Cluster analysis filter. More...

#include <clusterAnalysis.h>

Inheritance diagram for ClusterAnalysisFilter:

Collaboration diagram for ClusterAnalysisFilter:

Public Member Functions
	ClusterAnalysisFilter ()

Filter *	cloneUncached () const
	Duplicate filter contents, excluding cache. More...

virtual void	initFilter (const std::vector< const FilterStreamData > &dataIn, std::vector< const FilterStreamData > &dataOut)
	Initialise filter prior to tree propagation. More...

virtual size_t	numBytesForCache (size_t nObjects) const
	Returns -1, as range file cache size is dependant upon input. More...

unsigned int	getType () const
	Returns FILTER_TYPE_SPATIAL_ANALYSIS. More...

unsigned int	refresh (const std::vector< const FilterStreamData > &dataIn, std::vector< const FilterStreamData > &getOut, ProgressData &progress)
	Apply filter to new data, updating cache as needed. Vector of returned pointers must be deleted manually, first checking ->cached. More...

virtual std::string	typeString () const
	Get the type string for this filter. More...

std::string	getSpecificErrString (unsigned int i) const
	Get the per-filter error codes. More...

void	getProperties (FilterPropGroup &propertyList) const
	Get the properties of the filter, in key-value form. First std::vector is for each output. More...

bool	setProperty (unsigned int key, const std::string &value, bool &needUpdate)
	Set the properties for the nth filter. More...

bool	writeState (std::ostream &f, unsigned int format, unsigned int depth=0) const
	Dump state to output stream, using specified format. More...

bool	readState (xmlNodePtr &node, const std::string &packDir)
	Read the state of the filter from XML file. If this. More...

unsigned int	getRefreshBlockMask () const
	Get the stream types that will be dropped during ::refresh. More...

unsigned int	getRefreshEmitMask () const
	Get the stream types that will be generated during ::refresh. More...

unsigned int	getRefreshUseMask () const
	Get the stream types that will be generated during ::refresh. More...

void	setPropFromBinding (const SelectionBinding &b)
	Set internal property value using a selection binding (Disabled, this filter has no bindings) More...

Public Member Functions inherited from Filter
	Filter ()

virtual	~Filter ()

virtual void	clearCache ()
	Erase cache. More...

virtual void	clearDevices ()
	Erase any active devices. More...

std::string	getErrString (unsigned int code) const
	Get the human readable error string associated with a particular error code during refresh(...). Do not override this for specific filter errors. Override getSpecificErrString. More...

std::string	trueName () const
	Return the unique name for a given filter – DO NOT TRANSLATE. More...

virtual void	getStateOverrides (std::vector< std::string > &overrides) const
	Return the XML elements that refer to external entities (i.e. files) which do not move with the XML files. At this time, only files are supported. These will be looked for on the filesystem and moved as needed. More...

void	setCaching (bool enableCache)
	Enable/disable caching for this filter. More...

bool	haveCache () const
	Have cached output data? More...

virtual std::string	getUserString () const
	Return a user-specified string, or just the typestring if user set string not active. More...

virtual void	setUserString (const std::string &str)
	Set a user-specified string return value is. More...

virtual bool	writePackageState (std::ostream &f, unsigned int format, const std::vector< std::string > &valueOverrides, unsigned int depth=0) const
	Modified version of writeState for packaging. By default simply calls writeState. More...

void	getSelectionDevices (std::vector< SelectionDevice *> &devices) const
	Get the selection devices for this filter. MUST be called after refresh() More...

void	updateOutputInfo (const std::vector< const FilterStreamData *> &dataOut)
	Update the output statistics for this filter (num items of streams of each type output) More...

virtual void	setPropFromRegion (unsigned int method, unsigned int regionID, float newPos)
	Set a region update. More...

virtual bool	canBeHazardous () const
	Can this filter perform actions that are potentially a security concern? More...

unsigned int	getNumOutput (unsigned int streamType) const
	Get the number of outputs for the specified type during the filter's last refresh. More...

void	getConsoleStrings (std::vector< std::string > &v) const
	Get the filter messages from the console. To erase strings, either call erase, or erase cahche. More...

