public void actionPerformed(ActionEvent e) {
Button b = (Button) e.getSource();
if (b == null) return;
boolean imageThere = checkImage();
if (imageThere) {
if (b == originalB) {
reset(imp, ip);
filteredB.setEnabled(true);
} else if (b == filteredB) {
apply(imp, ip);
} else if (b == sampleB) {
reset(imp, ip);
sample();
apply(imp, ip);
} else if (b == stackB) {
applyStack();
} else if (b == helpB) {
IJ.showMessage(
"Help",
"Threshold Colour v1.0\n \n"
+ "Modification of Bob Dougherty's BandPass2 plugin by G.Landini to\n"
+ "threshold 24 bit RGB images based on Hue, Saturation and Brightness\n"
+ "or Red, Green and Blue components.\n \n"
+ "Pass: Band-pass filter (anything within range is displayed).\n \n"
+ "Stop: Band-reject filter (anything within range is NOT displayed).\n \n"
+ "Original: Shows the original image and updates the buffer when\n"
+ " switching to another image.\n \n"
+ "Filtered: Shows the filtered image.\n \n"
+ "Stack: Processes the rest of the slices in the stack (if any)\n"
+ " using the current settings.\n \n"
+ "Threshold: Shows the object/background in the foreground and\n"
+ " background colours selected in the ImageJ toolbar.\n \n"
+ "Invert: Swaps the fore/background colours.\n \n"
+ "Sample: (experimental) Sets the ranges of the filters based on the\n"
+ " pixel value componentd in a rectangular, user-defined, ROI.\n \n"
+ "HSB RGB: Selects HSB or RGB space and resets all the filters.\n \n"
+ "Note that the \'thresholded\' image is RGB, not 8 bit grey.");
}
updatePlot();
updateLabels();
imp.updateAndDraw();
} else {
IJ.beep();
IJ.showStatus("No Image");
}
notify();
}
private void showioerror() {
IJ.showMessage("Error in file io");
}
private void geterrors() {
GenericDialog gd = new GenericDialog("Options");
float conf = 0.67f;
gd.addNumericField("Confidence Limit", (int) (conf * 100.0f), 5, 10, null);
gd.addChoice("Error Parameter", paramsnames, paramsnames[0]);
double spacing = 0.01;
gd.addNumericField("Chi^2 plot spacing (% of value)?", spacing * 100.0, 2, 10, null);
boolean globalerror = false;
gd.addCheckbox("Global Fit Error?", globalerror);
int dataset = 0;
gd.addNumericField("Data Set (for Global Error)", dataset, 0);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
conf = 0.01f * (float) gd.getNextNumber();
int paramindex = (int) gd.getNextChoiceIndex();
spacing = 0.01 * gd.getNextNumber();
globalerror = gd.getNextBoolean();
dataset = (int) gd.getNextNumber();
if (globalerror) {
support_plane_errors erclass = new support_plane_errors(this, 0.0001, 50, true, 0.1);
int[] erindeces = {paramindex, dataset};
// need to set up all the matrices
int nsel = 0;
int nparams = 11;
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];
float[][] tempdata = new float[nsel][xpts * ypts];
float[][] tempweights = new float[nsel][xpts * ypts];
int nfit = 0;
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];
if (vflmatrix[counter][j] == 0 || (j == 0 && vflmatrix[counter][j] == 2)) {
nfit++;
}
}
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 dofnum = xpts * ypts * nsel - (nfit - 1) - 1;
int dofden = xpts * ypts * nsel - nfit - 1;
// double flim=FLimit(dofnum,dofden,(double)conf);
double flim = (new jdist()).FLimit(dofnum, dofden, (double) conf);
IJ.log("FLimit = " + (float) flim);
if (flim == Double.NaN && flim < 1.0) {
IJ.showMessage("Invalid Limiting F Value");
return;
}
double truespacing = Math.abs(params[erindeces[1]][erindeces[0]] * spacing);
double[][] c2plot =
erclass.geterrorsglobal(
params,
vflmatrix,
tempformulas,
paramsnames,
constraints,
tempdata,
tempweights,
flim,
truespacing,
erindeces);
IJ.log("upper limit = " + c2plot[1][0] + " lower limit = " + c2plot[0][0]);
int templength = c2plot[0].length;
float[][] c2plotf = new float[2][templength - 1];
for (int i = 0; i < (templength - 1); i++) {
c2plotf[0][i] = (float) c2plot[0][i + 1];
c2plotf[1][i] = (float) c2plot[1][i + 1];
}
new PlotWindow4(
"c2 plot",
paramsnames[paramindex] + "[" + dataset + "]",
"Chi^2",
c2plotf[0],
c2plotf[1])
.draw();
} else {
