/** * 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; }