public class TreeStatistics extends TreeAnalyzer
Tree
. For analysis of groups of Trees use
MultiTreeStatistics
.Modifier and Type | Field and Description |
---|---|
static String |
AVG_SPINE_DENSITY
Flag for "Average spine/varicosity density" statistics.
|
static String |
BRANCH_LENGTH
Flag for "Branch length" analysis.
|
static String |
CONTRACTION
Flag for "Contraction" statistics.
|
static String |
FRACTAL_DIMENSION
Flag for "Fractal dimension" statistics.
|
static String |
INNER_LENGTH
Flag for "Length of inner branches" analysis.
|
static String |
INTER_NODE_DISTANCE
Flag for "Inter-node distance" statistics.
|
static String |
INTER_NODE_DISTANCE_SQUARED
Flag for "Inter-node distance (squared)" statistics.
|
protected sc.fiji.snt.analysis.TreeStatistics.LastDstats |
lastDstats |
static String |
MEAN_RADIUS
Flag for "Path mean radius" statistics.
|
static String |
N_BRANCH_POINTS
Flag for "No. of branch points" statistics.
|
static String |
N_NODES
Flag for "No. of branch points" statistics.
|
static String |
N_SPINES
Flag for "No. of spines/varicosities" statistics.
|
static String |
NODE_RADIUS
Flag for "Node radius" statistics.
|
static String |
PARTITION_ASYMMETRY
Flag for "Partition asymmetry" statistics.
|
static String |
PATH_CHANNEL
Flag for "Path channel" statistics.
|
static String |
PATH_FRAME
Flag for "Path frame" statistics.
|
static String |
PATH_LENGTH
Flag for "Path length" analysis.
|
static String |
PATH_ORDER
Flag for "Path order" statistics.
|
static String |
PRIMARY_LENGTH
Flag for "Length of primary branches" analysis.
|
static String |
REMOTE_BIF_ANGLES
Flag for "Remote bif. angles" statistics.
|
static String |
TERMINAL_LENGTH
Flag for "Length of terminal branches" analysis.
|
static String |
VALUES
Flag for analysis of "Node intensity values", an optional numeric property that
can be assigned to Path nodes (e.g., voxel intensities, assigned via
PathProfiler . |
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.
|
displayService, innerBranches, primaryBranches, statusService, table, terminalBranches, tips, tree
Constructor and Description |
---|
TreeStatistics(Tree tree)
Instantiates a new instance from a collection of Paths
|
Modifier and Type | Method and Description |
---|---|
protected void |
assembleStats(sc.fiji.snt.analysis.TreeStatistics.StatisticsInstance stat,
String measurement) |
static TreeStatistics |
fromCollection(Collection<Tree> trees,
String metric) |
static List<String> |
getAllMetrics()
Gets the list of all supported metrics.
|
static List<String> |
getAnalyzerMetrics()
Gets the list of all
TreeAnalyzer supported metrics. |
protected static Map<BrainAnnotation,Double> |
getAnnotatedLength(DirectedWeightedGraph graph,
int level,
char lr) |
Map<BrainAnnotation,Double> |
getAnnotatedLength(int level)
Retrieves the amount of cable length present on each brain compartment
innervated by the analyzed neuron.
|
Map<BrainAnnotation,Double> |
getAnnotatedLength(int level,
String hemisphere)
Retrieves the amount of cable length present on each brain compartment
innervated by the analyzed neuron.
|
SNTChart |
getAnnotatedLengthHistogram()
Retrieves the of cable length frequencies across brain areas.
|
SNTChart |
getAnnotatedLengthHistogram(int depth)
Retrieves the histogram of cable length frequencies across brain areas of the
specified ontology level.
|
SNTChart |
getAnnotatedLengthHistogram(int depth,
String hemisphere)
Retrieves the histogram of cable length frequencies across brain areas of the
specified ontology level across the specified hemisphere.
|
protected SNTChart |
getAnnotatedLengthHistogram(Map<BrainAnnotation,Double> map,
int depth,
String secondaryLabel) |
protected static Map<BrainAnnotation,double[]> |
getAnnotatedLengthsByHemisphere(DirectedWeightedGraph graph,
int level) |
Map<BrainAnnotation,double[]> |
getAnnotatedLengthsByHemisphere(int level) |
protected SNTChart |
getAnnotatedLengthsByHemisphereHistogram(int depth) |
DescriptiveStatistics |
getDescriptiveStats(String metric)
Computes the
DescriptiveStatistics for the specified measurement. |
SNTChart |
getHistogram(String metric)
Retrieves the histogram of relative frequencies histogram for a univariate
measurement.
|
protected SNTChart |
getHistogram(String normMeasurement,
sc.fiji.snt.analysis.AnalysisUtils.HistogramDatasetPlus datasetPlus) |
static List<String> |
getMetrics()
Gets the list of most commonly used metrics.
