def get_embedding(self, points):
n = self.wanted_dimensions
try:
embedding, errors = locally_linear_embedding(points,
n_neighbors=self.knn,
n_components=n,
eigen_solver='dense',
n_jobs=-1)
except Exception:
embedding, errors = locally_linear_embedding(points,
n_neighbors=self.knn,
n_components=n,
eigen_solver='dense',
n_jobs=-1)
return (embedding, errors)
def test_singular_matrix():
M = np.ones((10, 3))
f = ignore_warnings
with pytest.raises(ValueError):
f(manifold.locally_linear_embedding(M, 2, 1,
method='standard',
eigen_solver='arpack'))
def improve_lle_alg(train_df, test_df=None, n_k=3, n_c=2, e_s='dense'):
"""
输入:
train_df 训练集; test_df 测试集; 均为 feature 数据, 无 label.
n_k lle 选取近邻数, 对应 n_neighbors;
n_c 选取嵌入数, 对应 n_components
e_s 特征值求解算法, eigen_solver 默认为 dense, 必能找到求解方式, 详细请 help
输出:
W 矩阵, 转化矩阵
求解 W, 线性表示的误差项.
"""
transform_array, error_result = manifold.locally_linear_embedding(X=train_df, n_neighbors=n_k,
n_components=n_c, eigen_solver=e_s)
# 数据类型转化
train_data_transform_df = pd.DataFrame(transform_array) # array to df
reduce_dim_matrix = np.matrix(transform_array)
train_data_matrix = np.matrix(train_df.astype('float')) # 是否存在逆??
train_data_matrix_inv = train_data_matrix.getI() # 求逆(不是方阵)
# 计算出 W 矩阵
w_transform_matrix = train_data_matrix_inv * reduce_dim_matrix
# 判断是否输入测试集
if test_df is None: # 输出: 局部线性嵌入转化后的训练集,W 矩阵, 误差项
return train_data_transform_df, w_transform_matrix, error_result
test_data_transform_matrix = np.matrix(test_df) * w_transform_matrix
test_data_transform_df = pd.DataFrame(test_data_transform_matrix)
# 输出4个指标, 转化后的train, test, W 矩阵, 以及 误差项
return train_data_transform_df, test_data_transform_df, w_transform_matrix, error_result
def test_locally_linear_embedding(self): np.random.seed(1234) pts = np.random.random((5, 3)) expected = locally_linear_embedding(pts, 3, 1)[0] G = neighbor_graph(pts, k=3).barycenter_edge_weights(pts, copy=False) actual = G.locally_linear_embedding(num_dims=1) assert_signless_array_almost_equal(expected, actual)
def perform_lle(X, d):
X_r, err = locally_linear_embedding(X.toarray(),
n_neighbors=12,
n_components=d,
random_state=32)
print("Done. Reconstruction error: %g" % err)
return X_r
def _train(self):
x = self._train_features
y = self._train_outputs
pipe = pipeline.Pipeline([
('drop', transformers.ColumnDropper(
columns=(0, 3, 5, 14, 26, 35, 40, 65, 72, 95, 99, 104, 124)
)),
('scale', preprocessing.StandardScaler(
with_mean=True,
with_std=True
)),
('select', feature_selection.SelectPercentile(
percentile=59,#59,
score_func=feature_selection.mutual_info_classif
)),
('select', feature_selection.SelectKBest(
k=101,
score_func=feature_selection.f_classif
)),
('estim', manifold.locally_linear_embedding(
x,
n_neighbors=6,
n_components=101,
eigen_solver='auto',
method='standard'
)),
])
pipe.fit_transform(x)
self._model = pipe.predict
def main_LLE2():
f3=open('projection vectors 1','w')
f4=open('projection vectors 2','w')
f5=open('projection vectors 3','w')
f6=open('scatter matrix in 3D','w')
k=40
images=[]
images,colors=load_images()
matrix_images=matrix_build(images)
newmatrix,squared_error=locally_linear_embedding(matrix_images,k,3,eigen_solver='auto')
print 'squared_error='+repr(squared_error)
print newmatrix.shape
M1=np.dot(newmatrix.T,matrix_images)
M2=np.linalg.inv(np.dot(matrix_images.T,matrix_images))
P_matrix=(np.dot(M1,M2)).T
print P_matrix.shape
for x in range(len(P_matrix)):
f3.write(repr(P_matrix[x][0])+'\n')
f4.write(repr(P_matrix[x][1])+'\n')
f5.write(repr(P_matrix[x][2])+'\n')
xx=[]
yy=[]
zz=[]
for x in range(len(newmatrix)):
xx.append(newmatrix[x][0])
yy.append(newmatrix[x][1])
zz.append(newmatrix[x][2])
f6.write(repr(newmatrix[x][0])+','+repr(newmatrix[x][1])+','+repr(newmatrix[x][2])+'\n')
fig = plt.figure()
ax = Axes3D(fig)
ax.scatter(xx,yy,zz,c=colors)
plt.show()
def lle(input,finaldim):
from sklearn.manifold import locally_linear_embedding
import numpy
if isinstance(input,numpy.ndarray)==False:
input= input.todense()
X_r, err = locally_linear_embedding(input, n_neighbors=12, n_components=finaldim)
# X_transformed = embedding.fit_transform(input.transpose())
# return X_transformed,np.asarray(np.asmatrix(input)*np.asmatrix(X_transformed))
# X_transformed = X_r.fit_transform(input)
return [],X_r
def network_to_es_df(network, labels): embedding = manifold.locally_linear_embedding(X=network, n_neighbors=5, n_components=2) embedded_x = embedding[0][:,0] embedded_y = embedding[0][:,1] embedded_df = pd.DataFrame() embedded_df['x'] = embedded_x embedded_df['y'] = embedded_y class_df = pd.DataFrame() class_df['class'] = labels return embedded_df, class_df
def dim_down(self, method='tsne', ndim=2, rand_seed=6):
"""
:param method: selected method of dimension reduction.
