public void fitSpline(int evaluationPoints) {
if (xpf == null) {
xpf = toFloat(xp);
ypf = toFloat(yp);
subPixel = true;
}
if (xSpline == null || splinePoints != evaluationPoints) {
splinePoints = evaluationPoints;
xSpline = new float[splinePoints];
ySpline = new float[splinePoints];
}
int nNodes = nPoints;
if (type == POLYGON) {
nNodes++;
if (nNodes >= xpf.length) enlargeArrays();
xpf[nNodes - 1] = xpf[0];
ypf[nNodes - 1] = ypf[0];
}
float[] xindex = new float[nNodes];
for (int i = 0; i < nNodes; i++) xindex[i] = i;
SplineFitter sfx = new SplineFitter(xindex, xpf, nNodes);
SplineFitter sfy = new SplineFitter(xindex, ypf, nNodes);
// Evaluate the splines at all points
double scale = (double) (nNodes - 1) / (splinePoints - 1);
float xs = 0f, ys = 0f;
float xmin = Float.MAX_VALUE, xmax = -xmin, ymin = xmin, ymax = xmax;
for (int i = 0; i < splinePoints; i++) {
double xvalue = i * scale;
xs = (float) sfx.evalSpline(xindex, xpf, nNodes, xvalue);
if (xs < xmin) xmin = xs;
if (xs > xmax) xmax = xs;
xSpline[i] = xs;
ys = (float) sfy.evalSpline(xindex, ypf, nNodes, xvalue);
if (ys < ymin) ymin = ys;
if (ys > ymax) ymax = ys;
ySpline[i] = ys;
}
int ixmin = (int) Math.floor(xmin + 0.5f);
int ixmax = (int) Math.floor(xmax + 0.5f);
int iymin = (int) Math.floor(ymin + 0.5f);
int iymax = (int) Math.floor(ymax + 0.5f);
if (ixmin != 0) {
for (int i = 0; i < nPoints; i++) xpf[i] -= ixmin;
for (int i = 0; i < splinePoints; i++) xSpline[i] -= ixmin;
}
if (iymin != 0) {
for (int i = 0; i < nPoints; i++) ypf[i] -= iymin;
for (int i = 0; i < splinePoints; i++) ySpline[i] -= iymin;
}
x += ixmin;
y += iymin;
width = ixmax - ixmin;
height = iymax - iymin;
bounds = null;
cachedMask = null;
// update protected xp and yp arrays for backward compatibility
xp = toInt(xpf, xp, nPoints);
yp = toInt(ypf, yp, nPoints);
}
void createEllipse(ImagePlus imp) {
IJ.showStatus("Fitting ellipse");
Roi roi = imp.getRoi();
if (roi == null) {
noRoi("Fit Ellipse");
return;
}
if (roi.isLine()) {
IJ.error("Fit Ellipse", "\"Fit Ellipse\" does not work with line selections");
return;
}
ImageProcessor ip = imp.getProcessor();
ip.setRoi(roi);
int options = Measurements.CENTROID + Measurements.ELLIPSE;
ImageStatistics stats = ImageStatistics.getStatistics(ip, options, null);
double dx = stats.major * Math.cos(stats.angle / 180.0 * Math.PI) / 2.0;
double dy = -stats.major * Math.sin(stats.angle / 180.0 * Math.PI) / 2.0;
double x1 = stats.xCentroid - dx;
double x2 = stats.xCentroid + dx;
double y1 = stats.yCentroid - dy;
double y2 = stats.yCentroid + dy;
double aspectRatio = stats.minor / stats.major;
imp.killRoi();
imp.setRoi(new EllipseRoi(x1, y1, x2, y2, aspectRatio));
}
double rodbard(double x) {
// y = c*((a-x/(x-d))^(1/b)
// a=3.9, b=.88, c=712, d=44
double ex;
if (x == 0.0) ex = 5.0;
else ex = Math.exp(Math.log(x / 700.0) * 0.88);
double y = 3.9 - 44.0;
y = y / (1.0 + ex);
return y + 44.0;
}
/* Creates a spline fitted polygon with one pixel segment lengths
that can be retrieved using the getFloatPolygon() method. */
public void fitSplineForStraightening() {
fitSpline((int) getUncalibratedLength() * 2);
if (splinePoints == 0) return;
float[] xpoints = new float[splinePoints * 2];
float[] ypoints = new float[splinePoints * 2];
xpoints[0] = xSpline[0];
ypoints[0] = ySpline[0];
int n = 1, n2;
double inc = 0.01;
double distance = 0.0, distance2 = 0.0, dx = 0.0, dy = 0.0, xinc, yinc;
double x, y, lastx, lasty, x1, y1, x2 = xSpline[0], y2 = ySpline[0];
for (int i = 1; i < splinePoints; i++) {
x1 = x2;
y1 = y2;
x = x1;
y = y1;
x2 = xSpline[i];
y2 = ySpline[i];
dx = x2 - x1;
dy = y2 - y1;
distance = Math.sqrt(dx * dx + dy * dy);
xinc = dx * inc / distance;
yinc = dy * inc / distance;
lastx = xpoints[n - 1];
lasty = ypoints[n - 1];
// n2 = (int)(dx/xinc);
n2 = (int) (distance / inc);
if (splinePoints == 2) n2++;
do {
dx = x - lastx;
dy = y - lasty;
distance2 = Math.sqrt(dx * dx + dy * dy);
// IJ.log(i+" "+IJ.d2s(xinc,5)+" "+IJ.d2s(yinc,5)+" "+IJ.d2s(distance,2)+"
// "+IJ.d2s(distance2,2)+" "+IJ.d2s(x,2)+" "+IJ.d2s(y,2)+" "+IJ.d2s(lastx,2)+"
// "+IJ.d2s(lasty,2)+" "+n+" "+n2);
if (distance2 >= 1.0 - inc / 2.0 && n < xpoints.length - 1) {
xpoints[n] = (float) x;
ypoints[n] = (float) y;
// IJ.log("--- "+IJ.d2s(x,2)+" "+IJ.d2s(y,2)+" "+n);
n++;
lastx = x;
lasty = y;
}
x += xinc;
y += yinc;
} while (--n2 > 0);
}
xSpline = xpoints;
ySpline = ypoints;
splinePoints = n;
}
String getAngleAsString() {
double angle1 = 0.0;
double angle2 = 0.0;
if (xpf != null) {
angle1 = getFloatAngle(xpf[0], ypf[0], xpf[1], ypf[1]);
angle2 = getFloatAngle(xpf[1], ypf[1], xpf[2], ypf[2]);
} else {
angle1 = getFloatAngle(xp[0], yp[0], xp[1], yp[1]);
angle2 = getFloatAngle(xp[1], yp[1], xp[2], yp[2]);
}
degrees = Math.abs(180 - Math.abs(angle1 - angle2));
if (degrees > 180.0) degrees = 360.0 - degrees;
double degrees2 = Prefs.reflexAngle && type == ANGLE ? 360.0 - degrees : degrees;
return ", angle=" + IJ.d2s(degrees2);
}
int[] smooth(int[] a, int n) {
FloatProcessor fp = new FloatProcessor(n, 1);
for (int i = 0; i < n; i++) fp.putPixelValue(i, 0, a[i]);
GaussianBlur gb = new GaussianBlur();
gb.blur1Direction(fp, 2.0, 0.01, true, 0);
for (int i = 0; i < n; i++) a[i] = (int) Math.round(fp.getPixelValue(i, 0));
return a;
}
/**
* Returns the perimeter length of ROIs created using the wand tool and the particle analyzer. The
* algorithm counts edge pixels as 1 and corner pixels as sqrt(2). It does this by calculating the
* total length of the ROI boundary and subtracting 2-sqrt(2) for each non-adjacent corner. For
* example, a 1x1 pixel ROI has a boundary length of 4 and 2 non-adjacent edges so the perimeter
* is 4-2*(2-sqrt(2)). A 2x2 pixel ROI has a boundary length of 8 and 4 non-adjacent edges so the
* perimeter is 8-4*(2-sqrt(2)).
