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.macro.Interpreter;
import ij.measure.Calibration;
import ij.measure.ResultsTable;
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.*;
/** This class consists of static utility methods. */
public class IJ {
public static final String URL = "http://imagej.nih.gov/ij";
public static final int ALL_KEYS = -1;
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, isJava2, isJava14, isJava15, isJava16, isJava17, isLinux, isVista, is64Bit;
private static boolean controlDown, altDown, spaceDown, shiftDown;
private static boolean macroRunning;
private static Thread previousThread;
private static TextPanel logPanel;
private static boolean checkForDuplicatePlugins = true;
private static ClassLoader classLoader;
private static boolean memMessageDisplayed;
private static long maxMemory;
private static boolean escapePressed;
private static boolean redirectErrorMessages, redirectErrorMessages2;
private static boolean suppressPluginNotFoundError;
private static Hashtable commandTable;
private static Vector eventListeners = new Vector();
static {
osname = System.getProperty("os.name");
isWin = osname.startsWith("Windows");
isMac = !isWin && osname.startsWith("Mac");
isLinux = osname.startsWith("Linux");
isVista = isWin && (osname.indexOf("Vista")!=-1||osname.indexOf(" 7")!=-1);
String version = System.getProperty("java.version").substring(0,3);
if (version.compareTo("2.9")<=0) { // JVM on Sharp Zaurus PDA claims to be "3.1"!
isJava2 = version.compareTo("1.1")>0;
isJava14 = version.compareTo("1.3")>0;
isJava15 = version.compareTo("1.4")>0;
isJava16 = version.compareTo("1.5")>0;
isJava17 = version.compareTo("1.6")>0;
}
}
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;
}
/** Runs the macro contained in the string <code>macro</code>.
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>.
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. ".txt" is
added if <code>name</code> does not have an extension.
The optional string argument (<code>arg</code>) can be retrieved in the called
macro or script (v1.42k or later) 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) {
if (ij==null && Menus.getCommands()==null)
init();
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. */
static Object runPlugIn(String commandName, String className, String arg) {
if (IJ.debugMode)
IJ.log("runPlugin: "+className+" "+arg);
if (arg==null) 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 (IJ.getApplet()==null)
log("Plugin or class not found: \"" + className + "\"\n(" + e+")");
}
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 (applet!=null) return null;
if (checkForDuplicatePlugins) {
// check for duplicate classes and jars in the plugins folder
IJ.runPlugIn("ij.plugin.ClassChecker", "");
checkForDuplicatePlugins = false;
}
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.indexOf('_')!=-1 && !suppressPluginNotFoundError)
error("Plugin or class not found: \"" + className + "\"\n(" + e+")");
}
catch (NoClassDefFoundError e) {
int dotIndex = className.indexOf('.');
if (dotIndex >= 0)
return runUserPlugIn(commandName, className.substring(dotIndex + 1), arg, createNewLoader);
if (className.indexOf('_')!=-1 && !suppressPluginNotFoundError)
error("Plugin or class not found: \"" + className + "\"\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 (redirectErrorMessages && !"HandleExtraFileTypes".equals(className))
redirectErrorMessages = false;
suppressPluginNotFoundError = false;
return thePlugIn;
}
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);
}
/** Starts executing a menu command in a separete thread and returns immediately. */
public static void doCommand(String command) {
if (ij!=null)
ij.doCommand(command);
}
/** 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. */
public static void run(String command, String options) {
//IJ.log("run1: "+command+" "+Thread.currentThread().hashCode());
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();
//IJ.log("run2: "+command+" "+Thread.currentThread().hashCode());
}
/** 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(23); // initial capacity should be increased as needed
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("New HyperStack...", "New Hyperstack...");
commandTable.put("Stack to HyperStack...", "Stack to Hyperstack...");
commandTable.put("HyperStack to Stack", "Hyperstack to Stack");
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 [-]");
}
String command2 = (String)commandTable.get(command);
if (command2!=null)
return command2;
else
return command;
}
/** Runs an ImageJ command using the specified image and options. */
public static void run(ImagePlus imp, String command, String options) {
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.*/
public static void showStatus(String s) {
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);
}
/**
* @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
logPanel.append(s);
} else
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.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.getTextPanel().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);
}
}
/** Deletes 'row1' through 'row2' of the "Results" window. Arguments
must be in the range 0-Analyzer.getCounter()-1. */
public static void deleteRows(int row1, int row2) {
int n = row2 - row1 + 1;
ResultsTable rt = Analyzer.getResultsTable();
for (int i=row1; i<row1+n; i++)
rt.deleteRow(row1);
rt.show("Results");
}
/** 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() {
error("No Image", "There are no images open.");
}
/** Displays an "out of memory" message to the "Log" window. */
public static void outOfMemory(String name) {
Undo.reset();
System.gc();
String tot = Runtime.getRuntime().totalMemory()/1048576L+"MB";
if (!memMessageDisplayed)
log(">>>>>>>>>>>>>>>>>>>>>>>>>>>");
log("<Out of memory>");
if (!memMessageDisplayed) {
log("<All available memory ("+tot+") has been>");
log("<used. Instructions for making more>");
log("<available can be found in the \"Memory\" >");
log("<sections of the installation notes at>");
log("<"+IJ.URL+"/docs/install/>");
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.
Does nothing if the ImageJ window is not present. */
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.
