public void run(String arg) {
GenericDialog gd = new GenericDialog("Options");
gd.addCheckbox("Add_Titles", true);
gd.addCheckbox("Close Original", false);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
boolean addtitles = gd.getNextBoolean();
boolean closeorig = gd.getNextBoolean();
// first get the table window
Frame[] niframes = WindowManager.getNonImageWindows();
boolean first = true;
TextWindow tw2 = null;
int ncols = 0;
String[] col_labels = null;
for (int i = 0; i < niframes.length; i++) {
if (niframes[i] instanceof TextWindow && !niframes[i].getTitle().equals("Log")) {
TextWindow tw = (TextWindow) niframes[i];
TextPanel tp = tw.getTextPanel();
List<List<String>> listtable = table_tools.table2listtable(tp);
if (listtable.size() == 0) {
col_labels = table_tools.getcollabels(tp);
ncols = col_labels.length;
ArrayList<String> temp = new ArrayList<String>();
for (int j = 0; j < ncols; j++) temp.add("");
listtable.add(temp);
}
if (first) {
col_labels = table_tools.getcollabels(tp);
ncols = col_labels.length;
String headings = tp.getColumnHeadings();
if (addtitles) {
String[] titles = repeated(tw.getTitle(), listtable.size());
table_tools.add_listtable_column(listtable, titles, 0);
headings = "name\t" + headings;
}
tw2 =
new TextWindow(
"Combined Table", headings, table_tools.print_listtable(listtable), 400, 200);
first = false;
} else {
if (addtitles) {
String[] titles = repeated(tw.getTitle(), listtable.size());
table_tools.add_listtable_column(listtable, titles, 0);
}
tw2.append(table_tools.print_listtable(listtable));
}
if (closeorig) tw.close();
}
}
}
public void showresults(String results) {
if (redirect) tw.append(results);
else IJ.log(results);
}
public boolean get_errors(double[] params, int[] fixes) {
GenericDialog gd = new GenericDialog("Error Options");
String[] methods = {"Support Plane", "Monte Carlo"};
gd.addChoice("Method", methods, methods[0]);
float conf = 0.67f;
gd.addNumericField("SP_Confidence Limit (%)", (int) (conf * 100.0f), 5, 10, null);
String[] labels = {"P1", "P2", "P3", "P4", "P5", "P6", "P7", "P8", "P9", "P10"};
gd.addChoice("SP_Parameter", labels, labels[0]);
double spacing = 0.01;
gd.addNumericField("SP_Chi^2_plot_spacing (% of value)?", spacing * 100.0, 2, 10, null);
int ntrials = 100;
gd.addNumericField("MC_#_Trials", ntrials, 0);
gd.showDialog();
if (gd.wasCanceled()) {
return false;
}
int methodindex = gd.getNextChoiceIndex();
conf = 0.01f * (float) gd.getNextNumber();
int paramindex = gd.getNextChoiceIndex();
spacing = 0.01 * gd.getNextNumber();
ntrials = (int) gd.getNextNumber();
if (methodindex == 0) {
support_plane_errors_v2 erclass = new support_plane_errors_v2(this, 0.0001, 50, false, 0.1);
int errindex = paramindex;
int nfit = 0;
for (int i = 0; i < labels.length; i++) {
if (fixes[i] == 0) {
nfit++;
}
}
int npts = tempdata.length;
int dofnum = npts - (nfit - 1) - 1;
int dofden = npts - 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 false;
}
double truespacing = Math.abs(params[errindex] * spacing);
double[][] c2plot =
erclass.geterrors(
params, fixes, constraints, tempdata, weights, flim, truespacing, errindex);
IJ.log("upper limit = " + c2plot[1][0] + " lower limit = " + c2plot[0][0]);
IJ.log(
"upper error = "
+ (c2plot[1][0] - params[errindex])
+ " lower error = "
+ (params[errindex] - 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", labels[errindex], "Chi^2", c2plotf[0], c2plotf[1]).draw();
} else {
StringBuffer sb = new StringBuffer();
sb.append("Trial\t");
for (int i = 0; i < labels.length; i++) {
if (fixes[i] == 0) sb.append(labels[i] + "\t");
}
sb.append("chi^2");
tw = new TextWindow("Monte Carlo Results", sb.toString(), "", 400, 400);
redirect = true;
monte_carlo_errors_v2 erclass = new monte_carlo_errors_v2(this, 0.0001, 50, false, 0.1);
double[][] errors = erclass.geterrors(params, fixes, constraints, tempdata, weights, ntrials);
sb = new StringBuffer();
sb.append("StDev\t");
for (int i = 0; i < errors.length; i++) {
