Micro-Manager beanshell script to get time interval between frames in a time series.

gistfile1.java

// Prints time intervals from most recently selected MDA data window.
//
// Reads "ElapsedTime-ms" property from image metadata to calculate
// image intervals. Sets first frame to 0 ms.
//
// One current limitation of the MM API (and therefore this script) is
// we to the most recently selected MDA data window (it's possible the
// user most recently selected the snap window or an ImageJ image
// window), so one has to prompt the user to select an MDA data
// window.  One could add a "getActiveAcquisitionName()" to the gui
// script API, and/or write an MM plugin that could e.g. refresh
// whenever the user selects an MDA data window.

// Preferences.
useHWTimestampIfAvailable = true;

// Find the current active window (can be MM MDA data, MM Snap/Live or
// ImageJ window).
import ij.WindowManager;
activeWindow = WindowManager.getActiveWindow();
if (activeWindow == null) {
   print("Error: No image window is open.  Please acquire or " +
     "open an image series.");
   return;
}
title = activeWindow.title;
print("Found most recently selected window \"" + title + "\".");

// Get number of time points (nFrames).
nFrames = activeWindow.getImagePlus().getNFrames();
// There is no easy way to get references to open MDA acquisitions, so
// we have to prompt the user to select an MDA data window (>_<).
if (nFrames == 1) {
   print("Error: Image window \"" + title + "\" should have at " +
     "least 2 time points to calculate frame intervals." +
     "  Please click on a valid MDA data window.");
   return;
}

// Get MM image cache.
cache = gui.getCacheForWindow(activeWindow);

// Prefer hardware timestamps if available.  The camera suppliers
// don't seem to define a consistent tag for this.  For now,  assume
// the hardware timestamp also contains "ElapsedTime-ms".
timestampSource = "builtin";
builtinTimestampTag = "ElapsedTime-ms";
timestampTag = builtinTimestampTag;
if (useHWTimestampIfAvailable) {
    keys = cache.getImageTags(0, 0, 0, 0).keys();
    for (k : keys)
        if(k.contains(builtinTimestampTag) && !k.equals(builtinTimestampTag)) {
            timestampTag = k;
            timestampSource = "hardware";
        }
}

// Get time of first image.
prevElapsedTime = cache.getImageTags(0, 0, 0, 0).get(timestampTag);

print("Reading " + timestampSource + " timestamps (Frame: Timestamp) ...");

parseAndorTimestamp(s) {
    // Andor cameras use a string format, which we have to work around:
    // Property="Neo 5.5 CL 3 Tap-ElapsedTime-ms"
    // Value="34.0011 [0.0340011 seconds]"
    spaceChar = s.indexOf(' ');
    s = s.substring(0, spaceChar);
    return Double.parseDouble(s);
}
if (prevElapsedTime.getClass().equals(String.class))
    prevElapsedTime = parseAndorTimestamp(prevElapsedTime);

// Get intervals between frames.
for (int i = 1; i < nFrames; i++) {
   elapsedTime = cache.getImageTags(0, 0, i, 0).get(timestampTag);
    if (elapsedTime.getClass().equals(String.class))
        elapsedTime = parseAndorTimestamp(elapsedTime);
    intervalTime = elapsedTime - prevElapsedTime;
   print(i + ": " + intervalTime);
   prevElapsedTime = elapsedTime;
}
print("Done.");