// for segmented lines, not polygons
public static double[] getSectors(float[] xxf, float[] yyf, double rad) {
int len = xxf.length;
double[] xx = new double[len];
double[] yy = new double[len];
for (int jj = 0; jj < xxf.length; jj++) {
xx[jj] = xxf[jj];
yy[jj] = yyf[jj];
}
double pi = Math.PI;
double[] vAngles = getVertexAngles(xx, yy);
double[] segAngles = getSegmentAngles(xx, yy);
double phiSym, phiArc, phi;
double dx, dy; // , px, py;
for (int jj = 1; jj < len - 1; jj++) {
phiSym = (segAngles[jj - 1] + segAngles[jj]) / 2;
phiArc = 180 - vAngles[jj];
int nPoints = 3;
float[] arcPointsX = new float[nPoints + 1];
float[] arcPointsY = new float[nPoints + 1];
for (int pt = 0; pt < nPoints; pt++) {
phi = phiSym - phiArc / 2 + pt * phiArc / (nPoints - 1);
dx = rad * Math.cos(phi / 180 * pi);
dy = rad * -Math.sin(phi / 180 * pi);
arcPointsX[pt] = (float) (xx[jj] + dx);
arcPointsY[pt] = (float) (yy[jj] + dy);
}
arcPointsX[nPoints] = (float) (xx[jj]);
arcPointsY[nPoints] = (float) (yy[jj]);
PolygonRoi polygon = new PolygonRoi(arcPointsX, arcPointsY, nPoints + 1, Roi.POLYGON);
IJ.getImage().setRoi(polygon, true);
}
return null;
}
public static void main(String args[]) {
// new ImageJ();
IJ.open("/Applications/ImageJ/Bilder/Bear.jpg");
// IJ.open("Z:/Pictures/Beispielbilder/orchid.jpg");
GRDM_U2 pw = new GRDM_U2();
pw.imp = IJ.getImage();
pw.run("");
}
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");
}
public boolean beadCalibration3d() {
imp = IJ.getImage();
if (imp == null) {
IJ.noImage();
return false;
} else if (imp.getStackSize() == 1) {
IJ.error("Stack required");
return false;
} else if (imp.getType() != ImagePlus.GRAY8 && imp.getType() != ImagePlus.GRAY16) {
// In order to support 32bit images, pict[] must be changed to float[], and getPixel(x, y);
// requires a Float.intBitsToFloat() conversion
IJ.error("8 or 16 bit greyscale image required");
return false;
}
width = imp.getWidth();
height = imp.getHeight();
nslices = imp.getStackSize();
imtitle = imp.getTitle();
models[0] = "*None*";
models[1] = "line";
models[2] = "2nd degree polynomial";
models[3] = "3rd degree polynomial";
models[4] = "4th degree polynomial";
GenericDialog gd = new GenericDialog("3D PALM calibration");
gd.addNumericField("Maximum FWHM (in px)", prefs.get("QuickPALM.3Dcal_fwhm", 20), 0);
gd.addNumericField(
"Particle local threshold (% maximum intensity)", prefs.get("QuickPALM.pthrsh", 20), 0);
gd.addNumericField("Z-spacing (nm)", prefs.get("QuickPALM.z-step", 10), 2);
gd.addNumericField("Calibration Z-smoothing (radius)", prefs.get("QuickPALM.window", 1), 0);
gd.addChoice("Model", models, prefs.get("QuickPALM.model", models[3]));
gd.addCheckbox(
"Show divergence of bead positions against model",
prefs.get("QuickPALM.3Dcal_showDivergence", false));
gd.addCheckbox("Show extra particle info", prefs.get("QuickPALM.3Dcal_showExtraInfo", false));
gd.addMessage("\n\nDon't forget to save the table in the end...");
gd.showDialog();
if (gd.wasCanceled()) return false;
fwhm = gd.getNextNumber();
prefs.set("QuickPALM.QuickPALM.3Dcal_fwhm", fwhm);
pthrsh = gd.getNextNumber() / 100;
prefs.set("QuickPALM.pthrsh", pthrsh * 100);
cal_z = gd.getNextNumber();
prefs.set("QuickPALM.z-step", cal_z);
window = (int) gd.getNextNumber();
prefs.set("QuickPALM.window", window);
model = gd.getNextChoice();
prefs.set("QuickPALM.model", model);
part_divergence = gd.getNextBoolean();
prefs.set("QuickPALM.3Dcal_showDivergence", part_divergence);
part_extrainfo = gd.getNextBoolean();
prefs.set("QuickPALM.3Dcal_showExtraInfo", part_extrainfo);
return true;
}
@Override
public String commandExecuting(String command) {
if (command.equalsIgnoreCase("Quit") && frame_ != null) {
try {
if (!frame_.closeSequence(true)) {
return null;
}
} catch (Exception ex) {
// do nothing, just make sure to continue quitting
}
return command;
} else if (command.equals("Crop")) {
if (IJ.getImage().getStack() instanceof AcquisitionVirtualStack) {
new Duplicator().run(IJ.getImage()).show();
// abort further processing of the Crop command
return null;
}
} else if (command.equals("Add Noise")) {
// blanket method to make sure that ImageJ filters do not execute on disk-cached images
// this may backfire!