:param ndim: number of retained dimensions.
:param rand_seed: seed used by the random number generator.
:return: embedding space with N cells * d feature.
"""
X = self.data
# http://scikit-learn.org/stable/modules/manifold.html
if method == 'tsne' or method == 'TSNE':
print(
"Dimension reduction with t-stochastic neighbor embedding(tSNE).\n"
)
V = manifold.TSNE(n_components=ndim,
random_state=rand_seed,
init='pca').fit_transform(X)
if method == 'lle' or method == 'LLE':
print("Dimension reduction with locally_linear_embedding(LLE).\n")
V, err = manifold.locally_linear_embedding(X,
n_neighbors=20,
n_components=ndim,
random_state=rand_seed,
method='modified')
if method == 'mds' or method == 'MDS':
print("Dimension reduction with Multidimensional scaling(MDS).\n")
V = manifold.MDS(n_components=ndim,
random_state=rand_seed,
max_iter=100,
n_init=1).fit_transform(X)
if method == 'se' or method == 'SE':
print("Dimension reduction with Spectral Embedding(SE).\n")
V = manifold.SpectralEmbedding(
n_components=ndim, random_state=rand_seed).fit_transform(X)
# http://scikit-learn.org/stable/modules/decomposition.html
if method == 'ica' or method == 'ICA':
print(
"Matrix decomposition with Independent component analysis(FastICA).\n"
)
V = decomposition.FastICA(n_components=ndim,
random_state=rand_seed).fit_transform(X)
if method == 'pca' or method == 'PCA':
print(
"Matrix decomposition with Principal component analysis(PCA).\n"
)
V = decomposition.PCA(n_components=ndim,
random_state=rand_seed).fit_transform(X)
return V
def test_singular_matrix():
M = np.ones((10, 3))
f = ignore_warnings
with pytest.raises(ValueError):
f(
manifold.locally_linear_embedding(
M,
n_neighbors=2,
n_components=1,
method="standard",
eigen_solver="arpack",
))
def preform_lle_on_dynamic_connectivity(input_path, output_path, brain_areas,
pattern):
"""
Computes the dynamic connectivity of brain areas with performing
a locally linear embedding returning its matrix.
