OmgModel Class Reference
[Library]

#include <omgmodel.h>

Inheritance diagram for OmgModel:

[legend]Collaboration diagram for OmgModel:

[legend]List of all members.

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Detailed Description

A representation of a model. Can be serialised to xml that openmodeller lib understands and can store rich model info returned by openModeller lib.

Definition at line 41 of file omgmodel.h.

Public Types
enum	LocalitiesFilterType { NO_FILTER, SPATIALLY_UNIQUE, ENVIRONMENTALLY_UNIQUE }
Public Slots
void	appendToLog (QString theMessage)
void	setLog (QString theLog)
Public Member Functions
	OmgModel ()
	~OmgModel ()
bool	isValid () const
QString	toString () const
QString	toHtml (bool theForceFlag=false) const
QString	toPrintHtml (bool theForceFlag=false) const
void	createRocGraph (bool theForceFlag=false) const
QString	projectionLayersXml ()
void	reset ()
bool	parseModelResult (QString theModelXml)
void	setCoordinateSystem (QString theCoordinateSystem)
void	setCoordinateSystemName (QString theName)
void	setOccurrencesFile (QString theSpeciesFile)
void	setSpeciesFile (QString theFileName)
void	setShapefileName (QString theFileName)
void	setCsvFileName (QString theFileName)
void	setTaxonName (QString theName)
void	setLocalities (OmgLocalities theLocalities)
void	setOutputFormatLayerName (QString theName)
void	setModelRasterFormat (QString theFormat)
void	setCreationLayerSet (OmgLayerSet theLayerSet)
void	setProjectionLayerSet (OmgLayerSet theLayerSet)
void	setCreationLayerNames (QStringList theNames)
void	setcreationMaskLayerName (QString theName)
void	setProjectionLayerNames (QStringList theNames)
void	setProjectionMaskLayerName (QString theName)
void	setAlgorithm (OmgAlgorithm theAlgorithm)
void	setCompleted (bool theFlag)
void	setError (bool theFlag)
void	setStartDateTimeStamp (QDateTime theDateTimeStamp)
void	setEndDateTimeStamp (QDateTime theDateTimeStamp)
void	setThumbnailFileName (QString theFileName)
void	setPreviewFileName (QString theFileName)
void	setLegendFileName (QString theFileName)
void	setRawImageFileName (QString theFileName)
void	setColouredImageFileName (QString theFileName)
void	setWorkDir (QString theDir)
void	setModelDefinition (QString theDefinition)
void	setNormalizationDefinition (QString theDefinition)
void	setRocScore (double theRocScore)
void	setAccuracy (double theAccuracy)
void	setOmission (double theOmission)
void	setCommission (double theCommission)
void	setPercentCellsPresent (double thePercent)
void	setTotalCells (double theTotal)
void	setLocalitiesFilterType (LocalitiesFilterType theFilterType=NO_FILTER)
QString	coordinateSystem () const
QString	coordinateSystemName () const
QString	speciesFile () const
QString	shapefileName () const
QString	csvFileName () const
QString	taxonName () const
OmgLayerSet	creationLayerSet () const
OmgLayerSet	projectionLayerSet () const
QString	creationMaskLayerName () const
QString	projectionMaskLayerName () const
QString	outputFormatLayerName () const
QStringList	creationLayerNames () const
QStringList	projectionLayerNames () const
OmgAlgorithm	algorithm () const
bool	isCompleted () const
bool	hasError () const
QDateTime	startDateTimeStamp () const
QDateTime	endDateTimeStamp () const
QString	thumbnailFileName () const
QString	previewFileName () const
QString	legendFileName () const
QString	rawImageFileName () const
QString	colouredImageFileName () const
QString	modelRasterFormat () const
QString	workDir () const
double	rocScore () const
double	accuracy () const
double	omission () const
double	commission () const
double	percentCellsPresent () const
double	totalCells () const
QString	modelDefinition () const
QString	normalizationDefinition () const
LocalitiesFilterType	localitiesFilterType () const
OmgLocalities	localities () const
QString	modelLog () const
unsigned int	loadLocalities ()
void	createThumbnail ()
QString	toXml () const
bool	fromXml (const QString theXml)
QString	toModelCreationXml () const
QString	toModelProjectionXml () const
QString	localitiesToCsv (QString theDelimiter="\t") const
bool	toShapefile (QString theShapefileName) const
void	addRocPoint (QPair< double, double > thePair)
void	clearRocPoints ()
OmgDataSeries	getRocPoints () const
bool	postProcess ()
Private Attributes
QString	mCoordinateSystem
	todo - make a class to represent a coordsys rather
QString	mCoordinateSystemName
QString	mSpeciesFile
QString	mTaxonName
OmgLayer	mOutputFormatLayer
OmgLayerSet	mProjectionLayerSet
OmgLayerSet	mCreationLayerSet
OmgAlgorithm	mAlgorithm
bool	mCompletedFlag
bool	mErrorFlag
OmgLocalities	mLocalities
QDateTime	mStartDateTimeStamp
QDateTime	mEndDateTimeStamp
QString	mThumbnailFileName
QString	mPreviewFileName
QString	mLegendFileName
QString	mRawImageFileName
QString	mShapefileName
QString	mCsvFileName
QString	mColouredImageFileName
QString	mWorkDir
QString	mModelDefinition
QString	mNormalizationDefinition
double	mRocScore
double	mAccuracy
double	mOmission
double	mCommission
double	mPercentCellsPresent
double	mTotalCells
QString	mModelLog
QList< QPair< double, double > >	mRocPoints
QString	mModelRasterFormat
LocalitiesFilterType	mLocalitiesFilterType

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Member Enumeration Documentation

enum OmgModel::LocalitiesFilterType

An enumerated type defining possible types of localities filter Enumeration values: NO_FILTER  SPATIALLY_UNIQUE  ENVIRONMENTALLY_UNIQUE  Definition at line 50 of file omgmodel.h.

