import unittest
import numpy
import apgl
@apgl.skipIf(not apgl.checkImport('pysparse'), 'No module pysparse')
class PySparseUtilsTest(unittest.TestCase):
def testSum(self):
try:
from pysparse import spmatrix
from apgl.util.PySparseUtils import PySparseUtils
except ImportError as error:
return
n = 10
X = spmatrix.ll_mat(n, n)
self.assertEquals(PySparseUtils.sum(X), 0.0)
X[1, 1] = 5
X[2, 4] = 6.1
X[3, 1] = 2.5
self.assertEquals(PySparseUtils.sum(X), 13.6)
def testNonzero(self):
try:
from pysparse import spmatrix
from apgl.util.PySparseUtils import PySparseUtils
except ImportError as error:
return
from apgl.util.PathDefaults import PathDefaults
import unittest
import logging
import sys
import apgl
from apgl.egograph.SvmEgoSimulator import SvmEgoSimulator
from apgl.generator import *
from apgl.graph import *
@apgl.skipIf(not apgl.checkImport('svm'), 'No module svm')
class SvmEgoSimulatorTest(unittest.TestCase):
def setUp(self):
logging.basicConfig(stream=sys.stdout, level=logging.INFO)
dataDir = PathDefaults.getDataDir() + "infoDiffusion/"
#dataDir = "/home/charanpal/Private/Postdoc/Code/APGL/data/"
matFileName = dataDir + "EgoAlterTransmissions.mat"
self.svmEgoSimulator = SvmEgoSimulator(matFileName)
def testSampleExamples(self):
self.svmEgoSimulator.sampleExamples(100)
self.assertEquals(self.svmEgoSimulator.examplesList.getNumSampledExamples(), 100)
def testModelSelection(self):
Cs = [1.0, 2.0]
kernel = "linear"
kernelParams = [0.0]
errorCosts = [0.1, 0.2]
folds = 5
import apgl
import numpy
import unittest
import pickle
import numpy.testing as nptst
from exp.viroscopy.model.HIVGraph import HIVGraph
from exp.viroscopy.model.HIVVertices import HIVVertices
@apgl.skipIf(not apgl.checkImport('sppy'), 'No module pysparse')
class HIVGraphTest(unittest.TestCase):
def setup(self):
pass
def testContructor(self):
numVertices = 10
graph = HIVGraph(numVertices)
self.assertEquals(numVertices, graph.getNumVertices())
self.assertEquals(8, graph.getVertexList().getNumFeatures())
self.assertTrue(graph.isUndirected() == True)
def testGetSusceptibleSet(self):
numVertices = 10
graph = HIVGraph(numVertices)
self.assertTrue(graph.getSusceptibleSet() == set(range(numVertices)))
for i in range(9):
import sys
import apgl
import numpy
import unittest
import logging
import pickle
import scipy.integrate
from apgl.util.Util import Util
from exp.viroscopy.model.HIVABCParameters import HIVABCParameters
from exp.viroscopy.model.HIVRates import HIVRates
from exp.viroscopy.model.HIVGraph import HIVGraph
@apgl.skipIf(not apgl.checkImport('sppy'), 'No module sppy')
class HIVABCParametersTest(unittest.TestCase):
def setUp(self):
numpy.seterr(invalid='raise')
logging.basicConfig(stream=sys.stdout, level=logging.DEBUG)
numpy.set_printoptions(suppress=True, precision=4, linewidth=100)
numpy.random.seed(21)
M = 1000
undirected = True
graph = HIVGraph(M, undirected)
alpha = 2
zeroVal = 0.9
p = Util.powerLawProbs(alpha, zeroVal)
hiddenDegSeq = Util.randomChoice(p, graph.getNumVertices())
rates = HIVRates(graph, hiddenDegSeq)
import apgl
import unittest
import numpy
import logging
from apgl.predictors.RandomForest import RandomForest
from apgl.util.PathDefaults import PathDefaults
from apgl.util.Evaluator import Evaluator
from apgl.util.Sampling import Sampling
@apgl.skipIf(not apgl.checkImport('sklearn'), 'Module sklearn is required')
