public int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr) {
this.pfr = pfr;
String macroOptions = Macro.getOptions();
if (macroOptions != null) {
if (macroOptions.indexOf(" interpolate") != -1)
macroOptions.replaceAll(" interpolate", " interpolation=Bilinear");
else if (macroOptions.indexOf(" interpolation=") == -1)
macroOptions = macroOptions + " interpolation=None";
Macro.setOptions(macroOptions);
}
gd = new GenericDialog("Rotate", IJ.getInstance());
gd.addNumericField("Angle (degrees):", angle, (int) angle == angle ? 1 : 2);
gd.addNumericField("Grid Lines:", gridLines, 0);
gd.addChoice("Interpolation:", methods, methods[interpolationMethod]);
if (bitDepth == 8 || bitDepth == 24)
gd.addCheckbox("Fill with Background Color", fillWithBackground);
if (canEnlarge) gd.addCheckbox("Enlarge Image to Fit Result", enlarge);
else enlarge = false;
gd.addPreviewCheckbox(pfr);
gd.addDialogListener(this);
gd.showDialog();
drawGridLines(0);
if (gd.wasCanceled()) {
return DONE;
}
if (!enlarge) flags |= KEEP_PREVIEW; // standard filter without enlarge
else if (imp.getStackSize() == 1) flags |= NO_CHANGES; // undoable as a "compound filter"
return IJ.setupDialog(imp, flags);
}
public int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr) {
if (doOptions) {
this.imp = imp;
this.pfr = pfr;
GenericDialog gd = new GenericDialog("Binary Options");
gd.addNumericField("Iterations (1-" + MAX_ITERATIONS + "):", iterations, 0, 3, "");
gd.addNumericField("Count (1-8):", count, 0, 3, "");
gd.addCheckbox("Black background", Prefs.blackBackground);
gd.addCheckbox("Pad edges when eroding", Prefs.padEdges);
gd.addChoice("EDM output:", outputTypes, outputTypes[EDM.getOutputType()]);
if (imp != null) {
gd.addChoice("Do:", operations, operation);
gd.addPreviewCheckbox(pfr);
gd.addDialogListener(this);
previewing = true;
}
gd.addHelp(IJ.URL + "/docs/menus/process.html#options");
gd.showDialog();
previewing = false;
if (gd.wasCanceled()) return DONE;
if (imp == null) { // options dialog only, no do/preview
dialogItemChanged(gd, null); // read dialog result
return DONE;
}
return operation.equals(NO_OPERATION) ? DONE : IJ.setupDialog(imp, flags);
} else { // no dialog, 'arg' is operation type
if (!((ByteProcessor) imp.getProcessor()).isBinary()) {
IJ.error("8-bit binary (black and white only) image required.");
return DONE;
}
return IJ.setupDialog(imp, flags);
}
}
/**
* 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);
}
}
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;
}
// DICOM options
void dicom() {
GenericDialog gd = new GenericDialog("DICOM Options");
gd.addCheckbox("Open as 32-bit float", Prefs.openDicomsAsFloat);
// gd.addCheckbox("Calculate voxel depth", Prefs.calculateDicomVoxelDepth);
gd.addMessage("Orthogonal Views");
gd.setInsets(5, 40, 0);
gd.addCheckbox("Rotate YZ", Prefs.rotateYZ);
gd.setInsets(0, 40, 0);
gd.addCheckbox("Flip XZ", Prefs.flipXZ);
gd.showDialog();
if (gd.wasCanceled()) return;
Prefs.openDicomsAsFloat = gd.getNextBoolean();
// Prefs.calculateDicomVoxelDepth = gd.getNextBoolean();
Prefs.rotateYZ = gd.getNextBoolean();
Prefs.flipXZ = gd.getNextBoolean();
}
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);
}
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);
}
/**
* 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;
}
void checkForCalibrationConflict(ImagePlus imp, Calibration cal) {
Calibration gcal = imp.getGlobalCalibration();
if (gcal == null || !showConflictMessage || IJ.isMacro()) return;
if (cal.pixelWidth == gcal.pixelWidth && cal.getUnit().equals(gcal.getUnit())) return;
GenericDialog gd = new GenericDialog(imp.getTitle());
gd.addMessage("The calibration of this image conflicts\nwith the current global calibration.");
gd.addCheckbox("Disable_Global Calibration", true);
gd.addCheckbox("Disable_these Messages", false);
gd.showDialog();
if (gd.wasCanceled()) return;
boolean disable = gd.getNextBoolean();
if (disable) {
imp.setGlobalCalibration(null);
imp.setCalibration(cal);
WindowManager.repaintImageWindows();
}
boolean dontShow = gd.getNextBoolean();
if (dontShow) showConflictMessage = false;
}
boolean showoptions(double[] params, int[] fixes) {
// GenericDialog gd=new NonBlockingGenericDialog("Options");
GenericDialog gd = new GenericDialog("Options");
gd.addCheckbox("Check Chi Squared", checkc2);
for (int i = 0; i < 10; i++) {
gd.addNumericField("P" + (i + 1), params[i], 5, 10, null);
gd.addCheckbox("Fix?", (fixes[i] == 1));
}
gd.addCheckbox("Get_Errors", false);
gd.addCheckbox("Set_Constraints", false);
gd.addNumericField("Iterations", iterations, 0, 10, null);
gd.addNumericField("chi squared", c2, 5, 10, null);
gd.addDialogListener(this);
gd.showDialog();
if (gd.wasCanceled()) {
return false;
}
checkc2 = gd.getNextBoolean();
for (int i = 0; i < 10; i++) {
params[i] = gd.getNextNumber();
if (gd.getNextBoolean()) {
fixes[i] = 1;
} else {
fixes[i] = 0;
}
}
boolean geterrors = gd.getNextBoolean();
boolean setconstraints = gd.getNextBoolean();
for (int i = 0; i < 10; i++) {
if (function.indexOf("P" + (i + 1)) < 0) {
fixes[i] = 1;
}
}
if (geterrors) {
if (!get_errors(params, fixes)) {
return false;
}
}
if (setconstraints) constraints = get_constraints(params);
return true;
}
// Conversion Options
void conversions() {
double[] weights = ColorProcessor.getWeightingFactors();
boolean weighted = !(weights[0] == 1d / 3d && weights[1] == 1d / 3d && weights[2] == 1d / 3d);
// boolean weighted = !(Math.abs(weights[0]-1d/3d)<0.0001 && Math.abs(weights[1]-1d/3d)<0.0001
// && Math.abs(weights[2]-1d/3d)<0.0001);
GenericDialog gd = new GenericDialog("Conversion Options");
gd.addCheckbox("Scale when converting", ImageConverter.getDoScaling());
String prompt = "Weighted RGB conversions";
if (weighted)
prompt +=
" (" + IJ.d2s(weights[0]) + "," + IJ.d2s(weights[1]) + "," + IJ.d2s(weights[2]) + ")";
gd.addCheckbox(prompt, weighted);
gd.showDialog();
if (gd.wasCanceled()) return;
ImageConverter.setDoScaling(gd.getNextBoolean());
Prefs.weightedColor = gd.getNextBoolean();
if (!Prefs.weightedColor) ColorProcessor.setWeightingFactors(1d / 3d, 1d / 3d, 1d / 3d);
else if (Prefs.weightedColor && !weighted)
ColorProcessor.setWeightingFactors(0.299, 0.587, 0.114);
return;
}
boolean init_functions() {
GenericDialog gd = new GenericDialog("Fitting Options");
gd.addStringField("Extra Definitions", exdef, 50);
gd.addCheckbox("Weight Using Plot Errors", false);
gd.addStringField("Weighting Equation (y is for data)", weightfunction, 50);
gd.addStringField("Fit_Equation", function, 50);
gd.showDialog();
if (gd.wasCanceled()) {
return false;
}
exdef = gd.getNextString();
boolean errweights = gd.getNextBoolean();
weightfunction = gd.getNextString();
function = gd.getNextString();
// first initialize the weights
weights = new float[tempdata.length];
if (errweights
|| weightfunction.equals("")
|| weightfunction == null
|| weightfunction == "1.0") {
if (errweights) {
for (int i = 0; i < tempdata.length; i++) weights[i] = 1.0f / (errs[i] * errs[i]);
} else {
for (int i = 0; i < tempdata.length; i++) weights[i] = 1.0f;
}
} else {
for (int i = 0; i < tempdata.length; i++) {
String script =
"y =" + tempdata[i] + "; " + "x =" + tempx[i] + "; " + "retval=" + weightfunction + ";";
Double temp = new Double(0.0);
try {
temp = (Double) engine.eval(script);
} catch (Exception e) {
IJ.log(e.getMessage());
}
if (!(temp.isInfinite() || temp.isNaN())) {
weights[i] = temp.floatValue();
}
}
}
// now compile the function script
try {
String script1 = exdef + "; retval=" + function + ";";
cs = ce.compile(script1);
} catch (Exception e) {
IJ.log(e.toString());
return false;
}
return true;
}
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 boolean showDialog(ImageStack stack) {