if (IJ.getImage().getStack() instanceof AcquisitionVirtualStack) {
AcquisitionVirtualStack avs = (AcquisitionVirtualStack) IJ.getImage().getStack();
if (avs.getVirtualAcquisitionDisplay().isDiskCached()) {
// duplicate the image and then run the ImageJ command on what is now the new image
new Duplicator().run(IJ.getImage()).show();
} else {
// Image is not disk chached. Warn that data will be lost
if (!IJ.showMessageWithCancel(
"Micro-Manager data not saved",
"Data are not saved and Undo is impossible. \n"
+ "Do you really want to execute the command?")) {
return null;
}
}
}
}
return command;
}
@Override
public void run(final String arg) {
imp = IJ.getImage();
if (imp == null) {
IJ.error("No image open.");
return;
}
if (!setup(imp)) return;
run(imp, width, height, minLambda, minPhi, hfov, vfov);
}
void addSelection() {
ImagePlus imp = IJ.getImage();
String macroOptions = Macro.getOptions();
if (macroOptions != null && IJ.macroRunning() && macroOptions.indexOf("remove") != -1) {
imp.setOverlay(null);
return;
}
Roi roi = imp.getRoi();
if (roi == null && imp.getOverlay() != null) {
GenericDialog gd = new GenericDialog("No Selection");
gd.addMessage("\"Overlay>Add\" requires a selection.");
gd.setInsets(15, 40, 0);
gd.addCheckbox("Remove existing overlay", false);
gd.showDialog();
if (gd.wasCanceled()) return;
if (gd.getNextBoolean()) imp.setOverlay(null);
return;
}
if (roi == null) {
IJ.error("This command requires a selection.");
return;
}
roi = (Roi) roi.clone();
if (roi.getStrokeColor() == null) roi.setStrokeColor(Toolbar.getForegroundColor());
int width = Line.getWidth();
Rectangle bounds = roi.getBounds();
boolean tooWide = width > Math.max(bounds.width, bounds.height) / 3.0;
if (roi.getStroke() == null && width > 1 && !tooWide) roi.setStrokeWidth(Line.getWidth());
Overlay overlay = imp.getOverlay();
if (overlay != null && overlay.size() > 0 && !roi.isDrawingTool()) {
Roi roi2 = overlay.get(overlay.size() - 1);
if (roi.getStroke() == null) roi.setStrokeWidth(roi2.getStrokeWidth());
if (roi.getFillColor() == null) roi.setFillColor(roi2.getFillColor());
}
boolean points = roi instanceof PointRoi && ((PolygonRoi) roi).getNCoordinates() > 1;
if (points) roi.setStrokeColor(Color.red);
if (!IJ.altKeyDown() && !(roi instanceof Arrow)) {
RoiProperties rp = new RoiProperties("Add to Overlay", roi);
if (!rp.showDialog()) return;
}
String name = roi.getName();
boolean newOverlay = name != null && name.equals("new-overlay");
if (overlay == null || newOverlay) overlay = new Overlay();
overlay.add(roi);
imp.setOverlay(overlay);
overlay2 = overlay;
if (points || (roi instanceof ImageRoi) || (roi instanceof Arrow)) imp.killRoi();
Undo.setup(Undo.OVERLAY_ADDITION, imp);
}
public void run(String arg) {
ImagePlus imp = IJ.getImage();
int size = imp.getStackSize();
if (size == 1) {
IJ.error("Z Project", "This command requires a stack");
return;
}
if (imp.isHyperStack()) {
new ZProjector().run("");
return;
}
if (!showDialog(imp)) return;
ImagePlus imp2 = groupZProject(imp, method, groupSize);
if (imp != null) imp2.show();
}
public void run(String arg) {
imp = IJ.getImage();
Roi roi = imp.getRoi();
if (roi != null && !roi.isArea()) imp.killRoi(); // ignore any line selection
ImageProcessor ip = imp.getProcessor();
if (!showDialog(ip)) return;
if (ip.getWidth() > 1 && ip.getHeight() > 1) ip.setInterpolate(interpolate);
else ip.setInterpolate(false);
ip.setBackgroundValue(bgValue);
imp.startTiming();
try {
if (newWindow && imp.getStackSize() > 1 && processStack) createNewStack(imp, ip);
else scale(ip);
} catch (OutOfMemoryError o) {
IJ.outOfMemory("Scale");
}
IJ.showProgress(1.0);
}
@Override
public void run(String arg) {
ImagePlus imp = IJ.getImage();
GenericDialog gd = new GenericDialog(name);
gd.addMessage("Requires SI raw data in OMX (CPZAT) order.");
