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IJ.java
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package ij;
import ij.gui.*;
import ij.process.*;
import ij.text.*;
import ij.io.*;
import ij.plugin.*;
import ij.plugin.filter.*;
import ij.util.Tools;
import ij.plugin.frame.Recorder;
import ij.plugin.frame.ThresholdAdjuster;
import ij.macro.Interpreter;
import ij.macro.MacroRunner;
import ij.measure.Calibration;
import ij.measure.ResultsTable;
import ij.measure.Measurements;
import java.awt.event.*;
import java.text.*;
import java.util.*;
import java.awt.*;
import java.applet.Applet;
import java.io.*;
import java.lang.reflect.*;
import java.net.*;
import javax.net.ssl.*;
import java.security.cert.*;
import java.security.KeyStore;
import java.nio.ByteBuffer;
import java.math.RoundingMode;
/** This class consists of static utility methods. */
public class IJ {
/** SansSerif, plain, 10-point font */
public static Font font10 = new Font("SansSerif", Font.PLAIN, 10);
/** SansSerif, plain, 12-point font */
public static Font font12 = ImageJ.SansSerif12;
/** SansSerif, plain, 14-point font */
public static Font font14 = ImageJ.SansSerif14;
/** Image display modes */
public static final int COMPOSITE=1, COLOR=2, GRAYSCALE=3;
/** @deprecated */
public static final String URL = "http://imagej.nih.gov/ij";
/** ImageJ website */
public static final String URL2 = "http://imagej.net/ij";
public static final int ALL_KEYS = -1;
/** Use setDebugMode(boolean) to enable/disable debug mode. */
public static boolean debugMode;
public static boolean hideProcessStackDialog;
public static final char micronSymbol = '\u00B5';
public static final char angstromSymbol = '\u00C5';
public static final char degreeSymbol = '\u00B0';
private static ImageJ ij;
private static java.applet.Applet applet;
private static ProgressBar progressBar;
private static TextPanel textPanel;
private static String osname, osarch;
private static boolean isMac, isWin, isLinux, is64Bit;
private static int javaVersion;
private static boolean controlDown, altDown, spaceDown, shiftDown;
private static boolean macroRunning;
private static Thread previousThread;
private static TextPanel logPanel;
private static ClassLoader classLoader;
private static boolean memMessageDisplayed;
private static long maxMemory;
private static boolean escapePressed;
private static boolean redirectErrorMessages;
private static boolean suppressPluginNotFoundError;
private static Hashtable commandTable;
private static Vector eventListeners = new Vector();
private static String lastErrorMessage;
private static Properties properties; private static DecimalFormat[] df;
private static DecimalFormat[] sf;
private static DecimalFormatSymbols dfs;
private static boolean trustManagerCreated;
private static String smoothMacro;
private static Interpreter macroInterpreter;
private static boolean protectStatusBar;
private static Thread statusBarThread;
static {
osname = System.getProperty("os.name");
isWin = osname.startsWith("Windows");
isMac = !isWin && osname.startsWith("Mac");
isLinux = osname.startsWith("Linux");
String version = System.getProperty("java.version");
if (version==null || version.length()<2)
version = "1.8";
if (version.startsWith("1.8"))
javaVersion = 8;
else if (version.charAt(0)=='1' && Character.isDigit(version.charAt(1)))
javaVersion = 10 + (version.charAt(1) - '0');
else if (version.charAt(0)=='2' && Character.isDigit(version.charAt(1)))
javaVersion = 20 + (version.charAt(1) - '0');
else if (version.startsWith("1.6"))
javaVersion = 6;
else if (version.startsWith("1.9")||version.startsWith("9"))
javaVersion = 9;
else if (version.startsWith("1.7"))
javaVersion = 7;
else
javaVersion = 8;
dfs = new DecimalFormatSymbols(Locale.US);
df = new DecimalFormat[10];
df[0] = new DecimalFormat("0", dfs);
df[1] = new DecimalFormat("0.0", dfs);
df[2] = new DecimalFormat("0.00", dfs);
df[3] = new DecimalFormat("0.000", dfs);
df[4] = new DecimalFormat("0.0000", dfs);
df[5] = new DecimalFormat("0.00000", dfs);
df[6] = new DecimalFormat("0.000000", dfs);
df[7] = new DecimalFormat("0.0000000", dfs);
df[8] = new DecimalFormat("0.00000000", dfs);
df[9] = new DecimalFormat("0.000000000", dfs);
df[0].setRoundingMode(RoundingMode.HALF_UP);
}
static void init(ImageJ imagej, Applet theApplet) {
ij = imagej;
applet = theApplet;
progressBar = ij.getProgressBar();
}
static void cleanup() {
ij=null; applet=null; progressBar=null; textPanel=null;
}
/**Returns a reference to the "ImageJ" frame.*/
public static ImageJ getInstance() {
return ij;
}
/**Enable/disable debug mode.*/
public static void setDebugMode(boolean b) {
debugMode = b;
LogStream.redirectSystem(debugMode);
}
/** Runs the macro contained in the string <code>macro</code>
on the current thread. Returns any string value returned by
the macro, null if the macro does not return a value, or
"[aborted]" if the macro was aborted due to an error. The
equivalent macro function is eval(). */
public static String runMacro(String macro) {
return runMacro(macro, "");
}
/** Runs the macro contained in the string <code>macro</code>
on the current thread. The optional string argument can be
retrieved in the called macro using the getArgument() macro
function. Returns any string value returned by the macro, null
if the macro does not return a value, or "[aborted]" if the
macro was aborted due to an error. */
public static String runMacro(String macro, String arg) {
Macro_Runner mr = new Macro_Runner();
return mr.runMacro(macro, arg);
}
/** Runs the specified macro or script file in the current thread.
