def compareClassesStep(self, i1, i2):
set1 = self.inputClasses1.get()
set2 = self.inputClasses2.get()
# Compare each pair of class from set1 and set2
# compute the Jaccard index for each (J = len(intersection) / len(union))
# Create a list will all pairs indexes and the sort them
jaccardList = []
f = open(self._getPath('jaccard.txt'), 'w')
f.write(
'; class1 class2 intersection(i) union(i) jaccard index = len(i)/len(u)\n'
)
for cls1 in set1:
ids1 = cls1.getIdSet()
for cls2 in set2:
ids2 = cls2.getIdSet()
inter = len(ids1.intersection(ids2))
union = len(ids1.union(ids2))
jaccardIndex = float(inter) / union
jaccardTuple = (cls1.getObjId(), cls2.getObjId(), inter, union,
jaccardIndex)
f.write('%d %d %d %d %0.3f\n' % jaccardTuple)
jaccardList.append(jaccardTuple)
f.close()
jaccardList.sort(key=lambda e: e[4], reverse=True)
visitedClasses = set()
outputFn = self._getPath('consensus.sqlite')
cleanPath(outputFn)
outputSet = EMSet(filename=outputFn)
for clsId1, clsId2, inter, union, jaccardIndex in jaccardList:
if clsId1 not in visitedClasses:
visitedClasses.add(clsId1) # mark as visited
cls1 = set1[clsId1]
cls2 = set2[clsId2]
o = Object()
o.setObjLabel('classes %d - %d' % (clsId1, clsId2))
o.class1 = cls1.clone()
o.class1.id = Integer(clsId1)
o.class2 = cls2.clone()
o.class2.id = Integer(clsId2)
o.jaccard = Float(jaccardIndex)
o.intersection = Integer(inter)
o.union = Integer(union)
outputSet.append(o)
self._defineOutputs(outputConsensus=outputSet)
def compareClassesStep(self, i1, i2):
set1 = self.inputClasses1.get()
set2 = self.inputClasses2.get()
# Compare each pair of class from set1 and set2
# compute the Jaccard index for each (J = len(intersection) / len(union))
# Create a list will all pairs indexes and the sort them
jaccardList = []
f = open(self._getPath('jaccard.txt'), 'w')
f.write('; class1 class2 intersection(i) union(i) jaccard index = len(i)/len(u)\n')
for cls1 in set1:
ids1 = cls1.getIdSet()
for cls2 in set2:
ids2 = cls2.getIdSet()
inter = len(ids1.intersection(ids2))
union = len(ids1.union(ids2))
jaccardIndex = float(inter) / union
jaccardTuple = (cls1.getObjId(), cls2.getObjId(), inter, union, jaccardIndex)
f.write('%d %d %d %d %0.3f\n' % jaccardTuple)
jaccardList.append(jaccardTuple)
f.close()
jaccardList.sort(key=lambda e: e[4], reverse=True)
visitedClasses = set()
outputFn = self._getPath('consensus.sqlite')
cleanPath(outputFn)
outputSet = EMSet(filename=outputFn)
for clsId1, clsId2, inter, union, jaccardIndex in jaccardList:
if clsId1 not in visitedClasses:
visitedClasses.add(clsId1) # mark as visited
cls1 = set1[clsId1]
cls2 = set2[clsId2]
o = Object()
o.setObjLabel('classes %d - %d' % (clsId1, clsId2))
o.class1 = cls1.clone()
o.class1.id = Integer(clsId1)
o.class2 = cls2.clone()
o.class2.id = Integer(clsId2)
o.jaccard = Float(jaccardIndex)
o.intersection = Integer(inter)
o.union = Integer(union)
outputSet.append(o)
self._defineOutputs(outputConsensus=outputSet)
def __init__(self, imag=0., real=0., **args):
Object.__init__(self, **args)
self.imag = Float(imag)
self.real = Float(real)
def createAnalyzeFilesStep(self):
""" This method will create two sqlite files that
will be used in by the viewer in the 'Analyze result' action.
ctfSet: a table with average ctf values between all methods.
ctfSetPair: a table where each row is a pair between two methods
"""
ctfSetFn, ctfSetPairFn = self._getAnalyzeFiles()
cleanPath(ctfSetFn, ctfSetPairFn)
ctfSet = Set(filename=ctfSetFn)
ctfSetPair = em.SetOfCTF(filename=ctfSetPairFn)
#import pdb
#pdb.set_trace()
minimumResolution = {}
maximumResolution = {}
averageResolution = {}
averageDefocusU = {}
averageDefocusV = {}
averageDefocusAngle = {}
for ctf in self.setOfCTF:
micFileName = self._getMicName(ctf)
minimumResolution[micFileName] = 0.
maximumResolution[micFileName] = 0.
averageResolution[micFileName] = 0.
averageDefocusU[micFileName] = 0.
averageDefocusV[micFileName] = 0.
averageDefocusAngle[micFileName] = 0.
