void setCalibration(ImagePlus imp) {
if (fi.fileType == FileInfo.GRAY16_SIGNED) {
if (IJ.debugMode) IJ.log("16-bit signed");
double[] coeff = new double[2];
coeff[0] = -32768.0;
coeff[1] = 1.0;
imp.getLocalCalibration().setFunction(Calibration.STRAIGHT_LINE, coeff, "gray value");
}
Properties props = decodeDescriptionString(fi);
Calibration cal = imp.getCalibration();
boolean calibrated = false;
if (fi.pixelWidth > 0.0 && fi.unit != null) {
cal.pixelWidth = fi.pixelWidth;
cal.pixelHeight = fi.pixelHeight;
cal.pixelDepth = fi.pixelDepth;
cal.setUnit(fi.unit);
calibrated = true;
}
if (fi.valueUnit != null) {
int f = fi.calibrationFunction;
if ((f >= Calibration.STRAIGHT_LINE && f <= Calibration.RODBARD2 && fi.coefficients != null)
|| f == Calibration.UNCALIBRATED_OD) {
boolean zeroClip = props != null && props.getProperty("zeroclip", "false").equals("true");
cal.setFunction(f, fi.coefficients, fi.valueUnit, zeroClip);
calibrated = true;
}
}
if (calibrated) checkForCalibrationConflict(imp, cal);
if (fi.frameInterval != 0.0) cal.frameInterval = fi.frameInterval;
if (props == null) return;
cal.xOrigin = getDouble(props, "xorigin");
cal.yOrigin = getDouble(props, "yorigin");
cal.zOrigin = getDouble(props, "zorigin");
cal.info = props.getProperty("info");
cal.fps = getDouble(props, "fps");
cal.loop = getBoolean(props, "loop");
cal.frameInterval = getDouble(props, "finterval");
cal.setTimeUnit(props.getProperty("tunit", "sec"));
double displayMin = getDouble(props, "min");
double displayMax = getDouble(props, "max");
if (!(displayMin == 0.0 && displayMax == 0.0)) {
int type = imp.getType();
ImageProcessor ip = imp.getProcessor();
if (type == ImagePlus.GRAY8 || type == ImagePlus.COLOR_256)
ip.setMinAndMax(displayMin, displayMax);
else if (type == ImagePlus.GRAY16 || type == ImagePlus.GRAY32) {
if (ip.getMin() != displayMin || ip.getMax() != displayMax)
ip.setMinAndMax(displayMin, displayMax);
}
}
int stackSize = imp.getStackSize();
if (stackSize > 1) {
int channels = (int) getDouble(props, "channels");
int slices = (int) getDouble(props, "slices");
int frames = (int) getDouble(props, "frames");
if (channels == 0) channels = 1;
if (slices == 0) slices = 1;
if (frames == 0) frames = 1;
// IJ.log("setCalibration: "+channels+" "+slices+" "+frames);
if (channels * slices * frames == stackSize) {
imp.setDimensions(channels, slices, frames);
if (getBoolean(props, "hyperstack")) imp.setOpenAsHyperStack(true);
}
}
}
/** Restores original disk or network version of image. */
public void revertToSaved(ImagePlus imp) {
Image img;
ProgressBar pb = IJ.getInstance().getProgressBar();
ImageProcessor ip;
String path = fi.directory + fi.fileName;
if (fi.fileFormat == fi.GIF_OR_JPG) {
// restore gif or jpg
img = Toolkit.getDefaultToolkit().createImage(path);
imp.setImage(img);
if (imp.getType() == ImagePlus.COLOR_RGB) Opener.convertGrayJpegTo8Bits(imp);
return;
}
if (fi.fileFormat == fi.DICOM) {
// restore DICOM
ImagePlus imp2 = (ImagePlus) IJ.runPlugIn("ij.plugin.DICOM", path);
if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
return;
}
if (fi.fileFormat == fi.BMP) {
// restore BMP
ImagePlus imp2 = (ImagePlus) IJ.runPlugIn("ij.plugin.BMP_Reader", path);
if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
return;
}
if (fi.fileFormat == fi.PGM) {
// restore PGM
ImagePlus imp2 = (ImagePlus) IJ.runPlugIn("ij.plugin.PGM_Reader", path);
if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
return;
}
if (fi.fileFormat == fi.ZIP_ARCHIVE) {
// restore ".zip" file
ImagePlus imp2 = (new Opener()).openZip(path);
if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
return;
}
// restore PNG or another image opened using ImageIO
if (fi.fileFormat == fi.IMAGEIO) {
ImagePlus imp2 = (new Opener()).openUsingImageIO(path);
if (imp2 != null) imp.setProcessor(null, imp2.getProcessor());
return;
}
if (fi.nImages > 1) return;
ColorModel cm;
if (fi.url == null || fi.url.equals("")) IJ.showStatus("Loading: " + path);
else IJ.showStatus("Loading: " + fi.url + fi.fileName);
Object pixels = readPixels(fi);
if (pixels == null) return;
cm = createColorModel(fi);
switch (fi.fileType) {
case FileInfo.GRAY8:
case FileInfo.COLOR8:
case FileInfo.BITMAP:
ip = new ByteProcessor(width, height, (byte[]) pixels, cm);
imp.setProcessor(null, ip);
break;
case FileInfo.GRAY16_SIGNED:
case FileInfo.GRAY16_UNSIGNED:
case FileInfo.GRAY12_UNSIGNED:
ip = new ShortProcessor(width, height, (short[]) pixels, cm);
imp.setProcessor(null, ip);
break;
case FileInfo.GRAY32_INT:
case FileInfo.GRAY32_FLOAT:
ip = new FloatProcessor(width, height, (float[]) pixels, cm);
imp.setProcessor(null, ip);
break;
case FileInfo.RGB:
case FileInfo.BGR:
case FileInfo.ARGB:
case FileInfo.ABGR:
case FileInfo.RGB_PLANAR:
img =
Toolkit.getDefaultToolkit()
.createImage(new MemoryImageSource(width, height, (int[]) pixels, 0, width));
imp.setImage(img);
break;
}
}