Re: Background substraction and LUT inconsitent on a folder

Posted by Krs5 on Feb 20, 2017; 4:57pm
URL: http://imagej.273.s1.nabble.com/Background-substraction-and-LUT-inconsitent-on-a-folder-tp5018144p5018148.html

I noticed that there is an overlay on your images. If I remove the overlay I can save with the new LUT or for example as 16-bit, what also does not seem to work for your images.

Not sure if this is intended behaviour...

Kees

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Eric Denarier
Sent: 20 February 2017 13:34
To: [hidden email]
Subject: Background substraction and LUT inconsitent on a folder

Hi All,
With the following code several of the images (image size 356ko) of a folder are saved with their original color instead of beeing all orange.
Any suggestion ?


It may seem that adding a wait(100); after run ("Orange Hot"); is working

but then how to know what should be the "wait" value???

Is there an other way to fix the problem ??


enclosed two files for a test.

Thanks for your help


I used Both FIJI : image2 2.0.0-rc-56/1.51h
and ImageJ 1.51i5
on Windows7 with the same problems


Thank you


/////////// Code here //////////

inputDir = getDirectory("Choose Source Directory ");
outputDir = getDirectory("Choose Destination Directory ");
list = getFileList(inputDir);

for (k=0; k<list.length; k++) {
open(inputDir +list[k]);

run ("Subtract Background...", "rolling=100");
run( "Orange Hot", "");
saveAs("Jpeg", outputDir +list[k]);
close(); }

--

Eric Denarier
Grenoble Institut des Neurosciences
Inserm U1216
Chemin Fortuné Ferrini
38700 La Tronche
France

Tél :[phone]

http://neurosciences.ujf-grenoble.fr/


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