*/
double getTracedPerimeter() {
int sumdx = 0;
int sumdy = 0;
int nCorners = 0;
int dx1 = xp[0] - xp[nPoints - 1];
int dy1 = yp[0] - yp[nPoints - 1];
int side1 = Math.abs(dx1) + Math.abs(dy1); // one of these is 0
boolean corner = false;
int nexti, dx2, dy2, side2;
for (int i = 0; i < nPoints; i++) {
nexti = i + 1;
if (nexti == nPoints) nexti = 0;
dx2 = xp[nexti] - xp[i];
dy2 = yp[nexti] - yp[i];
sumdx += Math.abs(dx1);
sumdy += Math.abs(dy1);
side2 = Math.abs(dx2) + Math.abs(dy2);
if (side1 > 1 || !corner) {
corner = true;
nCorners++;
} else corner = false;
dx1 = dx2;
dy1 = dy2;
side1 = side2;
}
double w = 1.0, h = 1.0;
if (imp != null) {
Calibration cal = imp.getCalibration();
w = cal.pixelWidth;
h = cal.pixelHeight;
}
return sumdx * w + sumdy * h - (nCorners * ((w + h) - Math.sqrt(w * w + h * h)));
}
PolygonRoi trimPolygon(PolygonRoi roi, double length) {
int[] x = roi.getXCoordinates();
int[] y = roi.getYCoordinates();
int n = roi.getNCoordinates();
x = smooth(x, n);
y = smooth(y, n);
float[] curvature = getCurvature(x, y, n);
Rectangle r = roi.getBounds();
double threshold = rodbard(length);
// IJ.log("trim: "+length+" "+threshold);
double distance = Math.sqrt((x[1] - x[0]) * (x[1] - x[0]) + (y[1] - y[0]) * (y[1] - y[0]));
x[0] += r.x;
y[0] += r.y;
int i2 = 1;
int x1, y1, x2 = 0, y2 = 0;
for (int i = 1; i < n - 1; i++) {
x1 = x[i];
y1 = y[i];
x2 = x[i + 1];
y2 = y[i + 1];
distance += Math.sqrt((x2 - x1) * (x2 - x1) + (y2 - y1) * (y2 - y1)) + 1;
distance += curvature[i] * 2;
if (distance >= threshold) {
x[i2] = x2 + r.x;
y[i2] = y2 + r.y;
i2++;
distance = 0.0;
}
}
int type = roi.getType() == Roi.FREELINE ? Roi.POLYLINE : Roi.POLYGON;
if (type == Roi.POLYLINE && distance > 0.0) {
x[i2] = x2 + r.x;
y[i2] = y2 + r.y;
i2++;
}
PolygonRoi p = new PolygonRoi(x, y, i2, type);
if (roi.getStroke() != null) p.setStrokeWidth(roi.getStrokeWidth());
p.setStrokeColor(roi.getStrokeColor());
p.setName(roi.getName());
imp.setRoi(p);
return p;
}
PolygonRoi trimFloatPolygon(PolygonRoi roi, double length) {
FloatPolygon poly = roi.getFloatPolygon();
float[] x = poly.xpoints;
float[] y = poly.ypoints;
int n = poly.npoints;
x = smooth(x, n);
y = smooth(y, n);
float[] curvature = getCurvature(x, y, n);
double threshold = rodbard(length);
// IJ.log("trim: "+length+" "+threshold);
double distance = Math.sqrt((x[1] - x[0]) * (x[1] - x[0]) + (y[1] - y[0]) * (y[1] - y[0]));
int i2 = 1;
double x1, y1, x2 = 0, y2 = 0;
for (int i = 1; i < n - 1; i++) {
x1 = x[i];
y1 = y[i];
x2 = x[i + 1];
y2 = y[i + 1];
distance += Math.sqrt((x2 - x1) * (x2 - x1) + (y2 - y1) * (y2 - y1)) + 1;
distance += curvature[i] * 2;
if (distance >= threshold) {
x[i2] = (float) x2;
y[i2] = (float) y2;
i2++;
distance = 0.0;
}
}
int type = roi.getType() == Roi.FREELINE ? Roi.POLYLINE : Roi.POLYGON;
if (type == Roi.POLYLINE && distance > 0.0) {
x[i2] = (float) x2;
y[i2] = (float) y2;
i2++;
}
PolygonRoi p = new PolygonRoi(x, y, i2, type);
if (roi.getStroke() != null) p.setStrokeWidth(roi.getStrokeWidth());
p.setStrokeColor(roi.getStrokeColor());
p.setDrawOffset(roi.getDrawOffset());
p.setName(roi.getName());
imp.setRoi(p);
return p;
}
void handleMouseMove(int sx, int sy) {
// Do rubber banding
int tool = Toolbar.getToolId();
if (!(tool == Toolbar.POLYGON || tool == Toolbar.POLYLINE || tool == Toolbar.ANGLE)) {
imp.deleteRoi();
imp.draw();
return;
}
drawRubberBand(sx, sy);
degrees = Double.NaN;
double len = -1;
if (nPoints > 1) {
double x1, y1, x2, y2;
if (xpf != null) {
x1 = xpf[nPoints - 2];
y1 = ypf[nPoints - 2];
x2 = xpf[nPoints - 1];
y2 = ypf[nPoints - 1];
} else {
x1 = xp[nPoints - 2];
y1 = yp[nPoints - 2];
x2 = xp[nPoints - 1];
y2 = yp[nPoints - 1];
}
degrees =
getAngle(
(int) Math.round(x1),
(int) Math.round(y1),
(int) Math.round(x2),
(int) Math.round(y2));
if (tool != Toolbar.ANGLE) {
Calibration cal = imp.getCalibration();
double pw = cal.pixelWidth, ph = cal.pixelHeight;
if (IJ.altKeyDown()) {
pw = 1.0;
ph = 1.0;
}
len = Math.sqrt((x2 - x1) * pw * (x2 - x1) * pw + (y2 - y1) * ph * (y2 - y1) * ph);
}
}
if (tool == Toolbar.ANGLE) {
if (nPoints == 2) angle1 = degrees;
else if (nPoints == 3) {
double angle2 = getAngle(xp[1], yp[1], xp[2], yp[2]);
degrees = Math.abs(180 - Math.abs(angle1 - angle2));