void	clearConsole ()

virtual bool	monitorNeedsRefresh () const

virtual bool	isPureDataSource () const

virtual bool	isUsefulAsAppend () const

template<>
bool	applyPropertyNow (bool &prop, const std::string &val, bool &needUp)

template<>
bool	applyPropertyNow (Point3D &prop, const std::string &val, bool &needUp)

template<>
bool	applyPropertyNow (std::string &prop, const std::string &val, bool &needUp)

Additional Inherited Members
Static Public Member Functions inherited from Filter
static void	setStrongRandom (bool strongRand)
	Should filters use strong randomisation (where applicable) or not? More...

template<typename T >
static void	getStreamsOfType (const std::vector< const FilterStreamData > &vec, std::vector< const T > &dataOut)

Static Public Attributes inherited from Filter
static ATOMIC_BOOL *	wantAbort = 0

Protected Member Functions inherited from Filter
void	convertFileStringToAbsolute (const string &basePath, std::string &s) const

void	propagateCache (std::vector< const FilterStreamData *> &dataOut) const
	Propagate the cache into output. More...

template<class T >
bool	applyPropertyNow (T &oldProp, const std::string &newVal, bool &needUp)

void	cacheAsNeeded (FilterStreamData *s)

Static Protected Member Functions inherited from Filter
static unsigned int	collateIons (const std::vector< const FilterStreamData *> &dataIn, std::vector< IonHit > &outVector, ProgressData &prog, size_t totalDataSize=(size_t) -1)

static unsigned int	collateIons (const std::vector< const FilterStreamData *> &dataIn, std::vector< Point3D > &outVector, ProgressData &prog, size_t totalDataSize=(size_t) -1)

static void	propagateStreams (const std::vector< const FilterStreamData > &dataIn, std::vector< const FilterStreamData > &dataOut, size_t mask=STREAMTYPE_MASK_ALL, bool invertMask=false)
	Propagate the given input data to an output vector. More...

static std::string	getBaseErrString (unsigned int errCode)
	Get the generic (applies to any filter) error codes. More...

template<class T >
static unsigned int	extendDataVector (std::vector< T > &dest, const std::vector< IonHit > &vIonData, unsigned int &progress, size_t offset)
	Extend a point data vector using some ion data. More...

template<class T >
static size_t	buildSplitPoints (const vector< const FilterStreamData > &dataIn, ProgressData &progress, size_t totalDataSize, const RangeFile rngF, const vector< bool > &pSourceEnabled, const vector< bool > &pTargetEnabled, vector< T > &pSource, vector< T > &pTarget)

static unsigned int	getIonstreamIonID (const IonStreamData d, const RangeFile r)

static void	demuxKey (unsigned int key, unsigned int &keyType, unsigned int &ionOffset)
	Hack to merge/extract two bits of information into a single property key. More...

static unsigned int	muxKey (unsigned int keyType, unsigned int ionOffset)

Protected Attributes inherited from Filter
bool	cache

bool	cacheOK

unsigned int	numStreamsLastRefresh [NUM_STREAM_TYPES]
	Array of the number of streams propagated on last refresh. More...

std::vector< std::string >	consoleOutput
	Temporary console output. Should be only nonzero size if messages are present. More...

std::string	userString
	User settable labelling string (human readable ID, etc etc) More...

std::vector< FilterStreamData * >	filterOutputs

std::vector< SelectionDevice * >	devices
	User interaction "Devices" associated with this filter. More...

Static Protected Attributes inherited from Filter
static bool	strongRandom = false

Detailed Description

Cluster analysis filter.

Constructor & Destructor Documentation

◆ ClusterAnalysisFilter()

ClusterAnalysisFilter::ClusterAnalysisFilter ( )

References Filter::cache, and Filter::cacheOK.

Referenced by cloneUncached(), and computeMatrixEntries().

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Member Function Documentation

◆ cloneUncached()

Filter * ClusterAnalysisFilter::cloneUncached ( ) const

virtual

Duplicate filter contents, excluding cache.

Implements Filter.

References Filter::cache, Filter::cacheOK, ClusterAnalysisFilter(), and Filter::userString.

◆ getProperties()

void ClusterAnalysisFilter::getProperties ( FilterPropGroup & propertyList ) const

virtual

Get the properties of the filter, in key-value form. First std::vector is for each output.

Implements Filter.