:param input_path: path to input dir
:type input_path: str
:param output_path: path to output directory
:type output_path: str
:param brain_areas: number of brain areas
:type brain_areas: int
:param pattern: pattern of input files
:type pattern: str
:return: LLE matrix, LLE matrix shape
:rtype: np.ndarray, tuple
"""
paths = return_paths_list(input_path, output_path, pattern=pattern)
n_subjects = len(paths)
array = np.genfromtxt(paths[0], delimiter=',')
t_phases = array.shape[0]
dFC = np.full((brain_areas, brain_areas), fill_value=0).astype(np.float64)
lle_components = np.full((n_subjects, t_phases, (brain_areas * 2)),
fill_value=0).astype(np.float64)
for n in tqdm(range(0, n_subjects)):
phases = convert_to_phases(paths[n], output_path, brain_areas,
t_phases, n)
for t in range(0, t_phases):
for i in range(0, brain_areas):
for z in range(0, brain_areas):
if np.absolute(phases[i, t] - phases[z, t]) > np.pi:
dFC[i,
z] = np.cos(2 * np.pi - np.absolute(phases[i, t] -
phases[z, t]))
else:
dFC[i, z] = np.cos(
np.absolute(phases[i, t] - phases[z, t]))
dfc_output = os.path.join(output_path, 'dFC')
create_dir(dfc_output)
np.savez(
os.path.join(dfc_output, 'subject_{}_time_{}'.format(n, t)),
dFC)
lle, err = manifold.locally_linear_embedding(dFC,
n_neighbors=12,
n_components=2)
with open(
os.path.join(output_path, 'LLE_error_{}_{}'.format(n, t)),
'w') as output:
json.dump(err, output)
lle_components[n, t, :] = np.squeeze(lle.flatten())
# save the LLE matrix into a .npz file
np.savez(os.path.join(output_path, 'components_matrix'), lle_components)
return lle_components, lle_components.shape
def local_linear_embedding(data, n_components=2, n_neighbors=5):
from sklearn.manifold import LocallyLinearEmbedding, locally_linear_embedding
# lle = LocallyLinearEmbedding(n_components=n_components,
# n_neighbors=n_neighbors)
[lle, er] = locally_linear_embedding(data,
n_neighbors=n_neighbors,
n_components=n_components,
method='modified')
return lle
def test_locally_linear_embedding(self):
iris = datasets.load_iris()
df = pdml.ModelFrame(iris)
result = df.manifold.locally_linear_embedding(3, 3)
expected = manifold.locally_linear_embedding(iris.data, 3, 3)
self.assertEqual(len(result), 2)
self.assertIsInstance(result[0], pdml.ModelFrame)
tm.assert_index_equal(result[0].index, df.index)
tm.assert_numpy_array_equal(result[0].values, expected[0])
self.assertEqual(result[1], expected[1])
def test_locally_linear_embedding(self):
iris = datasets.load_iris()
df = pdml.ModelFrame(iris)
result = df.manifold.locally_linear_embedding(3, 3)
expected = manifold.locally_linear_embedding(iris.data, 3, 3)
self.assertEqual(len(result), 2)
self.assertTrue(isinstance(result[0], pdml.ModelFrame))
self.assert_index_equal(result[0].index, df.index)
self.assert_numpy_array_equal(result[0].values, expected[0])
self.assertEqual(result[1], expected[1])
def plot_lle(pidata, nneigh=14):
lle_data = np.array(pidata)
n_components = 2 # 2 dimension
X_r, err = locally_linear_embedding(lle_data,
n_neighbors=nneigh,
n_components=n_components,
eigen_solver='dense',
method='standard')
print("Done. Reconstruction error: %g" % err)
plt.figure()
plt.scatter(X_r[:, 0],
X_r[:, 1],
s=5,
c=np.log10(np.array(pidata[['PI4']])))
plt.title("Local linear embedding")
def sampleBoundary(im, boundary, point, samples_x, samples_y):
# Identify connected boundary segment with size 'samples_y' via K-NN
# This can yield some errors if two different boundaries are very near. Fixing this later.
nbrs = NearestNeighbors(n_neighbors=samples_y,
algorithm='ball_tree').fit(boundary)
dist, ind = nbrs.kneighbors([point])
# Apply LLE in order to unravel the boundary manifold.
# Kind of an overkill but no other idea on how to do this.
X_r, err = manifold.locally_linear_embedding(boundary[ind[0]],
n_neighbors=2,
n_components=1)
X_r = np.concatenate((X_r, ind.transpose()), axis=1)
X_r_sorted = X_r[X_r[:, 0].argsort()]
# Some plotting
plt.figure()
plt.imshow(im)
samples = np.zeros((samples_y, samples_x * 2 + 1, 3), 'uint8')
# Iterate over boundary segments of size 10
for i in range(0, samples_y - 9, 10):
boundarySegment = boundary[X_r_sorted[:, 1].astype(int)[i:i + 10]]
plt.scatter(boundarySegment[:, 0],
boundarySegment[:, 1],
marker='.',
s=5)
# Fit line to boundary point coordinates
slope, intercept, _, _, _ = stats.linregress(boundarySegment[:, 0],
boundarySegment[:, 1])
line_x1 = min(boundarySegment[:, 0])
line_x2 = max(boundarySegment[:, 0])
line_y1 = slope * line_x1 + intercept
line_y2 = slope * line_x2 + intercept
plt.plot([line_x1, line_x2], [line_y1, line_y2], marker='.')