gd.addNumericField("angles", angles, 0);
gd.addNumericField("phases", phases, 0);
gd.showDialog();
if (gd.wasCanceled()) return;
if (gd.wasOKed()) {
angles = (int) gd.getNextNumber();
phases = (int) gd.getNextNumber();
}
if (!I1l.stackDivisibleBy(imp, phases * angles)) {
IJ.showMessage(name, "Error: stack size not consistent with phases/angles.");
return;
}
results = exec(imp);
results.report();
}
void fromRoiManager() {
ImagePlus imp = IJ.getImage();
RoiManager rm = RoiManager.getInstance();
if (rm == null) {
IJ.error("ROI Manager is not open");
return;
}
Roi[] rois = rm.getRoisAsArray();
if (rois.length == 0) {
IJ.error("ROI Manager is empty");
return;
}
Overlay overlay = new Overlay();
for (int i = 0; i < rois.length; i++) overlay.add((Roi) rois[i].clone());
imp.setOverlay(overlay);
ImageCanvas ic = imp.getCanvas();
if (ic != null) ic.setShowAllROIs(false);
rm.setEditMode(imp, false);
imp.killRoi();
}
public static void main(String[] args) {
String mriImage = args[0];
String outImage = args[1];
String segArgs = args[2];
String outTable = args[3];
String pdxArgs = args[4];
System.out.println("Open: " + mriImage);
IJ.open(mriImage);
COPD_LungSegment tjPlug = new COPD_LungSegment();
ImagePlus cImage = IJ.getImage();
tjPlug.setup(segArgs, cImage);
tjPlug.run(cImage.getProcessor());
IJ.save(cImage, outImage);
COPD_PDxLAAx pdxPlug = new COPD_PDxLAAx();
pdxPlug.setup("", cImage);
pdxPlug.run(cImage.getProcessor());
ResultsTable rt = Analyzer.getResultsTable();
try {
rt.saveAs(outTable);
} catch (IOException e) {
e.printStackTrace();
}
System.out.println("Results Table\n");
String prefix = "rtout, ";
for (int i = 0; i < ResultsTable.MAX_COLUMNS; i++) {
if (!rt.columnExists(i)) break;
String tempOut = rt.getColumnHeading(i);
for (double d : rt.getColumnAsDoubles(i)) {
tempOut += ", " + d;
}
System.out.println(prefix + tempOut);
}
}
void toRoiManager() {
ImagePlus imp = IJ.getImage();
Overlay overlay = imp.getOverlay();
if (overlay == null) {
IJ.error("Overlay required");
return;
}
RoiManager rm = RoiManager.getInstance();
if (rm == null) {
if (Macro.getOptions() != null && Interpreter.isBatchMode())
rm = Interpreter.getBatchModeRoiManager();
if (rm == 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)) return;
rm = (RoiManager) frame;
}
}
rm.runCommand("reset");
for (int i = 0; i < overlay.size(); i++) rm.add(imp, overlay.get(i), i);
rm.setEditMode(imp, true);
if (rm.getCount() == overlay.size()) imp.setOverlay(null);
}
public void run(String arg) {
imp = IJ.getImage();
if (imp == null) return;
stackSize = imp.getStackSize();
Roi roi = imp.getRoi();
Calibration cal = imp.getCalibration();
if (roi != null && roi.getBounds().equals(prevRoi) && cal.pixelWidth == prevPixelWidth)
roi = null;
if (roi != null) {
boolean rectOrOval =
roi != null && (roi.getType() == Roi.RECTANGLE || roi.getType() == Roi.OVAL);
oval = rectOrOval && (roi.getType() == Roi.OVAL); // Handle existing oval ROI
Rectangle r = roi.getBounds();
width = r.width;
height = r.height;
xRoi = r.x;
yRoi = r.y;
if (scaledUnits && cal.scaled()) {
xRoi = xRoi * cal.pixelWidth;
yRoi = yRoi * cal.pixelHeight;
width = width * cal.pixelWidth;
height = height * cal.pixelHeight;
}
if (centered) { // Make xRoi and yRoi consistent when centered mode is active
xRoi += width / 2.0;
yRoi += height / 2.0;
}
} else if (!validDialogValues()) {
width = imp.getWidth() / 2;
height = imp.getHeight() / 2;
xRoi = width / 2;
yRoi = height / 2;
}
iSlice = imp.getCurrentSlice();
showDialog();
}
void flatten() {
ImagePlus imp = IJ.getImage();
ImagePlus imp2 = imp.flatten();
imp2.setTitle(WindowManager.getUniqueName(imp.getTitle()));
imp2.show();
}
void show() {
ImagePlus imp = IJ.getImage();
if (overlay2 != null) imp.setOverlay(overlay2);
RoiManager rm = RoiManager.getInstance();
if (rm != null) rm.runCommand("show all");
}