Writes 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>"))
new HTMLDialog(title, msg);
else
new MessageDialog(ij, title, msg);
} else
System.out.println(msg);
}
/** Displays a message in a dialog box titled "ImageJ". If a
macro 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 is running, it is aborted. Writes to the Java
console if ImageJ is not present. */
public static void error(String title, String msg) {
String title2 = title!=null?title:"ImageJ";
boolean abortMacro = title!=null;
if (redirectErrorMessages || redirectErrorMessages2) {
IJ.log(title2 + ": " + msg);
if (abortMacro && (title.equals("Opener")||title.equals("Open URL")||title.equals("DicomDecoder")))
abortMacro = false;
} else
showMessage(title2, msg);
redirectErrorMessages = false;
if (abortMacro) Macro.abort();
}
/** 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();
}
/** Runs the garbage collector and 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;
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);
}
private static DecimalFormat[] df;
private static DecimalFormat[] sf;
private static DecimalFormatSymbols dfs;
/** 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))
return ""+n;
if (n==Float.MAX_VALUE) // divide by 0 in FloatProcessor
return "3.4e38";
double np = n;
if (n<0.0) np = -n;
if (df==null) {
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);
}
if (decimalPlaces<0) {
decimalPlaces = -decimalPlaces;
if (decimalPlaces>9) decimalPlaces=9;
if (sf==null) {
sf = new DecimalFormat[10];
sf[1] = new DecimalFormat("0.0E0",dfs);
sf[2] = new DecimalFormat("0.00E0",dfs);
sf[3] = new DecimalFormat("0.000E0",dfs);
sf[4] = new DecimalFormat("0.0000E0",dfs);
sf[5] = new DecimalFormat("0.00000E0",dfs);
sf[6] = new DecimalFormat("0.000000E0",dfs);
sf[7] = new DecimalFormat("0.0000000E0",dfs);
sf[8] = new DecimalFormat("0.00000000E0",dfs);
sf[9] = new DecimalFormat("0.000000000E0",dfs);
}
return sf[decimalPlaces].format(n); // use scientific notation
}
if (decimalPlaces<0) decimalPlaces = 0;
if (decimalPlaces>9) decimalPlaces = 9;
return df[decimalPlaces].format(n);
}
/** Pad 'n' with leading zeros to the specified number of digits. */
public static String pad(int n, int digits) {
String str = ""+n;
while (str.length()<digits)
str = "0"+str;
return str;
}
/** Adds the specified class to a Vector to keep it from being garbage
collected, which would cause the classes static fields to be reset.
Probably not needed with Java 1.2 or later. */
public static void register(Class c) {
if (ij!=null) ij.register(c);
}
/** Returns true if the space bar is down. */
public static boolean spaceBarDown() {
return spaceDown;
}
/** Returns true if the control key is down. */
public static boolean controlKeyDown() {
return controlDown;
}
/** Returns true if the alt key is down. */
public static boolean altKeyDown() {
return altDown;
}
/** Returns true if the shift key is down. */
public static boolean shiftKeyDown() {
return shiftDown;
}
public static void setKeyDown(int key) {
if (debugMode) IJ.log("setKeyDown: "+key);
switch (key) {
case KeyEvent.VK_CONTROL:
controlDown=true;
break;
case KeyEvent.VK_META:
if (isMacintosh()) controlDown=true;
break;
case KeyEvent.VK_ALT:
altDown=true;
break;
case KeyEvent.VK_SHIFT:
shiftDown=true;
if (debugMode) beep();
break;
case KeyEvent.VK_SPACE: {
spaceDown=true;
ImageWindow win = WindowManager.getCurrentWindow();
if (win!=null) win.getCanvas().setCursor(-1,-1,-1, -1);
break;
}
case KeyEvent.VK_ESCAPE: {
escapePressed = true;
break;
}
}
}
public static void setKeyUp(int key) {
if (debugMode) IJ.log("setKeyUp: "+key);
switch (key) {
case KeyEvent.VK_CONTROL: controlDown=false; break;
case KeyEvent.VK_META: if (isMacintosh()) controlDown=false; break;
case KeyEvent.VK_ALT: altDown=false; break;
case KeyEvent.VK_SHIFT: shiftDown=false; if (debugMode) beep(); break;
case KeyEvent.VK_SPACE:
spaceDown=false;
ImageWindow win = WindowManager.getCurrentWindow();
if (win!=null) win.getCanvas().setCursor(-1,-1,-1,-1);
break;
case ALL_KEYS:
shiftDown=controlDown=altDown=spaceDown=false;
break;
}
}
public static void setInputEvent(InputEvent e) {
altDown = e.isAltDown();
shiftDown = e.isShiftDown();
}
/** Returns true if this machine is a Macintosh. */
public static boolean isMacintosh() {
return isMac;
}
/** Returns true if this machine is a Macintosh running OS X. */
public static boolean isMacOSX() {
return isMacintosh();
}
/** Returns true if this machine is running Windows. */
public static boolean isWindows() {
return isWin;
}
/** Always returns true. */
public static boolean isJava2() {
return isJava2;
}
/** Returns true if ImageJ is running on a Java 1.4 or greater JVM. */
public static boolean isJava14() {
return isJava14;
}
/** Returns true if ImageJ is running on a Java 1.5 or greater JVM. */
public static boolean isJava15() {
return isJava15;
}
/** Returns true if ImageJ is running on a Java 1.6 or greater JVM. */
public static boolean isJava16() {
return isJava16;
}
/** Returns true if ImageJ is running on a Java 1.7 or greater JVM. */
public static boolean isJava17() {
return isJava17;
}
/** Returns true if ImageJ is running on Linux. */
public static boolean isLinux() {
return isLinux;
}
/** Returns true if ImageJ is running on Windows Vista. */
public static boolean isVista() {
return isVista;
}
/** Returns true if ImageJ is running a 64-bit version of Java. */
public static boolean is64Bit() {
if (osarch==null)
osarch = System.getProperty("os.arch");
return osarch!=null && osarch.indexOf("64")!=-1;
}
/** Displays an error message and returns false if the
ImageJ version is less than the one specified. */
public static boolean versionLessThan(String version) {
boolean lessThan = ImageJ.VERSION.compareTo(version)<0;
if (lessThan)
error("This plugin or macro requires ImageJ "+version+" or later. Use\nHelp>Update ImageJ to upgrade to the latest version.");
return lessThan;
}
/** Displays a "Process all images?" dialog. Returns
'flags'+PlugInFilter.DOES_STACKS if the user selects "Yes",
'flags' if the user selects "No" and PlugInFilter.DONE
if the user selects "Cancel".