The file is assumed to be in the macros folder
unless <code>name</code> is a full path.
The optional string argument (<code>arg</code>) can be retrieved in the called
macro or script using the getArgument() function.
Returns any string value returned by the macro, or null. Scripts always return null.
The equivalent macro function is runMacro(). */
public static String runMacroFile(String name, String arg) {
Macro_Runner mr = new Macro_Runner();
return mr.runMacroFile(name, arg);
}
/** Runs the specified macro file. */
public static String runMacroFile(String name) {
return runMacroFile(name, null);
}
/** Runs the specified plugin using the specified image. */
public static Object runPlugIn(ImagePlus imp, String className, String arg) {
if (imp!=null) {
ImagePlus temp = WindowManager.getTempCurrentImage();
WindowManager.setTempCurrentImage(imp);
Object o = runPlugIn("", className, arg);
WindowManager.setTempCurrentImage(temp);
return o;
} else
return runPlugIn(className, arg);
}
/** Runs the specified plugin and returns a reference to it. */
public static Object runPlugIn(String className, String arg) {
return runPlugIn("", className, arg);
}
/** Runs the specified plugin and returns a reference to it. */
public static Object runPlugIn(String commandName, String className, String arg) {
if (arg==null) arg = "";
if (IJ.debugMode)
IJ.log("runPlugIn: "+className+argument(arg));
// Load using custom classloader if this is a user
// plugin and we are not running as an applet
if (!className.startsWith("ij.") && applet==null)
return runUserPlugIn(commandName, className, arg, false);
Object thePlugIn=null;
try {
Class c = Class.forName(className);
thePlugIn = c.newInstance();
if (thePlugIn instanceof PlugIn)
((PlugIn)thePlugIn).run(arg);
else
new PlugInFilterRunner(thePlugIn, commandName, arg);
} catch (ClassNotFoundException e) {
if (!(className!=null && className.startsWith("ij.plugin.MacAdapter"))) {
log("Plugin or class not found: \"" + className + "\"\n(" + e+")");
String path = Prefs.getCustomPropsPath();
if (path!=null);
log("Error may be due to custom properties at " + path);
}
}
catch (InstantiationException e) {log("Unable to load plugin (ins)");}
catch (IllegalAccessException e) {log("Unable to load plugin, possibly \nbecause it is not public.");}
redirectErrorMessages = false;
return thePlugIn;
}
static Object runUserPlugIn(String commandName, String className, String arg, boolean createNewLoader) {
if (IJ.debugMode)
IJ.log("runUserPlugIn: "+className+", arg="+argument(arg));
if (applet!=null) return null;
if (createNewLoader)
classLoader = null;
ClassLoader loader = getClassLoader();
Object thePlugIn = null;
try {
thePlugIn = (loader.loadClass(className)).newInstance();
if (thePlugIn instanceof PlugIn)
((PlugIn)thePlugIn).run(arg);
else if (thePlugIn instanceof PlugInFilter)
new PlugInFilterRunner(thePlugIn, commandName, arg);
}
catch (ClassNotFoundException e) {
if (className.startsWith("macro:"))
runMacro(className.substring(6));
else if (className.contains("_") && !suppressPluginNotFoundError)
error("Plugin or class not found: \"" + className + "\"\n(" + e+")");
}
catch (NoClassDefFoundError e) {
int dotIndex = className.indexOf('.');
if (dotIndex>=0 && className.contains("_")) {
// rerun plugin after removing folder name
if (debugMode) IJ.log("runUserPlugIn: rerunning "+className);
return runUserPlugIn(commandName, className.substring(dotIndex+1), arg, createNewLoader);
}
if (className.contains("_") && !suppressPluginNotFoundError)
error("Run User Plugin", "Class not found while attempting to run \"" + className + "\"\n \n " + e);
}
catch (InstantiationException e) {error("Unable to load plugin (ins)");}
catch (IllegalAccessException e) {error("Unable to load plugin, possibly \nbecause it is not public.");}
if (thePlugIn!=null && !"HandleExtraFileTypes".equals(className))
redirectErrorMessages = false;
suppressPluginNotFoundError = false;
return thePlugIn;
}
private static String argument(String arg) {