support_plane_errors erclass = new support_plane_errors(this, 0.0001, 50, false, 0.1);
int errindex = paramindex;
float[] tempdata = new float[xpts * ypts];
float[] tempweights = new float[xpts * ypts];
for (int i = 0; i < xpts; i++) {
for (int j = 0; j < ypts; j++) {
tempdata[i + j * xpts] = (float) ((double) avg[i][j] / (double) nmeas[ncurves]);
tempweights[i + j * xpts] = avgweights[i][j];
}
}
int nfit = 0;
for (int i = 0; i < 7; i++) {
if (avgfixes[i] == 0) {
nfit++;
}
}
int dofnum = xpts * ypts - (nfit - 1) - 1;
int dofden = xpts * ypts - nfit - 1;
double flim = (new jdist()).FLimit(dofnum, dofden, (double) conf);
IJ.log("FLimit = " + (float) flim);
if (flim == Double.NaN && flim < 1.0) {
IJ.showMessage("Invalid Limiting F Value");
return;
}
double truespacing = Math.abs(avgparams[errindex] * spacing);
double[][] c2plot =
erclass.geterrors(
avgparams,
avgfixes,
avgconstraints,
tempdata,
tempweights,
flim,
truespacing,
errindex);
IJ.log("upper limit = " + c2plot[1][0] + " lower limit = " + c2plot[0][0]);
int templength = c2plot[0].length;
float[][] c2plotf = new float[2][templength - 1];
for (int i = 0; i < (templength - 1); i++) {
c2plotf[0][i] = (float) c2plot[0][i + 1];
c2plotf[1][i] = (float) c2plot[1][i + 1];
}
new PlotWindow4("c2 plot", paramsnames[errindex], "Chi^2", c2plotf[0], c2plotf[1]).draw();
}
}
void sample() {
byte[] hsSource, ssSource, bsSource;
// ImageProcessor ip2;
// ip2 = imp.getProcessor();
Rectangle myroi = ip.getRoi();
int swidth = myroi.width;
int sheight = myroi.height;
int sy = myroi.y;
int sx = myroi.x;
if (swidth == width && sheight == height) {
IJ.showMessage("Select a rectangular ROI");
IJ.beep();
return;
}
IJ.run("Select None");
int snumPixels = swidth * sheight;
hsSource = new byte[snumPixels];
ssSource = new byte[snumPixels];
bsSource = new byte[snumPixels];
int[] pixs = new int[snumPixels];
int[] bin = new int[256];
int counter = 0, pi = 0, rangePassH = 0, rangeStopH = 0, rangePassL = 0, rangeStopL = 0, i, j;
for (i = sy; i < sy + sheight; i++) {
for (j = sx; j < sx + swidth; j++) {
pixs[counter++] = ip.getPixel(j, i);
}
}
// Get hsb or rgb from roi.
ColorProcessor cp2 = new ColorProcessor(swidth, sheight, pixs);
int iminhue = 256, imaxhue = -1, iminsat = 256, imaxsat = -1, iminbri = 256, imaxbri = -1;
int iminred = 256, imaxred = -1, imingre = 256, imaxgre = -1, iminblu = 256, imaxblu = -1;
if (isRGB) cp2.getRGB(hsSource, ssSource, bsSource);
else cp2.getHSB(hsSource, ssSource, bsSource);
for (i = 0; i < snumPixels; i++) {
bin[hsSource[i] & 255] = 1;
if ((hsSource[i] & 255) > imaxhue) imaxhue = (hsSource[i] & 255);
if ((hsSource[i] & 255) < iminhue) iminhue = (hsSource[i] & 255);
if ((ssSource[i] & 255) > imaxsat) imaxsat = (ssSource[i] & 255);
if ((ssSource[i] & 255) < iminsat) iminsat = (ssSource[i] & 255);
if ((bsSource[i] & 255) > imaxbri) imaxbri = (bsSource[i] & 255);
if ((bsSource[i] & 255) < iminbri) iminbri = (bsSource[i] & 255);
// IJ.showMessage("h:"+minhue+"H:"+maxhue+"s:"+minsat+"S:"+maxsat+"b:"+minbri+"B:"+maxbri);
}
if (!isRGB) { // get pass or stop filter whichever has a narrower range
for (i = 0; i < 256; i++) {
if (bin[i] > 0) {
rangePassL = i;
break;
}
}
for (i = 255; i >= 0; i--) {
if (bin[i] > 0) {
rangePassH = i;
break;
}
}
for (i = 0; i < 256; i++) {
if (bin[i] == 0) {
rangeStopL = i;
break;
}
}
for (i = 255; i >= 0; i--) {
if (bin[i] == 0) {
rangeStopH = i;
break;
}
}
if ((rangePassH - rangePassL) < (rangeStopH - rangeStopL)) {
bandPassH.setState(true);
bandStopH.setState(false);
iminhue = rangePassL;
imaxhue = rangePassH;
} else {
bandPassH.setState(false);
bandStopH.setState(true);
iminhue = rangeStopL;
imaxhue = rangeStopH;
}
} else {
bandPassH.setState(true);
bandStopH.setState(false);
}
adjustMinHue(iminhue);
minSlider.setValue(iminhue);
adjustMaxHue(imaxhue);
maxSlider.setValue(imaxhue);
adjustMinSat(iminsat);
minSlider2.setValue(iminsat);
adjustMaxSat(imaxsat);
maxSlider2.setValue(imaxsat);
adjustMinBri(iminbri);
minSlider3.setValue(iminbri);
adjustMaxBri(imaxbri);
maxSlider3.setValue(imaxbri);
originalB.setEnabled(true);
// IJ.showStatus("done");
}
