| Package | Description |
|---|---|
| sc.fiji.snt |
SNT core classes
|
| sc.fiji.snt.analysis |
Analysis of
Trees. |
| sc.fiji.snt.analysis.sholl.parsers |
Parsers to retrieve Profiles from multiple sources (2D/3D images, reconstructions, and tables)
|
| sc.fiji.snt.util |
Miscellaneous SNT utilities, including classes defining reconstruction nodes.
|
| Modifier and Type | Field and Description |
|---|---|
protected PointInImage |
NearPoint.near |
protected PointInImage |
Path.startJoinsPoint |
| Modifier and Type | Method and Description |
|---|---|
PointInImage |
NearPoint.getNode() |
PointInImage |
Path.getNode(int pos)
Gets the node at the specified position.
|
protected PointInImage |
Path.getNodeWithoutChecks(int pos) |
PointInImage |
Tree.getRoot()
Gets the first node of the main primary path of this tree
|
PointInImage |
Path.getStartJoinsPoint() |
protected PointInImage |
Path.lastPoint() |
PointInImage |
Path.nearestNodeTo(PointInImage node,
double within)
Gets the closest node associated with the specified node.
|
PointInImage |
PathAndFillManager.AllPointsIterator.next() |
| Modifier and Type | Method and Description |
|---|---|
Iterator<PointInImage> |
PathAndFillManager.allPointsIterator() |
List<PointInImage> |
Path.findJunctions()
Returns the nodes which are indicated to be a join (junction/branch point),
either in this Path object, or any other that starts or ends on it.
|
Set<PointInImage> |
Path.getJunctionNodes()
This is a version of
Path.findJunctions() ensuring that a junction node
is only retrieved once even if multiple child paths are associated with it. |
List<PointInImage> |
Tree.getNodes()
Gets all the nodes (path points) forming this tree.
|
List<PointInImage> |
Path.getNodes()
Gets the nodes of this path.
|
List<PointInImage> |
Tree.getSomaNodes()
Gets the list of all nodes tagged as
Path.SWC_SOMA. |
| Modifier and Type | Method and Description |
|---|---|
void |
Path.addNode(PointInImage point)
Appends a node to this Path.
|
Path |
SNT.autoTrace(List<SNTPoint> pointList,
PointInImage forkPoint)
Automatically traces a path from a list of points and adds it to the active
PathAndFillManager instance. |
Path |
SNT.autoTrace(List<SNTPoint> pointList,
PointInImage forkPoint,
boolean headless) |
Path |
SNT.autoTrace(SNTPoint start,
SNTPoint end,
PointInImage forkPoint)
Automatically traces a path from a point A to a point B.
|
Path |
SNT.autoTrace(SNTPoint start,
SNTPoint end,
PointInImage forkPoint,
boolean headless) |
boolean |
Path.contains(PointInImage pim)
Check whether this Path contains the specified point
|
int |
Path.getNodeIndex(PointInImage pim)
Gets the first node index associated with the specified image coordinates.
|
void |
Path.insertNode(int index,
PointInImage point)
Inserts a node at a specified position.
|
void |
Path.moveNode(int index,
PointInImage destination)
Assigns a new location to the specified node.
|
PointInImage |
Path.nearestNodeTo(PointInImage node,
double within)
Gets the closest node associated with the specified node.
|
protected NearPoint |
PathAndFillManager.nearestPointOnAnyPath(Collection<Path> paths,
PointInImage pim,
double distanceLimitSquared,
boolean unScaledPositions) |
void |
Path.setStartJoin(Path other,
PointInImage joinPoint) |
protected void |
SNT.startSholl(PointInImage centerScaled) |
| Constructor and Description |
|---|
NearPoint(PointInImage nearPoint,
Path path,
int indexInPath) |
NearPoint(PointInImage nearPoint,
Path path,
int indexInPath,
boolean unScaledPositions) |
| Modifier and Type | Class and Description |
|---|---|
class |
NodeStatistics<T extends PointInImage>
Computes summary and descriptive statistics from a Collection of nodes.
