public Zipper<Map<Integer, MZipper<RoiContainer>>> exec(
Zipper<Map<Integer, MZipper<RoiContainer>>> z, int frame) {
JFileChooser fc = new JFileChooser();
int returnVal = fc.showOpenDialog(WindowManager.getCurrentWindow().getCanvas());
Map<Integer, MZipper<RoiContainer>> newRois;
if (returnVal == JFileChooser.APPROVE_OPTION) {
try {
FileInputStream f = new FileInputStream(fc.getSelectedFile().getCanonicalPath());
MroiLisp parser = new MroiLisp(f);
parser.ReInit(f);
newRois = parser.roiFile();
// z.rights.clear();
// z.rights.add(newRois);
// z = z.right();
// return z;
return z.insertAndStep(newRois);
} catch (IOException e) {
IJ.error("Couldn't open from " + fc.getSelectedFile().getName() + ": " + e.getMessage());
} catch (mroi.ParseException e) {
IJ.error("Failed in parsing: " + e.getMessage());
} catch (Exception e) {
IJ.error("Malformed input file: " + e.getMessage());
}
}
return z;
}
public void run(String arg) {
ImageWindow iw = WindowManager.getCurrentWindow();
pw = jutils.getPW4SelCopy(iw);
String title = pw.getTitle();
float[][] yvals = pw.getYValues();
float[][] xvals = pw.getXValues();
int length = yvals[0].length;
if (pw.getShowErrors()) errs = pw.getErrors(0, false);
int[] colors = pw.getColors();
colors[0] = 0;
ScriptEngineManager manager = new ScriptEngineManager();
engine = manager.getEngineByName("js");
ce = (Compilable) engine;
// hitcounter=0;
c2 = 0.0f;
iterations = 0;
checkc2 = false;
double[] stats = new double[3];
tempx = new float[length];
tempdata = new float[length];
System.arraycopy(xvals[0], 0, tempx, 0, length);
System.arraycopy(yvals[0], 0, tempdata, 0, length);
pw.addPoints(tempx, new float[tempx.length], false);
series = pw.getNpts().length - 1;
double[] params = new double[10];
int[] fixes = {0, 0, 0, 1, 1, 1, 1, 1, 1, 1};
init_options(params, fixes);
if (!init_functions()) {
return;
}
while (showoptions(params, fixes)) {
NLLSfit_v2 fitclass;
if (checkc2) {
fitclass = new NLLSfit_v2(this, 0);
} else {
fitclass = new NLLSfit_v2(this, 0.0001, 50, 0.1);
}
float[] fit = fitclass.fitdata(params, fixes, constraints, yvals[0], weights, stats, true);
pw.updateSeries(fit, series, false);
c2 = (float) stats[1];
iterations = (int) stats[0];
}
IJ.log("Chi Squared = " + (float) stats[1]);
IJ.log("Iterations = " + (int) stats[0]);
for (int i = 0; i < 10; i++) {
IJ.log("P" + (i + 1) + " = " + (float) params[i] + " fixed = " + fixes[i]);
}
IJ.log("AIC = " + (float) stats[2]);
// IJ.log("hits = "+hitcounter);
set_options(params, fixes);
}
public void render(int w, int h, Graphics2D g2) {
if (WindowManager.getImageCount() > 0) {
imp = WindowManager.getCurrentWindow().getImagePlus();
if (imp != null) {
Image img = imp.getImage();
g2.drawImage(img, 0, 0, imp.getWidth(), imp.getHeight(), null);
}
if (buff != null) {
g2.drawImage(buff, 0, 0, imp.getWidth(), imp.getHeight(), null);
}
}
}
public void render(int w, int h, Graphics2D g2) {
if (imagejEnabled == false) {
if (Quad2d.getQuad2dInstance() != null) {
Quad2d.getQuad2dInstance().malen(g2);
}
} else {
if (WindowManager.getImageCount() > 0) {
try {
imp = WindowManager.getCurrentWindow().getImagePlus();
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
if (imp != null) {
Image img = imp.getImage();
g2.drawImage(img, 0, 0, imp.getWidth(), imp.getHeight(), null);
}
}
}
}
public void run(String arg) {
GenericDialog gd = new GenericDialog("Options");