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Constructor & Destructor Documentation

OmgModel::OmgModel (   )

Definition at line 39 of file omgmodel.cpp.

OmgModel::~OmgModel (   )

Definition at line 76 of file omgmodel.cpp.

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Member Function Documentation

double OmgModel::accuracy (   )  const

Get the accuracy for this model (from confusion matrix) Definition at line 1500 of file omgmodel.cpp. References mAccuracy. Referenced by OmgExperiment::getStatsHtml(), and OmgExperiment::makeAlgorithmSummaryGraphs().

void OmgModel::addRocPoint (  QPair< double, double >  thePair  )

Add a point to the list of roc xy values for the roc graph. Parameters: QPair<double,double>  a pair of doubles representing the x,y values that are added to the roc curve. Definition at line 1039 of file omgmodel.cpp. References mRocPoints. Referenced by fromXml().

OmgAlgorithm OmgModel::algorithm (   )  const

Definition at line 1442 of file omgmodel.cpp. References mAlgorithm. Referenced by OmgExperiment::getStatsHtml(), OmgExperiment::makeAlgorithmSummaryGraphs(), OmgRasterThreshold::populateTree(), OmgMainWindow::populateTree(), OmgExperiment::removeAlgorithm(), OmgExperimentPrinter::run(), OmgExperiment::run(), OmgExperiment::setWorkDir(), OmgMainWindow::showAlgorithmSummary(), OmgExperiment::toAlgorithmSummaryHtml(), and OmgExperiment::toTaxonSummaryHtml().

void OmgModel::appendToLog (  QString  theMessage  )  [slot]

Append a message to the model log Definition at line 1367 of file omgmodel.cpp. References mModelLog. Referenced by postProcess(), and OmgExperiment::run().

void OmgModel::clearRocPoints (   )

Clear the list of roc xy values for the roc graph Definition at line 1044 of file omgmodel.cpp. References mRocPoints.

QString OmgModel::colouredImageFileName (   )  const

Definition at line 1487 of file omgmodel.cpp. References mColouredImageFileName.

double OmgModel::commission (   )  const

Get the commission score for this model (from confusion matrix) Returns: -1 if the commision is invalid ( in the case of models run with no absence data) Definition at line 1508 of file omgmodel.cpp. References mCommission. Referenced by OmgExperiment::getStatsHtml(), and OmgExperiment::makeAlgorithmSummaryGraphs().

QString OmgModel::coordinateSystem (   )  const

Retreive the globally unique identifier for this model Definition at line 1382 of file omgmodel.cpp. References mCoordinateSystem.

QString OmgModel::coordinateSystemName (   )  const

Definition at line 1387 of file omgmodel.cpp. References mCoordinateSystemName.

void OmgModel::createRocGraph (  bool  theForceFlag = false  )  const

Definition at line 1014 of file omgmodel.cpp. References OmgGraph::addSeries(), getRocPoints(), mTaxonName, mWorkDir, OmgGraph::render(), OmgGraph::setAreaFillEnabled(), OmgGraph::setDiagonalEnabled(), OmgDataSeries::setFillColor(), OmgGraph::setGridLinesEnabled(), OmgDataSeries::setLineColor(), OmgGraph::setSpliningEnabled(), OmgGraph::setVertexLabelsEnabled(), and OmgGraph::setVerticesEnabled(). Referenced by toHtml(), and toPrintHtml().

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void OmgModel::createThumbnail (   )

Create the thumbnail preview of the model for the thumbnail browser. Definition at line 1536 of file omgmodel.cpp. References Omgui::createThumbnail(), hasError(), isCompleted(), mAlgorithm, mTaxonName, mWorkDir, OmgAlgorithm::name(), rawImageFileName(), and setThumbnailFileName(). Referenced by postProcess(), and OmgMainWindow::refreshReports().

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QStringList OmgModel::creationLayerNames (   )  const

Definition at line 1434 of file omgmodel.cpp. References mCreationLayerSet, and OmgLayerSet::nameList(). Referenced by localitiesToCsv(), and OmgModelTest::run().

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OmgLayerSet OmgModel::creationLayerSet (   )  const

Definition at line 1414 of file omgmodel.cpp. References mCreationLayerSet.

QString OmgModel::creationMaskLayerName (   )  const

Definition at line 1422 of file omgmodel.cpp. References OmgLayerSet::maskName(), and mCreationLayerSet.

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QString OmgModel::csvFileName (   )  const

Definition at line 1404 of file omgmodel.cpp. References mCsvFileName.

