def createDataSet():
l = PointLayout()
l.add('a', RealType)
ds = DataSet()
# p1.a = (0.0, 0.0)
p = Point()
p.setName('p1')
p.setLayout(l)
p['a'] = (0.0, 0.0)
ds.addPoint(p)
# p2.a = (0.5, 1.0)
p = Point()
p.setName('p2')
p.setLayout(l)
p['a'] = (0.5, 1.0)
ds.addPoint(p)
if testdata.useFixedLength:
ds = testdata.fixLength(ds)
if testdata.useEnumerate:
ds = testdata.enumerateStrings(ds)
return ds
def newPoint(name):
l = PointLayout()
l.add('a', RealType)
p = Point()
p.setName(name)
p.setLayout(l)
return p
def createSimpleLayout():
l = PointLayout()
l.add('a.1', RealType)
l.add('a.2', RealType)
l.add('c', RealType)
l.add('b', RealType)
l.add('d', StringType)
l.add('e', RealType, FixedLength, 3)
return l
def testChronoIndependence(self):
#'''Layouts built using the same descriptors but in a different order should still be equal'''
l = PointLayout()
l.add('a', RealType)
l.add('b', RealType)
l2 = PointLayout()
l2.add('b', RealType)
l2.add('a', RealType)
self.assert_(l == l2)
def testForceIdentity(self):
l = PointLayout()
l.add('a', RealType, FixedLength, 1)
p = Point()
p.setLayout(l)
cd = MetricFactory.create('cosinesimilarity', p.layout(), { 'defaultValue': 0.5 })
self.assertEquals(cd(p, p), 0.5)
ficd = MetricFactory.create('forceidentity',
p.layout(),
{ 'distance': 'cosinesimilarity',
'params': { 'defaultValue': 0.5 }
})
self.assertEquals(ficd(p, p), 0.0)
p2 = Point(p)
p2.setName('p2')
self.assertEquals(ficd(p, p2), 0.5)
def testComplexReferenceCounting(self):
ds = DataSet()
self.assertEqual(ds.layout().ref(), 2) # 1 + 1 from temp object
p = Point()
p.setName('p1')
lext = PointLayout(p.layout()) # +1, {lext,p}.ref = 2
self.assertEqual(lext.ref(), 2)
lext = p.layout().copy() # copy, lext.ref = 1; p.ref -= 1, = 1
self.assertEqual(lext.ref(), 1)
ds.addPoint(p) # +3 (dataset + pointcopy), ref = 3
self.assertEqual(lext.ref(), 1)
self.assertEqual(ds.layout().ref(), 4) # 3 + 1 temp object
p2 = Point(p) # +1, {p,p2}.ref = 5
p2.setName('p2')
self.assertEqual(ds.layout().ref(), 5)
ds.addPoint(p2)
self.assertEqual(ds.layout().ref(), 6) # +1 pointcopy, ref = 6
def PCA(x):
points = []
layout = PointLayout()
layout.add('x', RealType)
for i, l in enumerate(x):
p = Point()
p.setName('p%d' % i)
p.setLayout(layout)
p['x'] = l
points.append(p)
ds = DataSet()
ds.addPoints(points)
ds = transform(ds, 'fixlength')
ds = transform(ds, 'pca', { 'dimension': len(x[0]), 'resultName': 'pca' })
result = []
for p in ds.points():
result.append(p['pca'])
return result
def PCA(x):
points = []
layout = PointLayout()
layout.add('x', RealType)
for i, l in enumerate(x):
p = Point()
p.setName('p%d' % i)
p.setLayout(layout)
p['x'] = l
points.append(p)
ds = DataSet()
ds.addPoints(points)
ds = transform(ds, 'fixlength')
ds = transform(ds, 'pca', {'dimension': len(x[0]), 'resultName': 'pca'})
result = []
for p in ds.points():
result.append(p['pca'])
return result
def testMerge(self):
l2 = testdata.createSimpleLayout()
self.assertEqual(self.l1, l2)
self.assertRaises(Exception, mergeLayouts, self.l1, l2)
l3 = PointLayout()
l3.add('a', RealType)
l3.add('a', '3', RealType)
l4 = mergeLayouts(l2, l3)
self.assertEqual(len(l4.descriptorNames()), len(l2.descriptorNames())+1)
self.assertEqual(l4.descriptorLocation('a').size(RealType, VariableLength), 3)
def readLibSVMDataSet(filename):
data = [l.split() for l in open(filename).readlines()]
minidx = maxidx = 1
for l in data:
for i in range(1, len(l)):
dim, value = l[i].split(':')
l[i] = (int(dim), float(value))
minidx = min(minidx, int(dim))
maxidx = max(maxidx, int(dim))
dimension = maxidx - minidx + 1
layout = PointLayout()
layout.add('class', StringType)
layout.add('value', RealType)
ds = DataSet()
n = 0
points = []
for l in data:
p = Point()
p.setLayout(layout)
p.setName('instance_%06d' % n)
n += 1
p['class'] = l[0]
desc = RealDescriptor(dimension, 0.0)
for dim, value in l[1:]:
desc[dim - minidx] = value
p['value'] = desc
points.append(p)
ds.addPoints(points)
return ds
def testBasicReferenceCounting(self):
l1 = PointLayout()
self.assertEqual(l1.ref(), 1)
# add python ref
l2 = l1
self.assertEqual(l1.ref(), 1)
self.assertEqual(l2.ref(), 1)
# add C++ ref
l3 = PointLayout(l2)
self.assertEqual(l1.ref(), 2)
self.assertEqual(l2.ref(), 2)
self.assertEqual(l3.ref(), 2)
# make different copy
l4 = l3.copy()
self.assertEqual(l4.ref(), 1)
# remove C++ ref
del l3
self.assertEqual(l1.ref(), 1)
self.assertEqual(l2.ref(), 1)
# add C++ ref
l3 = PointLayout(l2)
# remove python ref
del l1
self.assertEqual(l2.ref(), 2)
self.assertEqual(l3.ref(), 2)
# remove last python ref, hence remove C++ ref too
del l2
self.assertEqual(l3.ref(), 1)
def testCorrectNodes(self):
l = PointLayout()
self.assertRaises(Exception, l.add, 'undef')
l.add('blah', RealType)
l.add('', 'blah', StringType)
self.assertEqual(len(l.descriptorNames()), 1)
self.assertEqual(l.descriptorLocation('blah').type(), RealType)
l.add('blouh', StringType)
self.assertEqual(len(l.descriptorNames()), 2)
self.assertRaises(Exception, l.add, 'blouh', 'bluh', UndefinedType)
self.assertEqual(len(l.descriptorNames()), 2)
def testLibyaml1024CharLimit(self):
l = PointLayout()
l.add('a'*2000, RealType)
from gaia2 import fastyaml as yaml
yaml.load(l.toYaml())
def testIntersect(self):
l1 = PointLayout()
l1.add('a', RealType)
l1.add('b', RealType)
l2 = PointLayout()
l2.add('a', RealType)
l2.add('b', StringType)
l2.add('d', RealType)
lr = l1 & l2
self.assertEqual(lr.descriptorNames(), ('.a',))
self.assertEqual(l1.descriptorNames(), (l1 & l1).descriptorNames())
self.assertEqual(l2.descriptorNames(), (l2 & l2).descriptorNames())