void interpolate() {
Roi roi = imp.getRoi();
if (roi == null) {
noRoi("Interpolate");
return;
}
if (roi.getType() == Roi.POINT) return;
if (IJ.isMacro() && Macro.getOptions() == null) Macro.setOptions("interval=1");
GenericDialog gd = new GenericDialog("Interpolate");
gd.addNumericField("Interval:", 1.0, 1, 4, "pixel");
gd.addCheckbox("Smooth", IJ.isMacro() ? false : smooth);
gd.showDialog();
if (gd.wasCanceled()) return;
double interval = gd.getNextNumber();
smooth = gd.getNextBoolean();
Undo.setup(Undo.ROI, imp);
FloatPolygon poly = roi.getInterpolatedPolygon(interval, smooth);
int t = roi.getType();
int type = roi.isLine() ? Roi.FREELINE : Roi.FREEROI;
if (t == Roi.POLYGON && interval > 1.0) type = Roi.POLYGON;
if ((t == Roi.RECTANGLE || t == Roi.OVAL || t == Roi.FREEROI) && interval >= 5.0)
type = Roi.POLYGON;
if ((t == Roi.LINE || t == Roi.FREELINE) && interval >= 5.0) type = Roi.POLYLINE;
if (t == Roi.POLYLINE && interval >= 1.0) type = Roi.POLYLINE;
ImageCanvas ic = imp.getCanvas();
if (poly.npoints <= 150 && ic != null && ic.getMagnification() >= 12.0)
type = roi.isLine() ? Roi.POLYLINE : Roi.POLYGON;
Roi p = new PolygonRoi(poly, type);
if (roi.getStroke() != null) p.setStrokeWidth(roi.getStrokeWidth());
p.setStrokeColor(roi.getStrokeColor());
p.setName(roi.getName());
transferProperties(roi, p);
imp.setRoi(p);
}
void fitSpline() {
Roi roi = imp.getRoi();
if (roi == null) {
noRoi("Spline");
return;
}
int type = roi.getType();
boolean segmentedSelection = type == Roi.POLYGON || type == Roi.POLYLINE;
if (!(segmentedSelection
|| type == Roi.FREEROI
|| type == Roi.TRACED_ROI
|| type == Roi.FREELINE)) {
IJ.error("Spline", "Polygon or polyline selection required");
return;
}
if (roi instanceof EllipseRoi) return;
PolygonRoi p = (PolygonRoi) roi;
if (!segmentedSelection) {
if (p.subPixelResolution()) p = trimFloatPolygon(p, p.getUncalibratedLength());
else p = trimPolygon(p, p.getUncalibratedLength());
}
String options = Macro.getOptions();
if (options != null && options.indexOf("straighten") != -1) p.fitSplineForStraightening();
else if (options != null && options.indexOf("remove") != -1) p.removeSplineFit();
else p.fitSpline();
imp.draw();
LineWidthAdjuster.update();
}
void lineToArea(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null || !roi.isLine()) {
IJ.error("Line to Area", "Line selection required");
return;
}
if (roi.getType() == Roi.LINE && roi.getStrokeWidth() == 1) {
IJ.error("Line to Area", "Straight line width must be > 1");
return;
}
ImageProcessor ip2 = new ByteProcessor(imp.getWidth(), imp.getHeight());
ip2.setColor(255);
if (roi.getType() == Roi.LINE) ip2.fillPolygon(roi.getPolygon());
else {
roi.drawPixels(ip2);
// BufferedImage bi = new BufferedImage(imp.getWidth(), imp.getHeight(),
// BufferedImage.TYPE_BYTE_GRAY);
// Graphics g = bi.getGraphics();
// Roi roi2 = (Roi)roi.clone();
// roi2.setStrokeColor(Color.white);
// roi2.drawOverlay(g);
// ip2 = new ByteProcessor(bi);
}
// new ImagePlus("ip2", ip2.duplicate()).show();
ip2.setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
ThresholdToSelection tts = new ThresholdToSelection();
Roi roi2 = tts.convert(ip2);
imp.setRoi(roi2);
Roi.previousRoi = (Roi) roi.clone();
}
/*------------------------------------------------------------------*/
void setupProgressBar() {
int height = imp.getHeight();
int width = imp.getWidth();
completed = 0;
lastTime = System.currentTimeMillis();
switch (operation) {
case GRADIENT_MAGNITUDE:
processDuration = stackSize * (width + 2 * height);
break;
case GRADIENT_DIRECTION:
processDuration = stackSize * (width + 2 * height);
break;
case LAPLACIAN:
processDuration = stackSize * (width + 2 * height);
break;
case LARGEST_HESSIAN:
processDuration = stackSize * (2 * width + 3 * height);
break;
case SMALLEST_HESSIAN:
processDuration = stackSize * (2 * width + 3 * height);
break;
case HESSIAN_ORIENTATION:
processDuration = stackSize * (2 * width + 3 * height);
break;
default:
throw new IllegalArgumentException("Invalid operation");
}
} /* end setupProgressBar */
void createEllipse(ImagePlus imp) {
IJ.showStatus("Fitting ellipse");
Roi roi = imp.getRoi();
if (roi == null) {
noRoi("Fit Ellipse");
return;
}
