Commit 02a345846ea2b5cf0ac4249164e6b605a88abb41 - imagej

+4

-0

ij/CompositeImage.java less more

186	186	}
187	187
188	188	public void updateAndDraw() {
	189	if (win==null) {
	190	img = null;
	191	return;
	192	}
189	193	updateImage();
190	194	if (win!=null)
191	195	notifyListeners(UPDATED);

+1

-3

ij/IJ.java less more

2461	2461	return new String[0];
2462	2462	for (int i=0; i<lutsMenu.getItemCount(); i++) {
2463	2463	MenuItem menuItem = lutsMenu.getItem(i);
2464		if (menuItem.getActionListeners().length == 0) // separator?
2465		continue;
2466	2464	String label = menuItem.getLabel();
2467		if (label.equals("Invert LUT") \|\| label.equals("Apply LUT"))
	2465	if (label.equals("-") \|\| label.equals("Invert LUT") \|\| label.equals("Apply LUT"))
2468	2466	continue;
2469	2467	String command = (String)commands.get(label);
2470	2468	if (command==null \|\| command.startsWith("ij.plugin.LutLoader"))

+4

-3

ij/ImageJ.java less more

76	76	MouseListener, KeyListener, WindowListener, ItemListener, Runnable {
77	77
78	78	/** Plugins should call IJ.getVersion() or IJ.getFullVersion() to get the version string. */
79		public static final String VERSION = "1.53i";
80		public static final String BUILD = ""; //44
	79	public static final String VERSION = "1.53j";
	80	public static final String BUILD = ""; //46
81	81	public static Color backgroundColor = new Color(237,237,237);
82	82	/** SansSerif, 12-point, plain font. */
83	83	public static final Font SansSerif12 = new Font("SansSerif", Font.PLAIN, 12);

733	733	if (!noGUI && (ij==null \|\| (ij!=null && !ij.isShowing()))) {
734	734	ij = new ImageJ(null, mode);
735	735	ij.exitWhenQuitting = true;
736		}
	736	} else if (batchMode && noGUI)
	737	Prefs.load(null, null);
737	738	int macros = 0;
738	739	for (int i=0; i<nArgs; i++) {
739	740	String arg = args[i];

+14

-1

ij/ImagePlus.java less more

297	297	nothing if there is no window associated with
298	298	this image (i.e. show() has not been called).*/
299	299	public synchronized void updateAndDraw() {
	300	if (win==null) {
	301	img = null;
	302	return;
	303	}
300	304	if (stack!=null && !stack.isVirtual() && currentSlice>=1 && currentSlice<=stack.size()) {
301	305	if (stack.size()>1 && win!=null && !(win instanceof StackWindow)) {
302	306	setStack(stack); //adds scroll bar if stack size has changed to >1

421	425	/** ImageCanvas.paint() calls this method when the
422	426	ImageProcessor has generated a new image. */
423	427	public void updateImage() {
	428	if (win==null) {
	429	img = null;
	430	return;
	431	}
424	432	if (ip!=null)
425	433	img = ip.createImage();
426	434	}

428	436	/** Closes the window, if any, that is displaying this image. */
429	437	public void hide() {
430	438	if (win==null) {
	439	img = null;
431	440	Interpreter.removeBatchModeImage(this);
432	441	return;
433	442	}

542	551	img = ip.createImage();
543	552	return img;
544	553	}
545
	554
546	555	/** Returns a copy of this image as an 8-bit or RGB BufferedImage.
547	556	* @see ij.process.ShortProcessor#get16BitBufferedImage
548	557	*/

3346	3355	public void setBorderColor(Color borderColor) {
3347	3356	this.borderColor = borderColor;
3348	3357	}
	3358
	3359	public boolean windowActivated() {
	3360	return this.activated;
	3361	}
3349	3362
3350	3363	}

+6

-0

ij/Menus.java less more

825	825	/** Returns the specified ImageJ menu (e.g., "File>New") or null if it is not found. */
826	826	public static Menu getImageJMenu(String menuPath) {
827	827	if (menus==null)
	828	IJ.init();
	829	if (menus==null)
828	830	return null;
829	831	if (menus.get(menuPath)!=null)
830	832	return getMenu(menuPath, false);

1332	1334
1333	1335	/** Returns the hashtable that associates commands with plugins. */
1334	1336	public static Hashtable getCommands() {
	1337	if (pluginsTable==null)
	1338	IJ.init();
1335	1339	return pluginsTable;
1336	1340	}
1337	1341

1660	1664
1661	1665	/** Called once when ImageJ quits. */
1662	1666	public static void savePreferences(Properties prefs) {
	1667	if (pluginsPrefs==null)
	1668	return;
1663	1669	int index = 0;
1664	1670	for (Enumeration en=pluginsPrefs.elements(); en.hasMoreElements();) {
1665	1671	String key = "plugin" + (index/10)%10 + index%10;

+28

-24

ij/Prefs.java less more

287	287	public static String load(Object ij, Applet applet) {
288	288	if (ImageJDir==null)
289	289	ImageJDir = System.getProperty("user.dir");
290		InputStream f = null;
291		try { // Look for IJ_Props.txt in ImageJ folder
292		f = new FileInputStream(ImageJDir+"/"+PROPS_NAME);
293		propertiesPath = ImageJDir+"/"+PROPS_NAME;
294		} catch (FileNotFoundException e) {
295		f = null;
296		}
297		if (f==null) {
298		// Look in ij.jar if not found in ImageJ folder
299		f = ij.getClass().getResourceAsStream("/"+PROPS_NAME);
300		}
301		if (applet!=null)
302		return loadAppletProps(f, applet);
303		if (f==null)
304		return PROPS_NAME+" not found in ij.jar or in "+ImageJDir;
305		f = new BufferedInputStream(f);
306		try {
307		props.load(f);
308		f.close();
309		} catch (IOException e) {
310		return("Error loading "+PROPS_NAME);
311		}
312		imagesURL = props.getProperty(IJ.isJava18()?"images.location":"images.location2");
	290	if (ij!=null) {
	291	InputStream f = null;
	292	try { // Look for IJ_Props.txt in ImageJ folder
	293	f = new FileInputStream(ImageJDir+"/"+PROPS_NAME);
	294	propertiesPath = ImageJDir+"/"+PROPS_NAME;
	295	} catch (FileNotFoundException e) {
	296	f = null;
	297	}
	298	if (f==null) {
	299	// Look in ij.jar if not found in ImageJ folder
	300	f = ij.getClass().getResourceAsStream("/"+PROPS_NAME);
	301	}
	302	if (applet!=null)
	303	return loadAppletProps(f, applet);
	304	if (f==null)
	305	return PROPS_NAME+" not found in ij.jar or in "+ImageJDir;
	306	f = new BufferedInputStream(f);
	307	try {
	308	props.load(f);
	309	f.close();
	310	} catch (IOException e) {
	311	return("Error loading "+PROPS_NAME);
	312	}
	313	imagesURL = props.getProperty(IJ.isJava18()?"images.location":"images.location2");
	314	}
313	315	loadPreferences();
314	316	loadOptions();
315	317	guiScale = get(GUI_SCALE, 1.0);

461	463	if (!IJ.isLinux()) dialogCancelButtonOnRight = false;
462	464	saveOptions(prefs);
463	465	savePluginPrefs(prefs);
464		IJ.getInstance().savePreferences(prefs);
	466	ImageJ ij = IJ.getInstance();
	467	if (ij!=null)
	468	ij.savePreferences(prefs);
465	469	Menus.savePreferences(prefs);
466	470	ParticleAnalyzer.savePreferences(prefs);
467	471	Analyzer.savePreferences(prefs);

+19

-6

ij/gui/GenericDialog.java less more

721	721	}
722	722
723	723	/** Adds one or two (side by side) text areas.
724		* @param text1 initial contents of the first text area
725		* @param text2 initial contents of the second text area or null
726		* @param rows the number of rows
727		* @param columns the number of columns
	724	* Append "SCROLLBARS_VERTICAL_ONLY" to the text of
	725	* the first text area to get vertical scrollbars
	726	* and "SCROLLBARS_BOTH" to get both vertical and
	727	* horizontal scrollbars.
	728	* @param text1 initial contents of the first text area
	729	* @param text2 initial contents of the second text area or null
	730	* @param rows the number of rows
	731	* @param columns the number of columns
728	732	*/
729	733	public void addTextAreas(String text1, String text2, int rows, int columns) {
730	734	if (textArea1!=null) return;
731	735	Panel panel = new Panel();
	736	int scrollbars = TextArea.SCROLLBARS_NONE;
	737	if (text1.endsWith("SCROLLBARS_BOTH")) {
	738	scrollbars = TextArea.SCROLLBARS_BOTH;
	739	text1 = text1.substring(0, text1.length()-15);
	740	}
	741	if (text1.endsWith("SCROLLBARS_VERTICAL_ONLY")) {
	742	scrollbars = TextArea.SCROLLBARS_VERTICAL_ONLY;
	743	text1 = text1.substring(0, text1.length()-24);
	744	}
732	745	Font font = new Font("SansSerif", Font.PLAIN, (int)(14*Prefs.getGuiScale()));
733		textArea1 = new TextArea(text1,rows,columns,TextArea.SCROLLBARS_NONE);
	746	textArea1 = new TextArea(text1,rows,columns,scrollbars);
734	747	if (IJ.isLinux()) textArea1.setBackground(Color.white);
735	748	textArea1.setFont(font);
736	749	textArea1.addTextListener(this);
737	750	panel.add(textArea1);
738	751	if (text2!=null) {
739		textArea2 = new TextArea(text2,rows,columns,TextArea.SCROLLBARS_NONE);
	752	textArea2 = new TextArea(text2,rows,columns,scrollbars);
740	753	if (IJ.isLinux()) textArea2.setBackground(Color.white);
741	754	textArea2.setFont(font);
742	755	panel.add(textArea2);

+14

-3

ij/gui/HTMLDialog.java less more

72	72	if (dialogD.height > 0.80*screenD.height && screenD.height>400) //max 80% of screen height
73	73	dialogD.height = (int)(0.80*screenD.height);
74	74	setSize(dialogD);
75		GUI.centerOnImageJScreen(this);
76		if (!modal) WindowManager.addWindow(this);
77		show();
	75	GUI.centerOnImageJScreen(this);
	76	if (!modal) {
	77	WindowManager.addWindow(this);
	78	show();
	79	}
	80	final JScrollBar verticalScrollBar = scrollPane.getVerticalScrollBar();
	81	if (verticalScrollBar!=null) {
	82	EventQueue.invokeLater(new Runnable() {
	83	public void run() {
	84	verticalScrollBar.setValue(verticalScrollBar.getMinimum()); //start scrollbar at top
	85	}
	86	});
	87	}
	88	if (modal) show();
78	89	}
79	90
80	91	public void actionPerformed(ActionEvent e) {