QDateTime OmgModel::endDateTimeStamp (   )  const

Definition at line 1458 of file omgmodel.cpp. References mEndDateTimeStamp. Referenced by OmgExperiment::getStatsHtml(), and OmgExperiment::makeAlgorithmSummaryGraphs().

bool OmgModel::fromXml (  const QString  theXml  )  [virtual]

Implments the serialisable interface method to reinstate a model. It will try to populate all members of this class and fail gracefully when they are not available (typically by leaving the member tagged as [Not Set] Implements OmgSerialisable. Definition at line 126 of file omgmodel.cpp. References addRocPoint(), ENVIRONMENTALLY_UNIQUE, OmgLayerSet::fromXml(), OmgAlgorithm::fromXml(), mAccuracy, mCommission, mCompletedFlag, mCoordinateSystem, mCoordinateSystemName, mCreationLayerSet, mCsvFileName, mEndDateTimeStamp, mErrorFlag, mLocalities, mLocalitiesFilterType, mModelDefinition, mModelLog, mNormalizationDefinition, mOmission, mOutputFormatLayer, mPercentCellsPresent, mProjectionLayerSet, mRocPoints, mRocScore, mShapefileName, mSpeciesFile, mStartDateTimeStamp, mTaxonName, mTotalCells, mWorkDir, NO_FILTER, OmgLocality::setAbundance(), setAlgorithm(), OmgLayer::setCategorical(), setColouredImageFileName(), OmgGuid::setGuid(), OmgLocality::setId(), OmgLocality::setLatitude(), setLegendFileName(), OmgLocality::setLongitude(), setModelRasterFormat(), OmgLayer::setName(), setPreviewFileName(), setRawImageFileName(), OmgLocality::setSamples(), setThumbnailFileName(), and SPATIALLY_UNIQUE. Referenced by OmgExperiment::fromXml(), OmgLocalitiesModelTest::rowsAndColumns(), and OmgModelTest::run().

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OmgDataSeries OmgModel::getRocPoints (   )  const

Get the roc graph as an omgdataseries Definition at line 1049 of file omgmodel.cpp. References mRocPoints, and OmgDataSeries::setLabel(). Referenced by createRocGraph().

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bool OmgModel::hasError (   )  const

Definition at line 1446 of file omgmodel.cpp. References mErrorFlag. Referenced by createThumbnail(), OmgExperiment::getStatsHtml(), OmgMainWindow::populateTree(), and OmgExperiment::run().

bool OmgModel::isCompleted (   )  const

Definition at line 1450 of file omgmodel.cpp. References mCompletedFlag. Referenced by createThumbnail(), OmgExperiment::getStatsHtml(), OmgRasterThreshold::populateTree(), OmgMainWindow::populateTree(), OmgExperiment::removeCompleted(), and OmgExperiment::run().

bool OmgModel::isValid (   )  const

Todo: implement proper check here! Definition at line 81 of file omgmodel.cpp.

QString OmgModel::legendFileName (   )  const

Definition at line 1470 of file omgmodel.cpp. References mLegendFileName.

unsigned int OmgModel::loadLocalities (   )

Once the taxon name and species file properties have been set, you can call this method to populate the localities collection. Definition at line 1149 of file omgmodel.cpp. References OmgLocality::isValid(), mLocalities, mSpeciesFile, mTaxonName, OmgLocality::setAbundance(), OmgLocality::setId(), OmgLocality::setLabel(), OmgLocality::setLatitude(), and OmgLocality::setLongitude(). Referenced by OmgExperimentDesigner::getExperiment(), and OmgModelTest::loadLocalities().

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OmgLocalities OmgModel::localities (   )  const

Definition at line 1378 of file omgmodel.cpp. References mLocalities. Referenced by localitiesToCsv().

OmgModel::LocalitiesFilterType OmgModel::localitiesFilterType (   )  const

Whether the model creation should use a filter on the samples to remove duplicates Returns: LocalitiesFilterType Indicating the state of this setting Definition at line 1144 of file omgmodel.cpp. References mLocalitiesFilterType.

QString OmgModel::localitiesToCsv (  QString  theDelimiter = "\t"  )  const

A helper function for getting a CSV representation of the samples (sites plug environmental values) Parameters: theDelimter  - A QString containing the required delimiter Returns: A QString holding the CSV matrix Definition at line 1081 of file omgmodel.cpp. References creationLayerNames(), OmgLocality::id(), OmgLocality::latitude(), localities(), OmgLocality::longitude(), and OmgLocality::samples(). Referenced by postProcess(), and Localities2CsvTest::writeLocalities2Csv().

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QString OmgModel::modelDefinition (   )  const

Definition at line 1521 of file omgmodel.cpp. References mModelDefinition.

QString OmgModel::modelLog (   )  const

Definition at line 1531 of file omgmodel.cpp. References mModelLog.

QString OmgModel::modelRasterFormat (   )  const

The output raster format of the model as defined in the om lib Definition at line 1076 of file omgmodel.cpp. References mModelRasterFormat. Referenced by OmgRasterThreshold::accept().

QString OmgModel::normalizationDefinition (   )  const

Definition at line 1526 of file omgmodel.cpp. References mNormalizationDefinition.

double OmgModel::omission (   )  const

Get the omission score for this model (from confusion matrix) Definition at line 1504 of file omgmodel.cpp. References mOmission. Referenced by OmgExperiment::getStatsHtml(), and OmgExperiment::makeAlgorithmSummaryGraphs().

QString OmgModel::outputFormatLayerName (   )  const

Definition at line 1430 of file omgmodel.cpp. References mOutputFormatLayer, and OmgLayer::name().

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bool OmgModel::parseModelResult (  QString  theModelXml  )

Parse the model xml provided and get the samples and add them to the model. Also add the serialised model. Parameters: QString  theModelXml a model as returned by the modeller plugin Returns: bool true on success. Definition at line 1579 of file omgmodel.cpp. References OmgLocality::setAbundance(), OmgLocality::setId(), OmgLocality::setLatitude(), setLocalities(), OmgLocality::setLongitude(), setModelDefinition(), setNormalizationDefinition(), and OmgLocality::setSamples(). Referenced by OmgModelTest::run(), and OmgExperiment::run().

