def plot_loadings(components):
figs = []
for j in range(N_COMP):
legend = 'Loading #{j} for model {snr}'.format(j=j + 1, snr=snr)
plot_map2d(components[j, ].reshape(dice5_data.SHAPE), title=legend)
figs.append(plt.gcf())
return figs
def plot_map2d_of_PCA_models(models_dict, nrow, ncol, shape,N_COMP,folder,title_attr=None):
"""Plot 2 weight maps of models"""
#from .plot import plot_map2d
ax_i = 1
for k in models_dict.keys():
mod = models_dict[k]
if hasattr(mod, "V"):
w = mod.V
elif hasattr(mod, "components_"): # to work with sklean
w = mod.components_.T
if (title_attr is not None and hasattr(mod, title_attr)):
title = getattr(mod, title_attr)
else:
title = None
ax = plt.subplot(nrow, ncol, ax_i)
plt.tight_layout()
utils.plot_map2d(w[:,0].reshape(shape[:2]),ax,title=title)
ax_i += 1
ax = plt.subplot(nrow, ncol, ax_i)
utils.plot_map2d(w[:,1].reshape(shape[:2]),ax,title=title)
ax_i += 1
ax = plt.subplot(nrow, ncol, ax_i)
utils.plot_map2d(w[:,2].reshape(shape[:2]),ax,title=title)
ax_i += 1
plt.savefig(os.path.join(folder,'pca_fits.png'))
plt.close()
###########################################################################
## LogisticRegressionL1L2TV
# Minimize:
# f(beta, X, y) = - loglik/n_train
# + l2/2 * ||beta||^2_2
# + l1 * ||beta||_1
# + tv * TV(beta)
l1, l2, tv = alpha * np.array((.05, .75, .2)) # l1, l2, tv penalties
## Limit the precison to 1e-3
A = nesterov_tv.linear_operator_from_shape(beta3d.shape)
enettv = estimators.LogisticRegressionL1L2TV(l1, l2, tv, A, algorithm_params = dict(eps=1e-3))
yte_pred_enettv = enettv.fit(Xtr, ytr).predict(Xte)
_, recall_enettv, _, _ = precision_recall_fscore_support(yte, yte_pred_enettv, average=None)
###########################################################################
## Plot
plot = plt.subplot(221)
limits = None #np.array((beta3d.min(), beta3d.max())) / 2.
#limits = None
utils.plot_map2d(beta3d.reshape(shape), plot, title="beta star")
plot = plt.subplot(222)
utils.plot_map2d(enettv.beta.reshape(shape), plot, limits=limits,
title="L1+L2+TV (%.2f, %.2f)" % tuple(recall_enettv))
plot = plt.subplot(223)
utils.plot_map2d(ridge_sklrn.coef_.reshape(shape), plot, limits=limits,
title="Ridge (sklrn) (%.2f, %.2f)" % tuple(recall_ridge_sklrn))
plot = plt.subplot(224)
utils.plot_map2d(ridge_prsmy.beta.reshape(shape), plot,limits=limits,
title="Ridge (Parsimony) (%.2f, %.2f)" % tuple(recall_ridge_prsmy))
plt.show()
use_eg=False,
output=True)
t = timeit.timeit(stmt='e_con_sparse.fit(X)', setup="from __main__ import e_con_sparse, X", number=1)
print "CONESTA:", t
V_sparse_con = e_con_sparse.V
del e_con_sparse
sparsepca_sklearn = sklearn.decomposition.SparsePCA(n_components=N_COMP,
alpha=0.4)
t = timeit.timeit(stmt='sparsepca_sklearn.fit(X)', setup="from __main__ import sparsepca_sklearn, X", number=1)
print "Sparse PCA:", t
V_sparsepca_sklearn = sparsepca_sklearn.components_.transpose()
del sparsepca_sklearn
plot = plt.subplot(5, N_COMP, 1)
plot_map2d(beta3d.reshape(INPUT_SHAPE), plot, title="beta star")
for k in range(N_COMP):
# Plot PCA
plot = plt.subplot(5, N_COMP, N_COMP+1+k)
title = "PCA comp #{i}".format(i=k)
plot_map2d(V_pca_sklearn[:,k].reshape(INPUT_SHAPE), plot, title=title)
# Plot sparsepca_sklearn
plot = plt.subplot(5, N_COMP, 2*N_COMP+1+k)
title = "SparsePCA comp #{i}".format(i=k)
plot_map2d(V_sparsepca_sklearn[:,k].reshape(INPUT_SHAPE), plot, title=title)
# Plot the components EG
plot = plt.subplot(5, N_COMP, 3*N_COMP+1+k)
title = "PCA_L1L2TV EG comp #{i}".format(i=k)
plot_map2d(V_sparse_eg[:,k].reshape(INPUT_SHAPE), plot, title=title)
snr = float(input_str)
except:
print "Can't parse input"
continue
if snr not in dice5_data.ALL_SNRS:
print "Invalid SNR"
continue
# Reload weight maps
output_dir = OUTPUT_DIR_FORMAT.format(snr=snr)
full_filename = os.path.join(output_dir, OUTPUT_PCA_FILE)
with open(full_filename) as f:
pca = pickle.load(f)
for j in range(N_COMP):
legend = 'Loading #{j} for model {snr}'.format(j=j + 1, snr=snr)
plot_map2d(pca.components_[j, ].reshape(dice5_data.SHAPE),
title=legend)
f = plt.gcf()
filename = os.path.join(output_dir,
OUTPUT_LOADING_FILE_FMT.format(i=j + 1))
f.savefig(filename)
print "Figures are saved. Close them to continue."