+25

-0

ij/gui/Plot.java less more

993	993	public void setLabel(int index, String label) {
994	994	if (index < 0) index = allPlotObjects.size() + index;
995	995	allPlotObjects.get(index).label = label;
	996	}
	997
	998	/** Removes NaNs from the xValues and yValues arrays of all plot objects. */
	999	public void removeNaNs() {
	1000	for (PlotObject plotObj : allPlotObjects){
	1001	if(plotObj != null && plotObj.xValues!= null && plotObj.yValues != null ){
	1002	int oldSize = plotObj.xValues.length;
	1003	float[] xVals = new float[oldSize];
	1004	float[] yVals = new float[oldSize];
	1005	int newSize = 0;
	1006	for (int kk = 0; kk < oldSize; kk++) {
	1007	if (!Float.isNaN(plotObj.xValues[kk] + plotObj.yValues[kk])) {
	1008	xVals[newSize] = plotObj.xValues[kk];
	1009	yVals[newSize] = plotObj.yValues[kk];
	1010	newSize++;
	1011	}
	1012	}
	1013	if (newSize < oldSize) {
	1014	plotObj.xValues = new float[newSize];
	1015	plotObj.yValues = new float[newSize];
	1016	System.arraycopy(xVals, 0, plotObj.xValues, 0, newSize);
	1017	System.arraycopy(yVals, 0, plotObj.yValues, 0, newSize);
	1018	}
	1019	}
	1020	}
996	1021	}
997	1022
998	1023	/** Returns an array of the available curve types ("Line", "Bar", "Circle", etc). */

+11

-1

ij/gui/PointRoi.java less more

365	365	return this;
366	366	}
367	367
	368	/** Adds a point at the specified stack position. */
	369	public void addPoint(double x, double y, int position) {
	370	if (counters==null) {
	371	counters = new short[100];
	372	positions = new int[100];
	373	}
	374	addPoint(null, x, y);
	375	positions[nPoints-1] = position;
	376	}
	377
368	378	protected void deletePoint(int index) {
369	379	super.deletePoint(index);
370	380	if (index>=0 && index<=nPoints && counters!=null) {

404	414	if (rt!=null && WindowManager.getFrame(getCountsTitle())!=null)
405	415	displayCounts();
406	416	}
407
	417
408	418	/** Returns the index of the current counter. */
409	419	public int getCounter() {
410	420	return counter;

+30

-0

ij/gui/Toolbar.java less more

95	95
96	96	private static Color foregroundColor = Prefs.getColor(Prefs.FCOLOR,Color.white);
97	97	private static Color backgroundColor = Prefs.getColor(Prefs.BCOLOR,Color.black);
	98	private static double foregroundValue = Double.NaN;
	99	private static double backgroundValue = Double.NaN;
98	100	private static int ovalType = OVAL_ROI;
99	101	private static int rectType = RECT_ROI;
100	102	private static boolean multiPointMode = Prefs.multiPointMode;

935	937	if (c==null)
936	938	return;
937	939	foregroundColor = c;
	940	foregroundValue = Double.NaN;
938	941	IJ.notifyEventListeners(IJEventListener.FOREGROUND_COLOR_CHANGED);
939	942	if (instance==null)
940	943	return;

953	956	public static void setBackgroundColor(Color c) {
954	957	if (c!=null) {
955	958	backgroundColor = c;
	959	backgroundValue = Double.NaN;
956	960	repaintTool(DROPPER);
957	961	IJ.notifyEventListeners(IJEventListener.BACKGROUND_COLOR_CHANGED);
958	962	}
	963	}
	964
	965	public static double getForegroundValue() {
	966	return foregroundValue;
	967	}
	968
	969	public static void setForegroundValue(double value) {
	970	if (value>=0) {
	971	int v = (int)value;
	972	if (v>255) v=255;
	973	setForegroundColor(new Color(v,v,v));
	974	}
	975	foregroundValue = value;
	976	}
	977
	978	public static double getBackgroundValue() {
	979	return backgroundValue;
	980	}
	981
	982	public static void setBackgroundValue(double value) {
	983	if (value>=0) {
	984	int v = (int)value;
	985	if (v>255) v=255;
	986	setBackgroundColor(new Color(v,v,v));
	987	}
	988	backgroundValue = value;
959	989	}
960	990
961	991	private static void setRoiColor(Color c) {

+69

-26

ij/macro/Functions.java less more

278	278	case EXEC: str = exec(); break;
279	279	case LIST: str = doList(); break;
280	280	case DEBUG: str = debug(); break;
281		case IJ_CALL: str = ijCall(); break;
	281	case IJ_CALL: str = doIJ(); break;
282	282	case GET_RESULT_STRING: str = getResultString(null); break;
283	283	case TRIM: str = trim(); break;
284	284	default:

693	693	IJ.setKeyUp(IJ.ALL_KEYS);
694	694	shiftKeyDown = altKeyDown = false;
695	695	}
696
	696
697	697	private void selectWindow() {
698	698	String title = getStringArg();
699	699	if (resultsPending && "Results".equals(title)) {

2218	2218	return getPlotLimits(currentPlot);
2219	2219	} else if (name.equals("freeze")) {
2220	2220	currentPlot.setFrozen(getBooleanArg());
	2221	return Double.NaN;
	2222	} else if (name.equals("removeNaNs")) {
	2223	currentPlot.removeNaNs();
2221	2224	return Double.NaN;
2222	2225	} else if (name.equals("addLegend") \|\| name.equals("setLegend")) {
2223	2226	return addPlotLegend(currentPlot);

3886	3889	}
3887	3890	}
3888	3891	}
3889
	3892
3890	3893	String trim() {
3891	3894	if (interp.nextToken()=='=')
3892	3895	interp.error("'trim' is a reserved word");

5111	5114	return Toolbar.getForegroundColor().getRGB()&0xffffff;
5112	5115	else if (key.equals("rgb.background"))
5113	5116	return Toolbar.getBackgroundColor().getRGB()&0xffffff;
5114		else if (key.contains("foreground"))
5115		return getColorValue(Toolbar.getForegroundColor());
5116		else if (key.contains("background"))
5117		return getColorValue(Toolbar.getBackgroundColor());
5118		else if (key.equals("font.size")) {
	5117	else if (key.contains("foreground")) {
	5118	double value = Toolbar.getForegroundValue();
	5119	if (Double.isNaN(value))
	5120	return getColorValue(Toolbar.getForegroundColor());
	5121	else
	5122	return value;
	5123	} else if (key.contains("background")) {
	5124	double value = Toolbar.getBackgroundValue();
	5125	if (Double.isNaN(value))
	5126	return getColorValue(Toolbar.getBackgroundColor());
	5127	else
	5128	return value;
	5129	} else if (key.equals("font.size")) {
5119	5130	resetImage();
5120	5131	ImageProcessor ip = getProcessor();
5121	5132	setFont(ip);

5740	5751	props = new Properties();
5741	5752	String name = interp.tokenString;
5742	5753	if (name.equals("doFit"))
5743		return fitCurve();
	5754	return fitCurve(false);
	5755	if (name.equals("doWeightedFit"))
	5756	return fitCurve(true);
5744	5757	else if (name.equals("getEquation"))
5745	5758	return getEquation();
5746	5759	else if (name.equals("nEquations")) {

5776	5789	return Double.NaN;
5777	5790	}
5778	5791
5779		double fitCurve() {
	5792	double fitCurve(boolean withWeights) {
5780	5793	interp.getLeftParen();
5781	5794	int fit = -1;
5782	5795	String name = null;

5800	5813	double[] x = getNextArray();
5801	5814	interp.getComma();
5802	5815	double[] y = getNumericArray();
	5816	double[] weights = null;
	5817	if (withWeights) {
	5818	interp.getComma();
	5819	weights = getNumericArray();
	5820	}
5803	5821	if (interp.nextToken()==',') {
5804	5822	interp.getComma();
5805	5823	initialValues = getNumericArray();

5810	5828	if (x.length==0)
5811	5829	interp.error("Zero length array");
5812	5830	fitter = new CurveFitter(x, y);
	5831	if (withWeights)
	5832	fitter.setWeights(weights);
5813	5833	fitter.setStatusAndEsc(null, true);
5814	5834	if (fit==-1 && name!=null) {
5815	5835	Interpreter instance = Interpreter.getInstance();

5969	5989	contains = str.contains(filter);
5970	5990	if (contains)
5971	5991	list.add(a1[i]);
5972		}
	5992	}
5973	5993	}
5974	5994	return (Variable[])list.toArray(new Variable[list.size()]);
5975	5995	}
5976
	5996
5977	5997	Variable[] deleteArrayIndex() {
5978	5998	interp.getLeftParen();
5979	5999	Variable[] arr1 = getArray();

6486	6506	resetImage();
6487	6507	}
6488	6508
6489		private String ijCall() {
	6509	private String doIJ() {
6490	6510	interp.getToken();
6491	6511	if (interp.token!='.')
6492	6512	interp.error("'.' expected");

6514	6534	renameResults();
6515	6535	else if (name.equals("getFullVersion"))
6516	6536	{interp.getParens(); return ""+IJ.getFullVersion();}
	6537	else if (name.equals("checksum"))
	6538	return checksum();
6517	6539	else
6518	6540	interp.error("Unrecognized IJ function name");
6519	6541	return null;
	6542	}
	6543
	6544	private String checksum(){
	6545	String method = getFirstString();
	6546	String src = getLastString();
	6547	method = method.toUpperCase();
	6548	if (method.contains("FILE") && method.contains("MD5"))
	6549	return Tools.getHash("MD5", true, src);
	6550	if (method.contains("STRING") && method.contains("MD5"))
	6551	return Tools.getHash("MD5", false, src);
	6552	if (method.contains("FILE") && method.contains("SHA-256"))
	6553	return Tools.getHash("SHA-256", true, src);
	6554	if (method.contains("STRING") && method.contains("SHA-256"))
	6555	return Tools.getHash("SHA-256", false, src);
	6556	interp.error("must contain 'file' or 'string' and 'MD5' or 'SHA-256'");
	6557	return "0";
6520	6558	}
6521	6559
6522	6560	private String pad() {

6735	6773	interp.error("Unrecognized function name");
6736	6774	return Double.NaN;
6737	6775	}
6738
	6776
6739	6777	private double activateSelection(ImagePlus imp, Overlay overlay, boolean wait) {
6740	6778	int index = (int)getArg();
6741	6779	int size = overlay.size();

6764	6802	IJ.wait(5);
6765	6803	} while (ic!=null && ic.getPaintPending() && System.currentTimeMillis()-t0<50);
6766	6804	} else
6767		imp.setRoi(roi, !Interpreter.isBatchMode());
	6805	imp.setRoi(roi, !Interpreter.isBatchMode());
6768	6806	if (Analyzer.addToOverlay())
6769	6807	ResultsTable.selectRow(roi);
6770	6808	return Double.NaN;
6771		}
6772
	6809	}
	6810
6773	6811	private double getOverlayElementBounds(Overlay overlay) {
6774	6812	int index = (int)getFirstArg();
6775	6813	Variable x = getNextVariable();

7186	7224	resultsPending = false;
7187	7225	return null;
7188	7226	}
7189
	7227
7190	7228	private Variable resetTable() {
7191	7229	String title = getTitleArg();
7192	7230	ResultsTable rt = null;

7929	7967	interp.error("Unrecognized RoiManager function");
7930	7968	return null;
7931	7969	}
7932
	7970
7933	7971	private Variable doProperty() {
7934	7972	interp.getToken();
7935	7973	if (interp.token!='.')

