private static final int[] GetIntArrayTagValue(
final org.w3c.dom.Element eTag, final java.lang.String strTag) {
if (null == eTag || null == strTag || null == eTag.getElementsByTagName(strTag)) return null;
org.w3c.dom.NodeList nl = eTag.getElementsByTagName(strTag);
if (!(nl.item(0) instanceof org.w3c.dom.Element)) return null;
org.w3c.dom.Element elem = (org.w3c.dom.Element) nl.item(0);
if (null == elem
|| null == elem.getChildNodes()
|| null == elem.getChildNodes().item(0)
|| !(elem.getChildNodes().item(0) instanceof org.w3c.dom.Node)) return null;
java.lang.String strValue = elem.getChildNodes().item(0).getNodeValue();
if (null == strValue || strValue.isEmpty()) return null;
java.lang.String[] astrValue = strValue.split(",");
int[] ai = new int[astrValue.length];
for (int i = 0; i < astrValue.length; ++i)
ai[i] = new java.lang.Integer(astrValue[i]).intValue();
return ai;
}
protected void jparseargs(
java.lang.String jlocale, java.lang.String jchildid, java.lang.String joverride) {
this.jlocale = jlocale;
this.jchildid = jchildid;
if (jchildid != null && jchildid.length() > 0) jchildidx = jchildid + "_";
else jchildidx = "";
if (joverride != null && joverride.length() > 0) {
java.lang.String[] ss = joverride.split(" ");
for (int i = 0; i < ss.length; i++) setjnOverride(ss[i]);
}
}
public void run() {
line.trim();
elements = line.split("\t");
if (elements.length < 14) return;
lock.lock();
res.incrementCounter();
res.addValue("Intensity", Double.parseDouble(elements[1]));
res.addValue("X (px)", Double.parseDouble(elements[2]));
res.addValue("Y (px)", Double.parseDouble(elements[3]));
res.addValue("X (nm)", Double.parseDouble(elements[4]));
res.addValue("Y (nm)", Double.parseDouble(elements[5]));
res.addValue("Z (nm)", Double.parseDouble(elements[6]));
res.addValue("Left-StdDev (px)", Double.parseDouble(elements[7]));
res.addValue("Right-StdDev (px)", Double.parseDouble(elements[8]));
res.addValue("Up-StdDev (px)", Double.parseDouble(elements[9]));
res.addValue("Down-StdDev (px)", Double.parseDouble(elements[10]));
res.addValue("X Symmetry (%)", Double.parseDouble(elements[11]));
res.addValue("Y Symmetry (%)", Double.parseDouble(elements[12]));
res.addValue("Width minus Height (px)", Double.parseDouble(elements[13]));
res.addValue("Frame Number", Double.parseDouble(elements[14]));
lock.unlock();
}
public boolean analyseParticles(MyFunctions f) {
GenericDialog gd = new GenericDialog("Analyse PALM/STORM Particles");
gd.addNumericField("Minimum SNR", prefs.get("QuickPALM.snr", 5), 2);
gd.addNumericField("Maximum FWHM (in px)", prefs.get("QuickPALM.fwhm", 4), 0);
gd.addNumericField("Image plane pixel size (nm)", prefs.get("QuickPALM.pixelsize", 106), 2);
gd.addCheckbox("Smart SNR", prefs.get("QuickPALM.smartsnr", true));
gd.addCheckbox(
"3D PALM (astigmatism) - will require calibration file",
prefs.get("QuickPALM.is3d", false));
gd.addCheckbox("Online rendering", prefs.get("QuickPALM.view", true));
gd.addCheckbox("Attach to running acquisition", prefs.get("QuickPALM.attach", false));
gd.addCheckbox("Stream particle info directly into file", prefs.get("QuickPALM.stream", true));
gd.addMessage("\n");
// -----------------------------------------
gd.addMessage("-- Online rendering settings (used only if selected) --");
gd.addMessage("\n");
gd.addNumericField("Pixel size of rendered image (nm)", 30, 2);
gd.addNumericField("Accumulate last (0 to accumulate all frames)", 0, 0);
gd.addNumericField("Update every (frames)", 10, 0);
// gd.addNumericField("Allow color saturation (%)", 50, 0);
gd.addMessage("\n");
// -----------------------------------------
gd.addMessage("-- Attach to running acquisition settings (used only if selected) --");
gd.addMessage("\n");
gd.addStringField(
"_Image name pattern (NN...NN represents the numerical change)",
prefs.get("QuickPALM.pattern", "imgNNNNNNNNN.tif"),
20);
gd.addNumericField("Start NN...NN with", 0, 0);
gd.addNumericField("In acquisition max. wait time for new image (ms)", 50, 0);
gd.addMessage("\n");
// -----------------------------------------
gd.addMessage("-- Advanced settings (don't normally need to be changed) --");
gd.addMessage("\n");
gd.addNumericField("_Minimum symmetry (%)", prefs.get("QuickPALM.symmetry", 50), 0);
gd.addNumericField(
"Local threshold (% maximum intensity)", prefs.get("QuickPALM.lthreshold", 20), 0);
gd.addNumericField("_Maximum iterations per frame", prefs.get("QuickPALM.maxiter", 1000), 0);
gd.addNumericField(
"Threads (each takes ~3*[frame size] in memory)", prefs.get("QuickPALM.nthreads", 50), 0);
gd.addMessage("\n\nDon't forget to save the table in the end...");
gd.showDialog();
if (gd.wasCanceled()) return false;
snr = (int) gd.getNextNumber();
prefs.set("QuickPALM.snr", snr);
fwhm = gd.getNextNumber();
prefs.set("QuickPALM.fwhm", fwhm);
pixelsize = gd.getNextNumber();
prefs.set("QuickPALM.pixelsize", pixelsize);
smartsnr = gd.getNextBoolean();
prefs.set("QuickPALM.smartsnr", smartsnr);
is3d = gd.getNextBoolean();
prefs.set("QuickPALM.is3d", is3d);
view = gd.getNextBoolean();
prefs.set("QuickPALM.view", view);
attach = gd.getNextBoolean();
prefs.set("QuickPALM.attach", attach);
if (gd.getNextBoolean()) {
f.psave = new ParticleSaver();
f.psave.setup();
prefs.set("QuickPALM.stream", true);
} else prefs.set("QuickPALM.stream", false);
// --
magn = pixelsize / gd.getNextNumber();
viewer_accumulate = (int) gd.getNextNumber();
viewer_update = (int) gd.getNextNumber();
// --
pattern = gd.getNextString().trim();
prefs.set("QuickPALM.pattern", pattern);
prefix = pattern.substring(0, pattern.indexOf("N"));
sufix = pattern.substring(pattern.lastIndexOf("N") + 1, pattern.length());
nimchars = pattern.split("N").length - 1;
nimstart = (int) gd.getNextNumber();
waittime = (int) gd.getNextNumber();
// --
symmetry = gd.getNextNumber() / 100;
prefs.set("QuickPALM.symmetry", symmetry);
pthrsh = gd.getNextNumber() / 100;
prefs.set("QuickPALM.lthreshold", pthrsh * 100);
maxpart = (int) gd.getNextNumber();
prefs.set("QuickPALM.maxiter", maxpart);
threads = (int) gd.getNextNumber();
prefs.set("QuickPALM.nthreads", threads);
return true;
}