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double OmgModel::percentCellsPresent (   )  const

Get the percent cells present for this model (from confusion matrix) Definition at line 1512 of file omgmodel.cpp. References mPercentCellsPresent. Referenced by OmgExperiment::getStatsHtml(), and OmgExperiment::makeAlgorithmSummaryGraphs().

bool OmgModel::postProcess (   )

Perform post processing tasks on the model. This will generate a pseudocolor preview image, csv localities file and other products from the model output. Returns: bool true on success Definition at line 1707 of file omgmodel.cpp. References appendToLog(), Omgui::createTextFile(), createThumbnail(), localitiesToCsv(), OmgGdal::makeLegend(), rawImageFileName(), setCompleted(), setCsvFileName(), setEndDateTimeStamp(), setError(), setLegendFileName(), setPreviewFileName(), taxonName(), toHtml(), workDir(), and OmgGdal::writeImage(). Referenced by OmgExperiment::run().

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QString OmgModel::previewFileName (   )  const

Definition at line 1466 of file omgmodel.cpp. References mPreviewFileName.

QStringList OmgModel::projectionLayerNames (   )  const

Definition at line 1438 of file omgmodel.cpp. References mProjectionLayerSet, and OmgLayerSet::nameList(). Referenced by OmgModelTest::run().

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OmgLayerSet OmgModel::projectionLayerSet (   )  const

Definition at line 1418 of file omgmodel.cpp. References mProjectionLayerSet. Referenced by OmgExperimentPrinter::run().

QString OmgModel::projectionLayersXml (   )

Definition at line 590 of file omgmodel.cpp. References mProjectionLayerSet, and OmgLayerSet::toXml().

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QString OmgModel::projectionMaskLayerName (   )  const

Definition at line 1426 of file omgmodel.cpp. References OmgLayerSet::maskName(), and mProjectionLayerSet.

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QString OmgModel::rawImageFileName (   )  const

Definition at line 1474 of file omgmodel.cpp. References mRawImageFileName. Referenced by OmgRasterThreshold::accept(), createThumbnail(), postProcess(), and toHtml().

void OmgModel::reset (   )

Reset the model marking it as not started, not errored etc. Definition at line 87 of file omgmodel.cpp. References mCompletedFlag, and mErrorFlag. Referenced by OmgExperiment::reset().

double OmgModel::rocScore (   )  const

Get the rocScore for this model (from roc analysis) Definition at line 1496 of file omgmodel.cpp. References mRocScore. Referenced by OmgExperiment::getStatsHtml(), and OmgExperiment::makeAlgorithmSummaryGraphs().

void OmgModel::setAccuracy (  double  theAccuracy  )

set the accuracy for this model (from confusion matrix) Definition at line 1338 of file omgmodel.cpp. References mAccuracy.

void OmgModel::setAlgorithm (  OmgAlgorithm  theAlgorithm  )

Definition at line 1280 of file omgmodel.cpp. References mAlgorithm. Referenced by fromXml(), and OmgExperimentDesigner::getExperiment().

void OmgModel::setColouredImageFileName (  QString  theFileName  )

Definition at line 1321 of file omgmodel.cpp. References mColouredImageFileName. Referenced by fromXml().

void OmgModel::setCommission (  double  theCommission  )

set the commission score for this model (from confusion matrix) Definition at line 1346 of file omgmodel.cpp. References mCommission.

void OmgModel::setCompleted (  bool  theFlag  )

Definition at line 1289 of file omgmodel.cpp. References mCompletedFlag. Referenced by postProcess(), and OmgExperiment::run().

void OmgModel::setCoordinateSystem (  QString  theCoordinateSystem  )

Definition at line 1117 of file omgmodel.cpp. References mCoordinateSystem. Referenced by OmgExperimentDesigner::getExperiment().

void OmgModel::setCoordinateSystemName (  QString  theName  )

Definition at line 1121 of file omgmodel.cpp. References mCoordinateSystemName. Referenced by OmgExperimentDesigner::getExperiment().

void OmgModel::setCreationLayerNames (  QStringList  theNames  )

Definition at line 1254 of file omgmodel.cpp. References OmgLayerSet::addLayer(), mCreationLayerSet, OmgLayer::setCategorical(), and OmgLayer::setName(). Referenced by Localities2CsvTest::writeLocalities2Csv().

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void OmgModel::setCreationLayerSet (  OmgLayerSet  theLayerSet  )

Define the layerset that will be used for creationing this model. Parameters: theLayerSet  An OmgLayerSet that contains layers and mask for model creationing. Definition at line 1224 of file omgmodel.cpp. References mCreationLayerSet. Referenced by OmgExperimentDesigner::getExperiment().

void OmgModel::setcreationMaskLayerName (  QString  theName  )

Definition at line 1232 of file omgmodel.cpp. References mCreationLayerSet, OmgLayer::setCategorical(), OmgLayerSet::setMask(), and OmgLayer::setName().

