imgDir = os.environ['IMG_ROOT']
relImg = "/test/efi-test/bez-50X-1"
# strImg = gitDir + relImg + "/bridge.gif"
strImg = imgDir + relImg + "/out/bez-50X-1-ij-edf.tif"
print(strImg)
strFF = imgDir + relImg + "/ff/gain.tif"
# 1. Open an image and it's flat field
impExp = IJ.openImage(strImg)
name = impExp.getShortTitle()
impExp.show()
impBkg = IJ.openImage(strFF)
impSc = jmg.flatFieldCorrectRGB(impExp, impBkg)
impSc.show()
name = name + "-sc"
impSc.setTitle(name)
strImg = imgDir + relImg + "/out/" + name + ".tif"
IJ.saveAs("Tiff", strImg)
# flatFieldCorrect2.py
#
# Modifications
# Date Who Ver What
# ---------- --- ------ -------------------------------------------------
# 2014-11-26 JRM 0.1.00 Test function in jmFijiGen.py
from org.python.core import codecs
codecs.setDefaultEncoding('utf-8')
import os
from ij import IJ
import jmFijiGen as jmg
impImg = IJ.openImage("D:\\Data\\eds\\Oxford\\QM14-04-04E-Steele\\reports\\BX61\\qm-04229-49U003-922-Row-2-Bus-Line\\qm-04229-efi-20X-1.tif")
impFF = IJ.openImage("D:\\Data\\eds\\Oxford\\QM14-04-04E-Steele\\reports\\BX61\\qm-04229-49U003-922-Row-2-Bus-Line\\qm-04229-20x-1p6-col-pap-shade.tif")
impCor = jmg.flatFieldCorrectRGB(impImg, impFF, sigma=100)
impCor.show()
