public void run(ImageProcessor ip) {
dimz = stack.getSize();
dimy = stack.getWidth();
dimx = stack.getHeight();
SaveDialog sd = new SaveDialog("Save Measurements as Text...", "res", ".dat");
String name = sd.getFileName();
if (name == null) return;
String directory = sd.getDirectory();
nb = calculnb(stack); // -1;
IJ.showStatus("Measure parameters for the " + nb + " objects ...");
if (nb < 1) {
IJ.showMessage("volume must be labeled");
} else {
double[] volume_m = new double[nb];
int[] volume_p = new int[nb];
double[] surface = new double[nb];
double[] surfacenb = new double[nb];
double[][][] I = new double[3][3][nb];
double[][] J = new double[3][nb];
double[][][] dir = new double[3][3][nb];
double[] xg = new double[nb];
double[] yg = new double[nb];
double[] zg = new double[nb];
byte[] bord = new byte[nb];
// double[] a = new double[nb];
// double[] b = new double[nb];
// double[] c = new double[nb];
// double[] Fab = new double[nb];
// double[] Fac = new double[nb];
// double[] Fbc = new double[nb];
// double[] sp = new double[nb];
double[][] lmin = new double[nb][3];
double[][] lmax = new double[nb][3];
IJ.showStatus("Measure surfaces ...");
calculmarchsurfstack(stack, nb, surface, volume_m);
calculmarchsurfstacknb(stack, nb, surfacenb);
// calculvolumestack(stack,nb,volume_p);
IJ.showStatus("Measure volumes and inertia ...");
calculcgstack(stack, nb, volume_p, xg, yg, zg);
calculinertiestack(stack, nb, xg, yg, zg, I);
inertie(nb, I, J, dir);
IJ.showStatus("Measure bounding boxes ...");
boitestack(stack, nb, xg, yg, zg, dir, lmin, lmax);
borderstack(stack, nb, bord);
IJ.showStatus("Save results ...");
sauvegarde(
volume_p, volume_m, surface, surfacenb, xg, yg, zg, J, dir, nb, bord, lmin, lmax,
directory, name);
volume_m = null;
volume_p = null;
surface = null;
xg = null;
yg = null;
zg = null;
}
}
void loadParticleResults(String filename, ResultsTable res) {
try {
String line;
FileReader fr = new FileReader(filename);
BufferedReader br = new BufferedReader(fr);
java.lang.String header =
" Intensity X (px) Y (px) X (nm) Y (nm) Z (nm) Left-Width(px) Right-Width (px) Up-Height (px) Down-Height (px) X Symmetry (%) Y Symmetry (%) Width minus Height (px) Frame Number";
java.lang.String firstline = br.readLine();
if (!firstline.contains("X (px) Y (px) X (nm) Y (nm) Z (nm)")) {
IJ.error("File does not seam to be a Particles Table file");
IJ.log("Found header: " + firstline);
IJ.log("Expecting: " + header);
return;
}
res.reset();
int counter = 1;
java.util.concurrent.locks.Lock lock = new java.util.concurrent.locks.ReentrantLock();
ThreadedLoader tloader = new ThreadedLoader();
// java.lang.String txt = fr.read();
while ((line = br.readLine()) != null) {
tloader = new ThreadedLoader();
tloader.mysetup(res, lock, line);
tloader.start();
IJ.showStatus("Loading particle " + counter + "... sit back and relax.");
counter++;
}
try {
tloader.join();
} catch (Exception e) {
IJ.error("" + e);
}
if (res.getCounter() < 5000000) {
IJ.showStatus("Creating particle table, this should take a few seconds...");
res.show("Results");
} else
IJ.showMessage(
"Warning",
"Results table has too many particles, they will not be shown but the data still exists within it\nyou can still use all the plugin functionality or save table changes though the 'Save Particle Table' command.");
fr.close();
IJ.showStatus("Done loading table...");
} catch (FileNotFoundException e) {
IJ.error("File not found exception" + e);
return;
} catch (IOException e) {
IJ.error("IOException exception" + e);
return;
} catch (NumberFormatException e) {
IJ.error("Number format exception" + e);
return;
}
}
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();
}
}
public void run(String arg) {
Frame[] niframes = WindowManager.getNonImageWindows();
String[] titles = new String[niframes.length + 1];
for (int i = 0; i < niframes.length; i++) {
titles[i] = niframes[i].getTitle();
}
titles[niframes.length] = "Clipboard";
GenericDialog gd = new GenericDialog("Windows");
boolean importfile = false;
gd.addCheckbox("Import from file?", importfile);
gd.addChoice("Windows", titles, titles[0]);
boolean hasxvals = false;
