NodeStatistics (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- sc.fiji.snt.analysis.NodeStatistics<T>

Type Parameters:

T -
```
public class NodeStatistics<T extends PointInImage>
extends Object
```
Computes summary and descriptive statistics from a Collection of nodes.

Author:

Tiago Ferreira

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`BRANCH_LENGTH` Flag for "Branch length" analysis.
`static String`	`BRANCH_ORDER` Flag for "Branch order" statistics.
`static String`	`RADIUS` Flag for "Node radius" statistics.
`static String`	`VALUES` Flag for statistics on "Node intensity values"
`static String`	`X_COORDINATES` Flag for "X coordinates" statistics.
`static String`	`Y_COORDINATES` Flag for "Y coordinates" statistics.
`static String`	`Z_COORDINATES` Flag for "Z coordinates" statistics.

Constructor Summary

Constructors
Constructor and Description
`NodeStatistics(Collection<T> points)` Performs statistics on a collection of nodes.
`NodeStatistics(Collection<T> points, Tree tree)` Performs statistics on a collection of nodes.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected void`	`assessIfBranchesHaveBeenAssigned()`
`void`	`assignBranches(Tree tree)` Associates the nodes being analyzed to the branches of the specified tree
`List<T>`	`get(BrainAnnotation compartment)` Gets the list of nodes associated with the specified compartment (neuropil label).
`List<T>`	`get(BrainAnnotation compartment, boolean includeChildren)` Gets the list of nodes associated with the specified compartment (neuropil label).
`Map<BrainAnnotation,Integer>`	`getAnnotatedFrequencies()` Retrieves the count frequencies across brain compartment.
`Map<BrainAnnotation,Integer>`	`getAnnotatedFrequencies(int level)` Retrieves the count frequencies across brain compartment.
`Map<BrainAnnotation,Integer>`	`getAnnotatedFrequencies(int level, String hemisphere)` Retrieves the count frequencies across brain compartment.
`Map<BrainAnnotation,int[]>`	`getAnnotatedFrequenciesByHemisphere(int level, Tree tree)`
`SNTChart`	`getAnnotatedFrequencyHistogram(int depth, String hemisphere, Tree tree)` Retrieves the histogram of count frequencies across brain areas of the specified ontology level across the specified hemisphere.
`SNTChart`	`getAnnotatedHistogram()` Retrieves the histogram of count frequencies across brain areas.
`SNTChart`	`getAnnotatedHistogram(int depth)` Retrieves the histogram of count frequencies across brain areas of the specified ontology level.
`Map<BrainAnnotation,Set<T>>`	`getAnnotatedNodes()` Splits the nodes being analyzed into groups sharing the same brain annotation.
`Map<BrainAnnotation,Set<T>>`	`getAnnotatedNodes(int level)` Splits the nodes being analyzed into groups sharing the same brain annotation.
`DescriptiveStatistics`	`getDescriptiveStatistics(String metric)` Computes the `DescriptiveStatistics` for the specified measurement.
`SNTChart`	`getHistogram(String metric)` Gets the relative frequencies histogram for a univariate measurement.
`static List<String>`	`getMetrics()` Gets the list of supported metrics.
`protected static String`	`getNormalizedMeasurement(String measurement)`
`protected static String`	`getStandardizedMetric(String guess)`
`protected boolean`	`isBranchesAssigned()`
`static void`	`main(String[] args)`
`void`	`setLabel(String label)` Sets a descriptive label to this statistic analysis to be used in histograms, etc.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - BRANCH_LENGTH
```
public static final String BRANCH_LENGTH
```
    Flag for "Branch length" analysis.
    
    See Also:
    
    Constant Field Values
  - BRANCH_ORDER
```
public static final String BRANCH_ORDER
```
    Flag for "Branch order" statistics.
    
    See Also:
    
    Constant Field Values
  - RADIUS
```
public static final String RADIUS
```
    Flag for "Node radius" statistics.
    
