/**
* Finds local extrema in an image. A local extremum is defined as an image element whose value is
* either larger (maximum) or smaller (minimum) than those of all its neighboring elements. If the
* size of the image in the z-dimension equals {@code 1}, this method considers 8-connected
* neighbors in x-y space, otherwise it considers 26-connected neighbors in x-y-z space. For
* border elements, neighboring positions outside the image are ignored. The method searches for
* local extrema in every x-y(-z) subimage in a 5D image.
*
* @param image the input image in which local extrema are to be found.
* @param type the type of extrema to be found. Can be any or both (by addition) of {@link
* #MAXIMA} or {@link #MINIMA}.
* @param mode determines how the found extrema are stored and returned. Can be any or both (by
* addition) of {@link #DETECT} or {@link #EXTRACT}.
* @return if {@code mode} includes {@code DETECT}, the {@code image} is overwritten with the
* detection results: local maxima are set to {@code 255}, local minima to {@code 127}, and
* all other elements to {@code 0}. Otherwise the image is left unaltered. If {@code mode}
* includes {@code EXTRACT}, a new two-element {@code Vector} of {@code Vector<Coordinates>}
* objects is returned, containing the coordinates of all found local maxima (element {@code
* 0}) and local minima (element {@code 1}). Otherwise the method returns {@code null}.
* @exception NullPointerException if {@code image} is {@code null}.
*/
public Vector<Vector<Coordinates>> run(final Image image, final int type, final int mode) {
messenger.log(ImageScience.prelude() + "Extremizer");
final Timer timer = new Timer();
timer.messenger.log(messenger.log());
timer.start();
// Initialize:
final Dimensions dims = image.dimensions();
messenger.log(
"Input image dimensions: (x,y,z,t,c) = ("
+ dims.x
+ ","
+ dims.y
+ ","
+ dims.z
+ ","
+ dims.t
+ ","
+ dims.c
+ ")");
final boolean detect = (mode & DETECT) > 0;
final boolean extract = (mode & EXTRACT) > 0;
String detex = null;
if (detect) {
detex = extract ? "Detecting and extracting" : "Detecting";
} else if (extract) {
detex = "Extracting";
} else {
messenger.log("Neither detection nor extraction mode was selected");
return null;
}
final boolean maxima = (type & MAXIMA) > 0;
final boolean minima = (type & MINIMA) > 0;
String maxmin = null;
if (maxima) {
maxmin = minima ? "maxima and minima" : "maxima";
} else if (minima) {
maxmin = "minima";
} else {
messenger.log("Neither maxima nor minima type was selected");
return null;
}
final String demm = detex + " " + maxmin;
final Vector<Coordinates> camax = extract ? new Vector<Coordinates>(dims.x, dims.x) : null;
final Vector<Coordinates> camin = extract ? new Vector<Coordinates>(dims.x, dims.x) : null;
messenger.status("Finding extrema...");
// Find extrema:
if (dims.z == 1) { // 2D case
messenger.log(demm + " in 2D using 8-connectivity");
progressor.steps(dims.c * dims.t * dims.y);
progressor.start();
image.axes(Axes.X);
final Coordinates c0 = new Coordinates();
c0.x = -1;
final Coordinates c1 = new Coordinates();
c1.x = -1;
double[] mm = new double[dims.x + 2];
double[] a0 = new double[dims.x + 2];
double[] a1 = new double[dims.x + 2];
double[] a2 = new double[dims.x + 2];
