| Package | Description |
|---|---|
| ini.trakem2.analysis | |
| ini.trakem2.display | |
| ini.trakem2.vector |
| Modifier and Type | Field and Description |
|---|---|
VectorString3D |
Compare.Chain.vs |
| Modifier and Type | Method and Description |
|---|---|
static VectorString3D |
Compare.condense(Compare.CATAParameters cp,
VectorString3D[] vs,
Worker worker)
Do an all-to-all distance matrix of the given vs, then do a neighbor joining, do a weighted merge of the two VectorString3D being merged, and then finally output the resulting condensed unique VectorString3D with its source array full with all points that make each point in it.
|
| Modifier and Type | Method and Description |
|---|---|
static List<VectorString3D> |
Compare.transferVectorStrings(List<VectorString3D> vs,
List<Tuple3d> source,
List<Tuple3d> target,
Class<AffineModel3D> model_class)
Transform all points of all VectorString3D in vs using a Moving Least Squares Transform defined by the pairing of points in source to those in target.
|
static List<VectorString3D> |
Compare.transferVectorStrings(List<VectorString3D> vs,
Map<String,Tuple3d> source,
Map<String,Tuple3d> target)
Transfer vs via a moving least squares transform by matching source named points into equally named target named points.
|
static List<VectorString3D> |
Compare.transferVectorStrings(List<VectorString3D> vs,
ProjectThing source_fiduciary,
ProjectThing target_fiduciary) |
| Modifier and Type | Method and Description |
|---|---|
static VectorString3D |
Compare.condense(Compare.CATAParameters cp,
VectorString3D[] vs,
Worker worker)
Do an all-to-all distance matrix of the given vs, then do a neighbor joining, do a weighted merge of the two VectorString3D being merged, and then finally output the resulting condensed unique VectorString3D with its source array full with all points that make each point in it.
|
static Vector3d[] |
Compare.createOrigin(VectorString3D x,
VectorString3D y,
VectorString3D z,
int transform_type)
Returns an array of 4 Vector3d: the three unit vectors in the same order as the vector strings, and the origin of coordinates.
|
static Vector3d[] |
Compare.createOrigin(VectorString3D x,
VectorString3D y,
VectorString3D z,
int transform_type,
Vector3d[] o_ref) |
protected static Object[] |
Compare.findBestMatch(VectorString3D vs1,
VectorString3D vs2,
double delta,
boolean skip_ends,
int max_mut,
float min_chunk) |
protected static Object[] |
Compare.findBestMatch(VectorString3D vs1,
VectorString3D vs2,
double delta,
boolean skip_ends,
int max_mut,
float min_chunk,
int distance_type,
boolean direct,
boolean substring_matching)
Since comparing two sequences starting from one end or starting from the other
is not the same at all, this method performs the match starting first from one
end and then from the other.
|
static Object[] |
Compare.findBestMatch(VectorString3D vs1,
VectorString3D vs2,
double delta,
boolean skip_ends,
int max_mut,
float min_chunk,
int distance_type,
boolean direct,
boolean substring_matching,
double wi,
double wd,
double wm) |
static double[] |
Compare.makeEnvelope(Compare.CATAParameters cp,
VectorString3D c)
From a condensed VectorString3D, create the radius at each point.
|
static Plot |
Compare.makePlot(Compare.CATAParameters cp,
String name,
VectorString3D c) |
static float[][] |
Compare.scoreAllToAll(VectorString3D[] vs,
int distance_type,
double delta,
boolean skip_ends,
int max_mut,
float min_chunk,
boolean direct,
boolean substring_matching,
Worker worker)
Returns the half matrix of scores, with values copied from one half matrix to the other, and a diagonal of zeros.
|
static void |
Compare.testCreateOrigin(LayerSet ls,
VectorString3D vs1,
VectorString3D vs2,
VectorString3D vs3) |
| Modifier and Type | Method and Description |
|---|---|
static List<VectorString3D> |
Compare.transferVectorStrings(List<VectorString3D> vs,
List<Tuple3d> source,
List<Tuple3d> target,
Class<AffineModel3D> model_class)
Transform all points of all VectorString3D in vs using a Moving Least Squares Transform defined by the pairing of points in source to those in target.