7989	8027	interp.error("Unrecognized Property function");
7990	8028	return null;
7991	8029	}
7992
	8030
7993	8031	private void setPropertiesFromString(Properties props) {
7994	8032	String list = getStringArg();
7995	8033	props.clear();

8019	8057	}
8020	8058	return sb.toString();
8021	8059	}
8022
	8060
8023	8061	static boolean isStringFunction(String name, int type) {
8024	8062	boolean isString = false;
8025	8063	switch (type) {

8058	8096	}
8059	8097	return isString;
8060	8098	}
8061
	8099
8062	8100	private Variable doImage() {
8063	8101	interp.getToken();
8064	8102	if (interp.token!='.')

8078	8116	interp.getParens();
8079	8117	imp.copy();
8080	8118	return null;
8081		} else if (name.equals("paste")) {
	8119	} else if (name.equals("paste")) {
8082	8120	int x = (int)getFirstArg();
8083	8121	int y = (int)getNextArg();
8084	8122	String mode = null;

8119	8157	return setForegroundOrBackground(true);
8120	8158	} else if (name.equals("setBackground")) {
8121	8159	return setForegroundOrBackground(false);
	8160	} else if (name.equals("setForegroundValue")) {
	8161	Toolbar.setForegroundValue(getArg());
	8162	return null;
	8163	} else if (name.equals("setBackgroundValue")) {
	8164	Toolbar.setBackgroundValue(getArg());
	8165	return null;
8122	8166	} else if (name.equals("toString")) {
8123	8167	int red = (int)getFirstArg();
8124	8168	int green = (int)getNextArg();

8143	8187	interp.error("Unrecognized Color function");
8144	8188	return null;
8145	8189	}
8146
	8190
8147	8191	private Variable setForegroundOrBackground(boolean foreground) {
8148	8192	interp.getLeftParen();
8149	8193	Color color = null;

8157	8201	int blue = (int)getLastArg();
8158	8202	color = Colors.toColor(red, green, blue);
8159	8203	}
8160		if (foreground)
	8204	if (foreground)
8161	8205	Toolbar.setForegroundColor(color);
8162	8206	else
8163	8207	Toolbar.setBackgroundColor(color);

8165	8209	}
8166	8210
8167	8211	} // class Functions
8168

+1

-0

ij/macro/Interpreter.java less more

830	830	case Variable.STRING: doStringAssignment(); break;
831	831	case Variable.ARRAY: doArrayAssignment(); break;
832	832	case USER_FUNCTION: doUserFunctionAssignment(); break;
	833	case STRING_FUNCTION: doNumericStringAssignment(); break;
833	834	default:
834	835	putTokenBack();
835	836	double value = getAssignmentExpression();

+76

-45

ij/measure/CurveFitter.java less more

42	42	* 2016-11-28: added static getNumParams methods
43	43	* 2018-03-23: fixes NullPointerException for custom fit without initialParamVariations
44	44	* 2018-07-19: added error function erf (=integral over Gaussian)
	45	* 2021-04-30: data points can have weights
45	46	*/
46	47
47	48	public class CurveFitter implements UserFunction{

93	94	"y = a(1-exp(-bx))^c", //CHAPMAN
94	95	"y = a+b*erf((x-c)/d)" //ERF; note that the c parameter is sqrt2 times the Gaussian
95	96	};
96
	97
97	98	/** ImageJ Macro language code for the built-in functions */
98	99	public static final String[] fMacro = {
99	100	"y = a+xb","y = a+x(b+x*c)", //STRAIGHT_LINE,POLY2

122	123
123	124	private int fitType = -1; // Number of curve type to fit
124	125	private double[] xData, yData; // x,y data to fit
	126	private double[] weights; // weights for the data to fit
125	127	private double[] xDataSave, yDataSave; //saved original data after fitting modified data
126	128	private int numPoints; // number of data points in actual fit
127	129	private double ySign = 0; // remember sign of y data for power-law fit via regression
128		private double sumY = Double.NaN, sumY2 = Double.NaN; // sum(y), sum(y^2) of the data used for fitting
	130	private double sumY = Double.NaN, sumY2 = Double.NaN; // sum(yw), sum(y^2w) of the data used for fitting (w=weight, default 1)
	131	private double sumWeights = Double.NaN; //sum of weights (or numPoints, if no weigths are given)
129	132	private int numParams; // number of parameters
130	133	private double[] initialParams; // user specified or estimated initial parameters
131	134	private double[] initialParamVariations; // estimate of range of parameters

258	261	}
259	262
260	263	/** Fit a function defined as a macro String like "y = a + bx + cx*x".
	264	* When showSettings is true, pops up a dialog allowing the user to set the initial
	265	* fit parameters and various numbers controlling the Minimizer
261	266	* Returns the number of parameters, or 0 in case of a macro syntax error.
262	267	*
263		* For good performance, it is advisable to set also the typical variation range
264		* of the initial parameters by the
265		* getMinimizer().setInitialParamVariations(double[]) method (especially if one or
266		* more of the initialParams are zero).
267	268	* Use getStatus() and/or getStatusString() to see whether fitting was (probably) successful and
268	269	* getParams() to access the result.
	270	*
	271	* For complicated fits and good performance, it is advisable to use the doCustomFit method with
	272	* a (java) UserFunction, which also has more options.
	273	*
269	274	*/
270	275	public int doCustomFit(String equation, double[] initialParams, boolean showSettings) {
271	276	customFormula = null;

297	302	* Use getStatus() and/or getStatusString() to see whether fitting was (probably) successful and
298	303	* getParams() to access the result.
299	304	*
300		* @param userFunction A plugin where the fit function is defined by the
301		* userFunction(params, x) method.
302		* This function must allow simultaneous calls in multiple threads.
	305	* For getter performance, if possible it is advisable to first call setOffsetMultiplySlopeParams,
	306	* to avoid searching for one or two parameters that can be calculated directly by linear regression.
	307	*
	308	* @param userFunction A class instance implementing the userFunction interface. There, the
	309	* fit function hould be defined by the method userFunction(params, x).
	310	* This function must allow simultaneous calls in multiple threads.
303	311	* @param numParams Number of parameters of the fit function.
304	312	* @param formula A String describing the fit formula, may be null.
305		* @param initialParams Starting point for the parameters; may be null (than values
306		* of 0 are used). The fit function with these parameters must
307		* not return NaN for any of the data points given in the
308		* constructor (xData).
	313	* @param initialParams Starting point for the parameters; the fit function with these parameters
	314	* must not return NaN for any of the data points given in the constructor (xData).
	315	* initialParams may be null, then random values are used,
	316	* with repeated tries if the userFunction returns NaN.
309	317	* @param initialParamVariations Each parameter is initially varied by up to +/- this value.
310		* If not given (null), initial variations are taken as
311		* 10% of initial parameter value or 0.01 for parameters that are zero.
312		* When this array is given, all elements must be positive (nonzero).
313		* See Minimizer.minimize for details.
314		* @param showSettings Displays a popup dialog for modifying the initial parameters and
315		* a few numbers controlling the minimizer.
	318	* If not given (null), initial variations are taken as
	319	* 10% of initial parameter value or 0.01 for parameters that are zero.
	320	* When this array is given, all elements must be positive (nonzero).
	321	* See Minimizer.minimize for details. Providing this array is
	322	* especially valuable if one or more initial parameters have a value of 0.
	323	* @param showSettings Displays a popup dialog for modifying the initial parameters and
	324	* a few numbers controlling the minimizer.
316	325	*/
317	326	public void doCustomFit(UserFunction userFunction, int numParams, String formula,
318	327	double[] initialParams, double[] initialParamVariations, boolean showSettings) {

327	336	/** Sets the initial parameters, which override the default initial parameters. */
328	337	public void setInitialParameters(double[] initialParams) {
329	338	this.initialParams = initialParams;
	339	}
	340
	341	/** Sets weights of the data points. The 'weights' array must have the same length as the data arrays
	342	* passed with the constructor. If the error bars of the data points are known, the weights
	343	* should be proportional to 1/error^2.
	344	* When weights are specified, note that 'getSumResidualsSqr' will return the weighted sum. */
	345	public void setWeights(double[] weights) {
	346	this.weights = weights;
330	347	}
331	348
332	349	/** Returns a reference to the Minimizer used, for accessing Minimizer methods directly.

556	573	return residuals;
557	574	}
558	575
559		/* Get the sum of the residuals (may be NaN if the minimizer could not start properly
	576	/** Returns the sum of the residuals (may be NaN if the minimizer could not start properly
560	577	* i.e., if getStatus() returns Minimizer.INITILIZATION_FAILURE).
	578	* If weights have been specified, each of the residuals is multiplied by the corresponding
	579	* weight before summing.
561	580	*/
562	581	public double getSumResidualsSqr() {
563	582	return getParams()[numParams]; // value is stored as last element by the minimizer

566	585	/** Returns the standard deviation of the residuals.
567	586	* Here, the standard deviation is defined here as the root-mean-square of the residuals
568	587	* times sqrt(n/(n-1)); where n is the number of points.
	588	* If weights are provided, the standard deviation does not take the weights into account.
	589	* With weights, the standard deviation and getSumResidualsSqr (which uses weights)
	590	* are not related the usual way.
569	591	*/
570	592	public double getSD() {
571	593	double[] residuals = getResiduals();

579	601	return Math.sqrt(stdDev/(n-1.0));
580	602	}
581	603
582		/** Returns R^2, where 1.0 is best.
	604	/** Returns R^2, where 1.0 is best. For unweighted data,
583	605	<pre>
584	606	r^2 = 1 - SSE/SSD
585	607
586		where: SSE = sum of the squared errors
587		SSD = sum of the squared deviations about the mean.
	608	where: SSE = sum of the squared errors
	609	SSD = sum of the squared deviations about the mean.
588	610	</pre>
589	611	* For power, exp by linear regression and 'Rodbard NIH Image', this is calculated for the
590	612	* fit actually done, not for the residuals of the original data.
591		*/
	613	*/
592	614	public double getRSquared() {
593	615	if (Double.isNaN(sumY)) calculateSumYandY2();
594		double sumMeanDiffSqr = sumY2 - sumY*sumY/numPoints;
	616	double sumMeanDiffSqr = sumY2 - sumY*sumY/sumWeights;
595	617	double rSquared = 0.0;
596	618	if (sumMeanDiffSqr > 0.0)
597	619	rSquared = 1.0 - getSumResidualsSqr()/sumMeanDiffSqr;