float[] ferr = new float[errors[0].length];
for (int j = 0; j < ferr.length; j++) ferr[j] = (float) errors[i][j];
float stdev = jstatistics.getstatistic("StDev", ferr, null);
sb.append("" + stdev);
if (i < (errors.length - 1)) sb.append("\t");
}
tw.append(sb.toString());
redirect = false;
}
return true;
}
public void run(String arg) {
GenericDialog gd = new GenericDialog("Options");
gd.addCheckbox("Acceptor_First", true);
gd.showDialog();
if (gd.wasCanceled()) return;
boolean a1 = gd.getNextBoolean();
int asp = 0;
int dsp = 1;
int aop = 2;
int dop = 3;
int atp = 4;
int dtp = 5;
if (!a1) {
asp = 1;
dsp = 0;
aop = 3;
dop = 2;
atp = 5;
dtp = 4;
}
ImageWindow iw = WindowManager.getCurrentWindow();
float[][] xvals = (float[][]) jutils.runPW4VoidMethod(iw, "getXValues");
float[][] yvals = (float[][]) jutils.runPW4VoidMethod(iw, "getYValues");
int[] npts = (int[]) jutils.runPW4VoidMethod(iw, "getNpts");
int maxpts = (int) jstatistics.getstatistic("Max", npts, null);
int nsets = npts.length / 6;
float[][] rtxvals = new float[nsets][maxpts];
float[][] rtavals = new float[nsets][maxpts];
float[][] rtdvals = new float[nsets][maxpts];
int[] rtnpts = new int[nsets];
int fretlength = 10;
float[][] stfretvals = new float[nsets][fretlength];
float[][] offfretvals = new float[nsets][fretlength];
TextWindow tw = jutils.selectTable("DNA Damage FRET");
if (tw == null)
tw =
new TextWindow(
"DNA Damage FRET",
"title\tacceptor\tdonor\testripe\teoff\tmaxart\tmaxdrt",
"",
400,
200);
// note that st stands for stripe and off is for areas off the damage stripe
for (int i = 0; i < npts.length / 6; i++) {
int len = npts[i * 6];
int damageindex = findbleach(yvals[i * 6 + dsp], len);
int fretindex = findbleach(yvals[i * 6 + atp], len);
IJ.log("set " + i + " damage pos = " + damageindex + " , fret pos = " + fretindex);
int predamagestart = damageindex - 4;
int prefretstart = fretindex - 5;
float staccpredam = getavg(yvals[i * 6 + asp], len, predamagestart, damageindex - 1);
float stdonpredam = getavg(yvals[i * 6 + dsp], len, predamagestart, damageindex - 1);
float nucaccpredam = getavg(yvals[i * 6 + atp], len, predamagestart, damageindex - 1);
float nucdonpredam = getavg(yvals[i * 6 + dtp], len, predamagestart, damageindex - 1);
float stdonprefret = getavg(yvals[i * 6 + dsp], len, prefretstart, fretindex - 2);
float stdonafret = getavg(yvals[i * 6 + dsp], len, fretindex, fretindex + 3);
float offdonprefret = getavg(yvals[i * 6 + dop], len, prefretstart, fretindex - 2);
float offdonafret = getavg(yvals[i * 6 + dop], len, fretindex, fretindex + 3);
float estripe = 1.0f - stdonprefret / stdonafret;
float eoff = 1.0f - offdonprefret / offdonafret;
rtnpts[i] = len;
for (int j = 0; j < len; j++) {
rtxvals[i][j] = j - damageindex - 1;
rtavals[i][j] =
(yvals[i * 6 + asp][j] / staccpredam) / (yvals[i * 6 + atp][j] / nucaccpredam);
rtdvals[i][j] =
(yvals[i * 6 + dsp][j] / stdonpredam) / (yvals[i * 6 + dtp][j] / nucdonpredam);
}
float[] smart = (float[]) algutils.get_subarray(rtavals[i], 0, fretindex);
float[] smdrt = (float[]) algutils.get_subarray(rtdvals[i], 0, fretindex);
jsmooth.blur1D(smart, 2.0f);
jsmooth.blur1D(smdrt, 2.0f);
float maxart = 0.0f;
float maxdrt = 0.0f;
for (int j = 0; j < fretindex - 2; j++) {
if (smart[j] > maxart) maxart = smart[j];
if (smdrt[j] > maxdrt) maxdrt = smdrt[j];
}
stfretvals[i] = getregion(yvals[i * 6 + dsp], len, prefretstart, fretlength);
offfretvals[i] = getregion(yvals[i * 6 + dop], len, prefretstart, fretlength);
tw.append(
iw.getTitle()
+ "-"
+ (i + 1)
+ "\t"
+ staccpredam
+ "\t"
+ stdonpredam
+ "\t"
+ estripe
+ "\t"
+ eoff
+ "\t"
+ maxart
+ "\t"
+ maxdrt);
}
new PlotWindow4("Stripe_FRET_profiles", "time", "intensity", stfretvals, null).draw();
new PlotWindow4("OffStripe_FRET_profiles", "time", "intensity", offfretvals, null).draw();
new PlotWindow4("Acc_Rt_profiles", "time", "intensity", rtxvals, rtavals, rtnpts).draw();
new PlotWindow4("Don_Rt_profiles", "time", "intensity", rtxvals, rtdvals, rtnpts).draw();
}