|
static List<VectorString3D> |
Compare.transferVectorStrings(List<VectorString3D> vs,
Map<String,Tuple3d> source,
Map<String,Tuple3d> target)
Transfer vs via a moving least squares transform by matching source named points into equally named target named points.
|
static List<VectorString3D> |
Compare.transferVectorStrings(List<VectorString3D> vs,
ProjectThing source_fiduciary,
ProjectThing target_fiduciary) |
static Bureaucrat |
Compare.variabilityAnalysis(Project reference_project,
String regex,
String[] ignore,
boolean show_cata_dialog,
boolean generate_plots,
boolean show_plots,
String plot_dir_,
boolean show_3D,
boolean show_condensed_3D,
boolean show_sources_3D,
Map<Project,Color> sources_color_table,
boolean show_envelope_3D,
float envelope_alpha,
double delta_envelope,
int envelope_type,
boolean show_axes_3D,
boolean heat_map,
Map<String,VectorString3D> map_condensed,
Project[] projects) |
| Modifier and Type | Method and Description |
|---|---|
VectorString3D |
Polyline.asVectorString3D()
Returns a non-calibrated VectorString3D.
|
VectorString3D |
Pipe.asVectorString3D()
Returns a non-calibrated VectorString3D.
|
VectorString3D |
Line3D.asVectorString3D() |
| Modifier and Type | Method and Description |
|---|---|
static Future<Collection<Future<Content>>> |
Display3D.addMesh(LayerSet ref_ls,
VectorString3D vs,
String title,
Color color)
Creates a mesh from the given VectorString3D, which is unbound to any existing Pipe.
|
static Future<Collection<Future<Content>>> |
Display3D.addMesh(LayerSet ref_ls,
VectorString3D vs,
String title,
Color color,
double[] widths,
float alpha)
Creates a mesh from the given VectorString3D, which is unbound to any existing Pipe.
|
| Constructor and Description |
|---|
VectorStringContent(VectorString3D vs,
String title,
Color color,
double[] widths,
float alpha) |
| Modifier and Type | Method and Description |
|---|---|
VectorString3D |
VectorString3D.chain(VectorString3D vs)
Returns a new VectorString3D which is the result of the optimal chaining of this and the given VectorString.
|
static VectorString3D |
VectorString3D.createInterpolated(Editions ed,
double alpha) |
VectorString3D |
VectorString3D.createInterpolated(VectorString3D other,
Editions ed,
double alpha)
Create an interpolated VectorString3D between this and the given one, with the proper weight 'alpha' which must be 0 <= weight <= 1 (otherwise returns null)
|
static VectorString3D |
VectorString3D.createInterpolatedPoints(Editions ed,
double alpha)
Create a new VectorString3D which is the weighted average between the two VectorString3D that make the Editions.
|
static VectorString3D |
VectorString3D.createInterpolatedPoints(Editions ed,
double alpha,
int first,
int last)
Create a new VectorString3D which is the weighted average between the two VectorString3D that make the Editions.
|
static VectorString3D |
VectorString3D.createRandom(int length,
double delta,
boolean closed) |
VectorString3D |
VectorString3D.makeReversedCopy() |
VectorString3D |
VectorString3D.substring(int first,
int last)
Makes a substring starting at @param first (inclusive) and finishing at @param last (non-inclusive, aka last-1).
|
| Modifier and Type | Method and Description |
|---|---|
VectorString3D |
VectorString3D.chain(VectorString3D vs)
Returns a new VectorString3D which is the result of the optimal chaining of this and the given VectorString.
|
VectorString3D |
VectorString3D.createInterpolated(VectorString3D other,
Editions ed,
double alpha)
Create an interpolated VectorString3D between this and the given one, with the proper weight 'alpha' which must be 0 <= weight <= 1 (otherwise returns null)
|
static double |
VectorString3D.distance(VectorString3D vs1,
int i,
VectorString3D vs2,
int j) |
static double |
VectorString3D.getAverageVectorLength(int[] i,
VectorString3D[] vs) |
boolean |
VectorString3D.isNear(VectorString3D vs,
double radius)
Determine if any point of the given VectorString3D falls within a radius of any of the points in this VectorString3D.
|
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