PROG: Improved Statistics class coding standards. Added QDataStream, XML, HDF... (d3d2af24) · Commits · aflab / astrogeology / ISIS3

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

+560 −94

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

+106 −101

Original line number	Diff line number	Diff line
		@@ -20,11 +20,23 @@
		* http://www.usgs.gov/privacy.html.
		*/

		#include <QObject>

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

		#include "SpecialPixel.h"
		#include "Constants.h"
		#include "SpecialPixel.h"
		#include "XmlStackedHandler.h"

		class QDataStream;
		class QUuid;
		class QXmlStreamWriter;

		namespace Isis {
		class Project;// ??? does xml stuff need project???
		class XmlStackedHandlerReader;
		/**
		* @brief This class is used to accumulate statistics on double arrays.
		*
		@@ -50,104 +62,72 @@ namespace Isis {
		* Histogram object (inherits from Statistics) and the stats application,
		* stats.cpp (uses the Statistics child class Histogram).
		*
		* @ingroup Math
		* @ingroup Statistics
		*
		* @author 2002-05-06 Jeff Anderson
		*
		* @internal
		* @history 2002-05-08 Jeff Anderson - Added Chebyshev and Best
		* minimum/maximum methods.
		* @history 2004-05-11 Jeff Anderson - Moved Reset, AddData and RemoveData
		* methods into public space.
		* @history 2002-05-08 Jeff Anderson - Added Chebyshev and Best minimum/maximum methods.
		* @history 2004-05-11 Jeff Anderson - Moved Reset, AddData and RemoveData methods into public
		* space.
		* @history 2004-06-28 Jeff Anderson - Added Sum and SumSquare methods.
		* @history 2005-02-17 Deborah Lee Soltesz - Modified file to support Doxygen
		* documentation.
		* @history 2005-02-17 Deborah Lee Soltesz - Modified file to support Doxygen documentation.
		* @history 2005-05-23 Jeff Anderson - Changed to support 2GB+ files
		* @history 2006-02-15 Jacob Danton - Added Valid Range options/methods
		* @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 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 2011-06-13 Ken Edmundson - Added Rms method
		* @history 2010-03-18 Sharmila Prasad - Error message more meaningful for SetValidRange
		* function
		* @history 2011-06-13 Ken Edmundson - Added Rms method.
		* @history 2015-09-01 Tyler Wilson - Made SetValidRange and the destructor virtual.
		* See Ref #2188.
		* @todo 2005-02-07 Deborah Lee Soltesz - add example using cube data to the
		* class documentation
		* @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 {
		class Statistics : public QObject {
		Q_OBJECT
		public:
		Statistics();
		Statistics(QObject *parent = 0);
		Statistics(Project project, XmlStackedHandlerReader xmlReader, QObject *parent = 0);
		// TODO: does xml read/write stuff need Project input???
		Statistics(const Statistics &other);
		virtual ~Statistics();
		Statistics &operator=(const Statistics &other);

		void Reset();

		void AddData(const double *data, const unsigned int count);
		/**
		* Add a double to the accumulators and counters. This method
		* can be invoked multiple times (for example: once for each
		* pixel in a cube) before obtaining statistics.
		*
		* @param data The data to be added to the data set used for statistical
		* calculations.
		*
		*/
		inline void AddData(const double data) {
		p_totalPixels++;
		if(Isis::IsValidPixel(data) && InRange(data)) {
		p_sum += data;
		p_sumsum += data * data;
		if(data < p_minimum) p_minimum = data;
		if(data > p_maximum) p_maximum = data;
		p_validPixels++;
		}
		else if(Isis::IsNullPixel(data)) {
		p_nullPixels++;
		}
		else if(Isis::IsHisPixel(data)) {
		p_hisPixels++;
		}
		else if(Isis::IsHrsPixel(data)) {
		p_hrsPixels++;
		}
		else if(Isis::IsLisPixel(data)) {
		p_lisPixels++;
		}
		else if(Isis::IsLrsPixel(data)) {
		p_lrsPixels++;
		}
		else if(AboveRange(data)) {
		p_overRangePixels++;
		}
		else {
		p_underRangePixels++;
		}
		}
		void AddData(const double data);