if (roi.isLine()) {
IJ.error("Fit Ellipse", "\"Fit Ellipse\" does not work with line selections");
return;
}
ImageProcessor ip = imp.getProcessor();
ip.setRoi(roi);
int options = Measurements.CENTROID + Measurements.ELLIPSE;
ImageStatistics stats = ImageStatistics.getStatistics(ip, options, null);
double dx = stats.major * Math.cos(stats.angle / 180.0 * Math.PI) / 2.0;
double dy = -stats.major * Math.sin(stats.angle / 180.0 * Math.PI) / 2.0;
double x1 = stats.xCentroid - dx;
double x2 = stats.xCentroid + dx;
double y1 = stats.yCentroid - dy;
double y2 = stats.yCentroid + dy;
double aspectRatio = stats.minor / stats.major;
imp.killRoi();
imp.setRoi(new EllipseRoi(x1, y1, x2, y2, aspectRatio));
}
/** Generate output image whose type is same as input image. */
private ImagePlus makeOutputImage(ImagePlus imp, FloatProcessor fp, int ptype) {
int width = imp.getWidth();
int height = imp.getHeight();
float[] pixels = (float[]) fp.getPixels();
ImageProcessor oip = null;
// Create output image consistent w/ type of input image.
int size = pixels.length;
switch (ptype) {
case BYTE_TYPE:
oip = imp.getProcessor().createProcessor(width, height);
byte[] pixels8 = (byte[]) oip.getPixels();
for (int i = 0; i < size; i++) pixels8[i] = (byte) pixels[i];
break;
case SHORT_TYPE:
oip = imp.getProcessor().createProcessor(width, height);
short[] pixels16 = (short[]) oip.getPixels();
for (int i = 0; i < size; i++) pixels16[i] = (short) pixels[i];
break;
case FLOAT_TYPE:
oip = new FloatProcessor(width, height, pixels, null);
break;
}
// Adjust for display.
// Calling this on non-ByteProcessors ensures image
// processor is set up to correctly display image.
oip.resetMinAndMax();
// Create new image plus object. Don't use
// ImagePlus.createImagePlus here because there may be
// attributes of input image that are not appropriate for
// projection.
return new ImagePlus(makeTitle(), oip);
}
// Added by Marcel Boeglin 2013.09.22
private Overlay projectHyperStackRois(Overlay overlay) {
if (overlay == null) return null;
int t1 = imp.getFrame();
int channels = projImage.getNChannels();
int slices = 1;
int frames = projImage.getNFrames();
Overlay overlay2 = new Overlay();
Roi roi;
int c, z, t;
int size = channels * slices * frames;
for (Roi r : overlay.toArray()) {
c = r.getCPosition();
z = r.getZPosition();
t = r.getTPosition();
roi = (Roi) r.clone();
if (size == channels) { // current time frame
if (z >= startSlice && z <= stopSlice && t == t1 || c == 0) {
roi.setPosition(c);
overlay2.add(roi);
}
} else if (size == frames * channels) { // all time frames
if (z >= startSlice && z <= stopSlice) roi.setPosition(c, 1, t);
else if (z == 0) roi.setPosition(c, 0, t);
else continue;
overlay2.add(roi);
}
}
return overlay2;
}
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("");
}
}
/** 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);
}
}
/**
* 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();
}
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);
}
void showDialog() {
int width = imp.getWidth();
int height = imp.getHeight();
Calibration cal = imp.getCalibration();
int places;
if (cal.scaled()) {
pixelWidth = cal.pixelWidth;
pixelHeight = cal.pixelHeight;
units = cal.getUnits();
places = 2;
} else {
pixelWidth = 1.0;
pixelHeight = 1.0;
units = "pixels";
places = 0;
}
if (areaPerPoint == 0.0)
areaPerPoint =
(width * cal.pixelWidth * height * cal.pixelHeight) / 81.0; // default to 9x9 grid
ImageWindow win = imp.getWindow();
GenericDialog gd = new GenericDialog("Grid...");
gd.addChoice("Grid Type:", types, type);
gd.addNumericField("Area per Point:", areaPerPoint, places, 6, units + "^2");
gd.addChoice("Color:", colors, color);
gd.addCheckbox("Random Offset", randomOffset);
gd.addDialogListener(this);
gd.showDialog();
if (gd.wasCanceled()) showGrid(null);
}
private String getExifData(ImagePlus imp) {
FileInfo fi = imp.getOriginalFileInfo();
if (fi == null) return null;
String directory = fi.directory;
String name = fi.fileName;
if (directory == null) return null;
if ((name == null || name.equals("")) && imp.getStack().isVirtual())
name = imp.getStack().getSliceLabel(imp.getCurrentSlice());
