def __init__(self, subDir, pathDir, flChannel=4, isNeg=False):
self.subDir = subDir
self.pathDir = pathDir
self.isNeg = isNeg
if not self.isNeg:
negF = '/project/current/project/jagannath/projectfiles/EpiMicroscopy/rawFiles/2014-Oct/2014-10-17/rawImages/negShape.pkl'
self.negShapeProfile = pickle.load(open(negF))
self.beadsImg = BeadExpt(self.subDir, self.pathDir)
self.dicFname = self.beadsImg._getImageName(c=1)
self.flFname = self.beadsImg._getImageName(
c=flChannel) #Fluorescent channel
def getCircles(subDir, maskSource='DIC'):
expt = BeadExpt(subDir, pathDir)
imageDir = expt.imageDir
if maskSource is 'DIC':
dyeImage = expt._getImageName(1)
else:
dyeImage = expt._getImageName(4)
orig, cimg = expt._openImages(dyeImage)
circles = expt.findHoughCircles(orig)
orig, cimg = expt._openImages(expt._getImageName(4), -1)
return circles, orig, cimg