hyperstack = imp.isHyperStack();
boolean showCheckbox = false;
if (hyperstack && imp.getNSlices() > 1 && imp.getNFrames() > 1) showCheckbox = true;
else if (hyperstack && imp.getNSlices() > 1) reduceSlices = true;
int n = stack.getSize();
GenericDialog gd = new GenericDialog("Reduce Size");
gd.addNumericField("Reduction Factor:", factor, 0);
if (showCheckbox) gd.addCheckbox("Reduce in Z-Dimension", false);
gd.showDialog();
if (gd.wasCanceled()) return false;
factor = (int) gd.getNextNumber();
if (showCheckbox) reduceSlices = gd.getNextBoolean();
return true;
}
// Input/Output options
void io() {
GenericDialog gd = new GenericDialog("I/O Options");
gd.addNumericField("JPEG quality (0-100):", FileSaver.getJpegQuality(), 0, 3, "");
gd.addNumericField("GIF and PNG transparent index:", Prefs.getTransparentIndex(), 0, 3, "");
gd.addStringField(
"File extension for tables (.txt, .xls or .csv):", Prefs.get("options.ext", ".csv"), 4);
gd.addCheckbox("Use JFileChooser to open/save", Prefs.useJFileChooser);
if (!IJ.isMacOSX())
gd.addCheckbox("Use_file chooser to import sequences", Prefs.useFileChooser);
gd.addCheckbox("Save TIFF and raw in Intel byte order", Prefs.intelByteOrder);
gd.addCheckbox("Skip dialog when opening .raw files", Prefs.skipRawDialog);
gd.setInsets(15, 20, 0);
gd.addMessage("Results Table Options");
gd.setInsets(3, 40, 0);
gd.addCheckbox("Copy_column headers", Prefs.copyColumnHeaders);
gd.setInsets(0, 40, 0);
gd.addCheckbox("Copy_row numbers", !Prefs.noRowNumbers);
gd.setInsets(0, 40, 0);
gd.addCheckbox("Save_column headers", !Prefs.dontSaveHeaders);
gd.setInsets(0, 40, 0);
gd.addCheckbox("Save_row numbers", !Prefs.dontSaveRowNumbers);
gd.showDialog();
if (gd.wasCanceled()) return;
int quality = (int) gd.getNextNumber();
if (quality < 0) quality = 0;
if (quality > 100) quality = 100;
FileSaver.setJpegQuality(quality);
int transparentIndex = (int) gd.getNextNumber();
Prefs.setTransparentIndex(transparentIndex);
String extension = gd.getNextString();
if (!extension.startsWith(".")) extension = "." + extension;
Prefs.set("options.ext", extension);
Prefs.useJFileChooser = gd.getNextBoolean();
if (!IJ.isMacOSX()) Prefs.useFileChooser = gd.getNextBoolean();
Prefs.intelByteOrder = gd.getNextBoolean();
Prefs.skipRawDialog = gd.getNextBoolean();
Prefs.copyColumnHeaders = gd.getNextBoolean();
Prefs.noRowNumbers = !gd.getNextBoolean();
Prefs.dontSaveHeaders = !gd.getNextBoolean();
Prefs.dontSaveRowNumbers = !gd.getNextBoolean();
return;
}
// Miscellaneous Options
void miscOptions() {
String key = IJ.isMacintosh() ? "command" : "control";
GenericDialog gd = new GenericDialog("Miscellaneous Options", IJ.getInstance());
gd.addStringField("Divide by zero value:", "" + FloatBlitter.divideByZeroValue, 10);
gd.addCheckbox("Use pointer cursor", Prefs.usePointerCursor);
gd.addCheckbox("Hide \"Process Stack?\" dialog", IJ.hideProcessStackDialog);
gd.addCheckbox("Require " + key + " key for shortcuts", Prefs.requireControlKey);
gd.addCheckbox("Move isolated plugins to Misc. menu", Prefs.moveToMisc);
if (!IJ.isMacOSX()) gd.addCheckbox("Run single instance listener", Prefs.runSocketListener);
gd.addCheckbox("Enhanced line tool", Prefs.enhancedLineTool);
gd.addCheckbox("Reverse CZT order of \">\" and \"<\"", Prefs.reverseNextPreviousOrder);
gd.addCheckbox("Debug mode", IJ.debugMode);
gd.addHelp(IJ.URL + "/docs/menus/edit.html#misc");
gd.showDialog();
if (gd.wasCanceled()) return;
String divValue = gd.getNextString();
if (divValue.equalsIgnoreCase("infinity") || divValue.equalsIgnoreCase("infinite"))
FloatBlitter.divideByZeroValue = Float.POSITIVE_INFINITY;
else if (divValue.equalsIgnoreCase("NaN")) FloatBlitter.divideByZeroValue = Float.NaN;
else if (divValue.equalsIgnoreCase("max")) FloatBlitter.divideByZeroValue = Float.MAX_VALUE;
else {
Float f;
try {
f = new Float(divValue);
} catch (NumberFormatException e) {
f = null;
}
if (f != null) FloatBlitter.divideByZeroValue = f.floatValue();
}
IJ.register(FloatBlitter.class);
Prefs.usePointerCursor = gd.getNextBoolean();
IJ.hideProcessStackDialog = gd.getNextBoolean();
Prefs.requireControlKey = gd.getNextBoolean();
Prefs.moveToMisc = gd.getNextBoolean();
if (!IJ.isMacOSX()) Prefs.runSocketListener = gd.getNextBoolean();
Prefs.enhancedLineTool = gd.getNextBoolean();
Prefs.reverseNextPreviousOrder = gd.getNextBoolean();
IJ.setDebugMode(gd.getNextBoolean());
}
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) {
GenericDialog gd = new GenericDialog("Options");
double sfreq = 20000.0;
gd.addNumericField("Sampling Frequency?", sfreq, 1, 10, null);
String[] psfchoice = {"3D Gaussian", "Gaus-Lorentz^2", "2D Gaussian"};
gd.addChoice("PSF Type?", psfchoice, psfchoice[0]);
String[] filetypechoice = {
"Confocor 3 raw", "Short binary trajectory", "PlotWindow trajectory", "Ascii Text File"
};
gd.addChoice("File Type?", filetypechoice, filetypechoice[0]);
boolean ch2green = true;
gd.addCheckbox("Ch2 is green?", ch2green);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
sfreq = gd.getNextNumber();
int psfflag = gd.getNextChoiceIndex();
int fileflag = gd.getNextChoiceIndex();
ch2green = gd.getNextBoolean();
int nfiles = 0;
Object[] histograms = null;
int xmax = 0;
int ymax = 0;
String[] names = null;
if (fileflag < 2) {
jdataio ioclass = new jdataio();
File[] filearray = ioclass.openfiles(OpenDialog.getDefaultDirectory(), IJ.getInstance());
if (filearray.length == 0) {
return;
}
String dir = filearray[0].getAbsolutePath();
int sepindex = dir.lastIndexOf(File.separator);
String newdir = dir.substring(0, sepindex + 1);
OpenDialog.setDefaultDirectory(newdir);
nfiles = filearray.length / 2;
if (nfiles > 25) {
nfiles = 25;
}
histograms = new Object[nfiles];
names = organize_c3_files(filearray);
for (int i = 0; i < nfiles; i++) {
try {
int length1 = (int) (((double) filearray[2 * i].length() - 128.0) / 4.0);
int length2 = (int) (((double) filearray[2 * i + 1].length() - 128.0) / 4.0);
int length3 = (int) (((double) filearray[2 * i].length()) / 2.0);
int length4 = (int) (((double) filearray[2 * i + 1].length()) / 2.0);
InputStream instream = new BufferedInputStream(new FileInputStream(filearray[2 * i]));
InputStream instream2 =
new BufferedInputStream(new FileInputStream(filearray[2 * i + 1]));
if (fileflag == 0) {
int[] pmdata = new int[length1];
int[] pmdata2 = new int[length2];
if (!ioclass.skipstreambytes(instream, 128)) {
showioerror();
instream.close();
return;
}
if (!ioclass.skipstreambytes(instream2, 128)) {
showioerror();
instream2.close();
return;
}
if (!ioclass.readintelintfile(instream, length1, pmdata)) {
showioerror();
instream.close();
return;
}
if (!ioclass.readintelintfile(instream2, length2, pmdata2)) {
showioerror();
instream2.close();
return;
}
if (ch2green) {
histograms[i] = (new pmodeconvert()).pm2pch(pmdata2, pmdata, sfreq, 20000000);
} else {
histograms[i] = (new pmodeconvert()).pm2pch(pmdata, pmdata2, sfreq, 20000000);
}
} else {
float[] tmdata = new float[length3];
float[] tmdata2 = new float[length4];
if (!ioclass.readintelshortfile(instream, length3, tmdata)) {
showioerror();
instream.close();
return;
}
if (!ioclass.readintelshortfile(instream2, length4, tmdata2)) {
showioerror();
instream2.close();
return;
}
if (ch2green) {
histograms[i] = (new pmodeconvert()).create_2Dhistogram(tmdata2, tmdata);
} else {
histograms[i] = (new pmodeconvert()).create_2Dhistogram(tmdata, tmdata2);
}
}
if (((float[][]) histograms[i]).length > xmax) {
xmax = ((float[][]) histograms[i]).length;
}
if (((float[][]) histograms[i])[0].length > ymax) {
ymax = ((float[][]) histograms[i])[0].length;
}
instream.close();
instream2.close();
} catch (IOException e) {
showioerror();
return;
}
}
} else {
if (fileflag == 2) {
ImageWindow iw = WindowManager.getCurrentWindow();
