/**
* Implements ImageJ's Analyze Particles command.
*
* <p>
*
* <pre>
* for each line do
* for each pixel in this line do
* if the pixel value is "inside" the threshold range then
* trace the edge to mark the object
* do the measurement
* fill the object with a color outside the threshold range
* else
* continue the scan
* </pre>
*/
public class ParticleAnalyzer implements PlugInFilter, Measurements {
/** Display results in the ImageJ console. */
public static final int SHOW_RESULTS = 1;
/** Obsolete */
public static final int SHOW_SUMMARY = 2;
/** Display image containing outlines of measured particles. */
public static final int SHOW_OUTLINES = 4;
/** Do not measure particles touching edge of image. */
public static final int EXCLUDE_EDGE_PARTICLES = 8;
/** Display image containing grayscales masks that identify measured particles. */
public static final int SHOW_ROI_MASKS = 16;
/** Display a progress bar. */
public static final int SHOW_PROGRESS = 32;
/** Clear ImageJ console before starting. */
public static final int CLEAR_WORKSHEET = 64;
/** Record starting coordinates so outline can be recreated later using doWand(x,y). */
public static final int RECORD_STARTS = 128;
/** Display a summary. */
public static final int DISPLAY_SUMMARY = 256;
/** Do not display particle outline image. */
public static final int SHOW_NONE = 512;
/** Flood fill to ignore interior holes. */
public static final int INCLUDE_HOLES = 1024;
/** Add particles to ROI Manager. */
public static final int ADD_TO_MANAGER = 2048;
/** Display image containing binary masks of measured particles. */
public static final int SHOW_MASKS = 4096;
/** Use 4-connected particle tracing. */
public static final int FOUR_CONNECTED = 8192;
/** Replace original image with masks. */
public static final int IN_SITU_SHOW = 16384;
/** Display particle outlines as an overlay. */
public static final int SHOW_OVERLAY_OUTLINES = 32768;
/** Display filled particle as an overlay. */
public static final int SHOW_OVERLAY_MASKS = 65536;
static final String OPTIONS = "ap.options";
static final int BYTE = 0, SHORT = 1, FLOAT = 2, RGB = 3;
static final double DEFAULT_MIN_SIZE = 0.0;
static final double DEFAULT_MAX_SIZE = Double.POSITIVE_INFINITY;
private static double staticMinSize = 0.0;
private static double staticMaxSize = DEFAULT_MAX_SIZE;
private static boolean pixelUnits;
private static int staticOptions = Prefs.getInt(OPTIONS, CLEAR_WORKSHEET);
private static String[] showStrings = {
"Nothing",
"Outlines",
"Bare Outlines",
"Ellipses",
"Masks",
"Count Masks",
"Overlay Outlines",
"Overlay Masks"
};
private static double staticMinCircularity = 0.0, staticMaxCircularity = 1.0;
private static String prevHdr;
protected static final int NOTHING = 0,
OUTLINES = 1,
BARE_OUTLINES = 2,
ELLIPSES = 3,
MASKS = 4,
ROI_MASKS = 5,
OVERLAY_OUTLINES = 6,
OVERLAY_MASKS = 7;
protected static int staticShowChoice;
protected ImagePlus imp;
protected ResultsTable rt;
protected Analyzer analyzer;
protected int slice;
protected boolean processStack;
protected boolean showResults,
excludeEdgeParticles,
showSizeDistribution,
resetCounter,
showProgress,
recordStarts,
displaySummary,
floodFill,
addToManager,
inSituShow;
private String summaryHdr = "Slice\tCount\tTotal Area\tAverage Size\tArea Fraction";
private double level1, level2;
private double minSize, maxSize;
private double minCircularity, maxCircularity;
private int showChoice;
private int options;
private int measurements;
private Calibration calibration;
private String arg;
private double fillColor;
private boolean thresholdingLUT;
private ImageProcessor drawIP;
private int width, height;
private boolean canceled;
private ImageStack outlines;
private IndexColorModel customLut;
private int particleCount;
private int maxParticleCount = 0;
private int totalCount;
private TextWindow tw;
private Wand wand;
private int imageType, imageType2;
private boolean roiNeedsImage;
private int minX, maxX, minY, maxY;
private ImagePlus redirectImp;
private ImageProcessor redirectIP;
private PolygonFiller pf;
private Roi saveRoi;
private int beginningCount;
private Rectangle r;
private ImageProcessor mask;
private double totalArea;
private FloodFiller ff;
private Polygon polygon;
private RoiManager roiManager;
private ImagePlus outputImage;
private boolean hideOutputImage;
private int roiType;
private int wandMode = Wand.LEGACY_MODE;
private Overlay overlay;
boolean blackBackground;
private static int defaultFontSize = 9;
private static int nextFontSize = defaultFontSize;
private static int nextLineWidth = 1;
private int fontSize = nextFontSize;
private int lineWidth = nextLineWidth;
/**
* Constructs a ParticleAnalyzer.
*
* @param options a flag word created by Oring SHOW_RESULTS, EXCLUDE_EDGE_PARTICLES, etc.
* @param measurements a flag word created by ORing constants defined in the Measurements
* interface
* @param rt a ResultsTable where the measurements will be stored
* @param minSize the smallest particle size in pixels
* @param maxSize the largest particle size in pixels
* @param minCirc minimum circularity
* @param maxCirc maximum circularity
*/
public ParticleAnalyzer(
int options,
int measurements,
ResultsTable rt,
double minSize,
double maxSize,
double minCirc,
double maxCirc) {
this.options = options;
this.measurements = measurements;
this.rt = rt;
if (this.rt == null) this.rt = new ResultsTable();
this.minSize = minSize;
this.maxSize = maxSize;
this.minCircularity = minCirc;
this.maxCircularity = maxCirc;
slice = 1;
if ((options & SHOW_ROI_MASKS) != 0) showChoice = ROI_MASKS;
if ((options & SHOW_OVERLAY_OUTLINES) != 0) showChoice = OVERLAY_OUTLINES;
if ((options & SHOW_OVERLAY_MASKS) != 0) showChoice = OVERLAY_MASKS;
if ((options & SHOW_OUTLINES) != 0) showChoice = OUTLINES;
if ((options & SHOW_MASKS) != 0) showChoice = MASKS;
if ((options & SHOW_NONE) != 0) showChoice = NOTHING;
if ((options & FOUR_CONNECTED) != 0) {
wandMode = Wand.FOUR_CONNECTED;
options |= INCLUDE_HOLES;
}
nextFontSize = defaultFontSize;
nextLineWidth = 1;
}
/** Constructs a ParticleAnalyzer using the default min and max circularity values (0 and 1). */
public ParticleAnalyzer(
int options, int measurements, ResultsTable rt, double minSize, double maxSize) {
this(options, measurements, rt, minSize, maxSize, 0.0, 1.0);
}
/** Default constructor */
public ParticleAnalyzer() {
slice = 1;
}
public int setup(String arg, ImagePlus imp) {
this.arg = arg;
this.imp = imp;
IJ.register(ParticleAnalyzer.class);
if (imp == null) {
IJ.noImage();
return DONE;
}
if (imp.getBitDepth() == 24 && !isThresholdedRGB(imp)) {
IJ.error(
"Particle Analyzer",
"RGB images must be thresholded using\n" + "Image>Adjust>Color Threshold.");
return DONE;
}
if (!showDialog()) return DONE;
int baseFlags = DOES_ALL + NO_CHANGES + NO_UNDO;
int flags = IJ.setupDialog(imp, baseFlags);
processStack = (flags & DOES_STACKS) != 0;
slice = 0;
saveRoi = imp.getRoi();
if (saveRoi != null && saveRoi.getType() != Roi.RECTANGLE && saveRoi.isArea())
polygon = saveRoi.getPolygon();
imp.startTiming();
nextFontSize = defaultFontSize;
nextLineWidth = 1;
return flags;
}
public void run(ImageProcessor ip) {
if (canceled) return;
slice++;
if (imp.getStackSize() > 1 && processStack) imp.setSlice(slice);
if (imp.getType() == ImagePlus.COLOR_RGB) {
ip = (ImageProcessor) imp.getProperty("Mask");
ip.setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
}
if (!analyze(imp, ip)) canceled = true;
if (slice == imp.getStackSize()) {
imp.updateAndDraw();
if (saveRoi != null) imp.setRoi(saveRoi);
}
}
/** Displays a modal options dialog. */
public boolean showDialog() {
Calibration cal = imp != null ? imp.getCalibration() : (new Calibration());
double unitSquared = cal.pixelWidth * cal.pixelHeight;
if (pixelUnits) unitSquared = 1.0;
if (Macro.getOptions() != null) {
boolean oldMacro = updateMacroOptions();
if (oldMacro) unitSquared = 1.0;
staticMinSize = 0.0;
staticMaxSize = DEFAULT_MAX_SIZE;
staticMinCircularity = 0.0;
staticMaxCircularity = 1.0;
staticShowChoice = NOTHING;
}
GenericDialog gd = new GenericDialog("Analyze Particles");
minSize = staticMinSize;
maxSize = staticMaxSize;
minCircularity = staticMinCircularity;
maxCircularity = staticMaxCircularity;
showChoice = staticShowChoice;
if (maxSize == 999999) maxSize = DEFAULT_MAX_SIZE;
options = staticOptions;
String unit = cal.getUnit();
boolean scaled = cal.scaled();
if (unit.equals("inch")) {
unit = "pixel";
unitSquared = 1.0;
scaled = false;
pixelUnits = true;
}
String units = unit + "^2";
int places = 0;
double cmin = minSize * unitSquared;
if ((int) cmin != cmin) places = 2;
double cmax = maxSize * unitSquared;
if ((int) cmax != cmax && cmax != DEFAULT_MAX_SIZE) places = 2;
String minStr = ResultsTable.d2s(cmin, places);
if (minStr.indexOf("-") != -1) {
for (int i = places; i <= 6; i++) {
minStr = ResultsTable.d2s(cmin, i);
if (minStr.indexOf("-") == -1) break;
}
}
String maxStr = ResultsTable.d2s(cmax, places);
if (maxStr.indexOf("-") != -1) {
for (int i = places; i <= 6; i++) {
maxStr = ResultsTable.d2s(cmax, i);
if (maxStr.indexOf("-") == -1) break;
}
}
if (scaled) gd.setInsets(5, 0, 0);
gd.addStringField("Size (" + units + "):", minStr + "-" + maxStr, 12);
if (scaled) {
gd.setInsets(0, 40, 5);
gd.addCheckbox("Pixel units", pixelUnits);
}
gd.addStringField("Circularity:", IJ.d2s(minCircularity) + "-" + IJ.d2s(maxCircularity), 12);
gd.addChoice("Show:", showStrings, showStrings[showChoice]);
String[] labels = new String[8];
boolean[] states = new boolean[8];
labels[0] = "Display results";
states[0] = (options & SHOW_RESULTS) != 0;
labels[1] = "Exclude on edges";
states[1] = (options & EXCLUDE_EDGE_PARTICLES) != 0;
labels[2] = "Clear results";
states[2] = (options & CLEAR_WORKSHEET) != 0;
labels[3] = "Include holes";
states[3] = (options & INCLUDE_HOLES) != 0;
labels[4] = "Summarize";
states[4] = (options & DISPLAY_SUMMARY) != 0;
labels[5] = "Record starts";
states[5] = (options & RECORD_STARTS) != 0;
labels[6] = "Add to Manager";
states[6] = (options & ADD_TO_MANAGER) != 0;
labels[7] = "In_situ Show";
states[7] = (options & IN_SITU_SHOW) != 0;
gd.addCheckboxGroup(4, 2, labels, states);
gd.addHelp(IJ.URL + "/docs/menus/analyze.html#ap");
gd.showDialog();
if (gd.wasCanceled()) return false;
String size = gd.getNextString(); // min-max size
if (scaled) pixelUnits = gd.getNextBoolean();
if (pixelUnits) unitSquared = 1.0;
else unitSquared = cal.pixelWidth * cal.pixelHeight;
String[] minAndMax = Tools.split(size, " -");
double mins = gd.parseDouble(minAndMax[0]);
