public void showresults(String results) {
IJ.showStatus(results);
IJ.log(results);
}
private void fitglobal() {
int nparams = 11;
int nsel = 0;
for (int i = 0; i < ncurves; i++) {
if (include[i]) {
nsel++;
}
}
double[][] params = new double[nsel][nparams];
String[][] tempformulas = new String[nsel][nparams];
double[][][] constraints = new double[2][nsel][nparams];
int[][] vflmatrix = new int[nsel][nparams];
int counter = 0;
for (int i = 0; i < ncurves; i++) {
if (include[i]) {
for (int j = 0; j < nparams; j++) {
params[counter][j] = globalparams[i][j];
tempformulas[counter][j] = globalformulas[i][j];
constraints[0][counter][j] = globalconstraints[0][i][j];
constraints[1][counter][j] = globalconstraints[1][i][j];
vflmatrix[counter][j] = globalvflmatrix[i][j];
}
counter++;
}
for (int j = 0; j < nparams; j++) {
undoparams[i][j] = globalparams[i][j];
undoformulas[i][j] = globalformulas[i][j];
undovflmatrix[i][j] = globalvflmatrix[i][j];
}
for (int j = 0; j < xpts; j++) {
for (int k = 0; k < ypts; k++) {
undofit[i][j][k] = fit[i][j][k];
}
}
undoc2[i] = c2[i];
}
undoglobalc2 = globalc2;
if (showglobalfitdialog(params, tempformulas, vflmatrix)) {
counter = 0;
for (int i = 0; i < ncurves; i++) {
if (include[i]) {
for (int j = 0; j < nparams; j++) {
globalparams[i][j] = params[counter][j];
globalformulas[i][j] = tempformulas[counter][j];
globalvflmatrix[i][j] = vflmatrix[counter][j];
}
counter++;
}
}
double[] stats = new double[2];
float[][] tempdata = new float[nsel][xpts * ypts];
float[][] tempweights = new float[nsel][xpts * ypts];
counter = 0;
for (int i = 0; i < ncurves; i++) {
if (include[i]) {
for (int j = 0; j < xpts; j++) {
for (int k = 0; k < ypts; k++) {
tempdata[counter][j + k * xpts] = (float) ((double) pch[i][j][k] / (double) nmeas[i]);
tempweights[counter][j + k * xpts] = weights[i][j][k];
}
}
counter++;
}
}
int tempmaxiter = globalfitclass.maxiter;
if (checkc2) {
globalfitclass.changemaxiter(0);
}
double[] tempc2vals = new double[nsel];
IJ.showStatus("Fitting Globally");
float[][] tempfit =
globalfitclass.fitdata(
params,
vflmatrix,
tempformulas,
paramsnames,
constraints,
tempdata,
tempweights,
stats,
tempc2vals,
false);
IJ.showStatus("Fit Complete");
globalfitclass.changemaxiter(tempmaxiter);
globalc2 = stats[1];
globalc2label.setText("Global chi^2 = " + (float) globalc2);
counter = 0;
for (int i = 0; i < ncurves; i++) {
if (include[i]) {
for (int j = 0; j < xpts; j++) {
for (int k = 0; k < ypts; k++) {
fit[i][j][k] = tempfit[counter][j + xpts * k] * (float) nmeas[i];
}
}
if (i == dispcurve) {
pwfit.updateSeries(fit[dispcurve], 1, true);
}
for (int j = 0; j < nparams; j++) {
globalparams[i][j] = params[counter][j];
}
c2[i] = tempc2vals[counter];
c2array[i].setText("" + (float) c2[i]);
counter++;
}
}
float[] temp = pwfit.getLimits();
temp[4] = 1.0f;
pwfit.setLimits(temp);
}
}
public void run(String arg) {
ImagePlus imp = WindowManager.getCurrentImage();
Calibration cal = imp.getCalibration();
GenericDialog gd = new GenericDialog("Options");
int subsize = 32;
gd.addNumericField("Subregion Size (pixels)?", subsize, 0);
int stepsize = 16;
gd.addNumericField("Step Size?", stepsize, 0);
int shift = 3;
gd.addNumericField("STICS temporal Shift?", shift, 0);
float xoffset = 0.0f;
