/**
* File type operator accepts <code>"path/file.(type)"<code> and
* <code>"path/file.(type).other"</code> (as in
* <code>"path/file.(type).xml"</code> and
* <code>"path/file.(type).txt"</code>) conventions.
*
* @param path File path string
* @return File type string
*/
public static final java.lang.String FextI(java.lang.String path) {
if (null == path || 1 > path.length()) return null;
else {
java.lang.String p = path;
int idx = p.lastIndexOf('/');
if (-1 < idx)
/*
* (trim)
*/
p = p.substring(idx + 1);
int i0 = p.lastIndexOf('.');
if (-1 < i0) {
int i1 = p.lastIndexOf('.', (i0 - 1));
if (-1 < i1 && i1 < i0)
/*
* file.(type).xml
*/
return p.substring(i1 + 1, i0);
else
/*
* file.(type)
*/
return p.substring(i0 + 1);
} else
/*
* (punt)
*/
return p;
}
}
public void addExceptions(java.lang.String exceptionStr) {
if (Configuration.getShowImport().equalsIgnoreCase("true")) {
java.lang.String simplename = "";
java.lang.String fullName = exceptionStr;
int lastSlash = fullName.lastIndexOf("/");
if (lastSlash == -1) {
lastSlash = fullName.lastIndexOf(".");
}
if (lastSlash != -1) {
simplename = fullName.substring(lastSlash + 1);
} else simplename = fullName;
fullName = fullName.replace('/', '.');
ConsoleLauncher.addImportClass(fullName);
exceptions.add(simplename);
} else exceptions.add(exceptionStr);
}
public void parseDescriptor(java.lang.String descriptor) {
if (methodName.equalsIgnoreCase("<clinit>")) {
methodName = "static";
descriptor = "";
accessSpecifiers = new java.lang.String[] {""};
return;
}
int charIndex = 0;
java.lang.String parameterString = descriptor.substring(1, descriptor.lastIndexOf(")"));
java.lang.String returnString = descriptor.substring(descriptor.lastIndexOf(")") + 1);
if (returnString.trim().charAt(0) == 'L' || returnString.trim().charAt(0) == '[')
this.setReturnTypeAsObjectOrArrayType(true);
else this.setReturnTypeAsObjectOrArrayType(false);
java.lang.String arrString = "";
// while(charIndex < parameterString.length())
while (parameterString.length() > 0) {
if (parameterString.startsWith("L")) {
java.lang.String objectString = parameterString.substring(0, parameterString.indexOf(";"));
objectString = objectString.replace('/', '.');
parameters.add(objectString);
charIndex = charIndex + (objectString.length() + 2);
parameterString = parameterString.substring(parameterString.indexOf(";") + 1);
} else {
char parameterChar = parameterString.charAt(0);
if (parameterChar == '[') {
arrString = "";
while (parameterString.startsWith("[")) {
arrString += "[";
parameterString = parameterString.substring(1, parameterString.length());
isParameterArray = true;
}
java.lang.String objectString = "";
if (parameterString.charAt(0) == 'L') {
objectString = parameterString.substring(0, parameterString.indexOf(";"));
parameterString = parameterString.substring(parameterString.indexOf(";") + 1);
objectString = objectString.replace('/', '.');
parameters.add(arrString + objectString);
isParameterArray = false;
}
/*
* while(objectString.startsWith("[")) { arrString += "[";
* objectString =
* objectString.substring(1,objectString.length()); }
* objectString = objectString.substring(1); objectString =
* objectString.replace('/','.');
* parameters.add(objectString); charIndex = charIndex +
* (objectString.length() + 2);
* parameters.add(arrString+objectString);
*/
} else {
if (parameterChar == 'I') {
if (isParameterArray) {
parameters.add(arrString + "int");
isParameterArray = false;
} else {
parameters.add("int");
}
}
if (parameterChar == 'B') {
if (isParameterArray) {
parameters.add(arrString + "byte");
isParameterArray = false;
} else {
parameters.add("byte");
}
}
if (parameterChar == 'C') {
if (isParameterArray) {
parameters.add(arrString + "char");
isParameterArray = false;
} else {
parameters.add("char");
}
}
if (parameterChar == 'D') {
if (isParameterArray) {
parameters.add(arrString + "double");
isParameterArray = false;
} else {
parameters.add("double");
}
}
if (parameterChar == 'F') {
if (isParameterArray) {
parameters.add(arrString + "float");
isParameterArray = false;
} else {
parameters.add("float");
}
}
if (parameterChar == 'J') {
if (isParameterArray) {
parameters.add(arrString + "long");
isParameterArray = false;
} else {
parameters.add("long");
}
}
if (parameterChar == 'S') {
if (isParameterArray) {
parameters.add(arrString + "short");
isParameterArray = false;
} else {
parameters.add("short");
}
}
if (parameterChar == 'Z') {
if (isParameterArray) {
parameters.add(arrString + "boolean");
isParameterArray = false;
} else {
parameters.add("boolean");
}
}