# Sample patch
patch = bilinearInterpolation(slope, intercept, im, line_x1, line_x2,
samples_x, 10)
samples[i:i + 10, :] = patch
return samples
def compute(self):
matrix = self.getInputFromPort("X")
Y, squared_error = manifold.locally_linear_embedding(
X=matrix.values,
n_neighbors=self.forceGetInputFromPort("n_neighbors", 10),
n_components=self.forceGetInputFromPort("n_components", 2),
reg=self.forceGetInputFromPort("reg", 0.001),
eigen_solver=self.forceGetInputFromPort("eigen_solver", "auto"),
tol=self.forceGetInputFromPort("tol", 1e-06),
max_iter=self.forceGetInputFromPort("max_iter", 100),
method=self.method,
hessian_tol=self.hessian_tol,
modified_tol=self.modified_tol,
random_state=self.forceGetInputFromPort("random_state", None)
# out_dim = self.forceGetInputFromPort('out_dim', None)
)
proj_matrix = copy.deepcopy(matrix)
proj_matrix.values = Y
self.setResult("proj_matrix", proj_matrix)
self.setResult("squared_error", squared_error)
def compute(self):
matrix = self.getInputFromPort('X')
Y, squared_error = manifold.locally_linear_embedding(
X=matrix.values,
n_neighbors=self.forceGetInputFromPort('n_neighbors', 10),
n_components=self.forceGetInputFromPort('n_components', 2),
reg=self.forceGetInputFromPort('reg', 0.001),
eigen_solver=self.forceGetInputFromPort('eigen_solver', 'auto'),
tol=self.forceGetInputFromPort('tol', 1e-06),
max_iter=self.forceGetInputFromPort('max_iter', 100),
method=self.method,
hessian_tol=self.hessian_tol,
modified_tol=self.modified_tol,
random_state=self.forceGetInputFromPort('random_state', None)
# out_dim = self.forceGetInputFromPort('out_dim', None)
)
proj_matrix = copy.deepcopy(matrix)
proj_matrix.values = Y
self.setResult('proj_matrix', proj_matrix)
self.setResult('squared_error', squared_error)
def SwissRollTest01():
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
# Locally Linear Embedding of the swiss roll
from sklearn import manifold, datasets
#这里是生成数据集 X是1500 * 3 的矩阵(表示location)，color是1500 * 1的矩阵(表示label--颜色)
X, color = datasets.samples_generator.make_swiss_roll(n_samples = 1500)
#print X[1,:]
#print color[1]
X_r, err = manifold.locally_linear_embedding(X, n_neighbors=12, n_components=2)
#X_r是1500 * 2的矩阵，err是一个实数。
print X_r.shape
#print err
fig = plt.figure()
try:
ax = fig.add_subplot(211, projection='3d')
ax.scatter(X[:,0], X[:,1], X[:,2], c=color, cmap=plt.cm.Spectral)
except:
ax = fig.add_subplot(211)
ax.scatter(X[:,0],X[:,2],c=color, cmap=plt.cm.Spectral)
print ""
ax.set_title("Original data")
ax = fig.add_subplot(212)
#这里绘制的是projected data
ax.scatter(X_r[:,0], X_r[:,1], c=color, cmap=plt.cm.Spectral)
plt.axis('tight')
plt.xticks([]), plt.yticks([])
plt.title('Projected Data')
plt.show()
def main_LLE2():
f3 = open('projection vectors 1', 'w')
f4 = open('projection vectors 2', 'w')
f5 = open('projection vectors 3', 'w')
f6 = open('scatter matrix in 3D', 'w')
k = 40
images = []
images, colors = load_images()
matrix_images = matrix_build(images)
newmatrix, squared_error = locally_linear_embedding(matrix_images,
k,
3,
eigen_solver='auto')
print 'squared_error=' + repr(squared_error)
print newmatrix.shape
M1 = np.dot(newmatrix.T, matrix_images)
M2 = np.linalg.inv(np.dot(matrix_images.T, matrix_images))
P_matrix = (np.dot(M1, M2)).T
print P_matrix.shape
for x in range(len(P_matrix)):
f3.write(repr(P_matrix[x][0]) + '\n')
f4.write(repr(P_matrix[x][1]) + '\n')
f5.write(repr(P_matrix[x][2]) + '\n')
xx = []
yy = []
zz = []
for x in range(len(newmatrix)):
xx.append(newmatrix[x][0])
yy.append(newmatrix[x][1])
zz.append(newmatrix[x][2])
f6.write(
repr(newmatrix[x][0]) + ',' + repr(newmatrix[x][1]) + ',' +
repr(newmatrix[x][2]) + '\n')
fig = plt.figure()
ax = Axes3D(fig)
ax.scatter(xx, yy, zz, c=colors)
plt.show()
c=sr_color,
s=50,
alpha=0.8)
ax.set_title("Swiss Roll in Ambient Space")
ax.view_init(azim=-66, elev=12)
_ = ax.text2D(0.8, 0.05, s="n_samples=1500", transform=ax.transAxes)