class RandomForestTest(unittest.TestCase):
def setUp(self):
numpy.random.seed(21)
numExamples = 200
numFeatures = 5
self.X = numpy.random.rand(numExamples, numFeatures)
c = numpy.random.rand(numFeatures)
self.y = numpy.sign(self.X.dot(c) < numpy.mean(self.X.dot(c)))
def testLearnModel(self):
randomForest = RandomForest()
randomForest.learnModel(self.X, self.y)
tree = randomForest.getClassifier()
def testPredict(self):
randomForest = RandomForest()
randomForest.learnModel(self.X, self.y)
predY = randomForest.predict(self.X)
import apgl
import unittest
import numpy
import logging
from sandbox.predictors.RandomForest import RandomForest
from sandbox.util.PathDefaults import PathDefaults
from sandbox.util.Evaluator import Evaluator
from sandbox.util.Sampling import Sampling
@apgl.skipIf(not apgl.checkImport('sklearn'), 'Module sklearn is required')
class RandomForestTest(unittest.TestCase):
def setUp(self):
numpy.random.seed(21)
numExamples = 200
numFeatures = 5
self.X = numpy.random.rand(numExamples, numFeatures)
c = numpy.random.rand(numFeatures)
self.y = numpy.sign(self.X.dot(c) < numpy.mean(self.X.dot(c)))
def testLearnModel(self):
randomForest = RandomForest()
randomForest.learnModel(self.X, self.y)
tree = randomForest.getClassifier()
def testPredict(self):
randomForest = RandomForest()
randomForest.learnModel(self.X, self.y)
predY = randomForest.predict(self.X)
import unittest
import numpy
import apgl
import logging
from apgl.graph import *
try:
from apgl.clustering.LPKMeans import LPKMeans
except ImportError:
pass
@apgl.skipIf(not apgl.checkImport('cvxopt'), 'No module cvxopt')
class LPKMeansTest(unittest.TestCase):
def setUp(self):
numpy.set_printoptions(suppress=True, precision=3)
numpy.random.seed(21)
numpy.set_printoptions(threshold=numpy.nan, linewidth=100)
pass
def testCluster(self):
numFeatures = 2
X1 = numpy.random.randn(30, numFeatures) + numpy.array([1, 1])
X2 = numpy.random.randn(30, numFeatures) + numpy.array([-1, -1])
X = numpy.r_[X1, X2]
logging.debug(X.shape)
k = 2
import apgl
import numpy
import unittest
import pickle
import numpy.testing as nptst
from wallhack.viroscopy.model.HIVGraph import HIVGraph
from wallhack.viroscopy.model.HIVVertices import HIVVertices
@apgl.skipIf(not apgl.checkImport("sppy"), "No module pysparse")
class HIVGraphTest(unittest.TestCase):
def setup(self):
pass
def testContructor(self):
numVertices = 10
vertices = HIVVertices(numVertices)
self.assertEquals(numVertices, vertices.getNumVertices())
self.assertEquals(8, vertices.getNumFeatures())
def testAddVertices(self):
numVertices = 10
vertices = HIVVertices(numVertices)
v1 = vertices[4]
vertices.addVertices(5)
print(vertices.V.shape)
self.assertEquals(numVertices + 5, vertices.getNumVertices())
from apgl.generator.SmallWorldGenerator import SmallWorldGenerator
from apgl.graph.SparseGraph import SparseGraph
from apgl.graph.VertexList import VertexList
from apgl.util import *
import numpy
import numpy.random as rand
import unittest
import apgl
import logging
try:
import mlpy
except ImportError:
pass
@apgl.skipIf(not apgl.checkImport('mlpy'), 'No module mlpy')
class EgoSimulatorTest(unittest.TestCase):
def setUp(self):
numVertices = 500
numFeatures = 49
self.means = rand.randn(numFeatures)
self.vars = rand.randn(numFeatures, numFeatures)
self.vars = self.vars + self.vars.T #Make vars symmetric