// TODO split run method into more sensible methods
public void run(final String arg) {
if (!ImageCheck.checkEnvironment()) return;
final ImagePlus imp = IJ.getImage();
if (null == imp) {
IJ.noImage();
return;
}
final ImageCheck ic = new ImageCheck();
if (!ImageCheck.isBinary(imp)) {
IJ.showMessage("Fractal Count requires a binary image.");
return;
}
if (noGo) return;
final ImagePlus surfaceImp = findSurfaceVoxels(imp);
try {
// Fetch data
final int width = imp.getWidth();
final int height = imp.getHeight();
final int depth = imp.getStackSize();
if (autoParam) {
maxBox = Math.max(width, Math.max(height, depth)) / autoDiv;
if (verboseOutput) {
IJ.log("Automatic max box size " + maxBox + " selected");
}
}
// Create variables we need and set them
long bestCount; // keep track of best count so far
long count = 0; // current count
final ArrayList<Double> xList = new ArrayList<Double>();
final ArrayList<Double> yList = new ArrayList<Double>();
int xPos, yPos, zPos, yPart;
int xGrid, yGrid, zGrid;
int xStart, yStart, zStart;
int xEnd, yEnd, zEnd;
// Start timer
final long startTime = System.currentTimeMillis();
for (int boxSize = maxBox; boxSize >= minBox; boxSize /= divBox) {
if (verboseOutput) {
IJ.showStatus("Estimating dimension, box size: " + boxSize);
}
bestCount = Long.MAX_VALUE; // init count for this boxSize
final int increment = Math.max(1, boxSize / numOffsets);
for (int gridOffsetX = 0;
(gridOffsetX < boxSize) && (gridOffsetX < width);
gridOffsetX += increment) {
for (int gridOffsetY = 0;
(gridOffsetY < boxSize) && (gridOffsetY < height);
gridOffsetY += increment) {
for (int gridOffsetZ = 0;
(gridOffsetZ < boxSize) && (gridOffsetZ < depth);
gridOffsetZ += increment) {
count = 0;
final int iMax = width + gridOffsetX;
final int jMax = height + gridOffsetY;
final int kMax = depth + gridOffsetZ;
// Iterate over box-grid
for (int i = 0; i <= iMax; i += boxSize) {
xGrid = -gridOffsetX + i;
for (int j = 0; j <= jMax; j += boxSize) {
yGrid = -gridOffsetY + j;
for (int k = 0; k <= kMax; k += boxSize) {
zGrid = -gridOffsetZ + k;
xStart = 0;
if (xGrid < 0) {
xStart = -xGrid;
}
if ((boxSize + xGrid) >= width) {
xEnd = Math.min(width, (width - xGrid));
} else {
xEnd = boxSize;
}
yStart = 0;
if (yGrid < 0) {
yStart = -yGrid;
}
if ((boxSize + yGrid) >= height) {
yEnd = Math.min(height, (height - yGrid));
} else {
yEnd = boxSize;
}
zStart = 0;
if (zGrid < 0) {
zStart = -zGrid;
}
if ((boxSize + zGrid) >= depth) {
zEnd = Math.min(depth, (depth - zGrid));
} else {
zEnd = boxSize;
}
for (int x = xStart; x < xEnd; x++) {
xPos = x + xGrid;
for (int y = yStart; y < yEnd; y++) {
yPos = (y + yGrid);
yPart = yPos * width;
for (int z = zStart; z < zEnd; z++) {
zPos = z + zGrid;
// If pixel inside region,
// count it
if ((0xff
& ((byte[]) surfaceImp.getStack().getPixels(zPos + 1))
[xPos + yPart])
>= threshold) {
count++;
z = x = y = boxSize; // stops
// things
}
}
}
}
}
}
}
if (count < bestCount) {
bestCount = count;
}
}
}
}
xList.add(new Double(boxSize));
yList.add(new Double(bestCount));
}
if (verboseOutput) {
IJ.log("\nDuration: " + (System.currentTimeMillis() - startTime) / 1000.0 + " seconds\n");
}
final double[] boxSizes = new double[xList.size()];
final double[] boxCountSums = new double[yList.size()];
for (int i = 0; i < boxSizes.length; i++) {
boxSizes[i] = -Math.log((xList.get(i)).doubleValue());
boxCountSums[i] = Math.log((yList.get(i)).doubleValue());
}
if (verboseOutput) {
IJ.log(
"Used " + boxSizes.length + " different box sizes, from " + maxBox + " to " + minBox);
IJ.log(
"with a reduction rate of "
+ divBox
+ " and "
+ numOffsets
+ " translations of each box.");
}
if (boxSizes.length == 0) {
IJ.error(
"\nError: No boxes!\n"
+ "Make sure that starting and ending box size and"
+ "reduction rate allow for at least one"
+ " box size to exist!");
return;
}