		void RemoveData(const double *data, const unsigned int count);
		void RemoveData(const double data);
		virtual void SetValidRange(const double minimum = Isis::ValidMinimum,

		void SetValidRange(const double minimum = Isis::ValidMinimum,
		const double maximum = Isis::ValidMaximum);

		double ValidMinimum() const {
		return p_validMinimum;
		}
		double ValidMaximum() const {
		return p_validMaximum;
		}
		bool InRange(const double value) {
		return (value >= p_validMinimum && value <= p_validMaximum);
		}
		bool AboveRange(const double value) {
		return (value > p_validMaximum);
		}
		bool BelowRange(const double value) {
		return (value < p_validMinimum);
		}
		double ValidMinimum() const;
		double ValidMaximum() const;
		bool InRange(const double value);
		bool AboveRange(const double value);
		bool BelowRange(const double value);

		double Average() const;
		double StandardDeviation() const;
		double Variance() const;
		double Sum() const;
		double SumSquare() const;
		double Rms() const;

		double Minimum() const;
		@@ -168,45 +148,70 @@ namespace Isis {
		BigInt HisPixels() const;
		BigInt HrsPixels() const;
		BigInt OutOfRangePixels() const;
		bool RemovedData() const;

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

		/**
		* Returns the sum of all the data
		*
		* @return The sum of the data
		*/
		double Sum() const {
		return p_sum;
		};
		QDataStream &write(QDataStream &stream) const;
		QDataStream &read(QDataStream &stream);

		static H5::CompType compoundH5DataType();

		private:
		/**
		* Returns the sum of all the squared data
		*
		* @return The sum of the squared data
		* @author 2014-07-28 Jeannie Backer
		*
		* @internal
		*/
		double SumSquare() const {
		return p_sumsum;
		};
		class XmlHandler : public XmlStackedHandler {
		public:
		XmlHandler(Statistics statistics, Project project);
		// TODO: does xml stuff need project???
		~XmlHandler();

		virtual bool startElement(const QString &namespaceURI, const QString &localName,
		const QString &qName, const QXmlAttributes &atts);
		virtual bool characters(const QString &ch);
		virtual bool endElement(const QString &namespaceURI, const QString &localName,
		const QString &qName);

		private:
		double p_sum; //!< Sum accumulator.
		double p_sumsum; //!< Sum-squared accumulator.
		double p_minimum; //!< Minimum double value encountered.
		double p_maximum; //!< Maximum double value encountered.
		double p_validMinimum; //!< Minimum valid pixel value
		double p_validMaximum; //!< Maximum valid pixel value
		BigInt p_totalPixels; //!< Count of total pixels processed.
		BigInt p_validPixels; //!< Count of valid pixels (non-special) processed.
		BigInt p_nullPixels; //!< Count of null pixels processed.
		BigInt p_lrsPixels; //!< Count of low instrument saturation pixels processed.
		BigInt p_lisPixels; //!< Count of low representation saturation pixels processed.
		BigInt p_hrsPixels; //!< Count of high instrument saturation pixels processed.
		BigInt p_hisPixels; //!< Count of high instrument representation pixels processed.
		BigInt p_underRangePixels; //!< Count of pixels less than the valid range
		BigInt p_overRangePixels; //!< Count of pixels greater than the valid range
		bool p_removedData; /**< Indicates the RemoveData method was called which implies
		p_minimum and p_maximum are invalid. */
		Q_DISABLE_COPY(XmlHandler);