double maxs = minAndMax.length == 2 ? gd.parseDouble(minAndMax[1]) : Double.NaN;
minSize = Double.isNaN(mins) ? DEFAULT_MIN_SIZE : mins / unitSquared;
maxSize = Double.isNaN(maxs) ? DEFAULT_MAX_SIZE : maxs / unitSquared;
if (minSize < DEFAULT_MIN_SIZE) minSize = DEFAULT_MIN_SIZE;
if (maxSize < minSize) maxSize = DEFAULT_MAX_SIZE;
staticMinSize = minSize;
staticMaxSize = maxSize;
minAndMax = Tools.split(gd.getNextString(), " -"); // min-max circularity
double minc = gd.parseDouble(minAndMax[0]);
double maxc = minAndMax.length == 2 ? gd.parseDouble(minAndMax[1]) : Double.NaN;
minCircularity = Double.isNaN(minc) ? 0.0 : minc;
maxCircularity = Double.isNaN(maxc) ? 1.0 : maxc;
if (minCircularity < 0.0 || minCircularity > 1.0) minCircularity = 0.0;
if (maxCircularity < minCircularity || maxCircularity > 1.0) maxCircularity = 1.0;
if (minCircularity == 1.0 && maxCircularity == 1.0) minCircularity = 0.0;
staticMinCircularity = minCircularity;
staticMaxCircularity = maxCircularity;
if (gd.invalidNumber()) {
IJ.error("Bins invalid.");
canceled = true;
return false;
}
showChoice = gd.getNextChoiceIndex();
staticShowChoice = showChoice;
if (gd.getNextBoolean()) options |= SHOW_RESULTS;
else options &= ~SHOW_RESULTS;
if (gd.getNextBoolean()) options |= EXCLUDE_EDGE_PARTICLES;
else options &= ~EXCLUDE_EDGE_PARTICLES;
if (gd.getNextBoolean()) options |= CLEAR_WORKSHEET;
else options &= ~CLEAR_WORKSHEET;
if (gd.getNextBoolean()) options |= INCLUDE_HOLES;
else options &= ~INCLUDE_HOLES;
if (gd.getNextBoolean()) options |= DISPLAY_SUMMARY;
else options &= ~DISPLAY_SUMMARY;
if (gd.getNextBoolean()) options |= RECORD_STARTS;
else options &= ~RECORD_STARTS;
if (gd.getNextBoolean()) options |= ADD_TO_MANAGER;
else options &= ~ADD_TO_MANAGER;
if (gd.getNextBoolean()) options |= IN_SITU_SHOW;
else options &= ~IN_SITU_SHOW;
staticOptions = options;
options |= SHOW_PROGRESS;
if ((options & DISPLAY_SUMMARY) != 0)
Analyzer.setMeasurements(Analyzer.getMeasurements() | AREA);
return true;
}
private boolean isThresholdedRGB(ImagePlus imp) {
Object obj = imp.getProperty("Mask");
if (obj == null || !(obj instanceof ImageProcessor)) return false;
ImageProcessor mask = (ImageProcessor) obj;
return mask.getWidth() == imp.getWidth() && mask.getHeight() == imp.getHeight();
}
boolean updateMacroOptions() {
String options = Macro.getOptions();
int index = options.indexOf("maximum=");
if (index == -1) return false;
index += 8;
int len = options.length();
while (index < len - 1 && options.charAt(index) != ' ') index++;
if (index == len - 1) return false;
int min = (int) Tools.parseDouble(Macro.getValue(options, "minimum", "1"));
int max = (int) Tools.parseDouble(Macro.getValue(options, "maximum", "999999"));
options = "size=" + min + "-" + max + options.substring(index, len);
Macro.setOptions(options);
return true;
}
/** Performs particle analysis on the specified image. Returns false if there is an error. */
public boolean analyze(ImagePlus imp) {
return analyze(imp, imp.getProcessor());
}
/**
* Performs particle analysis on the specified ImagePlus and ImageProcessor. Returns false if
* there is an error.
*/
public boolean analyze(ImagePlus imp, ImageProcessor ip) {
if (this.imp == null) this.imp = imp;
showResults = (options & SHOW_RESULTS) != 0;
excludeEdgeParticles = (options & EXCLUDE_EDGE_PARTICLES) != 0;
resetCounter = (options & CLEAR_WORKSHEET) != 0;
showProgress = (options & SHOW_PROGRESS) != 0;
floodFill = (options & INCLUDE_HOLES) == 0;
recordStarts = (options & RECORD_STARTS) != 0;
addToManager = (options & ADD_TO_MANAGER) != 0;
displaySummary = (options & DISPLAY_SUMMARY) != 0;
inSituShow = (options & IN_SITU_SHOW) != 0;
outputImage = null;
ip.snapshot();
ip.setProgressBar(null);
if (Analyzer.isRedirectImage()) {
redirectImp = Analyzer.getRedirectImage(imp);
if (redirectImp == null) return false;
int depth = redirectImp.getStackSize();
if (depth > 1 && depth == imp.getStackSize()) {
ImageStack redirectStack = redirectImp.getStack();
redirectIP = redirectStack.getProcessor(imp.getCurrentSlice());
} else redirectIP = redirectImp.getProcessor();
} else if (imp.getType() == ImagePlus.COLOR_RGB) {
ImagePlus original = (ImagePlus) imp.getProperty("OriginalImage");
if (original != null
&& original.getWidth() == imp.getWidth()
&& original.getHeight() == imp.getHeight()) {
redirectImp = original;
redirectIP = original.getProcessor();
}
}
if (!setThresholdLevels(imp, ip)) return false;
width = ip.getWidth();
height = ip.getHeight();
if (!(showChoice == NOTHING || showChoice == OVERLAY_OUTLINES || showChoice == OVERLAY_MASKS)) {
blackBackground = Prefs.blackBackground && inSituShow;
if (slice == 1) outlines = new ImageStack(width, height);
if (showChoice == ROI_MASKS) drawIP = new ShortProcessor(width, height);
else drawIP = new ByteProcessor(width, height);
drawIP.setLineWidth(lineWidth);
if (showChoice == ROI_MASKS) {
} // Place holder for now...
else if (showChoice == MASKS && !blackBackground) drawIP.invertLut();
else if (showChoice == OUTLINES) {
if (!inSituShow) {
if (customLut == null) makeCustomLut();
drawIP.setColorModel(customLut);
}
drawIP.setFont(new Font("SansSerif", Font.PLAIN, fontSize));
if (fontSize > 12 && inSituShow) drawIP.setAntialiasedText(true);
}
outlines.addSlice(null, drawIP);
if (showChoice == ROI_MASKS || blackBackground) {
drawIP.setColor(Color.black);
drawIP.fill();
drawIP.setColor(Color.white);
} else {
drawIP.setColor(Color.white);
drawIP.fill();
drawIP.setColor(Color.black);
}
}
calibration = redirectImp != null ? redirectImp.getCalibration() : imp.getCalibration();
if (rt == null) {
rt = Analyzer.getResultsTable();
analyzer = new Analyzer(imp);
} else analyzer = new Analyzer(imp, measurements, rt);
if (resetCounter && slice == 1) {
if (!Analyzer.resetCounter()) return false;
}
beginningCount = Analyzer.getCounter();
byte[] pixels = null;
if (ip instanceof ByteProcessor) pixels = (byte[]) ip.getPixels();
if (r == null) {
r = ip.getRoi();
mask = ip.getMask();
if (displaySummary) {
if (mask != null) totalArea = ImageStatistics.getStatistics(ip, AREA, calibration).area;
else totalArea = r.width * calibration.pixelWidth * r.height * calibration.pixelHeight;
}
}
minX = r.x;
maxX = r.x + r.width;
minY = r.y;
maxY = r.y + r.height;
if (r.width < width || r.height < height || mask != null) {
if (!eraseOutsideRoi(ip, r, mask)) return false;
}
int offset;
double value;
int inc = Math.max(r.height / 25, 1);
int mi = 0;
ImageWindow win = imp.getWindow();
if (win != null) win.running = true;
if (measurements == 0) measurements = Analyzer.getMeasurements();
if (showChoice == ELLIPSES) measurements |= ELLIPSE;
measurements &= ~LIMIT; // ignore "Limit to Threshold"
roiNeedsImage =
(measurements & PERIMETER) != 0
|| (measurements & SHAPE_DESCRIPTORS) != 0
|| (measurements & FERET) != 0;
particleCount = 0;
wand = new Wand(ip);
pf = new PolygonFiller();
if (floodFill) {
ImageProcessor ipf = ip.duplicate();
ipf.setValue(fillColor);
ff = new FloodFiller(ipf);
}
roiType = Wand.allPoints() ? Roi.FREEROI : Roi.TRACED_ROI;
for (int y = r.y; y < (r.y + r.height); y++) {
offset = y * width;
for (int x = r.x; x < (r.x + r.width); x++) {
if (pixels != null) value = pixels[offset + x] & 255;
else if (imageType == SHORT) value = ip.getPixel(x, y);
else value = ip.getPixelValue(x, y);
if (value >= level1 && value <= level2) analyzeParticle(x, y, imp, ip);
}
if (showProgress && ((y % inc) == 0)) IJ.showProgress((double) (y - r.y) / r.height);
if (win != null) canceled = !win.running;
if (canceled) {
Macro.abort();
break;
}
}
if (showProgress) IJ.showProgress(1.0);
if (showResults) rt.updateResults();
imp.killRoi();
ip.resetRoi();
ip.reset();
if (displaySummary && IJ.getInstance() != null) updateSliceSummary();
if (addToManager && roiManager != null) roiManager.setEditMode(imp, true);
maxParticleCount = (particleCount > maxParticleCount) ? particleCount : maxParticleCount;
totalCount += particleCount;
if (!canceled) showResults();
return true;
}
void updateSliceSummary() {
int slices = imp.getStackSize();
float[] areas = rt.getColumn(ResultsTable.AREA);
if (areas == null) areas = new float[0];
String label = imp.getTitle();
if (slices > 1) {
label = imp.getStack().getShortSliceLabel(slice);
label = label != null && !label.equals("") ? label : "" + slice;
}
String aLine = null;
double sum = 0.0;
int start = areas.length - particleCount;
if (start < 0) return;
for (int i = start; i < areas.length; i++) sum += areas[i];
int places = Analyzer.getPrecision();
Calibration cal = imp.getCalibration();
String total = "\t" + ResultsTable.d2s(sum, places);
String average = "\t" + ResultsTable.d2s(sum / particleCount, places);
String fraction = "\t" + ResultsTable.d2s(sum * 100.0 / totalArea, 1);
aLine = label + "\t" + particleCount + total + average + fraction;
aLine = addMeans(aLine, areas.length > 0 ? start : -1);
if (slices == 1) {
Frame frame = WindowManager.getFrame("Summary");
if (frame != null && (frame instanceof TextWindow) && summaryHdr.equals(prevHdr))
tw = (TextWindow) frame;
}
if (tw == null) {
String title = slices == 1 ? "Summary" : "Summary of " + imp.getTitle();
tw = new TextWindow(title, summaryHdr, aLine, 450, 300);
prevHdr = summaryHdr;
} else tw.append(aLine);
}
String addMeans(String line, int start) {
if ((measurements & MEAN) != 0) line = addMean(ResultsTable.MEAN, line, start);
if ((measurements & MODE) != 0) line = addMean(ResultsTable.MODE, line, start);
if ((measurements & PERIMETER) != 0) line = addMean(ResultsTable.PERIMETER, line, start);
if ((measurements & ELLIPSE) != 0) {
line = addMean(ResultsTable.MAJOR, line, start);
line = addMean(ResultsTable.MINOR, line, start);
line = addMean(ResultsTable.ANGLE, line, start);
}
if ((measurements & SHAPE_DESCRIPTORS) != 0) {
line = addMean(ResultsTable.CIRCULARITY, line, start);
line = addMean(ResultsTable.SOLIDITY, line, start);
}
if ((measurements & FERET) != 0) {
line = addMean(ResultsTable.FERET, line, start);
line = addMean(ResultsTable.FERET_X, line, start);
line = addMean(ResultsTable.FERET_Y, line, start);
line = addMean(ResultsTable.FERET_ANGLE, line, start);
line = addMean(ResultsTable.MIN_FERET, line, start);
}
if ((measurements & INTEGRATED_DENSITY) != 0)
line = addMean(ResultsTable.INTEGRATED_DENSITY, line, start);
if ((measurements & MEDIAN) != 0) line = addMean(ResultsTable.MEDIAN, line, start);
if ((measurements & SKEWNESS) != 0) line = addMean(ResultsTable.SKEWNESS, line, start);
if ((measurements & KURTOSIS) != 0) line = addMean(ResultsTable.KURTOSIS, line, start);
return line;
}