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void OmgModel::setCsvFileName (  QString  theFileName  )

Definition at line 1135 of file omgmodel.cpp. References mCsvFileName. Referenced by postProcess().

void OmgModel::setEndDateTimeStamp (  QDateTime  theDateTimeStamp  )

Definition at line 1297 of file omgmodel.cpp. References mEndDateTimeStamp. Referenced by postProcess().

void OmgModel::setError (  bool  theFlag  )

Definition at line 1285 of file omgmodel.cpp. References mErrorFlag. Referenced by postProcess().

void OmgModel::setLegendFileName (  QString  theFileName  )

Definition at line 1311 of file omgmodel.cpp. References mLegendFileName. Referenced by fromXml(), and postProcess().

void OmgModel::setLocalities (  OmgLocalities  theLocalities  )

Definition at line 1112 of file omgmodel.cpp. References mLocalities. Referenced by parseModelResult(), and Localities2CsvTest::writeLocalities2Csv().

void OmgModel::setLocalitiesFilterType (  LocalitiesFilterType  theFilterType = NO_FILTER  )

Set whether the model creation should use only one sampler per distinct coordinate Parameters: LocalitiesFilterType  Indicating the state of this setting (default to none) Definition at line 1140 of file omgmodel.cpp. References mLocalitiesFilterType. Referenced by OmgExperimentDesigner::getExperiment().

void OmgModel::setLog (  QString  theLog  )  [slot]

Set the log to the provided message (overwriting any data that was previously there Definition at line 1372 of file omgmodel.cpp. References mModelLog.

void OmgModel::setModelDefinition (  QString  theDefinition  )

this is what is returned from om_create process. at the moment we just store this in a string member, but in the future we ill parse it out and store the individual constituents as properties of the model object Definition at line 1358 of file omgmodel.cpp. References mModelDefinition. Referenced by parseModelResult().

void OmgModel::setModelRasterFormat (  QString  theFormat  )

Set the output model raster format - the name should be in line with the names used in the openModeller library Definition at line 1062 of file omgmodel.cpp. References mModelRasterFormat. Referenced by fromXml(), and OmgExperimentDesigner::getExperiment().

void OmgModel::setNormalizationDefinition (  QString  theDefinition  )

Some algs will return a serialised normalization definition (since om lib supports different normalizer) Definition at line 1363 of file omgmodel.cpp. References mNormalizationDefinition. Referenced by parseModelResult().

void OmgModel::setOccurrencesFile (  QString  theSpeciesFile  )

void OmgModel::setOmission (  double  theOmission  )

set the omission score for this model (from confusion matrix) Definition at line 1342 of file omgmodel.cpp. References mOmission.

void OmgModel::setOutputFormatLayerName (  QString  theName  )

Definition at line 1248 of file omgmodel.cpp. References mOutputFormatLayer, OmgLayer::setCategorical(), and OmgLayer::setName(). Referenced by OmgExperimentDesigner::getExperiment().

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void OmgModel::setPercentCellsPresent (  double  thePercent  )

set the percent cells present for this model (from confusion matrix) Definition at line 1350 of file omgmodel.cpp. References mPercentCellsPresent.

void OmgModel::setPreviewFileName (  QString  theFileName  )

Definition at line 1306 of file omgmodel.cpp. References mPreviewFileName. Referenced by fromXml(), and postProcess().

void OmgModel::setProjectionLayerNames (  QStringList  theNames  )

Definition at line 1267 of file omgmodel.cpp. References OmgLayerSet::addLayer(), mProjectionLayerSet, OmgLayer::setCategorical(), and OmgLayer::setName().

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void OmgModel::setProjectionLayerSet (  OmgLayerSet  theLayerSet  )

Define the layerset that will be used for projecting this model. Parameters: theLayerSet  An OmgLayerSet that contains layers and mask for model projection. Definition at line 1228 of file omgmodel.cpp. References mProjectionLayerSet. Referenced by OmgExperimentDesigner::getExperiment().

void OmgModel::setProjectionMaskLayerName (  QString  theName  )

Definition at line 1240 of file omgmodel.cpp. References mProjectionLayerSet, OmgLayer::setCategorical(), OmgLayerSet::setMask(), and OmgLayer::setName().

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void OmgModel::setRawImageFileName (  QString  theFileName  )

Definition at line 1316 of file omgmodel.cpp. References mRawImageFileName. Referenced by fromXml().

void OmgModel::setRocScore (  double  theRocScore  )

set the rocScore for this model (from roc analysis) Definition at line 1334 of file omgmodel.cpp. References mRocScore.

void OmgModel::setShapefileName (  QString  theFileName  )

Definition at line 1130 of file omgmodel.cpp. References mShapefileName. Referenced by OmgExperiment::run().

void OmgModel::setSpeciesFile (  QString  theFileName  )

Set the species file to be used for the model. I will change this later so that it is not file based but rather the points will be added directly to the model. For now, calling this method will also cause the points to be loaded into the OmgLocalities collection associated with this model. Definition at line 1126 of file omgmodel.cpp. References mSpeciesFile. Referenced by OmgExperimentDesigner::getExperiment(), and OmgModelTest::loadLocalities().

void OmgModel::setStartDateTimeStamp (  QDateTime  theDateTimeStamp  )

Definition at line 1293 of file omgmodel.cpp. References mStartDateTimeStamp. Referenced by OmgExperiment::run().

void OmgModel::setTaxonName (  QString  theName  )

Definition at line 1219 of file omgmodel.cpp. References mTaxonName. Referenced by OmgExperimentDesigner::getExperiment(), and OmgModelTest::loadLocalities().

void OmgModel::setThumbnailFileName (  QString  theFileName  )

Definition at line 1301 of file omgmodel.cpp. References mThumbnailFileName. Referenced by createThumbnail(), and fromXml().

void OmgModel::setTotalCells (  double  theTotal  )

set the totalCells for this model (from confusion matrix) Definition at line 1354 of file omgmodel.cpp. References mTotalCells.

void OmgModel::setWorkDir (  QString  theDir  )

Definition at line 1327 of file omgmodel.cpp. References mWorkDir. Referenced by OmgLocalitiesModelTest::rowsAndColumns(), OmgModelTest::run(), OmgExperiment::run(), and OmgExperiment::setWorkDir().

