Package clickTrainDetector.clickTrainAlgorithms.mht.mhtvar

Class IDIManager

java.lang.Object
clickTrainDetector.clickTrainAlgorithms.mht.mhtvar.IDIManager
public class IDIManager extends Object
Calculates the inter-detection interval (IDI) (usually clicks) interval for a set of data units based either on the time stamp or a more complex sample rate and cross correlation calculation.

This is an important class in which all time calculations for tracks are based. It holds a master time list of all detections considered by the algorithm. The inter-click interval for an individual track is then calculated form this master list. This ensures that the no access to the data blocks and the list iterators which slow everything down are required by the MHT algorithms

Author:
Jamie Macaulay

  • Constructor Details

    • IDIManager

      public IDIManager()
      Constructor for the ICIManager.

  • Method Details

    • addDetection

      public void addDetection(PamDataUnit detection, int kcount)
      Add a detection to the ICIManager and update the master time series.
      Parameters:
      detection - - the current detection ion the kernel
      kcount - - the current kernel kcount. This should match ICICount

    • getLastTime

      public double getLastTime()
      Get the last time in seconds from the time series start. This is the last time of the last data unit to be added to the hypothesis mix. It is NOT the last time of the last hypothesis.
      Returns:
      the last time in seconds from the time series start.

    • setDataUnitList

      public void setDataUnitList(ArrayList<PamDataUnit> dataUnits, boolean useCorrelation)
      Set the current data unit list. Sets the current list and calculates time, ICI and correlation series values. Note: if the useCorrelation is set to false then all correlation series values will be set to zero.
      Parameters:
      dataUnits - - the data units to set.
      useCorrelation - - use cross correlation to get more accurate ICI measurements.

    • calcTime

      public double calcTime(PamDataUnit pamDataUnitPrev, PamDataUnit pamDataUnitNext)
      Calculate the time between two data units
      Parameters:
      pamDataUnitPrev - - the first data unit (in time)
      pamDataUnitNext - - the second data unit (in time)
      Returns:
      the time in SECONDS

    • calcTimeSR

      public double calcTimeSR(PamDataUnit pamDataUnitPrev, PamDataUnit pamDataUnitNext)
      Calculate the time between two data units
      Parameters:
      pamDataUnitPrev - - the first data unit (in time)
      pamDataUnitNext - - the second data unit (in time)
      Returns:
      the time in SAMPLES

    • isUseCorrelation

      public boolean isUseCorrelation()
      Check whether calculation is using cross correlation to increase ICI accuracy
      Returns:
      true if using correlation to increase ICI accuracy.

    • setUseCorrelation

      public void setUseCorrelation(boolean useCorrelation)
      Set whether calculation is using cross correlation to increase ICI accuracy
      Parameters:
      useCorrelation - - true to use cross correlation to increase accuracy.

    • clear

      public void clear()
      Clear all the info from the ICIManager. This deletes the master time list.

    • getTimeDiff

      public double getTimeDiff(BitSet bitSet)
      Get the time difference in seconds between the current last data unit and the last data unit a track
      Returns:

    • getIDISeries

      public double[] getIDISeries(BitSet bitSet)
      Get the IDI series for a track in seconds
      Parameters:
      bitSet - - the track bitset.
      Returns:
      the IDI series of the positive track detections.

    • getTimeSeries

      public double[] getTimeSeries(BitSet bitSet)
      Get the time series for a track in seconds
      Parameters:
      bitSet - - the track bitset.
      Returns:
      the IDI series of the positive track detections.

    • getIDIMedian

      public double getIDIMedian(BitSet bitSet)
      Get the IDI series for a track in seconds
      Parameters:
      bitSet - - the track bitset.
      Returns:
      the IDI series of the positive track detections.

    • getIDIStruct

      public IDIData getIDIStruct(BitSet bitSet)
      Get the IDI series for a track in seconds
      Parameters:
      bitSet - - the track bitset.
      Returns:
      the IDI series of the positive track detections.

    • timeSeries2IDI

      public static double[] timeSeries2IDI(double[] timeSeries)
      Simple conversation of a time series to an inter detection interval series/
      Parameters:
      timeSeries - - the time series in seconds
      Returns:
      - the inter detection interval in seconds. The size of the array will be one less than the time series array.

    • printTimeSeries

      public static void printTimeSeries(double[] timeSeries)
      Print out double array
      Parameters:
      timeSeries -

    • printICISeries

      public static void printICISeries(double[] timeSeries)
      Print out double array
      Parameters:
      timeSeries -

    • getMasterTimeSeries

      public double[] getMasterTimeSeries()
      Get the master time series.
      Returns:
      the master time series.

    • isForceCalc

      public boolean isForceCalc()
      Check whether force calc flag is set. If true then the IDI manager will recalculate the IDI series whether the bitset is the same or not. This is reset after the calculation to false.
      Returns:
      the forceCalc flag.

    • setForceCalc

      public void setForceCalc(boolean forceCalc)
      Set the force calc flag. If true then the IDI manager will recalculate the IDI series whether the bitset is the same or not. This is reset after the calculation to false.
      Parameters:
      the - forceCalc flag.

    • trimData

      public void trimData(int newRefIndex)
      Trims the front of all arrays to the specified index. This is used to junk old data that is no longer relevant.
      Parameters:
      newRefIndex - - the index to trim to.

    • getCorrelationManager

      public CorrelationManager getCorrelationManager()
      Get the correlation manager. This handles correlations between data units.
      Returns:
      the correlations manager.

    • getLastTime

      public double getLastTime(BitSet bitSet)
      Get the last positive detection time for a given track BitSet.
      Parameters:
      bitSet - - the BitSet.
      Returns:
      the positive detection time in SECONDS.

    • getTotalTime

      public double getTotalTime()
      The total time of the current set of detections.
      Returns:
      the total time in seconds.

    • getFirstDataUnit

      public PamDataUnit getFirstDataUnit()