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
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
class BeadsImage:
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 subDict(self, adict, negDict):
tmpDict = dict()
for k, v in adict.items():
tmpDict[k] = adict[k] - negDict[k]
return tmpDict
def makeHoughCircles(self):
self.dicFname = self.beadsImg._getImageName(c=1)
(dic_orig, dic_cimg) = self.beadsImg._openImages(self.dicFname)
circles = self.beadsImg.findHoughCircles(dic_orig)
if not circles is None:
self.beadsImg.overLayHoughCircles_SVG(circles,
dic_cimg) #SVG FILE MADE
overLayFname, overCimg = self.beadsImg.overLayHoughCircles(
circles, dic_cimg, idx=1, putNbr=True)
self.beadsImg._saveImage(overLayFname + '.png', overCimg)
return circles
def makeAllLinePlots(self, allCircles, minRad=30):
(fl_orig, fl_cimg) = self.beadsImg._openImages(self.flFname, flag=-1)
allNormDeviation_dict = collections.defaultdict(list)
for i, circle in enumerate(allCircles[0]):
if circle[2] > minRad:
oneBead = Bead(circle, fl_orig, fl_cimg)
allNormLineProfiles_dict = oneBead.makeLineProfile()
meanProfile, stdevProfile = combineVal_dict(
allNormLineProfiles_dict)
(med, factor
), devMedian, normDevMedian = calcDevMed_dict(meanProfile)
shapeProfile = normDevMedian
if not self.isNeg:
diffShape = self.subDict(shapeProfile,
self.negShapeProfile)
reNorm = dict([(k, (v * factor) + med)
for k, v in diffShape.items()])
allNormDeviation_dict = appendDict(allNormDeviation_dict,
reNorm)
else:
allNormDeviation_dict = appendDict(allNormDeviation_dict,
shapeProfile)
imageLineProfile, stdevLineProfile = combineVal_dict(
allNormDeviation_dict)
return imageLineProfile, stdevLineProfile
class BeadsImage:
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 subDict(self,adict,negDict):
tmpDict = dict()
for k,v in adict.items():
tmpDict[k] = adict[k] - negDict[k]
return tmpDict
def makeHoughCircles(self):
self.dicFname = self.beadsImg._getImageName(c=1)
(dic_orig, dic_cimg) = self.beadsImg._openImages(self.dicFname)
circles = self.beadsImg.findHoughCircles(dic_orig)
if not circles is None:
self.beadsImg.overLayHoughCircles_SVG(circles,dic_cimg)#SVG FILE MADE
overLayFname, overCimg = self.beadsImg.overLayHoughCircles(circles,dic_cimg,idx=1,putNbr= True)
self.beadsImg._saveImage(overLayFname+'.png', overCimg)
return circles
def makeAllLinePlots(self,allCircles,minRad=30):
(fl_orig,fl_cimg) = self.beadsImg._openImages(self.flFname,flag=-1)
allNormDeviation_dict = collections.defaultdict(list)
for i,circle in enumerate(allCircles[0]):
if circle[2]>minRad:
oneBead = Bead(circle,fl_orig,fl_cimg)
allNormLineProfiles_dict = oneBead.makeLineProfile()
meanProfile,stdevProfile = combineVal_dict(allNormLineProfiles_dict)
(med,factor), devMedian, normDevMedian = calcDevMed_dict(meanProfile)
shapeProfile = normDevMedian
if not self.isNeg:
diffShape = self.subDict(shapeProfile,self.negShapeProfile)
reNorm = dict([(k,(v*factor)+med) for k, v in diffShape.items()])
allNormDeviation_dict = appendDict(allNormDeviation_dict,reNorm)
else:
allNormDeviation_dict = appendDict(allNormDeviation_dict,shapeProfile)
imageLineProfile,stdevLineProfile = combineVal_dict(allNormDeviation_dict)
return imageLineProfile,stdevLineProfile