*/
public static int setupDialog(ImagePlus imp, int flags) {
if (imp==null || (ij!=null&&ij.hotkey))
return flags;
int stackSize = imp.getStackSize();
if (stackSize>1) {
if (imp.isComposite() && ((CompositeImage)imp).getMode()==CompositeImage.COMPOSITE)
return flags+PlugInFilter.DOES_STACKS;
String macroOptions = Macro.getOptions();
if (macroOptions!=null) {
if (macroOptions.indexOf("stack ")>=0)
return flags+PlugInFilter.DOES_STACKS;
else
return flags;
}
if (hideProcessStackDialog)
return flags;
String note = ((flags&PlugInFilter.NO_CHANGES)==0)?" There is\nno Undo if you select \"Yes\".":"";
YesNoCancelDialog d = new YesNoCancelDialog(getInstance(),
"Process Stack?", "Process all "+stackSize+" images?"+note);
if (d.cancelPressed())
return PlugInFilter.DONE;
else if (d.yesPressed()) {
if (imp.getStack().isVirtual() && ((flags&PlugInFilter.NO_CHANGES)==0)) {
int size = (stackSize*imp.getWidth()*imp.getHeight()*imp.getBytesPerPixel()+524288)/1048576;
String msg =
"Use the Process>Batch>Virtual Stack command\n"+
"to process a virtual stack ike this one or convert\n"+
"it to a normal stack using Image>Duplicate, which\n"+
"will require "+size+"MB of additional memory.";
error(msg);
return PlugInFilter.DONE;
}
if (Recorder.record)
Recorder.recordOption("stack");
return flags+PlugInFilter.DOES_STACKS;
}
if (Recorder.record)
Recorder.recordOption("slice");
}
return flags;
}
/** Creates a rectangular selection. Removes any existing
selection if width or height are less than 1. */
public static void makeRectangle(int x, int y, int width, int height) {
if (width<=0 || height<0)
getImage().killRoi();
else {
ImagePlus img = getImage();
if (Interpreter.isBatchMode())
img.setRoi(new Roi(x,y,width,height), false);
else
img.setRoi(x, y, width, height);
}
}
/** Creates an oval selection. Removes any existing
selection if width or height are less than 1. */
public static void makeOval(int x, int y, int width, int height) {
if (width<=0 || height<0)
getImage().killRoi();
else {
ImagePlus img = getImage();
img.setRoi(new OvalRoi(x, y, width, height));
}
}
/** Creates a straight line selection. */
public static void makeLine(int x1, int y1, int x2, int y2) {
getImage().setRoi(new Line(x1, y1, x2, y2));
}
/** Creates a point selection. */
public static void makePoint(int x, int y) {
ImagePlus img = getImage();
Roi roi = img.getRoi();
if (shiftKeyDown() && roi!=null && roi.getType()==Roi.POINT) {
Polygon p = roi.getPolygon();
p.addPoint(x, y);
img.setRoi(new PointRoi(p.xpoints, p.ypoints, p.npoints));
IJ.setKeyUp(KeyEvent.VK_SHIFT);
} else if (altKeyDown() && roi!=null && roi.getType()==Roi.POINT) {
((PolygonRoi)roi).deleteHandle(x, y);
IJ.setKeyUp(KeyEvent.VK_ALT);
} else
img.setRoi(new PointRoi(x, y));
}
/** Creates a straight line selection using double coordinates. */
public static void makeLine(double x1, double y1, double x2, double y2) {
getImage().setRoi(new Line(x1, y1, x2, y2));
}
/** Sets the display range (minimum and maximum displayed pixel values) of the current image. */
public static void setMinAndMax(double min, double max) {
setMinAndMax(getImage(), min, max, 7);
}
/** Sets the display range (minimum and maximum displayed pixel values) of the specified image. */
public static void setMinAndMax(ImagePlus img, double min, double max) {
setMinAndMax(img, min, max, 7);
}
/** Sets the minimum and maximum displayed pixel values on the specified RGB
channels, where 4=red, 2=green and 1=blue. */
public static void setMinAndMax(double min, double max, int channels) {
setMinAndMax(getImage(), min, max, channels);
}
private static void setMinAndMax(ImagePlus img, double min, double max, int channels) {
Calibration cal = img.getCalibration();
min = cal.getRawValue(min);
max = cal.getRawValue(max);
if (channels==7)
img.setDisplayRange(min, max);
else
img.setDisplayRange(min, max, channels);
img.updateAndDraw();
}
/** Resets the minimum and maximum displayed pixel values of the
current image to be the same as the min and max pixel values. */
public static void resetMinAndMax() {
resetMinAndMax(getImage());
}
/** Resets the minimum and maximum displayed pixel values of the
specified image to be the same as the min and max pixel values. */
public static void resetMinAndMax(ImagePlus img) {
img.resetDisplayRange();
img.updateAndDraw();
}
/** Sets the lower and upper threshold levels and displays the image
using red to highlight thresholded pixels. May not work correctly on
16 and 32 bit images unless the display range has been reset using IJ.resetMinAndMax().