if (degrees > 180.0) degrees = 360.0 - degrees;
}
}
String length = len != -1 ? ", length=" + IJ.d2s(len) : "";
double degrees2 =
tool == Toolbar.ANGLE && nPoints == 3 && Prefs.reflexAngle ? 360.0 - degrees : degrees;
String angle = !Double.isNaN(degrees) ? ", angle=" + IJ.d2s(degrees2) : "";
int ox = ic != null ? ic.offScreenX(sx) : sx;
int oy = ic != null ? ic.offScreenY(sy) : sy;
IJ.showStatus(imp.getLocationAsString(ox, oy) + length + angle);
}
double getFloatSmoothedPerimeter() {
double length = getSmoothedLineLength();
double w2 = 1.0, h2 = 1.0;
if (imp != null) {
Calibration cal = imp.getCalibration();
w2 = cal.pixelWidth * cal.pixelWidth;
h2 = cal.pixelHeight * cal.pixelHeight;
}
double dx = xpf[nPoints - 1] - xpf[0];
double dy = ypf[nPoints - 1] - ypf[0];
length += Math.sqrt(dx * dx * w2 + dy * dy * h2);
return length;
}
double getFloatSmoothedLineLength() {
double length = 0.0;
double w2 = 1.0;
double h2 = 1.0;
double dx, dy;
if (imp != null) {
Calibration cal = imp.getCalibration();
w2 = cal.pixelWidth * cal.pixelWidth;
h2 = cal.pixelHeight * cal.pixelHeight;
}
dx = (xpf[0] + xpf[1] + xpf[2]) / 3.0 - xpf[0];
dy = (ypf[0] + ypf[1] + ypf[2]) / 3.0 - ypf[0];
length += Math.sqrt(dx * dx * w2 + dy * dy * h2);
for (int i = 1; i < nPoints - 2; i++) {
dx = (xpf[i + 2] - xpf[i - 1]) / 3.0;
dy = (ypf[i + 2] - ypf[i - 1]) / 3.0;
length += Math.sqrt(dx * dx * w2 + dy * dy * h2);
}
dx = xpf[nPoints - 1] - (xpf[nPoints - 3] + xpf[nPoints - 2] + xpf[nPoints - 1]) / 3.0;
dy = ypf[nPoints - 1] - (ypf[nPoints - 3] + ypf[nPoints - 2] + ypf[nPoints - 1]) / 3.0;
length += Math.sqrt(dx * dx * w2 + dy * dy * h2);
return length;
}
/** Returns the perimeter (for ROIs) or length (for lines). */
public double getLength() {
if (type == TRACED_ROI) return getTracedPerimeter();
if (nPoints > 2) {
if (type == FREEROI) return getSmoothedPerimeter();
else if (type == FREELINE && !(width == 0 || height == 0)) return getSmoothedLineLength();
}
double length = 0.0;
int dx, dy;
double w2 = 1.0, h2 = 1.0;
if (imp != null) {
Calibration cal = imp.getCalibration();
w2 = cal.pixelWidth * cal.pixelWidth;
h2 = cal.pixelHeight * cal.pixelHeight;
}
if (xSpline != null) {
double fdx, fdy;
for (int i = 0; i < (splinePoints - 1); i++) {
fdx = xSpline[i + 1] - xSpline[i];
fdy = ySpline[i + 1] - ySpline[i];
length += Math.sqrt(fdx * fdx * w2 + fdy * fdy * h2);
}
if (type == POLYGON) {
fdx = xSpline[0] - xSpline[splinePoints - 1];
fdy = ySpline[0] - ySpline[splinePoints - 1];
length += Math.sqrt(fdx * fdx * w2 + fdy * fdy * h2);
}
} else if (xpf != null) {
double fdx, fdy;
for (int i = 0; i < (nPoints - 1); i++) {
fdx = xpf[i + 1] - xpf[i];
fdy = ypf[i + 1] - ypf[i];
length += Math.sqrt(fdx * fdx * w2 + fdy * fdy * h2);
}
if (type == POLYGON) {
fdx = xpf[0] - xpf[nPoints - 1];
fdy = ypf[0] - ypf[nPoints - 1];
length += Math.sqrt(fdx * fdx * w2 + fdy * fdy * h2);
}
} else {
for (int i = 0; i < (nPoints - 1); i++) {
dx = xp[i + 1] - xp[i];
dy = yp[i + 1] - yp[i];
length += Math.sqrt(dx * dx * w2 + dy * dy * h2);
}
if (type == POLYGON) {
dx = xp[0] - xp[nPoints - 1];
dy = yp[0] - yp[nPoints - 1];
length += Math.sqrt(dx * dx * w2 + dy * dy * h2);
}
}
return length;
}
float[] getCurvature(float[] x, float[] y, int n) {
float[] x2 = new float[n];
float[] y2 = new float[n];
for (int i = 0; i < n; i++) {
x2[i] = x[i];
y2[i] = y[i];
}
ImageProcessor ipx = new FloatProcessor(n, 1, x, null);
ImageProcessor ipy = new FloatProcessor(n, 1, y, null);
ipx.convolve(kernel, kernel.length, 1);
ipy.convolve(kernel, kernel.length, 1);
float[] indexes = new float[n];
float[] curvature = new float[n];
for (int i = 0; i < n; i++) {
indexes[i] = i;
curvature[i] =
(float) Math.sqrt((x2[i] - x[i]) * (x2[i] - x[i]) + (y2[i] - y[i]) * (y2[i] - y[i]));
}
return curvature;
}
/*
if selection is closed shape, create a circle with the same area and centroid, otherwise use<br>
the Pratt method to fit a circle to the points that define the line or multi-point selection.<br>
Reference: Pratt V., Direct least-squares fitting of algebraic surfaces", Computer Graphics, Vol. 21, pages 145-152 (1987).<br>
Original code: Nikolai Chernov's MATLAB script for Newton-based Pratt fit.<br>
(http://www.math.uab.edu/~chernov/cl/MATLABcircle.html)<br>