return arg!=null && !arg.equals("") && !arg.contains("\n")?"(\""+arg+"\")":"";
}
static void wrongType(int capabilities, String cmd) {
String s = "\""+cmd+"\" requires an image of type:\n \n";
if ((capabilities&PlugInFilter.DOES_8G)!=0) s += " 8-bit grayscale\n";
if ((capabilities&PlugInFilter.DOES_8C)!=0) s += " 8-bit color\n";
if ((capabilities&PlugInFilter.DOES_16)!=0) s += " 16-bit grayscale\n";
if ((capabilities&PlugInFilter.DOES_32)!=0) s += " 32-bit (float) grayscale\n";
if ((capabilities&PlugInFilter.DOES_RGB)!=0) s += " RGB color\n";
error(s);
}
/** Runs a menu command on a separete thread and returns immediately. */
public static void doCommand(String command) {
new Executer(command, null);
}
/** Runs a menu command on a separete thread, using the specified image. */
public static void doCommand(ImagePlus imp, String command) {
new Executer(command, imp);
}
/** Runs an ImageJ command. Does not return until
the command has finished executing. To avoid "image locked",
errors, plugins that call this method should implement
the PlugIn interface instead of PlugInFilter. */
public static void run(String command) {
run(command, null);
}
/** Runs an ImageJ command, with options that are passed to the
GenericDialog and OpenDialog classes. Does not return until
the command has finished executing. To generate run() calls,
start the recorder (Plugins/Macro/Record) and run commands
from the ImageJ menu bar.
*/
public static void run(String command, String options) {
//IJ.log("run1: "+command+" "+Thread.currentThread().hashCode()+" "+options);
if (ij==null && Menus.getCommands()==null)
init();
Macro.abort = false;
Macro.setOptions(options);
Thread thread = Thread.currentThread();
if (previousThread==null || thread!=previousThread) {
String name = thread.getName();
if (!name.startsWith("Run$_"))
thread.setName("Run$_"+name);
}
command = convert(command);
previousThread = thread;
macroRunning = true;
Executer e = new Executer(command);
e.run();
macroRunning = false;
Macro.setOptions(null);
testAbort();
macroInterpreter = null;
//IJ.log("run2: "+command+" "+Thread.currentThread().hashCode());
}
/** The macro interpreter uses this method to run commands. */
public static void run(Interpreter interpreter, String command, String options) {
macroInterpreter = interpreter;
run(command, options);
macroInterpreter = null;
}
/** Converts commands that have been renamed so
macros using the old names continue to work. */
private static String convert(String command) {
if (commandTable==null) {
commandTable = new Hashtable(30);
commandTable.put("New...", "Image...");
commandTable.put("Threshold", "Make Binary");
commandTable.put("Display...", "Appearance...");
commandTable.put("Start Animation", "Start Animation [\\]");
commandTable.put("Convert Images to Stack", "Images to Stack");
commandTable.put("Convert Stack to Images", "Stack to Images");
commandTable.put("Convert Stack to RGB", "Stack to RGB");
commandTable.put("Convert to Composite", "Make Composite");
commandTable.put("RGB Split", "Split Channels");
commandTable.put("RGB Merge...", "Merge Channels...");
commandTable.put("Channels...", "Channels Tool...");
commandTable.put("New... ", "Table...");
commandTable.put("Arbitrarily...", "Rotate... ");
commandTable.put("Measurements...", "Results... ");
commandTable.put("List Commands...", "Find Commands...");
commandTable.put("Capture Screen ", "Capture Screen");
commandTable.put("Add to Manager ", "Add to Manager");
commandTable.put("In", "In [+]");
commandTable.put("Out", "Out [-]");
commandTable.put("Enhance Contrast", "Enhance Contrast...");
commandTable.put("XY Coodinates... ", "XY Coordinates... ");
commandTable.put("Statistics...", "Statistics");
commandTable.put("Channels Tool... ", "Channels Tool...");
commandTable.put("Profile Plot Options...", "Plots...");
commandTable.put("AuPbSn 40 (56K)", "AuPbSn 40");
commandTable.put("Bat Cochlea Volume (19K)", "Bat Cochlea Volume");
commandTable.put("Bat Cochlea Renderings (449K)", "Bat Cochlea Renderings");
