private Double getNumber(Properties props, String key) {
String s = props.getProperty(key);
if (s != null) {
try {
return Double.valueOf(s);
} catch (NumberFormatException e) {
}
}
return null;
}
public Properties decodeDescriptionString(FileInfo fi) {
if (fi.description == null || fi.description.length() < 7) return null;
if (IJ.debugMode) IJ.log("Image Description: " + new String(fi.description).replace('\n', ' '));
if (!fi.description.startsWith("ImageJ")) return null;
Properties props = new Properties();
InputStream is = new ByteArrayInputStream(fi.description.getBytes());
try {
props.load(is);
is.close();
} catch (IOException e) {
return null;
}
fi.unit = props.getProperty("unit", "");
Double n = getNumber(props, "cf");
if (n != null) fi.calibrationFunction = n.intValue();
double c[] = new double[5];
int count = 0;
for (int i = 0; i < 5; i++) {
n = getNumber(props, "c" + i);
if (n == null) break;
c[i] = n.doubleValue();
count++;
}
if (count >= 2) {
fi.coefficients = new double[count];
for (int i = 0; i < count; i++) fi.coefficients[i] = c[i];
}
fi.valueUnit = props.getProperty("vunit");
n = getNumber(props, "images");
if (n != null && n.doubleValue() > 1.0) fi.nImages = (int) n.doubleValue();
if (fi.nImages > 1) {
double spacing = getDouble(props, "spacing");
if (spacing != 0.0) {
if (spacing < 0) spacing = -spacing;
fi.pixelDepth = spacing;
}
}
return props;
}
private boolean getBoolean(Properties props, String key) {
String s = props.getProperty(key);
return s != null && s.equals("true") ? true : false;
}
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);
}
}
}