Strange File Save Behavior with ImageJ - imagej

Question

I wrote an imageJ script to color and merge a series of black and white images. The script saves both the unmerged colored images and merged colored images. Everything works beautifully when I'm running in debug mode and step through the script. When I run it for real, however, it occasionally saves a couple of the original black and whites instead of the resulting colored image. All the merged images appear to be fine.
Why would everything work fine in debug mode but fail during regular usage?
Below is my code :
// Choose the directory with the images
dir = getDirectory("Choose a Directory ");
// Get a list of everything in the directory
list = getFileList(dir);
// Determine if a composite directory exists. If not create one.
if (File.exists(dir+"/composite") == 0) {
File.makeDirectory(dir+"/composite")
}
// Determine if a colored directory exists. If not create one.
if (File.exists(dir+"/colored") == 0) {
File.makeDirectory(dir+"/colored")
}
// Close all files currently open to be safe
run("Close All");
// Setup options
setOption("display labels", true);
setBatchMode(false);
// Counter 1 keeps track of if you're on the first or second image of the tumor/vessel pair
count = 1;
// Counter 2 keeps track of the number of pairs in the folder
count2 = 1;
// Default Radio Button State
RadioButtonDefault = "Vessel";
// Set Default SatLevel for Contrast Adjustment
// The contrast adjustment does a histogram equalization. The Sat Level is a percentage of pixels that are allowed to saturate. A larger number means more pixels can saturate making the image appear brighter.
satLevelDefault = 2.0;
// For each image in the list
for (i=0; i<list.length; i++) {
// As long as the name doesn't end with / or .jpg
if (endsWith(list[i], ".tif")) {
// Define the full path to the filename
fn = list[i];
path = dir+list[i];
// Open the file
open(path);
// Create a dialog box but don't show it yet
Dialog.create("Image Type");
Dialog.addRadioButtonGroup("Type:", newArray("Vessel", "Tumor"), 1, 2, RadioButtonDefault)
Dialog.addNumber("Image Brightness Adjustment", satLevelDefault, 2, 4, "(applied only to vessel images)")
// If it's the first image of the pair ...
if (count == 1) {
// Show the dialog box
Dialog.show();
// Get the result and put it into a new variable and change the Default Radio Button State for the next time through
if (Dialog.getRadioButton=="Vessel") {
imgType = "Vessel";
RadioButtonDefault = "Tumor";
} else {
imgType = "Tumor";
RadioButtonDefault = "Vessel";
}
// If it's the second image of the pair
} else {
// And the first image was a vessel assume the next image is a tumor
if (imgType=="Vessel") {
imgType="Tumor";
// otherwise assume the next image is a vessel
} else {
imgType="Vessel";
}
}
// Check to see the result of the dialog box input
// If vessel do this
if (imgType=="Vessel") {
// Make image Red
run("Red");
// Adjust Brightness
run("Enhance Contrast...", "saturated="+Dialog.getNumber+" normalize");
// Strip the .tif off the existing filename to use for the new filename
fnNewVessel = replace(fn,"\\.tif","");
// Save as jpg
saveAs("Jpeg", dir+"/colored/"+ fnNewVessel+"_colored");
// Get the title of the image for the merge
vesselTitle = getTitle();
// Othersie do this ...
} else {
// Make green
run("Green");
// Strip the .tif off the existing filename to use for the new filename
fnNewTumor = replace(fn,"\\.tif","");
// Save as jpg
saveAs("Jpeg", dir+"/colored/"+ fnNewTumor+"_colored");
// Get the title of the image for the merge
tumorTitle = getTitle();
}
// If it's the second in the pair ...
if (count == 2) {
// Merge the two images
run("Merge Channels...", "c1="+vesselTitle+" c2="+tumorTitle+" create");
// Save as Jpg
saveAs("Jpeg", dir+"/composite/composite_"+count2);
// Reset the number within the pair counter
count = count-1;
// Increment the number of pairs counter
count2 = count2+1;
// Otherwise
} else {
// Increment the number within the pair counter
count += 1;
}
}
}

Answer 1

Not sure why I'd need to do this but adding wait(100) immediately before saveAs() seems to do the trick

Answer 2

The best practice in this scenario would be to poll IJ.macroRunning(). This method will return true if a macro is running. I would suggest using helper methods that can eventually time out, like:
/** Run with default timeout of 30 seconds */
public boolean waitForMacro() {
return waitForMacro(30000);
}
/**
* #return True if no macro was running. False if a macro runs for longer than
* the specified timeOut value.
*/
public boolean waitForMacro(final long timeOut) {
final long time = System.currentTimeMillis();
while (IJ.macroRunning()) {
// Time out after 30 seconds.
if (System.currentTimeMillis() - time > timeOut) return false;
}
return true;
}
Then call one of these helper methods whenever you use run(), open(), or newImage().
Another direction that may require more work, but provide a more robust solution, is using ImageJ2. Then you can run things with a ThreadService, which gives you back a Java Future which can then guarantee execution completion.