Re: XY Coords in a Stack and in Macro Problem with Variable File Location

Posted by Wayne Rasband on Apr 13, 2006; 7:30pm
URL: http://imagej.273.s1.nabble.com/XY-Coords-in-a-Stack-and-in-Macro-Problem-with-Variable-File-Location-tp3703086p3703087.html

You have to use string concatenation (the "+" operator) to pass
variables to commands called using the run() function. There is an
example at

     http://rsb.info.nih.gov/ij/macros/ArgumentPassingDemo.txt

-wayne

On Apr 13, 2006, at 6:57 AM, Brian Sellar wrote:

> Hello.
>
> I'm using the save XY coords on a stack of images in a macro
> and it works fine but only for a single stack. I'm trying to
> do a batch job since I have 25000 images per test so
> splitting the images into groups of 100 or so. Everything
> seems to be working fine (i don't get any error messages)
> but the XY coord command doesn't seem to like being given a
> Variable as its file location so doesn't write any ouput
> file on each loop of the macro. Any ideas. Am i missing
> something obvious. Thanks in advance for any help.
>
> Heres my macro.........
>
>
> ..............................................................
>
> for (n=0; n<1; n++) {
>
> run("Image
> Sequence...",
> "open=C:\\BGS\\FOOTAGE\\BGSTEST2VIDEO\\IMAGES\\NECESSARY\\Imag
> e00000.bmp number=10 starting="+(n*100)+2+" increment=1 scale=100
> file=");
>
> makeRectangle(20, 150, 680, 250);
> run("Crop");
>
> for (i=1; i<=nSlices; i++) {
>               run("Set Slice...", "slice="+i);
>           run("8-bit");
> run("Min...", "value=100");
> setThreshold(240, 255);
> run("Threshold", "thresholded remaining black");
> }
>
> setThreshold(240, 255);
> run("Threshold", "stack");
> run("Skeletonize", "stack");
>
> //This works but will just overwrite NECESSARY.txt each time
> run("Save XY Coordinates...", "process
> save=C:\\BGS\\FOOTAGE\\BGSTEST2VIDEO\\JPEGRESULTS\\NECESSARY.txt");
>
> LABEL0="C:\\BGS\\FOOTAGE\\BGSTEST2VIDEO\\JPEGRESULTS\\";
> LABEL1="Sequence"+n;
> LABEL2=LABEL0+LABEL1;
> LABEL3=LABEL2+".txt";
> // Prints Something Like
> C:\\BGS\\FOOTAGE\\BGSTEST2VIDEO\\JPEGRESULTS\\Sequence#(loop
> number).txt
> print(LABEL3);
>
> //Trying to save XY Coords on each loop of the macro.
>
> run("Save XY Coordinates...", "process save=LABEL3");
>
> }
>