    See Also:
    
    Constant Field Values
  - X_COORDINATES
```
public static final String X_COORDINATES
```
    Flag for "X coordinates" statistics.
    
    See Also:
    
    Constant Field Values
  - Y_COORDINATES
```
public static final String Y_COORDINATES
```
    Flag for "Y coordinates" statistics.
    
    See Also:
    
    Constant Field Values
  - Z_COORDINATES
```
public static final String Z_COORDINATES
```
    Flag for "Z coordinates" statistics.
    
    See Also:
    
    Constant Field Values
  - VALUES
```
public static final String VALUES
```
    Flag for statistics on "Node intensity values"
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - NodeStatistics
```
public NodeStatistics(Collection<T> points)
```
    Performs statistics on a collection of nodes.
    
    Parameters:
    
    points - the points to be analyzed
  - NodeStatistics
```
public NodeStatistics(Collection<T> points,
                      Tree tree)
```
    Performs statistics on a collection of nodes.
    
    Parameters:
    
    points - the points to be analyzed
    
    tree - the Tree associated with points
- Method Detail
  - getMetrics
```
public static List<String> getMetrics()
```
    Gets the list of supported metrics.
    
    Returns:
    
    the list of supported metrics
  - setLabel
```
public void setLabel(String label)
```
    Sets a descriptive label to this statistic analysis to be used in histograms, etc.
    
    Parameters:
    
    label - the descriptive label
  - getDescriptiveStatistics
```
public DescriptiveStatistics getDescriptiveStatistics(String metric)
                                               throws sc.fiji.snt.analysis.UnknownMetricException
```
    Computes the DescriptiveStatistics for the specified measurement.
    
    Parameters:
    
    metric - the measurement (X_COORDINATES, Y_COORDINATES, etc.)
    
    Returns:
    
    the DescriptiveStatistics object.
    
    Throws:
    
    sc.fiji.snt.analysis.UnknownMetricException
  - getHistogram
```
public SNTChart getHistogram(String metric)
```
    Gets the relative frequencies histogram for a univariate measurement. The number of bins is determined using the Freedman-Diaconis rule.
    
    Parameters:
    
    metric - the measurement (X_COORDINATES, RADIUS, etc.)
    
    Returns:
    
    the frame holding the histogram
  - get
```
public List<T> get(BrainAnnotation compartment)
```
    Gets the list of nodes associated with the specified compartment (neuropil label).
    
    Parameters:
    
    compartment - the query compartment (null not allowed). All of its children will be considered
    
    Returns:
    
    the list of filtered nodes
  - get
```
public List<T> get(BrainAnnotation compartment,
                   boolean includeChildren)
```
    Gets the list of nodes associated with the specified compartment (neuropil label).
    
    Parameters:
    
    compartment - the query compartment (null not allowed)
    
    includeChildren - whether children of compartment should be included
    
    Returns:
    
    the list of filtered nodes
  - getAnnotatedNodes
```
public Map<BrainAnnotation,Set<T>> getAnnotatedNodes()
```
    Splits the nodes being analyzed into groups sharing the same brain annotation.
    
    Returns:
    
    the map containing the brain annotations as keys, and list of nodes as values.
  - getAnnotatedNodes
```
public Map<BrainAnnotation,Set<T>> getAnnotatedNodes(int level)
```
    Splits the nodes being analyzed into groups sharing the same brain annotation.
    
    Parameters:
    
    level - the ontological depth of the compartments to be considered
    
    Returns:
    
    the map containing the brain annotations as keys, and list of nodes as values.
  - getAnnotatedFrequencies
```
public Map<BrainAnnotation,Integer> getAnnotatedFrequencies()
```
    Retrieves the count frequencies across brain compartment.
    
    Returns:
    
    the map containing the brain compartments as keys, and count frequencies as values.
  - getAnnotatedFrequencies
```
public Map<BrainAnnotation,Integer> getAnnotatedFrequencies(int level)
```
    Retrieves the count frequencies across brain compartment.
    