final CurveFitter cf = new CurveFitter(boxSizes, boxCountSums);
cf.doFit(CurveFitter.STRAIGHT_LINE);
final double[] p = cf.getParams();
final double RSq = cf.getRSquared();
if (verboseOutput) {
IJ.log(
imp.getTitle()
+ ": Dimension estimate: "
+ IJ.d2s(p[1], 4)
+ ": R²: "
+ RSq
+ ": Settings: "
+ maxBox
+ ":"
+ minBox
+ ":"
+ divBox
+ ":"
+ numOffsets);
}
if (verboseOutput) {
IJ.log("Box Size Box Count");
for (int i = 0; i < boxSizes.length; i++) {
IJ.log(IJ.d2s(xList.get(i), 0) + " " + IJ.d2s(yList.get(i), 0));
}
}
final ResultInserter ri = ResultInserter.getInstance();
ri.setResultInRow(imp, "Fractal Dimension", p[1]);
ri.setResultInRow(imp, "R²", RSq);
ri.updateTable();
if (plotGraph && !Interpreter.isBatchMode()) {
drawGraph(p, boxSizes, boxCountSums);
}
} catch (final Exception e) {
e.printStackTrace();
}
UsageReporter.reportEvent(this).send();
}
public void run(String arg) {
ImageCheck ic = new ImageCheck();
if (!ImageCheck.checkEnvironment()) return;
ImagePlus imp = IJ.getImage();
if (!ic.isBinary(imp)) {
IJ.error("8-bit binary (black and white only) image required.");
return;
}
if (!ic.isVoxelIsotropic(imp, 1E-3)) {
if (IJ.showMessageWithCancel(
"Anisotropic voxels",
"This image contains anisotropic voxels, which will\n"
+ "result in incorrect thickness calculation.\n\n"
+ "Consider rescaling your data so that voxels are isotropic\n"
+ "(Image > Scale...).\n\n"
+ "Continue anyway?")) {
} else return;
}
GenericDialog gd = new GenericDialog("Options");
gd.addCheckbox("Thickness", true);
gd.addCheckbox("Spacing", false);
gd.addCheckbox("Graphic Result", true);
gd.addCheckbox("Use_ROI_Manager", false);
gd.addCheckbox("Mask thickness map", true);
gd.addHelp("http://bonej.org/thickness");
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
boolean doThickness = gd.getNextBoolean();
boolean doSpacing = gd.getNextBoolean();
boolean doGraphic = gd.getNextBoolean();
boolean doRoi = gd.getNextBoolean();
boolean doMask = gd.getNextBoolean();
long startTime = System.currentTimeMillis();
String title = stripExtension(imp.getTitle());
RoiManager roiMan = RoiManager.getInstance();
// calculate trabecular thickness (Tb.Th)
if (doThickness) {
boolean inverse = false;
ImagePlus impLTC = new ImagePlus();
if (doRoi && roiMan != null) {
ImageStack stack = RoiMan.cropStack(roiMan, imp.getStack(), true, 0, 1);
ImagePlus crop = new ImagePlus(imp.getTitle(), stack);
crop.setCalibration(imp.getCalibration());
impLTC = getLocalThickness(crop, inverse, doMask);
} else impLTC = getLocalThickness(imp, inverse, doMask);
impLTC.setTitle(title + "_Tb.Th");
impLTC.setCalibration(imp.getCalibration());
double[] stats = StackStats.meanStdDev(impLTC);
insertResults(imp, stats, inverse);
if (doGraphic && !Interpreter.isBatchMode()) {
impLTC.show();
impLTC.setSlice(1);
impLTC.getProcessor().setMinAndMax(0, stats[2]);
IJ.run("Fire");
}
}
if (doSpacing) {
boolean inverse = true;
ImagePlus impLTCi = new ImagePlus();
if (doRoi && roiMan != null) {
ImageStack stack = RoiMan.cropStack(roiMan, imp.getStack(), true, 255, 1);
ImagePlus crop = new ImagePlus(imp.getTitle(), stack);
crop.setCalibration(imp.getCalibration());
impLTCi = getLocalThickness(crop, inverse, doMask);
} else impLTCi = getLocalThickness(imp, inverse, doMask);
// check marrow cavity size (i.e. trabcular separation, Tb.Sp)
impLTCi.setTitle(title + "_Tb.Sp");
impLTCi.setCalibration(imp.getCalibration());
double[] stats = StackStats.meanStdDev(impLTCi);
insertResults(imp, stats, inverse);
if (doGraphic && !Interpreter.isBatchMode()) {
impLTCi.show();
impLTCi.setSlice(1);
impLTCi.getProcessor().setMinAndMax(0, stats[2]);
IJ.run("Fire");
}
}
IJ.showProgress(1.0);
IJ.showStatus("Done");
double duration = ((double) System.currentTimeMillis() - (double) startTime) / (double) 1000;
IJ.log("Duration = " + IJ.d2s(duration, 3) + " s");