QString OmgModel::shapefileName (   )  const

Definition at line 1397 of file omgmodel.cpp. References mShapefileName.

QString OmgModel::speciesFile (   )  const

Definition at line 1392 of file omgmodel.cpp. References mSpeciesFile.

QDateTime OmgModel::startDateTimeStamp (   )  const

Definition at line 1454 of file omgmodel.cpp. References mStartDateTimeStamp. Referenced by OmgExperiment::getStatsHtml(), and OmgExperiment::makeAlgorithmSummaryGraphs().

QString OmgModel::taxonName (   )  const

Definition at line 1409 of file omgmodel.cpp. References mTaxonName. Referenced by OmgRasterThreshold::populateTree(), OmgMainWindow::populateTree(), postProcess(), OmgExperiment::removeTaxon(), OmgExperimentPrinter::run(), OmgExperiment::run(), OmgPublishToCatalogue::setModel(), OmgMainWindow::showTaxonSummary(), and OmgExperiment::toTaxonSummaryHtml().

QString OmgModel::thumbnailFileName (   )  const

Definition at line 1462 of file omgmodel.cpp. References mThumbnailFileName. Referenced by OmgRasterThreshold::populateTree(), OmgPublishToCatalogue::setModel(), OmgMainWindow::showAlgorithmSummary(), OmgMainWindow::showTaxonSummary(), OmgExperiment::toAlgorithmSummaryHtml(), and OmgExperiment::toTaxonSummaryHtml().

QString OmgModel::toHtml (  bool  theForceFlag = false  )  const

Get the report file name for this model. Parameters: theForceFlag  - force recreation of the report and its graphs etc. Returns: QString with the filename of the html report Definition at line 595 of file omgmodel.cpp. References OmgGraph::addSeries(), createRocGraph(), Omgui::createTextFile(), Omgui::getHtmlFooter(), Omgui::getHtmlHeader(), OmgGuid::guid(), mAccuracy, mAlgorithm, mCommission, mCreationLayerSet, mEndDateTimeStamp, mLegendFileName, mLocalitiesFilterType, mModelLog, mModelRasterFormat, mOmission, mOutputFormatLayer, mPercentCellsPresent, mPreviewFileName, mProjectionLayerSet, mRocPoints, mRocScore, mStartDateTimeStamp, mTaxonName, mThumbnailFileName, mTotalCells, mWorkDir, OmgLayer::name(), OmgAlgorithm::name(), NO_FILTER, rawImageFileName(), OmgGraph::render(), OmgGraph::setAreaFillEnabled(), OmgDataSeries::setFillColor(), OmgGraph::setGridLinesEnabled(), OmgDataSeries::setLabel(), OmgDataSeries::setLineColor(), OmgGraph::setSpliningEnabled(), OmgGraph::setVertexLabelsEnabled(), OmgGraph::setVerticesEnabled(), SPATIALLY_UNIQUE, OmgLayerSet::toHtml(), OmgAlgorithm::toHtml(), and workDir(). Referenced by postProcess(), OmgMainWindow::printExperimentReport(), and OmgMainWindow::refreshReports().

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QString OmgModel::toModelCreationXml (   )  const

This is a special case serialiser needed for when preparing an xml representation of an model to send to the openmodeller library (or openmodeller web service interface). The xml produced will include no ancilliary meta information - only the essentials needed for the model. Returns: a string containing the model creation request xml representation or if something went wrong an empty string. Definition at line 469 of file omgmodel.cpp. References OmgLocality::abundance(), mAlgorithm, mCoordinateSystem, mCreationLayerSet, mLocalities, mLocalitiesFilterType, mTaxonName, NO_FILTER, SPATIALLY_UNIQUE, OmgAlgorithm::toModelCreationXml(), OmgLocality::toXml(), and OmgLayerSet::toXml(). Referenced by OmgLocalitiesModelTest::rowsAndColumns(), and OmgModelTest::run().

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QString OmgModel::toModelProjectionXml (   )  const

This is a special case serialiser needed for when preparing an xml representation of an model to send to the openmodeller library (or openmodeller web service interface). The xml produced will include no ancilliary meta information - only the essentials needed for the model. Returns: a string containing the model projection xml representation, or if something went wrong an empty string. Definition at line 553 of file omgmodel.cpp. References mAlgorithm, mModelDefinition, mModelRasterFormat, mNormalizationDefinition, mOutputFormatLayer, mProjectionLayerSet, OmgLayer::name(), OmgAlgorithm::toModelProjectionXml(), and OmgLayerSet::toXml().

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QString OmgModel::toPrintHtml (  bool  theForceFlag = false  )  const

Get the print ready reoport for this model. It excludes some portions of the on screen report such as model log. It also uses absolute paths for images so they are properly include into the printout. Parameters: theForceFlag  - force recreation of the report and its graphs etc. Returns: QString with the html report contents Definition at line 871 of file omgmodel.cpp. References createRocGraph(), mAccuracy, mAlgorithm, mCommission, mCreationLayerSet, mEndDateTimeStamp, mLegendFileName, mModelRasterFormat, mOmission, mOutputFormatLayer, mPercentCellsPresent, mPreviewFileName, mProjectionLayerSet, mRocPoints, mRocScore, mStartDateTimeStamp, mTaxonName, mTotalCells, mWorkDir, OmgLayer::name(), OmgLayerSet::name(), OmgAlgorithm::name(), and OmgAlgorithm::toHtml(). Referenced by OmgExperimentPrinter::run().