Java version: https://github.com/mdoube/BoneJ/blob/master/src/org/doube/geometry/FitCircle.java<br>
@authors Nikolai Chernov, Michael Doube, Ved Sharma
*/
void fitCircle(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null) {
noRoi("Fit Circle");
return;
}
if (roi.isArea()) { // create circle with the same area and centroid
ImageProcessor ip = imp.getProcessor();
ip.setRoi(roi);
ImageStatistics stats =
ImageStatistics.getStatistics(ip, Measurements.AREA + Measurements.CENTROID, null);
double r = Math.sqrt(stats.pixelCount / Math.PI);
imp.killRoi();
int d = (int) Math.round(2.0 * r);
IJ.makeOval(
(int) Math.round(stats.xCentroid - r), (int) Math.round(stats.yCentroid - r), d, d);
return;
}
Polygon poly = roi.getPolygon();
int n = poly.npoints;
int[] x = poly.xpoints;
int[] y = poly.ypoints;
if (n < 3) {
IJ.error("Fit Circle", "At least 3 points are required to fit a circle.");
return;
}
// calculate point centroid
double sumx = 0, sumy = 0;
for (int i = 0; i < n; i++) {
sumx = sumx + poly.xpoints[i];
sumy = sumy + poly.ypoints[i];
}
double meanx = sumx / n;
double meany = sumy / n;
// calculate moments
double[] X = new double[n], Y = new double[n];
double Mxx = 0, Myy = 0, Mxy = 0, Mxz = 0, Myz = 0, Mzz = 0;
for (int i = 0; i < n; i++) {
X[i] = x[i] - meanx;
Y[i] = y[i] - meany;
double Zi = X[i] * X[i] + Y[i] * Y[i];
Mxy = Mxy + X[i] * Y[i];
Mxx = Mxx + X[i] * X[i];
Myy = Myy + Y[i] * Y[i];
Mxz = Mxz + X[i] * Zi;
Myz = Myz + Y[i] * Zi;
Mzz = Mzz + Zi * Zi;
}
Mxx = Mxx / n;
Myy = Myy / n;
Mxy = Mxy / n;
Mxz = Mxz / n;
Myz = Myz / n;
Mzz = Mzz / n;
// calculate the coefficients of the characteristic polynomial
double Mz = Mxx + Myy;
double Cov_xy = Mxx * Myy - Mxy * Mxy;
double Mxz2 = Mxz * Mxz;
double Myz2 = Myz * Myz;
double A2 = 4 * Cov_xy - 3 * Mz * Mz - Mzz;
double A1 = Mzz * Mz + 4 * Cov_xy * Mz - Mxz2 - Myz2 - Mz * Mz * Mz;
double A0 = Mxz2 * Myy + Myz2 * Mxx - Mzz * Cov_xy - 2 * Mxz * Myz * Mxy + Mz * Mz * Cov_xy;
double A22 = A2 + A2;
double epsilon = 1e-12;
double ynew = 1e+20;
int IterMax = 20;
double xnew = 0;
int iterations = 0;
// Newton's method starting at x=0
for (int iter = 1; iter <= IterMax; iter++) {
iterations = iter;
double yold = ynew;
ynew = A0 + xnew * (A1 + xnew * (A2 + 4. * xnew * xnew));
if (Math.abs(ynew) > Math.abs(yold)) {
if (IJ.debugMode) IJ.log("Fit Circle: wrong direction: |ynew| > |yold|");
xnew = 0;
break;
}
double Dy = A1 + xnew * (A22 + 16 * xnew * xnew);
double xold = xnew;
xnew = xold - ynew / Dy;
if (Math.abs((xnew - xold) / xnew) < epsilon) break;
if (iter >= IterMax) {
if (IJ.debugMode) IJ.log("Fit Circle: will not converge");
xnew = 0;
}
if (xnew < 0) {
if (IJ.debugMode) IJ.log("Fit Circle: negative root: x = " + xnew);
xnew = 0;
}
}
if (IJ.debugMode)
IJ.log("Fit Circle: n=" + n + ", xnew=" + IJ.d2s(xnew, 2) + ", iterations=" + iterations);
// calculate the circle parameters
double DET = xnew * xnew - xnew * Mz + Cov_xy;
double CenterX = (Mxz * (Myy - xnew) - Myz * Mxy) / (2 * DET);
double CenterY = (Myz * (Mxx - xnew) - Mxz * Mxy) / (2 * DET);
double radius = Math.sqrt(CenterX * CenterX + CenterY * CenterY + Mz + 2 * xnew);
if (Double.isNaN(radius)) {
IJ.error("Fit Circle", "Points are collinear.");
return;
}
CenterX = CenterX + meanx;
CenterY = CenterY + meany;
imp.killRoi();
IJ.makeOval(
(int) Math.round(CenterX - radius),
(int) Math.round(CenterY - radius),
(int) Math.round(2 * radius),
(int) Math.round(2 * radius));
}
private void makeBand(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null) {
noRoi("Make Band");
return;
}
if (!roi.isArea()) {
IJ.error("Make Band", "Area selection required");
return;
}
Calibration cal = imp.getCalibration();
double pixels = bandSize;
double size = pixels * cal.pixelWidth;
int decimalPlaces = 0;
if ((int) size != size) decimalPlaces = 2;
GenericDialog gd = new GenericDialog("Make Band");
gd.addNumericField("Band Size:", size, decimalPlaces, 4, cal.getUnits());
gd.showDialog();
if (gd.wasCanceled()) return;
size = gd.getNextNumber();
if (Double.isNaN(size)) {
IJ.error("Make Band", "invalid number");
return;
}
int n = (int) Math.round(size / cal.pixelWidth);
if (n > 255) {
IJ.error("Make Band", "Cannot make bands wider that 255 pixels");
return;
}
int width = imp.getWidth();
int height = imp.getHeight();
