import jmFijiGen as jmg
homDir = os.environ['HOME']
edsDir = os.environ['EDS_ROOT']
ePrjDir = "QM14-04-04D1-Steele"
sampID = "qm-04227-49G003-456-R-15-FIB"
mapID = "7kV-map4"
datDir = "/Oxford/" + ePrjDir + "/reports/" + sampID + "/" + sampID + "-" + mapID
relWrk = datDir + "/work"
wrkDir = edsDir + relWrk
strROI = wrkDir + "/" + "ROI.png"
impRoi = IJ.openImage(strROI)
lName = ["O-K","Cu-L", "P-K", "Pd-L", "Ag-L"]
for name in lName:
strImg = wrkDir + "/" + name +".png"
impExp = IJ.openImage(strImg)
impOvr = jmg.makeFlattenedTransparentOverlay(impRoi, impExp, op=50)
impOvr.show()
strImg = wrkDir + "/" + name +"-ROI.png"
if os.access(strImg, os.R_OK):
os.remove(strImg)
IJ.saveAs(impOvr, "PNG", strImg)
impOvr.close()
# testHeadlessFlatten.py import os from ij import IJ import jmFijiGen as jmg imgDir = os.environ['IMG_ROOT'] edsDir = os.environ['EDS_ROOT'] relDir = "/Oxford/QM14-nn-nnA-Client/reports/qm-nnnnn-sampleID/qm-nnnnn-sampleID-nnkV-map1/work" inDir = edsDir + relDir pthRoi = inDir + "/ROI.png" pthCuL = inDir + "/Cu-L.png" impRoi = IJ.openImage(pthRoi) impCuL = IJ.openImage(pthCuL) # headlessFlatten is built into jmg.makeFlattenedTransparentOverlay impTol = jmg.makeFlattenedTransparentOverlay(impRoi, impCuL, op=50) # flat = headlessFlatten(impTol) impTol.show() outPth = imgDir + "/tmp/foo-fl.png" IJ.saveAs(impTol, "PNG", outPth) # imp.show() # impRoi.show()