if (name == null || !(name.endsWith("jpg") || name.endsWith("JPG"))) return null;
String path = directory + name;
String metadata = null;
try {
Class c = IJ.getClassLoader().loadClass("Exif_Reader");
if (c == null) return null;
String methodName = "getMetadata";
Class[] argClasses = new Class[1];
argClasses[0] = methodName.getClass();
Method m = c.getMethod("getMetadata", argClasses);
Object[] args = new Object[1];
args[0] = path;
Object obj = m.invoke(null, args);
metadata = obj != null ? obj.toString() : null;
} catch (Exception e) {
return null;
}
if (metadata != null && !metadata.startsWith("Error:")) return metadata;
else return null;
}
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;
}
void lineToArea(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null || !roi.isLine()) {
IJ.error("Line to Area", "Line selection required");
return;
}
Undo.setup(Undo.ROI, imp);
Roi roi2 = null;
if (roi.getType() == Roi.LINE) {
double width = roi.getStrokeWidth();
if (width <= 1.0) roi.setStrokeWidth(1.0000001);
FloatPolygon p = roi.getFloatPolygon();
roi.setStrokeWidth(width);
roi2 = new PolygonRoi(p, Roi.POLYGON);
roi2.setDrawOffset(roi.getDrawOffset());
} else {
ImageProcessor ip2 = new ByteProcessor(imp.getWidth(), imp.getHeight());
ip2.setColor(255);
roi.drawPixels(ip2);
// new ImagePlus("ip2", ip2.duplicate()).show();
ip2.setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE);
ThresholdToSelection tts = new ThresholdToSelection();
roi2 = tts.convert(ip2);
}
transferProperties(roi, roi2);
roi2.setStrokeWidth(0);
Color c = roi2.getStrokeColor();
if (c != null) // remove any transparency
roi2.setStrokeColor(new Color(c.getRed(), c.getGreen(), c.getBlue()));
imp.setRoi(roi2);
Roi.previousRoi = (Roi) roi.clone();
}
/**
* Creates a dialog box, allowing the user to enter the requested width, height, x & y
* coordinates, slice number for a Region Of Interest, option for oval, and option for whether x &
* y coordinates to be centered.
*/
void showDialog() {
Calibration cal = imp.getCalibration();
int digits = 0;
if (scaledUnits && cal.scaled()) digits = 2;
Roi roi = imp.getRoi();
if (roi == null) drawRoi();
GenericDialog gd = new GenericDialog("Specify");
gd.addNumericField("Width:", width, digits);
gd.addNumericField("Height:", height, digits);
gd.addNumericField("X coordinate:", xRoi, digits);
gd.addNumericField("Y coordinate:", yRoi, digits);
if (stackSize > 1) gd.addNumericField("Slice:", iSlice, 0);
gd.addCheckbox("Oval", oval);
gd.addCheckbox("Constrain square/circle", square);
gd.addCheckbox("Centered", centered);
if (cal.scaled()) {
boolean unitsMatch = cal.getXUnit().equals(cal.getYUnit());
String units = unitsMatch ? cal.getUnits() : cal.getXUnit() + " x " + cal.getYUnit();
gd.addCheckbox("Scaled units (" + units + ")", scaledUnits);
}
fields = gd.getNumericFields();
gd.addDialogListener(this);
gd.showDialog();
if (gd.wasCanceled()) {
if (roi == null) imp.deleteRoi();
else // *ALWAYS* restore initial ROI when cancelled
imp.setRoi(roi);
}
}
boolean validDialogValues() {
Calibration cal = imp.getCalibration();
double pw = cal.pixelWidth, ph = cal.pixelHeight;
if (width / pw < 1 || height / ph < 1) return false;
if (xRoi / pw > imp.getWidth() || yRoi / ph > imp.getHeight()) return false;
return true;
}
void remove() {
ImagePlus imp = WindowManager.getCurrentImage();
if (imp != null) imp.setOverlay(null);
overlay2 = null;
RoiManager rm = RoiManager.getInstance();
if (rm != null) rm.runCommand("show none");
}
/**
* Adds a checkbox labelled "Preview" for "automatic" preview. The reference to this checkbox can
* be retrieved by getPreviewCheckbox() and it provides the additional method previewRunning for
* optical feedback while preview is prepared. PlugInFilters can have their "run" method
* automatically called for preview under the following conditions: - the PlugInFilter must pass a
* reference to itself (i.e., "this") as an argument to the AddPreviewCheckbox - it must implement
* the DialogListener interface and set the filter parameters in the dialogItemChanged method. -
* it must have DIALOG and PREVIEW set in its flags. A previewCheckbox is always off when the
* filter is started and does not get recorded by the Macro Recorder.
