void runMacro(String arg) { Roi roi = imp.getRoi(); if (IJ.macroRunning()) { String options = Macro.getOptions(); if (options != null && (options.indexOf("grid=") != -1 || options.indexOf("interpolat") != -1)) { IJ.run("Rotate... ", options); // run Image>Transform>Rotate return; } } if (roi == null) { noRoi("Rotate>Selection"); return; } roi = (Roi) roi.clone(); if (arg.equals("rotate")) { double d = Tools.parseDouble(angle); if (Double.isNaN(d)) angle = "15"; String value = IJ.runMacroFile("ij.jar:RotateSelection", angle); if (value != null) angle = value; } else if (arg.equals("enlarge")) { String value = IJ.runMacroFile("ij.jar:EnlargeSelection", enlarge); if (value != null) enlarge = value; Roi.previousRoi = roi; } }
void lineToArea(ImagePlus imp) { Roi roi = imp.getRoi(); if (roi == null || !roi.isLine()) { IJ.error("Line to Area", "Line selection required"); return; } Undo.setup(Undo.ROI, imp); Roi roi2 = null; if (roi.getType() == Roi.LINE) { double width = roi.getStrokeWidth(); if (width <= 1.0) roi.setStrokeWidth(1.0000001); FloatPolygon p = roi.getFloatPolygon(); roi.setStrokeWidth(width); roi2 = new PolygonRoi(p, Roi.POLYGON); roi2.setDrawOffset(roi.getDrawOffset()); } else { ImageProcessor ip2 = new ByteProcessor(imp.getWidth(), imp.getHeight()); ip2.setColor(255); roi.drawPixels(ip2); // new ImagePlus("ip2", ip2.duplicate()).show(); ip2.setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE); ThresholdToSelection tts = new ThresholdToSelection(); roi2 = tts.convert(ip2); } transferProperties(roi, roi2); roi2.setStrokeWidth(0); Color c = roi2.getStrokeColor(); if (c != null) // remove any transparency roi2.setStrokeColor(new Color(c.getRed(), c.getGreen(), c.getBlue())); imp.setRoi(roi2); Roi.previousRoi = (Roi) roi.clone(); }
// 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; }
private void enlarge(ImagePlus imp) { Roi roi = imp.getRoi(); if (roi != null) { Undo.setup(Undo.ROI, imp); roi = (Roi) roi.clone(); (new RoiEnlarger()).run(""); } else noRoi("Enlarge"); }
// Added by Marcel Boeglin 2013.09.23 private Overlay projectStackRois(Overlay overlay) { if (overlay == null) return null; Overlay overlay2 = new Overlay(); Roi roi; int s; for (Roi r : overlay.toArray()) { s = r.getPosition(); roi = (Roi) r.clone(); if (s >= startSlice && s <= stopSlice || s == 0) { roi.setPosition(s); overlay2.add(roi); } } return overlay2; }
void lineToArea(ImagePlus imp) { Roi roi = imp.getRoi(); if (roi == null || !roi.isLine()) { IJ.error("Line to Area", "Line selection required"); return; } ImageProcessor ip2 = new ByteProcessor(imp.getWidth(), imp.getHeight()); ip2.setColor(255); if (roi.getType() == Roi.LINE && roi.getStrokeWidth() > 1) ip2.fillPolygon(roi.getPolygon()); else roi.drawPixels(ip2); // new ImagePlus("ip2", ip2.duplicate()).show(); ip2.setThreshold(255, 255, ImageProcessor.NO_LUT_UPDATE); ThresholdToSelection tts = new ThresholdToSelection(); Roi roi2 = tts.convert(ip2); imp.setRoi(roi2); Roi.previousRoi = (Roi) roi.clone(); }
// 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; }
void runMacro(String arg, ImagePlus imp) { boolean rotate = arg.equals("rotate"); Roi roi = imp.getRoi(); if (rotate && IJ.macroRunning()) { String options = Macro.getOptions(); if (options != null && (options.indexOf("grid=") != -1 || options.indexOf("interpolat") != -1)) { IJ.run("Rotate... ", options); // run Image>Transform>Rotate return; } } if (roi == null) { noRoi(rotate ? "Rotate" : "Enlarge"); return; } double dangle = Tools.parseDouble(angle); if (Double.isNaN(dangle)) { dangle = 15; angle = "" + dangle; } if (rotate && (roi instanceof ImageRoi)) { dangle = IJ.getNumber("Angle (degrees):", dangle); ((ImageRoi) roi).rotate(dangle); imp.draw(); angle = "" + dangle; return; } Undo.setup(Undo.ROI, imp); roi = (Roi) roi.clone(); if (rotate) { String value = IJ.runMacroFile("ij.jar:RotateSelection", angle); Roi roi2 = imp.getRoi(); transferProperties(roi, roi2); imp.setRoi(roi2); if (value != null) angle = value; } else if (arg.equals("enlarge")) (new RoiEnlarger()).run(""); }