Constructor Detail

• GroupedTreeStatistics

  public GroupedTreeStatistics()

  Instantiates a new grouped tree statistics.

Method Detail

• addGroup

  public void addGroup(Collection<Tree> group,
                       String groupLabel)

  Adds a comparison group to the analysis queue.

  Parameters:

  group - the group

  groupLabel - a unique label identifying the group

• addGroup

  public void addGroup(Collection<Tree> group,
                       String groupLabel,
                       String... swcTypes)
                throws NoSuchElementException

  Adds a comparison group to the analysis queue.

  Parameters:

  group - the collection of Trees to be analyzed

  groupLabel - a unique label identifying the group

  swcTypes - SWC type(s) a string with at least 2 characters describing the SWC type allowed in the subtree (e.g., 'axn', or 'dendrite')

  Throws:

  NoSuchElementException - swcTypes are not applicable to group

• getGroupStats

  public MultiTreeStatistics getGroupStats(String groupLabel)

  Gets the group statistics.

  Parameters:

  groupLabel - the unique label identifying the group

  Returns:

  the group statistics or null if no group is mapped to groupLabel

• getN

  public int getN(String groupLabel)

  Gets the number of Trees in a specified group.

  Parameters:

  groupLabel - the unique label identifying the group

  Returns:

  the number of Trees or -1 if no group is mapped to groupLabel

• getGroups

  public Collection<String> getGroups()

  Gets the group identifiers currently queued for analysis.

  Returns:

  the group identifiers

• getHistogram

  public SNTChart getHistogram(String measurement)

  Gets the relative frequencies histogram for a univariate measurement. The number of bins is determined using the Freedman-Diaconis rule.

  Parameters:

  measurement - the measurement (N_NODES, NODE_RADIUS, etc.)

  Returns:

  the frame holding the histogram

  See Also:

  MultiTreeStatistics.getMetrics(), TreeStatistics.getMetrics(), setMinNBins(int)

• getBoxPlot

  public SNTChart getBoxPlot(String measurement)

  Assembles a Box and Whisker Plot for the specified measurement (cell morphometry).

  Parameters:

  measurement - the measurement (N_NODES, NODE_RADIUS, etc.)

  Returns:

  the frame holding the box plot

  See Also:

  MultiTreeStatistics.getMetrics(), TreeStatistics.getMetrics()

• getBoxPlot

  public SNTChart getBoxPlot(String feature,
                             Collection<BrainAnnotation> annotations)

  Assembles a Box and Whisker Plot for the specified feature (absolute measurements).

  Parameters:

  feature - the feature (, , , etc.). Note that the majority of MultiTreeStatistics.getAllMetrics() metrics are currently not supported.

  annotations - the BrainAnnotation to be queried. Null not allowed.

  Returns:

  the frame holding the box plot

• getBoxPlot

  public SNTChart getBoxPlot(String feature,
                             Collection<BrainAnnotation> annotations,
                             double cutoff,
                             boolean normalize)

  Assembles a Box and Whisker Plot for the specified feature.

  Parameters:

  feature - the feature (, , , etc.). Note that the majority of MultiTreeStatistics.getAllMetrics() metrics are currently not supported.

  annotations - the BrainAnnotation to be queried. Null not allowed.

  cutoff - a filtering option. If the computed feature for an annotation is below this value, that annotation is excluded from the plot

  normalize - If true, values are retrieved as ratios. E.g., If feature is , and cutoff 0.1, BrainAnnotations in annotations associated with less than 10% of cable length are ignored.

  Returns:

  the frame holding the box plot

• main

  public static void main(String[] args)

• setMinNBins

  public void setMinNBins(int minNoOfBins)

  Sets the minimum number of bins when assembling histograms.

  Parameters:

  minNoOfBins - the minimum number of bins.