float[][] trajectories = (float[][]) jutils.runPW4VoidMethod(iw, "getYValues");
float[][] tempxvals = (float[][]) jutils.runPW4VoidMethod(iw, "getXValues");
sfreq = 1.0 / ((double) tempxvals[0][1]);
nfiles = trajectories.length / 2;
if (nfiles > 25) {
nfiles = 25;
}
names = new String[nfiles + 1];
names[nfiles] = "avg";
histograms = new Object[nfiles];
for (int i = 0; i < nfiles; i++) {
names[i] = "trajectory " + (i + 1);
if (ch2green) {
histograms[i] =
(new pmodeconvert())
.create_2Dhistogram(trajectories[2 * i + 1], trajectories[2 * i]);
} else {
histograms[i] =
(new pmodeconvert())
.create_2Dhistogram(trajectories[2 * i], trajectories[2 * i + 1]);
}
if (((float[][]) histograms[i]).length > xmax) {
xmax = ((float[][]) histograms[i]).length;
}
if (((float[][]) histograms[i])[0].length > ymax) {
ymax = ((float[][]) histograms[i])[0].length;
}
}
} else {
// here we read tab delimited lines from files
jdataio ioclass = new jdataio();
File[] filearray = ioclass.openfiles(OpenDialog.getDefaultDirectory(), IJ.getInstance());
if (filearray.length == 0) {
return;
}
String dir = filearray[0].getAbsolutePath();
int sepindex = dir.lastIndexOf(File.separator);
String newdir = dir.substring(0, sepindex + 1);
OpenDialog.setDefaultDirectory(newdir);
nfiles = filearray.length;
if (nfiles > 25) {
nfiles = 25;
}
histograms = new Object[nfiles];
names = new String[nfiles + 1];
names[nfiles] = "avg";
for (int i = 0; i < nfiles; i++) {
try {
names[i] = filearray[i].getName();
BufferedReader d = new BufferedReader(new FileReader(filearray[i]));
String[] lines = new String[256];
int counter = 0;
do {
lines[counter] = d.readLine();
counter++;
} while ((lines[counter - 1] != null && lines[counter - 1] != "") && counter < 256);
int numcolumns = 0;
for (int j = 0; j < counter - 1; j++) {
int temp = getncolumns(lines[j]);
if (temp > numcolumns) {
numcolumns = temp;
}
}
float[][] temphist2 = null;
if (ch2green) {
temphist2 = new float[numcolumns][counter - 1];
} else {
temphist2 = new float[counter - 1][numcolumns];
}
for (int k = 0; k < counter - 1; k++) {
float[] temp = tab_delim2float(lines[k]);
for (int j = 0; j < numcolumns; j++) {
if (ch2green) {
temphist2[j][k] = temp[j];
} else {
temphist2[k][j] = temp[j];
}
}
}
histograms[i] = temphist2;
d.close();
} catch (IOException e) {
showioerror();
return;
}
}
for (int i = 0; i < nfiles; i++) {
if (((float[][]) histograms[i]).length > xmax) {
xmax = ((float[][]) histograms[i]).length;
}
if (((float[][]) histograms[i])[0].length > ymax) {
ymax = ((float[][]) histograms[i])[0].length;
}
}
}
}
// note that here x is green and y is red
float[][][] pch = new float[nfiles][xmax][ymax];
for (int i = 0; i < nfiles; i++) {
for (int j = 0; j < ((float[][]) histograms[i]).length; j++) {
for (int k = 0; k < ((float[][]) histograms[i])[j].length; k++) {
pch[i][j][k] = ((float[][]) histograms[i])[j][k];
}
}
}
final PCH2DFitWindow cw = new PCH2DFitWindow();
cw.init(names, pch, psfflag);
final Frame f = new Frame("PCH 2D Analysis");
f.setLocation(10, 10);
f.addWindowListener(
new WindowAdapter() {
public void windowClosing(WindowEvent e) {
f.dispose();
}
});
f.add(cw);
f.pack();
f.setResizable(false);
Insets ins = f.getInsets();
cw.totalSize.height = PCH2DFitWindow.H + ins.bottom + ins.top + 65;
cw.totalSize.width = PCH2DFitWindow.WR + ins.left + ins.right;
f.setSize(cw.totalSize);
f.setVisible(true);
cw.requestFocus();
}
private void geterrors() {
GenericDialog gd = new GenericDialog("Options");
float conf = 0.67f;
gd.addNumericField("Confidence Limit", (int) (conf * 100.0f), 5, 10, null);
gd.addChoice("Error Parameter", paramsnames, paramsnames[0]);
double spacing = 0.01;
gd.addNumericField("Chi^2 plot spacing (% of value)?", spacing * 100.0, 2, 10, null);
boolean globalerror = false;
gd.addCheckbox("Global Fit Error?", globalerror);
int dataset = 0;
gd.addNumericField("Data Set (for Global Error)", dataset, 0);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
conf = 0.01f * (float) gd.getNextNumber();
int paramindex = (int) gd.getNextChoiceIndex();
spacing = 0.01 * gd.getNextNumber();
globalerror = gd.getNextBoolean();
dataset = (int) gd.getNextNumber();
if (globalerror) {
support_plane_errors erclass = new support_plane_errors(this, 0.0001, 50, true, 0.1);
int[] erindeces = {paramindex, dataset};
// need to set up all the matrices
int nsel = 0;
int nparams = 11;
for (int i = 0; i < ncurves; i++) {
if (include[i]) {
nsel++;
}
}
double[][] params = new double[nsel][nparams];
String[][] tempformulas = new String[nsel][nparams];
double[][][] constraints = new double[2][nsel][nparams];
int[][] vflmatrix = new int[nsel][nparams];
float[][] tempdata = new float[nsel][xpts * ypts];
float[][] tempweights = new float[nsel][xpts * ypts];
int nfit = 0;
int counter = 0;
for (int i = 0; i < ncurves; i++) {
if (include[i]) {
for (int j = 0; j < nparams; j++) {
params[counter][j] = globalparams[i][j];
tempformulas[counter][j] = globalformulas[i][j];
constraints[0][counter][j] = globalconstraints[0][i][j];
constraints[1][counter][j] = globalconstraints[1][i][j];
vflmatrix[counter][j] = globalvflmatrix[i][j];
if (vflmatrix[counter][j] == 0 || (j == 0 && vflmatrix[counter][j] == 2)) {
nfit++;
}
}
for (int j = 0; j < xpts; j++) {
for (int k = 0; k < ypts; k++) {
tempdata[counter][j + k * xpts] = (float) ((double) pch[i][j][k] / (double) nmeas[i]);
tempweights[counter][j + k * xpts] = weights[i][j][k];
}
}
counter++;
}
}
int dofnum = xpts * ypts * nsel - (nfit - 1) - 1;
int dofden = xpts * ypts * nsel - nfit - 1;
// double flim=FLimit(dofnum,dofden,(double)conf);
double flim = (new jdist()).FLimit(dofnum, dofden, (double) conf);
IJ.log("FLimit = " + (float) flim);
if (flim == Double.NaN && flim < 1.0) {
IJ.showMessage("Invalid Limiting F Value");
return;
}
double truespacing = Math.abs(params[erindeces[1]][erindeces[0]] * spacing);
double[][] c2plot =
erclass.geterrorsglobal(
params,
vflmatrix,
tempformulas,
paramsnames,
constraints,
tempdata,
tempweights,
flim,
truespacing,
erindeces);
IJ.log("upper limit = " + c2plot[1][0] + " lower limit = " + c2plot[0][0]);
int templength = c2plot[0].length;
float[][] c2plotf = new float[2][templength - 1];
for (int i = 0; i < (templength - 1); i++) {
c2plotf[0][i] = (float) c2plot[0][i + 1];
c2plotf[1][i] = (float) c2plot[1][i + 1];
}
new PlotWindow4(
"c2 plot",
paramsnames[paramindex] + "[" + dataset + "]",
"Chi^2",
c2plotf[0],
c2plotf[1])
.draw();
} else {
support_plane_errors erclass = new support_plane_errors(this, 0.0001, 50, false, 0.1);
int errindex = paramindex;
float[] tempdata = new float[xpts * ypts];
float[] tempweights = new float[xpts * ypts];
for (int i = 0; i < xpts; i++) {
for (int j = 0; j < ypts; j++) {
tempdata[i + j * xpts] = (float) ((double) avg[i][j] / (double) nmeas[ncurves]);
tempweights[i + j * xpts] = avgweights[i][j];
}
}
int nfit = 0;
for (int i = 0; i < 7; i++) {
if (avgfixes[i] == 0) {
nfit++;
}
}
int dofnum = xpts * ypts - (nfit - 1) - 1;
int dofden = xpts * ypts - nfit - 1;
double flim = (new jdist()).FLimit(dofnum, dofden, (double) conf);
IJ.log("FLimit = " + (float) flim);
if (flim == Double.NaN && flim < 1.0) {
IJ.showMessage("Invalid Limiting F Value");
return;
}
double truespacing = Math.abs(avgparams[errindex] * spacing);
double[][] c2plot =
erclass.geterrors(
avgparams,
avgfixes,
avgconstraints,
tempdata,
tempweights,
flim,
truespacing,
errindex);
IJ.log("upper limit = " + c2plot[1][0] + " lower limit = " + c2plot[0][0]);
int templength = c2plot[0].length;
float[][] c2plotf = new float[2][templength - 1];
for (int i = 0; i < (templength - 1); i++) {
c2plotf[0][i] = (float) c2plot[0][i + 1];
c2plotf[1][i] = (float) c2plot[1][i + 1];
}
new PlotWindow4("c2 plot", paramsnames[errindex], "Chi^2", c2plotf[0], c2plotf[1]).draw();