UsageReporter.reportEvent(this).send();
return;
}
public void run(String arg) {
int wOld, hOld, wNew, hNew;
boolean fIsStack = false;
ImagePlus imp = IJ.getImage();
wOld = imp.getWidth();
hOld = imp.getHeight();
ImageStack stackOld = imp.getStack();
if ((stackOld != null) && (stackOld.getSize() > 1)) fIsStack = true;
String[] sPositions = {
"Top-Left", "Top-Center", "Top-Right",
"Center-Left", "Center", "Center-Right",
"Bottom-Left", "Bottom-Center", "Bottom-Right"
};
String strTitle = fIsStack ? "Resize Stack Canvas" : "Resize Image Canvas";
GenericDialog gd = new GenericDialog(strTitle);
gd.addNumericField("Width:", wOld, 0, 5, "pixels");
gd.addNumericField("Height:", hOld, 0, 5, "pixels");
gd.addChoice("Position:", sPositions, sPositions[4]);
gd.addCheckbox("Zero Fill", zeroFill);
gd.showDialog();
if (gd.wasCanceled()) return;
wNew = (int) gd.getNextNumber();
hNew = (int) gd.getNextNumber();
int iPos = gd.getNextChoiceIndex();
zeroFill = gd.getNextBoolean();
Prefs.set("resizer.zero", zeroFill);
int xOff, yOff;
int xC = (wNew - wOld) / 2; // offset for centered
int xR = (wNew - wOld); // offset for right
int yC = (hNew - hOld) / 2; // offset for centered
int yB = (hNew - hOld); // offset for bottom
switch (iPos) {
case 0: // TL
xOff = 0;
yOff = 0;
break;
case 1: // TC
xOff = xC;
yOff = 0;
break;
case 2: // TR
xOff = xR;
yOff = 0;
break;
case 3: // CL
xOff = 0;
yOff = yC;
break;
case 4: // C
xOff = xC;
yOff = yC;
break;
case 5: // CR
xOff = xR;
yOff = yC;
break;
case 6: // BL
xOff = 0;
yOff = yB;
break;
case 7: // BC
xOff = xC;
yOff = yB;
break;
case 8: // BR
xOff = xR;
yOff = yB;
break;
default: // center
xOff = xC;
yOff = yC;
break;
}
if (fIsStack) {
ImageStack stackNew = expandStack(stackOld, wNew, hNew, xOff, yOff);
imp.setStack(null, stackNew);
} else {
if (!IJ.macroRunning()) Undo.setup(Undo.COMPOUND_FILTER, imp);
ImageWindow win = imp.getWindow();
if (win != null && (win instanceof PlotWindow)) ((PlotWindow) win).getPlot().setFrozen(true);
ImageProcessor newIP = expandImage(imp.getProcessor(), wNew, hNew, xOff, yOff);
imp.setProcessor(null, newIP);
if (!IJ.macroRunning()) Undo.setup(Undo.COMPOUND_FILTER_DONE, imp);
}
Overlay overlay = imp.getOverlay();
if (overlay != null) overlay.translate(xOff, yOff);
}
@Override
public void run(String arg) {
final ImagePlus imp = IJ.getImage();
run(IJ.getImage().getProcessor(), 0);
imp.updateAndDraw();
}
/** Ask for parameters and then execute. */
public void run(String arg) {
// 1 - Obtain the currently active image:
ImagePlus imp = IJ.getImage();
if (null == imp) {
IJ.showMessage("There must be at least one image open");
return;
}
if (imp.getBitDepth() != 8) {
IJ.showMessage("Error", "Only 8-bit images are supported");
return;
}
// 2 - Ask for parameters:
GenericDialog gd = new GenericDialog("Auto Local Threshold");
String[] methods = {
"Try all",
"Bernsen",
"Contrast",
"Mean",
"Median",
"MidGrey",
"Niblack",
"Otsu",
"Phansalkar",
"Sauvola"
};
gd.addMessage("Auto Local Threshold v1.5");
gd.addChoice("Method", methods, methods[0]);
gd.addNumericField("Radius", 15, 0);
gd.addMessage("Special paramters (if different from default)");
gd.addNumericField("Parameter_1", 0, 0);
gd.addNumericField("Parameter_2", 0, 0);
gd.addCheckbox("White objects on black background", true);
if (imp.getStackSize() > 1) {
gd.addCheckbox("Stack", false);
}
gd.addMessage("Thresholded result is always shown in white [255].");
gd.showDialog();
if (gd.wasCanceled()) return;
// 3 - Retrieve parameters from the dialog
String myMethod = gd.getNextChoice();
int radius = (int) gd.getNextNumber();
double par1 = (double) gd.getNextNumber();
double par2 = (double) gd.getNextNumber();
boolean doIwhite = gd.getNextBoolean();
boolean doIstack = false;
int stackSize = imp.getStackSize();
if (stackSize > 1) doIstack = gd.getNextBoolean();
// 4 - Execute!