# %%
# Computing the LLE and t-SNE embeddings, we find that LLE seems to unroll the
# Swiss Roll pretty effectively. t-SNE on the other hand, is able
# to preserve the general structure of the data, but, poorly represents the
# continous nature of our original data. Instead, it seems to unnecessarily
# clump sections of points together.
sr_lle, sr_err = manifold.locally_linear_embedding(sr_points,
n_neighbors=12,
n_components=2)
sr_tsne = manifold.TSNE(n_components=2,
learning_rate="auto",
perplexity=40,
init="pca",
random_state=0).fit_transform(sr_points)
fig, axs = plt.subplots(figsize=(8, 8), nrows=2)
axs[0].scatter(sr_lle[:, 0], sr_lle[:, 1], c=sr_color)
axs[0].set_title("LLE Embedding of Swiss Roll")
axs[1].scatter(sr_tsne[:, 0], sr_tsne[:, 1], c=sr_color)
_ = axs[1].set_title("t-SNE Embedding of Swiss Roll")
# %%
# Load the STL files and add the vectors
your_mesh = mesh.Mesh.from_file('Left_Thalamus.stl')
# Convert from groups of vertices (for each triangle) to list of vertices
tri, points, dim = np.shape(your_mesh.vectors)
data_mesh = np.zeros((tri * points, dim))
for index_t in range(tri):
for index_p in range(points):
data_mesh[index_t + index_p +
index_t * 2, :] = your_mesh.vectors[index_t, index_p, :]
# Isomap
#X_r = manifold.Isomap(n_neighbors=10,n_components=2).fit_transform(data_mesh)
# LLE
X_r, err = manifold.locally_linear_embedding(data_mesh,
n_neighbors=37,
n_components=2)
# T-sne
#tsne = manifold.TSNE(n_components=2, init='pca', random_state=0 )
#X_r = tsne.fit_transform(data_mesh)
# Plot original vertices
figure = pyplot.figure()
ax = figure.add_subplot(211, projection='3d')
ax.scatter(data_mesh[:, 0],
data_mesh[:, 1],
data_mesh[:, 2],
c=data_mesh[:, 0],
cmap=pyplot.cm.Spectral)
#pyplot.show()
ax.set_title("Original data")
train_df = pd.read_csv(data_root+"train_feature_pca500.csv")
test_df = pd.read_csv(data_root+"test_feature_pca500.csv")
photo_ids = np.vstack((train_df['photo_id'].reshape(-1,1),test_df['photo_id'].reshape(-1,1)))
train_df.drop('photo_id', axis=1, inplace=True)
test_df.drop('photo_id', axis=1, inplace=True)
X_std = np.vstack((train_df,test_df))
n_train = len(train_df)
from sklearn import manifold
X_lle, err = manifold.locally_linear_embedding(X_std, n_neighbors=10, n_components=300)
X_all = pd.DataFrame(X_lle)
X_all['photo_id'] = photo_ids
X_train = X_all[:n_train]
X_test = X_all[n_train:]
X_train.to_csv('train_feature_lle.csv', index=False)
X_test.to_csv('test_feature_lle.csv', index=False)
def lle(data): X_r, err = manifold.locally_linear_embedding(data, n_neighbors=5, n_components=2) return X_r
# License: BSD, (C) INRIA 2011
print __doc__
import pylab as pl
# This import is needed to modify the way figure behaves
from mpl_toolkits.mplot3d import Axes3D
#----------------------------------------------------------------------
# Locally linear embedding of the swiss roll
from sklearn import manifold, datasets
X, color = datasets.samples_generator.make_swiss_roll(n_samples=1500)
print "Computing LLE embedding"
X_r, err = manifold.locally_linear_embedding(X, n_neighbors=12, out_dim=2)
print "Done. Reconstruction error: %g" % err
#----------------------------------------------------------------------
# Plot result
fig = pl.figure()
try:
# compatibility matplotlib < 1.0
ax = fig.add_subplot(211, projection='3d')
ax.scatter(X[:, 0], X[:, 1], X[:, 2], c=color, cmap=pl.cm.Spectral)
except:
ax = fig.add_subplot(211)
ax.scatter(X[:, 0], X[:, 2], c=color, cmap=pl.cm.Spectral)
ax.set_title("Original data")
print __doc__
import pylab as pl
# This import is needed to modify the way figure behaves
from mpl_toolkits.mplot3d import Axes3D
#----------------------------------------------------------------------
# Locally linear embedding of the swiss roll
from sklearn import manifold, datasets
X, color = datasets.samples_generator.make_swiss_roll(n_samples=1500)
print "Computing LLE embedding"
X_r, err = manifold.locally_linear_embedding(X, n_neighbors=12, out_dim=2)
print "Done. Reconstruction error: %g" % err
#----------------------------------------------------------------------
# Plot result
fig = pl.figure()
try:
# compatibility matplotlib < 1.0
ax = fig.add_subplot(211, projection='3d')
ax.scatter(X[:, 0], X[:, 1], X[:, 2], c=color, cmap=pl.cm.Spectral)
except:
ax = fig.add_subplot(211)
ax.scatter(X[:, 0], X[:, 2], c=color, cmap=pl.cm.Spectral)
ax.set_title("Original data")
n_components = 4
pca = PCA(n_components, whiten=False)
param = pca.fit(dataset_matrix)
dataset_pca = pca.fit_transform(dataset_matrix)
print(pca.explained_variance_ratio_)
print(np.sum(pca.explained_variance_ratio_))
outdata_inter = dataset_pca.T
outdata = np.reshape(outdata_inter, (n_components, rows, cols))
