Re: PSF Generator in headless or macro

Posted by Daniel Sage on
URL: http://imagej.273.s1.nabble.com/PSF-Generator-in-headless-or-macro-tp5011899p5011901.html

Pen,

You can prepare a configuration file (.txt) that contains all the parameters of your PSF and run the following commands:

from the terminal: java -cp PSFGenerator.jar PSFGenerator config.txt
from the Matlab console: psf = PSFGenerator.compute('config.txt');

See the example below:

dsage:PSF dsage$ ls -l
-rw-r--r--   2532894 18 jul  2014 PSFGenerator.jar
-rw-r--r--       141  5 mar 23:29 config.txt

dsage:PSF dsage$ more config.txt
Lambda=610.0
LUT=Fire
NA=1.4
NX=256
NY=256
NZ=32
ResAxial=250.0
ResLateral=100.0
Scale=Linear
Type=double
psf-BW-accuracy=Good
psf-BW-NI=1.5

dsage:PSF dsage$ java -cp PSFGenerator.jar PSFGenerator config.txt
Computing BW
Save PSF BW

dsage:PSF dsage$ ls -l
-rw-r--r--    8393128  5 mar 23:30 PSF BW.tif
-rw-r--r--   2532894 18 jul  2014 PSFGenerator.jar
-rw-r--r--       141  5 mar 23:29 config.txt

At the end of the computation you get a PSF_BW.tif file containing the required PSF.

Best,

Daniel

> Hi,
>
> I was using the PSF generator from here:
>
> http://bigwww.epfl.ch/algorithms/psfgenerator/
>
> and was wondering if anyone knew if batch or macro is supported. If not,
> does anyone have any suggestions for a PSF generator that does support it
> since I have image stacks (3D) of different size which will need an
> individual PSF for each image.
>
> Thanks!
>
>
>
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