// long start = System.currentTimeMillis();
if (myMethod.equals("Try all")) {
ImageProcessor ip = imp.getProcessor();
int xe = ip.getWidth();
int ye = ip.getHeight();
int ml = methods.length;
ImagePlus imp2, imp3;
ImageStack tstack = null, stackNew;
if (stackSize > 1 && doIstack) {
boolean doItAnyway = true;
if (stackSize > 25) {
YesNoCancelDialog d =
new YesNoCancelDialog(
IJ.getInstance(),
"Auto Local Threshold",
"You might run out of memory.\n \nDisplay "
+ stackSize
+ " slices?\n \n \'No\' will process without display and\noutput results to the log window.");
if (!d.yesPressed()) {
// doIlog=true; //will show in the log window
doItAnyway = false;
}
if (d.cancelPressed()) return;
}
for (int j = 1; j <= stackSize; j++) {
imp.setSlice(j);
ip = imp.getProcessor();
tstack = new ImageStack(xe, ye);
for (int k = 1; k < ml; k++) tstack.addSlice(methods[k], ip.duplicate());
imp2 = new ImagePlus("Auto Threshold", tstack);
imp2.updateAndDraw();
for (int k = 1; k < ml; k++) {
imp2.setSlice(k);
Object[] result = exec(imp2, methods[k], radius, par1, par2, doIwhite);
}
// if (doItAnyway){
CanvasResizer cr = new CanvasResizer();
stackNew = cr.expandStack(tstack, (xe + 2), (ye + 18), 1, 1);
imp3 = new ImagePlus("Auto Threshold", stackNew);
imp3.updateAndDraw();
MontageMaker mm = new MontageMaker();
mm.makeMontage(imp3, 3, 3, 1.0, 1, (ml - 1), 1, 0, true); // 3 columns and 3 rows
}
imp.setSlice(1);
// if (doItAnyway)
IJ.run("Images to Stack", "method=[Copy (center)] title=Montage");
return;
} else { // single image try all
tstack = new ImageStack(xe, ye);
for (int k = 1; k < ml; k++) tstack.addSlice(methods[k], ip.duplicate());
imp2 = new ImagePlus("Auto Threshold", tstack);
imp2.updateAndDraw();
for (int k = 1; k < ml; k++) {
imp2.setSlice(k);
// IJ.log("analyzing slice with "+methods[k]);
Object[] result = exec(imp2, methods[k], radius, par1, par2, doIwhite);
}
// imp2.setSlice(1);
CanvasResizer cr = new CanvasResizer();
stackNew = cr.expandStack(tstack, (xe + 2), (ye + 18), 1, 1);
imp3 = new ImagePlus("Auto Threshold", stackNew);
imp3.updateAndDraw();
MontageMaker mm = new MontageMaker();
mm.makeMontage(imp3, 3, 3, 1.0, 1, (ml - 1), 1, 0, true);
return;
}
} else { // selected a method
if (stackSize > 1 && doIstack) { // whole stack
// if (doIstackHistogram) {// one global histogram
// Object[] result = exec(imp, myMethod, noWhite, noBlack, doIwhite, doIset, doIlog,
// doIstackHistogram );
// }
// else{ // slice by slice
for (int k = 1; k <= stackSize; k++) {
imp.setSlice(k);
Object[] result = exec(imp, myMethod, radius, par1, par2, doIwhite);
}
// }
imp.setSlice(1);
} else { // just one slice
Object[] result = exec(imp, myMethod, radius, par1, par2, doIwhite);
}
// 5 - If all went well, show the image:
// not needed here as the source image is binarised
}
}
void addImage() {
ImagePlus imp = IJ.getImage();
int[] wList = WindowManager.getIDList();
if (wList == null || wList.length < 2) {
IJ.error("Add Image...", "The command requires at least two open images.");
return;
}
String[] titles = new String[wList.length];
for (int i = 0; i < wList.length; i++) {
ImagePlus imp2 = WindowManager.getImage(wList[i]);
titles[i] = imp2 != null ? imp2.getTitle() : "";
}
int x = 0, y = 0;
Roi roi = imp.getRoi();
if (roi != null && roi.isArea()) {
Rectangle r = roi.getBounds();
x = r.x;
y = r.y;
}
int index = 0;
if (wList.length == 2) {
ImagePlus i1 = WindowManager.getImage(wList[0]);
ImagePlus i2 = WindowManager.getImage(wList[1]);
if (i2.getWidth() < i1.getWidth() && i2.getHeight() < i1.getHeight()) index = 1;
} else if (imp.getID() == wList[0]) index = 1;
