def _object(n, x, y, yp):
obj = pwobj.Object()
obj.n = n
obj.x = x
obj.y = y
obj.yp = yp
return obj
def addObj(objId, name, output='', size='', parent=None):
obj = pwobj.Object(objId=objId)
obj.name = name
obj.output = output
obj.outSize = size
obj._objParent = parent
objects.append(obj)
return obj
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')
pwutils.cleanPath(outputFn)
outputSet = emobj.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 = pwobj.Object()
o.setObjLabel('classes %d - %d' % (clsId1, clsId2))
o.class1 = cls1.clone()
o.class1.id = pwobj.Integer(clsId1)
o.class2 = cls2.clone()
o.class2.id = pwobj.Integer(clsId2)
o.jaccard = pwobj.Float(jaccardIndex)
o.intersection = pwobj.Integer(inter)
o.union = pwobj.Integer(union)
outputSet.append(o)
self._defineOutputs(outputConsensus=outputSet)
def testWithPointer(self):
obj = pwobj.Integer(10)
self.assertFalse(obj.hasPointer(),
"Default instantiation off Integer has a pointer.")
self.assertEqual(obj.get(), 10, "Integer.get(), without pointer fails.")
pointee = pwobj.Object()
setattr(pointee, "value", pwobj.Integer(20))
# Set a pointer (not a real case though, but enough here)
obj.setPointer(pwobj.Pointer(pointee, extended='value'))
self.assertEqual(obj.get(), 20, "Integer.get() fails with a pointer.")