private String addMean(int column, String line, int start) {
if (start == -1) {
line += "\tNaN";
summaryHdr += "\t" + ResultsTable.getDefaultHeading(column);
} else {
float[] c = column >= 0 ? rt.getColumn(column) : null;
if (c != null) {
ImageProcessor ip = new FloatProcessor(c.length, 1, c, null);
if (ip == null) return line;
ip.setRoi(start, 0, ip.getWidth() - start, 1);
ip = ip.crop();
ImageStatistics stats = new FloatStatistics(ip);
if (stats == null) return line;
line += n(stats.mean);
} else line += "\tNaN";
summaryHdr += "\t" + rt.getColumnHeading(column);
}
return line;
}
String n(double n) {
String s;
if (Math.round(n) == n) s = ResultsTable.d2s(n, 0);
else s = ResultsTable.d2s(n, Analyzer.getPrecision());
return "\t" + s;
}
boolean eraseOutsideRoi(ImageProcessor ip, Rectangle r, ImageProcessor mask) {
int width = ip.getWidth();
int height = ip.getHeight();
ip.setRoi(r);
if (excludeEdgeParticles && polygon != null) {
ImageStatistics stats = ImageStatistics.getStatistics(ip, MIN_MAX, null);
if (fillColor >= stats.min && fillColor <= stats.max) {
double replaceColor = level1 - 1.0;
if (replaceColor < 0.0 || replaceColor == fillColor) {
replaceColor = level2 + 1.0;
int maxColor = imageType == BYTE ? 255 : 65535;
if (replaceColor > maxColor || replaceColor == fillColor) {
IJ.error("Particle Analyzer", "Unable to remove edge particles");
return false;
}
}
for (int y = minY; y < maxY; y++) {
for (int x = minX; x < maxX; x++) {
int v = ip.getPixel(x, y);
if (v == fillColor) ip.putPixel(x, y, (int) replaceColor);
}
}
}
}
ip.setValue(fillColor);
if (mask != null) {
mask = mask.duplicate();
mask.invert();
ip.fill(mask);
}
ip.setRoi(0, 0, r.x, height);
ip.fill();
ip.setRoi(r.x, 0, r.width, r.y);
ip.fill();
ip.setRoi(r.x, r.y + r.height, r.width, height - (r.y + r.height));
ip.fill();
ip.setRoi(r.x + r.width, 0, width - (r.x + r.width), height);
ip.fill();
ip.resetRoi();
// IJ.log("erase: "+fillColor+" "+level1+" "+level2+" "+excludeEdgeParticles);
// (new ImagePlus("ip2", ip.duplicate())).show();
return true;
}
boolean setThresholdLevels(ImagePlus imp, ImageProcessor ip) {
double t1 = ip.getMinThreshold();
double t2 = ip.getMaxThreshold();
boolean invertedLut = imp.isInvertedLut();
boolean byteImage = ip instanceof ByteProcessor;
if (ip instanceof ShortProcessor) imageType = SHORT;
else if (ip instanceof FloatProcessor) imageType = FLOAT;
else imageType = BYTE;
if (t1 == ImageProcessor.NO_THRESHOLD) {
ImageStatistics stats = imp.getStatistics();
if (imageType != BYTE || (stats.histogram[0] + stats.histogram[255] != stats.pixelCount)) {
IJ.error(
"Particle Analyzer",
"A thresholded image or 8-bit binary image is\n"
+ "required. Threshold levels can be set using\n"
+ "the Image->Adjust->Threshold tool.");
canceled = true;
return false;
}
boolean threshold255 = invertedLut;
if (Prefs.blackBackground) threshold255 = !threshold255;
if (threshold255) {
level1 = 255;
level2 = 255;
fillColor = 64;
} else {
level1 = 0;
level2 = 0;
fillColor = 192;
}
} else {
level1 = t1;
level2 = t2;
if (imageType == BYTE) {
if (level1 > 0) fillColor = 0;
else if (level2 < 255) fillColor = 255;
} else if (imageType == SHORT) {
if (level1 > 0) fillColor = 0;
else if (level2 < 65535) fillColor = 65535;
} else if (imageType == FLOAT) fillColor = -Float.MAX_VALUE;
else return false;
}
imageType2 = imageType;
if (redirectIP != null) {
if (redirectIP instanceof ShortProcessor) imageType2 = SHORT;
else if (redirectIP instanceof FloatProcessor) imageType2 = FLOAT;
else if (redirectIP instanceof ColorProcessor) imageType2 = RGB;
else imageType2 = BYTE;
}
return true;
}
int counter = 0;
void analyzeParticle(int x, int y, ImagePlus imp, ImageProcessor ip) {
// Wand wand = new Wand(ip);
ImageProcessor ip2 = redirectIP != null ? redirectIP : ip;
wand.autoOutline(x, y, level1, level2, wandMode);
if (wand.npoints == 0) {
IJ.log("wand error: " + x + " " + y);
return;
}
Roi roi = new PolygonRoi(wand.xpoints, wand.ypoints, wand.npoints, roiType);
Rectangle r = roi.getBounds();
if (r.width > 1 && r.height > 1) {
PolygonRoi proi = (PolygonRoi) roi;
pf.setPolygon(proi.getXCoordinates(), proi.getYCoordinates(), proi.getNCoordinates());
ip2.setMask(pf.getMask(r.width, r.height));
if (floodFill) ff.particleAnalyzerFill(x, y, level1, level2, ip2.getMask(), r);
}
ip2.setRoi(r);
ip.setValue(fillColor);
ImageStatistics stats = getStatistics(ip2, measurements, calibration);
boolean include = true;
if (excludeEdgeParticles) {
if (r.x == minX || r.y == minY || r.x + r.width == maxX || r.y + r.height == maxY)
include = false;
if (polygon != null) {
Rectangle bounds = roi.getBounds();
int x1 = bounds.x + wand.xpoints[wand.npoints - 1];
int y1 = bounds.y + wand.ypoints[wand.npoints - 1];
int x2, y2;
for (int i = 0; i < wand.npoints; i++) {
x2 = bounds.x + wand.xpoints[i];
y2 = bounds.y + wand.ypoints[i];
if (!polygon.contains(x2, y2)) {
include = false;
break;
}
if ((x1 == x2 && ip.getPixel(x1, y1 - 1) == fillColor)
|| (y1 == y2 && ip.getPixel(x1 - 1, y1) == fillColor)) {
include = false;
break;
}
x1 = x2;
y1 = y2;
}
}
}
ImageProcessor mask = ip2.getMask();
if (minCircularity > 0.0 || maxCircularity < 1.0) {
double perimeter = roi.getLength();
double circularity =
perimeter == 0.0 ? 0.0 : 4.0 * Math.PI * (stats.pixelCount / (perimeter * perimeter));
if (circularity > 1.0) circularity = 1.0;
// IJ.log(circularity+" "+perimeter+" "+stats.area);
if (circularity < minCircularity || circularity > maxCircularity) include = false;
}
if (stats.pixelCount >= minSize && stats.pixelCount <= maxSize && include) {
particleCount++;
if (roiNeedsImage) roi.setImage(imp);
stats.xstart = x;
stats.ystart = y;
saveResults(stats, roi);
if (showChoice != NOTHING) drawParticle(drawIP, roi, stats, mask);
}
if (redirectIP != null) ip.setRoi(r);
ip.fill(mask);
}
ImageStatistics getStatistics(ImageProcessor ip, int mOptions, Calibration cal) {
switch (imageType2) {
case BYTE:
return new ByteStatistics(ip, mOptions, cal);
case SHORT:
return new ShortStatistics(ip, mOptions, cal);
case FLOAT:
return new FloatStatistics(ip, mOptions, cal);
case RGB:
return new ColorStatistics(ip, mOptions, cal);
default:
return null;
}
}
/**
* Saves statistics for one particle in a results table. This is a method subclasses may want to
* override.
*/
protected void saveResults(ImageStatistics stats, Roi roi) {
analyzer.saveResults(stats, roi);
if (recordStarts) {
rt.addValue("XStart", stats.xstart);
rt.addValue("YStart", stats.ystart);
}
if (addToManager) {
if (roiManager == null) {
if (Macro.getOptions() != null && Interpreter.isBatchMode())
roiManager = Interpreter.getBatchModeRoiManager();
if (roiManager == null) {
Frame frame = WindowManager.getFrame("ROI Manager");
if (frame == null) IJ.run("ROI Manager...");
frame = WindowManager.getFrame("ROI Manager");
if (frame == null || !(frame instanceof RoiManager)) {
addToManager = false;
return;
}
roiManager = (RoiManager) frame;
}
if (resetCounter) roiManager.runCommand("reset");
}
if (imp.getStackSize() > 1) roi.setPosition(imp.getCurrentSlice());
if (lineWidth != 1) roi.setStrokeWidth(lineWidth);
roiManager.add(imp, roi, rt.getCounter());
}
if (showResults) rt.addResults();
}
/**
* Draws a selected particle in a separate image. This is another method subclasses may want to
* override.
*/
protected void drawParticle(
ImageProcessor drawIP, Roi roi, ImageStatistics stats, ImageProcessor mask) {
switch (showChoice) {
case MASKS:
drawFilledParticle(drawIP, roi, mask);
break;
case OUTLINES:
case BARE_OUTLINES:
case OVERLAY_OUTLINES:
case OVERLAY_MASKS:
drawOutline(drawIP, roi, rt.getCounter());
break;
case ELLIPSES:
drawEllipse(drawIP, stats, rt.getCounter());
break;
case ROI_MASKS:
drawRoiFilledParticle(drawIP, roi, mask, rt.getCounter());
break;
default:
}
}
void drawFilledParticle(ImageProcessor ip, Roi roi, ImageProcessor mask) {
// IJ.write(roi.getBounds()+" "+mask.length);
ip.setRoi(roi.getBounds());
ip.fill(mask);
}
void drawOutline(ImageProcessor ip, Roi roi, int count) {
if (showChoice == OVERLAY_OUTLINES || showChoice == OVERLAY_MASKS) {
if (overlay == null) {
overlay = new Overlay();
overlay.drawLabels(true);
overlay.setLabelFont(new Font("SansSerif", Font.PLAIN, fontSize));
}
Roi roi2 = (Roi) roi.clone();
roi2.setStrokeColor(Color.cyan);
if (lineWidth != 1) roi2.setStrokeWidth(lineWidth);
if (showChoice == OVERLAY_MASKS) roi2.setFillColor(Color.cyan);
overlay.add(roi2);
} else {
Rectangle r = roi.getBounds();
int nPoints = ((PolygonRoi) roi).getNCoordinates();
int[] xp = ((PolygonRoi) roi).getXCoordinates();
int[] yp = ((PolygonRoi) roi).getYCoordinates();
int x = r.x, y = r.y;
if (!inSituShow) ip.setValue(0.0);
ip.moveTo(x + xp[0], y + yp[0]);
for (int i = 1; i < nPoints; i++) ip.lineTo(x + xp[i], y + yp[i]);
ip.lineTo(x + xp[0], y + yp[0]);
if (showChoice != BARE_OUTLINES) {
String s = ResultsTable.d2s(count, 0);
ip.moveTo(r.x + r.width / 2 - ip.getStringWidth(s) / 2, r.y + r.height / 2 + fontSize / 2);
if (!inSituShow) ip.setValue(1.0);
ip.drawString(s);
}
}
}
void drawEllipse(ImageProcessor ip, ImageStatistics stats, int count) {
stats.drawEllipse(ip);
}
void drawRoiFilledParticle(ImageProcessor ip, Roi roi, ImageProcessor mask, int count) {
int grayLevel = (count < 65535) ? count : 65535;
ip.setValue((double) grayLevel);
ip.setRoi(roi.getBounds());
ip.fill(mask);
}
void showResults() {
int count = rt.getCounter();
// if (count==0) return;
boolean lastSlice = !processStack || slice == imp.getStackSize();
if ((showChoice == OVERLAY_OUTLINES || showChoice == OVERLAY_MASKS) && slice == 1 && count > 0)
imp.setOverlay(overlay);
else if (outlines != null && lastSlice) {
String title = imp != null ? imp.getTitle() : "Outlines";
String prefix;
if (showChoice == MASKS) prefix = "Mask of ";
else if (showChoice == ROI_MASKS) prefix = "Count Masks of ";
else prefix = "Drawing of ";
outlines.update(drawIP);
outputImage = new ImagePlus(prefix + title, outlines);
if (inSituShow) {
if (imp.getStackSize() == 1) Undo.setup(Undo.TRANSFORM, imp);
imp.setStack(null, outputImage.getStack());
} else if (!hideOutputImage) outputImage.show();
}
if (showResults && !processStack) {
TextPanel tp = IJ.getTextPanel();
if (beginningCount > 0 && tp != null && tp.getLineCount() != count) rt.show("Results");
Analyzer.firstParticle = beginningCount;
Analyzer.lastParticle = Analyzer.getCounter() - 1;
} else Analyzer.firstParticle = Analyzer.lastParticle = 0;
}
/**
* Returns the "Outlines", "Masks", "Elipses" or "Count Masks" image, or null if "Nothing" is
* selected in the "Show:" menu.