}
}
public void run(String arg) {
String[] labels = {
"Masked_Chromosomes", "Unmixed_Image", "Spectral_Image(optional)", "Spectra(optional)"
};
ImagePlus[] imps = jutils.selectImages(true, 4, labels);
if (imps == null) {
return;
}
if (imps[0] == null) {
return;
}
float[] mask = (float[]) imps[0].getStack().getPixels(2);
findblobs3 fb = new findblobs3(imps[0].getWidth(), imps[0].getHeight());
float[] objects = fb.dofindblobs(mask, 0.5f);
WaitForUserDialog dg =
new WaitForUserDialog(
"Optional Input", "Place RoiManager Points on Chromosome Segments (if desired)");
dg.show();
if (!dg.escPressed()) {
RoiManager rman = RoiManager.getInstance();
while (rman != null && rman.getCount() > 1) {
Roi[] rois = rman.getRoisAsArray();
int[] ids = new int[rois.length];
for (int i = 0; i < rois.length; i++) {
Rectangle r = rois[i].getBounds();
ids[i] = (int) objects[r.x + fb.width * r.y];
}
objects = fb.link_objects(objects, ids);
rman.reset();
dg =
new WaitForUserDialog(
"Optional Input",
"Place More RoiManager Points on Chromosome Segments (if desired)");
dg.show();
if (dg.escPressed()) break;
}
}
int[] areas = fb.get_areas(objects);
int[] temprank = jsort.get_javasort_order(areas);
int[] arearank = jsort.get_javasort_order(temprank);
for (int i = 0; i < fb.nobjects; i++) {
arearank[i] = fb.nobjects - arearank[i] - 1;
}
// if the spectra are available, get them
float[][][] spectra = null;
Object[] data = null;
if (imps[1] != null && imps[2] != null && imps[3] != null) {
ImageWindow iw = imps[3].getWindow();
if (iw.getClass().getName().equals("jguis.PlotWindow4")) {
float[][] yvals = (float[][]) jutils.runPW4VoidMethod(iw, "getYValues");
data = jutils.stack2array(imps[2].getStack());
Object[] coef = jutils.stack2array(imps[1].getStack());
spectra = new float[fb.nobjects][2][];
for (int i = 0; i < fb.nobjects; i++) {
spectra[i][0] = fb.get_object_spectrum(objects, (i + 1), data, "Sum");
spectra[i][1] = new float[yvals[0].length];
float[] tempcoef = fb.get_object_spectrum(objects, (i + 1), coef, "Sum");
for (int j = 0; j < yvals[0].length; j++) {
for (int k = 0; k < 5; k++) {
spectra[i][1][j] += tempcoef[k] * yvals[k][j];
}
}
}
}
}
CompositeImage imp = (CompositeImage) imps[0];
imp.setPosition(1, 1, 1);
LUT graylut = jutils.get_lut_for_color(Color.white);
imp.setChannelColorModel(graylut);
imp.setPosition(2, 1, 1);
LUT redlut = jutils.get_lut_for_color(Color.red);
imp.setChannelColorModel(redlut);
imp.setPosition(1, 1, 1);
imp.updateAndRepaintWindow();
SkyPanel_v3 sp = new SkyPanel_v3();
int skychan = 6;
if (imps[1] != null) skychan = imps[1].getNChannels();
// assume that the sky image has 6 channels and that the second is the unknown green
// shift the unknown green to the end
ImagePlus skyimp = null;
if (imps[1] != null) {
Object[] skystack = jutils.stack2array(imps[1].getStack());
// Object[]
// skystack2={skystack[0],skystack[2],skystack[3],skystack[4],skystack[5],skystack[1]};
Object[] skystack2 = null;
if (skychan == 6)
skystack2 = new Object[] {skystack[0], skystack[2], skystack[3], skystack[4], skystack[5]};
else
skystack2 = new Object[] {skystack[0], skystack[1], skystack[2], skystack[3], skystack[4]};
skyimp =
new ImagePlus(
"rearranged", jutils.array2stack(skystack2, imps[1].getWidth(), imps[1].getHeight()));
}
int nch = 5;
if (skyimp != null) nch = skyimp.getStack().getSize();
GenericDialog gd2 = new GenericDialog("Options");
gd2.addNumericField("Area Accuracy (percent)", 30, 0);
for (int i = 0; i < nch; i++) {
gd2.addNumericField("Ch_" + (i + 1) + "_Contr_Thresh", 0.35, 5, 15, null);
}
// gd2.addNumericField("Contribution Threshold",0.35,5,15,null);
gd2.addCheckbox("Mouse?", false);
gd2.addNumericField("Box_Width", 150, 0);
gd2.addNumericField("Box_Height", 100, 0);
gd2.showDialog();
if (gd2.wasCanceled()) {
return;
}
sp.areathresh = (float) gd2.getNextNumber();
sp.objthresh2 = new float[nch];
for (int i = 0; i < nch; i++) sp.objthresh2[i] = (float) gd2.getNextNumber();
// sp.objthresh=(float)gd2.getNextNumber();
boolean mouse = gd2.getNextBoolean();
int bwidth = (int) gd2.getNextNumber();
int bheight = (int) gd2.getNextNumber();
int[] colorindices = {4, 1, 2, 6, 3};
GenericDialog gd3 = new GenericDialog("Color Options");
for (int i = 0; i < 5; i++)
gd3.addChoice(
"Ch" + (i + 1) + " Color",
SkyPanel_v3.colornames,
SkyPanel_v3.colornames[colorindices[i]]);
gd3.showDialog();
if (gd3.wasCanceled()) return;
for (int i = 0; i < 5; i++) colorindices[i] = gd3.getNextChoiceIndex();
sp.colorindices = colorindices;
sp.nch = 5;
sp.dapilast = false;
sp.cellwidth = bwidth;
sp.cellheight = bheight;
sp.init(imps[0], skyimp, objects, areas, arearank, fb, true, spectra, data, mouse);
SkyPanel_v3.launch_frame(sp);
}
public boolean reconstructDataset() {
view_modes[0] = "3D color";
view_modes[1] = "2D histogram";
view_modes[2] = "2D particle intensity (16-bit)";
view_modes[3] = "2D particle intensity (8-bit)";
GenericDialog gd = new GenericDialog("Reconstruct PALM/STORM Dataset");
gd.addNumericField(
"Target pixel size for the rendered image (nm)",
prefs.get("QuickPALM.viewer_tpixelsize", 30),
2);
gd.addNumericField("Original image width (px)", prefs.get("QuickPALM.viewer_owidth", 512), 2);
gd.addNumericField("Original image height (px)", prefs.get("QuickPALM.viewer_oheight", 512), 2);
gd.addChoice("View mode", view_modes, prefs.get("QuickPALM.view_mode", view_modes[1]));
// gd.addNumericField("Allow image saturation (%)", prefs.get("QuickPALM.saturation", 50), 0);
gd.addCheckbox(
"Simulate sub-difraction spot (gaussian convolution - only 2D)",
prefs.get("QuickPALM.viewer_doConvolve", true));
// gd.addCheckbox("Make 3D stack", prefs.get("QuickPALM.viewer_do3d", false));
// gd.addCheckbox("Make movie", prefs.get("QuickPALM.viewer_doMovie", false));
gd.addCheckbox("Make 3D stack", false);
gd.addCheckbox("Make movie", false);
// gd.addCheckbox("Save only and don't show", prefs.get("QuickPALM.viewer_doSave", false));
gd.addMessage("\n");
// -----------------------------------------
gd.addMessage("-- Simulate sub-difraction spot settings (used only if selected) --");
gd.addNumericField("FWHM of the spot", prefs.get("QuickPALM.viewer_fwhm", 30), 2);
gd.addMessage("\n");
// -----------------------------------------
gd.addMessage("-- Make 3D stack settings (used only if selected) --");
gd.addNumericField("Z-spacing between slices (nm)", prefs.get("QuickPALM.viewer_zstep", 50), 2);
gd.addNumericField(
"Merge particle Z-position above (nm - 0 for full Z range)",
prefs.get("QuickPALM.viewer_mergeabove", 0),
2);
gd.addNumericField(
"Merge particle Z-position bellow (nm - 0 for full Z range)",
prefs.get("QuickPALM.viewer_mergebellow", 0),
2);
gd.addMessage("\n");
// -----------------------------------------
gd.addMessage("-- Make movie settings (used only if selected) --");
gd.addNumericField(
"Make a reconstruction in every N frames", prefs.get("QuickPALM.viewer_update", 10), 0);
gd.addNumericField(
"Accumulate N neighboring frames for each reconstruction\n(set to 0 to accumulate all the preceding frames)",
prefs.get("QuickPALM.viewer_accumulate", 100),
0);
gd.showDialog();
if (gd.wasCanceled()) return false;
viewer_tpixelsize = gd.getNextNumber();
prefs.set("QuickPALM.viewer_tpixelsize", viewer_tpixelsize);
viewer_owidth = (int) gd.getNextNumber();
prefs.set("QuickPALM.viewer_owidth", viewer_owidth);
viewer_oheight = (int) gd.getNextNumber();
prefs.set("QuickPALM.viewer_oheight", viewer_oheight);
view_mode = gd.getNextChoice();
prefs.set("QuickPALM.view_mode", view_mode);
viewer_doConvolve = gd.getNextBoolean();
prefs.set("QuickPALM.viewer_doConvolve", viewer_doConvolve);
viewer_do3d = gd.getNextBoolean();
prefs.set("QuickPALM.viewer_do3d", viewer_do3d);