*/
public static void setThreshold(double lowerThreshold, double upperThresold) {
setThreshold(lowerThreshold, upperThresold, null);
}
/** Sets the lower and upper threshold levels and displays the image using
the specified <code>displayMode</code> ("Red", "Black & White", "Over/Under" or "No Update"). */
public static void setThreshold(double lowerThreshold, double upperThreshold, String displayMode) {
setThreshold(getImage(), lowerThreshold, upperThreshold, displayMode);
}
/** Sets the lower and upper threshold levels of the specified image. */
public static void setThreshold(ImagePlus img, double lowerThreshold, double upperThreshold) {
setThreshold(img, lowerThreshold, upperThreshold, "Red");
}
/** Sets the lower and upper threshold levels of the specified image and updates the display using
the specified <code>displayMode</code> ("Red", "Black & White", "Over/Under" or "No Update"). */
public static void setThreshold(ImagePlus img, double lowerThreshold, double upperThreshold, String displayMode) {
int mode = ImageProcessor.RED_LUT;
if (displayMode!=null) {
displayMode = displayMode.toLowerCase(Locale.US);
if (displayMode.indexOf("black")!=-1)
mode = ImageProcessor.BLACK_AND_WHITE_LUT;
else if (displayMode.indexOf("over")!=-1)
mode = ImageProcessor.OVER_UNDER_LUT;
else if (displayMode.indexOf("no")!=-1)
mode = ImageProcessor.NO_LUT_UPDATE;
}
Calibration cal = img.getCalibration();
lowerThreshold = cal.getRawValue(lowerThreshold);
upperThreshold = cal.getRawValue(upperThreshold);
img.getProcessor().setThreshold(lowerThreshold, upperThreshold, mode);
if (mode != ImageProcessor.NO_LUT_UPDATE) {
img.getProcessor().setLutAnimation(true);
img.updateAndDraw();
}
}
public static void setAutoThreshold(ImagePlus imp, String method) {
ImageProcessor ip = imp.getProcessor();
if (ip instanceof ColorProcessor)
throw new IllegalArgumentException("Non-RGB image required");
ip.setRoi(imp.getRoi());
if (method!=null) {
try {
if (method.indexOf("stack")!=-1)
setStackThreshold(imp, ip, method);
else
ip.setAutoThreshold(method);
} catch (Exception e) {
log(e.getMessage());
}
} else
ip.setAutoThreshold(ImageProcessor.ISODATA2, ImageProcessor.RED_LUT);
imp.updateAndDraw();
}
private static void setStackThreshold(ImagePlus imp, ImageProcessor ip, String method) {
boolean darkBackground = method.indexOf("dark")!=-1;
ImageStatistics stats = new StackStatistics(imp);
AutoThresholder thresholder = new AutoThresholder();
double min=0.0, max=255.0;
if (imp.getBitDepth()!=8) {
min = stats.min;
max = stats.max;
}
int threshold = thresholder.getThreshold(method, stats.histogram);
double lower, upper;
if (darkBackground) {
if (ip.isInvertedLut())
{lower=0.0; upper=threshold;}
else
{lower=threshold+1; upper=255.0;}
} else {
if (ip.isInvertedLut())
{lower=threshold+1; upper=255.0;}
else
{lower=0.0; upper=threshold;}
}
if (lower>255) lower = 255;
if (max>min) {
lower = min + (lower/255.0)*(max-min);
upper = min + (upper/255.0)*(max-min);
} else
lower = upper = min;
ip.setMinAndMax(min, max);
ip.setThreshold(lower, upper, ImageProcessor.RED_LUT);
imp.updateAndDraw();
}
/** Disables thresholding on the current image. */
public static void resetThreshold() {
resetThreshold(getImage());
}
/** Disables thresholding on the specified image. */
public static void resetThreshold(ImagePlus img) {
ImageProcessor ip = img.getProcessor();
ip.resetThreshold();
ip.setLutAnimation(true);
img.updateAndDraw();
}
/** For IDs less than zero, activates the image with the specified ID.
For IDs greater than zero, activates the Nth image. */
public static void selectWindow(int id) {
if (id>0)
id = WindowManager.getNthImageID(id);
ImagePlus imp = WindowManager.getImage(id);
if (imp==null)
error("Macro Error", "Image "+id+" not found or no images are open.");
if (Interpreter.isBatchMode()) {
ImagePlus imp2 = WindowManager.getCurrentImage();
if (imp2!=null && imp2!=imp) imp2.saveRoi();
WindowManager.setTempCurrentImage(imp);
WindowManager.setWindow(null);
} else {
ImageWindow win = imp.getWindow();
win.toFront();
WindowManager.setWindow(win);
long start = System.currentTimeMillis();
// timeout after 2 seconds unless current thread is event dispatch thread
String thread = Thread.currentThread().getName();
int timeout = thread!=null&&thread.indexOf("EventQueue")!=-1?0:2000;
while (true) {
wait(10);
imp = WindowManager.getCurrentImage();
if (imp!=null && imp.getID()==id)
return; // specified image is now active
if ((System.currentTimeMillis()-start)>timeout) {
WindowManager.setCurrentWindow(win);
return;
}
}
}
}
/** Activates the window with the specified title. */
public static void selectWindow(String title) {
if (title.equals("ImageJ")&&ij!=null)
{ij.toFront(); return;}
long start = System.currentTimeMillis();
while (System.currentTimeMillis()-start<3000) { // 3 sec timeout
Frame frame = WindowManager.getFrame(title);
if (frame!=null && !(frame instanceof ImageWindow)) {
selectWindow(frame);
return;
}
int[] wList = WindowManager.getIDList();
int len = wList!=null?wList.length:0;
for (int i=0; i<len; i++) {
ImagePlus imp = WindowManager.getImage(wList[i]);
if (imp!=null) {
if (imp.getTitle().equals(title)) {
selectWindow(imp.getID());
return;
}
}
}
wait(10);
}
error("Macro Error", "No window with the title \""+title+"\" found.");