		Statistics *m_xmlHandlerStatistics;
		Project *m_xmlHandlerProject;
		// TODO: does xml stuff need project???
		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; //!< 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
		double m_validMaximum; //!< Maximum valid pixel value
		BigInt m_totalPixels; //!< Count of total pixels processed.
		BigInt m_validPixels; //!< Count of valid pixels (non-special) processed.
		BigInt m_nullPixels; //!< Count of null pixels processed.
		BigInt m_lrsPixels; //!< Count of low instrument saturation pixels processed.
		BigInt m_lisPixels; //!< Count of low representation saturation pixels processed.
		BigInt m_hrsPixels; //!< Count of high instrument saturation pixels processed.
		BigInt m_hisPixels; //!< Count of high instrument representation pixels processed.
		BigInt m_underRangePixels; //!< Count of pixels less than the valid range
		BigInt m_overRangePixels; //!< Count of pixels greater than the valid range
		bool m_removedData; /**< Indicates the RemoveData method was called which implies
		m_minimum and m_maximum are invalid. */
		};

		// operators to read/write Statistics to/from binary data
		QDataStream &operator<<(QDataStream &stream, const Statistics &statistics);
		QDataStream &operator>>(QDataStream &stream, Statistics &statistics);

		} // end namespace isis

		#endif

isis/src/base/objs/Statistics/Statistics.truth

+226 −12

Original line number	Diff line number	Diff line
		Unit test for Statistics...
		For data set: 5, 5
		Average: 5
		ZScore(5.0): 0

		Testing Reset...
		Average: -1.79769e+308
		Variance: -1.79769e+308
		Rms: -1.79769e+308
		Std Deviation: -1.79769e+308
		Minimum: -1.79769e+308
		Maximum: -1.79769e+308
		ChebyShev Min: -1.79769e+308
		ChebyShev Max: -1.79769e+308
		Best Minimum: -1.79769e+308
		Best Maximum: -1.79769e+308
		Valid Minimum: -1.79769e+308
		Valid Maximum: 1.79769e+308
		Total Pixels: 0
		Valid Pixels: 0
		Null Pixels: 0
		Lis Pixels: 0
		Lrs Pixels: 0
		His Pixels: 0
		Hrs Pixels: 0
		Out of Range Pixels: 0
		Over Range Pixels: 0
		Under Range Pixels: 0
		Sum: 0
		SumSquare: 0
		Removed Data? false
		Z-Score at 1.0 -1

		SetValidRange(1, 6) and AddData( 1, 2, 3, Null, HRS, LRS, HIS, LIS, 10, -1)
		InRange(0.0)? false
		InRange(2.0)? true
		InRange(7.0)? false
		Average: 2
		Variance: 1
		Rms: 2.16025
		@@ -9,16 +45,24 @@ ChebyShev Min: -12.1421
		ChebyShev Max: 16.1421
		Best Minimum: 1
		Best Maximum: 3
		Total Pixels: 8
		Valid Minimum: 1
		Valid Maximum: 6
		Total Pixels: 10
		Valid Pixels: 3
		Null Pixels: 1
		Lis Pixels: 1
		Lrs Pixels: 1
		His Pixels: 1
		Hrs Pixels: 1
		Out of Range Pixels: 2
		Over Range Pixels: 1
		Under Range Pixels: 1
		Sum: 6
		SumSquare: 14
		Removed Data? false
		Z-Score at 1.0 -1

		AddData( 4, 5, 6, Null)
		Average: 3.5
		Variance: 3.5
		Rms: 3.89444
		@@ -29,38 +73,198 @@ ChebyShev Min: -22.9575
		ChebyShev Max: 29.9575
		Best Minimum: 1
		Best Maximum: 6
		Total Pixels: 12
		Valid Minimum: 1
		Valid Maximum: 6
		Total Pixels: 14
		Valid Pixels: 6
		Null Pixels: 2
		Lis Pixels: 1
		Lrs Pixels: 1
		His Pixels: 1
		Hrs Pixels: 1
		Out of Range Pixels: 2
		Over Range Pixels: 1
		Under Range Pixels: 1
		Sum: 21
		SumSquare: 91
		Removed Data? false
		Z-Score at 1.0 -1.33631