*/
public ImagePlus getOutputImage() {
return outputImage;
}
/** Set 'hideOutputImage' true to not display the "Show:" image. */
public void setHideOutputImage(boolean hideOutputImage) {
this.hideOutputImage = hideOutputImage;
}
/** Sets the size of the font used to label outlines in the next particle analyzer instance. */
public static void setFontSize(int size) {
nextFontSize = size;
}
/** Sets the outline line width for the next particle analyzer instance. */
public static void setLineWidth(int width) {
nextLineWidth = width;
}
int getColumnID(String name) {
int id = rt.getFreeColumn(name);
if (id == ResultsTable.COLUMN_IN_USE) id = rt.getColumnIndex(name);
return id;
}
void makeCustomLut() {
IndexColorModel cm = (IndexColorModel) LookUpTable.createGrayscaleColorModel(false);
byte[] reds = new byte[256];
byte[] greens = new byte[256];
byte[] blues = new byte[256];
cm.getReds(reds);
cm.getGreens(greens);
cm.getBlues(blues);
reds[1] = (byte) 255;
greens[1] = (byte) 0;
blues[1] = (byte) 0;
customLut = new IndexColorModel(8, 256, reds, greens, blues);
}
/** Called once when ImageJ quits. */
public static void savePreferences(Properties prefs) {
prefs.put(OPTIONS, Integer.toString(staticOptions));
}
}
public void run(ImageProcessor ip) {
String[] imageNames = getOpenImageNames();
if (imageNames[0] == "None") {
IJ.error("need at least 2 binary open images");
return;
}
double previousMinOverlap = Prefs.get("BVTB.BinaryFeatureExtractor.minOverlap", 0);
boolean previousCombine = Prefs.get("BVTB.BinaryFeatureExtractor.combine", false);
GenericDialog gd = new GenericDialog("Binary Feature Extractor");
gd.addChoice("Objects image", imageNames, imageNames[0]);
gd.addChoice("Selector image", imageNames, imageNames[1]);
gd.addNumericField("Object_overlap in % (0=off)", previousMinOverlap, 0, 9, "");
gd.addCheckbox("Combine objects and selectors", previousCombine);
gd.addCheckbox("Count output", true);
gd.addCheckbox("Analysis tables", false);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
String objectsImgTitle = gd.getNextChoice();
String selectorsImgTitle = gd.getNextChoice();
double minOverlap = gd.getNextNumber();
boolean combineImages = gd.getNextBoolean();
boolean showCountOutput = gd.getNextBoolean();
boolean showAnalysis = gd.getNextBoolean();
if (gd.invalidNumber() || minOverlap < 0 || minOverlap > 100) {
IJ.error("invalid number");
return;
}
Prefs.set("BVTB.BinaryFeatureExtractor.minOverlap", minOverlap);
Prefs.set("BVTB.BinaryFeatureExtractor.combine", combineImages);
if (objectsImgTitle.equals(selectorsImgTitle)) {
IJ.error("images need to be different");
return;
}
ImagePlus objectsImp = WindowManager.getImage(objectsImgTitle);
ImageProcessor objectsIP = objectsImp.getProcessor();
ImagePlus selectorsImp = WindowManager.getImage(selectorsImgTitle);
ImageProcessor selectorsIP = selectorsImp.getProcessor();
if (!objectsIP.isBinary() || !selectorsIP.isBinary()) {
IJ.error("works with 8-bit binary images only");
return;
}
if ((objectsImp.getWidth() != selectorsImp.getWidth())
|| objectsImp.getHeight() != selectorsImp.getHeight()) {
IJ.error("images need to be of the same size");
return;
}
// close any existing RoiManager before instantiating a new one for this analysis
RoiManager oldRM = RoiManager.getInstance2();
if (oldRM != null) {
oldRM.close();
}
RoiManager objectsRM = new RoiManager(true);
ResultsTable objectsRT = new ResultsTable();
ParticleAnalyzer analyzeObjects =
new ParticleAnalyzer(analyzerOptions, measurementFlags, objectsRT, 0.0, 999999999.9);
analyzeObjects.setRoiManager(objectsRM);
analyzeObjects.analyze(objectsImp);
objectsRM.runCommand("Show None");
int objectNumber = objectsRT.getCounter();
Roi[] objectRoi = objectsRM.getRoisAsArray();
ResultsTable measureSelectorsRT = new ResultsTable();
Analyzer overlapAnalyzer = new Analyzer(selectorsImp, measurementFlags, measureSelectorsRT);
ImagePlus outputImp =
IJ.createImage("output", "8-bit black", objectsImp.getWidth(), objectsImp.getHeight(), 1);
ImageProcessor outputIP = outputImp.getProcessor();
double[] measuredOverlap = new double[objectNumber];
outputIP.setValue(255.0);
for (int o = 0; o < objectNumber; o++) {
selectorsImp.killRoi();
selectorsImp.setRoi(objectRoi[o]);
overlapAnalyzer.measure();
measuredOverlap[o] = measureSelectorsRT.getValue("%Area", o);
if (minOverlap != 0.0 && measuredOverlap[o] >= minOverlap) {
outputIP.fill(objectRoi[o]);
finalCount++;
} else if (minOverlap == 0.0 && measuredOverlap[o] > 0.0) {
outputIP.fill(objectRoi[o]);
finalCount++;
}
}
// measureSelectorsRT.show("Objects");
selectorsImp.killRoi();
RoiManager selectorRM = new RoiManager(true);
ResultsTable selectorRT = new ResultsTable();
ParticleAnalyzer.setRoiManager(selectorRM);
ParticleAnalyzer analyzeSelectors =
new ParticleAnalyzer(analyzerOptions, measurementFlags, selectorRT, 0.0, 999999999.9);
analyzeSelectors.analyze(selectorsImp);
selectorRM.runCommand("Show None");
int selectorNumber = selectorRT.getCounter();
if (combineImages) {
outputImp.updateAndDraw();
Roi[] selectorRoi = selectorRM.getRoisAsArray();
ResultsTable measureObjectsRT = new ResultsTable();
Analyzer selectorAnalyzer = new Analyzer(outputImp, measurementFlags, measureObjectsRT);
double[] selectorOverlap = new double[selectorNumber];
outputIP.setValue(255.0);
for (int s = 0; s < selectorNumber; s++) {
outputImp.killRoi();
outputImp.setRoi(selectorRoi[s]);
selectorAnalyzer.measure();
selectorOverlap[s] = measureObjectsRT.getValue("%Area", s);
if (selectorOverlap[s] > 0.0d) {
outputIP.fill(selectorRoi[s]);
}
}
selectorRoi = null;
selectorAnalyzer = null;
measureObjectsRT = null;
}
// selectorRT.show("Selectors");
outputImp.killRoi();
String outputImageTitle = WindowManager.getUniqueName("Extracted_" + objectsImgTitle);
outputImp.setTitle(outputImageTitle);
outputImp.show();
outputImp.changes = true;
if (showCountOutput) {
String[] openTextWindows = WindowManager.getNonImageTitles();
boolean makeNewTable = true;
for (int w = 0; w < openTextWindows.length; w++) {
if (openTextWindows[w].equals("BFE_Results")) {
makeNewTable = false;
}
}
TextWindow existingCountTable = ResultsTable.getResultsWindow();
if (makeNewTable) {
countTable = new ResultsTable();
countTable.setPrecision(0);
countTable.setValue("Image", 0, outputImageTitle);
countTable.setValue("Objects", 0, objectNumber);
countTable.setValue("Selectors", 0, selectorNumber);
countTable.setValue("Extracted", 0, finalCount);
countTable.show("BFE_Results");
} else {
IJ.renameResults("BFE_Results", "Results");
countTable = ResultsTable.getResultsTable();
countTable.setPrecision(0);
countTable.incrementCounter();
countTable.addValue("Image", outputImageTitle);
countTable.addValue("Objects", objectNumber);
countTable.addValue("Selectors", selectorNumber);
countTable.addValue("Extracted", finalCount);
IJ.renameResults("Results", "BFE_Results");
countTable.show("BFE_Results");
}
}
if (showAnalysis) {
ResultsTable extractedRT = new ResultsTable();
ParticleAnalyzer analyzeExtracted =
new ParticleAnalyzer(
ParticleAnalyzer.CLEAR_WORKSHEET | ParticleAnalyzer.RECORD_STARTS,
measurementFlags,
extractedRT,
0.0,
999999999.9);
analyzeExtracted.analyze(outputImp);
objectsRT.show("Objects");
selectorRT.show("Selectors");
extractedRT.show("Extracted");
} else {
objectsRT = null;
selectorRT = null;
}
objectsRM = null;
measureSelectorsRT = null;
analyzeObjects = null;
overlapAnalyzer = null;
objectRoi = null;
selectorRM = null;
objectsImp.killRoi();
objectsImp.changes = false;
selectorsImp.changes = false;
}
/** This is a Canvas used to display images in a Window. */
public class ImageCanvas extends Canvas implements MouseListener, MouseMotionListener, Cloneable {
protected static Cursor defaultCursor = new Cursor(Cursor.DEFAULT_CURSOR);
protected static Cursor handCursor = new Cursor(Cursor.HAND_CURSOR);
protected static Cursor moveCursor = new Cursor(Cursor.MOVE_CURSOR);
protected static Cursor crosshairCursor = new Cursor(Cursor.CROSSHAIR_CURSOR);
public static boolean usePointer = Prefs.usePointerCursor;
protected ImagePlus imp;
protected boolean imageUpdated;
protected Rectangle srcRect;
protected int imageWidth, imageHeight;
protected int xMouse; // current cursor offscreen x location
protected int yMouse; // current cursor offscreen y location
private boolean showCursorStatus = true;
private int sx2, sy2;
private boolean disablePopupMenu;
private boolean showAllROIs;
private static Color zoomIndicatorColor;
private static Font smallFont, largeFont;
private Font font;
private Rectangle[] labelRects;
private boolean maxBoundsReset;
private Overlay overlay, showAllList;
private static final int LIST_OFFSET = 100000;
private static Color showAllColor = Prefs.getColor(Prefs.SHOW_ALL_COLOR, new Color(0, 255, 255));
private Color defaultColor = showAllColor;
private static Color labelColor, bgColor;
private int resetMaxBoundsCount;
private Roi currentRoi;
protected ImageJ ij;
protected double magnification;
protected int dstWidth, dstHeight;
protected int xMouseStart;
protected int yMouseStart;
protected int xSrcStart;
protected int ySrcStart;
protected int flags;
private Image offScreenImage;
private int offScreenWidth = 0;
private int offScreenHeight = 0;
private boolean mouseExited = true;
private boolean customRoi;
private boolean drawNames;
public ImageCanvas(ImagePlus imp) {
this.imp = imp;
ij = IJ.getInstance();
int width = imp.getWidth();
int height = imp.getHeight();
imageWidth = width;
imageHeight = height;
srcRect = new Rectangle(0, 0, imageWidth, imageHeight);
setDrawingSize(imageWidth, (int) (imageHeight));
magnification = 1.0;
addMouseListener(this);
addMouseMotionListener(this);
addKeyListener(ij); // ImageJ handles keyboard shortcuts
setFocusTraversalKeysEnabled(false);
}
void updateImage(ImagePlus imp) {
this.imp = imp;
int width = imp.getWidth();
int height = imp.getHeight();
imageWidth = width;
imageHeight = height;
srcRect = new Rectangle(0, 0, imageWidth, imageHeight);
setDrawingSize(imageWidth, (int) imageHeight);
magnification = 1.0;
}
/** Update this ImageCanvas to have the same zoom and scale settings as the one specified. */
void update(ImageCanvas ic) {
if (ic == null || ic == this || ic.imp == null) return;
if (ic.imp.getWidth() != imageWidth || ic.imp.getHeight() != imageHeight) return;
srcRect = new Rectangle(ic.srcRect.x, ic.srcRect.y, ic.srcRect.width, ic.srcRect.height);
setMagnification(ic.magnification);
setDrawingSize(ic.dstWidth, ic.dstHeight);
}
public void setSourceRect(Rectangle r) {
srcRect = r;
}
void setSrcRect(Rectangle srcRect) {
this.srcRect = srcRect;
}
public Rectangle getSrcRect() {
return srcRect;
}
public void setDrawingSize(int width, int height) {
dstWidth = width;
dstHeight = height;
setSize(dstWidth, dstHeight);
}
/**
* ImagePlus.updateAndDraw calls this method to force the paint() method to update the image from
* the ImageProcessor.