600	622
601	623	/** Get a measure of "goodness of fit" where 1.0 is best.
602	624	* Approaches R^2 if the number of points is much larger than the number of fit parameters.
	625	* Assumes that the data points are independent (i.e., each point having a different x value).
603	626	* For power, exp by linear regression and 'Rodbard NIH Image', this is calculated for the
604	627	* fit actually done, not for the residuals of the original data.
605	628	*/
606	629	public double getFitGoodness() {
607	630	if (Double.isNaN(sumY)) calculateSumYandY2();
608		double sumMeanDiffSqr = sumY2 - sumY*sumY/numPoints;
	631	double sumMeanDiffSqr = sumY2 - sumY*sumY/sumWeights;
609	632	double fitGoodness = 0.0;
610	633	int degreesOfFreedom = numPoints - getNumParams();
611	634	if (sumMeanDiffSqr > 0.0 && degreesOfFreedom > 0)

739	762	fitType = RODBARD;
740	763	return fList[fitType];
741	764	}
742
	765
743	766	/** Returns macro code of the form "y = ...x" for the fit function used.
744	767	* Note that this is not neccessarily the equation acutally used for the fit
745	768	* (for the various "linear regression" types and RODBARD2, the fit is done

790	813	if (numRegressionParams == 0) { // simply calculate sum of residuals
791	814	for (int i=0; i<numPoints; i++) {
792	815	double fValue = f(params,xData[i]);
793		sumResidualsSqr += sqr(fValue-yData[i]);
	816	double resSqr = sqr(fValue-yData[i]);
	817	if (weights != null) resSqr *= weights[i];
	818	sumResidualsSqr += resSqr;
794	819	}
795	820	//IJ.log(IJ.d2s(params[0],3,5)+","+IJ.d2s(params[1],3,5)+": r="+IJ.d2s(sumResidualsSqr,3,5)+Thread.currentThread().getName() );
796	821	} else { // handle simple linear dependencies by linear regression:

845	870	private void doRegression(double[] params) {
846	871	double sumX=0, sumX2=0, sumXY=0; //sums for regression; here 'x' are function values
847	872	double sumY=0, sumY2=0; //only calculated for 'slope', otherwise we use the values calculated already
	873	double sumWeights=0;
848	874	for (int i=0; i<numPoints; i++) {
849	875	double fValue = fitType == STRAIGHT_LINE ? 0 : f(params, xData[i]); // function value
850	876	if (Double.isNaN(fValue)) { //check for NaN now; later we need NaN checking for division-by-zero check.
851	877	params[numParams] = Double.NaN;
852	878	return; //sum of squared residuals is NaN if any value is NaN
853	879	}
	880	double w = weights==null ? 1 : weights[i];
	881	sumWeights += w;
854	882	//if(getIterations()==0)IJ.log(xData[i]+"\t"+yData[i]+"\t"+fValue); //x,y,function
855	883	if (hasSlopeParam) { // fit y = offset + slope*x + function(of other params)
856	884	double x = xData[i];
857	885	double y = yData[i] - fValue;
858		sumX += x;
859		sumX2 += x*x;
860		sumXY += x*y;
861		sumY2 += y*y;
862		sumY += y;
	886	sumX += x*w;
	887	sumX2 += xxw;
	888	sumXY += xyw;
	889	sumY2 += yyw;
	890	sumY += y*w;
863	891	} else { // fit y = offset + factor * function(of other params)
864	892	double x = fValue;
865	893	double y = yData[i];
866		sumX += fValue;
867		sumX2 += fValue*fValue;
868		sumXY += fValue*yData[i];
	894	sumX += fValue*w;
	895	sumX2 += fValuefValuew;
	896	sumXY += fValueyData[i]w;
869	897	}
870	898	}
871	899	if (!hasSlopeParam) {

883	911	sumResidualsSqr = 2e-15*sumY2;
884	912	} else { // full linear regression or offset only. Slope is named 'factor' here
885	913	if (factorParam >= 0) {
886		factor = (sumXY-sumXsumY/numPoints)/(sumX2-sumXsumX/numPoints);
	914	factor = (sumXY-sumXsumY/sumWeights)/(sumX2-sumXsumX/sumWeights);
887	915	if (restrictPower & factor<=0) // power-law fit with (0,0) point: power must be >0
888	916	factor = 1e-100;
889	917	else if (Double.isNaN(factor) \|\| Double.isInfinite(factor))
890	918	factor = 0; // all 'x' values are equal, any factor (slope) will fit
891	919	}
892		double offset = (sumY-factor*sumX)/numPoints;
	920	double offset = (sumY-factor*sumX)/sumWeights;
893	921	params[offsetParam] = offset;
894		sumResidualsSqr = sqr(factor)sumX2 + numPointssqr(offset) + sumY2 +
	922	sumResidualsSqr = sqr(factor)sumX2 + sumWeightssqr(offset) + sumY2 +
895	923	2factoroffsetsumX - 2factorsumXY - 2offset*sumY;
896	924	// check for accuracy problem: large difference of small numbers?
897	925	// Don't report unrealistic or even negative values, otherwise minimization could lead
898	926	// into parameters where we have a numeric problem
899		if (sumResidualsSqr < 2e-15(sqr(factor)sumX2 + numPoints*sqr(offset) + sumY2))
900		sumResidualsSqr = 2e-15(sqr(factor)sumX2 + numPoints*sqr(offset) + sumY2);
	927	if (sumResidualsSqr < 2e-15(sqr(factor)sumX2 + sumWeights*sqr(offset) + sumY2))
	928	sumResidualsSqr = 2e-15(sqr(factor)sumX2 + sumWeights*sqr(offset) + sumY2);
901	929	//if(){IJ.log("sumX="+sumX+" sumX2="+sumX2+" sumXY="+sumXY+" factor="+factor+" offset=="+offset);}
902	930	}
903	931	params[numParams] = sumResidualsSqr;

1215	1243	}
1216	1244
1217	1245
1218		/** calculates the sum of y and y^2 */
	1246	/** calculates the sum of y and y^2 (weighted sum if we have weights) */
1219	1247	private void calculateSumYandY2() {
1220		sumY = 0.0; sumY2 = 0.0;
	1248	sumY = 0.0; sumY2 = 0.0; sumWeights = 0.0;
	1249	double w = 1.0;
1221	1250	for (int i=0; i<numPoints; i++) {
1222	1251	double y = yData[i];
1223		sumY += y;
1224		sumY2 += y*y;
	1252	if (weights != null) w = weights[i];
	1253	sumY += y*w;
	1254	sumY2 += yyw;
	1255	sumWeights += w;
1225	1256	}
1226	1257	}
1227	1258

+30

-3

ij/plugin/Benchmark.java less more

1	1	import ij.*;
2	2	import ij.process.*;
3	3	import ij.gui.*;
	4	import ij.measure.ResultsTable;
	5	import ij.util.Tools;
4	6
5	7	/** Implements the Plugins/Utilities/Run Benchmark command.
6	8	* Suppresses subordinate status bar messages by using

9	11	* IJ.showProgress(-currentIndex,finalIndex).
10	12	*/
11	13	public class Benchmark implements PlugIn {
12		int size = 5000;
13		int ops = 62;
14		int counter;
	14	private String[] results = {
	15	"10.9\|MacBook Air (M1, 2020, Native)",
	16	"17.2\|iMac Pro (2017)",
	17	"18.1\|MacBook Air (M1, 2020, Rosetta)",
	18	"22.8\|Dell T7920 (Dual Xeon, 282GB RAM, 2018)",
	19	"24.7\|27\" iMac (Early 2015)",
	20	"29.7\|13\" MacBook Pro (Late 2015)",
	21	"29.7\|15\" MacBook Pro (Early 2013)",
	22	"62.3\|Acer Aspire laptop (Core i5, 2014)"
	23	};
	24	private int size = 5000;
	25	private int ops = 62;
	26	private int counter;
15	27
16	28	public void run(String arg) {
17	29	ImagePlus cImp = WindowManager.getCurrentImage();

55	67	scale = scale*1.2;
56	68	}
57	69	double time = (System.currentTimeMillis()-t0)/1000.0;
	70	ResultsTable rt = new ResultsTable();
	71	rt.showRowNumbers(true);
	72	for (int i=0; i<results.length; i++) {
	73	String[] columns = Tools.split(results[i],"\|");
	74	rt.addRow();
	75	rt.addValue("Time", columns[0]);
	76	rt.addValue("Computer", columns[1]);
	77	}
	78	rt.addRow();
	79	String t = IJ.d2s(time,1);
	80	if (t.length()<4) t=" "+t;
	81	rt.addValue("Time", t);
	82	rt.addValue("Computer", "<<THIS MACHINE ("+Prefs.getThreads()+" THREADS)>>");
	83	rt.sort("Time");
	84	rt.show("Benchmark Results");
58	85	IJ.showStatus("!"+IJ.d2s(time,1)+" seconds to perform "+counter+" operations on a "+size+"x"+size+" 16-bit image");
59	86	}
60	87

+3

-5

ij/plugin/CanvasResizer.java less more

97	97
98	98	public ImageStack expandStack(ImageStack stackOld, int wNew, int hNew, int xOff, int yOff) {
99	99	int nFrames = stackOld.getSize();
100		ImageProcessor ipOld = stackOld.getProcessor(1);
101		java.awt.Color colorBack = Toolbar.getBackgroundColor();
102
	100	ImageProcessor ipOld = stackOld.getProcessor(1);
103	101	ImageStack stackNew = new ImageStack(wNew, hNew, stackOld.getColorModel());
104	102	ImageProcessor ipNew;
105	103

109	107	if (zeroFill)
110	108	ipNew.setValue(0.0);
111	109	else
112		ipNew.setColor(colorBack);
	110	ipNew.setGlobalBackgroundColor();
113	111	ipNew.fill();
114	112	ipNew.insert(stackOld.getProcessor(i), xOff, yOff);
115	113	stackNew.addSlice(stackOld.getSliceLabel(i), ipNew);

122	120	if (zeroFill)
123	121	ipNew.setValue(0.0);
124	122	else
125		ipNew.setColor(Toolbar.getBackgroundColor());
	123	ipNew.setGlobalBackgroundColor();
126	124	ipNew.fill();
127	125	ipNew.insert(ipOld, xOff, yOff);
128	126	return ipNew;

+0

-3

ij/plugin/ChannelSplitter.java less more

41	41	ImagePlus rImp = new ImagePlus(title+" (red)", channels[0]);
42	42	rImp.setCalibration(cal);
43	43	rImp.setIJMenuBar(false);
44		rImp.setBorderColor(new Color(255,180,180));
45	44	rImp.show();
46	45	rImp.setSlice(pos);
47	46	if (IJ.isMacOSX()) IJ.wait(500);
48	47	ImagePlus gImp = new ImagePlus(title+" (green)", channels[1]);
49	48	gImp.setCalibration(cal);
50	49	gImp.setIJMenuBar(false);
51		gImp.setBorderColor(new Color(180,255,180));
52	50	gImp.show();
53	51	gImp.setSlice(pos);
54	52	if (IJ.isMacOSX()) IJ.wait(500);
55	53	ImagePlus bImp = new ImagePlus(title+" (blue)", channels[2]);
56	54	bImp.setCalibration(cal);
57		bImp.setBorderColor(new Color(180,180,255));
58	55	bImp.show();
59	56	bImp.setSlice(pos);
60	57	}

