// Added by Marcel Boeglin 2013.09.22 private Overlay projectHyperStackRois(Overlay overlay) { if (overlay == null) return null; int t1 = imp.getFrame(); int channels = projImage.getNChannels(); int slices = 1; int frames = projImage.getNFrames(); Overlay overlay2 = new Overlay(); Roi roi; int c, z, t; int size = channels * slices * frames; for (Roi r : overlay.toArray()) { c = r.getCPosition(); z = r.getZPosition(); t = r.getTPosition(); roi = (Roi) r.clone(); if (size == channels) { // current time frame if (z >= startSlice && z <= stopSlice && t == t1 || c == 0) { roi.setPosition(c); overlay2.add(roi); } } else if (size == frames * channels) { // all time frames if (z >= startSlice && z <= stopSlice) roi.setPosition(c, 1, t); else if (z == 0) roi.setPosition(c, 0, t); else continue; overlay2.add(roi); } } return overlay2; }
/** * 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; }
public void doHyperStackProjection(boolean allTimeFrames) { int start = startSlice; int stop = stopSlice; int firstFrame = 1; int lastFrame = imp.getNFrames(); if (!allTimeFrames) firstFrame = lastFrame = imp.getFrame(); ImageStack stack = new ImageStack(imp.getWidth(), imp.getHeight()); int channels = imp.getNChannels(); int slices = imp.getNSlices(); if (slices == 1) { slices = imp.getNFrames(); firstFrame = lastFrame = 1; } int frames = lastFrame - firstFrame + 1; increment = channels; boolean rgb = imp.getBitDepth() == 24; for (int frame = firstFrame; frame <= lastFrame; frame++) { for (int channel = 1; channel <= channels; channel++) { startSlice = (frame - 1) * channels * slices + (start - 1) * channels + channel; stopSlice = (frame - 1) * channels * slices + (stop - 1) * channels + channel; if (rgb) doHSRGBProjection(imp); else doProjection(); stack.addSlice(null, projImage.getProcessor()); } } projImage = new ImagePlus(makeTitle(), stack); projImage.setDimensions(channels, 1, frames); if (channels > 1) { projImage = new CompositeImage(projImage, 0); ((CompositeImage) projImage).copyLuts(imp); if (method == SUM_METHOD || method == SD_METHOD) ((CompositeImage) projImage).resetDisplayRanges(); } if (frames > 1) projImage.setOpenAsHyperStack(true); Overlay overlay = imp.getOverlay(); if (overlay != null) { startSlice = start; stopSlice = stop; if (imp.getType() == ImagePlus.COLOR_RGB) projImage.setOverlay(projectRGBHyperStackRois(overlay)); else projImage.setOverlay(projectHyperStackRois(overlay)); } IJ.showProgress(1, 1); }
// Added by Marcel Boeglin 2013.09.22 private Overlay projectRGBHyperStackRois(Overlay overlay) { if (overlay == null) return null; int frames = projImage.getNFrames(); int t1 = imp.getFrame(); Overlay overlay2 = new Overlay(); Roi roi; int c, z, t; for (Roi r : overlay.toArray()) { c = r.getCPosition(); z = r.getZPosition(); t = r.getTPosition(); roi = (Roi) r.clone(); if (z >= startSlice && z <= stopSlice || z == 0 || c == 0 || t == 0) { if (frames == 1 && t != t1 && t != 0) // current time frame continue; roi.setPosition(t); overlay2.add(roi); } } return overlay2; }
public void textValueChanged(TextEvent e) { Object source = e.getSource(); double newXScale = xscale; double newYScale = yscale; double newZScale = zscale; if (source == xField && fieldWithFocus == xField) { String newXText = xField.getText(); newXScale = Tools.parseDouble(newXText, 0); if (newXScale == 0) return; if (newXScale != xscale) { int newWidth = (int) (newXScale * r.width); widthField.setText("" + newWidth); if (constainAspectRatio) { yField.setText(newXText); int newHeight = (int) (newXScale * r.height); heightField.setText("" + newHeight); } } } else if (source == yField && fieldWithFocus == yField) { String newYText = yField.getText(); newYScale = Tools.parseDouble(newYText, 0); if (newYScale == 0) return; if (newYScale != yscale) { int newHeight = (int) (newYScale * r.height); heightField.setText("" + newHeight); } } else if (source == zField && fieldWithFocus == zField) { String newZText = zField.getText(); newZScale = Tools.parseDouble(newZText, 0); if (newZScale == 0) return; if (newZScale != zscale) { int nSlices = imp.getStackSize(); if (imp.isHyperStack()) { int slices = imp.getNSlices(); int frames = imp.getNFrames(); if (slices == 1 && frames > 1) nSlices = frames; else nSlices = slices; } int newDepth = (int) (newZScale * nSlices); depthField.setText("" + newDepth); } } else if (source == widthField && fieldWithFocus == widthField) { int newWidth = (int) Tools.parseDouble(widthField.getText(), 0.0); if (newWidth != 0) { int newHeight = (int) (newWidth * (double) r.height / r.width); heightField.setText("" + newHeight); xField.setText("-"); yField.setText("-"); newXScale = 0.0; newYScale = 0.0; } } else if (source == depthField && fieldWithFocus == depthField) { int newDepth = (int) Tools.parseDouble(depthField.getText(), 0.0); if (newDepth != 0) { zField.setText("-"); newZScale = 0.0; } } xscale = newXScale; yscale = newYScale; zscale = newZScale; }
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) { 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; }