plt.show()
# Store chosen SNR
CHOSEN_SNR = []
while True:
input_str = raw_input("Enter a SNR value to store (or q to quit):")
if input_str == "q":
break
try:
###########################################################################
## Fit LinearRegressionL1L2TV
# Min: (1 / (2 * n)) * ||Xbeta - y||^2_2
# + l1 * ||beta||_1
# + (l2 / 2) * ||beta||^2_2
# + tv * TV(beta)
#
l1, l2, tv = alpha * np.array((.33, .33, .33)) # l1, l2, tv penalties
A = nesterov_tv.linear_operator_from_shape(shape)
algo = algorithms.proximal.CONESTA(max_iter=500)
enettv = estimators.LinearRegressionL1L2TV(l1, l2, tv, A, algorithm=algo)
yte_pred_enettv = enettv.fit(Xtr, ytr).predict(Xte)
###########################################################################
## Plot
# TODO: Please remove dependence on scikit-learn. Add required functionality
# to parsimony instead.
plot = plt.subplot(131)
utils.plot_map2d(beta3d.reshape(shape), plot, title="beta star")
plot = plt.subplot(132)
utils.plot_map2d(enet.beta.reshape(shape), plot, title="beta enet (R2=%.2f)" %
r2_score(yte, yte_pred_enet))
#utils.plot_map2d(enet.coef_.reshape(shape), plot, title="beta enet (R2=%.2f)" %
# r2_score(yte, yte_pred_enet), limits=limits/1.)
plot = plt.subplot(133)
utils.plot_map2d(enettv.beta.reshape(shape), plot,
title="beta enettv (R2=%.2f)" % r2_score(yte, yte_pred_enettv))
plt.show()
yte_pred_enet = enet.fit(Xtr, ytr).predict(Xte)
###########################################################################
## Fit LinearRegressionL1L2TV
#
l1, l2, tv = alpha * np.array((.4, .1, .5)) # l2, l1, tv penalties
A, n_compacts = tv_helper.A_from_shape(shape)
#import parsimony.functions as functions
#functions.RR_L1_TV(X, y, k, l, g, A=A)
enettv = LinearRegressionL1L2TV(l1, l2, tv, A, algorithm=StaticCONESTA(max_iter=500))
yte_pred_enettv = enettv.fit(Xtr, ytr).predict(Xte)
###########################################################################
## Plot
# TODO: Please remove dependence on scikit-learn. Add required functionality
# to parsimony instead.
plot = plt.subplot(131)
plot_map2d(beta3d.reshape(shape), plot, title="beta star")
plot = plt.subplot(132)
plot_map2d(enet.coef_.reshape(shape), plot, title="beta enet (R2=%.2f)" %
r2_score(yte, yte_pred_enet),
limits=(beta3d.min(), beta3d.max()))
plot = plt.subplot(133)
plot_map2d(enettv.beta.reshape(shape), plot,
title="beta enettv (R2=%.2f)" \
% r2_score(yte, yte_pred_enettv),
limits=(beta3d.min(), beta3d.max()))
plt.show()
enettv = estimators.LogisticRegressionL1L2TV(l1,
l2,
tv,
A,
algorithm_params=dict(eps=1e-3))
yte_pred_enettv = enettv.fit(Xtr, ytr).predict(Xte)
_, recall_enettv, _, _ = precision_recall_fscore_support(yte,
yte_pred_enettv,
average=None)
###########################################################################
## Plot
plot = plt.subplot(221)
limits = None #np.array((beta3d.min(), beta3d.max())) / 2.
