/** * Adds a checkbox labelled "Preview" for "automatic" preview. The reference to this checkbox can * be retrieved by getPreviewCheckbox() and it provides the additional method previewRunning for * optical feedback while preview is prepared. PlugInFilters can have their "run" method * automatically called for preview under the following conditions: - the PlugInFilter must pass a * reference to itself (i.e., "this") as an argument to the AddPreviewCheckbox - it must implement * the DialogListener interface and set the filter parameters in the dialogItemChanged method. - * it must have DIALOG and PREVIEW set in its flags. A previewCheckbox is always off when the * filter is started and does not get recorded by the Macro Recorder. * * @param pfr A reference to the PlugInFilterRunner calling the PlugInFilter if automatic preview * is desired, null otherwise. */ public void addPreviewCheckbox(PlugInFilterRunner pfr) { if (previewCheckbox != null) return; ImagePlus imp = WindowManager.getCurrentImage(); if (imp != null && imp.isComposite() && ((CompositeImage) imp).getMode() == IJ.COMPOSITE) return; this.pfr = pfr; addCheckbox(previewLabel, false, true); }
void addScrollbars(ImagePlus imp) { ImageStack s = imp.getStack(); int stackSize = s.getSize(); nSlices = stackSize; hyperStack = imp.getOpenAsHyperStack(); // imp.setOpenAsHyperStack(false); int[] dim = imp.getDimensions(); int nDimensions = 2 + (dim[2] > 1 ? 1 : 0) + (dim[3] > 1 ? 1 : 0) + (dim[4] > 1 ? 1 : 0); if (nDimensions <= 3 && dim[2] != nSlices) hyperStack = false; if (hyperStack) { nChannels = dim[2]; nSlices = dim[3]; nFrames = dim[4]; } // IJ.log("StackWindow: "+hyperStack+" "+nChannels+" "+nSlices+" "+nFrames); if (nSlices == stackSize) hyperStack = false; if (nChannels * nSlices * nFrames != stackSize) hyperStack = false; if (cSelector != null || zSelector != null || tSelector != null) removeScrollbars(); ImageJ ij = IJ.getInstance(); if (nChannels > 1) { cSelector = new ScrollbarWithLabel(this, 1, 1, 1, nChannels + 1, 'c'); add(cSelector); if (ij != null) cSelector.addKeyListener(ij); cSelector.addAdjustmentListener(this); cSelector.setFocusable(false); // prevents scroll bar from blinking on Windows cSelector.setUnitIncrement(1); cSelector.setBlockIncrement(1); } if (nSlices > 1) { char label = nChannels > 1 || nFrames > 1 ? 'z' : 't'; if (stackSize == dim[2] && imp.isComposite()) label = 'c'; zSelector = new ScrollbarWithLabel(this, 1, 1, 1, nSlices + 1, label); if (label == 't') animationSelector = zSelector; add(zSelector); if (ij != null) zSelector.addKeyListener(ij); zSelector.addAdjustmentListener(this); zSelector.setFocusable(false); int blockIncrement = nSlices / 10; if (blockIncrement < 1) blockIncrement = 1; zSelector.setUnitIncrement(1); zSelector.setBlockIncrement(blockIncrement); sliceSelector = zSelector.bar; } if (nFrames > 1) { animationSelector = tSelector = new ScrollbarWithLabel(this, 1, 1, 1, nFrames + 1, 't'); add(tSelector); if (ij != null) tSelector.addKeyListener(ij); tSelector.addAdjustmentListener(this); tSelector.setFocusable(false); int blockIncrement = nFrames / 10; if (blockIncrement < 1) blockIncrement = 1; tSelector.setUnitIncrement(1); tSelector.setBlockIncrement(blockIncrement); } }
void createNewStack(ImagePlus imp, ImageProcessor ip) { int nSlices = imp.getStackSize(); int w = imp.getWidth(), h = imp.getHeight(); ImagePlus imp2 = imp.createImagePlus(); Rectangle r = ip.getRoi(); boolean crop = r.width != imp.getWidth() || r.height != imp.getHeight(); ImageStack stack1 = imp.getStack(); ImageStack stack2 = new ImageStack(newWidth, newHeight); ImageProcessor ip1, ip2; int method = interpolationMethod; if (w == 1 || h == 1) method = ImageProcessor.NONE; for (int i = 1; i <= nSlices; i++) { IJ.showStatus("Scale: " + i + "/" + nSlices); ip1 = stack1.getProcessor(i); String label = stack1.getSliceLabel(i); if (crop) { ip1.setRoi(r); ip1 = ip1.crop(); } ip1.setInterpolationMethod(method); ip2 = ip1.resize(newWidth, newHeight, averageWhenDownsizing); if (ip2 != null) stack2.addSlice(label, ip2); IJ.showProgress(i, nSlices); } imp2.setStack(title, stack2); Calibration cal = imp2.getCalibration(); if (cal.scaled()) { cal.pixelWidth *= 1.0 / xscale; cal.pixelHeight *= 1.0 / yscale; } IJ.showProgress(1.0); int[] dim = imp.getDimensions(); imp2.setDimensions(dim[2], dim[3], dim[4]); if (imp.isComposite()) { imp2 = new CompositeImage(imp2, ((CompositeImage) imp).getMode()); ((CompositeImage) imp2).copyLuts(imp); } if (imp.isHyperStack()) imp2.setOpenAsHyperStack(true); if (newDepth > 0 && newDepth != oldDepth) imp2 = (new Resizer()).zScale(imp2, newDepth, interpolationMethod); if (imp2 != null) { imp2.show(); imp2.changes = true; } }
void createNewStack(ImagePlus imp, ImageProcessor ip) { Rectangle r = ip.getRoi(); boolean crop = r.width != imp.getWidth() || r.height != imp.getHeight(); int nSlices = imp.getStackSize(); ImageStack stack1 = imp.getStack(); ImageStack stack2 = new ImageStack(newWidth, newHeight); ImageProcessor ip1, ip2; boolean interp = interpolate; if (imp.getWidth() == 1 || imp.getHeight() == 1) interp = false; for (int i = 1; i <= nSlices; i++) { IJ.showStatus("Scale: " + i + "/" + nSlices); ip1 = stack1.getProcessor(i); String label = stack1.getSliceLabel(i); if (crop) { ip1.setRoi(r); ip1 = ip1.crop(); } ip1.setInterpolate(interp); ip2 = ip1.resize(newWidth, newHeight); if (ip2 != null) stack2.addSlice(label, ip2); IJ.showProgress(i, nSlices); } ImagePlus imp2 = imp.createImagePlus(); imp2.setStack(title, stack2); Calibration cal = imp2.getCalibration(); if (cal.scaled()) { cal.pixelWidth *= 1.0 / xscale; cal.pixelHeight *= 1.0 / yscale; } int[] dim = imp.getDimensions(); imp2.setDimensions(dim[2], dim[3], dim[4]); IJ.showProgress(1.0); if (imp.isComposite()) { imp2 = new CompositeImage(imp2, 0); ((CompositeImage) imp2).copyLuts(imp); } if (imp.isHyperStack()) imp2.setOpenAsHyperStack(true); imp2.show(); imp2.changes = 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 itemStateChanged(ItemEvent e) { ImagePlus imp = WindowManager.getCurrentImage(); if (imp == null) return; if (!imp.isComposite()) { int channels = imp.getNChannels(); if (channels == 1 && imp.getStackSize() <= 4) channels = imp.getStackSize(); if (imp.getBitDepth() == 24 || (channels > 1 && channels < CompositeImage.MAX_CHANNELS)) { GenericDialog gd = new GenericDialog(imp.getTitle()); gd.addMessage("Convert to multi-channel composite image?"); gd.showDialog(); if (gd.wasCanceled()) return; else IJ.doCommand("Make Composite"); } else { IJ.error( "Channels", "A composite image is required (e.g., " + moreLabel + " Open HeLa Cells),\nor create one using " + moreLabel + " Make Composite."); return; } } if (!imp.isComposite()) return; CompositeImage ci = (CompositeImage) imp; Object source = e.getSource(); if (source == choice) { int index = ((Choice) source).getSelectedIndex(); switch (index) { case 0: ci.setMode(IJ.COMPOSITE); break; case 1: ci.setMode(IJ.COLOR); break; case 2: ci.setMode(IJ.GRAYSCALE); break; } ci.updateAndDraw(); if (Recorder.record) { String mode = null; switch (index) { case 0: mode = "composite"; break; case 1: mode = "color"; break; case 2: mode = "grayscale"; break; } Recorder.record("Stack.setDisplayMode", mode); } } else if (source instanceof Checkbox) { for (int i = 0; i < checkbox.length; i++) { Checkbox cb = (Checkbox) source; if (cb == checkbox[i]) { if (ci.getMode() == IJ.COMPOSITE) { boolean[] active = ci.getActiveChannels(); active[i] = cb.getState(); if (Recorder.record) { String str = ""; for (int c = 0; c < ci.getNChannels(); c++) str += active[c] ? "1" : "0"; Recorder.record("Stack.setActiveChannels", str); Recorder.record("//Stack.toggleChannel", imp.getChannel()); } } else { imp.setPosition(i + 1, imp.getSlice(), imp.getFrame()); if (Recorder.record) Recorder.record("Stack.setChannel", i + 1); } ci.updateAndDraw(); return; } } } }
CompositeImage getImage() { ImagePlus imp = WindowManager.getCurrentImage(); if (imp == null || !imp.isComposite()) return null; else return (CompositeImage) imp; }