*/
public void setImageUpdated() {
imageUpdated = true;
}
public void update(Graphics g) {
paint(g);
}
public void paint(Graphics g) {
Roi roi = imp.getRoi();
if (roi != null || showAllROIs || overlay != null) {
if (roi != null) roi.updatePaste();
if (!IJ.isMacOSX() && imageWidth != 0) {
paintDoubleBuffered(g);
return;
}
}
try {
if (imageUpdated) {
imageUpdated = false;
imp.updateImage();
}
Java2.setBilinearInterpolation(g, Prefs.interpolateScaledImages);
Image img = imp.getImage();
if (img != null)
g.drawImage(
img,
0,
0,
(int) (srcRect.width * magnification),
(int) (srcRect.height * magnification),
srcRect.x,
srcRect.y,
srcRect.x + srcRect.width,
srcRect.y + srcRect.height,
null);
if (overlay != null) drawOverlay(g);
if (showAllROIs) drawAllROIs(g);
if (roi != null) drawRoi(roi, g);
if (srcRect.width < imageWidth || srcRect.height < imageHeight) drawZoomIndicator(g);
if (IJ.debugMode) showFrameRate(g);
} catch (OutOfMemoryError e) {
IJ.outOfMemory("Paint");
}
}
private void drawRoi(Roi roi, Graphics g) {
if (roi == currentRoi) {
Color lineColor = roi.getStrokeColor();
Color fillColor = roi.getFillColor();
float lineWidth = roi.getStrokeWidth();
roi.setStrokeColor(null);
roi.setFillColor(null);
boolean strokeSet = roi.getStroke() != null;
if (strokeSet) roi.setStrokeWidth(1);
roi.draw(g);
roi.setStrokeColor(lineColor);
if (strokeSet) roi.setStrokeWidth(lineWidth);
roi.setFillColor(fillColor);
currentRoi = null;
} else roi.draw(g);
}
void drawAllROIs(Graphics g) {
RoiManager rm = RoiManager.getInstance();
if (rm == null) {
rm = Interpreter.getBatchModeRoiManager();
if (rm != null && rm.getList().getItemCount() == 0) rm = null;
}
if (rm == null) {
// if (showAllList!=null)
// overlay = showAllList;
showAllROIs = false;
repaint();
return;
}
initGraphics(g, null, showAllColor);
Hashtable rois = rm.getROIs();
java.awt.List list = rm.getList();
boolean drawLabels = rm.getDrawLabels();
currentRoi = null;
int n = list.getItemCount();
if (IJ.debugMode) IJ.log("paint: drawing " + n + " \"Show All\" ROIs");
if (labelRects == null || labelRects.length != n) labelRects = new Rectangle[n];
if (!drawLabels) showAllList = new Overlay();
else showAllList = null;
if (imp == null) return;
int currentImage = imp.getCurrentSlice();
int channel = 0, slice = 0, frame = 0;
boolean hyperstack = imp.isHyperStack();
if (hyperstack) {
channel = imp.getChannel();
slice = imp.getSlice();
frame = imp.getFrame();
}
drawNames = Prefs.useNamesAsLabels;
for (int i = 0; i < n; i++) {
String label = list.getItem(i);
Roi roi = (Roi) rois.get(label);
if (roi == null) continue;
if (showAllList != null) showAllList.add(roi);
if (i < 200 && drawLabels && roi == imp.getRoi()) currentRoi = roi;
if (Prefs.showAllSliceOnly && imp.getStackSize() > 1) {
if (hyperstack && roi.getPosition() == 0) {
int c = roi.getCPosition();
int z = roi.getZPosition();
int t = roi.getTPosition();
if ((c == 0 || c == channel) && (z == 0 || z == slice) && (t == 0 || t == frame))
drawRoi(g, roi, drawLabels ? i : -1);
} else {
int position = roi.getPosition();
if (position == 0) position = getSliceNumber(roi.getName());
if (position == 0 || position == currentImage) drawRoi(g, roi, drawLabels ? i : -1);
}
} else drawRoi(g, roi, drawLabels ? i : -1);
}
((Graphics2D) g).setStroke(Roi.onePixelWide);
drawNames = false;
}
public int getSliceNumber(String label) {
int slice = 0;
if (label.length() >= 14 && label.charAt(4) == '-' && label.charAt(9) == '-')
slice = (int) Tools.parseDouble(label.substring(0, 4), -1);
else if (label.length() >= 17 && label.charAt(5) == '-' && label.charAt(11) == '-')
slice = (int) Tools.parseDouble(label.substring(0, 5), -1);
else if (label.length() >= 20 && label.charAt(6) == '-' && label.charAt(13) == '-')
slice = (int) Tools.parseDouble(label.substring(0, 6), -1);
return slice;
}
void drawOverlay(Graphics g) {
if (imp != null && imp.getHideOverlay()) return;
Color labelColor = overlay.getLabelColor();
if (labelColor == null) labelColor = Color.white;
initGraphics(g, labelColor, Roi.getColor());
int n = overlay.size();
if (IJ.debugMode) IJ.log("paint: drawing " + n + " ROI display list");
int currentImage = imp != null ? imp.getCurrentSlice() : -1;
if (imp.getStackSize() == 1) currentImage = -1;
int channel = 0, slice = 0, frame = 0;
boolean hyperstack = imp.isHyperStack();
if (hyperstack) {
channel = imp.getChannel();
slice = imp.getSlice();
frame = imp.getFrame();
}
drawNames = overlay.getDrawNames();
boolean drawLabels = drawNames || overlay.getDrawLabels();
for (int i = 0; i < n; i++) {
if (overlay == null) break;
Roi roi = overlay.get(i);
if (hyperstack && roi.getPosition() == 0) {
int c = roi.getCPosition();
int z = roi.getZPosition();
int t = roi.getTPosition();
if ((c == 0 || c == channel) && (z == 0 || z == slice) && (t == 0 || t == frame))
drawRoi(g, roi, drawLabels ? i + LIST_OFFSET : -1);
} else {
int position = roi.getPosition();
if (position == 0 || position == currentImage)
drawRoi(g, roi, drawLabels ? i + LIST_OFFSET : -1);
}
}
((Graphics2D) g).setStroke(Roi.onePixelWide);
drawNames = false;
}
void initGraphics(Graphics g, Color textColor, Color defaultColor) {
if (smallFont == null) {
smallFont = new Font("SansSerif", Font.PLAIN, 9);
largeFont = new Font("SansSerif", Font.PLAIN, 12);
}
if (textColor != null) {
labelColor = textColor;
if (overlay != null && overlay.getDrawBackgrounds())
bgColor =
new Color(
255 - labelColor.getRed(), 255 - labelColor.getGreen(), 255 - labelColor.getBlue());
else bgColor = null;
} else {
int red = defaultColor.getRed();
int green = defaultColor.getGreen();
int blue = defaultColor.getBlue();
if ((red + green + blue) / 3 < 128) labelColor = Color.white;
else labelColor = Color.black;
bgColor = defaultColor;
}
this.defaultColor = defaultColor;
g.setColor(defaultColor);
}
void drawRoi(Graphics g, Roi roi, int index) {
int type = roi.getType();
ImagePlus imp2 = roi.getImage();
roi.setImage(imp);
Color saveColor = roi.getStrokeColor();
if (saveColor == null) roi.setStrokeColor(defaultColor);
if (roi instanceof TextRoi) ((TextRoi) roi).drawText(g);
else roi.drawOverlay(g);
roi.setStrokeColor(saveColor);
if (index >= 0) {
if (roi == currentRoi) g.setColor(Roi.getColor());
else g.setColor(defaultColor);
drawRoiLabel(g, index, roi);
}
if (imp2 != null) roi.setImage(imp2);
else roi.setImage(null);
}
void drawRoiLabel(Graphics g, int index, Roi roi) {
Rectangle r = roi.getBounds();
int x = screenX(r.x);
int y = screenY(r.y);
double mag = getMagnification();
int width = (int) (r.width * mag);
int height = (int) (r.height * mag);
int size = width > 40 && height > 40 ? 12 : 9;
if (font != null) {
g.setFont(font);
size = font.getSize();
} else if (size == 12) g.setFont(largeFont);
else g.setFont(smallFont);
boolean drawingList = index >= LIST_OFFSET;
if (drawingList) index -= LIST_OFFSET;
String label = "" + (index + 1);
if (drawNames && roi.getName() != null) label = roi.getName();
FontMetrics metrics = g.getFontMetrics();
int w = metrics.stringWidth(label);
x = x + width / 2 - w / 2;
y = y + height / 2 + Math.max(size / 2, 6);
int h = metrics.getAscent() + metrics.getDescent();
if (bgColor != null) {
g.setColor(bgColor);
g.fillRoundRect(x - 1, y - h + 2, w + 1, h - 3, 5, 5);
}
if (!drawingList && labelRects != null && index < labelRects.length)
labelRects[index] = new Rectangle(x - 1, y - h + 2, w + 1, h);
g.setColor(labelColor);
g.drawString(label, x, y - 2);
g.setColor(defaultColor);
}
void drawZoomIndicator(Graphics g) {
int x1 = 10;
int y1 = 10;
double aspectRatio = (double) imageHeight / imageWidth;
int w1 = 64;
if (aspectRatio > 1.0) w1 = (int) (w1 / aspectRatio);
int h1 = (int) (w1 * aspectRatio);
if (w1 < 4) w1 = 4;
if (h1 < 4) h1 = 4;
int w2 = (int) (w1 * ((double) srcRect.width / imageWidth));
int h2 = (int) (h1 * ((double) srcRect.height / imageHeight));
if (w2 < 1) w2 = 1;
if (h2 < 1) h2 = 1;
int x2 = (int) (w1 * ((double) srcRect.x / imageWidth));
int y2 = (int) (h1 * ((double) srcRect.y / imageHeight));
if (zoomIndicatorColor == null) zoomIndicatorColor = new Color(128, 128, 255);
g.setColor(zoomIndicatorColor);
((Graphics2D) g).setStroke(Roi.onePixelWide);
g.drawRect(x1, y1, w1, h1);
if (w2 * h2 <= 200 || w2 < 10 || h2 < 10) g.fillRect(x1 + x2, y1 + y2, w2, h2);
else g.drawRect(x1 + x2, y1 + y2, w2, h2);
}
// Use double buffer to reduce flicker when drawing complex ROIs.