commandTable.put("Blobs (25K)", "Blobs");
commandTable.put("Boats (356K)", "Boats");
commandTable.put("Cardio (768K, RGB DICOM)", "Cardio (RGB DICOM)");
commandTable.put("Cell Colony (31K)", "Cell Colony");
commandTable.put("Clown (14K)", "Clown");
commandTable.put("Confocal Series (2.2MB)", "Confocal Series");
commandTable.put("CT (420K, 16-bit DICOM)", "CT (16-bit DICOM)");
commandTable.put("Dot Blot (7K)", "Dot Blot");
commandTable.put("Embryos (42K)", "Embryos");
commandTable.put("Fluorescent Cells (400K)", "Fluorescent Cells");
commandTable.put("Fly Brain (1MB)", "Fly Brain");
commandTable.put("Gel (105K)", "Gel");
commandTable.put("HeLa Cells (1.3M, 48-bit RGB)", "HeLa Cells (48-bit RGB)");
commandTable.put("Leaf (36K)", "Leaf");
commandTable.put("Line Graph (21K)", "Line Graph");
commandTable.put("Mitosis (26MB, 5D stack)", "Mitosis (5D stack)");
commandTable.put("MRI Stack (528K)", "MRI Stack");
commandTable.put("M51 Galaxy (177K, 16-bits)", "M51 Galaxy (16-bits)");
commandTable.put("Neuron (1.6M, 5 channels)", "Neuron (5 channels)");
commandTable.put("Nile Bend (1.9M)", "Nile Bend");
commandTable.put("Organ of Corti (2.8M, 4D stack)", "Organ of Corti (4D stack)");
commandTable.put("Particles (75K)", "Particles");
commandTable.put("T1 Head (2.4M, 16-bits)", "T1 Head (16-bits)");
commandTable.put("T1 Head Renderings (736K)", "T1 Head Renderings");
commandTable.put("TEM Filter (112K)", "TEM Filter");
commandTable.put("Tree Rings (48K)", "Tree Rings");
}
String command2 = (String)commandTable.get(command);
if (command2!=null)
return command2;
else
return command;
}
/** Runs an ImageJ command using the specified image and options.
To generate run() calls, start the recorder (Plugins/Macro/Record)
and run commands from the ImageJ menu bar.*/
public static void run(ImagePlus imp, String command, String options) {
if (ij==null && Menus.getCommands()==null)
init();
if (imp!=null) {
ImagePlus temp = WindowManager.getTempCurrentImage();
WindowManager.setTempCurrentImage(imp);
run(command, options);
WindowManager.setTempCurrentImage(temp);
} else
run(command, options);
}
static void init() {
Menus m = new Menus(null, null);
Prefs.load(m, null);
m.addMenuBar();
}
private static void testAbort() {
if (Macro.abort)
abort();
}
/** Returns true if the run(), open() or newImage() method is executing. */
public static boolean macroRunning() {
return macroRunning;
}
/** Returns true if a macro is running, or if the run(), open()
or newImage() method is executing. */
public static boolean isMacro() {
return macroRunning || Interpreter.getInstance()!=null;
}
/**Returns the Applet that created this ImageJ or null if running as an application.*/
public static java.applet.Applet getApplet() {
return applet;
}
/**Displays a message in the ImageJ status bar. If 's' starts
with '!', subsequent showStatus() calls in the current
thread (without "!" in the message) are suppressed. */
public static void showStatus(String s) {
if ((Interpreter.getInstance()==null&&statusBarThread==null)
|| (statusBarThread!=null&&Thread.currentThread()!=statusBarThread))
protectStatusBar(false);
boolean doProtect = s.startsWith("!"); // suppress subsequent showStatus() calls
if (doProtect) {
protectStatusBar(true);
statusBarThread = Thread.currentThread();
s = s.substring(1);
}
if (doProtect || !protectStatusBar) {
if (ij!=null)
ij.showStatus(s);
ImagePlus imp = WindowManager.getCurrentImage();
ImageCanvas ic = imp!=null?imp.getCanvas():null;
if (ic!=null)
ic.setShowCursorStatus(s.length()==0?true:false);
}
}
/**Displays a message in the status bar and flashes
* either the status bar or the active image.<br>
* See: http://wsr.imagej.net/macros/FlashingStatusMessages.txt
*/
public static void showStatus(String message, String options) {
showStatus(message);
if (options==null)
return;
options = options.replace("flash", "");
options = options.replace("ms", "");
Color optionalColor = null;
int index1 = options.indexOf("#");
if (index1>=0) { // hex color?