viewer_doMovie = gd.getNextBoolean();
prefs.set("QuickPALM.viewer_doMovie", viewer_doMovie);
// viewer_doSave = gd.getNextBoolean();
// prefs.set("QuickPALM.viewer_doSave", viewer_doSave);
// -- Simulate sub-difraction spot
viewer_fwhm = gd.getNextNumber();
prefs.set("QuickPALM.viewer_fwhm", viewer_fwhm);
// -- Show B&W
// viewer_is8bit = gd.getNextBoolean();
// prefs.set("QuickPALM.viewer_is8bit", viewer_is8bit);
// -- Make 3D stack
viewer_zstep = gd.getNextNumber();
prefs.set("QuickPALM.viewer_zstep", viewer_zstep);
viewer_mergeabove = gd.getNextNumber();
prefs.set("QuickPALM.viewer_mergeabove", viewer_mergeabove);
viewer_mergebellow = gd.getNextNumber();
prefs.set("QuickPALM.viewer_mergebellow", viewer_mergebellow);
// -- Make Movie
viewer_update = (int) gd.getNextNumber();
prefs.set("QuickPALM.viewer_update", viewer_update);
viewer_accumulate = (int) gd.getNextNumber();
prefs.set("QuickPALM.viewer_accumulate", viewer_accumulate);
return true;
}
boolean showDialog(ImageProcessor ip) {
String macroOptions = Macro.getOptions();
if (macroOptions != null) {
if (macroOptions.indexOf(" interpolate") != -1)
macroOptions.replaceAll(" interpolate", " interpolation=Bilinear");
else if (macroOptions.indexOf(" interpolation=") == -1)
macroOptions = macroOptions + " interpolation=None";
Macro.setOptions(macroOptions);
}
int bitDepth = imp.getBitDepth();
int stackSize = imp.getStackSize();
boolean isStack = stackSize > 1;
oldDepth = stackSize;
if (isStack) {
xstr = "1.0";
ystr = "1.0";
zstr = "1.0";
}
r = ip.getRoi();
int width = newWidth;
if (width == 0) width = r.width;
int height = (int) ((double) width * r.height / r.width);
xscale = Tools.parseDouble(xstr, 0.0);
yscale = Tools.parseDouble(ystr, 0.0);
zscale = 1.0;
if (xscale != 0.0 && yscale != 0.0) {
width = (int) (r.width * xscale);
height = (int) (r.height * yscale);
} else {
xstr = "-";
ystr = "-";
}
GenericDialog gd = new GenericDialog("Scale");
gd.addStringField("X Scale:", xstr);
gd.addStringField("Y Scale:", ystr);
if (isStack) gd.addStringField("Z Scale:", zstr);
gd.setInsets(5, 0, 5);
gd.addStringField("Width (pixels):", "" + width);
gd.addStringField("Height (pixels):", "" + height);
if (isStack) {
String label = "Depth (images):";
if (imp.isHyperStack()) {
int slices = imp.getNSlices();
int frames = imp.getNFrames();
if (slices == 1 && frames > 1) {
label = "Depth (frames):";
oldDepth = frames;
} else {
label = "Depth (slices):";
oldDepth = slices;
}
}
gd.addStringField(label, "" + oldDepth);
}
fields = gd.getStringFields();
for (int i = 0; i < fields.size(); i++) {
((TextField) fields.elementAt(i)).addTextListener(this);
((TextField) fields.elementAt(i)).addFocusListener(this);
}
xField = (TextField) fields.elementAt(0);
yField = (TextField) fields.elementAt(1);
if (isStack) {
zField = (TextField) fields.elementAt(2);
widthField = (TextField) fields.elementAt(3);
heightField = (TextField) fields.elementAt(4);
depthField = (TextField) fields.elementAt(5);
} else {
widthField = (TextField) fields.elementAt(2);
heightField = (TextField) fields.elementAt(3);
}
fieldWithFocus = xField;
gd.addChoice("Interpolation:", methods, methods[interpolationMethod]);
if (bitDepth == 8 || bitDepth == 24)
gd.addCheckbox("Fill with background color", fillWithBackground);
gd.addCheckbox("Average when downsizing", averageWhenDownsizing);
boolean hyperstack = imp.isHyperStack() || imp.isComposite();
if (isStack && !hyperstack) gd.addCheckbox("Process entire stack", processStack);
gd.addCheckbox("Create new window", newWindow);
title = WindowManager.getUniqueName(imp.getTitle());
gd.setInsets(10, 0, 0);
gd.addStringField("Title:", title, 12);
gd.showDialog();
if (gd.wasCanceled()) return false;
xstr = gd.getNextString();
ystr = gd.getNextString();
xscale = Tools.parseDouble(xstr, 0.0);
yscale = Tools.parseDouble(ystr, 0.0);
if (isStack) {
zstr = gd.getNextString();
zscale = Tools.parseDouble(ystr, 0.0);
}
String wstr = gd.getNextString();
newWidth = (int) Tools.parseDouble(wstr, 0);
newHeight = (int) Tools.parseDouble(gd.getNextString(), 0);
if (newHeight != 0 && (wstr.equals("-") || wstr.equals("0")))
newWidth = (int) (newHeight * (double) r.width / r.height);
if (newWidth == 0 || newHeight == 0) {
IJ.error("Scaler", "Width or height is 0");
return false;
}
if (xscale > 0.0 && yscale > 0.0) {
newWidth = (int) (r.width * xscale);
newHeight = (int) (r.height * yscale);
}
if (isStack) newDepth = (int) Tools.parseDouble(gd.getNextString(), 0);
interpolationMethod = gd.getNextChoiceIndex();
if (bitDepth == 8 || bitDepth == 24) fillWithBackground = gd.getNextBoolean();
averageWhenDownsizing = gd.getNextBoolean();
if (isStack && !hyperstack) processStack = gd.getNextBoolean();
if (hyperstack) processStack = true;
newWindow = gd.getNextBoolean();
if (xscale == 0.0) {
xscale = (double) newWidth / r.width;
yscale = (double) newHeight / r.height;
}
title = gd.getNextString();
if (fillWithBackground) {
Color bgc = Toolbar.getBackgroundColor();
if (bitDepth == 8) bgValue = ip.getBestIndex(bgc);
else if (bitDepth == 24) bgValue = bgc.getRGB();
} else bgValue = 0.0;
return true;
}
public void run(String arg) {
ImagePlus imp = WindowManager.getCurrentImage();
Calibration cal = imp.getCalibration();
GenericDialog gd = new GenericDialog("Options");
int subsize = 32;
gd.addNumericField("Subregion Size (pixels)?", subsize, 0);
int stepsize = 16;
gd.addNumericField("Step Size?", stepsize, 0);
int shift = 3;
gd.addNumericField("STICS temporal Shift?", shift, 0);
float xoffset = 0.0f;
gd.addNumericField("X_Offset", xoffset, 5, 15, null);
float yoffset = 0.0f;
gd.addNumericField("Y_Offset", yoffset, 5, 15, null);
float multiplier = 8.0f;
gd.addNumericField("Velocity Multiplier", multiplier, 5, 15, null);
float ftime = 1.0f;
gd.addNumericField("Frame_Time(min)", ftime, 5, 15, null);
float scaling = (float) cal.pixelWidth;
gd.addNumericField("Pixel_Size(um)", scaling, 5, 15, null);
boolean norm = true;
gd.addCheckbox("Normalize_Vector_lengths?", norm);
boolean centered = true;
gd.addCheckbox("Center_Vectors?", centered);
float magthresh = 0.0f;
gd.addNumericField("Magnitude_Threshhold?", magthresh, 5, 15, null);
int rlength = 10;
gd.addNumericField("Running_avg_length", rlength, 0);
int inc = 5;
gd.addNumericField("Start_frame_increment", inc, 0);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
subsize = (int) gd.getNextNumber();
stepsize = (int) gd.getNextNumber();
shift = (int) gd.getNextNumber();
xoffset = (float) gd.getNextNumber();
yoffset = (float) gd.getNextNumber();
multiplier = (float) gd.getNextNumber();
ftime = (float) gd.getNextNumber();
scaling = (float) gd.getNextNumber();
norm = gd.getNextBoolean();
centered = gd.getNextBoolean();
magthresh = (float) gd.getNextNumber();
rlength = (int) gd.getNextNumber();
inc = (int) gd.getNextNumber();
int width = imp.getWidth();
int xregions = 1 + (int) (((float) width - (float) subsize) / (float) stepsize);
int newwidth = xregions * subsize;
int height = imp.getHeight();
int yregions = 1 + (int) (((float) height - (float) subsize) / (float) stepsize);
int newheight = yregions * subsize;
ImageStack stack = imp.getStack();
int slices = imp.getNSlices();
int channels = imp.getNChannels();
int frames = imp.getNFrames();
if (frames == 1) {
frames = slices;
slices = 1;
}
Roi roi = imp.getRoi();
if (roi == null) {
roi = new Roi(0, 0, width, height);
}
STICS_map map = new STICS_map(subsize, stepsize);
Object[] tseries = jutils.get3DTSeries(stack, 0, 0, frames, slices, channels);
map.update_STICS_map(tseries, width, height, 0, rlength, roi.getPolygon(), shift);
FloatProcessor fp =
map.get_map(scaling, ftime, stepsize, centered, norm, multiplier, stepsize, magthresh);
ImageStack vector_stack = new ImageStack(fp.getWidth(), fp.getHeight());