*
* @param pfr A reference to the PlugInFilterRunner calling the PlugInFilter if automatic preview
* is desired, null otherwise.
*/
public void addPreviewCheckbox(PlugInFilterRunner pfr) {
if (previewCheckbox != null) return;
ImagePlus imp = WindowManager.getCurrentImage();
if (imp != null && imp.isComposite() && ((CompositeImage) imp).getMode() == IJ.COMPOSITE)
return;
this.pfr = pfr;
addCheckbox(previewLabel, false, true);
}
/**
* 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();
}
protected void hideRois() {
if (currentImage == null) return;
currentImage.killRoi();
if (currentImage.isVisible()) {
currentImage.updateAndDraw();
ImageUtils.removeScrollListener(currentImage, this, this);
}
currentImage = null;
}
/**
* Builds dialog to query users for projection parameters.
*
* @param start starting slice to display
* @param stop last slice
*/
protected GenericDialog buildControlDialog(int start, int stop) {
GenericDialog gd = new GenericDialog("ZProjection", IJ.getInstance());
gd.addNumericField("Start slice:", startSlice, 0 /*digits*/);
gd.addNumericField("Stop slice:", stopSlice, 0 /*digits*/);
gd.addChoice("Projection type", METHODS, METHODS[method]);
if (isHyperstack && imp.getNFrames() > 1 && imp.getNSlices() > 1)
gd.addCheckbox("All time frames", allTimeFrames);
return gd;
}
/** 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();
}
}
void toBoundingBox(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null) {
noRoi("To Bounding Box");
return;
}
Rectangle r = roi.getBounds();
imp.killRoi();
imp.setRoi(new Roi(r.x, r.y, r.width, r.height));
}
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;
}
void hide() {
ImagePlus imp = IJ.getImage();
Overlay overlay = imp.getOverlay();
if (overlay != null) {
overlay2 = overlay;
imp.setOverlay(null);
}
RoiManager rm = RoiManager.getInstance();
if (rm != null) rm.runCommand("show none");
}
protected void updateRoi() {
// System.out.println("image:"+currentImage.getTitle()+ " slice:"+currentImage.getSlice());
Roi r = currentROIs.get(currentImage.getSlice());
if (r != null) {
currentImage.setRoi(r);
} else {
currentImage.killRoi();
}
currentImage.updateAndDraw();
}
void addScrollbars(ImagePlus imp) {
ImageStack s = imp.getStack();
int stackSize = s.getSize();
nSlices = stackSize;
hyperStack = imp.getOpenAsHyperStack();
// imp.setOpenAsHyperStack(false);
int[] dim = imp.getDimensions();
int nDimensions = 2 + (dim[2] > 1 ? 1 : 0) + (dim[3] > 1 ? 1 : 0) + (dim[4] > 1 ? 1 : 0);
if (nDimensions <= 3 && dim[2] != nSlices) hyperStack = false;
if (hyperStack) {
nChannels = dim[2];
nSlices = dim[3];
nFrames = dim[4];
}
// IJ.log("StackWindow: "+hyperStack+" "+nChannels+" "+nSlices+" "+nFrames);
if (nSlices == stackSize) hyperStack = false;
if (nChannels * nSlices * nFrames != stackSize) hyperStack = false;
if (cSelector != null || zSelector != null || tSelector != null) removeScrollbars();
ImageJ ij = IJ.getInstance();
if (nChannels > 1) {
cSelector = new ScrollbarWithLabel(this, 1, 1, 1, nChannels + 1, 'c');
add(cSelector);
if (ij != null) cSelector.addKeyListener(ij);
cSelector.addAdjustmentListener(this);
cSelector.setFocusable(false); // prevents scroll bar from blinking on Windows
cSelector.setUnitIncrement(1);