p1 = 0.1
self.egoGenerator = EgoGenerator()
vList = self.egoGenerator.generateIndicatorVertices(numVertices, self.means, self.vars, p1)
sGraph = SparseGraph(vList)
p2 = 0.1
class EvaluatorTestCase(unittest.TestCase):
#def setUp(self):
# self.foo = Evaluator()
#
def testRootMeanSqError(self):
y = numpy.array([1, 2, 3])
predY = numpy.array([1, 2, 3])
self.assertEquals(Evaluator.rootMeanSqError(y, predY), 0.0)
y = numpy.array([1, 2, 3])
predY = numpy.array([1, 2, 2])
self.assertEquals(Evaluator.rootMeanSqError(y, predY),
float(1) / numpy.sqrt(3))
predY = numpy.array([1, 2])
self.assertRaises(ValueError, Evaluator.rootMeanSqError, y, predY)
def testWeightedRootMeanSqError(self):
y = numpy.array([0.1, 0.2, 0.3])
predY = numpy.array([0.1, 0.2, 0.3])
self.assertEquals(Evaluator.weightedRootMeanSqError(y, predY), 0.0)
#Errors on larger ys are weighted more
predY = numpy.array([0.0, 0.2, 0.3])
predY2 = numpy.array([0.1, 0.2, 0.4])
self.assertTrue(
Evaluator.weightedRootMeanSqError(y, predY) <
Evaluator.weightedRootMeanSqError(y, predY2))
def testBinaryError(self):
testY = numpy.array([1, 1, -1, 1])
predY = numpy.array([-1, 1, -1, 1])
predY2 = numpy.array([-1, -1, -1, 1])
predY3 = numpy.array([-1, -1, 1, -1])
self.assertTrue(Evaluator.binaryError(testY, predY) == 0.25)
self.assertTrue(Evaluator.binaryError(testY, testY) == 0.0)
self.assertTrue(Evaluator.binaryError(predY, predY) == 0.0)
self.assertTrue(Evaluator.binaryError(testY, predY2) == 0.5)
self.assertTrue(Evaluator.binaryError(testY, predY3) == 1.0)
def testBinaryErrorP(self):
testY = numpy.array([1, 1, -1, 1])
predY = numpy.array([-1, 1, -1, 1])
predY2 = numpy.array([-1, -1, -1, 1])
predY3 = numpy.array([-1, -1, 1, -1])
self.assertTrue(Evaluator.binaryErrorP(testY, predY) == 1.0 / 3.0)
self.assertTrue(Evaluator.binaryErrorP(testY, testY) == 0.0)
self.assertTrue(Evaluator.binaryErrorP(predY, predY) == 0.0)
self.assertTrue(Evaluator.binaryErrorP(testY, predY2) == 2.0 / 3.0)
self.assertTrue(Evaluator.binaryErrorP(testY, predY3) == 1.0)
testY = numpy.array([-1, -1, -1, -1])
predY = numpy.array([-1, 1, -1, 1])
self.assertTrue(Evaluator.binaryErrorP(testY, predY) == 0.0)
def testBinaryErrorN(self):
testY = numpy.array([1, 1, -1, 1])
predY = numpy.array([-1, 1, -1, 1])
predY2 = numpy.array([-1, -1, -1, 1])
predY3 = numpy.array([-1, -1, 1, -1])
self.assertTrue(Evaluator.binaryErrorN(testY, predY) == 0.0)
self.assertTrue(Evaluator.binaryErrorN(testY, testY) == 0.0)
self.assertTrue(Evaluator.binaryErrorN(predY, predY) == 0.0)
self.assertTrue(Evaluator.binaryErrorN(testY, predY2) == 0.0)
self.assertTrue(Evaluator.binaryErrorN(testY, predY3) == 1.0)
testY = numpy.array([-1, -1, -1, -1])
predY = numpy.array([-1, 1, -1, 1])
self.assertTrue(Evaluator.binaryErrorN(testY, predY) == 0.5)
testY = numpy.array([1, 1, 1, 1])
predY = numpy.array([-1, 1, -1, 1])
self.assertTrue(Evaluator.binaryErrorN(testY, predY) == 0.0)
@apgl.skipIf(not apgl.checkImport('sklearn'), 'No module scikits.learn')
def testAuc(self):
testY = numpy.array([-1, -1, 1, 1])
predY = numpy.array([-1, 0, 1, 1])
predY2 = numpy.array([0.1, 0.2, 0.3, 0.4])
self.assertEquals(Evaluator.auc(predY, testY), 1.0)
self.assertEquals(Evaluator.auc(predY2, testY), 1.0)
self.assertEquals(Evaluator.auc(-predY, testY), 0.0)
numExamples = 1000
