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#ifndef CLUSTERANALYSIS_H
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#define CLUSTERANALYSIS_H
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#include "../translation.h"
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//!Cluster analysis filter
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class ClusterAnalysisFilter : public Filter
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//Clustering algorithm to use
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unsigned int algorithm;
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//Algorithm parameters
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//Core-linkage "core" classification distance
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//Link distance for core
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//Link distance for bulk
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//Erosion distance for bulk from nonclustered bulk
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//post processing options
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//Minimum/max number of "core" entires to qualify as,
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//well, a meaningful cluster
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bool wantClusterSizeDist,logClusterSize;
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//Do we want the composition data for the cluster
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bool wantClusterComposition, normaliseComposition;
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//Do we want a morphological analysis
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bool wantClusterMorphology;
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//!Do we have range data to use
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//!The names of the incoming ions
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std::vector<std::string > ionNames;
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//!Which ions are core/builk for a particular incoming range?
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std::vector<bool> ionCoreEnabled,ionBulkEnabled;
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//Do cluster refresh using Link Algorithm (Core + max sep)
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unsigned int refreshLinkClustering(const std::vector<const FilterStreamData *> &dataIn,
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std::vector< std::vector<IonHit> > &clusteredCore,
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std::vector<std::vector<IonHit> > &clusteredBulk,ProgressData &progress,
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bool (*callback)(bool));
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//Helper function to create core and bulk vectors of ions from input ionstreams
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void createRangedIons(const std::vector<const FilterStreamData *> &dataIn,
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std::vector<IonHit> &core,std::vector<IonHit> &bulk,
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ProgressData &p,bool (*callback)(bool)) const;
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//Check to see if there are any core or bulk ions enabled respectively.
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void checkIonEnabled(bool &core, bool &bulk) const;
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void buildRangeEnabledMap(const RangeStreamData *r,
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map<size_t,size_t> &rangeEnabledMap) const;
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//Strip out clusters with a given number of elements
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bool stripClusterBySize(vector<vector<IonHit> > &clusteredCore,
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vector<vector<IonHit> > &clusteredBulk,
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bool (*callback)(bool), ProgressData &p) const;
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//Build a plot that is the cluster size distribution as afunction of cluster size
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PlotStreamData *clusterSizeDistribution(const vector<vector<IonHit> > &solutes,
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const vector<vector<IonHit> > &matrix) const;
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//Build plots that are the cluster size distribution as
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// a function of cluster size, specific to each ion type.
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void genCompositionVersusSize(const vector<vector<IonHit> > &clusteredCore,
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const vector<vector<IonHit> > &clusteredBulk, const RangeFile *rng,
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vector<PlotStreamData *> &plots) const;
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//COmpute the singular values that area associated with each cluster
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void getSingularValues(const vector<vector<IonHit> > &clusteredCore,
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const vector<vector<IonHit> > &clusteredBulk, vector<vector<float> > &singularValues) const;
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bool paranoidDebugAssert(const std::vector<std::vector<IonHit > > &core,
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const std::vector<std::vector<IonHit> > &bulk) const;
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ClusterAnalysisFilter();
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//!Duplicate filter contents, excluding cache.
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Filter *cloneUncached() const;
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//!Initialise filter prior to tree propagation
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virtual void initFilter(const std::vector<const FilterStreamData *> &dataIn,
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std::vector<const FilterStreamData *> &dataOut);
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//!Returns -1, as range file cache size is dependant upon input.
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virtual size_t numBytesForCache(size_t nObjects) const;
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//!Returns FILTER_TYPE_SPATIAL_ANALYSIS
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unsigned int getType() const { return FILTER_TYPE_CLUSTER_ANALYSIS;};
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unsigned int refresh(const std::vector<const FilterStreamData *> &dataIn,
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std::vector<const FilterStreamData *> &getOut,
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ProgressData &progress, bool (*callback)(bool));
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//!Get the type string for this fitler
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virtual std::string typeString() const { return std::string(TRANS("Cluster Analysis"));};
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std::string getErrString(unsigned int i) const;
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//!Get the properties of the filter, in key-value form. First vector is for each output.
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void getProperties(FilterProperties &propertyList) const;
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//!Set the properties for the nth filter
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bool setProperty(unsigned int set,unsigned int key,
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const std::string &value, bool &needUpdate);
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//!Dump state to output stream, using specified format
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bool writeState(std::ofstream &f,unsigned int format,
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unsigned int depth=0) const;
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//!Read the state of the filter from XML file. If this
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//fails, filter will be in an undefined state.
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bool readState(xmlNodePtr &node, const std::string &packDir);
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//!Get the stream types that will be dropped during ::refresh
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unsigned int getRefreshBlockMask() const;
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//!Get the stream types that will be generated during ::refresh
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unsigned int getRefreshEmitMask() const;
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//!Set internal property value using a selection binding (Disabled, this filter has no bindings)
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void setPropFromBinding(const SelectionBinding &b) {ASSERT(false);} ;
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bool wantParanoidDebug;
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src/filters/clusterAnalysis.h