		Average: 5
		Variance: 1
		Rms: 5.06623
		Std Deviation: 1
		ChebyShev Min: -9.14214
		ChebyShev Max: 19.1421
		Total Pixels: 9
		Valid Pixels: 3
		Testing copy constructor...
		Average: 3.5
		Variance: 3.5
		Rms: 3.89444
		Std Deviation: 1.87083
		Minimum: 1
		Maximum: 6
		ChebyShev Min: -22.9575
		ChebyShev Max: 29.9575
		Best Minimum: 1
		Best Maximum: 6
		Valid Minimum: 1
		Valid Maximum: 6
		Total Pixels: 14
		Valid Pixels: 6
		Null Pixels: 2
		Lis Pixels: 1
		Lrs Pixels: 1
		His Pixels: 1
		Hrs Pixels: 1
		Out of Range Pixels: 2
		Over Range Pixels: 1
		Under Range Pixels: 1
		Sum: 21
		SumSquare: 91
		Removed Data? false
		Z-Score at 1.0 -1.33631

		Testing assignment operator=...
		Average: 3.5
		Variance: 3.5
		Rms: 3.89444
		Std Deviation: 1.87083
		Minimum: 1
		Maximum: 6
		ChebyShev Min: -22.9575
		ChebyShev Max: 29.9575
		Best Minimum: 1
		Best Maximum: 6
		Valid Minimum: 1
		Valid Maximum: 6
		Total Pixels: 14
		Valid Pixels: 6
		Null Pixels: 2
		Lis Pixels: 1
		Lrs Pixels: 1
		His Pixels: 1
		Hrs Pixels: 1
		Out of Range Pixels: 2
		Over Range Pixels: 1
		Under Range Pixels: 1
		Sum: 21
		SumSquare: 91
		Removed Data? false
		Z-Score at 1.0 -1.33631

		Average: 3.5
		Variance: 3.5
		Rms: 3.89444
		Std Deviation: 1.87083
		Minimum: 1
		Maximum: 6
		ChebyShev Min: -22.9575
		ChebyShev Max: 29.9575
		Best Minimum: 1
		Best Maximum: 6
		Valid Minimum: 1
		Valid Maximum: 6
		Total Pixels: 14
		Valid Pixels: 6
		Null Pixels: 2
		Lis Pixels: 1
		Lrs Pixels: 1
		His Pixels: 1
		Hrs Pixels: 1
		Sum: 15
		SumSquare: 77
		Out of Range Pixels: 2
		Over Range Pixels: 1
		Under Range Pixels: 1
		Sum: 21
		SumSquare: 91
		Removed Data? false
		Z-Score at 1.0 -1.33631

		Testing RemoveData(3, Null, HRS, LRS, HIS, LIS, 10, -1)
		Average: 3.6
		Variance: 4.3
		Rms: 4.04969
		Std Deviation: 2.07364
		ChebyShev Min: -25.7258
		ChebyShev Max: 32.9258
		Total Pixels: 6
		Valid Pixels: 5
		Null Pixels: 1
		Lis Pixels: 0
		Lrs Pixels: 0
		His Pixels: 0
		Hrs Pixels: 0
		Out of Range Pixels: 0
		Over Range Pixels: 0
		Under Range Pixels: 0
		Sum: 18
		SumSquare: 82
		Removed Data? true
		Z-Score at 1.0 -1.25383

		Testing serialization from copy constructor object...
		Average: 3.5
		Variance: 3.5
		Rms: 3.89444
		Std Deviation: 1.87083
		Minimum: 1
		Maximum: 6
		ChebyShev Min: -22.9575
		ChebyShev Max: 29.9575
		Best Minimum: 1
		Best Maximum: 6
		Valid Minimum: 1
		Valid Maximum: 6
		Total Pixels: 14
		Valid Pixels: 6
		Null Pixels: 2
		Lis Pixels: 1
		Lrs Pixels: 1
		His Pixels: 1
		Hrs Pixels: 1
		Out of Range Pixels: 2
		Over Range Pixels: 1
		Under Range Pixels: 1
		Sum: 21
		SumSquare: 91
		Removed Data? false
		Z-Score at 1.0 -1.33631