gd.addNumericField("X_Offset", xoffset, 5, 15, null);
float yoffset = 0.0f;
gd.addNumericField("Y_Offset", yoffset, 5, 15, null);
float multiplier = 8.0f;
gd.addNumericField("Velocity Multiplier", multiplier, 5, 15, null);
float ftime = 1.0f;
gd.addNumericField("Frame_Time(min)", ftime, 5, 15, null);
float scaling = (float) cal.pixelWidth;
gd.addNumericField("Pixel_Size(um)", scaling, 5, 15, null);
boolean norm = true;
gd.addCheckbox("Normalize_Vector_lengths?", norm);
boolean centered = true;
gd.addCheckbox("Center_Vectors?", centered);
float magthresh = 0.0f;
gd.addNumericField("Magnitude_Threshhold?", magthresh, 5, 15, null);
int rlength = 10;
gd.addNumericField("Running_avg_length", rlength, 0);
int inc = 5;
gd.addNumericField("Start_frame_increment", inc, 0);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
subsize = (int) gd.getNextNumber();
stepsize = (int) gd.getNextNumber();
shift = (int) gd.getNextNumber();
xoffset = (float) gd.getNextNumber();
yoffset = (float) gd.getNextNumber();
multiplier = (float) gd.getNextNumber();
ftime = (float) gd.getNextNumber();
scaling = (float) gd.getNextNumber();
norm = gd.getNextBoolean();
centered = gd.getNextBoolean();
magthresh = (float) gd.getNextNumber();
rlength = (int) gd.getNextNumber();
inc = (int) gd.getNextNumber();
int width = imp.getWidth();
int xregions = 1 + (int) (((float) width - (float) subsize) / (float) stepsize);
int newwidth = xregions * subsize;
int height = imp.getHeight();
int yregions = 1 + (int) (((float) height - (float) subsize) / (float) stepsize);
int newheight = yregions * subsize;
ImageStack stack = imp.getStack();
int slices = imp.getNSlices();
int channels = imp.getNChannels();
int frames = imp.getNFrames();
if (frames == 1) {
frames = slices;
slices = 1;
}
Roi roi = imp.getRoi();
if (roi == null) {
roi = new Roi(0, 0, width, height);
}
STICS_map map = new STICS_map(subsize, stepsize);
Object[] tseries = jutils.get3DTSeries(stack, 0, 0, frames, slices, channels);
map.update_STICS_map(tseries, width, height, 0, rlength, roi.getPolygon(), shift);
FloatProcessor fp =
map.get_map(scaling, ftime, stepsize, centered, norm, multiplier, stepsize, magthresh);
ImageStack vector_stack = new ImageStack(fp.getWidth(), fp.getHeight());
vector_stack.addSlice("", fp);
float[][] vel = map.get_scaled_velocities(scaling, ftime, stepsize);
ImageStack velstack = new ImageStack(map.xregions, map.yregions);
velstack.addSlice("", vel[0]);
velstack.addSlice("", vel[1]);
int velframes = 2;
IJ.showStatus("frame " + 0 + " calculated");
for (int i = inc; i < (frames - rlength); i += inc) {
map.update_STICS_map(tseries, width, height, i, rlength, roi.getPolygon(), shift);
FloatProcessor fp2 =
map.get_map(scaling, ftime, stepsize, centered, norm, multiplier, stepsize, magthresh);
vector_stack.addSlice("", fp2);
vel = map.get_scaled_velocities(scaling, ftime, stepsize);
velstack.addSlice("", vel[0]);
velstack.addSlice("", vel[1]);
velframes += 2;
IJ.showStatus("frame " + i + " calculated");
}
(new ImagePlus("STICS Vectors", vector_stack)).show();
ImagePlus imp3 = new ImagePlus("Velocities", velstack);
imp3.setOpenAsHyperStack(true);
imp3.setDimensions(2, 1, velframes / 2);
new CompositeImage(imp3, CompositeImage.COLOR).show();
}