|
| Modifier and Type | Field and Description |
|---|---|
protected Set<PointInImage> |
TreeAnalyzer.tips |
| Modifier and Type | Method and Description |
|---|---|
Set<PointInImage> |
TreeAnalyzer.getBranchPoints()
Gets the position of all the branch points in the analyzed tree.
|
Set<PointInImage> |
MultiTreeStatistics.getBranchPoints() |
Set<PointInImage> |
TreeAnalyzer.getBranchPoints(BrainAnnotation annot)
Gets the position of all the branch points in the analyzed tree associated
with the specified annotation.
|
Set<PointInImage> |
TreeAnalyzer.getTips()
Gets the position of all the tips in the analyzed tree.
|
Set<PointInImage> |
MultiTreeStatistics.getTips() |
Set<PointInImage> |
TreeAnalyzer.getTips(BrainAnnotation annot)
Gets the position of all the tips in the analyzed tree associated with the
specified annotation.
|
| Modifier and Type | Method and Description |
|---|---|
void |
TreeColorMapper.map(Collection<? extends PointInImage> points,
String measurement,
String lut)
Colorizes a collection of points after the specified measurement.
|
| Modifier and Type | Method and Description |
|---|---|
PointInImage |
TreeParser.getCenter()
Returns the center coordinates
|
| Modifier and Type | Method and Description |
|---|---|
void |
TreeParser.setCenter(PointInImage center)
Sets the center of the profile.
|
| Modifier and Type | Class and Description |
|---|---|
class |
PointInCanvas
Defines a Point in a tracing canvas in pixel coordinates.
|
class |
ShollPoint
Convenience flavor of
PointInImage defining 2D/3D points for Sholll Analysis. |
class |
SWCPoint
Defines a node in an SWC reconstruction.
|
| Modifier and Type | Field and Description |
|---|---|
protected PointInImage |
BoundingBox.origin
The bounding box origin (SE, lower corner)
|
protected PointInImage |
BoundingBox.originOpposite
The origin opposite (NW, upper corner)
|
| Modifier and Type | Method and Description |
|---|---|
PointInImage |
PointInImage.clone() |
PointInImage |
PointInCanvas.getScaledPoint()
Converts the pixels coordinates of this point into a physical location if
this point is associated with a Path.
|
PointInImage |
BoundingBox.origin()
Retrieves the origin of this box.
|
PointInImage |
BoundingBox.originOpposite()
Retrieves the origin opposite of this box.
|
PointInImage |
PointInImage.transform(PathTransformer transformer) |
PointInImage |
BoundingBox.unscaledOrigin()
Retrieves the origin of this box in unscaled ("pixel" units)
|
PointInImage |
BoundingBox.unscaledOriginOpposite()
Retrieves the origin opposite of this box in unscaled ("pixel" units)
|
| Modifier and Type | Method and Description |
|---|---|
double |
PointInImage.chebyshevDxTo(PointInImage point) |
double |
PointInImage.chebyshevXYdxTo(PointInImage point) |
double |
PointInImage.chebyshevZdxTo(PointInImage point) |
double |
PointInImage.distanceSquaredTo(PointInImage o) |
double |
PointInImage.distanceTo(PointInImage o) |
double |
PointInImage.euclideanDxTo(PointInImage point) |
boolean |
PointInImage.isSameLocation(PointInImage pim) |
void |
BoundingBox.setOrigin(PointInImage origin)
Sets the origin for this box, i.e., its (xMin, yMin, zMin) vertex.
|
void |
BoundingBox.setOriginOpposite(PointInImage originOpposite)
Sets the origin opposite for this box, i.e., its (xMax, yMax, zMax) vertex.
|
| Constructor and Description |
|---|
ShollPoint(PointInImage pim) |
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