double[] at = null;
final int dimsxp1 = dims.x + 1;
final int dimsym1 = dims.y - 1;
final boolean dimsyis1 = (dims.y == 1);
for (c0.c = c1.c = 0; c0.c < dims.c; ++c0.c, ++c1.c) {
for (c0.t = c1.t = 0; c0.t < dims.t; ++c0.t, ++c1.t) {
for (c0.y = 0, c1.y = 1; c0.y < dims.y; ++c0.y, ++c1.y) {
set(mm, NEX);
if (c0.y == 0) {
image.get(c0, a1);
if (!dimsyis1) image.get(c1, a2);
} else {
at = a0;
a0 = a1;
a1 = a2;
a2 = at;
if (c0.y < dimsym1) image.get(c1, a2);
}
// Find maxima:
if (maxima) {
if (c0.y == 0) {
set(a0, DMIN);
if (dimsyis1) set(a2, DMIN);
} else if (c0.y == dimsym1) set(a2, DMIN);
border(a0, DMIN);
border(a1, DMIN);
border(a2, DMIN);
for (int x = 1, xm1 = 0, xp1 = 2; x < dimsxp1; ++x, ++xm1, ++xp1) {
final double vx = a1[x];
if (vx > a0[xm1]
&& vx > a0[x]
&& vx > a0[xp1]
&& vx > a2[xm1]
&& vx > a2[x]
&& vx > a2[xp1]
&& vx > a1[xm1]
&& vx > a1[xp1]) {
if (extract) camax.add(new Coordinates(xm1, c0.y, 0, c0.t, c0.c));
mm[x] = MAX;
}
}
}
// Find minima:
if (minima) {
if (c0.y == 0) {
set(a0, DMAX);
if (dimsyis1) set(a2, DMAX);
} else if (c0.y == dimsym1) set(a2, DMAX);
border(a0, DMAX);
border(a1, DMAX);
border(a2, DMAX);
for (int x = 1, xm1 = 0, xp1 = 2; x < dimsxp1; ++x, ++xm1, ++xp1) {
final double vx = a1[x];
if (vx < a0[xm1]
&& vx < a0[x]
&& vx < a0[xp1]
&& vx < a2[xm1]
&& vx < a2[x]
&& vx < a2[xp1]
&& vx < a1[xm1]
&& vx < a1[xp1]) {
if (extract) camin.add(new Coordinates(xm1, c0.y, 0, c0.t, c0.c));
mm[x] = MIN;
}
}
}
if (detect) image.set(c0, mm);
progressor.step();
}
}
}
} else { // 3D case
messenger.log(demm + " in 3D using 26-connectivity");
final int ysteps = (maxima ? dims.y : 0) + (minima ? dims.y : 0);
progressor.steps(dims.c * dims.t * dims.z * ysteps);
progressor.start();
image.axes(Axes.X + Axes.Y);
final Coordinates c0 = new Coordinates();
c0.x = c0.y = -1;
final Coordinates c1 = new Coordinates();
c1.x = c1.y = -1;
double[][] mm = new double[dims.y + 2][dims.x + 2];
double[][] a0 = new double[dims.y + 2][dims.x + 2];
double[][] a1 = new double[dims.y + 2][dims.x + 2];
double[][] a2 = new double[dims.y + 2][dims.x + 2];
double[][] at = null;
final int dimsxp1 = dims.x + 1;
final int dimsyp1 = dims.y + 1;
final int dimszm1 = dims.z - 1;
for (c0.c = c1.c = 0; c0.c < dims.c; ++c0.c, ++c1.c) {
for (c0.t = c1.t = 0; c0.t < dims.t; ++c0.t, ++c1.t) {
for (c0.z = 0, c1.z = 1; c0.z < dims.z; ++c0.z, ++c1.z) {
set(mm, NEX);
if (c0.z == 0) {
image.get(c0, a1);
image.get(c1, a2);
} else {
at = a0;
a0 = a1;
a1 = a2;
a2 = at;
if (c0.z < dimszm1) image.get(c1, a2);
}
// Find maxima:
if (maxima) {
if (c0.z == 0) set(a0, DMIN);
else if (c0.z == dimszm1) set(a2, DMIN);
border(a0, DMIN);
border(a1, DMIN);
border(a2, DMIN);
for (int y = 1, ym1 = 0, yp1 = 2; y < dimsyp1; ++y, ++ym1, ++yp1) {
final double[] a0ym1 = a0[ym1], a0y = a0[y], a0yp1 = a0[yp1];
final double[] a1ym1 = a1[ym1], a1y = a1[y], a1yp1 = a1[yp1];
final double[] a2ym1 = a2[ym1], a2y = a2[y], a2yp1 = a2[yp1];
final double[] mmy = mm[y];
for (int x = 1, xm1 = 0, xp1 = 2; x < dimsxp1; ++x, ++xm1, ++xp1) {
final double vx = a1y[x];
if (vx > a0ym1[xm1]
&& vx > a0ym1[x]
&& vx > a0ym1[xp1]
&& vx > a0y[xm1]
&& vx > a0y[x]
&& vx > a0y[xp1]
&& vx > a0yp1[xm1]
&& vx > a0yp1[x]
&& vx > a0yp1[xp1]
&& vx > a1ym1[xm1]
&& vx > a1ym1[x]
&& vx > a1ym1[xp1]