testY = numpy.array(numpy.random.rand(numExamples) > 0.5, numpy.int)
predY = numpy.random.rand(numExamples) > 0.5
#For a random score the AUC is approximately 0.5
self.assertAlmostEquals(Evaluator.auc(predY, testY), 0.5, 1)
@apgl.skipIf(not apgl.checkImport('sklearn'), 'No module scikits.learn')
def testLocalAuc(self):
testY = numpy.array([-1, -1, 1, 1, 1, 1, 1, -1, -1, 1])
predY = numpy.array([
0.987, 0.868, 0.512, 0.114, 0.755, 0.976, 0.05, 0.371, 0.629, 0.819
])
self.assertEquals(Evaluator.localAuc(testY, predY, 1.0),
Evaluator.auc(predY, testY))
self.assertEquals(Evaluator.localAuc(testY, predY, 0.0), 0)
self.assertEquals(Evaluator.localAuc(testY, testY, 0.2), 1.0)
#Ask stephan if correct - needs extra tests
def testBinaryBootstrapError(self):
testY = numpy.array([-1, -1, 1, 1, 1])
predY = 1 - testY
trainY = numpy.array([-1, -1, 1, 1, 1])
predTrainY = 1 - trainY
self.assertEquals(
Evaluator.binaryBootstrapError(testY, testY, trainY, trainY, 0.5),
0.0)
self.assertEquals(
Evaluator.binaryBootstrapError(testY, testY, trainY, predTrainY,
0.5), 0.5)
self.assertEquals(
Evaluator.binaryBootstrapError(testY, testY, trainY, predTrainY,
0.1), 0.9)
self.assertEquals(
Evaluator.binaryBootstrapError(testY, predY, trainY, trainY, 0.1),
0.1)
def testMeanAbsError(self):
testY = numpy.array([1, 2, 1.5])
predY = numpy.array([2, 1, 0.5])
self.assertEquals(Evaluator.meanAbsError(testY, predY), 1.0)
self.assertEquals(Evaluator.meanAbsError(testY, testY), 0.0)
testY = numpy.random.rand(10)
predY = numpy.random.rand(10)
error = numpy.abs(testY - predY).mean()
self.assertEquals(error, Evaluator.meanAbsError(testY, predY))
@apgl.skipIf(not apgl.checkImport('sklearn'), 'No module scikits.learn')
def testPrecisionFromIndLists(self):
predList = [4, 2, 10]
testList = [4, 2]
self.assertEquals(Evaluator.precisionFromIndLists(testList, predList),
2.0 / 3)
testList = [4, 2, 10]
self.assertEquals(Evaluator.precisionFromIndLists(testList, predList),
1)
predList = [10, 2, 4]
self.assertEquals(Evaluator.precisionFromIndLists(testList, predList),
1)
testList = [1, 9, 11]
self.assertEquals(Evaluator.precisionFromIndLists(testList, predList),
0)
predList = [1, 2, 3, 4, 5]
testList = [1, 9, 11]
self.assertEquals(Evaluator.precisionFromIndLists(testList, predList),
1.0 / 5)
def testAveragePrecisionFromLists(self):
predList = [4, 2, 10]
testList = [4, 2, 15, 16]
self.assertEquals(
Evaluator.averagePrecisionFromLists(testList, predList), 0.5)
predList = [0, 1, 2, 3, 4, 5]
testList = [0, 3, 4, 5]
self.assertAlmostEquals(
Evaluator.averagePrecisionFromLists(testList, predList),
0.691666666666)
import apgl
from apgl.graph.VertexList import VertexList
from apgl.util import *
from apgl.graph.test.MatrixGraphTest import MatrixGraphTest
import unittest
import numpy
try:
from apgl.graph.CsArrayGraph import CsArrayGraph
except ImportError:
pass
@apgl.skipIf(not apgl.checkImport('sppy'), 'No module sppy')
class CsArrayGraphTest(unittest.TestCase, MatrixGraphTest):
def setUp(self):
self.GraphType = CsArrayGraph
self.initialise()
def testInit(self):
numVertices = 0
numFeatures = 1
vList = VertexList(numVertices, numFeatures)
graph = CsArrayGraph(vList)
self.assertEquals(graph.weightMatrixDType(), numpy.float)
graph = CsArrayGraph(vList, dtype=numpy.int16)
self.assertEquals(graph.weightMatrixDType(), numpy.int16)
#Test just specifying number of vertices