References FilterPropGroup::addProperty(), ASSERT, boolStrEnc(), choiceString(), CLUSTER_ALGORITHM_ENUM_END, CLUSTER_LINK_ERODE, FilterProperty::data, FilterProperty::helpText, FilterProperty::key, KEY_BULK_ALL, KEY_BULK_OFFSET, KEY_BULKLINK, KEY_BULKLINK_ENABLE, KEY_CLUSTERANALYSIS_ALGORITHM, KEY_CORE_OFFSET, KEY_CORECLASSIFY_ENABLE, KEY_CORECLASSIFYDIST, KEY_CORECLASSIFYKNN, KEY_CROP_NMAX, KEY_CROP_NMIN, KEY_CROP_SIZE, KEY_ERODE_ENABLE, KEY_ERODEDIST, KEY_LINKDIST, KEY_NORMALISE_COMPOSITION, KEY_WANT_CLUSTERID, KEY_WANT_CLUSTERMORPHOLOGY, KEY_WANT_CLUSTERSIZEDIST, KEY_WANT_COMPOSITIONDIST, KEY_WANT_LOGSIZEDIST, FilterProperty::name, PROPERTY_TYPE_BOOL, PROPERTY_TYPE_CHOICE, PROPERTY_TYPE_INTEGER, PROPERTY_TYPE_REAL, FilterPropGroup::setGroupTitle(), stream_cast(), TRANS, and FilterProperty::type.

Referenced by typeString().

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◆ getRefreshBlockMask()

unsigned int ClusterAnalysisFilter::getRefreshBlockMask ( ) const

virtual

Get the stream types that will be dropped during ::refresh.

Implements Filter.

References STREAM_TYPE_IONS.

Referenced by typeString().

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◆ getRefreshEmitMask()

unsigned int ClusterAnalysisFilter::getRefreshEmitMask ( ) const

virtual

Get the stream types that will be generated during ::refresh.

Implements Filter.

References STREAM_TYPE_DRAW, STREAM_TYPE_IONS, STREAM_TYPE_PLOT, and STREAM_TYPE_PLOT2D.

Referenced by typeString().

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◆ getRefreshUseMask()

unsigned int ClusterAnalysisFilter::getRefreshUseMask ( ) const

virtual

Get the stream types that will be generated during ::refresh.

Implements Filter.

References STREAM_TYPE_IONS, and STREAM_TYPE_RANGE.

Referenced by typeString().

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◆ getSpecificErrString()

std::string ClusterAnalysisFilter::getSpecificErrString ( unsigned int errCode ) const

virtual

Get the per-filter error codes.

Implements Filter.

References ASSERT, CLUSTER_ERR_ENUM_END, COMPILE_ASSERT, and THREEDEP_ARRAYSIZE.

Referenced by typeString().

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◆ getType()

unsigned int ClusterAnalysisFilter::getType ( ) const

inlinevirtual

Returns FILTER_TYPE_SPATIAL_ANALYSIS.

Implements Filter.

References FILTER_TYPE_CLUSTER_ANALYSIS, and refresh().

◆ initFilter()

void ClusterAnalysisFilter::initFilter	(	const std::vector< const FilterStreamData *> &	dataIn,
		std::vector< const FilterStreamData *> &	dataOut
	)

virtual

Initialise filter prior to tree propagation.

Reimplemented from Filter.

References RangeStreamData::enabledIons, RangeFile::getName(), RangeFile::getNumIons(), RangeFile::getNumRanges(), RangeStreamData::rangeFile, and STREAM_TYPE_RANGE.

Referenced by computeMatrixEntries().

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◆ numBytesForCache()

size_t ClusterAnalysisFilter::numBytesForCache ( size_t nObjects ) const

virtual

Returns -1, as range file cache size is dependant upon input.

Implements Filter.

References IONDATA_SIZE.

◆ readState()

bool ClusterAnalysisFilter::readState	(	xmlNodePtr &	node,
		const std::string &	packDir
	)

virtual

Read the state of the filter from XML file. If this.

Implements Filter.

References ASSERT, CLUSTER_ALGORITHM_ENUM_END, CLUSTER_LINK_ERODE, Filter::userString, XMLGetAttrib(), XMLGetNextElemAttrib(), XMLHelpFwdToElem(), and XMLHelpGetProp().

Referenced by typeString().

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◆ refresh()

unsigned int ClusterAnalysisFilter::refresh	(	const std::vector< const FilterStreamData *> &	dataIn,
		std::vector< const FilterStreamData *> &	dataOut,
		ProgressData &	progress
	)