int index2 = options.indexOf(" ", index1);
if (index2==-1) index2 = options.length();
String hexColor = options.substring(index1, index2);
optionalColor = Colors.decode(hexColor, null);
options = options.replace(hexColor, "");
}
if (optionalColor==null) { // "red", "green", etc.
for (String c : Colors.colors) {
if (options.contains(c)) {
optionalColor = Colors.getColor(c, ImageJ.backgroundColor);
options = options.replace(c, "");
break;
}
}
}
boolean flashImage = options.contains("image");
Color defaultColor = new Color(255,255,245);
int defaultDelay = 500;
ImagePlus imp = WindowManager.getCurrentImage();
if (flashImage) {
options = options.replace("image", "");
if (imp!=null && imp.getWindow()!=null) {
defaultColor = Color.black;
defaultDelay = 100;
}
else
flashImage = false;
}
Color color = optionalColor!=null?optionalColor:defaultColor;
int delay = (int)Tools.parseDouble(options, defaultDelay);
if (delay>8000)
delay = 8000;
String colorString = null;
ImageJ ij = IJ.getInstance();
if (flashImage) {
Color previousColor = imp.getWindow().getBackground();
imp.getWindow().setBackground(color);
if (delay>0) {
wait(delay);
imp.getWindow().setBackground(previousColor);
}
} else if (ij!=null) {
ij.getStatusBar().setBackground(color);
wait(delay);
ij.getStatusBar().setBackground(ij.backgroundColor);
}
}
/**
* @deprecated
* replaced by IJ.log(), ResultsTable.setResult() and TextWindow.append().
* There are examples at
* http://imagej.nih.gov/ij/plugins/sine-cosine.html
*/
public static void write(String s) {
if (textPanel==null && ij!=null)
showResults();
if (textPanel!=null)
textPanel.append(s);
else
System.out.println(s);
}
private static void showResults() {
TextWindow resultsWindow = new TextWindow("Results", "", 400, 250);
textPanel = resultsWindow.getTextPanel();
textPanel.setResultsTable(Analyzer.getResultsTable());
}
public static synchronized void log(String s) {
if (s==null) return;
if (logPanel==null && ij!=null) {
TextWindow logWindow = new TextWindow("Log", "", 400, 250);
logPanel = logWindow.getTextPanel();
logPanel.setFont(new Font("SansSerif", Font.PLAIN, 16));
}
if (logPanel!=null) {
if (s.startsWith("\\"))
handleLogCommand(s);
else {
if (s.endsWith("\n")) {
if (s.equals("\n\n"))
s= "\n \n ";
else if (s.endsWith("\n\n"))
s = s.substring(0, s.length()-2)+"\n \n ";
else
s = s+" ";
}
logPanel.append(s);
}
} else {
LogStream.redirectSystem(false);
System.out.println(s);
}
}
static void handleLogCommand(String s) {
if (s.equals("\\Closed"))
logPanel = null;
else if (s.startsWith("\\Update:")) {
int n = logPanel.getLineCount();
String s2 = s.substring(8, s.length());
if (n==0)
logPanel.append(s2);
else
logPanel.setLine(n-1, s2);
} else if (s.startsWith("\\Update")) {
int cindex = s.indexOf(":");
if (cindex==-1)
{logPanel.append(s); return;}
String nstr = s.substring(7, cindex);
int line = (int)Tools.parseDouble(nstr, -1);
if (line<0 || line>25)
{logPanel.append(s); return;}
int count = logPanel.getLineCount();
while (line>=count) {
log("");
count++;
}
String s2 = s.substring(cindex+1, s.length());
logPanel.setLine(line, s2);
} else if (s.equals("\\Clear")) {
logPanel.clear();
} else if (s.startsWith("\\Heading:")) {
logPanel.updateColumnHeadings(s.substring(10));
} else if (s.equals("\\Close")) {
Frame f = WindowManager.getFrame("Log");
if (f!=null && (f instanceof TextWindow))
((TextWindow)f).close();
} else
logPanel.append(s);
}
/** Returns the contents of the Log window or null if the Log window is not open. */
