#!/usr/bin/env jython

from ij import IJ
import os

from mpicbg.ij.clahe import Flat
from ij.process import ImageConverter

# http://fiji.sc/wiki/index.php/Enhance_Local_Contrast_(CLAHE)
# http://fiji.sc/cgi-bin/gitweb.cgi?p=mpicbg.git;a=blob;f=mpicbg/ij/clahe/PlugIn.java;h=663153764493547de560c08ee11f2e6b1e7e1a32;hb=HEAD

dir = "/usr/people/tmacrina/Desktop/test/"

blocksize = 50
histogram_bins = 128
maximum_slope = 3
mask = "*None*"
composite = False
mask = None

files = os.listdir(dir)
files.sort()
for file in files:
     if file.endswith(".tif")
          fn = os.path.join(dir, file)
          imp = IJ.openImage(path)
          output_fn = os.path.splitext(fn)[0] + "_CLAHE_8bit.tif"
          imp = IJ.openImage(fn)
            
          Flat.getFastInstance().run( imp, 
                                  blocksize,
                                  histogram_bins,
                                  maximum_slope,
                                  mask,
                                  composite )
          ImageConverter(imp).convertToGray8()

          IJ.save(imp, output_fn)

Add script to CLAHE images in a directory via FIJI
Add script to CLAHE images in a directory via FIJI