+7

-4

ij/plugin/DICOM.java less more

257	257	private static final int AE=0x4145, AS=0x4153, AT=0x4154, CS=0x4353, DA=0x4441, DS=0x4453, DT=0x4454,
258	258	FD=0x4644, FL=0x464C, IS=0x4953, LO=0x4C4F, LT=0x4C54, PN=0x504E, SH=0x5348, SL=0x534C,
259	259	SS=0x5353, ST=0x5354, TM=0x544D, UI=0x5549, UL=0x554C, US=0x5553, UT=0x5554,
260		OB=0x4F42, OW=0x4F57, SQ=0x5351, UN=0x554E, QQ=0x3F3F;
	260	OB=0x4F42, OW=0x4F57, SQ=0x5351, UN=0x554E, QQ=0x3F3F,
	261	OF=0x4F46, OL=0x4F4C, OD=0x4F44, UC=0x5543, UR=0x5552, OV=0x4F56, SV=0x5356, UV=0x5556;
	262
261	263
262	264	private static Properties dictionary;
263	265

460	462
461	463	switch (vr) {
462	464	case OB: case OW: case SQ: case UN: case UT:
	465	case OF: case OL: case OD: case UC: case UR:
	466	case OV: case SV: case UV:
463	467	// Explicit VR with 32-bit length if other two bytes are zero
464	468	if ( (b2 == 0) \|\| (b3 == 0) ) return getInt();
465	469	// Implicit VR with 32-bit length

467	471	if (littleEndian)
468	472	return ((b3<<24) + (b2<<16) + (b1<<8) + b0);
469	473	else
470		return ((b0<<24) + (b1<<16) + (b2<<8) + b3);
	474	return ((b0<<24) + (b1<<16) + (b2<<8) + b3);
471	475	case AE: case AS: case AT: case CS: case DA: case DS: case DT: case FD:
472	476	case FL: case IS: case LO: case LT: case PN: case SH: case SL: case SS:
473		case ST: case TM:case UI: case UL: case US: case QQ:
	477	case ST: case TM: case UI: case UL: case US: case QQ:
474	478	// Explicit vr with 16-bit length
475	479	if (littleEndian)
476	480	return ((b3<<8) + b2);

1716	1720	};
1717	1721
1718	1722	}
1719

+0

-1

ij/plugin/Duplicator.java less more

280	280	* @see ij.ImagePlus#crop(String)
281	281	*/
282	282	public ImagePlus crop(ImagePlus imp) {
283		//if (imp!=null) throw new IllegalArgumentException();
284	283	if (imp.getNChannels()>1 && imp.getCompositeMode()==IJ.COMPOSITE) {
285	284	int z = imp.getSlice();
286	285	int t = imp.getFrame();

+5

-2

ij/plugin/FolderOpener.java less more

17	17	private static final int MAX_SEPARATE = 40;
18	18	private static final String DIR_KEY = "import.sequence.dir";
19	19	private static final String[] types = {"default", "16-bit", "32-bit", "RGB"};
20		private static String[] excludedTypes = {".txt", ".lut", ".roi", ".pty", ".hdr", ".java", ".ijm", ".py", ".js", ".bsh", ".xml"};
	20	private static String[] excludedTypes = {".txt",".lut",".roi",".pty",".hdr",".java",".ijm",".py",".js",".bsh",".xml",".rar",".h5",".doc",".xls"};
21	21	private static boolean staticSortFileNames = true;
22	22	private static boolean staticOpenAsVirtualStack;
23	23	private boolean convertToRGB;

421	421	}
422	422	}
423	423	if (imp2.getStackSize()==1) {
424		imp2.setProperty("Label", list[0]);
	424	int idx = this.start-1;
	425	if (idx<0 \|\| idx>=list.length)
	426	idx = 0;
	427	imp2.setProperty("Label", list[idx]);
425	428	if (info1!=null)
426	429	imp2.setProperty("Info", info1);
427	430	}

+6

-4

ij/plugin/ImagesToStack.java less more

91	91	gd.addChoice("Method:", methods, methods[staticMethod]);
92	92	}
93	93	gd.addStringField("Name:", name, 12);
94		gd.addStringField("Title Contains:", "", 12);
	94	gd.addStringField("Title contains:", "", 12);
95	95	if (sizesDiffer)
96		gd.addCheckbox("Bicubic Interpolation", staticBicubic);
97		gd.addCheckbox("Use Titles as Labels", staticTitlesAsLabels);
98		gd.addCheckbox("Keep Source Images", staticKeep);
	96	gd.addCheckbox("Bicubic interpolation", staticBicubic);
	97	gd.addCheckbox("Use titles as labels", staticTitlesAsLabels);
	98	gd.addCheckbox("Keep source images", staticKeep);
99	99	gd.showDialog();
100	100	if (gd.wasCanceled()) return;
101	101	if (sizesDiffer)

149	149	if (ip.getMin()<min) min = ip.getMin();
150	150	if (ip.getMax()>max) max = ip.getMax();
151	151	String label = titlesAsLabels?images[i].getTitle():null;
	152	if (label==null)
	153	label = (String)images[i].getProperty("Label");
152	154	if (label!=null) {
153	155	String info = (String)images[i].getProperty("Info");
154	156	if (info!=null) label += "\n" + info;

+8

-2

ij/plugin/MontageMaker.java less more

181	181	bgColor = Color.white;
182	182	}
183	183	}
184		montage.setColor(bgColor);
	184	if (Double.isNaN(Toolbar.getBackgroundValue()))
	185	montage.setColor(bgColor);
	186	else
	187	montage.setGlobalBackgroundColor();
185	188	montage.fill();
186		montage.setColor(fgColor);
	189	if (Double.isNaN(Toolbar.getForegroundValue()))
	190	montage.setColor(fgColor);
	191	else
	192	montage.setGlobalForegroundColor();
187	193	montage.setFont(new Font("SansSerif", Font.PLAIN, fontSize));
188	194	montage.setAntialiasedText(true);
189	195	ImageStack stack = imp.getStack();

+5

-0

ij/plugin/OverlayCommands.java less more

409	409	public static void listRois(Roi[] rois) {
410	410	ImagePlus imp = WindowManager.getCurrentImage();
411	411	ResultsTable rt = new ResultsTable();
	412	rt.showRowNumbers(true);
412	413	for (int i=0; i<rois.length; i++) {
413	414	if (rois[i]==null)
414	415	continue;

437	438	Rectangle2D.Double bounds = rois[i].getFloatBounds();
438	439	rt.setValue("X", i, (int)Math.round(bounds.x));
439	440	rt.setValue("Y", i, (int)Math.round(bounds.y));
	441	} else if (rois[i] instanceof Arrow) {
	442	Polygon p = ((Arrow)rois[i]).getPoints();
	443	rt.setValue("X", i, p.xpoints[1]);
	444	rt.setValue("Y", i, p.ypoints[1]);
440	445	} else {
441	446	rt.setValue("X", i, r.x);
442	447	rt.setValue("Y", i, r.y);

+2

-1

ij/plugin/PNG_Writer.java less more

36	36	msg = ""+e;
37	37	msg = "An error occured writing the file.\n \n" + msg;
38	38	if (msg.contains("NullPointerException"))
39		msg = "Incorrect file path: \""+path+"\"";
	39	msg = "Incorrect file path:";
	40	msg += "\n \n"+path;
40	41	IJ.error("PNG Writer", msg);
41	42	}
42	43	IJ.showStatus("");

+98

-22

ij/plugin/RoiEnlarger.java less more

4	4	import ij.measure.Calibration;
5	5	import ij.plugin.filter.EDM;
6	6	import ij.plugin.filter.ThresholdToSelection;
	7	import ij.plugin.frame.Recorder;
7	8	import java.awt.*;
	9	import java.util.Vector;
8	10
9	11	/** This plugin, which enlarges or shrinks selections, implements the Edit/Selection/Enlarge command. */
10		public class RoiEnlarger implements PlugIn {
11		private static double defaultDistance = 15; // pixels
	12	public class RoiEnlarger implements PlugIn, DialogListener {
	13	private static final String DISTANCE_KEY = "enlarger.distance";
	14	private static final String USE_PIXELS_KEY = "enlarger.pixels";
	15	private double defaultDistance = Prefs.get(DISTANCE_KEY, 15); // pixels
	16	private boolean defaultUsePixels = Prefs.get(USE_PIXELS_KEY, false);
	17	private Calibration cal;
	18	private Label unitsLabel;
12	19
13	20	public void run(String arg) {
14	21	ImagePlus imp = IJ.getImage();