}
static void selectWindow(Frame frame) {
frame.toFront();
long start = System.currentTimeMillis();
while (true) {
wait(10);
if (WindowManager.getFrontWindow()==frame)
return; // specified window is now in front
if ((System.currentTimeMillis()-start)>1000) {
WindowManager.setWindow(frame);
return; // 1 second timeout
}
}
}
/** Sets the foreground color. */
public static void setForegroundColor(int red, int green, int blue) {
setColor(red, green, blue, true);
}
/** Sets the background color. */
public static void setBackgroundColor(int red, int green, int blue) {
setColor(red, green, blue, false);
}
static void setColor(int red, int green, int blue, boolean foreground) {
if (red<0) red=0; if (green<0) green=0; if (blue<0) blue=0;
if (red>255) red=255; if (green>255) green=255; if (blue>255) blue=255;
Color c = new Color(red, green, blue);
if (foreground) {
Toolbar.setForegroundColor(c);
ImagePlus img = WindowManager.getCurrentImage();
if (img!=null)
img.getProcessor().setColor(c);
} else
Toolbar.setBackgroundColor(c);
}
/** Switches to the specified tool, where id = Toolbar.RECTANGLE (0),
Toolbar.OVAL (1), etc. */
public static void setTool(int id) {
Toolbar.getInstance().setTool(id);
}
/** Switches to the specified tool, where 'name' is "rect", "elliptical",
"brush", etc. Returns 'false' if the name is not recognized. */
public static boolean setTool(String name) {
return Toolbar.getInstance().setTool(name);
}
/** Returns the name of the current tool. */
public static String getToolName() {
return Toolbar.getToolName();
}
/** Equivalent to clicking on the current image at (x,y) with the
wand tool. Returns the number of points in the resulting ROI. */
public static int doWand(int x, int y) {
return doWand(getImage(), x, y, 0, null);
}
/** Traces the boundary of the area with pixel values within
* 'tolerance' of the value of the pixel at the starting location.
* 'tolerance' is in uncalibrated units.
* 'mode' can be "4-connected", "8-connected" or "Legacy".
* "Legacy" is for compatibility with previous versions of ImageJ;
* it is ignored if 'tolerance' > 0.
*/
public static int doWand(int x, int y, double tolerance, String mode) {
return doWand(getImage(), x, y, tolerance, mode);
}
/** This version of doWand adds an ImagePlus argument. */
public static int doWand(ImagePlus img, int x, int y, double tolerance, String mode) {
ImageProcessor ip = img.getProcessor();
if ((img.getType()==ImagePlus.GRAY32) && Double.isNaN(ip.getPixelValue(x,y)))
return 0;
int imode = Wand.LEGACY_MODE;
if (mode!=null) {
if (mode.startsWith("4"))
imode = Wand.FOUR_CONNECTED;
else if (mode.startsWith("8"))
imode = Wand.EIGHT_CONNECTED;
}
Wand w = new Wand(ip);
double t1 = ip.getMinThreshold();
if (t1==ImageProcessor.NO_THRESHOLD || (ip.getLutUpdateMode()==ImageProcessor.NO_LUT_UPDATE&& tolerance>0.0))
w.autoOutline(x, y, tolerance, imode);
else
w.autoOutline(x, y, t1, ip.getMaxThreshold(), imode);
if (w.npoints>0) {
Roi previousRoi = img.getRoi();
int type = Wand.allPoints()?Roi.FREEROI:Roi.TRACED_ROI;
Roi roi = new PolygonRoi(w.xpoints, w.ypoints, w.npoints, type);
img.killRoi();
img.setRoi(roi);
// add/subtract this ROI to the previous one if the shift/alt key is down
if (previousRoi!=null)
roi.update(shiftKeyDown(), altKeyDown());
}
return w.npoints;
}
/** Sets the transfer mode used by the <i>Edit/Paste</i> command, where mode is "Copy", "Blend", "Average", "Difference",
"Transparent", "Transparent2", "AND", "OR", "XOR", "Add", "Subtract", "Multiply", or "Divide". */
public static void setPasteMode(String mode) {
mode = mode.toLowerCase(Locale.US);
int m = Blitter.COPY;
if (mode.startsWith("ble") || mode.startsWith("ave"))
m = Blitter.AVERAGE;
else if (mode.startsWith("diff"))
m = Blitter.DIFFERENCE;
else if (mode.indexOf("zero")!=-1)
m = Blitter.COPY_ZERO_TRANSPARENT;
else if (mode.startsWith("tran"))
m = Blitter.COPY_TRANSPARENT;
else if (mode.startsWith("and"))
m = Blitter.AND;
else if (mode.startsWith("or"))
m = Blitter.OR;
else if (mode.startsWith("xor"))
m = Blitter.XOR;
else if (mode.startsWith("sub"))
m = Blitter.SUBTRACT;
else if (mode.startsWith("add"))
m = Blitter.ADD;
else if (mode.startsWith("div"))
m = Blitter.DIVIDE;
else if (mode.startsWith("mul"))
m = Blitter.MULTIPLY;
else if (mode.startsWith("min"))
m = Blitter.MIN;
else if (mode.startsWith("max"))
m = Blitter.MAX;
Roi.setPasteMode(m);
}
/** Returns a reference to the active image. Displays an error
message and aborts the macro if no images are open. */
public static ImagePlus getImage() { //ts
ImagePlus img = WindowManager.getCurrentImage();
if (img==null) {
IJ.noImage();
if (ij==null)
System.exit(0);
else
abort();
}
return img;
}
/** Switches to the specified stack slice, where 1<='slice'<=stack-size. */
public static void setSlice(int slice) {
getImage().setSlice(slice);
}
/** Returns the ImageJ version number as a string. */
public static String getVersion() {
return ImageJ.VERSION;
}
/** Returns the path to the home ("user.home"), startup, ImageJ, plugins, macros,
luts, temp, current or image directory if <code>title</code> is "home", "startup",
"imagej", "plugins", "macros", "luts", "temp", "current" or "image", otherwise,
displays a dialog and returns the path to the directory selected by the user.
