def dimreduce_test(self):
# Check to see if intrinsically 2D data
# can be transformed to 2D and back exactly
p = PCA(dim=2, eps=0.)
new = p.fit_transform(self.data)
new = p.inv_transform(new)
assert np.allclose(new,self.data)
def transform_test(self):
# Check to see if data can
# be transformed and inverse transformed exactly
p = PCA(eps=0.)
new = p.fit_transform(self.data)
new = p.inv_transform(new)
assert np.allclose(new,self.data)
def transform_zca_whiten_test(self):
# Check to see if data can
# be transformed and inverse transformed exactly
p = PCA(whiten=True, eps=0.)
data = self.rng.randn(100,10)
p.fit(data)
new = p.transform_zca(data)
old = p.inv_transform_zca(new)
assert np.allclose(old,data)
def get_length_from_list( image_sequence ):
""" Function to get PCs of given image sequence """
N, D = len(image_sequence), len(sitk.GetArrayFromImage( image_sequence[0] ).ravel())
X = np.zeros([D,N])
for n in range(N):
X[:,n] = sitk.GetArrayFromImage( image_sequence[n] ).ravel()
ipca = PCA( X.T, np.eye(N), fraction=fraction, ptype='dual' )
iZ = ipca.transform()
length = 0
for n in range(N-1):
length += np.linalg.norm( iZ[n,:]-iZ[n+1,:] )
del X, ipca
return length
def train(self):
self.construct_graph()
tf.global_variables_initializer().run()
for _ in range(self.epoch):
x, y = self.shuffle_data(self.x_train, self.y_train)
for i in range(self.x_train.shape[0] // self.batch_size):
x_batch = x[i * self.batch_size:(i + 1) * self.batch_size]
y_batch = y[i * self.batch_size:(i + 1) * self.batch_size]
feed_dict = {self.x: x_batch, self.y: y_batch}
self.sess.run(self.opt, feed_dict=feed_dict)
b, w = self.sess.run([self.b, self.W])
self.coeff = np.concatenate((b.reshape((-1, 1)), w), axis=0)
PCA.save(self)
def get_pca_distance( tseq, wseq, mask, perimeter, vis ):
""" Function to compute the distance between PCA manifolds """
#==============================================================================
# Create matrices to store the sequences
#==============================================================================
n_t, n_w, D = len(tseq), len(wseq), len(sitk.GetArrayFromImage( tseq[0] ).ravel())
tX, wX = np.zeros([D,n_t]), np.zeros([D,n_w])
for n in range(n_t):
tX[:,n] = sitk.GetArrayFromImage( tseq[n] ).ravel()
for n in range(n_w):
wX[:,n] = sitk.GetArrayFromImage( wseq[n] ).ravel()
#==============================================================================
# Reduce dimensionality of target sequence
#==============================================================================
tpca = PCA( tX[mask,:].T, np.eye(n_t), fraction=fraction, ptype='dual' )
tZ = tpca.transform()
U = np.dot( np.dot( tpca.psi, tpca.eigVec ), \
np.linalg.inv(np.diag(np.sqrt( tpca.eigVal )) ) )
#==============================================================================
# Project warped sequence onto reduced subspace of target
#==============================================================================
wpca = PCA( wX[mask,:].T, np.eye(n_w), fraction=fraction, ptype='dual' )
wtZ = np.real( np.dot( U.T, wpca.A ).T )
length = 0
for n in range(n_w-1):
length += np.linalg.norm( wtZ[n,:]-wtZ[n+1,:] )
#==============================================================================
# Find correspondences if sequences have different number of frames
#==============================================================================
n_vertices = np.max( [n_t, n_w])
idx_t, idx_w = np.zeros( n_vertices, dtype = np.uint ),\
np.zeros( n_vertices, dtype = np.uint )
at, aw = np.linspace(0,1,num=n_t), np.linspace(0,1,num=n_w)
if n_t>n_w:
idx_t = np.arange( n_vertices )
for ni in np.arange( n_vertices ):
idx_w[ni] = find_nearest( aw, at[ni] )
elif n_t<n_w:
idx_w = np.arange( n_vertices )
for ni in np.arange(n_vertices):
idx_t[ni] = find_nearest( at, aw[ni] )
else:
idx_t = np.arange( n_vertices )
idx_w = np.arange( n_vertices )
return _GAMMA*np.sum( np.linalg.norm(wtZ[idx_w,:]-tZ[idx_t,:], axis=1) ) +\
(1-_GAMMA)*(perimeter-length)
def change_test(self):
# Check to see if functions touch original data
# They should not
data_init = np.copy(self.data)
p = PCA(eps=0.)