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bool OmgModel::toShapefile (  QString  theShapefileName  )  const

A helper method to easily write a shapefile to disk. Parameters: theFileName  - the filename to be created or overwritten Returns: bool - false if the file could not be written Definition at line 1106 of file omgmodel.cpp. References Omgui::localitiesToShapefile(), and mLocalities. Referenced by OmgExperiment::run().

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QString OmgModel::toString (   )  const

Create an html formatted sumary of the model and save it to disk. Parameters: bool  flag indicating whether to force recreating the report or whether to just return the existing one if it was made previously. If the file does not exist the flag is ignored and the report is created anyway. By default this flag is false. Returns: QString containing the full file name and path to the summary report. Definition at line 93 of file omgmodel.cpp. References mAlgorithm, OmgLayerSet::maskName(), mCoordinateSystem, mCoordinateSystemName, mCreationLayerSet, mLegendFileName, mLocalities, mOutputFormatLayer, mPreviewFileName, mProjectionLayerSet, mSpeciesFile, mTaxonName, OmgLayer::name(), OmgAlgorithm::toString(), and OmgLayerSet::toString(). Referenced by OmgExperiment::toString().

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double OmgModel::totalCells (   )  const

Get the totalCells for this model (from confusion matrix) Definition at line 1516 of file omgmodel.cpp. References mTotalCells.

QString OmgModel::toXml (   )  const [virtual]

This method is required for the serialiseable interface. It will encapsulate *all* model properties so that its complete state can be serialised and later deserialised. See also: toModelCreationXml() Implements OmgSerialisable. Definition at line 347 of file omgmodel.cpp. References OmgGuid::guid(), mAccuracy, mAlgorithm, mColouredImageFileName, mCommission, mCompletedFlag, mCoordinateSystem, mCoordinateSystemName, mCreationLayerSet, mCsvFileName, mEndDateTimeStamp, mErrorFlag, mLegendFileName, mLocalities, mLocalitiesFilterType, mModelDefinition, mModelLog, mModelRasterFormat, mNormalizationDefinition, mOmission, mOutputFormatLayer, mPercentCellsPresent, mPreviewFileName, mProjectionLayerSet, mRawImageFileName, mRocPoints, mRocScore, mShapefileName, mSpeciesFile, mStartDateTimeStamp, mTaxonName, mThumbnailFileName, mTotalCells, mWorkDir, NO_FILTER, SPATIALLY_UNIQUE, OmgLocality::toXml(), OmgAlgorithm::toXml(), OmgLayerSet::toXml(), and OmgLayer::toXml(). Referenced by OmgLocalitiesModelTest::rowsAndColumns(), OmgModelTest::run(), OmgModelTest::saveAndLoadModel(), and OmgExperiment::toXml().

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QString OmgModel::workDir (   )  const

The directory where the working files were stored for this model Definition at line 1492 of file omgmodel.cpp. References mWorkDir. Referenced by OmgRasterThreshold::accept(), OmgRasterThreshold::populateTree(), postProcess(), OmgExperiment::run(), OmgPublishToCatalogue::setModel(), OmgMainWindow::showAlgorithmSummary(), OmgMainWindow::showTaxonSummary(), and toHtml().

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Member Data Documentation

double OmgModel::mAccuracy [private]

Definition at line 335 of file omgmodel.h. Referenced by accuracy(), fromXml(), setAccuracy(), toHtml(), toPrintHtml(), and toXml().

OmgAlgorithm OmgModel::mAlgorithm [private]

Definition at line 317 of file omgmodel.h. Referenced by algorithm(), createThumbnail(), setAlgorithm(), toHtml(), toModelCreationXml(), toModelProjectionXml(), toPrintHtml(), toString(), and toXml().

QString OmgModel::mColouredImageFileName [private]

Definition at line 330 of file omgmodel.h. Referenced by colouredImageFileName(), setColouredImageFileName(), and toXml().

double OmgModel::mCommission [private]

-1 indicates invalid since commission only applies to presence/absence models Definition at line 339 of file omgmodel.h. Referenced by commission(), fromXml(), setCommission(), toHtml(), toPrintHtml(), and toXml().

bool OmgModel::mCompletedFlag [private]

Definition at line 318 of file omgmodel.h. Referenced by fromXml(), isCompleted(), reset(), setCompleted(), and toXml().

QString OmgModel::mCoordinateSystem [private]

todo - make a class to represent a coordsys rather Definition at line 310 of file omgmodel.h. Referenced by coordinateSystem(), fromXml(), setCoordinateSystem(), toModelCreationXml(), toString(), and toXml().

QString OmgModel::mCoordinateSystemName [private]

Definition at line 311 of file omgmodel.h. Referenced by coordinateSystemName(), fromXml(), setCoordinateSystemName(), toString(), and toXml().

OmgLayerSet OmgModel::mCreationLayerSet [private]

Definition at line 316 of file omgmodel.h. Referenced by creationLayerNames(), creationLayerSet(), creationMaskLayerName(), fromXml(), setCreationLayerNames(), setCreationLayerSet(), setcreationMaskLayerName(), toHtml(), toModelCreationXml(), toPrintHtml(), toString(), and toXml().

QString OmgModel::mCsvFileName [private]

Definition at line 329 of file omgmodel.h. Referenced by csvFileName(), fromXml(), setCsvFileName(), and toXml().