Returns null if the specified directory is not found or the user
cancels the dialog box. Also aborts the macro if the user cancels
the dialog box.*/
public static String getDirectory(String title) {
if (title.equals("plugins"))
return Menus.getPlugInsPath();
else if (title.equals("macros"))
return Menus.getMacrosPath();
else if (title.equals("luts")) {
String ijdir = getIJDir();
if (ijdir!=null)
return ijdir + "luts" + File.separator;
else
return null;
} else if (title.equals("home"))
return System.getProperty("user.home") + File.separator;
else if (title.equals("startup"))
return Prefs.getHomeDir() + File.separator;
else if (title.equals("imagej"))
return getIJDir();
else if (title.equals("current"))
return OpenDialog.getDefaultDirectory();
else if (title.equals("temp")) {
String dir = System.getProperty("java.io.tmpdir");
if (isMacintosh()) dir = "/tmp/";
if (dir!=null && !dir.endsWith(File.separator)) dir += File.separator;
return dir;
} else if (title.equals("image")) {
ImagePlus imp = WindowManager.getCurrentImage();
FileInfo fi = imp!=null?imp.getOriginalFileInfo():null;
if (fi!=null && fi.directory!=null)
return fi.directory;
else
return null;
} else {
DirectoryChooser dc = new DirectoryChooser(title);
String dir = dc.getDirectory();
if (dir==null) Macro.abort();
return dir;
}
}
private static String getIJDir() {
String path = Menus.getPlugInsPath();
if (path==null) return null;
String ijdir = (new File(path)).getParent();
if (ijdir!=null) ijdir += File.separator;
return ijdir;
}
/** Displays a file open dialog box and then opens the tiff, dicom,
fits, pgm, jpeg, bmp, gif, lut, roi, or text file selected by
the user. Displays an error message if the selected file is not
in one of the supported formats, or if it is not found. */
public static void open() {
open(null);
}
/** Opens and displays a tiff, dicom, fits, pgm, jpeg, bmp, gif, lut,
roi, or text file. Displays an error message if the specified file
is not in one of the supported formats, or if it is not found.
With 1.41k or later, opens images specified by a URL.
*/
public static void open(String path) {
if (ij==null && Menus.getCommands()==null) init();
Opener o = new Opener();
macroRunning = true;
if (path==null || path.equals(""))
o.open();
else
o.open(path);
macroRunning = false;
}
/** Opens and displays the nth image in the specified tiff stack. */
public static void open(String path, int n) {
if (ij==null && Menus.getCommands()==null) init();
ImagePlus imp = openImage(path, n);
if (imp!=null) imp.show();
}
/** Opens the specified file as a tiff, bmp, dicom, fits, pgm, gif
or jpeg image and returns an ImagePlus object if successful.
Calls HandleExtraFileTypes plugin if the file type is not recognised.
Displays a file open dialog if 'path' is null or an empty string.
Note that 'path' can also be a URL. Some reader plugins, including
the Bio-Formats plugin, display the image and return null. */
public static ImagePlus openImage(String path) {
return (new Opener()).openImage(path);
}
/** Opens the nth image of the specified tiff stack. */
public static ImagePlus openImage(String path, int n) {
return (new Opener()).openImage(path, n);
}
/** Opens an image using a file open dialog and returns it as an ImagePlus object. */
public static ImagePlus openImage() {
return openImage(null);
}
/** Opens a URL and returns the contents as a string.
Returns "<Error: message>" if there an error, including
host or file not found. */
public static String openUrlAsString(String url) {
StringBuffer sb = null;
url = url.replaceAll(" ", "%20");
try {
URL u = new URL(url);
URLConnection uc = u.openConnection();
long len = uc.getContentLength();
if (len>1048576L)
return "<Error: file is larger than 1MB>";
InputStream in = u.openStream();
BufferedReader br = new BufferedReader(new InputStreamReader(in));
sb = new StringBuffer() ;
String line;
while ((line=br.readLine()) != null)
sb.append (line + "\n");
in.close ();
} catch (Exception e) {
return("<Error: "+e+">");
}
if (sb!=null)
return new String(sb);
else
return "";
}
/** Saves the current image, lookup table, selection or text window to the specified file path.
The path must end in ".tif", ".jpg", ".gif", ".zip", ".raw", ".avi", ".bmp", ".fits", ".pgm", ".png", ".lut", ".roi" or ".txt". */
public static void save(String path) {
save(null, path);
}
/** Saves the specified image, lookup table or selection to the specified file path.