for method1, method2, ctfId in self._freqResol:
ctf = em.CTFModel()
ctf1 = self.inputCTFs[method1].get()[ctfId]
ctf2 = self.inputCTFs[method2].get()[ctfId]
ctf.setDefocusU( (ctf1.getDefocusU() + ctf2.getDefocusU())/2. )
ctf.setDefocusV( (ctf1.getDefocusV() + ctf2.getDefocusV())/2. )
ctf.setDefocusAngle((ctf1.getDefocusAngle() + ctf2.getDefocusAngle())/2. )
ctf.setMicrograph( ctf1.getMicrograph())
#Clean objId since we can have ctf from the same micrograph
# and by default it is set to micrograph id
ctf.cleanObjId()
resolution = self._freqResol[(method1, method2, ctfId)]
ctf.resolution = Float(resolution)
ctf.method1 = String(self.methodNames[method1])
ctf.method2 = String(self.methodNames[method2])
# save the values of defocus for each micrograph in a list
ctfSetPair.append(ctf)
micFileName = self._getMicName(ctf1)
if (not micFileName in minimumResolution or
not micFileName in maximumResolution):
pass
if resolution < minimumResolution[micFileName]:
minimumResolution[micFileName] = resolution
if resolution > maximumResolution[micFileName]:
maximumResolution[micFileName] = resolution
averageResolution[micFileName] += resolution
averageDefocusU[micFileName] += ctf.getDefocusU()
averageDefocusV[micFileName] += ctf.getDefocusV()
averageDefocusAngle[micFileName] += ctf.getDefocusAngle()
size = float(len(self.setOfCTF))
for ctf in self.setOfCTF:
ctfAvg = Object()
micFileName = self._getMicName(ctf)
ctfAvg._micObj = ctf.getMicrograph()
ctfAvg.averageDefocusU = Float(averageDefocusU[micFileName] / size)
ctfAvg.averageDefocusV = Float(averageDefocusV[micFileName] / size)
ctfAvg.averageDefocusAngle = Float(averageDefocusAngle[micFileName] / size)
ctfAvg.averageResolution = Float(averageResolution[micFileName] / size)
ctfSet.append(ctfAvg)
ctfSetPair.write()
ctfSet.write()
def __init__(self, imag=0.0, real=0.0, **args):
Object.__init__(self, **args)
self.imag = Float(imag)
self.real = Float(real)
def createAnalyzeFilesStep(self):
""" This method will create two sqlite files that
will be used in by the viewer in the 'Analyze result' action.
ctfSet: a table with average ctf values between all methods.
ctfSetPair: a table where each row is a pair between two methods
"""
ctfSetFn, ctfSetPairFn = self._getAnalyzeFiles()
cleanPath(ctfSetFn, ctfSetPairFn)
ctfSet = Set(filename=ctfSetFn)
ctfSetPair = em.SetOfCTF(filename=ctfSetPairFn)
#import pdb
#pdb.set_trace()
minimumResolution = {}
maximumResolution = {}
averageResolution = {}
averageDefocusU = {}
averageDefocusV = {}
averageDefocusAngle = {}
for ctf in self.setOfCTF:
micFileName = self._getMicName(ctf)
minimumResolution[micFileName] = 0.
maximumResolution[micFileName] = 0.
averageResolution[micFileName] = 0.
averageDefocusU[micFileName] = 0.
averageDefocusV[micFileName] = 0.
averageDefocusAngle[micFileName] = 0.
for method1, method2, ctfId in self._freqResol:
ctf = em.CTFModel()
ctf1 = self.inputCTFs[method1].get()[ctfId]
ctf2 = self.inputCTFs[method2].get()[ctfId]
ctf.setDefocusU((ctf1.getDefocusU() + ctf2.getDefocusU()) / 2.)
ctf.setDefocusV((ctf1.getDefocusV() + ctf2.getDefocusV()) / 2.)
ctf.setDefocusAngle(
(ctf1.getDefocusAngle() + ctf2.getDefocusAngle()) / 2.)
ctf.setMicrograph(ctf1.getMicrograph())
#Clean objId since we can have ctf from the same micrograph
# and by default it is set to micrograph id
ctf.cleanObjId()
resolution = self._freqResol[(method1, method2, ctfId)]
ctf.resolution = Float(resolution)
ctf.method1 = String(self.methodNames[method1])
ctf.method2 = String(self.methodNames[method2])
# save the values of defocus for each micrograph in a list
ctfSetPair.append(ctf)
micFileName = self._getMicName(ctf1)
if (not micFileName in minimumResolution
or not micFileName in maximumResolution):
pass
if resolution < minimumResolution[micFileName]:
minimumResolution[micFileName] = resolution
if resolution > maximumResolution[micFileName]:
maximumResolution[micFileName] = resolution
averageResolution[micFileName] += resolution
averageDefocusU[micFileName] += ctf.getDefocusU()
averageDefocusV[micFileName] += ctf.getDefocusV()
averageDefocusAngle[micFileName] += ctf.getDefocusAngle()
size = float(len(self.setOfCTF))
for ctf in self.setOfCTF:
ctfAvg = Object()
micFileName = self._getMicName(ctf)
ctfAvg._micObj = ctf.getMicrograph()
ctfAvg.averageDefocusU = Float(averageDefocusU[micFileName] / size)
ctfAvg.averageDefocusV = Float(averageDefocusV[micFileName] / size)
ctfAvg.averageDefocusAngle = Float(
averageDefocusAngle[micFileName] / size)
ctfAvg.averageResolution = Float(averageResolution[micFileName] /
size)
ctfSet.append(ctfAvg)
ctfSetPair.write()
ctfSet.write()