Rectangle r = roi.getBounds();
ImageProcessor ip = roi.getMask();
if (ip == null) {
ip = new ByteProcessor(r.width, r.height);
ip.invert();
}
ImageProcessor mask = new ByteProcessor(width, height);
mask.insert(ip, r.x, r.y);
ImagePlus edm = new ImagePlus("mask", mask);
boolean saveBlackBackground = Prefs.blackBackground;
Prefs.blackBackground = false;
IJ.run(edm, "Distance Map", "");
Prefs.blackBackground = saveBlackBackground;
ip = edm.getProcessor();
ip.setThreshold(0, n, ImageProcessor.NO_LUT_UPDATE);
int xx = -1, yy = -1;
for (int x = r.x; x < r.x + r.width; x++) {
for (int y = r.y; y < r.y + r.height; y++) {
if (ip.getPixel(x, y) < n) {
xx = x;
yy = y;
break;
}
}
if (xx >= 0 || yy >= 0) break;
}
int count = IJ.doWand(edm, xx, yy, 0, null);
if (count <= 0) {
IJ.error("Make Band", "Unable to make band");
return;
}
ShapeRoi roi2 = new ShapeRoi(edm.getRoi());
if (!(roi instanceof ShapeRoi)) roi = new ShapeRoi(roi);
ShapeRoi roi1 = (ShapeRoi) roi;
roi2 = roi2.not(roi1);
imp.setRoi(roi2);
bandSize = n;
}
public void drawPixels(ImageProcessor ip) {
int saveWidth = ip.getLineWidth();
if (getStrokeWidth() > 1f) ip.setLineWidth((int) Math.round(getStrokeWidth()));
double offset = getOffset(0.5);
if (xSpline != null) {
ip.moveTo(
x + (int) (Math.round(xSpline[0]) + offset), y + (int) Math.round(ySpline[0] + offset));
for (int i = 1; i < splinePoints; i++)
ip.lineTo(
x + (int) (Math.round(xSpline[i]) + offset), y + (int) Math.round(ySpline[i] + offset));
if (type == POLYGON || type == FREEROI || type == TRACED_ROI)
ip.lineTo(
x + (int) (Math.round(xSpline[0]) + offset), y + (int) Math.round(ySpline[0] + offset));
} else if (xpf != null) {
ip.moveTo(x + (int) (Math.round(xpf[0]) + offset), y + (int) Math.round(ypf[0] + offset));
for (int i = 1; i < nPoints; i++)
ip.lineTo(x + (int) (Math.round(xpf[i]) + offset), y + (int) Math.round(ypf[i] + offset));
if (type == POLYGON || type == FREEROI || type == TRACED_ROI)
ip.lineTo(x + (int) (Math.round(xpf[0]) + offset), y + (int) Math.round(ypf[0] + offset));
} else {
ip.moveTo(x + xp[0], y + yp[0]);
for (int i = 1; i < nPoints; i++) ip.lineTo(x + xp[i], y + yp[i]);
if (type == POLYGON || type == FREEROI || type == TRACED_ROI) ip.lineTo(x + xp[0], y + yp[0]);
}
ip.setLineWidth(saveWidth);
updateFullWindow = true;
}
public void build_bricks() {
ImagePlus imp;
ImagePlus orgimp;
ImageStack stack;
FileInfo finfo;
if (lvImgTitle.isEmpty()) return;
orgimp = WindowManager.getImage(lvImgTitle.get(0));
imp = orgimp;
finfo = imp.getFileInfo();
if (finfo == null) return;
int[] dims = imp.getDimensions();
int imageW = dims[0];
int imageH = dims[1];
int nCh = dims[2];
int imageD = dims[3];
int nFrame = dims[4];
int bdepth = imp.getBitDepth();
double xspc = finfo.pixelWidth;
double yspc = finfo.pixelHeight;
double zspc = finfo.pixelDepth;
double z_aspect = Math.max(xspc, yspc) / zspc;
int orgW = imageW;
int orgH = imageH;
int orgD = imageD;
double orgxspc = xspc;
double orgyspc = yspc;
double orgzspc = zspc;
lv = lvImgTitle.size();
if (filetype == "JPEG") {
for (int l = 0; l < lv; l++) {
if (WindowManager.getImage(lvImgTitle.get(l)).getBitDepth() != 8) {
IJ.error("A SOURCE IMAGE MUST BE 8BIT GLAYSCALE");
return;
}
}
}
// calculate levels
/* int baseXY = 256;
int baseZ = 256;
if (z_aspect < 0.5) baseZ = 128;
if (z_aspect > 2.0) baseXY = 128;
if (z_aspect >= 0.5 && z_aspect < 1.0) baseZ = (int)(baseZ*z_aspect);
if (z_aspect > 1.0 && z_aspect <= 2.0) baseXY = (int)(baseXY/z_aspect);
IJ.log("Z_aspect: " + z_aspect);
IJ.log("BaseXY: " + baseXY);
IJ.log("BaseZ: " + baseZ);
*/
int baseXY = 256;
int baseZ = 128;
int dbXY = Math.max(orgW, orgH) / baseXY;
if (Math.max(orgW, orgH) % baseXY > 0) dbXY *= 2;
int dbZ = orgD / baseZ;
if (orgD % baseZ > 0) dbZ *= 2;
lv = Math.max(log2(dbXY), log2(dbZ)) + 1;
int ww = orgW;
int hh = orgH;
int dd = orgD;
for (int l = 0; l < lv; l++) {
int bwnum = ww / baseXY;
if (ww % baseXY > 0) bwnum++;
int bhnum = hh / baseXY;
if (hh % baseXY > 0) bhnum++;
int bdnum = dd / baseZ;
if (dd % baseZ > 0) bdnum++;
if (bwnum % 2 == 0) bwnum++;
if (bhnum % 2 == 0) bhnum++;
if (bdnum % 2 == 0) bdnum++;
int bw = (bwnum <= 1) ? ww : ww / bwnum + 1 + (ww % bwnum > 0 ? 1 : 0);
int bh = (bhnum <= 1) ? hh : hh / bhnum + 1 + (hh % bhnum > 0 ? 1 : 0);