The file path must end with ".tif", ".jpg", ".gif", ".zip", ".raw", ".avi", ".bmp",
".fits", ".pgm", ".png", ".lut", ".roi" or ".txt". */
public static void save(ImagePlus imp, String path) {
int dotLoc = path.lastIndexOf('.');
if (dotLoc!=-1) {
ImagePlus imp2 = imp;
if (imp2==null) imp2 = WindowManager.getCurrentImage();
String title = imp2!=null?imp2.getTitle():null;
saveAs(imp, path.substring(dotLoc+1), path);
if (title!=null) imp2.setTitle(title);
} else
error("The file path passed to IJ.save() method or save()\nmacro function is missing the required extension.\n \n\""+path+"\"");
}
/* Saves the active image, lookup table, selection, measurement results, selection XY
coordinates or text window to the specified file path. The format argument must be "tiff",
"jpeg", "gif", "zip", "raw", "avi", "bmp", "fits", "pgm", "png", "text image", "lut", "selection", "measurements",
"xy Coordinates" or "text". If <code>path</code> is null or an emply string, a file
save dialog is displayed. */
public static void saveAs(String format, String path) {
saveAs(null, format, path);
}
/* Saves the specified image. The format argument must be "tiff",
"jpeg", "gif", "zip", "raw", "avi", "bmp", "fits", "pgm", "png",
"text image", "lut", "selection" or "xy Coordinates". */
public static void saveAs(ImagePlus imp, String format, String path) {
if (format==null) return;
if (path!=null && path.length()==0) path = null;
format = format.toLowerCase(Locale.US);
if (format.indexOf("tif")!=-1) {
if (path!=null&&!path.endsWith(".tiff"))
path = updateExtension(path, ".tif");
format = "Tiff...";
} else if (format.indexOf("jpeg")!=-1 || format.indexOf("jpg")!=-1) {
path = updateExtension(path, ".jpg");
format = "Jpeg...";
} else if (format.indexOf("gif")!=-1) {
path = updateExtension(path, ".gif");
format = "Gif...";
} else if (format.indexOf("text image")!=-1) {
path = updateExtension(path, ".txt");
format = "Text Image...";
} else if (format.indexOf("text")!=-1 || format.indexOf("txt")!=-1) {
if (path!=null && !path.endsWith(".xls"))
path = updateExtension(path, ".txt");
format = "Text...";
} else if (format.indexOf("zip")!=-1) {
path = updateExtension(path, ".zip");
format = "ZIP...";
} else if (format.indexOf("raw")!=-1) {
//path = updateExtension(path, ".raw");
format = "Raw Data...";
} else if (format.indexOf("avi")!=-1) {
path = updateExtension(path, ".avi");
format = "AVI... ";
} else if (format.indexOf("bmp")!=-1) {
path = updateExtension(path, ".bmp");
format = "BMP...";
} else if (format.indexOf("fits")!=-1) {
path = updateExtension(path, ".fits");
format = "FITS...";
} else if (format.indexOf("png")!=-1) {
path = updateExtension(path, ".png");
format = "PNG...";
} else if (format.indexOf("pgm")!=-1) {
path = updateExtension(path, ".pgm");
format = "PGM...";
} else if (format.indexOf("lut")!=-1) {
path = updateExtension(path, ".lut");
format = "LUT...";
} else if (format.indexOf("results")!=-1 || format.indexOf("measurements")!=-1) {
format = "Results...";
} else if (format.indexOf("selection")!=-1 || format.indexOf("roi")!=-1) {
path = updateExtension(path, ".roi");
format = "Selection...";
} else if (format.indexOf("xy")!=-1 || format.indexOf("coordinates")!=-1) {
path = updateExtension(path, ".txt");
format = "XY Coordinates...";
} else
error("Unsupported save() or saveAs() file format: \""+format+"\"\n \n\""+path+"\"");
if (path==null)
run(format);
else
run(imp, format, "save=["+path+"]");
}
static String updateExtension(String path, String extension) {
if (path==null) return null;
int dotIndex = path.lastIndexOf(".");
int separatorIndex = path.lastIndexOf(File.separator);
if (dotIndex>=0 && dotIndex>separatorIndex && (path.length()-dotIndex)<=5) {
if (dotIndex+1<path.length() && Character.isDigit(path.charAt(dotIndex+1)))
path += extension;
else
path = path.substring(0, dotIndex) + extension;
} else
path += extension;
return path;
}
/** Saves a string as a file. Displays a file save dialog if
'path' is null or blank. Returns an error message
if there is an exception, otherwise returns null. */
public static String saveString(String string, String path) {
return write(string, path, false);
}
/** Appends a string to the end of a file. A newline character ("\n")
is added to the end of the string before it is written. Returns an
error message if there is an exception, otherwise returns null. */
public static String append(String string, String path) {
return write(string+"\n", path, true);
}
private static String write(String string, String path, boolean append) {
if (path==null || path.equals("")) {
String msg = append?"Append String...":"Save String...";
SaveDialog sd = new SaveDialog(msg, "Untitled", ".txt");
String name = sd.getFileName();
if (name==null) return null;
path = sd.getDirectory() + name;
}
try {
BufferedWriter out = new BufferedWriter(new FileWriter(path, append));
out.write(string);
out.close();
} catch (IOException e) {
return ""+e;
}
return null;
}
/** Opens a text file as a string. Displays a file open dialog
if path is null or blank. Returns null if the user cancels
the file open dialog. If there is an error, returns a
message in the form "Error: message". */
public static String openAsString(String path) {
if (path==null || path.equals("")) {
OpenDialog od = new OpenDialog("Open Text File", "");
String directory = od.getDirectory();
String name = od.getFileName();
if (name==null) return null;
path = directory + name;
}
String str = "";
File file = new File(path);
if (!file.exists())
return "Error: file not found";
try {
StringBuffer sb = new StringBuffer(5000);
BufferedReader r = new BufferedReader(new FileReader(file));
while (true) {
String s=r.readLine();
if (s==null)
break;
else
sb.append(s+"\n");
}
r.close();
str = new String(sb);
}
catch (Exception e) {
str = "Error: "+e.getMessage();
}
return str;
}
/** Creates a new imagePlus. <code>Type</code> should contain "8-bit", "16-bit", "32-bit" or "RGB".
In addition, it can contain "white", "black" or "ramp" (the default is "white"). <code>Width</code>
and <code>height</code> specify the width and height of the image in pixels.
