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("");
}