int bd = (bdnum <= 1) ? dd : dd / bdnum + 1 + (dd % bdnum > 0 ? 1 : 0);
bwlist.add(bw);
bhlist.add(bh);
bdlist.add(bd);
IJ.log("LEVEL: " + l);
IJ.log(" width: " + ww);
IJ.log(" hight: " + hh);
IJ.log(" depth: " + dd);
IJ.log(" bw: " + bw);
IJ.log(" bh: " + bh);
IJ.log(" bd: " + bd);
int xyl2 = Math.max(ww, hh) / baseXY;
if (Math.max(ww, hh) % baseXY > 0) xyl2 *= 2;
if (lv - 1 - log2(xyl2) <= l) {
ww /= 2;
hh /= 2;
}
IJ.log(" xyl2: " + (lv - 1 - log2(xyl2)));
int zl2 = dd / baseZ;
if (dd % baseZ > 0) zl2 *= 2;
if (lv - 1 - log2(zl2) <= l) dd /= 2;
IJ.log(" zl2: " + (lv - 1 - log2(zl2)));
if (l < lv - 1) {
lvImgTitle.add(lvImgTitle.get(0) + "_level" + (l + 1));
IJ.selectWindow(lvImgTitle.get(0));
IJ.run(
"Scale...",
"x=- y=- z=- width="
+ ww
+ " height="
+ hh
+ " depth="
+ dd
+ " interpolation=Bicubic average process create title="
+ lvImgTitle.get(l + 1));
}
}
for (int l = 0; l < lv; l++) {
IJ.log(lvImgTitle.get(l));
}
Document doc = newXMLDocument();
Element root = doc.createElement("BRK");
root.setAttribute("version", "1.0");
root.setAttribute("nLevel", String.valueOf(lv));
root.setAttribute("nChannel", String.valueOf(nCh));
root.setAttribute("nFrame", String.valueOf(nFrame));
doc.appendChild(root);
for (int l = 0; l < lv; l++) {
IJ.showProgress(0.0);
int[] dims2 = imp.getDimensions();
IJ.log(
"W: "
+ String.valueOf(dims2[0])
+ " H: "
+ String.valueOf(dims2[1])
+ " C: "
+ String.valueOf(dims2[2])
+ " D: "
+ String.valueOf(dims2[3])
+ " T: "
+ String.valueOf(dims2[4])
+ " b: "
+ String.valueOf(bdepth));
bw = bwlist.get(l).intValue();
bh = bhlist.get(l).intValue();
bd = bdlist.get(l).intValue();
boolean force_pow2 = false;
/* if(IsPowerOf2(bw) && IsPowerOf2(bh) && IsPowerOf2(bd)) force_pow2 = true;
if(force_pow2){
//force pow2
if(Pow2(bw) > bw) bw = Pow2(bw)/2;
if(Pow2(bh) > bh) bh = Pow2(bh)/2;
if(Pow2(bd) > bd) bd = Pow2(bd)/2;
}
if(bw > imageW) bw = (Pow2(imageW) == imageW) ? imageW : Pow2(imageW)/2;
if(bh > imageH) bh = (Pow2(imageH) == imageH) ? imageH : Pow2(imageH)/2;
if(bd > imageD) bd = (Pow2(imageD) == imageD) ? imageD : Pow2(imageD)/2;
*/
if (bw > imageW) bw = imageW;
if (bh > imageH) bh = imageH;
if (bd > imageD) bd = imageD;
if (bw <= 1 || bh <= 1 || bd <= 1) break;
if (filetype == "JPEG" && (bw < 8 || bh < 8)) break;
Element lvnode = doc.createElement("Level");
lvnode.setAttribute("lv", String.valueOf(l));
lvnode.setAttribute("imageW", String.valueOf(imageW));
lvnode.setAttribute("imageH", String.valueOf(imageH));
lvnode.setAttribute("imageD", String.valueOf(imageD));
lvnode.setAttribute("xspc", String.valueOf(xspc));
lvnode.setAttribute("yspc", String.valueOf(yspc));
lvnode.setAttribute("zspc", String.valueOf(zspc));
lvnode.setAttribute("bitDepth", String.valueOf(bdepth));
root.appendChild(lvnode);
Element brksnode = doc.createElement("Bricks");
brksnode.setAttribute("brick_baseW", String.valueOf(bw));
brksnode.setAttribute("brick_baseH", String.valueOf(bh));
brksnode.setAttribute("brick_baseD", String.valueOf(bd));
lvnode.appendChild(brksnode);
ArrayList<Brick> bricks = new ArrayList<Brick>();
int mw, mh, md, mw2, mh2, md2;
double tx0, ty0, tz0, tx1, ty1, tz1;
double bx0, by0, bz0, bx1, by1, bz1;
for (int k = 0; k < imageD; k += bd) {
if (k > 0) k--;
for (int j = 0; j < imageH; j += bh) {
if (j > 0) j--;
for (int i = 0; i < imageW; i += bw) {
if (i > 0) i--;
mw = Math.min(bw, imageW - i);
mh = Math.min(bh, imageH - j);
md = Math.min(bd, imageD - k);
if (force_pow2) {
mw2 = Pow2(mw);
mh2 = Pow2(mh);
md2 = Pow2(md);
} else {
mw2 = mw;
mh2 = mh;
md2 = md;
}
if (filetype == "JPEG") {
if (mw2 < 8) mw2 = 8;
if (mh2 < 8) mh2 = 8;
}
tx0 = i == 0 ? 0.0d : ((mw2 - mw + 0.5d) / mw2);
ty0 = j == 0 ? 0.0d : ((mh2 - mh + 0.5d) / mh2);
tz0 = k == 0 ? 0.0d : ((md2 - md + 0.5d) / md2);
tx1 = 1.0d - 0.5d / mw2;
if (mw < bw) tx1 = 1.0d;
if (imageW - i == bw) tx1 = 1.0d;
ty1 = 1.0d - 0.5d / mh2;
if (mh < bh) ty1 = 1.0d;
if (imageH - j == bh) ty1 = 1.0d;
tz1 = 1.0d - 0.5d / md2;
if (md < bd) tz1 = 1.0d;
if (imageD - k == bd) tz1 = 1.0d;
bx0 = i == 0 ? 0.0d : (i + 0.5d) / (double) imageW;
by0 = j == 0 ? 0.0d : (j + 0.5d) / (double) imageH;
bz0 = k == 0 ? 0.0d : (k + 0.5d) / (double) imageD;
bx1 = Math.min((i + bw - 0.5d) / (double) imageW, 1.0d);