|
NodeStatistics<SWCPoint> |
getNodeStatistics() |
NodeStatistics<SWCPoint> |
getNodeStatistics(String type) |
protected static String |
getNormalizedMeasurement(String measurement) |
SummaryStatistics |
getSummaryStats(String metric)
Computes the
SummaryStatistics for the specified measurement. |
protected boolean |
lastDstatsCanBeRecycled(String normMeasurement) |
static void |
main(String[] args) |
protected static String |
tryReallyHardToGuessMetric(String guess) |
getAnnotations, getAnnotations, getAvgBranchLength, getAvgContraction, getAvgFractalDimension, getAvgFragmentation, getAvgPartitionAsymmetry, getAvgRemoteBifAngle, getBranches, getBranchPoints, getBranchPoints, getCableLength, getCableLength, getCableLength, getCableLengthNorm, getCol, getDepth, getFractalDimension, getHeight, getHighestPathOrder, getInnerBranches, getInnerLength, getMetric, getMetricInternal, getMetricWithoutChecks, getNBranches, getNbranchPoints, getNbranchPointsNorm, getNextRow, getNFittedPaths, getNoSpinesOrVaricosities, getNPaths, getNtips, getNtipsNorm, getParsedTree, getPartitionAsymmetry, getPrimaryBranches, getPrimaryLength, getPrimaryPaths, getRemoteBifAngles, getShollAnalyzer, getSinglePointPaths, getSpineOrVaricosityDensity, getStrahlerAnalyzer, getStrahlerBifurcationRatio, getStrahlerNumber, getSWCTypesAsString, getTable, getTerminalBranches, getTerminalLength, getTips, getTips, getWidth, ignoreSWCType, isSameOrParentAnnotation, isValid, measure, measure, resetRestrictions, restrictToLength, restrictToNamePattern, restrictToOrder, restrictToSize, restrictToSWCType, run, setTable, setTable, summarize, summarize, updateAndDisplayTable
cancel, getCancelReason, isCanceled
context, getContext
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
setContext
public static final String PATH_LENGTH
public static final String BRANCH_LENGTH
public static final String TERMINAL_LENGTH
public static final String PRIMARY_LENGTH
public static final String INNER_LENGTH
public static final String PATH_ORDER
public static final String PATH_CHANNEL
public static final String PATH_FRAME
public static final String INTER_NODE_DISTANCE
public static final String INTER_NODE_DISTANCE_SQUARED
public static final String N_BRANCH_POINTS
public static final String N_NODES
public static final String N_SPINES
public static final String NODE_RADIUS
public static final String MEAN_RADIUS
public static final String AVG_SPINE_DENSITY
public static final String X_COORDINATES
public static final String Y_COORDINATES
public static final String Z_COORDINATES
public static final String CONTRACTION
public static final String REMOTE_BIF_ANGLES
public static final String PARTITION_ASYMMETRY
public static final String FRACTAL_DIMENSION
public static final String VALUES
PathProfiler
. Note that an IllegalArgumentException
is
triggered if no values have been assigned to the tree being analyzed.protected sc.fiji.snt.analysis.TreeStatistics.LastDstats lastDstats
public TreeStatistics(Tree tree)
tree
- the collection of paths to be analyzedpublic static List<String> getAnalyzerMetrics()
TreeAnalyzer
supported metrics.TreeAnalyzer.getAllMetrics()
public static List<String> getAllMetrics()
public static List<String> getMetrics()
public SummaryStatistics getSummaryStats(String metric)
SummaryStatistics
for the specified measurement.metric
- the measurement (N_NODES
, NODE_RADIUS
,
etc.)public DescriptiveStatistics getDescriptiveStats(String metric)
DescriptiveStatistics
for the specified measurement.metric
- the measurement (N_NODES
, NODE_RADIUS
,
etc.)public Map<BrainAnnotation,Double> getAnnotatedLength(int level)
level
- the ontological depth of the compartments to be consideredAllenCompartment.getOntologyDepth()
public Map<BrainAnnotation,Double> getAnnotatedLength(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()
protected static Map<BrainAnnotation,Double> getAnnotatedLength(DirectedWeightedGraph graph, int level, char lr)
public Map<BrainAnnotation,double[]> getAnnotatedLengthsByHemisphere(int level)
protected static Map<BrainAnnotation,double[]> getAnnotatedLengthsByHemisphere(DirectedWeightedGraph graph, int level)
public SNTChart getAnnotatedLengthHistogram()
public SNTChart getAnnotatedLengthHistogram(int depth)
depth
- the ontological depth of the compartments to be consideredAllenCompartment.getOntologyDepth()
public SNTChart getAnnotatedLengthHistogram(int depth, String hemisphere)
depth
- the ontological depth of the compartments to be consideredhemisphere
- 'left', 'right' or 'ratio' (case insensitive). Ignored if
not a recognized optionAllenCompartment.getOntologyDepth()
protected SNTChart getAnnotatedLengthsByHemisphereHistogram(int depth)
protected SNTChart getAnnotatedLengthHistogram(Map<BrainAnnotation,Double> map, int depth, String secondaryLabel)
public SNTChart getHistogram(String metric)
metric
- the measurement (N_NODES
, NODE_RADIUS
, etc.)public static TreeStatistics fromCollection(Collection<Tree> trees, String metric)
protected SNTChart getHistogram(String normMeasurement, sc.fiji.snt.analysis.AnalysisUtils.HistogramDatasetPlus datasetPlus)
protected void assembleStats(sc.fiji.snt.analysis.TreeStatistics.StatisticsInstance stat, String measurement)
protected boolean lastDstatsCanBeRecycled(String normMeasurement)
public NodeStatistics<SWCPoint> getNodeStatistics()
public NodeStatistics<SWCPoint> getNodeStatistics(String type)
public static void main(String[] args)
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