&& vx > a1y[xm1]
&& vx > a1y[xp1]
&& vx > a1yp1[xm1]
&& vx > a1yp1[x]
&& vx > a1yp1[xp1]
&& vx > a2ym1[xm1]
&& vx > a2ym1[x]
&& vx > a2ym1[xp1]
&& vx > a2y[xm1]
&& vx > a2y[x]
&& vx > a2y[xp1]
&& vx > a2yp1[xm1]
&& vx > a2yp1[x]
&& vx > a2yp1[xp1]) {
if (extract) camax.add(new Coordinates(xm1, ym1, c0.z, c0.t, c0.c));
mmy[x] = MAX;
}
}
progressor.step();
}
}
// Find minima:
if (minima) {
if (c0.z == 0) set(a0, DMAX);
else if (c0.z == dimszm1) set(a2, DMAX);
border(a0, DMAX);
border(a1, DMAX);
border(a2, DMAX);
for (int y = 1, ym1 = 0, yp1 = 2; y < dimsyp1; ++y, ++ym1, ++yp1) {
final double[] a0ym1 = a0[ym1], a0y = a0[y], a0yp1 = a0[yp1];
final double[] a1ym1 = a1[ym1], a1y = a1[y], a1yp1 = a1[yp1];
final double[] a2ym1 = a2[ym1], a2y = a2[y], a2yp1 = a2[yp1];
final double[] mmy = mm[y];
for (int x = 1, xm1 = 0, xp1 = 2; x < dimsxp1; ++x, ++xm1, ++xp1) {
final double vx = a1y[x];
if (vx < a0ym1[xm1]
&& vx < a0ym1[x]
&& vx < a0ym1[xp1]
&& vx < a0y[xm1]
&& vx < a0y[x]
&& vx < a0y[xp1]
&& vx < a0yp1[xm1]
&& vx < a0yp1[x]
&& vx < a0yp1[xp1]
&& vx < a1ym1[xm1]
&& vx < a1ym1[x]
&& vx < a1ym1[xp1]
&& vx < a1y[xm1]
&& vx < a1y[xp1]
&& vx < a1yp1[xm1]
&& vx < a1yp1[x]
&& vx < a1yp1[xp1]
&& vx < a2ym1[xm1]
&& vx < a2ym1[x]
&& vx < a2ym1[xp1]
&& vx < a2y[xm1]
&& vx < a2y[x]
&& vx < a2y[xp1]
&& vx < a2yp1[xm1]
&& vx < a2yp1[x]
&& vx < a2yp1[xp1]) {
if (extract) camin.add(new Coordinates(xm1, ym1, c0.z, c0.t, c0.c));
mmy[x] = MIN;
}
}
progressor.step();
}
}
if (detect) image.set(c0, mm);
}
}
}
}
// Finish up:
messenger.status("");
progressor.stop();
timer.stop();
if (detect) image.name(image.name() + " extrema");
final Vector<Vector<Coordinates>> vvc = new Vector<Vector<Coordinates>>(2);
vvc.add(camax);
vvc.add(camin);
return vvc;
}
/**
* Mirrors an image.
*
* @param image the input image to be mirrored. The image is overwritten with the results of
* mirroring.
* @param axes indicates the axes along which to mirror. The image is mirrored in each dimension
* for which the corresponding boolean field of this parameter is {@code true}.
* @exception NullPointerException if any of the parameters is {@code null}.
*/
public void run(final Image image, final Axes axes) {
messenger.log(ImageScience.prelude() + "Mirror");
// Initialize timer:
final Timer timer = new Timer();
timer.messenger.log(messenger.log());
timer.start();
// Check parameters:
messenger.log("Checking parameters");
final Dimensions dims = image.dimensions();
messenger.log(
"Input image dimensions: (x,y,z,t,c) = ("
+ dims.x
+ ","
+ dims.y
+ ","
+ dims.z
+ ","
+ dims.t
+ ","
+ dims.c
+ ")");
// Mirror input image:
messenger.log("Mirroring " + image.type());
progressor.steps(
(axes.x ? dims.c * dims.t * dims.z : 0)
+ (axes.y ? dims.c * dims.t * dims.z : 0)
+ (axes.z ? dims.c * dims.t * (1 + (dims.z - 1) / 2) : 0)
+ (axes.t ? dims.c * (1 + (dims.t - 1) / 2) * dims.z : 0)
+ (axes.c ? (1 + (dims.c - 1) / 2) * dims.t * dims.z : 0));
progressor.start();
image.axes(Axes.X);
// Mirror in x-dimension if requested:
if (axes.x) {
messenger.log("Mirroring in x-dimension");
messenger.status("Mirroring in x-dimension...");
final Coordinates c = new Coordinates();
final double[] a = new double[dims.x];
final int dimsxm1 = dims.x - 1;
final int maxx = dimsxm1 / 2;
