumsum; //!< Sum-squared accumulator.
		// QUuid m_id; /*< A unique ID for this object (useful for others to reference
		// this object when saving to disk).*/
		double m_sum; //!< The sum accumulator, i.e. the sum of added data values.
		double m_sumsum; /**< The sum-squared accumulator, i.e. the sum of the squares
		of the data values.*/
		double m_minimum; //!< Minimum double value encountered.
		double m_maximum; //!< Maximum double value encountered.
		double m_validMinimum; //!< Minimum valid pixel value

isis/src/control/objs/BundleAdjust/BundleAdjust.cpp

+57 −37

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isis/src/control/objs/BundleAdjust/BundleAdjust.h

+10 −2

Original line number	Diff line number	Diff line
		@@ -196,6 +196,12 @@ namespace Isis {
		* users to use the outputFilePrefix to specify a file path without
		* adding an underscore to the file name. If the underscore is wanted,
		* it should be added to the prefix when entered by the user.
		* @history 2015-09-03 Jeannie Backer - Changed the name of the output correlation matrix file
		* from ["inverseMatrix" + random unique code + ".dat"] to
		* [BundleSettings::outputFilePrefix() + "inverseMatrix.dat"]. So that
		* the prefix can be used to specify the path of the location where the
		* matrix file should be written. Some improvements made to comply with
		* coding standards.
		*/
		class BundleAdjust : public QObject {
		Q_OBJECT
		@@ -495,6 +501,10 @@ namespace Isis {

		BundleSettings m_bundleSettings; // pointer ??? then bundle settings method needs copy constructor ???
		// or constructors here take a const ref ???
		BundleResults m_bundleResults;
		// BundleSolutionInfo m_bundleSolveInformation;


		// unused variable ??? int m_nHeldPoints; //!< number of 'held' points (define)
		// unused variable ??? int m_nHeldObservations; //!< number of 'held' observations (define)
		// ??? moved to bundle stats class //!< vectors for statistical computations...
		@@ -503,8 +513,6 @@ Statistics m_Statsy; //!< y errors
		Statistics m_Statsrx; //!< x residuals
		Statistics m_Statsry; //!< y residuals
		Statistics m_Statsrxy; //!< xy residuals
		BundleResults m_bundleResults;
		// BundleSolutionInfo m_bundleSolveInformation;
		};
		}

isis/src/control/objs/BundleResults/BundleResults.cpp

+625 −254

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