def test_mutual_info_calculation(self):
X, Y = utils.load_digits()
X = mutual_information_old.normalize_data_for_MI(X)
for i in range(X.shape[1]):
for j in range(i+1, X.shape[1]):
X1 = np.array(X[:,i])
X2 = np.array(X[:,j])
mi_pyfeast = self.__calculate_MI(X1, X2)
mi_ours = mutual_information_old.calculate_mutual_information_histogram_binning(X1, X2)
logger.debug("mutual_info: features: %d and %d; pyfeast: %f \t ours: %f"%(i, j, mi_pyfeast, mi_ours))
self.assertTrue(np.isclose(mi_pyfeast, mi_ours, rtol=0.01, atol=0.00001))
def test_CIFE(self):
X, Y = utils.load_digits()
X = mutual_information_old.normalize_data_for_MI(X)
X = X.astype("float64")
selector = ilastik_feature_selection.filter_feature_selection.FilterFeatureSelection(X, Y, "CIFE")
num_feat = 10
our_set = selector.run(num_feat)
feast_set = np.array(feast.CIFE(X, Y, num_feat)).astype("int")
logger.debug("CIFE")
logger.debug("ours\t%s"%str(our_set))
logger.debug("feast\t%s"%str(feast_set))
self.assertEqual(set(our_set), set(feast_set))
def test_JMI(self):
X, Y = utils.load_digits()
X = mutual_information_old.normalize_data_for_MI(X)
X = X.astype("float64")
selector = ilastik_feature_selection.filter_feature_selection.FilterFeatureSelection(
X, Y, "JMI")
num_feat = 10
our_set = selector.run(num_feat)
feast_set = np.array(feast.JMI(X, Y, num_feat)).astype("int")
logger.debug("JMI")
logger.debug("ours\t%s" % str(our_set))
logger.debug("feast\t%s" % str(feast_set))
self.assertEqual(set(our_set), set(feast_set))
def test_cond_mutual_info(self):
X, Y = utils.load_digits()
Y = Y.astype("int")
X = mutual_information_old.normalize_data_for_MI(X)
for i in range(X.shape[1]):
for j in range(i+1, X.shape[1]):
X1 = np.array(X[:,i])
X2 = np.array(X[:,j])
cond_mi_pyfeast = self.__calculate_cond_MI(X1, X2, Y)
cond_mi_ours = mutual_information_old.calculate_conditional_MI(X1, X2, Y)
logger.debug("class cond mutual info: features: %d and %d; pyfeast: %f \t ours: %f"%(i, j, cond_mi_pyfeast, cond_mi_ours))
self.assertTrue(np.isclose(cond_mi_pyfeast, cond_mi_ours, rtol=0.01, atol=0.00001))
def test_MIFS(self):
X, Y = utils.load_digits()
X = mutual_information_old.normalize_data_for_MI(X)
X = X.astype("float64")
selector = ilastik_feature_selection.filter_feature_selection.FilterFeatureSelection(X, Y, "MIFS")
num_feat = 10
our_set = selector.run(num_feat)
feast_set = np.array(feast.BetaGamma(X, Y, num_feat, 1.0, 0.0)).astype("int") # MIFS in feast is buggy
# (beta=0 although it should be =1)
logger.debug("MIFS")
logger.debug("ours\t%s"%str(our_set))
logger.debug("feast\t%s"%str(feast_set))
self.assertEqual(set(our_set), set(feast_set))
def test_class_cond_mi_calculation(self):
X, Y = utils.load_digits()
X = mutual_information_old.normalize_data_for_MI(X)
X = X.astype("float64")
selector = ilastik_feature_selection.filter_feature_selection.FilterFeatureSelection(X, Y, "CIFE")
for i in range(X.shape[1]):
for j in range(i+1, X.shape[1]):
X1 = np.array(X[:,i])
X2 = np.array(X[:,j])
cond_mi_pyfeast = self.__calculate_cond_MI(X1, X2, Y)
cond_mi_ours = selector._calculate_class_conditional_MI(X1.astype("int"), X2.astype("int"), Y)
logger.debug("class cond mutual info: features: %d and %d; pyfeast: %f \t ours: %f"%(i, j, cond_mi_pyfeast, cond_mi_ours))
self.assertTrue(np.isclose(cond_mi_pyfeast, cond_mi_ours, rtol=0.01, atol=0.00001))
def test_mutual_info_calculation(self):
X, Y = utils.load_digits()
X = mutual_information_old.normalize_data_for_MI(X)
for i in range(X.shape[1]):
for j in range(i + 1, X.shape[1]):
X1 = np.array(X[:, i])
X2 = np.array(X[:, j])
mi_pyfeast = self.__calculate_MI(X1, X2)
mi_ours = mutual_information_old.calculate_mutual_information_histogram_binning(
X1, X2)
logger.debug(
"mutual_info: features: %d and %d; pyfeast: %f \t ours: %f"
% (i, j, mi_pyfeast, mi_ours))
self.assertTrue(
np.isclose(mi_pyfeast, mi_ours, rtol=0.01, atol=0.00001))
def test_MIFS(self):
X, Y = utils.load_digits()
X = mutual_information_old.normalize_data_for_MI(X)
X = X.astype("float64")
selector = ilastik_feature_selection.filter_feature_selection.FilterFeatureSelection(
X, Y, "MIFS")
num_feat = 10
our_set = selector.run(num_feat)
feast_set = np.array(feast.BetaGamma(X, Y, num_feat, 1.0, 0.0)).astype(
"int") # MIFS in feast is buggy
# (beta=0 although it should be =1)
logger.debug("MIFS")
logger.debug("ours\t%s" % str(our_set))
logger.debug("feast\t%s" % str(feast_set))
self.assertEqual(set(our_set), set(feast_set))
def test_cond_mutual_info(self):
X, Y = utils.load_digits()
Y = Y.astype("int")
X = mutual_information_old.normalize_data_for_MI(X)
for i in range(X.shape[1]):
for j in range(i + 1, X.shape[1]):
X1 = np.array(X[:, i])
X2 = np.array(X[:, j])
cond_mi_pyfeast = self.__calculate_cond_MI(X1, X2, Y)
cond_mi_ours = mutual_information_old.calculate_conditional_MI(
X1, X2, Y)
logger.debug(
"class cond mutual info: features: %d and %d; pyfeast: %f \t ours: %f"
% (i, j, cond_mi_pyfeast, cond_mi_ours))
self.assertTrue(
np.isclose(cond_mi_pyfeast,
cond_mi_ours,
rtol=0.01,
atol=0.00001))
def test_class_cond_mi_calculation(self):
X, Y = utils.load_digits()
X = mutual_information_old.normalize_data_for_MI(X)
X = X.astype("float64")
selector = ilastik_feature_selection.filter_feature_selection.FilterFeatureSelection(
X, Y, "CIFE")
for i in range(X.shape[1]):
for j in range(i + 1, X.shape[1]):
X1 = np.array(X[:, i])
X2 = np.array(X[:, j])
cond_mi_pyfeast = self.__calculate_cond_MI(X1, X2, Y)
cond_mi_ours = selector._calculate_class_conditional_MI(
X1.astype("int"), X2.astype("int"), Y)
logger.debug(
"class cond mutual info: features: %d and %d; pyfeast: %f \t ours: %f"
% (i, j, cond_mi_pyfeast, cond_mi_ours))
self.assertTrue(
np.isclose(cond_mi_pyfeast,
cond_mi_ours,
rtol=0.01,
atol=0.00001))