<code>Depth</code> specifies the number of stack slices. */
public static ImagePlus createImage(String title, String type, int width, int height, int depth) {
type = type.toLowerCase(Locale.US);
int bitDepth = 8;
if (type.indexOf("16")!=-1) bitDepth = 16;
if (type.indexOf("24")!=-1||type.indexOf("rgb")!=-1) bitDepth = 24;
if (type.indexOf("32")!=-1) bitDepth = 32;
int options = NewImage.FILL_WHITE;
if (bitDepth==16 || bitDepth==32)
options = NewImage.FILL_BLACK;
if (type.indexOf("white")!=-1)
options = NewImage.FILL_WHITE;
else if (type.indexOf("black")!=-1)
options = NewImage.FILL_BLACK;
else if (type.indexOf("ramp")!=-1)
options = NewImage.FILL_RAMP;
options += NewImage.CHECK_AVAILABLE_MEMORY;
return NewImage.createImage(title, width, height, depth, bitDepth, options);
}
/** Opens a new image. <code>Type</code> should contain "8-bit", "16-bit", "32-bit" or "RGB".
In addition, it can contain "white", "black" or "ramp" (the default is "white"). <code>Width</code>
and <code>height</code> specify the width and height of the image in pixels.
<code>Depth</code> specifies the number of stack slices. */
public static void newImage(String title, String type, int width, int height, int depth) {
ImagePlus imp = createImage(title, type, width, height, depth);
if (imp!=null) {
macroRunning = true;
imp.show();
macroRunning = false;
}
}
/** Returns true if the <code>Esc</code> key was pressed since the
last ImageJ command started to execute or since resetEscape() was called. */
public static boolean escapePressed() {
return escapePressed;
}
/** This method sets the <code>Esc</code> key to the "up" position.
The Executer class calls this method when it runs
an ImageJ command in a separate thread. */
public static void resetEscape() {
escapePressed = false;
}
/** Causes IJ.error() output to be temporarily redirected to the "Log" window. */
public static void redirectErrorMessages() {
redirectErrorMessages = true;
}
/** Set 'true' and IJ.error() output will be redirected to the "Log" window. */
public static void redirectErrorMessages(boolean redirect) {
redirectErrorMessages2 = redirect;
}
/** Returns the state of the 'redirectErrorMessages' flag. The File/Import/Image Sequence command sets this flag.*/
public static boolean redirectingErrorMessages() {
return redirectErrorMessages || redirectErrorMessages2;
}
/** Temporarily suppress "plugin not found" errors. */
public static void suppressPluginNotFoundError() {
suppressPluginNotFoundError = true;
}
/** Returns the class loader ImageJ uses to run plugins or the
system class loader if Menus.getPlugInsPath() returns null. */
public static ClassLoader getClassLoader() {
if (classLoader==null) {
String pluginsDir = Menus.getPlugInsPath();
if (pluginsDir==null) {
String home = System.getProperty("plugins.dir");
if (home!=null) {
if (!home.endsWith(Prefs.separator)) home+=Prefs.separator;
pluginsDir = home+"plugins"+Prefs.separator;
if (!(new File(pluginsDir)).isDirectory()) pluginsDir = home;
}
}
if (pluginsDir==null)
return IJ.class.getClassLoader();
else {
if (Menus.jnlp)
classLoader = new PluginClassLoader(pluginsDir, true);
else
classLoader = new PluginClassLoader(pluginsDir);
}
}
return classLoader;
}
/** Returns the size, in pixels, of the primary display. */
public static Dimension getScreenSize() {
if (isWindows()) // GraphicsEnvironment.getConfigurations is *very* slow on Windows
return Toolkit.getDefaultToolkit().getScreenSize();
if (GraphicsEnvironment.isHeadless())
return new Dimension(0, 0);
// Can't use Toolkit.getScreenSize() on Linux because it returns
// size of all displays rather than just the primary display.
GraphicsEnvironment ge = GraphicsEnvironment.getLocalGraphicsEnvironment();
GraphicsDevice[] gd = ge.getScreenDevices();
GraphicsConfiguration[] gc = gd[0].getConfigurations();
Rectangle bounds = gc[0].getBounds();
if (bounds.x==0&&bounds.y==0)
return new Dimension(bounds.width, bounds.height);
else
return Toolkit.getDefaultToolkit().getScreenSize();
}
static void abort() {
if (ij!=null || Interpreter.isBatchMode())
throw new RuntimeException(Macro.MACRO_CANCELED);
}
static void setClassLoader(ClassLoader loader) {
classLoader = loader;
}
/** Displays a stack trace. Use the setExceptionHandler
method() to override with a custom exception handler. */
public static void handleException(Throwable e) {
if (exceptionHandler!=null) {
exceptionHandler.handle(e);
return;
}
CharArrayWriter caw = new CharArrayWriter();
PrintWriter pw = new PrintWriter(caw);
e.printStackTrace(pw);
String s = caw.toString();
if (getInstance()!=null)
new TextWindow("Exception", s, 500, 300);
else
log(s);
}
/** Installs a custom exception handler that
overrides the handleException() method. */
public static void setExceptionHandler(ExceptionHandler handler) {
exceptionHandler = handler;
}
public interface ExceptionHandler {
public void handle(Throwable e);
}
static ExceptionHandler exceptionHandler;
public static void addEventListener(IJEventListener listener) {
eventListeners.addElement(listener);
}
public static void removeEventListener(IJEventListener listener) {
eventListeners.removeElement(listener);
}
public static void notifyEventListeners(int eventID) {
synchronized (eventListeners) {
for (int i=0; i<eventListeners.size(); i++) {
IJEventListener listener = (IJEventListener)eventListeners.elementAt(i);
listener.eventOccurred(eventID);
}
}
}
}