T
- public class NodeStatistics<T extends PointInImage> extends Object
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 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.
|
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.
|
public static final String BRANCH_LENGTH
public static final String BRANCH_ORDER
public static final String RADIUS
public static final String X_COORDINATES
public static final String Y_COORDINATES
public static final String Z_COORDINATES
public static final String VALUES
public NodeStatistics(Collection<T> points)
points
- the points to be analyzedpublic NodeStatistics(Collection<T> points, Tree tree)
points
- the points to be analyzedtree
- the Tree associated with points
public static List<String> getMetrics()
public void setLabel(String label)
label
- the descriptive labelpublic DescriptiveStatistics getDescriptiveStatistics(String metric) throws sc.fiji.snt.analysis.UnknownMetricException
DescriptiveStatistics
for the specified measurement.metric
- the measurement (X_COORDINATES
, Y_COORDINATES
,
etc.)sc.fiji.snt.analysis.UnknownMetricException
public SNTChart getHistogram(String metric)
metric
- the measurement (X_COORDINATES
, RADIUS
,
etc.)public List<T> get(BrainAnnotation compartment)
compartment
- the query compartment (null not allowed). All of its
children will be consideredpublic List<T> get(BrainAnnotation compartment, boolean includeChildren)
compartment
- the query compartment (null not allowed)includeChildren
- whether children of compartment
should be includedpublic Map<BrainAnnotation,Set<T>> getAnnotatedNodes()
public Map<BrainAnnotation,Set<T>> getAnnotatedNodes(int level)
level
- the ontological depth of the compartments to be consideredpublic Map<BrainAnnotation,Integer> getAnnotatedFrequencies()
public Map<BrainAnnotation,Integer> getAnnotatedFrequencies(int level)
level
- the ontological depth of the compartments to be consideredAllenCompartment.getOntologyDepth()
public Map<BrainAnnotation,Integer> getAnnotatedFrequencies(int level, String hemisphere)
level
- the ontological depth of the compartments to be consideredhemisphere
- 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 optionAllenCompartment.getOntologyDepth()
public Map<BrainAnnotation,int[]> getAnnotatedFrequenciesByHemisphere(int level, Tree tree)
public SNTChart getAnnotatedHistogram()
public SNTChart getAnnotatedHistogram(int depth)
depth
- the ontological depth of the compartments to be consideredAllenCompartment.getOntologyDepth()
public SNTChart getAnnotatedFrequencyHistogram(int depth, String hemisphere, Tree tree)
depth
- the ontological depth of the compartments to be consideredhemisphere
- 'left', 'right' or 'ratio' (case insensitive). Ignored if
not a recognized optiontree
- the Tree associated with the nodes being analyzed. Only
used if hemisphere is 'ratio'.AllenCompartment.getOntologyDepth()
public void assignBranches(Tree tree)
tree
- the association treeprotected boolean isBranchesAssigned()
protected void assessIfBranchesHaveBeenAssigned()
public static void main(String[] args)
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