QDateTime OmgModel::mEndDateTimeStamp [private]

Definition at line 323 of file omgmodel.h. Referenced by endDateTimeStamp(), fromXml(), setEndDateTimeStamp(), toHtml(), toPrintHtml(), and toXml().

bool OmgModel::mErrorFlag [private]

Definition at line 319 of file omgmodel.h. Referenced by fromXml(), hasError(), reset(), setError(), and toXml().

QString OmgModel::mLegendFileName [private]

Definition at line 326 of file omgmodel.h. Referenced by legendFileName(), setLegendFileName(), toHtml(), toPrintHtml(), toString(), and toXml().

OmgLocalities OmgModel::mLocalities [private]

Definition at line 321 of file omgmodel.h. Referenced by fromXml(), loadLocalities(), localities(), setLocalities(), toModelCreationXml(), toShapefile(), toString(), and toXml().

LocalitiesFilterType OmgModel::mLocalitiesFilterType [private]

Definition at line 345 of file omgmodel.h. Referenced by fromXml(), localitiesFilterType(), setLocalitiesFilterType(), toHtml(), toModelCreationXml(), and toXml().

QString OmgModel::mModelDefinition [private]

Definition at line 332 of file omgmodel.h. Referenced by fromXml(), modelDefinition(), setModelDefinition(), toModelProjectionXml(), and toXml().

QString OmgModel::mModelLog [private]

Definition at line 342 of file omgmodel.h. Referenced by appendToLog(), fromXml(), modelLog(), setLog(), toHtml(), and toXml().

QString OmgModel::mModelRasterFormat [private]

Definition at line 344 of file omgmodel.h. Referenced by modelRasterFormat(), setModelRasterFormat(), toHtml(), toModelProjectionXml(), toPrintHtml(), and toXml().

QString OmgModel::mNormalizationDefinition [private]

Definition at line 333 of file omgmodel.h. Referenced by fromXml(), normalizationDefinition(), setNormalizationDefinition(), toModelProjectionXml(), and toXml().

double OmgModel::mOmission [private]

Definition at line 336 of file omgmodel.h. Referenced by fromXml(), omission(), setOmission(), toHtml(), toPrintHtml(), and toXml().

OmgLayer OmgModel::mOutputFormatLayer [private]

Definition at line 314 of file omgmodel.h. Referenced by fromXml(), outputFormatLayerName(), setOutputFormatLayerName(), toHtml(), toModelProjectionXml(), toPrintHtml(), toString(), and toXml().

double OmgModel::mPercentCellsPresent [private]

Definition at line 340 of file omgmodel.h. Referenced by fromXml(), percentCellsPresent(), setPercentCellsPresent(), toHtml(), toPrintHtml(), and toXml().

QString OmgModel::mPreviewFileName [private]

Definition at line 325 of file omgmodel.h. Referenced by previewFileName(), setPreviewFileName(), toHtml(), toPrintHtml(), toString(), and toXml().

OmgLayerSet OmgModel::mProjectionLayerSet [private]

Definition at line 315 of file omgmodel.h. Referenced by fromXml(), projectionLayerNames(), projectionLayerSet(), projectionLayersXml(), projectionMaskLayerName(), setProjectionLayerNames(), setProjectionLayerSet(), setProjectionMaskLayerName(), toHtml(), toModelProjectionXml(), toPrintHtml(), toString(), and toXml().

QString OmgModel::mRawImageFileName [private]

Definition at line 327 of file omgmodel.h. Referenced by rawImageFileName(), setRawImageFileName(), and toXml().

QList< QPair <double,double> > OmgModel::mRocPoints [private]

Definition at line 343 of file omgmodel.h. Referenced by addRocPoint(), clearRocPoints(), fromXml(), getRocPoints(), toHtml(), toPrintHtml(), and toXml().

double OmgModel::mRocScore [private]

Definition at line 334 of file omgmodel.h. Referenced by fromXml(), rocScore(), setRocScore(), toHtml(), toPrintHtml(), and toXml().

QString OmgModel::mShapefileName [private]

Definition at line 328 of file omgmodel.h. Referenced by fromXml(), setShapefileName(), shapefileName(), and toXml().

QString OmgModel::mSpeciesFile [private]

Definition at line 312 of file omgmodel.h. Referenced by fromXml(), loadLocalities(), setSpeciesFile(), speciesFile(), toString(), and toXml().

QDateTime OmgModel::mStartDateTimeStamp [private]

Definition at line 322 of file omgmodel.h. Referenced by fromXml(), setStartDateTimeStamp(), startDateTimeStamp(), toHtml(), toPrintHtml(), and toXml().

QString OmgModel::mTaxonName [private]

Definition at line 313 of file omgmodel.h. Referenced by createRocGraph(), createThumbnail(), fromXml(), loadLocalities(), setTaxonName(), taxonName(), toHtml(), toModelCreationXml(), toPrintHtml(), toString(), and toXml().

QString OmgModel::mThumbnailFileName [private]

Definition at line 324 of file omgmodel.h. Referenced by setThumbnailFileName(), thumbnailFileName(), toHtml(), and toXml().

double OmgModel::mTotalCells [private]

Definition at line 341 of file omgmodel.h. Referenced by fromXml(), setTotalCells(), toHtml(), toPrintHtml(), totalCells(), and toXml().

QString OmgModel::mWorkDir [private]

Definition at line 331 of file omgmodel.h. Referenced by createRocGraph(), createThumbnail(), fromXml(), setWorkDir(), toHtml(), toPrintHtml(), toXml(), and workDir().

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

• lib/omgmodel.h
• lib/omgmodel.cpp

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