20	27	if (!imp.okToDeleteRoi())
21	28	return;
22	29	double n = showDialog(imp, defaultDistance);
23		if (n==Double.NaN)
24		return;
	30	if (Double.isNaN(n))
	31	return;
	32	Prefs.set(DISTANCE_KEY, defaultDistance);
	33	Prefs.set(USE_PIXELS_KEY, defaultUsePixels);
25	34	Roi roi2 = Math.abs(n)<256?enlarge255(roi,n):enlarge(roi,n);
26	35	if (roi2!=null) {
27	36	imp.setRoi(roi2);
28	37	Roi.setPreviousRoi(roi);
29	38	defaultDistance = n;
30	39	}
31		}
32
	40	int pixels = (int)Math.round(n);
	41	Recorder.recordCall("RoiEnlarger.enlarge(imp, "+pixels+");");
	42	}
	43
	44	public static void enlarge(ImagePlus imp, int pixels) {
	45	Roi roi = imp.getRoi();
	46	if (roi==null \|\| roi.isLine() \|\| (roi instanceof PointRoi))
	47	return;
	48	Roi roi2 = Math.abs(pixels)<256?enlarge255(roi,pixels):enlarge(roi,pixels);
	49	if (roi2!=null)
	50	imp.setRoi(roi2);
	51	}
	52
33	53	public double showDialog(ImagePlus imp, double pixels) {
34		Calibration cal = imp.getCalibration();
	54	cal = imp.getCalibration();
35	55	boolean scaled = cal.scaled();
36		boolean usePixels = false;
37		double n = pixels*cal.pixelWidth;
	56	double pixelWidth = cal.pixelWidth;
	57	boolean xyScaleDifferent = scaled && cal.pixelWidth != cal.pixelHeight;
	58	boolean usePixels = defaultUsePixels;
	59	double n = pixels;
38	60	int decimalPlaces = 0;
39		if (Math.floor(n)!=n)
40		decimalPlaces = 2;
	61	if (scaled && !usePixels) {
	62	n *= pixelWidth;
	63	decimalPlaces = getDecimalPlaces(pixelWidth, n);
	64	}
41	65	GenericDialog gd = new GenericDialog("Enlarge Selection");
42		gd.addNumericField("Enlarge by", n, decimalPlaces, 4, cal.getUnits());
	66	gd.addNumericField("Enlarge by", n, decimalPlaces);
	67	String units = scaled && !usePixels ? cal.getUnits()+" " : "pixels ";
	68	gd.addToSameRow();
	69	gd.addMessage(units.replace('\n', ' ')); //just in case of a newline character, which would make it a MultiLineLabel
	70	unitsLabel = (Label)gd.getMessage();
43	71	if (scaled) {
44		gd.setInsets(0, 20, 0);
	72	gd.setInsets(0, 20, 0); //top left bottom
45	73	gd.addCheckbox("Pixel units", usePixels);
46	74	}
47	75	gd.setInsets(10, 0, 0);
48	76	gd.addMessage("Enter negative number to shrink", null, Color.darkGray);
	77	if (xyScaleDifferent) {
	78	gd.setInsets(5, 0, 0);
	79	gd.addMessage(" \n ", null, Color.RED);
	80	}
	81	gd.addDialogListener(this);
	82	if (xyScaleDifferent && Macro.getOptions()==null)
	83	updateWarning(gd); //in interactive mode only
49	84	gd.showDialog();
50	85	if (gd.wasCanceled())
51	86	return Double.NaN;
52	87	n = gd.getNextNumber();
53	88	if (scaled)
54	89	usePixels = gd.getNextBoolean();
55		pixels = usePixels?n:n/cal.pixelWidth;
	90	pixels = usePixels ? n : n/pixelWidth;
	91	defaultDistance = pixels;
	92	defaultUsePixels = usePixels;
56	93	return pixels;
57	94	}
58
	95
	96	public boolean dialogItemChanged(GenericDialog gd, AWTEvent e) {
	97	Vector checkboxes = gd.getCheckboxes();
	98	Checkbox usePixelsCbx = checkboxes == null ? null : (Checkbox)checkboxes.get(0);
	99	double n = gd.getNextNumber();
	100	boolean usePixels = cal.scaled() ? gd.getNextBoolean() : true; //getNextBoolean also needed for macro recorded
	101	if (e != null && e.getSource() == usePixelsCbx) {
	102	double pixelWidth = cal.pixelWidth;
	103	int decimalPlaces = 0;
	104	if (usePixels) {
	105	n /= pixelWidth; //scaled to pixels
	106	} else {
	107	n *= pixelWidth; //pixels to scaled
	108	decimalPlaces = getDecimalPlaces(pixelWidth, n);
	109	}
	110	TextField numberField = (TextField)gd.getNumericFields().get(0);
	111	numberField.setText(IJ.d2s(n, decimalPlaces));
	112	if (unitsLabel != null) unitsLabel.setText(usePixels ? "pixels" : cal.getUnits());
	113	boolean xyScaleDifferent = cal.scaled() && cal.pixelWidth != cal.pixelHeight;
	114	if (xyScaleDifferent && usePixelsCbx != null) updateWarning(gd);
	115	}
	116	return !gd.invalidNumber();
	117	}
	118
	119	private void updateWarning(GenericDialog gd) {
	120	Checkbox usePixelsCbx = (Checkbox)gd.getCheckboxes().get(0);
	121	MultiLineLabel warningLabel = (MultiLineLabel)gd.getMessage();
	122	boolean showWarning = !usePixelsCbx.getState(); //warn if not pixels units
	123	warningLabel.setText(showWarning ? "WARNING: x & y scales differ\nConversion to pixels uses x scale" : " \n ");
	124	}
	125
	126	//decimal places for displaying the scaled enlarge/shrink value
	127	private static int getDecimalPlaces(double pixelWidth, double number) {
	128	if (number == (int)number \|\| pixelWidth == 1) return 0;
	129	int decimalPlaces = (int)(-Math.log10(pixelWidth)+1.9);
	130	if (decimalPlaces < 0) decimalPlaces = 0;
	131	if (decimalPlaces >9) decimalPlaces = 9;
	132	return decimalPlaces;
	133	}
	134
59	135	public static Roi enlarge(Roi roi, double pixels) {
60	136	if (pixels==0)
61	137	return roi;

85	161	edm.setThreshold(0, n, ImageProcessor.NO_LUT_UPDATE);
86	162	roi2 = (new ThresholdToSelection()).convert(edm);
87	163	if (roi2==null)
88		return roi;
	164	return roi;
89	165	roi2.copyAttributes(roi);
90	166	roi2.setLocation(bounds.x-n+xoffset, bounds.y-n+yoffset);
91	167	if (roi.getStroke()!=null)
92	168	roi2.setStroke(roi.getStroke());
93	169	return roi2;
94	170	}
95
	171
96	172	private static Roi enlargeRectOrOval(Roi roi, int n) {
97	173	Rectangle bounds = roi.getBounds();
98	174	bounds.x -= n;

109	185	roi2.copyAttributes(roi);
110	186	return roi2;
111	187	}
112
	188
113	189	private static Roi shrink(Roi roi, int n) {
114	190	Rectangle bounds = roi.getBounds();
115	191	int width = bounds.width + 2;

119	195	ip.setColor(255);
120	196	ip.fill(roi);
121	197	roi.setLocation(bounds.x, bounds.y);
122		FloatProcessor edm = new EDM().makeFloatEDM (ip, 0, false);
	198	FloatProcessor edm = new EDM().makeFloatEDM (ip, 0, false);
123	199	edm.setThreshold(n+1, Float.MAX_VALUE, ImageProcessor.NO_LUT_UPDATE);
124	200	Roi roi2 = (new ThresholdToSelection()).convert(edm);
125	201	if (roi2==null)

131	207	roi2.setLocation(bounds.x+bounds2.x-1, bounds.y+bounds2.y-1);
132	208	return roi2;
133	209	}
134
	210
135	211	public static Roi enlarge255(Roi roi, double pixels) {
136	212	if (pixels==0)
137	213	return roi;

164	240	ip.setThreshold(0, n, ImageProcessor.NO_LUT_UPDATE);
165	241	roi2 = (new ThresholdToSelection()).convert(ip);
166	242	if (roi2==null)
167		return roi;
	243	return roi;
168	244	roi2.copyAttributes(roi);
169	245	roi2.setLocation(bounds.x-n+xoffset, bounds.y-n+yoffset);
170	246	if (roi.getStroke()!=null)
171	247	roi2.setStroke(roi.getStroke());
172	248	return roi2;
173	249	}
174
	250
175	251	private static Roi shrink255(Roi roi, int n) {
176	252	Rectangle bounds = roi.getBounds();
177	253	int width = bounds.width + 2;

+81

-17

ij/plugin/Zoom.java less more

24	24	Zoom zoom = new Zoom();
25	25	zoom.setZoom(imp, magnification, x, y);
26	26	}
	27
	28	public static void in(ImagePlus imp) {
	29	ImageCanvas ic = imp.getCanvas();
	30	if (ic==null) return;
	31	waitUntilActivated(imp);
	32	int x = ic.screenX(imp.getWidth()/2);
	33	int y = ic.screenY(imp.getHeight()/2);
	34	ic.zoomIn(x, y);
	35	if (ic.getMagnification()<=1.0)
	36	imp.repaintWindow();
	37	}
	38
	39	public static void out(ImagePlus imp) {
	40	ImageCanvas ic = imp.getCanvas();
	41	if (ic==null) return;
	42	waitUntilActivated(imp);
	43	int x = ic.screenX(imp.getWidth()/2);
	44	int y = ic.screenY(imp.getHeight()/2);
	45	ic.zoomOut(x, y);
	46	if (ic.getMagnification()<=1.0)
	47	imp.repaintWindow();
	48	}
	49
	50	public static void unzoom(ImagePlus imp) {
	51	ImageCanvas ic = imp.getCanvas();
	52	if (ic!=null) {
	53	waitUntilActivated(imp);
	54	ic.unzoom();
	55	}
	56	}
	57
	58	public static void maximize(ImagePlus imp) {
	59	ImageWindow win = imp.getWindow();
	60	if (win!=null) {
	61	waitUntilActivated(imp);
	62	win.maximize();
	63	IJ.wait(100);
	64	}
	65	}
	66
	67	private static void waitUntilActivated(ImagePlus imp) {
	68	int count = 0;
	69	boolean isCanvas = imp.getCanvas()!=null;
	70	if (isCanvas) {
	71	long t0 = System.currentTimeMillis();
	72	while (!imp.windowActivated() && (System.currentTimeMillis()-t0)<=1000) {
	73	IJ.wait(10);
	74	count++;
	75	}
	76	}
	77	if (IJ.debugMode)
	78	IJ.log("Zoom: "+ count+" "+imp.windowActivated()+" "+isCanvas+" "+imp);
	79	}
27	80
28	81	public void run(String arg) {
29	82	ImagePlus imp = WindowManager.getCurrentImage();
30		if (imp==null)
31		{IJ.noImage(); return;}
	83	if (imp==null) {
	84	IJ.noImage();
	85	return;
	86	}
32	87	ImageCanvas ic = imp.getCanvas();
33	88	if (ic==null) return;
34	89	if (ic instanceof PlotCanvas && !((PlotCanvas)ic).isFrozen()) {

44	99	int x = ic.screenX(loc.x);
45	100	int y = ic.screenY(loc.y);
46	101	if (arg.equals("in")) {
47		ic.zoomIn(x, y);
48		if (ic.getMagnification()<=1.0) imp.repaintWindow();
	102	waitUntilActivated(imp);
	103	ic.zoomIn(x, y);
	104	if (ic.getMagnification()<=1.0)
	105	imp.repaintWindow();
	106	Recorder.recordCall("Zoom.in(imp);");
49	107	} else if (arg.equals("out")) {
	108	waitUntilActivated(imp);
50	109	ic.zoomOut(x, y);
51		if (ic.getMagnification()<1.0) imp.repaintWindow();
52		} else if (arg.equals("orig"))
53		ic.unzoom();
54		else if (arg.equals("100%"))
	110	if (ic.getMagnification()<1.0)
	111	imp.repaintWindow();
	112	Recorder.recordCall("Zoom.out(imp);");
	113	} else if (arg.equals("orig")) {
	114	unzoom(imp);
	115	Recorder.recordCall("Zoom.unzoom(imp);");
	116	} else if (arg.equals("100%")) {
	117	waitUntilActivated(imp);
55	118	ic.zoom100Percent();
56		else if (arg.equals("to")) {
	119	} else if (arg.equals("to")) {
57	120	zoomToSelection(imp, ic);
58	121	Recorder.recordCall("Zoom.toSelection(imp);");
59		} else if (arg.equals("set"))
	122	} else if (arg.equals("set")) {
60	123	setZoom(imp, -1, -1, -1);
61		else if (arg.equals("max")) {
62		ImageWindow win = imp.getWindow();
63		if (win!=null) {
64		win.maximize();
65		IJ.wait(100);
66		}
	124	} else if (arg.equals("max")) {
	125	maximize(imp);
	126	Recorder.recordCall("Zoom.maximize(imp);");
67	127	} else if (arg.equals("scale"))
68	128	scaleToFit(imp);
69	129	}
70	130
71	131	void zoomToSelection(ImagePlus imp, ImageCanvas ic) {
	132	waitUntilActivated(imp);
72	133	Roi roi = imp.getRoi();
73	134	ic.unzoom();
74	135	if (roi==null) return;

