- calibrate(Calibration) - Method in class ini.trakem2.vector.VectorString2D
-
Scale to match cal.pixelWidth, cal.pixelHeight and computed depth.
- calibrate(Calibration) - Method in class ini.trakem2.vector.VectorString3D
-
Scale to match cal.pixelWidth, cal.pixelHeight and computed depth.
- chain(VectorString3D) - Method in class ini.trakem2.vector.VectorString3D
-
Returns a new VectorString3D which is the result of the optimal chaining of this and the given VectorString.
- CircularSequence(int) - Constructor for class ini.trakem2.vector.Util.CircularSequence
-
A sequence of integers from 0 to
size
that cycle back to zero when reaching the end;
the starting point is the last point in the sequence,
so that a call to
Util.CircularSequence.next() delivers the first value, 0.
- clone() - Method in class ini.trakem2.vector.VectorString2D
-
Does NOT clone the vector arrays, which are initialized to NULL; only the x,y,delta,z.
- clone() - Method in class ini.trakem2.vector.VectorString3D
-
- closed - Variable in class ini.trakem2.vector.Editions
-
- CLOSED - Static variable in class ini.trakem2.vector.VectorString3D
-
- computeCenterOfMass() - Method in class ini.trakem2.vector.VectorString3D
-
- computeLength() - Method in class ini.trakem2.vector.VectorString3D
-
The physical length of this sequence of points.
- convolveGaussianSigma1(double[], double[], Util.CircularSequence) - Static method in class ini.trakem2.vector.Util
-
- copy(double[], int) - Static method in class ini.trakem2.vector.Util
-
Will make a new double[] array, then fit in it as many points from the given array as possible according to the desired new length.
- copy(double[], int, int) - Static method in class ini.trakem2.vector.Util
-
- createInterpolated(Editions, double) - Static method in class ini.trakem2.vector.VectorString3D
-
- createInterpolated(VectorString3D, Editions, double) - Method in class ini.trakem2.vector.VectorString3D
-
Create an interpolated VectorString3D between this and the given one, with the proper weight 'alpha' which must be 0 <= weight <= 1 (otherwise returns null)
- createInterpolatedPoints(Editions, double) - Static method in class ini.trakem2.vector.VectorString3D
-
Create a new VectorString3D which is the weighted average between the two VectorString3D that make the Editions.
- createInterpolatedPoints(Editions, double, int, int) - Static method in class ini.trakem2.vector.VectorString3D
-
Create a new VectorString3D which is the weighted average between the two VectorString3D that make the Editions.
- createInterpolatedPolygon(Util.DoublePolygon, double, boolean) - Static method in class ini.trakem2.vector.Util
-
Copied from ImageJ's ij.gui.PolygonRoi.getInterpolatedPolygon, by Wayne Rasband and collaborators.
- createRandom(int, double, boolean) - Static method in class ini.trakem2.vector.VectorString3D
-
- generateTriangles(VectorString2D[], int, double, boolean) - Static method in class ini.trakem2.vector.SkinMaker
-
From an array of VectorString2D, obtain a list of Point3f which define, every three, a triangle of a skin.
- generateTriangles(boolean) - Method in class ini.trakem2.vector.SkinMaker.Match
-
Generate a list of Point3f points, every three defining a triangle, between vs1 and vs2 using the given sequence of editions.
- getAngle(double, double) - Static method in class ini.trakem2.vector.Util
-
Returns the angle in radians of the given polar coordinates, correcting the Math.atan2 output.
- getAverageDelta() - Method in class ini.trakem2.vector.VectorString2D
-
- getAverageDelta() - Method in class ini.trakem2.vector.VectorString3D
-
Return the average point interdistance.
- getAverageVectorLength(int[], VectorString3D[]) - Static method in class ini.trakem2.vector.VectorString3D
-
- getCalibrationCopy() - Method in class ini.trakem2.vector.VectorString2D
-
- getCalibrationCopy() - Method in class ini.trakem2.vector.VectorString3D
-
- getDelta() - Method in interface ini.trakem2.vector.VectorString
-
- getDelta() - Method in class ini.trakem2.vector.VectorString2D
-
If not resampled, returns zero.
- getDelta() - Method in class ini.trakem2.vector.VectorString3D
-
If not resampled, the returned delta is zero.
- getDependent(int) - Method in class ini.trakem2.vector.VectorString3D
-
- getDiffVectorLength(int, int, VectorString) - Method in interface ini.trakem2.vector.VectorString
-
- getDiffVectorLength(int, int, VectorString) - Method in class ini.trakem2.vector.VectorString2D
-
Subtracts vs2 vector j to this vector i and returns its length, without changing any data.
- getDiffVectorLength(int, int, VectorString) - Method in class ini.trakem2.vector.VectorString3D
-
Subtracts vs2 vector j to this vector i and returns its length, without changing any data.
