[ImageJ-bugs] [Bug 1171] batch mode not working

[bugzilla at fiji.sc]

http://fiji.sc/bugzilla/show_bug.cgi?id=1171

Wayne Rasband <wsr at nih.gov> changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEEDSINFO                   |RESOLVED
         Resolution|---                         |FIXED

--- Comment #7 from Wayne Rasband <wsr at nih.gov> ---
Here is a version of your macro that should work better. I marked the changes
with "//**".

dir = getDirectory("Choose Sorce Directory"); //with slash at the end
dir2 = getDirectory("Choose Destination Directory");
acq = getFileList(dir);
setBatchMode(true); 
for (i=0; i<acq.length; i++) {
    if (endsWith(acq[i], "tif")) {
        open(dir+acq[i]);
        run("Make Composite");
        run("Split Channels");
        close("C3-"+acq[i]);
        imageCalculator("Subtract stack", "C2-"+acq[i], "C1-"+acq[i]);
        //Save Z-projection of 169
        selectWindow("C2-"+acq[i]);
        run("Despeckle", "stack");   //**
        run("Z Project...", "projection=[Average Intensity]");
        selectWindow("AVG_C2-"+acq[i]);
        path = dir2+"Zproj-169-BGsubtr-"+acq[i]; //**
        run("Save", "save=&path"); //**
        close("AVG_C2-"+acq[i]);
        //Save Z-projection of SHG
        selectWindow("C4-"+acq[i]);
        run("Despeckle", "stack"); //**
        run("Z Project...", "projection=[Average Intensity]");
        selectWindow("AVG_C4-"+acq[i]);
        path = dir2+"Zproj-SHG-BGsubtr-"+acq[i]; //**
        run("Save", "save=&path"); //**
        close("*");
    }
}

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