add resolution calibration function and export

calibrate.ijm

+//Batch macro to set spatial and temporal resolution of supplied tiff stacks
+//Arguments are:
+//  frame-interval frame-unit xy-pixelsize xy-unit file1 file2 ...
+//  (apparently file path must be absolute)
+
+//This macro can be called in Fiji's headless mode e.g.
+// fiji --headless -macro /path-to-macro.ijm /path-to-file.tif
+// or by runMacro(macro, arg)
+
+arguments = split(getArgument());
+tInterval = parseFloat(arguments[0]);
+tUnit = arguments[1];
+xySize = parseFloat(arguments[2]);
+xyUnit = arguments[3];
+fileList = Array.slice(arguments,4);
+
+if (isNaN(tInterval)) { exit("Frame interval is not a valid number."); }
+
+setBatchMode(true);
+for (i = 0; i < fileList.length; i++) {
+    open(fileList[i]);
+
+    //processing steps
+    Stack.setFrameInterval(tInterval);
+    Stack.setTUnit(tUnit);
+    setVoxelSize(xySize, xySize, xySize, xyUnit);
+
+    save(fileList[i]);
+    close();
+}
+setBatchMode(false);

exportAvi.ijm

 //Batch macro to export avi files from supplied tiff stacks.
+// Also prints scale bar and time stamp onto the video.
 // Arguments string should be a list of absolute file paths to process.
 
 //This macro can be called in Fiji's headless mode e.g.
@@ -7,6 +8,10 @@
 
 outExtension = ".avi";
 frameRate = 20;
+barWidth = 2; //µm
+barHeight = 4; //px
+tUnit = "";
+tInterval = 1;
 
 fileList = split(getArgument());
 
@@ -31,7 +36,16 @@ for (i = 0; i < fileList.length; i++) {
 
     //processing steps
     //frameRate = Stack.getFrameRate();
+    Stack.getUnits(xUnit, yUnit, zUnit, tUnit, vUnit);
+    tInterval = Stack.getFrameInterval();
+    print("frame= "+tInterval+" "+tUnit);
+    getVoxelSize(x, y, z, u); print("vx size= "+x+"x"+y+"x"+z+" "+u);
     run("8-bit");
+    run("Scale Bar...", "width="+barWidth+" height="+barHeight+" font=12 color=White background=None location=[Lower Right] bold label");
+    if (tInterval > 0) {
+        run("Time Stamper", "starting=0 interval="+tInterval+" x=2 y=15 font=12 decimal=0 anti-aliased or="+tUnit);
+        print("muh");
+    }
     run("AVI... ", "compression=JPEG frame="+frameRate+" save="+outFile);
 
     close();