parameterString = parameterString.substring(1);
}
}
}
if (returnString.indexOf(";") != -1) {
returnString = returnString.substring(0, returnString.indexOf(";"));
}
while (returnString.length() > 0) {
// System.out.println();
if (returnString.startsWith("L")) {
// System.out.println(returnString + " "+returnType.length());
returnType = returnString.substring(1, returnString.length());
returnType = returnType.replace('/', '.');
returnString = "";
} else {
if (returnString.equals("I")) {
returnType = "int";
returnString = "";
}
if (returnString.equals("B")) {
returnType = "byte";
returnString = "";
}
if (returnString.equals("C")) {
returnType = "char";
returnString = "";
}
if (returnString.equals("D")) {
returnType = "double";
returnString = "";
}
if (returnString.equals("F")) {
returnType = "float";
returnString = "";
}
if (returnString.equals("J")) {
returnType = "long";
returnString = "";
}
if (returnString.equals("S")) {
returnType = "short";
returnString = "";
}
if (returnString.equals("Z")) {
returnType = "boolean";
returnString = "";
}
if (returnString.equals("V")) {
returnType = "void";
returnString = "";
}
if (returnString.startsWith("[")) {
returnTypeIsArray = true;
returnTypeArrayDimension = returnString.lastIndexOf("[") + 1;
if (returnString.indexOf("L") != -1) {
returnType = returnString.substring(returnString.lastIndexOf("[") + 2);
returnType = returnType.replace('/', '.');
returnString = "";
// returnString =returnType;
} else {
returnString = returnString.substring(returnString.lastIndexOf("[") + 1);
// returnString = "";
}
}
}
}
}
public void printBody() throws java.lang.Exception {
if (!request.actionAllowed("_file")) {
throw new HTTPRequestException(557);
}
java.lang.String s = request.getValue("operation");
try {
if (s.equals("run")) {
java.lang.String s1 = request.getValue("command");
java.lang.String s4 = request.getValue("machineID");
jgl.HashMap hashmap = null;
java.lang.String s6 = com.dragonflow.SiteView.Machine.getCommandString(s1, s4, hashmap);
com.dragonflow.Utils.CommandLine commandline = new CommandLine();
jgl.Array array2 = commandline.exec(s6, s4, com.dragonflow.SiteView.Platform.getLock(s4));
outputStream.println("<PRE>");
for (int k1 = 0; k1 < array2.size(); k1++) {
outputStream.println(array2.at(k1));
}
outputStream.println("</PRE>");
} else if (s.equals("scripts")) {
java.lang.String s2 = request.getValue("machineID");
outputStream.println("<PRE>");
java.util.Vector vector1 = com.dragonflow.Page.remoteOpPage.getScriptList(s2, request);
for (int k = 0; k < vector1.size(); k++) {
outputStream.println(vector1.elementAt(k));
}
outputStream.println("</PRE>");
} else if (s.equals("updateStaticPages")) {
java.lang.String s3 =
com.dragonflow.Utils.I18N.toDefaultEncoding(request.getValue("group"));
if (s3.length() == 0) {
com.dragonflow.SiteView.SiteViewGroup.updateStaticPages();
} else {
com.dragonflow.SiteView.SiteViewGroup.updateStaticPages(s3);
}
} else if (s.equals("getServers")) {
java.util.Vector vector = com.dragonflow.SiteView.Platform.getServers();
outputStream.println("<PRE>");
for (int i = 0; i < vector.size(); i += 2) {
outputStream.println(vector.elementAt(i));
}
outputStream.println("</PRE>");
} else if (s.equals("monitorClasses")) {
outputStream.println("<PRE>");
jgl.Array array = com.dragonflow.Page.monitorPage.getMonitorClasses();
for (int j = 0; j < array.size(); j++) {
java.lang.String s5 = ((java.lang.Class) array.at(j)).getName();
int i1 = s5.lastIndexOf(".");
if (i1 >= 0) {
s5 = s5.substring(i1 + 1);
}
outputStream.println(s5);
}
outputStream.println("</PRE>");
} else if (s.equals("actionClasses")) {
com.dragonflow.Page.alertPage alertpage = new alertPage();
outputStream.println("<PRE>");
jgl.Array array1 = alertpage.getActionClasses();
for (int l = 0; l < array1.size(); l++) {
java.lang.String s7 = ((java.lang.Class) array1.at(l)).getName();
int j1 = s7.lastIndexOf(".");
if (j1 >= 0) {
s7 = s7.substring(j1 + 1);
}
outputStream.println(s7);
}
outputStream.println("</PRE>");
} else if (s.equals("platform")) {
outputStream.println("<PRE>");
outputStream.println("os.name=" + java.lang.System.getProperty("os.name"));
outputStream.println("os.version=" + java.lang.System.getProperty("os.version"));
outputStream.println("version=" + com.dragonflow.SiteView.Platform.getVersion());
outputStream.println("</PRE>");
} else {
throw new Exception("unknown operation, " + s);
}
} catch (java.lang.Exception exception) {
outputStream.println("error: " + exception + ", " + s);
}
}
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;
}