for (c.c = 0; c.c < dims.c; ++c.c) {
for (c.t = 0; c.t < dims.t; ++c.t) {
for (c.z = 0; c.z < dims.z; ++c.z) {
for (c.y = 0; c.y < dims.y; ++c.y) {
image.get(c, a);
for (int x1 = 0, x2 = dimsxm1; x1 <= maxx; ++x1, --x2) {
final double tmp = a[x2];
a[x2] = a[x1];
a[x1] = tmp;
}
image.set(c, a);
}
progressor.step();
}
}
}
}
// Mirror in y-dimension if requested:
if (axes.y) {
messenger.log("Mirroring in y-dimension");
messenger.status("Mirroring in y-dimension...");
final Coordinates c1 = new Coordinates();
final Coordinates c2 = new Coordinates();
final double[] a1 = new double[dims.x];
final double[] a2 = new double[dims.x];
final int dimsym1 = dims.y - 1;
final int maxy = dimsym1 / 2;
for (c1.c = c2.c = 0; c1.c < dims.c; ++c1.c, ++c2.c) {
for (c1.t = c2.t = 0; c1.t < dims.t; ++c1.t, ++c2.t) {
for (c1.z = c2.z = 0; c1.z < dims.z; ++c1.z, ++c2.z) {
for (c1.y = 0, c2.y = dimsym1; c1.y <= maxy; ++c1.y, --c2.y) {
image.get(c1, a1);
image.get(c2, a2);
image.set(c1, a2);
image.set(c2, a1);
}
progressor.step();
}
}
}
}
// Mirror in z-dimension if requested:
if (axes.z) {
messenger.log("Mirroring in z-dimension");
messenger.status("Mirroring in z-dimension...");
final Coordinates c1 = new Coordinates();
final Coordinates c2 = new Coordinates();
final double[] a1 = new double[dims.x];
final double[] a2 = new double[dims.x];
final int dimszm1 = dims.z - 1;
final int maxz = dimszm1 / 2;
for (c1.c = c2.c = 0; c1.c < dims.c; ++c1.c, ++c2.c) {
for (c1.t = c2.t = 0; c1.t < dims.t; ++c1.t, ++c2.t) {
for (c1.z = 0, c2.z = dimszm1; c1.z <= maxz; ++c1.z, --c2.z) {
for (c1.y = c2.y = 0; c1.y < dims.y; ++c1.y, ++c2.y) {
image.get(c1, a1);
image.get(c2, a2);
image.set(c1, a2);
image.set(c2, a1);
}
progressor.step();
}
}
}
}
// Mirror in t-dimension if requested:
if (axes.t) {
messenger.log("Mirroring in t-dimension");
messenger.status("Mirroring in t-dimension...");
final Coordinates c1 = new Coordinates();
final Coordinates c2 = new Coordinates();
final double[] a1 = new double[dims.x];
final double[] a2 = new double[dims.x];
final int dimstm1 = dims.t - 1;
final int maxt = dimstm1 / 2;
for (c1.c = c2.c = 0; c1.c < dims.c; ++c1.c, ++c2.c) {
for (c1.t = 0, c2.t = dimstm1; c1.t <= maxt; ++c1.t, --c2.t) {
for (c1.z = c2.z = 0; c1.z < dims.z; ++c1.z, ++c2.z) {
for (c1.y = c2.y = 0; c1.y < dims.y; ++c1.y, ++c2.y) {
image.get(c1, a1);
image.get(c2, a2);
image.set(c1, a2);
image.set(c2, a1);
}
progressor.step();
}
}
}
}
// Mirror in c-dimension if requested:
if (axes.c) {
messenger.log("Mirroring in c-dimension");
messenger.status("Mirroring in c-dimension...");
final Coordinates c1 = new Coordinates();
final Coordinates c2 = new Coordinates();
final double[] a1 = new double[dims.x];
final double[] a2 = new double[dims.x];
final int dimscm1 = dims.c - 1;
final int maxc = dimscm1 / 2;
for (c1.c = 0, c2.c = dimscm1; c1.c <= maxc; ++c1.c, --c2.c) {
for (c1.t = c2.t = 0; c1.t < dims.t; ++c1.t, ++c2.t) {
for (c1.z = c2.z = 0; c1.z < dims.z; ++c1.z, ++c2.z) {
for (c1.y = c2.y = 0; c1.y < dims.y; ++c1.y, ++c2.y) {
image.get(c1, a1);
image.get(c2, a2);
image.set(c1, a2);
image.set(c2, a1);
}
progressor.step();
}
}
}
}
// Finish up:
image.name(image.name() + " mirrored");
messenger.status("");
progressor.stop();
timer.stop();
}