double sfreq = 20000.0;
gd.addNumericField("Sampling Frequency?", sfreq, 1, 10, null);
String[] psfchoice = {"3D Gaussian", "Gaus-Lorentz^2", "2D Gaussian"};
gd.addChoice("PSF Type?", psfchoice, psfchoice[0]);
String[] filetypechoice = {
"Confocor 3 raw", "Short binary trajectory", "PlotWindow trajectory", "Ascii Text File"
};
gd.addChoice("File Type?", filetypechoice, filetypechoice[0]);
boolean ch2green = true;
gd.addCheckbox("Ch2 is green?", ch2green);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
sfreq = gd.getNextNumber();
int psfflag = gd.getNextChoiceIndex();
int fileflag = gd.getNextChoiceIndex();
ch2green = gd.getNextBoolean();
int nfiles = 0;
Object[] histograms = null;
int xmax = 0;
int ymax = 0;
String[] names = null;
if (fileflag < 2) {
jdataio ioclass = new jdataio();
File[] filearray = ioclass.openfiles(OpenDialog.getDefaultDirectory(), IJ.getInstance());
if (filearray.length == 0) {
return;
}
String dir = filearray[0].getAbsolutePath();
int sepindex = dir.lastIndexOf(File.separator);
String newdir = dir.substring(0, sepindex + 1);
OpenDialog.setDefaultDirectory(newdir);
nfiles = filearray.length / 2;
if (nfiles > 25) {
nfiles = 25;
}
histograms = new Object[nfiles];
names = organize_c3_files(filearray);
for (int i = 0; i < nfiles; i++) {
try {
int length1 = (int) (((double) filearray[2 * i].length() - 128.0) / 4.0);
int length2 = (int) (((double) filearray[2 * i + 1].length() - 128.0) / 4.0);
int length3 = (int) (((double) filearray[2 * i].length()) / 2.0);
int length4 = (int) (((double) filearray[2 * i + 1].length()) / 2.0);
InputStream instream = new BufferedInputStream(new FileInputStream(filearray[2 * i]));
InputStream instream2 =
new BufferedInputStream(new FileInputStream(filearray[2 * i + 1]));
if (fileflag == 0) {
int[] pmdata = new int[length1];
int[] pmdata2 = new int[length2];
if (!ioclass.skipstreambytes(instream, 128)) {
showioerror();
instream.close();
return;
}
if (!ioclass.skipstreambytes(instream2, 128)) {
showioerror();
instream2.close();
return;
}
if (!ioclass.readintelintfile(instream, length1, pmdata)) {
showioerror();
instream.close();
return;
}
if (!ioclass.readintelintfile(instream2, length2, pmdata2)) {
showioerror();
instream2.close();
return;
}
if (ch2green) {
histograms[i] = (new pmodeconvert()).pm2pch(pmdata2, pmdata, sfreq, 20000000);
} else {
histograms[i] = (new pmodeconvert()).pm2pch(pmdata, pmdata2, sfreq, 20000000);
}
} else {
float[] tmdata = new float[length3];
float[] tmdata2 = new float[length4];
if (!ioclass.readintelshortfile(instream, length3, tmdata)) {
showioerror();
instream.close();
return;
}
if (!ioclass.readintelshortfile(instream2, length4, tmdata2)) {
showioerror();
instream2.close();
return;
}
if (ch2green) {
histograms[i] = (new pmodeconvert()).create_2Dhistogram(tmdata2, tmdata);
} else {
histograms[i] = (new pmodeconvert()).create_2Dhistogram(tmdata, tmdata2);
}
}
if (((float[][]) histograms[i]).length > xmax) {
xmax = ((float[][]) histograms[i]).length;
}
if (((float[][]) histograms[i])[0].length > ymax) {
ymax = ((float[][]) histograms[i])[0].length;
}
instream.close();
instream2.close();
} catch (IOException e) {
showioerror();
return;
}
}
} else {
if (fileflag == 2) {
ImageWindow iw = WindowManager.getCurrentWindow();
float[][] trajectories = (float[][]) jutils.runPW4VoidMethod(iw, "getYValues");