// Author: Erik Meijering
void paintDoubleBuffered(Graphics g) {
final int srcRectWidthMag = (int) (srcRect.width * magnification);
final int srcRectHeightMag = (int) (srcRect.height * magnification);
if (offScreenImage == null
|| offScreenWidth != srcRectWidthMag
|| offScreenHeight != srcRectHeightMag) {
offScreenImage = createImage(srcRectWidthMag, srcRectHeightMag);
offScreenWidth = srcRectWidthMag;
offScreenHeight = srcRectHeightMag;
}
Roi roi = imp.getRoi();
try {
if (imageUpdated) {
imageUpdated = false;
imp.updateImage();
}
Graphics offScreenGraphics = offScreenImage.getGraphics();
Java2.setBilinearInterpolation(offScreenGraphics, Prefs.interpolateScaledImages);
Image img = imp.getImage();
if (img != null)
offScreenGraphics.drawImage(
img,
0,
0,
srcRectWidthMag,
srcRectHeightMag,
srcRect.x,
srcRect.y,
srcRect.x + srcRect.width,
srcRect.y + srcRect.height,
null);
if (overlay != null) drawOverlay(offScreenGraphics);
if (showAllROIs) drawAllROIs(offScreenGraphics);
if (roi != null) drawRoi(roi, offScreenGraphics);
if (srcRect.width < imageWidth || srcRect.height < imageHeight)
drawZoomIndicator(offScreenGraphics);
if (IJ.debugMode) showFrameRate(offScreenGraphics);
g.drawImage(offScreenImage, 0, 0, null);
} catch (OutOfMemoryError e) {
IJ.outOfMemory("Paint");
}
}
public void resetDoubleBuffer() {
offScreenImage = null;
}
long firstFrame;
int frames, fps;
void showFrameRate(Graphics g) {
frames++;
if (System.currentTimeMillis() > firstFrame + 1000) {
firstFrame = System.currentTimeMillis();
fps = frames;
frames = 0;
}
g.setColor(Color.white);
g.fillRect(10, 12, 50, 15);
g.setColor(Color.black);
g.drawString((int) (fps + 0.5) + " fps", 10, 25);
}
public Dimension getPreferredSize() {
return new Dimension(dstWidth, dstHeight);
}
int count;
/*
public Graphics getGraphics() {
Graphics g = super.getGraphics();
IJ.write("getGraphics: "+count++);
if (IJ.altKeyDown())
throw new IllegalArgumentException("");
return g;
}
*/
/** Returns the current cursor location in image coordinates. */
public Point getCursorLoc() {
return new Point(xMouse, yMouse);
}
/** Returns 'true' if the cursor is over this image. */
public boolean cursorOverImage() {
return !mouseExited;
}
/** Returns the mouse event modifiers. */
public int getModifiers() {
return flags;
}
/** Returns the ImagePlus object that is associated with this ImageCanvas. */
public ImagePlus getImage() {
return imp;
}
/** Sets the cursor based on the current tool and cursor location. */
public void setCursor(int sx, int sy, int ox, int oy) {
xMouse = ox;
yMouse = oy;
mouseExited = false;
Roi roi = imp.getRoi();
ImageWindow win = imp.getWindow();
if (win == null) return;
if (IJ.spaceBarDown()) {
setCursor(handCursor);
return;
}
int id = Toolbar.getToolId();
switch (Toolbar.getToolId()) {
case Toolbar.MAGNIFIER:
setCursor(moveCursor);
break;
case Toolbar.HAND:
setCursor(handCursor);
break;
default: // selection tool
if (id == Toolbar.SPARE1 || id >= Toolbar.SPARE2) {
if (Prefs.usePointerCursor) setCursor(defaultCursor);
else setCursor(crosshairCursor);
} else if (roi != null && roi.getState() != roi.CONSTRUCTING && roi.isHandle(sx, sy) >= 0)
setCursor(handCursor);
else if (Prefs.usePointerCursor
|| (roi != null && roi.getState() != roi.CONSTRUCTING && roi.contains(ox, oy)))
setCursor(defaultCursor);
else setCursor(crosshairCursor);
}
}
/** Converts a screen x-coordinate to an offscreen x-coordinate. */
public int offScreenX(int sx) {
return srcRect.x + (int) (sx / magnification);
}
/** Converts a screen y-coordinate to an offscreen y-coordinate. */
public int offScreenY(int sy) {
return srcRect.y + (int) (sy / magnification);
}
/** Converts a screen x-coordinate to a floating-point offscreen x-coordinate. */
public double offScreenXD(int sx) {
return srcRect.x + sx / magnification;
}
/** Converts a screen y-coordinate to a floating-point offscreen y-coordinate. */
public double offScreenYD(int sy) {
return srcRect.y + sy / magnification;
}
/** Converts an offscreen x-coordinate to a screen x-coordinate. */
public int screenX(int ox) {
return (int) ((ox - srcRect.x) * magnification);
}
/** Converts an offscreen y-coordinate to a screen y-coordinate. */
public int screenY(int oy) {
return (int) ((oy - srcRect.y) * magnification);
}
/** Converts a floating-point offscreen x-coordinate to a screen x-coordinate. */
public int screenXD(double ox) {
return (int) ((ox - srcRect.x) * magnification);
}
/** Converts a floating-point offscreen x-coordinate to a screen x-coordinate. */
public int screenYD(double oy) {
return (int) ((oy - srcRect.y) * magnification);
}
public double getMagnification() {
return magnification;
}
public void setMagnification(double magnification) {
setMagnification2(magnification);
}
void setMagnification2(double magnification) {
if (magnification > 32.0) magnification = 32.0;
if (magnification < 0.03125) magnification = 0.03125;
this.magnification = magnification;
imp.setTitle(imp.getTitle());
}
/** Enlarge the canvas if the user enlarges the window. */
void resizeCanvas(int width, int height) {
ImageWindow win = imp.getWindow();
// IJ.log("resizeCanvas: "+srcRect+" "+imageWidth+" "+imageHeight+" "+width+" "+height+"
// "+dstWidth+" "+dstHeight+" "+win.maxBounds);
if (!maxBoundsReset
&& (width > dstWidth || height > dstHeight)
&& win != null
&& win.maxBounds != null
&& width != win.maxBounds.width - 10) {
if (resetMaxBoundsCount != 0)
resetMaxBounds(); // Works around problem that prevented window from being larger than
// maximized size
resetMaxBoundsCount++;
}
if (IJ.altKeyDown()) {
fitToWindow();
return;
}
if (srcRect.width < imageWidth || srcRect.height < imageHeight) {
if (width > imageWidth * magnification) width = (int) (imageWidth * magnification);
if (height > imageHeight * magnification) height = (int) (imageHeight * magnification);
setDrawingSize(width, height);
srcRect.width = (int) (dstWidth / magnification);
srcRect.height = (int) (dstHeight / magnification);
if ((srcRect.x + srcRect.width) > imageWidth) srcRect.x = imageWidth - srcRect.width;
if ((srcRect.y + srcRect.height) > imageHeight) srcRect.y = imageHeight - srcRect.height;
repaint();
}
// IJ.log("resizeCanvas2: "+srcRect+" "+dstWidth+" "+dstHeight+" "+width+" "+height);
}
public void fitToWindow() {
ImageWindow win = imp.getWindow();
if (win == null) return;
Rectangle bounds = win.getBounds();
Insets insets = win.getInsets();
int sliderHeight = (win instanceof StackWindow) ? 20 : 0;
double xmag = (double) (bounds.width - 10) / srcRect.width;
double ymag = (double) (bounds.height - (10 + insets.top + sliderHeight)) / srcRect.height;
setMagnification(Math.min(xmag, ymag));
int width = (int) (imageWidth * magnification);
int height = (int) (imageHeight * magnification);
if (width == dstWidth && height == dstHeight) return;
srcRect = new Rectangle(0, 0, imageWidth, imageHeight);
setDrawingSize(width, height);
getParent().doLayout();
}
void setMaxBounds() {
if (maxBoundsReset) {
maxBoundsReset = false;
ImageWindow win = imp.getWindow();
if (win != null && !IJ.isLinux() && win.maxBounds != null) {
win.setMaximizedBounds(win.maxBounds);
win.setMaxBoundsTime = System.currentTimeMillis();
}
}
}
void resetMaxBounds() {
ImageWindow win = imp.getWindow();
if (win != null && (System.currentTimeMillis() - win.setMaxBoundsTime) > 500L) {
win.setMaximizedBounds(win.maxWindowBounds);
maxBoundsReset = true;
}
}
private static final double[] zoomLevels = {
1 / 72.0, 1 / 48.0, 1 / 32.0, 1 / 24.0, 1 / 16.0, 1 / 12.0, 1 / 8.0, 1 / 6.0, 1 / 4.0, 1 / 3.0,
1 / 2.0, 0.75, 1.0, 1.5, 2.0, 3.0, 4.0, 6.0, 8.0, 12.0, 16.0, 24.0, 32.0
};
public static double getLowerZoomLevel(double currentMag) {
double newMag = zoomLevels[0];
for (int i = 0; i < zoomLevels.length; i++) {
if (zoomLevels[i] < currentMag) newMag = zoomLevels[i];
else break;
}
return newMag;
}
public static double getHigherZoomLevel(double currentMag) {
double newMag = 32.0;
for (int i = zoomLevels.length - 1; i >= 0; i--) {
if (zoomLevels[i] > currentMag) newMag = zoomLevels[i];
else break;
}
return newMag;
}
/**
* Zooms in by making the window bigger. If it can't be made bigger, then make the source
* rectangle (srcRect) smaller and center it at (sx,sy). Note that sx and sy are screen
* coordinates.
*/
public void zoomIn(int sx, int sy) {
if (magnification >= 32) return;
double newMag = getHigherZoomLevel(magnification);
int newWidth = (int) (imageWidth * newMag);
int newHeight = (int) (imageHeight * newMag);
Dimension newSize = canEnlarge(newWidth, newHeight);
if (newSize != null) {
setDrawingSize(newSize.width, newSize.height);
if (newSize.width != newWidth || newSize.height != newHeight)
adjustSourceRect(newMag, sx, sy);
else setMagnification(newMag);
imp.getWindow().pack();
} else adjustSourceRect(newMag, sx, sy);
repaint();
if (srcRect.width < imageWidth || srcRect.height < imageHeight) resetMaxBounds();
}
void adjustSourceRect(double newMag, int x, int y) {
// IJ.log("adjustSourceRect1: "+newMag+" "+dstWidth+" "+dstHeight);
int w = (int) Math.round(dstWidth / newMag);
if (w * newMag < dstWidth) w++;
int h = (int) Math.round(dstHeight / newMag);
if (h * newMag < dstHeight) h++;
x = offScreenX(x);
y = offScreenY(y);
Rectangle r = new Rectangle(x - w / 2, y - h / 2, w, h);
if (r.x < 0) r.x = 0;
if (r.y < 0) r.y = 0;
if (r.x + w > imageWidth) r.x = imageWidth - w;
if (r.y + h > imageHeight) r.y = imageHeight - h;
srcRect = r;
setMagnification(newMag);
// IJ.log("adjustSourceRect2: "+srcRect+" "+dstWidth+" "+dstHeight);
}
protected Dimension canEnlarge(int newWidth, int newHeight) {
// if ((flags&Event.CTRL_MASK)!=0 || IJ.controlKeyDown()) return null;
ImageWindow win = imp.getWindow();
if (win == null) return null;
Rectangle r1 = win.getBounds();
Insets insets = win.getInsets();
Point loc = getLocation();
if (loc.x > insets.left + 5 || loc.y > insets.top + 5) {
r1.width = newWidth + insets.left + insets.right + 10;
r1.height = newHeight + insets.top + insets.bottom + 10;
if (win instanceof StackWindow) r1.height += 20;
} else {
r1.width = r1.width - dstWidth + newWidth + 10;
r1.height = r1.height - dstHeight + newHeight + 10;
}
Rectangle max = win.getMaxWindow(r1.x, r1.y);
boolean fitsHorizontally = r1.x + r1.width < max.x + max.width;
boolean fitsVertically = r1.y + r1.height < max.y + max.height;
if (fitsHorizontally && fitsVertically) return new Dimension(newWidth, newHeight);
else if (fitsVertically && newHeight < dstWidth) return new Dimension(dstWidth, newHeight);
else if (fitsHorizontally && newWidth < dstHeight) return new Dimension(newWidth, dstHeight);
else return null;
}
/**
* Zooms out by making the source rectangle (srcRect) larger and centering it on (x,y). If we
* can't make it larger, then make the window smaller.