		Testing XML: write XML from Statistics object...
		Testing XML: read XML to Statistics object...
		Average: 3.5
		Variance: 3.5
		Rms: 3.89444
		Std Deviation: 1.87083
		Minimum: 1
		Maximum: 6
		ChebyShev Min: -22.9575
		ChebyShev Max: 29.9575
		Best Minimum: 1
		Best Maximum: 6
		Valid Minimum: 1
		Valid Maximum: 6
		Total Pixels: 14
		Valid Pixels: 6
		Null Pixels: 2
		Lis Pixels: 1
		Lrs Pixels: 1
		His Pixels: 1
		Hrs Pixels: 1
		Out of Range Pixels: 2
		Over Range Pixels: 1
		Under Range Pixels: 1
		Sum: 21
		SumSquare: 91
		Removed Data? false
		Z-Score at 1.0 -1.33631

		Testing XML: read XML with no attributes or values to Statistics object...
		Average: -1.79769e+308
		Variance: -1.79769e+308
		Rms: -1.79769e+308
		Std Deviation: -1.79769e+308
		Minimum: -1.79769e+308
		Maximum: -1.79769e+308
		ChebyShev Min: -1.79769e+308
		ChebyShev Max: -1.79769e+308
		Best Minimum: -1.79769e+308
		Best Maximum: -1.79769e+308
		Valid Minimum: -1.79769e+308
		Valid Maximum: 1.79769e+308
		Total Pixels: 0
		Valid Pixels: 0
		Null Pixels: 0
		@@ -68,11 +272,21 @@ Lis Pixels: 0
		Lrs Pixels: 0
		His Pixels: 0
		Hrs Pixels: 0
		Out of Range Pixels: 0
		Over Range Pixels: 0
		Under Range Pixels: 0
		Sum: 0
		SumSquare: 0
		Removed Data? false
		Z-Score at 1.0 -1

		Testing error throws...
		PROGRAMMER ERROR You are removing non-existant data in [Statistics::RemoveData].
		PROGRAMMER ERROR Minimum is invalid since you removed data.
		PROGRAMMER ERROR Maximum is invalid since you removed data.
		PROGRAMMER ERROR Invalid value for percent.
		PROGRAMMER ERROR Invalid value for percent.
		PROGRAMMER ERROR Invalid value for percent.
		PROGRAMMER ERROR Invalid value for percent.
		PROGRAMMER ERROR Invalid Range: Minimum [100.0] must be less than the Maximum [0.0].
		PROGRAMMER ERROR Undefined Z-score. Standard deviation is zero and the input value[0.0] is out of range [5.0].

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

+442 −93

File changed.

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isis/src/base/objs/Statistics/unitTest_NoElementValues.xml

0 → 100755

+24 −0

Original line number	Diff line number	Diff line
		<?xml version="1.0" encoding="UTF-8"?>
		<statistics>
		<id></id>
		<sum></sum>
		<sumSquares></sumSquares>
		<range>
		<minimum></minimum>
		<maximum></maximum>
		<validMinimum></validMinimum>
		<validMaximum></validMaximum>
		</range>
		<pixelCounts>
		<totalPixels></totalPixels>
		<validPixels></validPixels>
		<nullPixels></nullPixels>
		<lisPixels></lisPixels>
		<lrsPixels></lrsPixels>
		<hisPixels></hisPixels>
		<hrsPixels></hrsPixels>
		<underRangePixels></underRangePixels>
		<overRangePixels></overRangePixels>
		</pixelCounts>
		<removedData></removedData>
		</statistics>

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

+1 −1

File changed.

Contains only whitespace changes.