gd.addCheckbox("X Vals Column?", hasxvals);
boolean multix = false;
gd.addCheckbox("Multi_X_Columns?", multix);
boolean skipendzeros = false;
gd.addCheckbox("Skip_end_zeros?", skipendzeros);
String[] delimiters = {"Tab", "Comma", "Space"};
gd.addChoice("Delimiter", delimiters, delimiters[0]);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
importfile = gd.getNextBoolean();
int index = gd.getNextChoiceIndex();
hasxvals = gd.getNextBoolean();
multix = gd.getNextBoolean();
skipendzeros = gd.getNextBoolean();
int delimindex = gd.getNextChoiceIndex();
if (multix) hasxvals = true;
String textdata = "";
if (importfile) {
OpenDialog od = new OpenDialog("Open File", "", ".txt");
String directory = od.getDirectory();
String name = od.getFileName();
if (name == null) {
return;
}
try {
File infile = new File(directory + name);
BufferedReader b = new BufferedReader(new FileReader(infile));
textdata = (new jdataio()).readstringfile(b);
b.close();
} catch (IOException e) {
return;
}
} else {
if (index == niframes.length) {
// here we get the data from the clipboard
Transferable t = Toolkit.getDefaultToolkit().getSystemClipboard().getContents(null);
try {
if (t != null && t.isDataFlavorSupported(DataFlavor.stringFlavor)) {
textdata = (String) t.getTransferData(DataFlavor.stringFlavor);
}
} catch (UnsupportedFlavorException e) {
} catch (IOException e) {
}
if (textdata.equals("")) {
IJ.error("Error copying from clipboard.");
return;
}
} else {
if (niframes[index] instanceof Editor) {
Editor tw = (Editor) niframes[index];
textdata = tw.getText();
} else {
if (niframes[index] instanceof TextWindow) {
TextWindow tw = (TextWindow) niframes[index];
textdata = tw.getTextPanel().getText();
} else {
IJ.showMessage("Not a valid text window");
return;
}
}
}
}
if (textdata == null) {
IJ.showMessage("Error in Obtaining String");
return;
}
if (textdata.indexOf("\r") >= 0) {
textdata = textdata.replace('\r', '\n');
}
char[] delims = {'\t', ',', ' '};
delimit_string ds = new delimit_string(delims[delimindex]);
String[] rows = ds.getrows(textdata);
int lines = rows.length;
int columns = ds.getnumcolumns(rows[0]);
int ycolumns = columns;
if (hasxvals) {
if (multix) {
ycolumns /= 2;
} else {
ycolumns--;
}
}
if (multix) {
float[][] ydata = new float[ycolumns][lines];
float[][] xdata = new float[ycolumns][lines];
for (int i = 0; i < lines; i++) {
float[] temp = ds.delim2float(rows[i], columns);
for (int j = 0; j < ycolumns; j++) {
ydata[j][i] = temp[2 * j + 1];
xdata[j][i] = temp[2 * j];
}
}
int[] npts = new int[ycolumns];
for (int i = 0; i < ycolumns; i++) {
npts[i] = lines;
}
if (skipendzeros) {
for (int i = 0; i < ycolumns; i++) {
int counter = lines - 1;
while ((xdata[i][counter] == 0.0f || Float.isNaN(xdata[i][counter])) && counter > 0) {
xdata[i][counter] = 0.0f;
ydata[i][counter] = 0.0f;
npts[i]--;
counter--;
}
}
}
(new PlotWindow4("Text Plot", "x", "y", xdata, ydata, npts)).draw();
} else {
float[][] tempydata = new float[ycolumns][lines];
float[] tempxdata = new float[lines];
float[][] xdata = null;
float[][] ydata = null;
int startcolumn = 0;
if (hasxvals) startcolumn = 1;
for (int i = 0; i < lines; i++) {
float[] temp = ds.delim2float(rows[i], columns);
if (hasxvals) {
tempxdata[i] = temp[0];
} else {
tempxdata[i] = (float) (i + 1);
}
for (int j = 0; j < ycolumns; j++) {
tempydata[j][i] = temp[j + startcolumn];
}
}
int[] npts = new int[ycolumns];
npts[0] = lines;
if (skipendzeros) {
int maxpts = 0;
for (int i = 0; i < ycolumns; i++) {
int counter = lines - 1;
npts[i] = lines;
while ((tempydata[i][counter] == 0.0f || Float.isNaN(tempydata[i][counter]))
&& counter > 0) {
npts[i]--;
counter--;
}
if (npts[i] > maxpts) maxpts = npts[i];
IJ.log("" + npts[i]);
}
ydata = new float[ycolumns][maxpts];
xdata = new float[ycolumns][maxpts];
for (int i = 0; i < ycolumns; i++) {
// npts[i]=npts[0];
System.arraycopy(tempxdata, 0, xdata[i], 0, npts[i]);
System.arraycopy(tempydata[i], 0, ydata[i], 0, npts[i]);
}
} else {
ydata = tempydata;
xdata = new float[ycolumns][];
for (int i = 0; i < ycolumns; i++) {
npts[i] = npts[0];
xdata[i] = tempxdata.clone();
}
}
(new PlotWindow4("Text Plot", "x", "y", xdata, ydata, npts)).draw();
}
}