public static synchronized String getLog() {
if (logPanel==null || ij==null)
return null;
else
return logPanel.getText();
}
/** Clears the "Results" window and sets the column headings to
those in the tab-delimited 'headings' String. Writes to
System.out.println if the "ImageJ" frame is not present.*/
public static void setColumnHeadings(String headings) {
if (textPanel==null && ij!=null)
showResults();
if (textPanel!=null)
textPanel.setColumnHeadings(headings);
else
System.out.println(headings);
}
/** Returns true if the "Results" window is open. */
public static boolean isResultsWindow() {
return textPanel!=null;
}
/** Renames a results window. */
public static void renameResults(String title) {
Frame frame = WindowManager.getFrontWindow();
if (frame!=null && (frame instanceof TextWindow)) {
TextWindow tw = (TextWindow)frame;
if (tw.getResultsTable()==null) {
IJ.error("Rename", "\""+tw.getTitle()+"\" is not a results table");
return;
}
tw.rename(title);
} else if (isResultsWindow()) {
TextPanel tp = getTextPanel();
TextWindow tw = (TextWindow)tp.getParent();
tw.rename(title);
}
}
/** Changes the name of a table window from 'oldTitle' to 'newTitle'. */
public static void renameResults(String oldTitle, String newTitle) {
Frame frame = WindowManager.getFrame(oldTitle);
if (frame==null) {
error("Rename", "\""+oldTitle+"\" not found");
return;
} else if (frame instanceof TextWindow) {
TextWindow tw = (TextWindow)frame;
if (tw.getResultsTable()==null) {
error("Rename", "\""+oldTitle+"\" is not a table");
return;
}
tw.rename(newTitle);
} else
error("Rename", "\""+oldTitle+"\" is not a table");
}
/** Deletes 'row1' through 'row2' of the "Results" window, where
'row1' and 'row2' must be in the range 0-Analyzer.getCounter()-1. */
public static void deleteRows(int row1, int row2) {
ResultsTable rt = Analyzer.getResultsTable();
int tableSize = rt.size();
rt.deleteRows(row1, row2);
ImagePlus imp = WindowManager.getCurrentImage();
if (imp!=null)
Overlay.updateTableOverlay(imp, row1, row2, tableSize);
rt.show("Results");
}
/** Returns a measurement result, where 'measurement' is "Area",
* "Mean", "StdDev", "Mode", "Min", "Max", "X", "Y", "XM", "YM",
* "Perim.", "BX", "BY", "Width", "Height", "Major", "Minor", "Angle",
* "Circ.", "Feret", "IntDen", "Median", "Skew", "Kurt", "%Area",
* "RawIntDen", "Ch", "Slice", "Frame", "FeretX", "FeretY",
* "FeretAngle", "MinFeret", "AR", "Round", "Solidity", "MinThr"
* or "MaxThr". Add " raw" to the argument to disable calibration,
* for example IJ.getValue("Mean raw"). Add " limit" to enable
* the "limit to threshold" option.
*/
public static double getValue(ImagePlus imp, String measurement) {
String options = "";
int index = measurement.indexOf(" ");
if (index>0) {
if (index<measurement.length()-1)
options = measurement.substring(index+1, measurement.length());
measurement = measurement.substring(0, index);
}
int measurements = Measurements.ALL_STATS + Measurements.SLICE;
if (options.contains("limit"))
measurements += Measurements.LIMIT;
Calibration cal = null;
if (options.contains("raw")) {
cal = imp.getCalibration();
imp.setCalibration(null);
}
ResultsTable rt = new ResultsTable();
Analyzer analyzer = new Analyzer(imp, measurements, rt);
analyzer.measure();
double value = Double.NaN;
try {
value = rt.getValue(measurement, 0);
} catch (Exception e) {};
if (cal!=null)
imp.setCalibration(cal);
return value;
}
/** Returns a reference to the "Results" window TextPanel.
Opens the "Results" window if it is currently not open.