if (imageW - i == bw) bx1 = 1.0d;
by1 = Math.min((j + bh - 0.5d) / (double) imageH, 1.0d);
if (imageH - j == bh) by1 = 1.0d;
bz1 = Math.min((k + bd - 0.5d) / (double) imageD, 1.0d);
if (imageD - k == bd) bz1 = 1.0d;
int x, y, z;
x = i - (mw2 - mw);
y = j - (mh2 - mh);
z = k - (md2 - md);
bricks.add(
new Brick(
x, y, z, mw2, mh2, md2, 0, 0, tx0, ty0, tz0, tx1, ty1, tz1, bx0, by0, bz0, bx1,
by1, bz1));
}
}
}
Element fsnode = doc.createElement("Files");
lvnode.appendChild(fsnode);
stack = imp.getStack();
int totalbricknum = nFrame * nCh * bricks.size();
int curbricknum = 0;
for (int f = 0; f < nFrame; f++) {
for (int ch = 0; ch < nCh; ch++) {
int sizelimit = bdsizelimit * 1024 * 1024;
int bytecount = 0;
int filecount = 0;
int pd_bufsize = Math.max(sizelimit, bw * bh * bd * bdepth / 8);
byte[] packed_data = new byte[pd_bufsize];
String base_dataname =
basename
+ "_Lv"
+ String.valueOf(l)
+ "_Ch"
+ String.valueOf(ch)
+ "_Fr"
+ String.valueOf(f);
String current_dataname = base_dataname + "_data" + filecount;
Brick b_first = bricks.get(0);
if (b_first.z_ != 0) IJ.log("warning");
int st_z = b_first.z_;
int ed_z = b_first.z_ + b_first.d_;
LinkedList<ImageProcessor> iplist = new LinkedList<ImageProcessor>();
for (int s = st_z; s < ed_z; s++)
iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
// ImagePlus test;
// ImageStack tsst;
// test = NewImage.createByteImage("test", imageW, imageH, imageD,
// NewImage.FILL_BLACK);
// tsst = test.getStack();
for (int i = 0; i < bricks.size(); i++) {
Brick b = bricks.get(i);
if (ed_z > b.z_ || st_z < b.z_ + b.d_) {
if (b.z_ > st_z) {
for (int s = 0; s < b.z_ - st_z; s++) iplist.pollFirst();
st_z = b.z_;
} else if (b.z_ < st_z) {
IJ.log("warning");
for (int s = st_z - 1; s > b.z_; s--)
iplist.addFirst(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
st_z = b.z_;
}
if (b.z_ + b.d_ > ed_z) {
for (int s = ed_z; s < b.z_ + b.d_; s++)
iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
ed_z = b.z_ + b.d_;
} else if (b.z_ + b.d_ < ed_z) {
IJ.log("warning");
for (int s = 0; s < ed_z - (b.z_ + b.d_); s++) iplist.pollLast();
ed_z = b.z_ + b.d_;
}
} else {
IJ.log("warning");
iplist.clear();
st_z = b.z_;
ed_z = b.z_ + b.d_;
for (int s = st_z; s < ed_z; s++)
iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
}
if (iplist.size() != b.d_) {
IJ.log("Stack Error");
return;
}
// int zz = st_z;
int bsize = 0;
byte[] bdata = new byte[b.w_ * b.h_ * b.d_ * bdepth / 8];
Iterator<ImageProcessor> ipite = iplist.iterator();
while (ipite.hasNext()) {
// ImageProcessor tsip = tsst.getProcessor(zz+1);
ImageProcessor ip = ipite.next();
ip.setRoi(b.x_, b.y_, b.w_, b.h_);
if (bdepth == 8) {
byte[] data = (byte[]) ip.crop().getPixels();
System.arraycopy(data, 0, bdata, bsize, data.length);
bsize += data.length;
} else if (bdepth == 16) {
ByteBuffer buffer = ByteBuffer.allocate(b.w_ * b.h_ * bdepth / 8);
buffer.order(ByteOrder.LITTLE_ENDIAN);
short[] data = (short[]) ip.crop().getPixels();
for (short e : data) buffer.putShort(e);
System.arraycopy(buffer.array(), 0, bdata, bsize, buffer.array().length);
bsize += buffer.array().length;
} else if (bdepth == 32) {
ByteBuffer buffer = ByteBuffer.allocate(b.w_ * b.h_ * bdepth / 8);
buffer.order(ByteOrder.LITTLE_ENDIAN);
float[] data = (float[]) ip.crop().getPixels();
for (float e : data) buffer.putFloat(e);
System.arraycopy(buffer.array(), 0, bdata, bsize, buffer.array().length);
bsize += buffer.array().length;
}
}
String filename =
basename
+ "_Lv"
+ String.valueOf(l)
+ "_Ch"
+ String.valueOf(ch)
+ "_Fr"
+ String.valueOf(f)
+ "_ID"
+ String.valueOf(i);
int offset = bytecount;
int datasize = bdata.length;
if (filetype == "RAW") {
int dummy = -1;
// do nothing
}
if (filetype == "JPEG" && bdepth == 8) {
try {
DataBufferByte db = new DataBufferByte(bdata, datasize);
Raster raster = Raster.createPackedRaster(db, b.w_, b.h_ * b.d_, 8, null);
BufferedImage img =
new BufferedImage(b.w_, b.h_ * b.d_, BufferedImage.TYPE_BYTE_GRAY);
img.setData(raster);
ByteArrayOutputStream baos = new ByteArrayOutputStream();
ImageOutputStream ios = ImageIO.createImageOutputStream(baos);
String format = "jpg";
Iterator<javax.imageio.ImageWriter> iter =
ImageIO.getImageWritersByFormatName("jpeg");
javax.imageio.ImageWriter writer = iter.next();