*/
public void zoomOut(int x, int y) {
if (magnification <= 0.03125) return;
double oldMag = magnification;
double newMag = getLowerZoomLevel(magnification);
double srcRatio = (double) srcRect.width / srcRect.height;
double imageRatio = (double) imageWidth / imageHeight;
double initialMag = imp.getWindow().getInitialMagnification();
if (Math.abs(srcRatio - imageRatio) > 0.05) {
double scale = oldMag / newMag;
int newSrcWidth = (int) Math.round(srcRect.width * scale);
int newSrcHeight = (int) Math.round(srcRect.height * scale);
if (newSrcWidth > imageWidth) newSrcWidth = imageWidth;
if (newSrcHeight > imageHeight) newSrcHeight = imageHeight;
int newSrcX = srcRect.x - (newSrcWidth - srcRect.width) / 2;
int newSrcY = srcRect.y - (newSrcHeight - srcRect.height) / 2;
if (newSrcX < 0) newSrcX = 0;
if (newSrcY < 0) newSrcY = 0;
srcRect = new Rectangle(newSrcX, newSrcY, newSrcWidth, newSrcHeight);
// IJ.log(newMag+" "+srcRect+" "+dstWidth+" "+dstHeight);
int newDstWidth = (int) (srcRect.width * newMag);
int newDstHeight = (int) (srcRect.height * newMag);
setMagnification(newMag);
setMaxBounds();
// IJ.log(newDstWidth+" "+dstWidth+" "+newDstHeight+" "+dstHeight);
if (newDstWidth < dstWidth || newDstHeight < dstHeight) {
// IJ.log("pack");
setDrawingSize(newDstWidth, newDstHeight);
imp.getWindow().pack();
} else repaint();
return;
}
if (imageWidth * newMag > dstWidth) {
int w = (int) Math.round(dstWidth / newMag);
if (w * newMag < dstWidth) w++;
int h = (int) Math.round(dstHeight / newMag);
if (h * newMag < dstHeight) h++;
x = offScreenX(x);
y = offScreenY(y);
Rectangle r = new Rectangle(x - w / 2, y - h / 2, w, h);
if (r.x < 0) r.x = 0;
if (r.y < 0) r.y = 0;
if (r.x + w > imageWidth) r.x = imageWidth - w;
if (r.y + h > imageHeight) r.y = imageHeight - h;
srcRect = r;
} else {
srcRect = new Rectangle(0, 0, imageWidth, imageHeight);
setDrawingSize((int) (imageWidth * newMag), (int) (imageHeight * newMag));
// setDrawingSize(dstWidth/2, dstHeight/2);
imp.getWindow().pack();
}
// IJ.write(newMag + " " + srcRect.x+" "+srcRect.y+" "+srcRect.width+" "+srcRect.height+"
// "+dstWidth + " " + dstHeight);
setMagnification(newMag);
// IJ.write(srcRect.x + " " + srcRect.width + " " + dstWidth);
setMaxBounds();
repaint();
}
/** Implements the Image/Zoom/Original Scale command. */
public void unzoom() {
double imag = imp.getWindow().getInitialMagnification();
if (magnification == imag) return;
srcRect = new Rectangle(0, 0, imageWidth, imageHeight);
ImageWindow win = imp.getWindow();
setDrawingSize((int) (imageWidth * imag), (int) (imageHeight * imag));
setMagnification(imag);
setMaxBounds();
win.pack();
setMaxBounds();
repaint();
}
/** Implements the Image/Zoom/View 100% command. */
public void zoom100Percent() {
if (magnification == 1.0) return;
double imag = imp.getWindow().getInitialMagnification();
if (magnification != imag) unzoom();
if (magnification == 1.0) return;
if (magnification < 1.0) {
while (magnification < 1.0) zoomIn(imageWidth / 2, imageHeight / 2);
} else if (magnification > 1.0) {
while (magnification > 1.0) zoomOut(imageWidth / 2, imageHeight / 2);
} else return;
int x = xMouse, y = yMouse;
if (mouseExited) {
x = imageWidth / 2;
y = imageHeight / 2;
}
int sx = screenX(x);
int sy = screenY(y);
adjustSourceRect(1.0, sx, sy);
repaint();
}
protected void scroll(int sx, int sy) {
int ox = xSrcStart + (int) (sx / magnification); // convert to offscreen coordinates
int oy = ySrcStart + (int) (sy / magnification);
// IJ.log("scroll: "+ox+" "+oy+" "+xMouseStart+" "+yMouseStart);
int newx = xSrcStart + (xMouseStart - ox);
int newy = ySrcStart + (yMouseStart - oy);
if (newx < 0) newx = 0;
if (newy < 0) newy = 0;
if ((newx + srcRect.width) > imageWidth) newx = imageWidth - srcRect.width;
if ((newy + srcRect.height) > imageHeight) newy = imageHeight - srcRect.height;
srcRect.x = newx;
srcRect.y = newy;
// IJ.log(sx+" "+sy+" "+newx+" "+newy+" "+srcRect);
imp.draw();
Thread.yield();
}
Color getColor(int index) {
IndexColorModel cm = (IndexColorModel) imp.getProcessor().getColorModel();
// IJ.write(""+index+" "+(new Color(cm.getRGB(index))));
return new Color(cm.getRGB(index));
}
protected void setDrawingColor(int ox, int oy, boolean setBackground) {
// IJ.log("setDrawingColor: "+setBackground+this);
int type = imp.getType();
int[] v = imp.getPixel(ox, oy);
switch (type) {
case ImagePlus.GRAY8:
{
if (setBackground) setBackgroundColor(getColor(v[0]));
else setForegroundColor(getColor(v[0]));
break;
}
case ImagePlus.GRAY16:
case ImagePlus.GRAY32:
{
double min = imp.getProcessor().getMin();
double max = imp.getProcessor().getMax();
double value = (type == ImagePlus.GRAY32) ? Float.intBitsToFloat(v[0]) : v[0];
int index = (int) (255.0 * ((value - min) / (max - min)));
if (index < 0) index = 0;
if (index > 255) index = 255;
if (setBackground) setBackgroundColor(getColor(index));
else setForegroundColor(getColor(index));
break;
}
case ImagePlus.COLOR_RGB:
case ImagePlus.COLOR_256:
{
Color c = new Color(v[0], v[1], v[2]);
if (setBackground) setBackgroundColor(c);
else setForegroundColor(c);
break;
}
}
Color c;
if (setBackground) c = Toolbar.getBackgroundColor();
else {
c = Toolbar.getForegroundColor();
imp.setColor(c);
}
IJ.showStatus("(" + c.getRed() + ", " + c.getGreen() + ", " + c.getBlue() + ")");
}
private void setForegroundColor(Color c) {
Toolbar.setForegroundColor(c);
if (Recorder.record)
Recorder.record("setForegroundColor", c.getRed(), c.getGreen(), c.getBlue());
}
private void setBackgroundColor(Color c) {
Toolbar.setBackgroundColor(c);
if (Recorder.record)
Recorder.record("setBackgroundColor", c.getRed(), c.getGreen(), c.getBlue());
}
public void mousePressed(MouseEvent e) {
// if (ij==null) return;
showCursorStatus = true;
int toolID = Toolbar.getToolId();
ImageWindow win = imp.getWindow();
if (win != null && win.running2 && toolID != Toolbar.MAGNIFIER) {
if (win instanceof StackWindow) ((StackWindow) win).setAnimate(false);
else win.running2 = false;
return;
}
int x = e.getX();
int y = e.getY();
flags = e.getModifiers();
// IJ.log("Mouse pressed: " + e.isPopupTrigger() + " " + ij.modifiers(flags));
// if (toolID!=Toolbar.MAGNIFIER && e.isPopupTrigger()) {
if (toolID != Toolbar.MAGNIFIER
&& (e.isPopupTrigger() || (!IJ.isMacintosh() && (flags & Event.META_MASK) != 0))) {
handlePopupMenu(e);
return;
}
int ox = offScreenX(x);
int oy = offScreenY(y);
xMouse = ox;
yMouse = oy;
if (IJ.spaceBarDown()) {
// temporarily switch to "hand" tool of space bar down
setupScroll(ox, oy);
return;
}
if (showAllROIs) {
Roi roi = imp.getRoi();
if (!(roi != null && (roi.contains(ox, oy) || roi.isHandle(x, y) >= 0))
&& roiManagerSelect(x, y)) return;
}
if (customRoi && overlay != null) return;
switch (toolID) {
case Toolbar.MAGNIFIER:
if (IJ.shiftKeyDown()) zoomToSelection(ox, oy);
else if ((flags & (Event.ALT_MASK | Event.META_MASK | Event.CTRL_MASK)) != 0) {
// IJ.run("Out");
zoomOut(x, y);
if (getMagnification() < 1.0) imp.repaintWindow();
} else {
// IJ.run("In");
zoomIn(x, y);
if (getMagnification() <= 1.0) imp.repaintWindow();
}
break;
case Toolbar.HAND:
setupScroll(ox, oy);
break;
case Toolbar.DROPPER:
setDrawingColor(ox, oy, IJ.altKeyDown());
break;
case Toolbar.WAND:
Roi roi = imp.getRoi();
if (roi != null && roi.contains(ox, oy)) {
Rectangle r = roi.getBounds();
if (r.width == imageWidth && r.height == imageHeight) imp.killRoi();
else if (!e.isAltDown()) {
handleRoiMouseDown(e);
return;
}
}
if (roi != null) {
int handle = roi.isHandle(x, y);
if (handle >= 0) {
roi.mouseDownInHandle(handle, x, y);
return;
}
}
setRoiModState(e, roi, -1);
String mode = WandToolOptions.getMode();
double tolerance = WandToolOptions.getTolerance();
int npoints = IJ.doWand(ox, oy, tolerance, mode);
if (Recorder.record && npoints > 0) {
if (tolerance == 0.0 && mode.equals("Legacy")) Recorder.record("doWand", ox, oy);
else
Recorder.recordString(
"doWand(" + ox + ", " + oy + ", " + tolerance + ", \"" + mode + "\");\n");
}
break;
case Toolbar.OVAL:
if (Toolbar.getBrushSize() > 0) new RoiBrush();
else handleRoiMouseDown(e);
break;
case Toolbar.SPARE1:
case Toolbar.SPARE2:
case Toolbar.SPARE3:
case Toolbar.SPARE4:
case Toolbar.SPARE5:
case Toolbar.SPARE6:
case Toolbar.SPARE7:
case Toolbar.SPARE8:
case Toolbar.SPARE9:
Toolbar.getInstance().runMacroTool(toolID);
break;
default: // selection tool
handleRoiMouseDown(e);
}
}
boolean roiManagerSelect(int x, int y) {
RoiManager rm = RoiManager.getInstance();
if (rm == null) return false;
Hashtable rois = rm.getROIs();
java.awt.List list = rm.getList();
int n = list.getItemCount();
if (labelRects == null || labelRects.length != n) return false;
boolean stackMode = imp != null && imp.getStackSize() > 1 && Prefs.showAllSliceOnly;
for (int i = 0; i < n; i++) {
if (labelRects[i] != null && labelRects[i].contains(x, y)) {
if (stackMode) {
int slice = getSliceNumber(list.getItem(i));
if (slice != imp.getCurrentSlice()) continue;
}
// rm.select(i);
// this needs to run on a separate thread, at least on OS X
// "update2" does not clone the ROI so the "Show All"
// outline moves as the user moves the RO.