cSelector.setBlockIncrement(1);
}
if (nSlices > 1) {
char label = nChannels > 1 || nFrames > 1 ? 'z' : 't';
if (stackSize == dim[2] && imp.isComposite()) label = 'c';
zSelector = new ScrollbarWithLabel(this, 1, 1, 1, nSlices + 1, label);
if (label == 't') animationSelector = zSelector;
add(zSelector);
if (ij != null) zSelector.addKeyListener(ij);
zSelector.addAdjustmentListener(this);
zSelector.setFocusable(false);
int blockIncrement = nSlices / 10;
if (blockIncrement < 1) blockIncrement = 1;
zSelector.setUnitIncrement(1);
zSelector.setBlockIncrement(blockIncrement);
sliceSelector = zSelector.bar;
}
if (nFrames > 1) {
animationSelector = tSelector = new ScrollbarWithLabel(this, 1, 1, 1, nFrames + 1, 't');
add(tSelector);
if (ij != null) tSelector.addKeyListener(ij);
tSelector.addAdjustmentListener(this);
tSelector.setFocusable(false);
int blockIncrement = nFrames / 10;
if (blockIncrement < 1) blockIncrement = 1;
tSelector.setUnitIncrement(1);
tSelector.setBlockIncrement(blockIncrement);
}
}
public int setup(String arg, ImagePlus imp) {
this.arg = arg;
this.imp = imp;
// return IJ.setupDialog(imp, DOES_8G+DOES_8C+SUPPORTS_MASKING);
if (imp != null) {
Roi roi = imp.getRoi();
if (roi != null && !roi.isArea()) imp.killRoi(); // ignore any line selection
}
int flags = IJ.setupDialog(imp, DOES_ALL - DOES_8C + SUPPORTS_MASKING);
return flags;
}
/** Performs actual projection using specified method. */
public void doProjection() {
if (imp == null) return;
sliceCount = 0;
if (method < AVG_METHOD || method > MEDIAN_METHOD) method = AVG_METHOD;
for (int slice = startSlice; slice <= stopSlice; slice += increment) sliceCount++;
if (method == MEDIAN_METHOD) {
projImage = doMedianProjection();
return;
}
// Create new float processor for projected pixels.
FloatProcessor fp = new FloatProcessor(imp.getWidth(), imp.getHeight());
ImageStack stack = imp.getStack();
RayFunction rayFunc = getRayFunction(method, fp);
if (IJ.debugMode == true) {
IJ.log("\nProjecting stack from: " + startSlice + " to: " + stopSlice);
}
// Determine type of input image. Explicit determination of
// processor type is required for subsequent pixel
// manipulation. This approach is more efficient than the
// more general use of ImageProcessor's getPixelValue and
// putPixel methods.
int ptype;
if (stack.getProcessor(1) instanceof ByteProcessor) ptype = BYTE_TYPE;
else if (stack.getProcessor(1) instanceof ShortProcessor) ptype = SHORT_TYPE;
else if (stack.getProcessor(1) instanceof FloatProcessor) ptype = FLOAT_TYPE;
else {
IJ.error("Z Project", "Non-RGB stack required");
return;
}
// Do the projection.
for (int n = startSlice; n <= stopSlice; n += increment) {
IJ.showStatus("ZProjection " + color + ": " + n + "/" + stopSlice);
IJ.showProgress(n - startSlice, stopSlice - startSlice);
projectSlice(stack.getPixels(n), rayFunc, ptype);
}
// Finish up projection.
if (method == SUM_METHOD) {
fp.resetMinAndMax();
projImage = new ImagePlus(makeTitle(), fp);
} else if (method == SD_METHOD) {
rayFunc.postProcess();
fp.resetMinAndMax();
projImage = new ImagePlus(makeTitle(), fp);
} else {
rayFunc.postProcess();
projImage = makeOutputImage(imp, fp, ptype);
}
if (projImage == null) IJ.error("Z Project", "Error computing projection.");
}