turboReg in batch mode

Posted by C.Oldfield on
URL: http://imagej.273.s1.nabble.com/turboReg-in-batch-mode-tp5008351.html

Hi everyone,

I am writing a macro using turboReg to regsiter every frame of a time series to the average image of that series. Can I call turboReg on the whole batch of images from the time series, or do I have to run turboReg on every single frame?

When I use the turboReg plugin from the GUI, there is a "batch" button which performs the operation I'm looking for, but I don't know how to code it into the macro.

Thanks!!

Claire

This is my code so far:
run("TurboReg ",
        "-align " // Register the two images that we have just prepared.
        + "-window " + sourceName + " "// Source (window reference).
        + "0 0 " + (width - 1) + " " + (height - 1) + " " // No cropping.
        + "-window " + targetName + " "// Target (file reference).
        + "0 0 " + (width - 1) + " " + (height - 1) + " " // No cropping.
        + "-affine "
        + (width / 2) + " " + (height / 2) + " " // Source translation landmark.
        + (width / 2) + " " + (height / 2) + " " // Target translation landmark.
        + "0 " + (height / 2) + " " // Source first rotation landmark.
        + "0 " + (height / 2) + " " // Target first rotation landmark.
        + (width - 1) + " " + (height / 2) + " " // Source second rotation landmark.
        + (width - 1) + " " + (height / 2) + " " // Target second rotation landmark.
        + "-showOutput");