vector_stack.addSlice("", fp);
float[][] vel = map.get_scaled_velocities(scaling, ftime, stepsize);
ImageStack velstack = new ImageStack(map.xregions, map.yregions);
velstack.addSlice("", vel[0]);
velstack.addSlice("", vel[1]);
int velframes = 2;
IJ.showStatus("frame " + 0 + " calculated");
for (int i = inc; i < (frames - rlength); i += inc) {
map.update_STICS_map(tseries, width, height, i, rlength, roi.getPolygon(), shift);
FloatProcessor fp2 =
map.get_map(scaling, ftime, stepsize, centered, norm, multiplier, stepsize, magthresh);
vector_stack.addSlice("", fp2);
vel = map.get_scaled_velocities(scaling, ftime, stepsize);
velstack.addSlice("", vel[0]);
velstack.addSlice("", vel[1]);
velframes += 2;
IJ.showStatus("frame " + i + " calculated");
}
(new ImagePlus("STICS Vectors", vector_stack)).show();
ImagePlus imp3 = new ImagePlus("Velocities", velstack);
imp3.setOpenAsHyperStack(true);
imp3.setDimensions(2, 1, velframes / 2);
new CompositeImage(imp3, CompositeImage.COLOR).show();
}
public void run(String arg) {
GenericDialog gd = new GenericDialog("Options");
gd.addCheckbox("Acceptor_First", true);
gd.showDialog();
if (gd.wasCanceled()) return;
boolean a1 = gd.getNextBoolean();
int asp = 0;
int dsp = 1;
int aop = 2;
int dop = 3;
int atp = 4;
int dtp = 5;
if (!a1) {
asp = 1;
dsp = 0;
aop = 3;
dop = 2;
atp = 5;
dtp = 4;
}
ImageWindow iw = WindowManager.getCurrentWindow();
float[][] xvals = (float[][]) jutils.runPW4VoidMethod(iw, "getXValues");
float[][] yvals = (float[][]) jutils.runPW4VoidMethod(iw, "getYValues");
int[] npts = (int[]) jutils.runPW4VoidMethod(iw, "getNpts");
int maxpts = (int) jstatistics.getstatistic("Max", npts, null);
int nsets = npts.length / 6;
float[][] rtxvals = new float[nsets][maxpts];
float[][] rtavals = new float[nsets][maxpts];
float[][] rtdvals = new float[nsets][maxpts];
int[] rtnpts = new int[nsets];
int fretlength = 10;
float[][] stfretvals = new float[nsets][fretlength];
float[][] offfretvals = new float[nsets][fretlength];
TextWindow tw = jutils.selectTable("DNA Damage FRET");
if (tw == null)
tw =
new TextWindow(
"DNA Damage FRET",
"title\tacceptor\tdonor\testripe\teoff\tmaxart\tmaxdrt",
"",
400,
200);
// note that st stands for stripe and off is for areas off the damage stripe
for (int i = 0; i < npts.length / 6; i++) {
int len = npts[i * 6];
int damageindex = findbleach(yvals[i * 6 + dsp], len);
int fretindex = findbleach(yvals[i * 6 + atp], len);
IJ.log("set " + i + " damage pos = " + damageindex + " , fret pos = " + fretindex);
int predamagestart = damageindex - 4;
int prefretstart = fretindex - 5;
float staccpredam = getavg(yvals[i * 6 + asp], len, predamagestart, damageindex - 1);
float stdonpredam = getavg(yvals[i * 6 + dsp], len, predamagestart, damageindex - 1);
float nucaccpredam = getavg(yvals[i * 6 + atp], len, predamagestart, damageindex - 1);
float nucdonpredam = getavg(yvals[i * 6 + dtp], len, predamagestart, damageindex - 1);
float stdonprefret = getavg(yvals[i * 6 + dsp], len, prefretstart, fretindex - 2);
float stdonafret = getavg(yvals[i * 6 + dsp], len, fretindex, fretindex + 3);
float offdonprefret = getavg(yvals[i * 6 + dop], len, prefretstart, fretindex - 2);
float offdonafret = getavg(yvals[i * 6 + dop], len, fretindex, fretindex + 3);
float estripe = 1.0f - stdonprefret / stdonafret;
float eoff = 1.0f - offdonprefret / offdonafret;
rtnpts[i] = len;
for (int j = 0; j < len; j++) {
rtxvals[i][j] = j - damageindex - 1;
rtavals[i][j] =
(yvals[i * 6 + asp][j] / staccpredam) / (yvals[i * 6 + atp][j] / nucaccpredam);
rtdvals[i][j] =
(yvals[i * 6 + dsp][j] / stdonpredam) / (yvals[i * 6 + dtp][j] / nucdonpredam);
}
float[] smart = (float[]) algutils.get_subarray(rtavals[i], 0, fretindex);
float[] smdrt = (float[]) algutils.get_subarray(rtdvals[i], 0, fretindex);
jsmooth.blur1D(smart, 2.0f);
jsmooth.blur1D(smdrt, 2.0f);
float maxart = 0.0f;
float maxdrt = 0.0f;
for (int j = 0; j < fretindex - 2; j++) {
if (smart[j] > maxart) maxart = smart[j];
if (smdrt[j] > maxdrt) maxdrt = smdrt[j];
}
stfretvals[i] = getregion(yvals[i * 6 + dsp], len, prefretstart, fretlength);
offfretvals[i] = getregion(yvals[i * 6 + dop], len, prefretstart, fretlength);
tw.append(
iw.getTitle()
+ "-"
+ (i + 1)
+ "\t"
+ staccpredam
+ "\t"
+ stdonpredam
+ "\t"
+ estripe
+ "\t"
+ eoff
+ "\t"
+ maxart
+ "\t"
+ maxdrt);
}
new PlotWindow4("Stripe_FRET_profiles", "time", "intensity", stfretvals, null).draw();
new PlotWindow4("OffStripe_FRET_profiles", "time", "intensity", offfretvals, null).draw();
new PlotWindow4("Acc_Rt_profiles", "time", "intensity", rtxvals, rtavals, rtnpts).draw();
new PlotWindow4("Don_Rt_profiles", "time", "intensity", rtxvals, rtdvals, rtnpts).draw();
}
public void run(String arg) {
int[] wList = WindowManager.getIDList();
if (wList==null) {
IJ.error("No images are open.");
return;
}
double kernel=3;
double kernelsum = 0;
double kernelvarsum =0;
double kernalvar = 0;
double sigmawidth = 2;
int kernelindex, minpixnumber;
String[] kernelsize = { "3�,"5�, "7�, "9�};
GenericDialog gd = new GenericDialog("Sigma Filter");
gd.addChoice("Kernel size", kernelsize, kernelsize[0]);
gd.addNumericField("Sigma width",sigmawidth , 2);
gd.addNumericField("Minimum number of pixels", 1, 0);
gd.addCheckbox("Keep source:",true);
gd.addCheckbox("Do all stack:",true);
gd.addCheckbox("Modified Lee's FIlter:",true);
gd.showDialog();
if (gd.wasCanceled()) return ;
kernelindex = gd.getNextChoiceIndex();
sigmawidth = gd.getNextNumber();
minpixnumber = ((int)gd.getNextNumber());
boolean keep = gd.getNextBoolean();
boolean doallstack = gd.getNextBoolean();
boolean modified = gd.getNextBoolean();
if (kernelindex==0) kernel = 3;
if (kernelindex==1) kernel = 5;
if (kernelindex==2) kernel = 7;
if (kernelindex==3) kernel = 9;
long start = System.currentTimeMillis();
if (minpixnumber> (kernel*kernel)){
IJ.showMessage("Sigma filter", "There must be more pixels in the kernel than+\n" + "the minimum number to be included");
return;
}
double v, midintensity;
int x, y, ix, iy;
double sum = 0;
double backupsum =0;
int count = 0;
int n = 0;
if (keep) {IJ.run("Select All"); IJ.run("Duplicate...", "title='Sigma filtered' duplicate");}
int radius = (int)(kernel-1)/2;
ImagePlus imp = WindowManager.getCurrentImage();
ImageStack stack1 = imp.getStack();
int width = imp.getWidth();
int height = imp.getHeight();
int nslices = stack1.getSize();
int cslice = imp.getCurrentSlice();
double status = width*height*nslices;
ImageProcessor ip = imp.getProcessor();
int sstart = 1;
if (!doallstack) {sstart = cslice; nslices=sstart;status = status/nslices;};
for (int i=sstart; i<=nslices; i++) {
imp.setSlice(i);
for (x=radius;x<width+radius;x++) {
for (y=radius;y<height+radius;y++) {
midintensity = ip.getPixelValue(x,y);
count = 0;
sum = 0;
kernelsum =0;
kernalvar =0;
kernelvarsum =0;
backupsum = 0;
//calculate mean of kernel value
for (ix=0;ix<kernel;ix++) {
for (iy=0;iy<kernel;iy++) {
v = ip.getPixelValue(x+ix-radius,y+iy-radius);
kernelsum = kernelsum+v;
}
}
double sigmacalcmean = (kernelsum/(kernel*kernel));
//calculate variance of kernel
for (ix=0;ix<kernel;ix++) {
for (iy=0;iy<kernel;iy++) {
v = ip.getPixelValue(x+ix-radius,y+iy-radius);
kernalvar = (v-sigmacalcmean)*(v-sigmacalcmean);
kernelvarsum = kernelvarsum + kernalvar;
}
}
//double variance = kernelvarsum/kernel;
double sigmacalcvar = kernelvarsum/((kernel*kernel)-1);
//calcuate sigma range = sqrt(variance/(mean^2)) � sigmawidth
double sigmarange = sigmawidth*(Math.sqrt((sigmacalcvar) /(sigmacalcmean*sigmacalcmean)));
//calulate sigma top value and bottom value
double sigmatop = midintensity*(1+sigmarange);
double sigmabottom = midintensity*(1-sigmarange);
//calculate mean of values that differ are in sigma range.