float[][] tempxvals = (float[][]) jutils.runPW4VoidMethod(iw, "getXValues");
sfreq = 1.0 / ((double) tempxvals[0][1]);
nfiles = trajectories.length / 2;
if (nfiles > 25) {
nfiles = 25;
}
names = new String[nfiles + 1];
names[nfiles] = "avg";
histograms = new Object[nfiles];
for (int i = 0; i < nfiles; i++) {
names[i] = "trajectory " + (i + 1);
if (ch2green) {
histograms[i] =
(new pmodeconvert())
.create_2Dhistogram(trajectories[2 * i + 1], trajectories[2 * i]);
} else {
histograms[i] =
(new pmodeconvert())
.create_2Dhistogram(trajectories[2 * i], trajectories[2 * i + 1]);
}
if (((float[][]) histograms[i]).length > xmax) {
xmax = ((float[][]) histograms[i]).length;
}
if (((float[][]) histograms[i])[0].length > ymax) {
ymax = ((float[][]) histograms[i])[0].length;
}
}
} else {
// here we read tab delimited lines from files
jdataio ioclass = new jdataio();
File[] filearray = ioclass.openfiles(OpenDialog.getDefaultDirectory(), IJ.getInstance());
if (filearray.length == 0) {
return;
}
String dir = filearray[0].getAbsolutePath();
int sepindex = dir.lastIndexOf(File.separator);
String newdir = dir.substring(0, sepindex + 1);
OpenDialog.setDefaultDirectory(newdir);
nfiles = filearray.length;
if (nfiles > 25) {
nfiles = 25;
}
histograms = new Object[nfiles];
names = new String[nfiles + 1];
names[nfiles] = "avg";
for (int i = 0; i < nfiles; i++) {
try {
names[i] = filearray[i].getName();
BufferedReader d = new BufferedReader(new FileReader(filearray[i]));
String[] lines = new String[256];
int counter = 0;
do {
lines[counter] = d.readLine();
counter++;
} while ((lines[counter - 1] != null && lines[counter - 1] != "") && counter < 256);
int numcolumns = 0;
for (int j = 0; j < counter - 1; j++) {
int temp = getncolumns(lines[j]);
if (temp > numcolumns) {
numcolumns = temp;
}
}
float[][] temphist2 = null;
if (ch2green) {
temphist2 = new float[numcolumns][counter - 1];
} else {
temphist2 = new float[counter - 1][numcolumns];
}
for (int k = 0; k < counter - 1; k++) {
float[] temp = tab_delim2float(lines[k]);
for (int j = 0; j < numcolumns; j++) {
if (ch2green) {
temphist2[j][k] = temp[j];
} else {
temphist2[k][j] = temp[j];
}
}
}
histograms[i] = temphist2;
d.close();
} catch (IOException e) {
showioerror();
return;
}
}
for (int i = 0; i < nfiles; i++) {
if (((float[][]) histograms[i]).length > xmax) {
xmax = ((float[][]) histograms[i]).length;
}
if (((float[][]) histograms[i])[0].length > ymax) {
ymax = ((float[][]) histograms[i])[0].length;
}
}
}
}
// note that here x is green and y is red
float[][][] pch = new float[nfiles][xmax][ymax];
for (int i = 0; i < nfiles; i++) {
for (int j = 0; j < ((float[][]) histograms[i]).length; j++) {
for (int k = 0; k < ((float[][]) histograms[i])[j].length; k++) {
pch[i][j][k] = ((float[][]) histograms[i])[j][k];
}
}
}
final PCH2DFitWindow cw = new PCH2DFitWindow();
cw.init(names, pch, psfflag);
final Frame f = new Frame("PCH 2D Analysis");
f.setLocation(10, 10);
f.addWindowListener(
new WindowAdapter() {
public void windowClosing(WindowEvent e) {
f.dispose();
}
});
f.add(cw);
f.pack();
f.setResizable(false);
Insets ins = f.getInsets();
cw.totalSize.height = PCH2DFitWindow.H + ins.bottom + ins.top + 65;
cw.totalSize.width = PCH2DFitWindow.WR + ins.left + ins.right;
f.setSize(cw.totalSize);
f.setVisible(true);
cw.requestFocus();
}
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();
}