http://imagej.273.s1.nabble.com/Writing-a-macro-to-save-image-stack-as-series-of-separate-files-tp5009571p5009572.html
In order for newFileName to be recognised as a variable inside this string, you need to write it as
run("Image Sequence... ", "format=TIFF name="+newFileName+" start=0 digits=3
Note the "+ before the variable and the +" after the variable - this will insert the content of your variable into the string.
I assume firstPlaneName at the end of that command is also a varibale. So, you will have to add "+ before that variable name as well. You don't need a +" at the end as there is no more text to be added to that string.
brackets. For more examples, see theArgumentPassingDemo
> Hi, I'm trying to write a macro to open image stacks, manually look at them
> and adjust brightness/contrast, then save as a series of separate files,
> each in its own folder. The way the files are named is not flexible because
> they have to be named in a certain way to feed into another Matlab program
> that is already written. Here is the code I have:
>
>
> function prepareForMatlab(input, output, filename) {
> setBatchMode(false);
> open(input + filename);
> run("Brightness/Contrast...");
> waitForUser('Adjust brightness and contrast');
> run("Close"); //The filename is automatically extracted but we have to
> modify this to get it without the extension
> name = getTitle; //Includes .tif
> dotIndex = indexOf(name, ".");
> title = substring(name, 0, dotIndex); //name without the extension
> mouseAndRegionNumber = substring(output,33); //Extracts the mouse and
> region number, in this case delta_1. Will change if file structure changes
> print(mouseAndRegionNumber);
> newFileName = mouseAndRegionNumber + "_" + title + "_";
> print(newFileName);
> firstPlaneName = output + "/" + title + "/";
> print(firstPlaneName);
> run("Image Sequence... ", "format=TIFF name=newFileName start=0 digits=3
> save=firstPlaneName");
>
> run("Close All");
> }
>
> input = "/C:/.../Raw/"; //Here i've omitted some directories with a ... just
> for the purpose of posting this question
> output = "/C:/.../delta_1";
>
> list = getFileList(input);
> for (i = 0; i < list.length; i++){
> setBatchMode(false);
> prepareForMatlab(input, output, list[i]);
> }
>
>
> I know this code is probably not the most elegant way to do this (accepting
> suggestions on that as well!) but the problem I'm having now is that in the
> line
> run("Image Sequence... ", "format=TIFF name=newFileName start=0 digits=3
> save=firstPlaneName")
> newFileName is not treated as a variable with a string value but rather as a
> string itself (so all the files end up having the word newFileName in them).
> How do I fix this?
>
> This code also has another weird problem where the images open one by one
> and allow the user to move the sliders to see different z planes and then
> adjust brightness/contrast. This works fine unless you try to switch back
> and forth between toggling z planes and toggling brightness. (Then the macro
> gives and error "no image open") No idea why this would happen...it works
> fine if you do one and then the other, just not if you switch back and
> forth.
>
> Any help would be greatly appreciated!!!
>
>
>
> --
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>
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