for (ix=0;ix<kernel;ix++) {
for (iy=0;iy<kernel;iy++) {
v = ip.getPixelValue(x+ix-radius,y+iy-radius);
if ((v>=sigmabottom)&&(v<=sigmatop)){
sum = sum+v;
count = count+1; }
backupsum = v+ backupsum;
}
}
//if there are too few pixels in the kernal that are within sigma range, the
//mean of the entire kernal is taken. My modification of Lee's filter is to exclude the central value
//from the calculation of the mean as I assume it to be spuriously high or low
if (!(count>(minpixnumber)))
{sum = (backupsum-midintensity);
count = (int)((kernel*kernel)-1);
if (!modified)
{sum = (backupsum);
count = (int)(kernel*kernel);}
}
double val = (sum/count);
ip.putPixelValue(x,y, val);
n = n+1;
double percentage = (((double)n/status)*100);
IJ.showStatus(IJ.d2s(percentage,0) +"% done");
}
// IJ.showProgress(i, status);
}}
imp.updateAndDraw();
IJ.showStatus(IJ.d2s((System.currentTimeMillis()-start)/1000.0, 2)+" seconds"); }
/* Setup GUI */
protected final boolean setup() {
if (IJ.versionLessThan("1.40c")) {
return false;
} else {
int[] ids = WindowManager.getIDList();
if (ids != null && ids.length >= 2) {
ArrayList titlesList = new ArrayList();
ArrayList idsList = new ArrayList();
String currentTitle = null;
for (int titles = 0; titles < ids.length; ++titles) {
ImagePlus var1 = WindowManager.getImage(ids[titles]);
titlesList.add(var1.getTitle());
idsList.add(Integer.valueOf(ids[titles]));
if (var1 == WindowManager.getCurrentImage()) {
currentTitle = var1.getTitle();
}
}
if (titlesList.size() < 2) {
IJ.showMessage("You should have at least two stacks - stimulus and response.");
return false;
} else {
String[] var8 = new String[titlesList.size()];
titlesList.toArray(var8);
if (currentTitle == null) {
currentTitle = var8[0];
}
SubstackMaker sm = new SubstackMaker();
GenericDialog gd = new GenericDialog("AAP - 1.1.0");
// gd.setInsets(10, 45, 0);
gd.addChoice("Stimulus stack", var8, currentTitle);
gd.addChoice("Response stack", var8, currentTitle.equals(var8[0]) ? var8[1] : var8[0]);
String defautltSlices =
"1-" + WindowManager.getImage(((Integer) idsList.get(0)).intValue()).getStackSize();
gd.addMessage("Enter a range (e.g. 2-14)...", null, Color.darkGray);
gd.addStringField("Slices of Response:", defautltSlices, 40);
gd.addCheckbox("Remove first slice", true);
gd.addCheckbox("Use Artifact from response", true);
gd.showDialog();
if (gd.wasCanceled()) {
return false;
} else {
this.imp_s =
WindowManager.getImage(((Integer) idsList.get(gd.getNextChoiceIndex())).intValue());
this.imp_r =
WindowManager.getImage(((Integer) idsList.get(gd.getNextChoiceIndex())).intValue());
String userInput = gd.getNextString();
this.dt_r = Activity_Analysis.findSignalDt(this.imp_r.getTitle());
if (userInput == null) {
return false;
}
IJ.showStatus(" Making substack copy of selection...");
this.imp_r = sm.makeSubstack(this.imp_r, userInput);
this.imp_s_index = getFirstNLast(this.imp_r, userInput);
if (this.imp_s_index[0] != 1 | !gd.getNextBoolean()) this.removeFirst = false;
if (gd.getNextBoolean()) this.useArtifact = true;
// this.imp_s = makeStimSubstack(this.imp_s , userInput);
return true;
}
}
} else {
IJ.showMessage("You should have at least two stacks open.");
return false;
}
}
}
public void run(String arg) {
Frame[] niframes = WindowManager.getNonImageWindows();
String[] titles = new String[niframes.length + 1];
for (int i = 0; i < niframes.length; i++) {
titles[i] = niframes[i].getTitle();
}
titles[niframes.length] = "Clipboard";
GenericDialog gd = new GenericDialog("Windows");
boolean importfile = false;
gd.addCheckbox("Import from file?", importfile);
gd.addChoice("Windows", titles, titles[0]);
boolean hasxvals = false;
gd.addCheckbox("X Vals Column?", hasxvals);
boolean multix = false;
gd.addCheckbox("Multi_X_Columns?", multix);
boolean skipendzeros = false;
gd.addCheckbox("Skip_end_zeros?", skipendzeros);
String[] delimiters = {"Tab", "Comma", "Space"};
gd.addChoice("Delimiter", delimiters, delimiters[0]);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
importfile = gd.getNextBoolean();
int index = gd.getNextChoiceIndex();
hasxvals = gd.getNextBoolean();
multix = gd.getNextBoolean();
skipendzeros = gd.getNextBoolean();
int delimindex = gd.getNextChoiceIndex();
if (multix) hasxvals = true;
String textdata = "";
if (importfile) {
OpenDialog od = new OpenDialog("Open File", "", ".txt");
String directory = od.getDirectory();
String name = od.getFileName();
if (name == null) {
return;
}
try {
File infile = new File(directory + name);
BufferedReader b = new BufferedReader(new FileReader(infile));
textdata = (new jdataio()).readstringfile(b);
b.close();
} catch (IOException e) {
return;
}
} else {
if (index == niframes.length) {
// here we get the data from the clipboard
Transferable t = Toolkit.getDefaultToolkit().getSystemClipboard().getContents(null);
try {
if (t != null && t.isDataFlavorSupported(DataFlavor.stringFlavor)) {
textdata = (String) t.getTransferData(DataFlavor.stringFlavor);
}
} catch (UnsupportedFlavorException e) {
} catch (IOException e) {
}
if (textdata.equals("")) {
IJ.error("Error copying from clipboard.");
return;
}
} else {
if (niframes[index] instanceof Editor) {
Editor tw = (Editor) niframes[index];
textdata = tw.getText();
} else {
if (niframes[index] instanceof TextWindow) {
TextWindow tw = (TextWindow) niframes[index];
textdata = tw.getTextPanel().getText();
} else {
IJ.showMessage("Not a valid text window");
return;
}
}
}
}
if (textdata == null) {
IJ.showMessage("Error in Obtaining String");
return;
}
if (textdata.indexOf("\r") >= 0) {
textdata = textdata.replace('\r', '\n');
}
char[] delims = {'\t', ',', ' '};
delimit_string ds = new delimit_string(delims[delimindex]);
String[] rows = ds.getrows(textdata);
int lines = rows.length;
int columns = ds.getnumcolumns(rows[0]);
int ycolumns = columns;
if (hasxvals) {
if (multix) {
ycolumns /= 2;
} else {
ycolumns--;
}
}
if (multix) {
float[][] ydata = new float[ycolumns][lines];
float[][] xdata = new float[ycolumns][lines];
for (int i = 0; i < lines; i++) {
float[] temp = ds.delim2float(rows[i], columns);
for (int j = 0; j < ycolumns; j++) {
ydata[j][i] = temp[2 * j + 1];
xdata[j][i] = temp[2 * j];
}
}
int[] npts = new int[ycolumns];
for (int i = 0; i < ycolumns; i++) {
npts[i] = lines;
}
if (skipendzeros) {
for (int i = 0; i < ycolumns; i++) {
int counter = lines - 1;
while ((xdata[i][counter] == 0.0f || Float.isNaN(xdata[i][counter])) && counter > 0) {
xdata[i][counter] = 0.0f;
ydata[i][counter] = 0.0f;
npts[i]--;
counter--;
}
}
}
(new PlotWindow4("Text Plot", "x", "y", xdata, ydata, npts)).draw();
} else {
float[][] tempydata = new float[ycolumns][lines];
float[] tempxdata = new float[lines];
float[][] xdata = null;
float[][] ydata = null;
int startcolumn = 0;
if (hasxvals) startcolumn = 1;
for (int i = 0; i < lines; i++) {
float[] temp = ds.delim2float(rows[i], columns);
if (hasxvals) {
tempxdata[i] = temp[0];
} else {
tempxdata[i] = (float) (i + 1);
}
for (int j = 0; j < ycolumns; j++) {
tempydata[j][i] = temp[j + startcolumn];
}
}
int[] npts = new int[ycolumns];
npts[0] = lines;
if (skipendzeros) {
int maxpts = 0;
for (int i = 0; i < ycolumns; i++) {
int counter = lines - 1;
npts[i] = lines;
while ((tempydata[i][counter] == 0.0f || Float.isNaN(tempydata[i][counter]))
&& counter > 0) {