80	141	int x = r.x+r.width/2;
81	142	int y = r.y+r.height/2;
82	143	mag = ic.getHigherZoomLevel(mag);
83		while(r.widthmag<w.width - marginw && r.heightmag<w.height - marginh) {
	144	while (r.widthmag<w.width-marginw && r.heightmag<w.height-marginh) {
84	145	ic.zoomIn(ic.screenX(x), ic.screenY(y));
85	146	double cmag = ic.getMagnification();
86	147	if (cmag==32.0) break;

92	153	/** Based on Albert Cardona's ZoomExact plugin:
93	154	http://albert.rierol.net/software.html */
94	155	void setZoom(ImagePlus imp, double mag, int x, int y) {
	156	waitUntilActivated(imp);
95	157	ImageCanvas ic = imp.getCanvas();
96	158	if (ic==null)
97	159	return;

155	217	int canvasHeight = (int)(srcHeightmag+insets.top+insets.bottom+ImageWindow.VGAP2+win.getSliderHeight());
156	218	ic.setSourceRect(new Rectangle(x-srcWidth/2,y-srcHeight/2,srcWidth,srcHeight));
157	219	ic.setMagnification(mag);
	220	ic.setSize(new Dimension((int)(srcWidthmag), (int)(srcHeightmag)));
158	221	win.setSize(canvasWidth, canvasHeight);
159	222	return;
160	223	}

193	256	}
194	257
195	258	private void scaleToFit(ImagePlus imp) {
	259	waitUntilActivated(imp);
196	260	ImageCanvas ic = imp.getCanvas();
197	261	if (ic==null)
198	262	return;

+6

-6

ij/plugin/filter/Filler.java less more

76	76	}
77	77
78	78	public void clear(ImageProcessor ip) {
79		ip.setColor(Toolbar.getBackgroundColor());
	79	ip.setGlobalBackgroundColor();
80	80	if (isLineSelection()) {
81	81	if (isStraightLine() && roi.getStrokeWidth()>1)
82	82	ip.fillPolygon(roi.getPolygon());

86	86	((TextRoi)roi).clear(ip);
87	87	else
88	88	ip.fill(); // fill with background color
89		ip.setColor(Toolbar.getForegroundColor());
	89	ip.setGlobalForegroundColor();
90	90	}
91	91
92	92	/**

95	95	*/
96	96	public void fill(ImageProcessor ip) {
97	97	if (!IJ.isMacro() \|\| !ip.fillValueSet())
98		ip.setColor(Toolbar.getForegroundColor());
	98	ip.setGlobalForegroundColor();
99	99	if (isLineSelection()) {
100	100	if (isStraightLine() && roi.getStrokeWidth()>1 && !(roi instanceof Arrow)) {
101	101	Roi roi2=Roi.convertLineToArea(roi);

113	113	* replaced by ImageProcessor.draw(Roi)
114	114	*/
115	115	public void draw(ImageProcessor ip) {
116		ip.setColor(Toolbar.getForegroundColor());
	116	ip.setGlobalForegroundColor();
117	117	roi.drawPixels(ip);
118	118	if (IJ.altKeyDown())
119	119	drawLabel(ip);

215	215	Rectangle r = ip.getRoi();
216	216	if (mask==null)
217	217	makeMask(ip, r);
218		ip.setColor(Toolbar.getBackgroundColor());
	218	ip.setGlobalBackgroundColor();
219	219	int stackSize = imp.getStackSize();
220	220	if (stackSize>1)
221	221	ip.snapshot();

233	233	ip.fill();
234	234	ip.setRoi(r); // restore original ROI
235	235	if (sliceCount==stackSize) {
236		ip.setColor(Toolbar.getForegroundColor());
	236	ip.setGlobalForegroundColor();
237	237	Roi roi = imp.getRoi();
238	238	imp.deleteRoi();
239	239	imp.updateAndDraw();

+11

-8

ij/plugin/filter/ParticleAnalyzer.java less more

1032	1032	overlay.add(roi2);
1033	1033	} else {
1034	1034	Rectangle r = roi.getBounds();
1035		int nPoints = ((PolygonRoi)roi).getNCoordinates();
1036		int[] xp = ((PolygonRoi)roi).getXCoordinates();
1037		int[] yp = ((PolygonRoi)roi).getYCoordinates();
1038		int x=r.x, y=r.y;
1039	1035	if (!inSituShow)
1040	1036	ip.setValue(0.0);
1041		ip.moveTo(x+xp[0], y+yp[0]);
1042		for (int i=1; i<nPoints; i++)
1043		ip.lineTo(x+xp[i], y+yp[i]);
1044		ip.lineTo(x+xp[0], y+yp[0]);
	1037	if (roi instanceof PolygonRoi) {
	1038	int nPoints = ((PolygonRoi)roi).getNCoordinates();
	1039	int[] xp = ((PolygonRoi)roi).getXCoordinates();
	1040	int[] yp = ((PolygonRoi)roi).getYCoordinates();
	1041	int x=r.x, y=r.y;
	1042	ip.moveTo(x+xp[0], y+yp[0]);
	1043	for (int i=1; i<nPoints; i++)
	1044	ip.lineTo(x+xp[i], y+yp[i]);
	1045	ip.lineTo(x+xp[0], y+yp[0]);
	1046	} else
	1047	roi.drawPixels(ip);
1045	1048	if (showChoice!=BARE_OUTLINES) {
1046	1049	String s = ResultsTable.d2s(count,0);
1047	1050	ip.moveTo(r.x+r.width/2-ip.getStringWidth(s)/2, r.y+r.height/2+fontSize/2);

+1

-1

ij/plugin/filter/PlugInFilterRunner.java less more

105	105	((ExtendedPlugInFilter)theFilter).setNPasses(nPasses);
106	106	if ((flags&PlugInFilter.NO_CHANGES)==0) { // for filters modifying the image
107	107	boolean disableUndo = Prefs.disableUndo \|\| (flags&PlugInFilter.NO_UNDO)!=0;
108		if (!disableUndo) {
	108	if (!disableUndo \|\| ((ip instanceof ColorProcessor)&&WindowManager.getWindow("B&C")!=null)) {
109	109	ip.snapshot();
110	110	snapshotPixels = ip.getSnapshotPixels();
111	111	}

+21

-9

ij/plugin/filter/Rotator.java less more

22	22	private String[] methods = ImageProcessor.getInterpolationMethods();
23	23	private static int interpolationMethod = ImageProcessor.BILINEAR;
24	24	private Overlay overlay;
	25	private boolean done;
25	26
26	27	public int setup(String arg, ImagePlus imp) {
27	28	this.imp = imp;

80	81	imp.updateAndDraw();
81	82	Undo.setup(Undo.COMPOUND_FILTER_DONE, imp);
82	83	}
	84	if (done) { // remove grid
	85	Overlay ovly = imp.getOverlay();
	86	if (ovly!=null) {
	87	ovly.remove(GRID);
	88	if (ovly.size()==0) imp.setOverlay(null);
	89	}
	90	}
83	91	}
84	92
85	93	void enlargeCanvas() {
86	94	imp.unlock();
87		IJ.run("Select All");
88		IJ.run("Rotate...", "angle="+angle);
	95	IJ.run(imp, "Select All", "");
	96	IJ.run(imp, "Rotate...", "angle="+angle);
89	97	Roi roi = imp.getRoi();
90	98	Rectangle r = roi.getBounds();
91	99	if (r.width<imp.getWidth()) r.width = imp.getWidth();

93	101	IJ.showStatus("Rotate: Enlarging...");
94	102	if (imp.getStackSize()==1)
95	103	Undo.setup(Undo.COMPOUND_FILTER, imp);
96		IJ.run("Canvas Size...", "width="+r.width+" height="+r.height+" position=Center "+(fillWithBackground?"":"zero"));
	104	IJ.run(imp, "Canvas Size...", "width="+r.width+" height="+r.height+" position=Center "+(fillWithBackground?"":"zero"));
97	105	IJ.showStatus("Rotating...");
98	106	}
99	107
100	108	void drawGridLines(int lines) {
101		//if (overlay.size()>0 && GRID.equals(overlay.get(0).getName()))
102		// overlay.remove(0);
	109	if (overlay==null)
	110	return;
103	111	overlay.remove(GRID);
104	112	if (lines==0)
105	113	return;

153	161	return DONE;
154	162	}
155	163	Overlay ovly = imp.getOverlay();
156		if (ovly!=null) ovly.remove(GRID);
157		if (!enlarge)
	164	if (ovly!=null) {
	165	ovly.remove(GRID);
	166	if (ovly.size()==0) imp.setOverlay(null);
	167	}
	168	if (enlarge)
	169	flags \|= NO_CHANGES; // undoable as a "compound filter"
	170	else if (imp.getStackSize()==1)
158	171	flags \|= KEEP_PREVIEW; // standard filter without enlarge
159		else if (imp.getStackSize()==1)
160		flags \|= NO_CHANGES; // undoable as a "compound filter"
	172	done = true;
161	173	return IJ.setupDialog(imp, flags);
162	174	}
163	175

+8

-3

ij/plugin/frame/RoiManager.java less more

704	704	//IJ.log("restore: "+roi.getPosition()+" "+roi.getZPosition()+" "+imp.getNSlices()+" "+imp.getStackSize());
705	705	if (setSlice) {
706	706	boolean hyperstack = imp.isHyperStack();
	707	int position = roi.getPosition();
707	708	if (hyperstack && roi.hasHyperStackPosition())
708	709	imp.setPosition(roi.getCPosition(), roi.getZPosition(), roi.getTPosition());
	710	else if (hyperstack && imp.getNSlices()==1)
	711	imp.setPosition(imp.getChannel(), 1, position);
	712	else if (hyperstack)
	713	imp.setPosition(imp.getChannel(), position, imp.getChannel());
709	714	else if (roi.getZPosition()>0 && imp.getNSlices()==imp.getStackSize())
710		imp.setSlice(roi.getZPosition());
711		else if (roi.getPosition()>0 && roi.getPosition()<=imp.getStackSize())
712		imp.setSlice(roi.getPosition());
	715	imp.setSlice(roi.getZPosition());
	716	else if (position>0 && position<=imp.getStackSize())
	717	imp.setSlice(position);
713	718	else {
714	719	String label = (String)listModel.getElementAt(index);
715	720	int n = getSliceNumber(roi, label);