#limits = None
utils.plot_map2d(beta3d.reshape(shape), plot, title="beta star")
plot = plt.subplot(222)
utils.plot_map2d(enettv.beta.reshape(shape),
plot,
limits=limits,
title="L1+L2+TV (%.2f, %.2f)" % tuple(recall_enettv))
plot = plt.subplot(223)
utils.plot_map2d(ridge_sklrn.coef_.reshape(shape),
plot,
limits=limits,
title="Ridge (sklrn) (%.2f, %.2f)" %
tuple(recall_ridge_sklrn))
plot = plt.subplot(224)
utils.plot_map2d(ridge_prsmy.beta.reshape(shape),
plot,
limits=limits,
ridge2 = LogisticRegressionL1L2TV(0, alpha, 0, A, algorithm=StaticCONESTA(max_iter=500))
yte_pred_ridge2 = ridge2.fit(Xtr, ytr).predict(Xte)
_, recall_ridge2, _, _ = precision_recall_fscore_support(yte, yte_pred_ridge2, average=None)
###########################################################################
## LogisticRegressionL1L2TV
# Minimize:
# f(beta, X, y) = - loglik/n_train
# + k/2 * ||beta||^2_2
# + l * ||beta||_1
# + g * TV(beta)
l1, l2, tv = alpha * np.array((.4, .1, .5)) / 10 # l2, l1, tv penalties
A, n_compacts = tv_helper.A_from_shape(beta3d.shape)
enettv = LogisticRegressionL1L2TV(l1, l2, tv, A, algorithm=StaticCONESTA(max_iter=500))
yte_pred_enettv = enettv.fit(Xtr, ytr).predict(Xte)
_, recall_enettv, _, _ = precision_recall_fscore_support(yte, yte_pred_enettv, average=None)
###########################################################################
## Plot
plot = plt.subplot(221)
plot_map2d(beta3d.reshape(shape), plot, title="beta star")
plot = plt.subplot(222)
plot_map2d(enettv.beta.reshape(shape), plot, limits=(beta3d.min(), beta3d.max()),
title="L1+L2+TV (%.2f, %.2f)" % tuple(recall_enettv))
plot = plt.subplot(223)
plot_map2d(ridge.coef_.reshape(shape), plot, limits=(beta3d.min(), beta3d.max()),
title="Ridge (%.2f, %.2f)" % tuple(recall_ridge))
plot = plt.subplot(224)
plot_map2d(ridge2.beta.reshape(shape), plot, limits=(beta3d.min(), beta3d.max()),
title="Ridge (parsimony) (%.2f, %.2f)" % tuple(recall_ridge2))
plt.show()
#Load result of minimization
beta_path = os.path.join(BETA_DIR, "components.npz")
components = np.load(beta_path)
components = components['arr_0'].reshape(100, 100, 3)
for k in range(0, 3):
components[:, :, k] = components[:, :, k] - components[:, :, k].mean()
components[:, :, k] = components[:, :, k] / components[:, :, k].std()
true = np.abs(true)
components = np.abs(components)
for k in range(3):
plot = plt.subplot(3, 3, 3 + 1 + k)
title = "comp #{i}".format(i=k)
plot_map2d(components[:, :, k], plot, title=title)
f = plt.gcf()
plt.show()
filename = os.path.join(BASE_DIR,
"eps_components_0.1/eps_1e-%r.svg") % (EPS)
f.savefig(filename)
plt.clf()
mean_mse = 0
for k in range(0, 2):
data = np.zeros((10000, 2))
data[:, 0] = true[:, :, k].reshape(10000)
R = np.zeros((2))
for i in range(0, 2):
data[:, 1] = components[:, :, i].reshape(10000)
R[i] = np.abs(np.corrcoef(np.abs(data.T))[0, 1])
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
from brainomics import plot_utilities
from parsimony.utils import plot_map2d
#FIGURES OF PAPER
#################################################################################################################################################
#reconstruction with Standard PCA
components = np.load(
"/neurospin/brainomics/2014_pca_struct/dice5_ad_validation/results_0.1_1e-6/data_100_100_0/results/0/pca_0.0_0.0_0.0/components.npz"
)
components = components['arr_0']
for k in range(3):
fig = plot_map2d(components[:, k].reshape(100, 100))
#reconstruction with Sparse PCA
components = np.load(
"/neurospin/brainomics/2014_pca_struct/dice5_ad_validation/results_0.1_1e-6/data_100_100_0/results/0/sparse_pca_0.0_0.0_1.0/components.npz"
)
components = components['arr_0']
for k in range(3):
fig = plots.map2d(components[:, k].reshape(100, 100))
#reconstruction with ElasticNet PCA
components = np.load(
"/neurospin/brainomics/2014_pca_struct/dice5_ad_validation/results_0.1_1e-6/data_100_100_0/results/0/struct_pca_0.01_1e-05_0.5/components.npz"
)
components = components['arr_0']
for k in range(3):