GenericDialog gd = new GenericDialog("Add Image...");
gd.addChoice("Image to add:", titles, titles[index]);
gd.addNumericField("X location:", x, 0);
gd.addNumericField("Y location:", y, 0);
gd.addNumericField("Opacity (0-100%):", 100, 0);
gd.addCheckbox("Create image selection", createImageRoi);
gd.showDialog();
if (gd.wasCanceled()) return;
index = gd.getNextChoiceIndex();
x = (int) gd.getNextNumber();
y = (int) gd.getNextNumber();
double opacity = gd.getNextNumber() / 100.0;
createImageRoi = gd.getNextBoolean();
ImagePlus overlay = WindowManager.getImage(wList[index]);
if (wList.length == 2) {
ImagePlus i1 = WindowManager.getImage(wList[0]);
ImagePlus i2 = WindowManager.getImage(wList[1]);
if (i2.getWidth() < i1.getWidth() && i2.getHeight() < i1.getHeight()) {
imp = i1;
overlay = i2;
}
}
if (overlay == imp) {
IJ.error(
"Add Image...", "Image to be added cannot be the same as\n\"" + imp.getTitle() + "\".");
return;
}
if (overlay.getWidth() > imp.getWidth() && overlay.getHeight() > imp.getHeight()) {
IJ.error(
"Add Image...", "Image to be added cannnot be larger than\n\"" + imp.getTitle() + "\".");
return;
}
if (createImageRoi && x == 0 && y == 0) {
x = imp.getWidth() / 2 - overlay.getWidth() / 2;
y = imp.getHeight() / 2 - overlay.getHeight() / 2;
}
roi = new ImageRoi(x, y, overlay.getProcessor());
roi.setName(overlay.getShortTitle());
if (opacity != 1.0) ((ImageRoi) roi).setOpacity(opacity);
if (createImageRoi) imp.setRoi(roi);
else {
Overlay overlayList = imp.getOverlay();
if (overlayList == null) overlayList = new Overlay();
overlayList.add(roi);
imp.setOverlay(overlayList);
overlay2 = overlayList;
Undo.setup(Undo.OVERLAY_ADDITION, imp);
}
}
public void run(String arg) {
imp = IJ.getImage();
showDialog();
}
public void run(String arg) {
imp = IJ.getImage();
int stackSize = imp.getStackSize();
if (imp == null) {
IJ.noImage();
return;
}
// Make sure input image is a stack.
if (stackSize == 1) {
IJ.error("Z Project", "Stack required");
return;
}
// Check for inverting LUT.
if (imp.getProcessor().isInvertedLut()) {
if (!IJ.showMessageWithCancel("ZProjection", lutMessage)) return;
}
// Set default bounds.
int channels = imp.getNChannels();
int frames = imp.getNFrames();
int slices = imp.getNSlices();
isHyperstack =
imp.isHyperStack()
|| (ij.macro.Interpreter.isBatchMode()
&& ((frames > 1 && frames < stackSize) || (slices > 1 && slices < stackSize)));
boolean simpleComposite = channels == stackSize;
if (simpleComposite) isHyperstack = false;
startSlice = 1;
if (isHyperstack) {
int nSlices = imp.getNSlices();
if (nSlices > 1) stopSlice = nSlices;
else stopSlice = imp.getNFrames();
} else stopSlice = stackSize;
// Build control dialog
GenericDialog gd = buildControlDialog(startSlice, stopSlice);
gd.showDialog();
if (gd.wasCanceled()) return;
if (!imp.lock()) return; // exit if in use
long tstart = System.currentTimeMillis();
setStartSlice((int) gd.getNextNumber());
setStopSlice((int) gd.getNextNumber());
method = gd.getNextChoiceIndex();
Prefs.set(METHOD_KEY, method);
if (isHyperstack) {
allTimeFrames = imp.getNFrames() > 1 && imp.getNSlices() > 1 ? gd.getNextBoolean() : false;
doHyperStackProjection(allTimeFrames);
} else if (imp.getType() == ImagePlus.COLOR_RGB) doRGBProjection(true);
else doProjection(true);
if (arg.equals("") && projImage != null) {
long tstop = System.currentTimeMillis();
projImage.setCalibration(imp.getCalibration());
if (simpleComposite) IJ.run(projImage, "Grays", "");
projImage.show("ZProjector: " + IJ.d2s((tstop - tstart) / 1000.0, 2) + " seconds");
}
imp.unlock();
IJ.register(ZProjector.class);
return;
}