- getDimensions() - Method in interface ini.trakem2.vector.VectorString
-
- getDimensions() - Method in class ini.trakem2.vector.VectorString2D
-
- getDimensions() - Method in class ini.trakem2.vector.VectorString3D
-
- getDistance() - Method in class ini.trakem2.vector.Editions
-
- getEditions() - Method in class ini.trakem2.vector.Editions
-
- getMorphedPerimeter(VectorString2D, VectorString2D, double, Editions) - Static method in class ini.trakem2.vector.SkinMaker
-
Returns a weighted VectorString2D.
- getMorphedPerimeters(VectorString2D, VectorString2D, int, Editions) - Static method in class ini.trakem2.vector.SkinMaker
-
From two VectorString2D, return an array of x,y points ( in the form [2][n] ) defining all necessary intermediate, morphed perimeters that describe a skin between them (not including the two VectorString2D)
- getMorphedPerimeters(VectorString2D[], int, double, boolean) - Static method in class ini.trakem2.vector.SkinMaker
-
From an array of VectorString2D, return a new array of VectorString2D defining all necessary intermediate, morphed perimeters that describe a skin between each consecutive pair; includes the originals inserted at the proper locations.
- getNSources() - Method in class ini.trakem2.vector.VectorString3D
-
Returns the number of VectorString3D that have contributed to this VectorString3D, via merging with createInterpolated(...).
- getPhysicalDistance(boolean, int, float, boolean) - Method in class ini.trakem2.vector.Editions
-
Returns the distance between all points involved in a mutation; if average is false, then it returns the cummulative.
- getPoint(int, int) - Method in interface ini.trakem2.vector.VectorString
-
Get the value at index i for dimension dim; dimensions start at 0 and go up to n-dimensions -1, for example for VectorString3D, 0=X, 1=Y, 2=Z; to get y[32] call getPoint(1, 32);
- getPoint(int, int) - Method in class ini.trakem2.vector.VectorString2D
-
- getPoint(int, int) - Method in class ini.trakem2.vector.VectorString3D
-
- getPoints(int) - Method in interface ini.trakem2.vector.VectorString
-
Get the array at dimension dim which ranges from 0 to n-dimensions -1; 0=X, 1=Y, 2=Z, et cetera depending on how many dimensions this VectorString supports.
- getPoints(int) - Method in class ini.trakem2.vector.VectorString2D
-
- getPoints(int) - Method in class ini.trakem2.vector.VectorString3D
-
- getRelativeVector(int, int) - Method in class ini.trakem2.vector.VectorString3D
-
- getSimilarity(boolean, int, float) - Method in class ini.trakem2.vector.Editions
-
A mutation is considered an equal or near equal, and thus does not count.
- getSimilarity() - Method in class ini.trakem2.vector.Editions
-
- getSimilarity2() - Method in class ini.trakem2.vector.Editions
-
- getSimilarity2(boolean, int, float) - Method in class ini.trakem2.vector.Editions
-
Returns the number of mutations / max(len(vs1), len(vs2)) : 1.0 means all are mutations and the sequences have the same lengths.
- getSource() - Method in class ini.trakem2.vector.VectorString3D
-
Returns a list of lists of Point3d, one list of lists for each point in this VectorString3D; may be null.
- getStatistics(boolean, int, float, boolean) - Method in class ini.trakem2.vector.Editions
-
Returns {average distance, cummulative distance, stdDev, median, prop_mut} which are:
[0] - average distance: the average physical distance between mutation pairs
[1] - cummulative distance: the sum of the distances between mutation pairs
[2] - stdDev: of the physical distances between mutation pairs relative to the average
[3] - median: the average medial physical distance between mutation pairs, more robust than the average to extreme values
[4] - prop_mut: the proportion of mutation pairs relative to the length of the queried sequence vs1.
- getStdDev(boolean, int, float) - Method in class ini.trakem2.vector.Editions
-
- getStdDevAtEachPoint() - Method in class ini.trakem2.vector.VectorString3D
-
If null != source, compute the StdDev at each point in this VectorString3D, by comparing it with its associated source points.
- getTags() - Method in class ini.trakem2.vector.VectorString3D
-
- getVector(int, int) - Method in interface ini.trakem2.vector.VectorString
-
- getVector(int, int) - Method in class ini.trakem2.vector.VectorString2D
-
- getVector(int, int) - Method in class ini.trakem2.vector.VectorString3D
-
- getVectors(int) - Method in interface ini.trakem2.vector.VectorString
-
- getVectors(int) - Method in class ini.trakem2.vector.VectorString2D
-
- getVectors(int) - Method in class ini.trakem2.vector.VectorString3D
-
- getVS1() - Method in class ini.trakem2.vector.Editions
-
- getVS2() - Method in class ini.trakem2.vector.Editions
-