Re: Apply bUnwarpJ in macro
Posted by nellypledge on May 10, 2016; 5:07pm
URL: http://imagej.273.s1.nabble.com/Apply-bUnwarpJ-in-macro-tp5016374p5016388.html
Hi Philippe, thanks for all your time taken to help me out on this.
Alas, I don't seem to be able to get your adapted plugin to work... I downloaded your jar file and moved it to the plugins folder of my Fiji folder. I didn't receive any errors on start, which I was a little surprised by as there is another plugin with the name UnwarpJ_-v2.0.0. When I attempted to apply the marco line to a simple test pair of images it didn't appear to do anything...
I then renamed the v2.0.0 plugin to have extension .jar.tmp and restarted. I then got errors regarding my path to the transform text file. It turns out that if I locate it in a folder and name without spaces it doesn't error and it provides the text out in the results window as follows:
Target image : trg.tif
Source image : src.tif
Transformation file : R://Code//transf.txt
Output : output
If I then overlay the trg and output image I see that the transform was not performed...? The beads are not overlapping as they should be. When I manually create the transform the beads shown in the first two channels of the UnwarpJ output do overlap.
Sorry to take up your time, but could you please look at the below to make sure I'm not mixed up with my macro steps?
Thanks
Neil
Test Macro:
selectWindow("20160509_Tetx60_2_MMStack_Pos0.ome.tif");
run("Duplicate...", "title=dup duplicate slices=1");
run("Split Channels");
selectWindow("C1-dup");
rename("src.tif");
selectWindow("C2-dup");
rename("trg.tif");
trans = "R://Code//transf.txt";
run("UnwarpJ ", "-transformMemory trg.tif src.tif " + trans + " output");
selectWindow("output");
run("16-bit");
run("Merge Channels...", "c1=trg.tif c2=output create keep ignore");