p.fit(self.data)
assert np.allclose(self.data,data_init)
p.fit_transform(self.data)
assert np.allclose(self.data,data_init)
p.inv_transform(self.data)
assert np.allclose(self.data,data_init)
def plot_in_2d(X, y=None, title=None, accuracy=None, legend_labels=None):
cmap = plt.get_cmap('viridis')
X_transformed = PCA().transform(X, 2)
x1 = X_transformed[:, 0]
x2 = X_transformed[:, 1]
class_distr = []
y = np.array(y).astype(int)
colors = [cmap(i) for i in np.linspace(0, 1, len(np.unique(y)))]
# Plot the different class distributions
for i, l in enumerate(np.unique(y)):
_x1 = x1[y == l]
_x2 = x2[y == l]
_y = y[y == l]
class_distr.append(plt.scatter(_x1, _x2, color=colors[i]))
# Plot legend
if not legend_labels is None:
plt.legend(class_distr, legend_labels, loc=1)
# Plot title
if title:
if accuracy:
perc = 100 * accuracy
plt.suptitle(title)
plt.title("Accuracy: %.1f%%" % perc, fontsize=10)
else:
plt.title(title)
# Axis labels
plt.xlabel('Principal Component 1')
plt.ylabel('Principal Component 2')
plt.show()
@author: Eric
"""
from os import chdir
chdir("..")
import numpy as np
import matplotlib.pyplot as plt
import scipy.io
from pca.pca import PCA
import SAILnet
imfile = "patches.mat"
imname = "patches"
nullpca = PCA()
normalpca = PCA()
whiteningpca = PCA(whiten=True)
patches = scipy.io.loadmat(imfile)[imname]
origshape = patches.shape
veclength = origshape[0] * origshape[1]
nimages = origshape[2]
# unroll images
patches = patches.reshape((veclength, nimages))
scipy.io.savemat("unrolledpatches.mat", {"patches": patches})
# the PCA object wants each row to be a data point by default
patches = np.transpose(patches)
def ready_test(self):
p = PCA(dim=2, eps=0.)
assert p.ready == False
new = p.fit(self.data)
assert p.ready == True
def whiten_test(self):
data = self.data+self.rng.rand(*self.data.shape)
p = PCA(whiten=True, eps=0.)
new = p.fit_transform(data)
cov = new.T.dot(new)
assert np.allclose(cov,np.eye(data.shape[1]))
import numpy as np
from pca.pca import PCA
def sd_normalize(mat: np.ndarray):
sd = np.sqrt(np.var(mat, 0))
return mat / sd
def eigen_normalize(mat, eigen, ep):
return mat / np.array(np.sqrt(eigen[0:2] + ep))
if __name__ == '__main__':
data = np.array([[5, 0, 1], [0, 1, 1], [1, 0, 1], [1, 1, 1], [0, 0, 1],
[1, 2, 1], [2, 3, 4], [0, 0, 1]])
pca = PCA(data)
out, eigen, vector = pca.fit()
pca_whitening_mat = sd_normalize(out)
pca_whitening_mat2 = eigen_normalize(out, eigen, 0.01)
print(pca_whitening_mat)
a = 1