#LLE DR method
n_neighbors = 5
n_components = 4
dataset_lle, err = manifold.locally_linear_embedding(dataset_matrix,
n_neighbors,
n_components,
eigen_solver='auto',
method='standard')
print("Reconstruction error: %g" % err)
outdata_inter = dataset_lle
outdata = np.reshape(outdata_inter, (n_components, rows, cols))
#ISOMAP Method
from sklearn.manifold import Isomap
n_neighbors = 5
n_components = 4
dataset_isomap = manifold.Isomap(n_neighbors,
n_components).fit_transform(dataset_matrix)
outdata_inter = dataset_isomap
outdata = np.reshape(outdata_inter, (n_components, rows, cols))
# angles = np.linspace(0,2*np.pi,100)
angles = np.linspace(0, 2 * np.pi, 50)
# angles = [5.3]
newData = True
if newData:
print("Integrating data")
# data = sim.states(duration=500)
data = sim.states(duration=2400, split=0.01) # max modified 850
data = data[1000:]
data = sim.interpolateCurve()[1000:]
print("Computing LLE embedding of data")
manifoldData, err = manifold.locally_linear_embedding(
data, n_neighbors=12, n_components=2, method='standard'
) # weird results, can see that it is rossler but it doesn't look as excpected
# Modified provides a smoother manifold, the return map still sucks
# Hessians manifold is weird.... and the return maps suck
print("Done. Reconstruction error: %g" % err)
print("Storing data")
sim.storeData("TestRossler")
np.savetxt("ManifoldRossler.txt", manifoldData)
else:
print("Loading data")
sim.loadData("TestRossler")
data = sim.getData()
manifoldData = np.loadtxt("ManifoldRossler.txt")
i = 0
print(__doc__)
import pylab as pl
# This import is needed to modify the way figure behaves
from mpl_toolkits.mplot3d import Axes3D
Axes3D
#----------------------------------------------------------------------
# Locally linear embedding of the swiss roll
from sklearn import manifold, datasets
X, color = datasets.samples_generator.make_swiss_roll(n_samples=1500)
print("Computing LLE embedding")
X_r, err = manifold.locally_linear_embedding(X, n_neighbors=12, n_components=2)
print("Done. Reconstruction error: %g" % err)
#----------------------------------------------------------------------
# Plot result
fig = pl.figure()
try:
# compatibility matplotlib < 1.0
ax = fig.add_subplot(211, projection='3d')
ax.scatter(X[:, 0], X[:, 1], X[:, 2], c=color, cmap=pl.cm.Spectral)
except:
ax = fig.add_subplot(211)
ax.scatter(X[:, 0], X[:, 2], c=color, cmap=pl.cm.Spectral)
ax.set_title("Original data")
poincareSection2 = np.array(
[point for point in poincareSection if (point[2] < 0.1)])
extremeEvents = []
index = []
for i, point in enumerate(poincareSection):
if point[2] > 0.1:
extremeEvents.append(i)
else:
index.append(i)
extremeEvents = np.array(extremeEvents)
print('Number of extreme events = %g' % len(extremeEvents))
print("Computing LLE embedding of return map")
manifoldOfPoincareSection, err = manifold.locally_linear_embedding(
poincareSection2, n_neighbors=8, n_components=2,
method='modified') # return map then manifold
print("Done. Reconstruction error: %g" % err)
## Fix colors for Plot
col = col = cm.get_cmap('plasma')
normdata = [np.linalg.norm(point) for point in poincareSection2]
normalize = colors.Normalize(vmin=min(normdata), vmax=max(normdata))
dataColors = [col(normalize(value)) for value in normdata]
poincColor = [dataColors[i] for i in range(0, len(poincareSection2))]
print('Plotting data')
fig = plt.figure()
ax = fig.add_subplot(221)
ax.set_title('Oscillator 1')
from sklearn import manifold,datasets
import pandas as pd
from sklearn import svm
from sklearn import cross_validation
from sklearn.metrics import confusion_matrix
from sklearn.cross_validation import cross_val_score
from unbalanced_dataset import SMOTE
import numpy as np
train=pd.read_csv('./cmv.csv')
train['Defective']=train['Defective'].map({'Y':1,'N':0})
print type(train.values)
train=train.values
print train[0:1]
X_r,err=manifold.locally_linear_embedding(train[:,0:-1],n_neighbors=12,n_components=4)
print("Done. Reconstruction error: %g" % err)
data=X_r
label=train[:,-1]
#print label
x_train,x_test,y_train,y_test=cross_validation.train_test_split(data,label,test_size=0.3,random_state=0)
verbose = False
ratio = float(np.count_nonzero(y_train==0)) / float(np.count_nonzero(y_train==1))
smote = SMOTE(ratio=ratio, verbose=verbose, kind='regular')
smox, smoy = smote.fit_transform(x_train, y_train)
print np.count_nonzero(smoy==1)
print np.count_nonzero(smoy==0)
clf=svm.SVC(C=10000,gamma=0.0078125)
#print y_train.astype(int)
clf.fit(smox,smoy)
y_pred=clf.predict(x_test)
print y_test
if not DBexists:
logging.info("Starting to build index into DB file %s" % outputf)
index.fit()
logging.info("Index fitted!!")