new ij.macro.MacroRunner("roiManager('select', " + i + "); roiManager('update2');");
return true;
}
}
return false;
}
void zoomToSelection(int x, int y) {
IJ.setKeyUp(IJ.ALL_KEYS);
String macro =
"args = split(getArgument);\n"
+ "x1=parseInt(args[0]); y1=parseInt(args[1]); flags=20;\n"
+ "while (flags&20!=0) {\n"
+ "getCursorLoc(x2, y2, z, flags);\n"
+ "if (x2>=x1) x=x1; else x=x2;\n"
+ "if (y2>=y1) y=y1; else y=y2;\n"
+ "makeRectangle(x, y, abs(x2-x1), abs(y2-y1));\n"
+ "wait(10);\n"
+ "}\n"
+ "run('To Selection');\n";
new MacroRunner(macro, x + " " + y);
}
protected void setupScroll(int ox, int oy) {
xMouseStart = ox;
yMouseStart = oy;
xSrcStart = srcRect.x;
ySrcStart = srcRect.y;
}
protected void handlePopupMenu(MouseEvent e) {
if (disablePopupMenu) return;
if (IJ.debugMode) IJ.log("show popup: " + (e.isPopupTrigger() ? "true" : "false"));
int x = e.getX();
int y = e.getY();
Roi roi = imp.getRoi();
if (roi != null
&& (roi.getType() == Roi.POLYGON
|| roi.getType() == Roi.POLYLINE
|| roi.getType() == Roi.ANGLE)
&& roi.getState() == roi.CONSTRUCTING) {
roi.handleMouseUp(x, y); // simulate double-click to finalize
roi.handleMouseUp(x, y); // polygon or polyline selection
return;
}
PopupMenu popup = Menus.getPopupMenu();
if (popup != null) {
add(popup);
if (IJ.isMacOSX()) IJ.wait(10);
popup.show(this, x, y);
}
}
public void mouseExited(MouseEvent e) {
// autoScroll(e);
ImageWindow win = imp.getWindow();
if (win != null) setCursor(defaultCursor);
IJ.showStatus("");
mouseExited = true;
}
/*
public void autoScroll(MouseEvent e) {
Roi roi = imp.getRoi();
if (roi==null || roi.getState()!=roi.CONSTRUCTING || srcRect.width>=imageWidth || srcRect.height>=imageHeight
|| !(roi.getType()==Roi.POLYGON || roi.getType()==Roi.POLYLINE || roi.getType()==Roi.ANGLE))
return;
int sx = e.getX();
int sy = e.getY();
xMouseStart = srcRect.x+srcRect.width/2;
yMouseStart = srcRect.y+srcRect.height/2;
Rectangle r = roi.getBounds();
Dimension size = getSize();
int deltax=0, deltay=0;
if (sx<0)
deltax = srcRect.width/4;
else if (sx>size.width)
deltax = -srcRect.width/4;
if (sy<0)
deltay = srcRect.height/4;
else if (sy>size.height)
deltay = -srcRect.height/4;
//IJ.log("autoscroll: "+sx+" "+sy+" "+deltax+" "+deltay+" "+r);
scroll(screenX(xMouseStart+deltax), screenY(yMouseStart+deltay));
}
*/
public void mouseDragged(MouseEvent e) {
int x = e.getX();
int y = e.getY();
xMouse = offScreenX(x);
yMouse = offScreenY(y);
flags = e.getModifiers();
// IJ.log("mouseDragged: "+flags);
if (flags == 0) // workaround for Mac OS 9 bug
flags = InputEvent.BUTTON1_MASK;
if (Toolbar.getToolId() == Toolbar.HAND || IJ.spaceBarDown()) scroll(x, y);
else {
IJ.setInputEvent(e);
Roi roi = imp.getRoi();
if (roi != null) roi.handleMouseDrag(x, y, flags);
}
}
protected void handleRoiMouseDown(MouseEvent e) {
int sx = e.getX();
int sy = e.getY();
int ox = offScreenX(sx);
int oy = offScreenY(sy);
Roi roi = imp.getRoi();
int handle = roi != null ? roi.isHandle(sx, sy) : -1;
boolean multiPointMode =
roi != null
&& (roi instanceof PointRoi)
&& handle == -1
&& Toolbar.getToolId() == Toolbar.POINT
&& Toolbar.getMultiPointMode();
if (multiPointMode) {
imp.setRoi(((PointRoi) roi).addPoint(ox, oy));
return;
}
setRoiModState(e, roi, handle);
if (roi != null) {
if (handle >= 0) {
roi.mouseDownInHandle(handle, sx, sy);
return;
}
Rectangle r = roi.getBounds();
int type = roi.getType();
if (type == Roi.RECTANGLE
&& r.width == imp.getWidth()
&& r.height == imp.getHeight()
&& roi.getPasteMode() == Roi.NOT_PASTING
&& !(roi instanceof ImageRoi)) {
imp.killRoi();
return;
}
if (roi.contains(ox, oy)) {
if (roi.modState == Roi.NO_MODS) roi.handleMouseDown(sx, sy);
else {
imp.killRoi();
imp.createNewRoi(sx, sy);
}
return;
}
if ((type == Roi.POLYGON || type == Roi.POLYLINE || type == Roi.ANGLE)
&& roi.getState() == roi.CONSTRUCTING) return;
int tool = Toolbar.getToolId();
if ((tool == Toolbar.POLYGON || tool == Toolbar.POLYLINE || tool == Toolbar.ANGLE)
&& !(IJ.shiftKeyDown() || IJ.altKeyDown())) {
imp.killRoi();
return;
}
}
imp.createNewRoi(sx, sy);
}
void setRoiModState(MouseEvent e, Roi roi, int handle) {
if (roi == null || (handle >= 0 && roi.modState == Roi.NO_MODS)) return;
if (roi.state == Roi.CONSTRUCTING) return;
int tool = Toolbar.getToolId();
if (tool > Toolbar.FREEROI && tool != Toolbar.WAND && tool != Toolbar.POINT) {
roi.modState = Roi.NO_MODS;
return;
}
if (e.isShiftDown()) roi.modState = Roi.ADD_TO_ROI;
else if (e.isAltDown()) roi.modState = Roi.SUBTRACT_FROM_ROI;
else roi.modState = Roi.NO_MODS;
// IJ.log("setRoiModState: "+roi.modState+" "+ roi.state);
}
/** Disable/enable popup menu. */
public void disablePopupMenu(boolean status) {
disablePopupMenu = status;
}
/** Enables/disables the ROI Manager "Show All" mode. */
public void setShowAllROIs(boolean showAllROIs) {
this.showAllROIs = showAllROIs;
}
/** Returns the state of the ROI Manager "Show All" flag. */
public boolean getShowAllROIs() {
return showAllROIs;
}
/** Return the ROI Manager "Show All" list as an overlay. */
public Overlay getShowAllList() {
if (!showAllROIs) return null;
if (showAllList != null) return showAllList;
RoiManager rm = RoiManager.getInstance();
if (rm == null) return null;
Roi[] rois = rm.getRoisAsArray();
if (rois.length == 0) return null;
Overlay overlay = new Overlay();
for (int i = 0; i < rois.length; i++) overlay.add((Roi) rois[i].clone());
return overlay;
}
/** Returns the color used for "Show All" mode. */
public static Color getShowAllColor() {
if (showAllColor != null && showAllColor.getRGB() == 0xff80ffff) showAllColor = Color.cyan;
return showAllColor;
}
/** Sets the color used used for the ROI Manager "Show All" mode. */
public static void setShowAllColor(Color c) {
if (c == null) return;
showAllColor = c;
labelColor = null;
ImagePlus img = WindowManager.getCurrentImage();
if (img != null) {
ImageCanvas ic = img.getCanvas();
if (ic != null && ic.getShowAllROIs()) img.draw();
}
}
/** Use ImagePlus.setOverlay(ij.gui.Overlay). */
public void setOverlay(Overlay overlay) {
this.overlay = overlay;
if (overlay != null) font = overlay.getLabelsFont();
repaint();
}
/** Use ImagePlus.getOverlay(). */
public Overlay getOverlay() {
return overlay;
}
/** @deprecated replaced by ImagePlus.setOverlay(ij.gui.Overlay) */
public void setDisplayList(Vector list) {
if (list != null) {
Overlay list2 = new Overlay();
list2.setVector(list);
setOverlay(list2);
} else setOverlay(null);
if (overlay != null)
overlay.drawLabels(overlay.size() > 0 && overlay.get(0).getStrokeColor() == null);
else customRoi = false;
repaint();
}
/** @deprecated replaced by ImagePlus.setOverlay(Shape, Color, BasicStroke) */
public void setDisplayList(Shape shape, Color color, BasicStroke stroke) {
if (shape == null) {
setOverlay(null);
return;
}
Roi roi = new ShapeRoi(shape);
roi.setStrokeColor(color);
roi.setStroke(stroke);
Overlay list = new Overlay();
list.add(roi);
setOverlay(list);
}
/** @deprecated replaced by ImagePlus.setOverlay(Roi, Color, int, Color) */
public void setDisplayList(Roi roi, Color color) {
roi.setStrokeColor(color);
Overlay list = new Overlay();
list.add(roi);
setOverlay(list);
}
/** @deprecated replaced by ImagePlus.getOverlay() */
public Vector getDisplayList() {
if (overlay == null) return null;
Vector displayList = new Vector();
for (int i = 0; i < overlay.size(); i++) displayList.add(overlay.get(i));
return displayList;
}
/** Allows plugins (e.g., Orthogonal_Views) to create a custom ROI using a display list. */
public void setCustomRoi(boolean customRoi) {
this.customRoi = customRoi;
}
public boolean getCustomRoi() {
return customRoi;
}
/**
* Called by IJ.showStatus() to prevent status bar text from being overwritten until the cursor
* moves at least 12 pixels.
*/
public void setShowCursorStatus(boolean status) {
showCursorStatus = status;
if (status == true) sx2 = sy2 = -1000;
else {
sx2 = screenX(xMouse);
sy2 = screenY(yMouse);
}
}
public void mouseReleased(MouseEvent e) {
flags = e.getModifiers();
flags &= ~InputEvent.BUTTON1_MASK; // make sure button 1 bit is not set
flags &= ~InputEvent.BUTTON2_MASK; // make sure button 2 bit is not set
flags &= ~InputEvent.BUTTON3_MASK; // make sure button 3 bit is not set
Roi roi = imp.getRoi();
if (roi != null) {
Rectangle r = roi.getBounds();
int type = roi.getType();
if ((r.width == 0 || r.height == 0)
&& !(type == Roi.POLYGON || type == Roi.POLYLINE || type == Roi.ANGLE || type == Roi.LINE)
&& !(roi instanceof TextRoi)
&& roi.getState() == roi.CONSTRUCTING
&& type != roi.POINT) imp.killRoi();
else {
roi.handleMouseUp(e.getX(), e.getY());
if (roi.getType() == Roi.LINE && roi.getLength() == 0.0) imp.killRoi();
}
}
}
public void mouseMoved(MouseEvent e) {
// if (ij==null) return;
int sx = e.getX();
int sy = e.getY();
int ox = offScreenX(sx);
int oy = offScreenY(sy);
flags = e.getModifiers();
setCursor(sx, sy, ox, oy);
IJ.setInputEvent(e);
Roi roi = imp.getRoi();
if (roi != null
&& (roi.getType() == Roi.POLYGON
|| roi.getType() == Roi.POLYLINE
|| roi.getType() == Roi.ANGLE)
&& roi.getState() == roi.CONSTRUCTING) {
PolygonRoi pRoi = (PolygonRoi) roi;
pRoi.handleMouseMove(ox, oy);
} else {
if (ox < imageWidth && oy < imageHeight) {
ImageWindow win = imp.getWindow();
// Cursor must move at least 12 pixels before text
// displayed using IJ.showStatus() is overwritten.
if ((sx - sx2) * (sx - sx2) + (sy - sy2) * (sy - sy2) > 144) showCursorStatus = true;
if (win != null && showCursorStatus) win.mouseMoved(ox, oy);
} else IJ.showStatus("");
}
}
public void mouseClicked(MouseEvent e) {}
public void mouseEntered(MouseEvent e) {}
}