npts[i]--;
counter--;
}
if (npts[i] > maxpts) maxpts = npts[i];
IJ.log("" + npts[i]);
}
ydata = new float[ycolumns][maxpts];
xdata = new float[ycolumns][maxpts];
for (int i = 0; i < ycolumns; i++) {
// npts[i]=npts[0];
System.arraycopy(tempxdata, 0, xdata[i], 0, npts[i]);
System.arraycopy(tempydata[i], 0, ydata[i], 0, npts[i]);
}
} else {
ydata = tempydata;
xdata = new float[ycolumns][];
for (int i = 0; i < ycolumns; i++) {
npts[i] = npts[0];
xdata[i] = tempxdata.clone();
}
}
(new PlotWindow4("Text Plot", "x", "y", xdata, ydata, npts)).draw();
}
}
public boolean analyseParticles(MyFunctions f) {
GenericDialog gd = new GenericDialog("Analyse PALM/STORM Particles");
gd.addNumericField("Minimum SNR", prefs.get("QuickPALM.snr", 5), 2);
gd.addNumericField("Maximum FWHM (in px)", prefs.get("QuickPALM.fwhm", 4), 0);
gd.addNumericField("Image plane pixel size (nm)", prefs.get("QuickPALM.pixelsize", 106), 2);
gd.addCheckbox("Smart SNR", prefs.get("QuickPALM.smartsnr", true));
gd.addCheckbox(
"3D PALM (astigmatism) - will require calibration file",
prefs.get("QuickPALM.is3d", false));
gd.addCheckbox("Online rendering", prefs.get("QuickPALM.view", true));
gd.addCheckbox("Attach to running acquisition", prefs.get("QuickPALM.attach", false));
gd.addCheckbox("Stream particle info directly into file", prefs.get("QuickPALM.stream", true));
gd.addMessage("\n");
// -----------------------------------------
gd.addMessage("-- Online rendering settings (used only if selected) --");
gd.addMessage("\n");
gd.addNumericField("Pixel size of rendered image (nm)", 30, 2);
gd.addNumericField("Accumulate last (0 to accumulate all frames)", 0, 0);
gd.addNumericField("Update every (frames)", 10, 0);
// gd.addNumericField("Allow color saturation (%)", 50, 0);
gd.addMessage("\n");
// -----------------------------------------
gd.addMessage("-- Attach to running acquisition settings (used only if selected) --");
gd.addMessage("\n");
gd.addStringField(
"_Image name pattern (NN...NN represents the numerical change)",
prefs.get("QuickPALM.pattern", "imgNNNNNNNNN.tif"),
20);
gd.addNumericField("Start NN...NN with", 0, 0);
gd.addNumericField("In acquisition max. wait time for new image (ms)", 50, 0);
gd.addMessage("\n");
// -----------------------------------------
gd.addMessage("-- Advanced settings (don't normally need to be changed) --");
gd.addMessage("\n");
gd.addNumericField("_Minimum symmetry (%)", prefs.get("QuickPALM.symmetry", 50), 0);
gd.addNumericField(
"Local threshold (% maximum intensity)", prefs.get("QuickPALM.lthreshold", 20), 0);
gd.addNumericField("_Maximum iterations per frame", prefs.get("QuickPALM.maxiter", 1000), 0);
gd.addNumericField(
"Threads (each takes ~3*[frame size] in memory)", prefs.get("QuickPALM.nthreads", 50), 0);
gd.addMessage("\n\nDon't forget to save the table in the end...");
gd.showDialog();
if (gd.wasCanceled()) return false;
snr = (int) gd.getNextNumber();
prefs.set("QuickPALM.snr", snr);
fwhm = gd.getNextNumber();
prefs.set("QuickPALM.fwhm", fwhm);
pixelsize = gd.getNextNumber();
prefs.set("QuickPALM.pixelsize", pixelsize);
smartsnr = gd.getNextBoolean();
prefs.set("QuickPALM.smartsnr", smartsnr);
is3d = gd.getNextBoolean();
prefs.set("QuickPALM.is3d", is3d);
view = gd.getNextBoolean();
prefs.set("QuickPALM.view", view);
attach = gd.getNextBoolean();
prefs.set("QuickPALM.attach", attach);
if (gd.getNextBoolean()) {
f.psave = new ParticleSaver();
f.psave.setup();
prefs.set("QuickPALM.stream", true);
} else prefs.set("QuickPALM.stream", false);
// --
magn = pixelsize / gd.getNextNumber();
viewer_accumulate = (int) gd.getNextNumber();
viewer_update = (int) gd.getNextNumber();
// --
pattern = gd.getNextString().trim();
prefs.set("QuickPALM.pattern", pattern);
prefix = pattern.substring(0, pattern.indexOf("N"));
sufix = pattern.substring(pattern.lastIndexOf("N") + 1, pattern.length());
nimchars = pattern.split("N").length - 1;
nimstart = (int) gd.getNextNumber();
waittime = (int) gd.getNextNumber();
// --
symmetry = gd.getNextNumber() / 100;
prefs.set("QuickPALM.symmetry", symmetry);
pthrsh = gd.getNextNumber() / 100;
prefs.set("QuickPALM.lthreshold", pthrsh * 100);
maxpart = (int) gd.getNextNumber();
prefs.set("QuickPALM.maxiter", maxpart);
threads = (int) gd.getNextNumber();
prefs.set("QuickPALM.nthreads", threads);
return true;
}
/** 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;
}
boolean showDialog(ImageProcessor ip) {
int bitDepth = imp.getBitDepth();
boolean isStack = imp.getStackSize() > 1;
r = ip.getRoi();
int width = newWidth;
if (width == 0) width = r.width;
int height = (int) ((double) width * r.height / r.width);
xscale = Tools.parseDouble(xstr, 0.0);
yscale = Tools.parseDouble(ystr, 0.0);
if (xscale != 0.0 && yscale != 0.0) {
width = (int) (r.width * xscale);
height = (int) (r.height * yscale);
} else {
xstr = "-";
ystr = "-";
}
GenericDialog gd = new GenericDialog("Scale");
gd.addStringField("X Scale (0.05-25):", xstr);
gd.addStringField("Y Scale (0.05-25):", ystr);
gd.setInsets(5, 0, 5);
gd.addStringField("Width (pixels):", "" + width);
gd.addStringField("Height (pixels):", "" + height);
fields = gd.getStringFields();
for (int i = 0; i < 3; i++) {
((TextField) fields.elementAt(i)).addTextListener(this);
((TextField) fields.elementAt(i)).addFocusListener(this);
}
xField = (TextField) fields.elementAt(0);
yField = (TextField) fields.elementAt(1);
widthField = (TextField) fields.elementAt(2);
heightField = (TextField) fields.elementAt(3);
fieldWithFocus = xField;
gd.addCheckbox("Interpolate", interpolate);
if (bitDepth == 8 || bitDepth == 24)
gd.addCheckbox("Fill with Background Color", fillWithBackground);
if (isStack) gd.addCheckbox("Process Entire Stack", processStack);
gd.addCheckbox("Create New Window", newWindow);
title = WindowManager.getUniqueName(imp.getTitle());
gd.setInsets(10, 0, 0);
gd.addStringField("Title:", title, 12);
gd.showDialog();
if (gd.wasCanceled()) return false;
xstr = gd.getNextString();
ystr = gd.getNextString();
xscale = Tools.parseDouble(xstr, 0.0);
yscale = Tools.parseDouble(ystr, 0.0);
String wstr = gd.getNextString();
newWidth = (int) Tools.parseDouble(wstr, 0);
newHeight = (int) Tools.parseDouble(gd.getNextString(), 0);
if (newHeight != 0 && (wstr.equals("-") || wstr.equals("0")))
newWidth = (int) (newHeight * (double) r.width / r.height);
if (newWidth == 0 || newHeight == 0) {
IJ.error("Invalid width or height entered");
return false;
}
if (xscale > 25.0) xscale = 25.0;
if (yscale > 25.0) yscale = 25.0;
if (xscale > 0.0 && yscale > 0.0) {
newWidth = (int) (r.width * xscale);
newHeight = (int) (r.height * yscale);
}
interpolate = gd.getNextBoolean();
if (bitDepth == 8 || bitDepth == 24) fillWithBackground = gd.getNextBoolean();
if (isStack) processStack = gd.getNextBoolean();
newWindow = gd.getNextBoolean();
if (!newWindow && xscale == 0.0) {
xscale = (double) newWidth / r.width;
yscale = (double) newHeight / r.height;
}
title = gd.getNextString();
if (fillWithBackground) {
Color bgc = Toolbar.getBackgroundColor();
if (bitDepth == 8) bgValue = ip.getBestIndex(bgc);
else if (bitDepth == 24) bgValue = bgc.getRGB();
} else {
if (bitDepth == 8) bgValue = ip.isInvertedLut() ? 0.0 : 255.0; // white
else if (bitDepth == 24) bgValue = 0xffffffff; // white
}
return true;
}
