I've tried using the fast filters plugin - http://imagejdocu.tudor.lu/doku.php?id=plugin:filter:fast_filters:start - by Michael Schmid. But when I integrated it with my own Java program, the results are different even when I used the same parameters I tried in the ImageJ software.
Are there other techniques should be done before feeding it to the plugin?
As far as I know the fast filters use a square or rectangular kernel.
The default ImageJ Filters use aproximate circular kernels.
You can view them under
Process -> Filters -> Show Circular Masks