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);
}
public void run(String arg) {
ImagePlus image = WindowManager.getCurrentImage();
try {
Image3DUniverse univ = new Image3DUniverse();
univ.show();
GUI.center(univ.getWindow());
// only when there is an image and we are not called
// from a macro
if (image != null && !IJ.isMacro()) univ.getExecuter().addContent(image, null);
} catch (Exception e) {
StringBuffer buf = new StringBuffer();
StackTraceElement[] st = e.getStackTrace();
buf.append(
"An unexpected exception occurred. \n"
+ "Please mail me the following lines if you \n"
+ "need help.\n"
+ "[email protected]\n \n");
buf.append(e.getClass().getName() + ":" + e.getMessage() + "\n");
for (int i = 0; i < st.length; i++) {
buf.append(
" at "
+ st[i].getClassName()
+ "."
+ st[i].getMethodName()
+ "("
+ st[i].getFileName()
+ ":"
+ st[i].getLineNumber()
+ ")\n");
}
new ij.text.TextWindow("Error", buf.toString(), 500, 400);
}
}
/**
* Opens a single TIFF or DICOM contained in a ZIP archive, or a ZIPed collection of ".roi" files
* created by the ROI manager.
*/
public ImagePlus openZip(String path) {
ImagePlus imp = null;
try {
ZipInputStream zis = new ZipInputStream(new FileInputStream(path));
ZipEntry entry = zis.getNextEntry();
if (entry == null) {
zis.close();
return null;
}
String name = entry.getName();
if (name.endsWith(".roi")) {
zis.close();
if (!silentMode)
if (IJ.isMacro() && Interpreter.isBatchMode() && RoiManager.getInstance() == null)
IJ.log(
"Use roiManager(\"Open\", path) instead of open(path)\nto open ROI sets in batch mode macros.");
else IJ.runMacro("roiManager(\"Open\", getArgument());", path);
return null;
}
if (name.endsWith(".tif")) {
imp = openTiff(zis, name);
} else if (name.endsWith(".dcm")) {
DICOM dcm = new DICOM(zis);
dcm.run(name);
imp = dcm;
} else {
zis.close();
IJ.error(
"Opener",
"This ZIP archive does not appear to contain a \nTIFF (\".tif\") or DICOM (\".dcm\") file, or ROIs (\".roi\").");
return null;
}
zis.close();
} catch (Exception e) {
IJ.error("Opener", "" + e);
return null;
}
File f = new File(path);
FileInfo fi = imp.getOriginalFileInfo();
if (fi != null) {
fi.fileFormat = FileInfo.ZIP_ARCHIVE;
fi.fileName = f.getName();
fi.directory = f.getParent() + File.separator;
}
return imp;
}
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;
}
/**
* Opens and displays the specified tiff, dicom, fits, pgm, jpeg, bmp, gif, lut, roi, or text
* file. Displays an error message if the file is not in a supported format.
*
* @see ij.IJ#open(String)
* @see ij.IJ#openImage(String)
*/
public void open(String path) {
boolean isURL = path.indexOf("://") > 0;
if (isURL && isText(path)) {
openTextURL(path);
return;
}
if (path.endsWith(".jar") || path.endsWith(".class")) {
(new PluginInstaller()).install(path);
return;
}
boolean fullPath =
path.startsWith("/") || path.startsWith("\\") || path.indexOf(":\\") == 1 || isURL;
if (!fullPath) {
String defaultDir = OpenDialog.getDefaultDirectory();
if (defaultDir != null) path = defaultDir + path;
else path = (new File(path)).getAbsolutePath();
}
if (!silentMode) IJ.showStatus("Opening: " + path);
long start = System.currentTimeMillis();
ImagePlus imp = openImage(path);
if (imp == null && isURL) return;
if (imp != null) {
WindowManager.checkForDuplicateName = true;
if (isRGB48) openRGB48(imp);
else imp.show(getLoadRate(start, imp));
} else {
switch (fileType) {
case LUT:
imp = (ImagePlus) IJ.runPlugIn("ij.plugin.LutLoader", path);
if (imp.getWidth() != 0) imp.show();
break;
case ROI:
IJ.runPlugIn("ij.plugin.RoiReader", path);
break;
case JAVA_OR_TEXT:
case TEXT:
if (IJ.altKeyDown()) { // open in TextWindow if alt key down
new TextWindow(path, 400, 450);
IJ.setKeyUp(KeyEvent.VK_ALT);
break;
}
File file = new File(path);
int maxSize = 250000;
long size = file.length();
if (size >= 28000) {
String osName = System.getProperty("os.name");
if (osName.equals("Windows 95")
|| osName.equals("Windows 98")
|| osName.equals("Windows Me")) maxSize = 60000;
}
if (size < maxSize) {
Editor ed = (Editor) IJ.runPlugIn("ij.plugin.frame.Editor", "");
if (ed != null) ed.open(getDir(path), getName(path));
} else new TextWindow(path, 400, 450);
break;
case OJJ: // ObjectJ project
IJ.runPlugIn("ObjectJ_", path);
break;
case TABLE: // ImageJ Results table
openResultsTable(path);
break;
case RAW:
IJ.runPlugIn("ij.plugin.Raw", path);
break;
case UNKNOWN:
String msg =
"File is not in a supported format, a reader\n"
+ "plugin is not available, or it was not found.";
if (path != null) {
if (path.length() > 64) path = (new File(path)).getName();
if (path.length() <= 64) {
if (IJ.redirectingErrorMessages()) msg += " \n " + path;
else msg += " \n \n" + path;
}
}
if (openUsingPlugins) msg += "\n \nNOTE: The \"OpenUsingPlugins\" option is set.";
IJ.wait(IJ.isMacro() ? 500 : 100); // work around for OS X thread deadlock problem
IJ.error("Opener", msg);
error = true;
break;
}
}
}