+26

-0

ij/process/ImageProcessor.java less more

429	429
430	430	/** Returns the background fill value. */
431	431	public abstract double getBackgroundValue();
	432
	433	/** Sets the global (Color Picker) foreground color
	434	* as the fill/draw color.
	435	* @see ij.gui.Toolbar#setForegroundColor(Color)
	436	* @see ij.gui.Toolbar#setForegroundValue(double)
	437	*/
	438	public void setGlobalForegroundColor() {
	439	double value = Toolbar.getForegroundValue();
	440	if (Double.isNaN(value))
	441	setColor(Toolbar.getForegroundColor());
	442	else
	443	setValue(value);
	444	}
	445
	446	/** Sets the global (Color Picker) background color
	447	* as the fill/draw color.
	448	* @see ij.gui.Toolbar#setBackgroundColor(Color)
	449	* @see ij.gui.Toolbar#setBackgroundValue(double)
	450	*/
	451	public void setGlobalBackgroundColor() {
	452	double value = Toolbar.getBackgroundValue();
	453	if (Double.isNaN(value))
	454	setColor(Toolbar.getBackgroundColor());
	455	else
	456	setValue(value);
	457	}
432	458
433	459	/** Returns the smallest displayed pixel value. */
434	460	public abstract double getMin();

+11

-0

ij/text/TableListener.java less more

	0	package ij.text;
	1
	2	/** Plugins that implement this interface are notified when
	3	a table is opened, closed or updated. The
	4	Plugins/Utilities/Monitor Events command uses this interface.
	5	*/
	6	public interface TableListener {
	7
	8	public void TableUpdated(TextPanel table, String event, int row);
	9
	10	}

+43

-0

ij/util/Tools.java less more

4	4	import java.io.*;
5	5	import java.util.Comparator;
6	6	import java.nio.channels.FileChannel;
	7	import java.nio.file.*;
	8	import java.security.MessageDigest;
	9
7	10
8	11	/** This class contains static utility methods. */
9	12	public class Tools {

417	420	default: return c;
418	421	}
419	422	}
	423
	424	/** Returns the checksum of a string or file, or "0" if no success.
	425	The 'method' argument must be "MD5" or "SHA-256".
	426	*/
	427	public static String getHash(String method, boolean fromFile, String pathOrString) {
	428	method = method.toUpperCase();
	429	boolean md5 = method.contains("MD5");
	430	boolean sha_256 = method.contains("SHA-256");
	431	try {
	432	MessageDigest digest = null;
	433	if (md5)
	434	digest = MessageDigest.getInstance("MD5");
	435	else if(sha_256)
	436	digest = MessageDigest.getInstance("SHA-256");
	437	else
	438	return "0";
	439	Path path = Paths.get(pathOrString);
	440	byte[] encodedhash;
	441	if (fromFile)
	442	encodedhash = digest.digest(Files.readAllBytes(path));
	443	else
	444	encodedhash = digest.digest(pathOrString.getBytes());
	445
	446	return bytesToHex(encodedhash);
	447
	448	} catch (Exception e) {}
	449	return "0";
	450	}
	451
	452	private static String bytesToHex(byte[] hash) {
	453	StringBuilder hexString = new StringBuilder(2 * hash.length);
	454	for (int i = 0; i < hash.length; i++) {
	455	String hex = Integer.toHexString(0xff & hash[i]);
	456	if (hex.length() == 1) {
	457	hexString.append('0');
	458	}
	459	hexString.append(hex);
	460	}
	461	return hexString.toString();
	462	}
420	463
421	464	}

+77

-10

release-notes.html less more

3	3	<title>Release Notes</title>
4	4	</head>
5	5	<body>
	6
	7	<li> <u>1.53j 13 May 2021</u>
	8	<ul>
	9	<li> Thanks to 'VolkerH', the table created by
	10	<i>Image>Overlay>List Elements</i> now
	11	displays row numbers and arrow selection 'X' and 'Y'
	12	values are the coordinates of the arrow tip.
	13	<li> Thanks to Stein Rorvik, added the Color.setForegroundValue()
	14	and Color.setBackgroundValue() macro functions and the
	15	Toolbar.setForegroundValue(), Toolbar.setBackgroundValue(),
	16	ImageProcessor.setGlobalForegroundColor() and
	17	ImageProcessor.setGlobalBackgroundColor() methods.
	18	<li> Thanks to Norbert Vischer, added the IJ.checksum() macro
	19	function, which returns the MD5 (or SHA-256) checksum from
	20	a string or file
	21	(<a href="http://wsr.imagej.net/macros/ChecksumTest.txt">example</a>).
	22	<li> Thanks to Michael Schmid, added the
	23	Fit.doWeightedFit(equation,x,y,weights[,initialGuesses])
	24	macro function.
	25	<li> Thanks to Norbert Vischer, added the Plot.removeNaNs macro function.
	26	<li> Thanks to Laurent Thomas, added support for scrollbars in
	27	GenericDialog TextAreas.
	28	<li> Thanks to Fred Damen, added the Zoom.in(imp), Zoom.out(imp),
	29	Zoom.unzoom(imp) and Zoom.maximize(imp) methods.
	30	<li> Thanks to John Dunsmuir, added the PointRoi.addPoint(x,y,position) method.
	31	<li> Thanks to Fred Damen, fixed bugs that caused programmatic image
	32	window zooming to not work reliably
	33	(<a href="http://wsr.imagej.net/macros/js/ZoomTest.js">example</a>).
	34	<li> Thanks to Michael Schmid, fixed a bug with HTMLDialogs that
	35	caused the initial scroll position to be at the end when displaying
	36	more text than what fits in the window.
	37	<li> Thanks to 'Sethur', fixed bugs that caused DICOM
	38	files using newer VRs (from 2014 and later), such as
	39	UC and UR, to fail.
	40	<li> Thanks to Bruno Vellutini, fixed a bug that caused images rotated
	41	interactively using the "Enlarge image" and "Preview" options to not
	42	have the grid lines removed after the rotation.
	43	<li> Thanks to Jerome Mutterer, fixed a bug that caused the
	44	Prefs.savePreferences() method to throw a null pointer
	45	exception if the "ImageJ" window was not open.
	46	<li> Thanks to Stein Rorvik, fixed a bug that caused the slice
	47	label to be incorrect after importing an image sequence and
	48	"Start" was greater than 1 and "Count" was 1.
	49	<li> Thanks to Stein Rorvik, fixed a bug that caused
	50	the <i>Images to Stack</i> command to ignore slice labels
	51	when the "Use titles as labels" option was not enabled.
	52	<li> Thanks to 'ghf', worked around a Fiji bug that caused the
	53	<i>File>Import>Image Sequence</i> command to fail
	54	if the folder contained a ".h5" file.
	55	<li> Thanks to Jerome Mutterer, fixed bugs that caused the
	56	Stack.setDisplayMode(), Stack.setSlice(), Stack.setFrame()
	57	and Stack.setPosition() macro functions to not work as expected
	58	in batch mode, and the ImagePlus.setDisplayMode(),
	59	ImagePlus.setZ(), ImagePlus.setSetT() and
	60	ImagePlus.setPosition() methods to not work as expected when
	61	the image was not displayed.
	62	<li> Thanks to Nicolas Montes, fixed a bug that caused the
	63	particle analyzer to throw an exception when both the
	64	"Composite ROIs" and "Show: Outlines" options where used.
	65	<li> Thanks to Christian Kremser, fixed a 1.53i regression
	66	that caused macro statements like "n=Dialog.getNumber()+1"
	67	to generate and error.
	68	<li> Thanks to Christian Tischer, fixed a regression that
	69	caused the ROI Manager to not set the hyperstack position
	70	of ROIs without a c,z,t position.
	71
	72	</ul>
6	73
7	74	<li> <u>1.53i 24 March 2021</u>
8	75	<ul>

14	81	is displayed in the status bar. The total number of lines is
15	82	displayed after <i>Select All</i>.
16	83	<li> Thanks to Norbert Vischer, ImageJ now corrects the orientation of
17		phone camera photos. This does not work on Fiji because it is
	84	phone camera photos. Does not work on Fiji because it is
18	85	missing Exif_Reader.jar.
19	86	<li> Improved the Plugins>Utilities>Benchmark command. It now
20	87	suppresses subordinate status bar messages and displays

24	91	in the Log window if it was not called from a macro and a
25	92	threshold was not set.
26	93	<li> Thanks to Laurent Thomas, <i>File>Save As>Image Sequence</i>,
27		with "Use slice labels as names" enabled, now supports file names as
	94	when "Use slice labels as names" is enabled, now supports file names as
28	95	long as 111 characters, excluding the extension.
29		<li> Thanks to Michael Schmid, ImageJ displays “horizontal” in the
30		image info line of column average plots and “vertical” for
	96	<li> Thanks to Michael Schmid, ImageJ displays "horizontal" in the
	97	image info line of column average plots and "vertical" with
31	98	row average plots.
32	99	<li> Thanks to Jerome Mutterer, added the showStatus(message,options)
33	100	macro function and the IJ.showStatus(message,options) method
34	101	(<a href="http://wsr.imagej.net/macros/FlashingStatusMessages.txt">example</a>).
35		<li> Added the Overlay.update(index) macro function. DOCUMENT
	102	<li> Added the Overlay.update(index) macro function.
36	103	<li> Added the ImagePlus.setBorderColor() method,
37	104	used by <i>Image>Color>Split Channels</i> to
38	105	colorize image borders.

41	108	methods.
42	109	<li> Thanks to Herbie Gluender, fixed a bug that caused the status bar
43	110	to stop being updated after activating an overlay selection.
44		<li> Thanks to Fred Damen, fixed a bug with one slice stacks where the slice label
45		is not displayed on the image window info line or in the <i>Image>Show Info</i>
46		window.
	111	<li> Thanks to Fred Damen, fixed a bug with one slice stacks that caused the
	112	slice label to not be displayed on the image info line or in the
	113	<i>Image>Show Info</i> window.
47	114	<li> Thanks to Antoneta, fixed a bug with the <i>Flatten</i> command that caused
48	115	multi-point selections on stacks to lose counter information.
49	116	<li> Thanks to Herbie Gluender, fixed a bug that caused unexpected overlay

63	130	WaitForUserDialogs to not be scaled on high-resolution
64	131	screens.
65	132	<li> Thanks to Stein Rorvik, fixed a macro interpreter bug that caused
66		if statements using built in string functions to fail
	133	if statements using string functions to sometimes fail
67	134	(e.g., "if (getTitle.length>10) ...").
68	135	<li> Thanks to Norbert Vischer, fixed a bug that caused the
69	136	first column of tables copied to the clipboard to be missing

74	141	the "Properties..." command in the ROI Manager to not work as
75	142	expected when changing the stroke color.
76	143	<li> Thanks to Stein Rorvik, fixed a 1.53i regression that caused
77		the str.trim() macro function to fail.
	144	the str.trim() macro function to sometimes fail.
78	145	</ul>
79	146
80	147	<li> <u>1.53h 04 February 2021</u>