logging.info("Output database: {}".format(outputf))
else:
logging.info("Index loaded from DB file %s" % outputf)
sparse_word_centroids = wordCentroids(db=index, vect=vectorizer)
# Tal vez pueda cargar la matrix dipersa de word_centroids en ram y hacer NMF.
logging.info("Fitting Isomap for sparse coding ...")
X_s = Dict(sorted({w: v for w, v in sparse_word_centroids
if not v is None}.items(), key=lambda t: len(t[0])))
word_embeddings, err = locally_linear_embedding(vstack(list(X_s.values())), method='ltsa',
n_neighbors=5, n_components=args.dim, n_jobs=-1)
#word_embeddings = factorizer.fit_transform(csr_matrix(vstack(list(X_s.values()))))
logging.info("Recosntruction error %f ..." % err)
logging.info("DB Vocabulary size %d ..." % index.vocab_size)
logging.info("Vectorizer vocabulary size %d ..." % len(vectorizer.vocabulary_.keys()))
logging.info("Shape of resulting embedding matrix:")
#logging.info("({} {})".format(factorizer.embedding_.shape[0], factorizer.embedding_.shape[1]))
logging.info("Writing word vectors into file %s ..." % args.output)
write = partial(indexing.write_given_embedding, fname=args.output)
with open(args.output, "w") as f:
f.write("{} {}\n".format(len(X_s.keys()), word_embeddings.shape[1]) )
Parallel(#backend='threading',
n_jobs=20
N2=(Y==2)
N3=(Y==3)
pca=PCA(copy=True, n_components=2, whiten=False)
pcaX=pca.fit_transform(X)
lda = LinearDiscriminantAnalysis(n_components=2)
ldaX = lda.fit(X, Y).transform(X)
kpca = KernelPCA(kernel="rbf",n_components=2)
kpcaX = kpca.fit_transform(X)
isomap=Isomap(n_neighbors=15,n_components=2)
isomapX=isomap.fit_transform(X)
iieX,err=locally_linear_embedding(X,n_neighbors=12,n_components=2)
print("Done. Reconstruction error: %g" % err)
distX=np.zeros([len(Y),len(Y)])
nbrs = NearestNeighbors(n_neighbors=15, algorithm='ball_tree').fit(X)
distances, indices = nbrs.kneighbors(X)
for i in range(0,len(Y)):
distX[indices[i,0],indices[i,1:15]]=distances[i,1:15]
print(distX)
leX=spectral_embedding(distX,n_components=2)
plt.figure()
ax=plt.subplot(projection='3d')
ax.scatter(X[N1, 0], X[N1, 1], X[N1, 2], c='b')
ax.scatter(X[N2, 0], X[N2, 1], X[N2, 2], c='g')
components_ = pca.components_
print(components_)
data1 = data_pca[0:3000]
data2 = data_pca[3000:6000]
data3 = data_pca[6000:9000]
fig = plt.figure()
plt.scatter(data1[:, 0], np.zeros((3000, )), s=1, c="b", marker="1")
plt.scatter(data2[:, 0], np.zeros((3000, )), s=1, c="y", marker="1")
plt.scatter(data3[:, 0], np.zeros((3000, )), s=1, c="r", marker="1")
plt.show()
from sklearn.manifold import locally_linear_embedding
for neis in [5, 10, 20, 30, 40, 50]:
(data_lle, _) = locally_linear_embedding(data,
n_neighbors=neis,
n_components=1)
data1 = data_lle[0:3000]
data2 = data_lle[3000:6000]
data3 = data_lle[6000:9000]
fig = plt.figure()
plt.scatter(data1[:, 0], np.zeros((3000, )), s=1, c="b", marker="1")
plt.scatter(data2[:, 0], np.zeros((3000, )), s=1, c="y", marker="1")
plt.scatter(data3[:, 0], np.zeros((3000, )), s=1, c="r", marker="1")
plt.show()
#print(np.all(np.isfinite(K_train)))