Returns null if the "ImageJ" window is not open. */
public static TextPanel getTextPanel() {
if (textPanel==null && ij!=null)
showResults();
return textPanel;
}
/** TextWindow calls this method with a null argument when the "Results" window is closed. */
public static void setTextPanel(TextPanel tp) {
textPanel = tp;
}
/**Displays a "no images are open" dialog box.*/
public static void noImage() {
String msg = "There are no images open";
if (macroInterpreter!=null) {
macroInterpreter.abort(msg);
macroInterpreter = null;
} else
error("No Image", msg);
}
/** Displays an "out of memory" message to the "Log" window. */
public static void outOfMemory(String name) {
Undo.reset();
System.gc();
lastErrorMessage = "out of memory";
String tot = Runtime.getRuntime().maxMemory()/1048576L+"MB";
if (!memMessageDisplayed)
log(">>>>>>>>>>>>>>>>>>>>>>>>>>>");
log("<Out of memory>");
if (!memMessageDisplayed) {
log("<All available memory ("+tot+") has been>");
log("<used. To make more available, use the>");
log("<Edit>Options>Memory & Threads command.>");
log(">>>>>>>>>>>>>>>>>>>>>>>>>>>");
memMessageDisplayed = true;
}
Macro.abort();
}
/** Updates the progress bar, where 0<=progress<=1.0. The progress bar is
not shown in BatchMode and erased if progress>=1.0. The progress bar is
updated only if more than 90 ms have passes since the last call. Does nothing
if the ImageJ window is not present. */
public static void showProgress(double progress) {
if (progressBar!=null) progressBar.show(progress, false);
}
/** Updates the progress bar, where the length of the bar is set to
* (<code>currentValue+1)/finalValue</code> of the maximum bar length.
* The bar is erased if <code>currentValue>=finalValue</code>.
* The bar is updated only if more than 90 ms have passed since the
* last call. Displays subordinate progress bars as dots if
* 'currentIndex' is negative (example: Plugins/Utilities/Benchmark).
*/
public static void showProgress(int currentIndex, int finalIndex) {
if (progressBar!=null) {
progressBar.show(currentIndex, finalIndex);
if (currentIndex==finalIndex)
progressBar.setBatchMode(false);
}
}
/** Displays a message in a dialog box titled "Message".
Writes the Java console if ImageJ is not present. */
public static void showMessage(String msg) {
showMessage("Message", msg);
}
/** Displays a message in a dialog box with the specified title.
Displays HTML formatted text if 'msg' starts with "<html>".
There are examples at
"http://imagej.nih.gov/ij/macros/HtmlDialogDemo.txt".
Writes to the Java console if ImageJ is not present. */
public static void showMessage(String title, String msg) {
if (ij!=null) {
if (msg!=null && (msg.startsWith("<html>")||msg.startsWith("<HTML>"))) {
HTMLDialog hd = new HTMLDialog(title, msg);
if (isMacro() && hd.escapePressed())
throw new RuntimeException(Macro.MACRO_CANCELED);
} else {
MessageDialog md = new MessageDialog(ij, title, msg);
if (isMacro() && md.escapePressed())
throw new RuntimeException(Macro.MACRO_CANCELED);
}
} else
System.out.println(msg);
}
/** Displays a message in a dialog box titled "ImageJ". If a
macro or JavaScript is running, it is aborted. Writes to the
Java console if the ImageJ window is not present.*/
public static void error(String msg) {
error(null, msg);
if (Thread.currentThread().getName().endsWith("JavaScript"))
throw new RuntimeException(Macro.MACRO_CANCELED);
else
Macro.abort();
}
/** Displays a message in a dialog box with the specified title. If a
macro or JavaScript is running, it is aborted. Writes to the
Java console if the ImageJ window is not present. */
public static void error(String title, String msg) {
if (macroInterpreter!=null) {
macroInterpreter.abort(msg);
macroInterpreter = null;
return;
}
if (msg!=null && msg.endsWith(Macro.MACRO_CANCELED))
return;
String title2 = title!=null?title:"ImageJ";
boolean abortMacro = title!=null;
lastErrorMessage = msg;
if (redirectErrorMessages) {
IJ.log(title2 + ": " + msg);
if (abortMacro && (title.contains("Open")||title.contains("Reader")))
abortMacro = false;
} else
showMessage(title2, msg);
redirectErrorMessages = false;
if (abortMacro)
Macro.abort();
}
/** Aborts any currently running JavaScript, or use IJ.error(string)
to abort a JavaScript with a message. */
public static void exit() {
if (Thread.currentThread().getName().endsWith("JavaScript"))
throw new RuntimeException(Macro.MACRO_CANCELED);
}
/**
* Returns the last error message written by IJ.error() or null if there
* was no error since the last time this method was called.
* @see #error(String)
*/
public static String getErrorMessage() {
String msg = lastErrorMessage;
lastErrorMessage = null;
return msg;
}
/** Displays a message in a dialog box with the specified title.