ImageWriteParam iwp = writer.getDefaultWriteParam();
iwp.setCompressionMode(ImageWriteParam.MODE_EXPLICIT);
iwp.setCompressionQuality((float) jpeg_quality * 0.01f);
writer.setOutput(ios);
writer.write(null, new IIOImage(img, null, null), iwp);
// ImageIO.write(img, format, baos);
bdata = baos.toByteArray();
datasize = bdata.length;
} catch (IOException e) {
e.printStackTrace();
return;
}
}
if (filetype == "ZLIB") {
byte[] tmpdata = new byte[b.w_ * b.h_ * b.d_ * bdepth / 8];
Deflater compresser = new Deflater();
compresser.setInput(bdata);
compresser.setLevel(Deflater.DEFAULT_COMPRESSION);
compresser.setStrategy(Deflater.DEFAULT_STRATEGY);
compresser.finish();
datasize = compresser.deflate(tmpdata);
bdata = tmpdata;
compresser.end();
}
if (bytecount + datasize > sizelimit && bytecount > 0) {
BufferedOutputStream fis = null;
try {
File file = new File(directory + current_dataname);
fis = new BufferedOutputStream(new FileOutputStream(file));
fis.write(packed_data, 0, bytecount);
} catch (IOException e) {
e.printStackTrace();
return;
} finally {
try {
if (fis != null) fis.close();
} catch (IOException e) {
e.printStackTrace();
return;
}
}
filecount++;
current_dataname = base_dataname + "_data" + filecount;
bytecount = 0;
offset = 0;
System.arraycopy(bdata, 0, packed_data, bytecount, datasize);
bytecount += datasize;
} else {
System.arraycopy(bdata, 0, packed_data, bytecount, datasize);
bytecount += datasize;
}
Element filenode = doc.createElement("File");
filenode.setAttribute("filename", current_dataname);
filenode.setAttribute("channel", String.valueOf(ch));
filenode.setAttribute("frame", String.valueOf(f));
filenode.setAttribute("brickID", String.valueOf(i));
filenode.setAttribute("offset", String.valueOf(offset));
filenode.setAttribute("datasize", String.valueOf(datasize));
filenode.setAttribute("filetype", String.valueOf(filetype));
fsnode.appendChild(filenode);
curbricknum++;
IJ.showProgress((double) (curbricknum) / (double) (totalbricknum));
}
if (bytecount > 0) {
BufferedOutputStream fis = null;
try {
File file = new File(directory + current_dataname);
fis = new BufferedOutputStream(new FileOutputStream(file));
fis.write(packed_data, 0, bytecount);
} catch (IOException e) {
e.printStackTrace();
return;
} finally {
try {
if (fis != null) fis.close();
} catch (IOException e) {
e.printStackTrace();
return;
}
}
}
}
}
for (int i = 0; i < bricks.size(); i++) {
Brick b = bricks.get(i);
Element bricknode = doc.createElement("Brick");
bricknode.setAttribute("id", String.valueOf(i));
bricknode.setAttribute("st_x", String.valueOf(b.x_));
bricknode.setAttribute("st_y", String.valueOf(b.y_));
bricknode.setAttribute("st_z", String.valueOf(b.z_));
bricknode.setAttribute("width", String.valueOf(b.w_));
bricknode.setAttribute("height", String.valueOf(b.h_));
bricknode.setAttribute("depth", String.valueOf(b.d_));
brksnode.appendChild(bricknode);
Element tboxnode = doc.createElement("tbox");
tboxnode.setAttribute("x0", String.valueOf(b.tx0_));
tboxnode.setAttribute("y0", String.valueOf(b.ty0_));
tboxnode.setAttribute("z0", String.valueOf(b.tz0_));
tboxnode.setAttribute("x1", String.valueOf(b.tx1_));
tboxnode.setAttribute("y1", String.valueOf(b.ty1_));
tboxnode.setAttribute("z1", String.valueOf(b.tz1_));
bricknode.appendChild(tboxnode);
Element bboxnode = doc.createElement("bbox");
bboxnode.setAttribute("x0", String.valueOf(b.bx0_));
bboxnode.setAttribute("y0", String.valueOf(b.by0_));
bboxnode.setAttribute("z0", String.valueOf(b.bz0_));
bboxnode.setAttribute("x1", String.valueOf(b.bx1_));
bboxnode.setAttribute("y1", String.valueOf(b.by1_));
bboxnode.setAttribute("z1", String.valueOf(b.bz1_));
bricknode.appendChild(bboxnode);
}
if (l < lv - 1) {
imp = WindowManager.getImage(lvImgTitle.get(l + 1));
int[] newdims = imp.getDimensions();
imageW = newdims[0];
imageH = newdims[1];
imageD = newdims[3];
xspc = orgxspc * ((double) orgW / (double) imageW);
yspc = orgyspc * ((double) orgH / (double) imageH);
zspc = orgzspc * ((double) orgD / (double) imageD);
bdepth = imp.getBitDepth();
}
}
File newXMLfile = new File(directory + basename + ".vvd");
writeXML(newXMLfile, doc);
for (int l = 1; l < lv; l++) {
imp = WindowManager.getImage(lvImgTitle.get(l));
imp.changes = false;
imp.close();
}
}