    Parameters:
    
    level - the ontological depth of the compartments to be considered
    
    Returns:
    
    the map containing the brain compartments as keys, and count frequencies as values.
    
    See Also:
    
    AllenCompartment.getOntologyDepth()
  - getAnnotatedFrequencies
```
public Map<BrainAnnotation,Integer> getAnnotatedFrequencies(int level,
                                                            String hemisphere)
```
    Retrieves the count frequencies across brain compartment.
    
    Parameters:
    
    level - the ontological depth of the compartments to be considered
    
    hemisphere - typically 'left' or 'right'. The hemisphere flag ( BrainAnnotation.LEFT_HEMISPHERE or BrainAnnotation.RIGHT_HEMISPHERE) is extracted from the first character of the string (case insensitive). Ignored if not a recognized option
    
    Returns:
    
    the map containing the brain compartments as keys, and frequencies as values.
    
    See Also:
    
    AllenCompartment.getOntologyDepth()
  - getAnnotatedFrequenciesByHemisphere
```
public Map<BrainAnnotation,int[]> getAnnotatedFrequenciesByHemisphere(int level,
                                                                      Tree tree)
```
  - getAnnotatedHistogram
```
public SNTChart getAnnotatedHistogram()
```
    Retrieves the histogram of count frequencies across brain areas.
    
    Returns:
    
    the annotated frequencies histogram
  - getAnnotatedHistogram
```
public SNTChart getAnnotatedHistogram(int depth)
```
    Retrieves the histogram of count frequencies across brain areas of the specified ontology level.
    
    Parameters:
    
    depth - the ontological depth of the compartments to be considered
    
    Returns:
    
    the annotated frequencies histogram
    
    See Also:
    
    AllenCompartment.getOntologyDepth()
  - getAnnotatedFrequencyHistogram
```
public SNTChart getAnnotatedFrequencyHistogram(int depth,
                                               String hemisphere,
                                               Tree tree)
```
    Retrieves the histogram of count frequencies across brain areas of the specified ontology level across the specified hemisphere.
    
    Parameters:
    
    depth - the ontological depth of the compartments to be considered
    
    hemisphere - 'left', 'right' or 'ratio' (case insensitive). Ignored if not a recognized option
    
    tree - the Tree associated with the nodes being analyzed. Only used if hemisphere is 'ratio'.
    
    Returns:
    
    the annotated frequencies histogram
    
    See Also:
    
    AllenCompartment.getOntologyDepth()
  - getStandardizedMetric
```
protected static String getStandardizedMetric(String guess)
```
  - assignBranches
```
public void assignBranches(Tree tree)
```
    Associates the nodes being analyzed to the branches of the specified tree
    
    Parameters:
    
    tree - the association tree
  - isBranchesAssigned
```
protected boolean isBranchesAssigned()
```
  - getNormalizedMeasurement
```
protected static String getNormalizedMeasurement(String measurement)
```
  - assessIfBranchesHaveBeenAssigned
```
protected void assessIfBranchesHaveBeenAssigned()
```
  - main
```
public static void main(String[] args)
```

Class NodeStatistics<T extends PointInImage>

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

BRANCH_LENGTH

BRANCH_ORDER

RADIUS

X_COORDINATES

Y_COORDINATES

Z_COORDINATES

VALUES

Constructor Detail

NodeStatistics

NodeStatistics

Method Detail

getMetrics

setLabel

getDescriptiveStatistics

getHistogram

get

get

getAnnotatedNodes

getAnnotatedNodes

getAnnotatedFrequencies

getAnnotatedFrequencies

getAnnotatedFrequencies

getAnnotatedFrequenciesByHemisphere

getAnnotatedHistogram

getAnnotatedHistogram

getAnnotatedFrequencyHistogram

getStandardizedMetric

assignBranches

isBranchesAssigned

getNormalizedMeasurement

assessIfBranchesHaveBeenAssigned

main