Returns false if the user pressed "Cancel". */
public static boolean showMessageWithCancel(String title, String msg) {
GenericDialog gd = new GenericDialog(title);
gd.addMessage(msg);
gd.showDialog();
return !gd.wasCanceled();
}
public static final int CANCELED = Integer.MIN_VALUE;
/** Allows the user to enter a number in a dialog box. Returns the
value IJ.CANCELED (-2,147,483,648) if the user cancels the dialog box.
Returns 'defaultValue' if the user enters an invalid number. */
public static double getNumber(String prompt, double defaultValue) {
GenericDialog gd = new GenericDialog("");
int decimalPlaces = (int)defaultValue==defaultValue?0:2;
gd.addNumericField(prompt, defaultValue, decimalPlaces);
gd.showDialog();
if (gd.wasCanceled())
return CANCELED;
double v = gd.getNextNumber();
if (gd.invalidNumber())
return defaultValue;
else
return v;
}
/** Allows the user to enter a string in a dialog box. Returns
"" if the user cancels the dialog box. */
public static String getString(String prompt, String defaultString) {
GenericDialog gd = new GenericDialog("");
gd.addStringField(prompt, defaultString, 20);
gd.showDialog();
if (gd.wasCanceled())
return "";
return gd.getNextString();
}
/**Delays 'msecs' milliseconds.*/
public static void wait(int msecs) {
try {Thread.sleep(msecs);}
catch (InterruptedException e) { }
}
/** Emits an audio beep. */
public static void beep() {
java.awt.Toolkit.getDefaultToolkit().beep();
}
/** Returns a string something like "64K of 256MB (25%)"
* that shows how much of the available memory is in use.
* This is the string displayed when the user clicks in the
* status bar.
*/
public static String freeMemory() {
long inUse = currentMemory();
String inUseStr = inUse<10000*1024?inUse/1024L+"K":inUse/1048576L+"MB";
String maxStr="";
long max = maxMemory();
if (max>0L) {
double percent = inUse*100/max;
maxStr = " of "+max/1048576L+"MB ("+(percent<1.0?"<1":d2s(percent,0)) + "%)";
}
return inUseStr + maxStr;
}
/** Returns the amount of memory currently being used by ImageJ. */
public static long currentMemory() {
long freeMem = Runtime.getRuntime().freeMemory();
long totMem = Runtime.getRuntime().totalMemory();
return totMem-freeMem;
}
/** Returns the maximum amount of memory available to ImageJ or
zero if ImageJ is unable to determine this limit. */
public static long maxMemory() {
if (maxMemory==0L) {
Memory mem = new Memory();
maxMemory = mem.getMemorySetting();
if (maxMemory==0L) maxMemory = mem.maxMemory();
}
return maxMemory;
}
public static void showTime(ImagePlus imp, long start, String str) {
showTime(imp, start, str, 1);
}
public static void showTime(ImagePlus imp, long start, String str, int nslices) {
if (Interpreter.isBatchMode())
return;
double seconds = (System.currentTimeMillis()-start)/1000.0;
if (seconds<=0.5 && macroRunning())
return;
double pixels = (double)imp.getWidth() * imp.getHeight();
double rate = pixels*nslices/seconds;
String str2;
if (rate>1000000000.0)
str2 = "";
else if (rate<1000000.0)
str2 = ", "+d2s(rate,0)+" pixels/second";
else
str2 = ", "+d2s(rate/1000000.0,1)+" million pixels/second";
showStatus(str+seconds+" seconds"+str2);
}
/** Experimental */
public static String time(ImagePlus imp, long startNanoTime) {
double planes = imp.getStackSize();
double seconds = (System.nanoTime()-startNanoTime)/1000000000.0;
double mpixels = imp.getWidth()*imp.getHeight()*planes/1000000.0;
String time = seconds<1.0?d2s(seconds*1000.0,0)+" ms":d2s(seconds,1)+" seconds";
return time+", "+d2s(mpixels/seconds,1)+" million pixels/second";
}
/** Converts a number to a formatted string using
2 digits to the right of the decimal point. */
public static String d2s(double n) {
return d2s(n, 2);
}
/** Converts a number to a rounded formatted string.
The 'decimalPlaces' argument specifies the number of
digits to the right of the decimal point (0-9). Uses
scientific notation if 'decimalPlaces is negative. */
public static String d2s(double n, int decimalPlaces) {
if (Double.isNaN(n)||Double.isInfinite(n))