# Initialise an SVM and fit data using random walk Kernel.
clf = svm.SVC(kernel='precomputed', C=1)
clf.fit(K_train, y_train)
# Predict and test.
y_pred = clf.predict(K_test)
# Calculate accuracy of classification.
acc = accuracy_score(y_test, y_pred)
print("Accuracy:", str(round(acc * 100, 2)))
K_train = manifold.locally_linear_embedding(K_train,
n_neighbors=5,
n_components=3)
K_test = manifold.locally_linear_embedding(K_test,
n_neighbors=5,
n_components=3)
clf.fit(
K_train,
y_train,
)
# Predict and test.
y_pred = clf.predict(K_test)
# Calculate accuracy of classification.
acc = accuracy_score(y_test, y_pred)
import pylab as pl
# This import is needed to modify the way figure behaves
from mpl_toolkits.mplot3d import Axes3D
Axes3D
# ----------------------------------------------------------------------
# Locally linear embedding of the swiss roll
from sklearn import manifold, datasets
X, color = datasets.samples_generator.make_swiss_roll(n_samples=1500)
print "Computing LLE embedding"
X_r, err = manifold.locally_linear_embedding(X, n_neighbors=12, n_components=2)
print "Done. Reconstruction error: %g" % err
# ----------------------------------------------------------------------
# Plot result
fig = pl.figure()
try:
# compatibility matplotlib < 1.0
ax = fig.add_subplot(211, projection="3d")
ax.scatter(X[:, 0], X[:, 1], X[:, 2], c=color, cmap=pl.cm.Spectral)
except:
ax = fig.add_subplot(211)
ax.scatter(X[:, 0], X[:, 2], c=color, cmap=pl.cm.Spectral)
ax.set_title("Original data")
def def_lenses_dimred(df, fs, get_PCA, get_isomap, get_LLE, get_MDS,
get_spectral_embedding, get_SVD):
scaler = MinMaxScaler()
mapper = km.KeplerMapper()
X = df[fs].as_matrix()
keys = []
values = []
minmax_scaler = MinMaxScaler()
df_minmax = minmax_scaler.fit_transform(df[fs].as_matrix())
# PCA
if get_PCA == True:
keys.append('lens_pca_0')
keys.append('lens_pca_1')
pca = mapper.fit_transform(df_minmax,
projection=PCA(n_components=2),
scaler=None)
values.append(scaler.fit_transform(pca[:, 0].reshape(-1, 1)))
values.append(scaler.fit_transform(pca[:, 1].reshape(-1, 1)))
# Isomap
if get_isomap == True:
keys.append('lens_isomap_0')
keys.append('lens_isomap_1')
isomap = manifold.Isomap(n_components=2,
n_neighbors=3).fit_transform(df_minmax)
values.append(scaler.fit_transform(isomap[:, 0].reshape(-1, 1)))
values.append(scaler.fit_transform(isomap[:, 1].reshape(-1, 1)))
# Locally linear embedding
if get_LLE == True:
keys.append('lens_LLE_0')
keys.append('lens_LLE_1')
LLE = manifold.locally_linear_embedding(df_minmax,
n_neighbors=3,
n_components=2,
random_state=0)[0]
values.append(scaler.fit_transform(LLE[:, 0].reshape(-1, 1)))
values.append(scaler.fit_transform(LLE[:, 1].reshape(-1, 1)))
# Multi-dimensional scaling
if get_MDS == True:
keys.append('lens_MDS_0')
keys.append('lens_MDS_1')
MDS = manifold.MDS(n_components=2).fit_transform(df_minmax)
values.append(scaler.fit_transform(MDS[:, 0].reshape(-1, 1)))
values.append(scaler.fit_transform(MDS[:, 1].reshape(-1, 1)))
# Spectral embedding
if get_spectral_embedding == True:
keys.append('lens_spectral_embedding_0')
keys.append('lens_spectral_embedding_1')
L = manifold.SpectralEmbedding(n_components=2,
n_neighbors=1,
random_state=0).fit_transform(df_minmax)
values.append(scaler.fit_transform(L[:, 0].reshape(-1, 1)))
values.append(scaler.fit_transform(L[:, 1].reshape(-1, 1)))
# truncated SVD
if get_SVD == True:
keys.append('lens_SVD_0')
keys.append('lens_SVD_1')
svd = TruncatedSVD(n_components=2,
random_state=42).fit_transform(df_minmax)
values.append(scaler.fit_transform(svd[:, 0].reshape(-1, 1)))
values.append(scaler.fit_transform(svd[:, 1].reshape(-1, 1)))
lenses_dimred = dict(zip(keys, values))
return (lenses_dimred)