def mapper(key, output_collector):
import mapreduce as GLOBAL # access to global variables:
model_name, global_pen, tv_ratio, l1_ratio = key
if model_name == 'pca':
# Force the key
global_pen = tv_ratio = l1_ratio = 0
if model_name == 'sparse_pca':
global_pen = tv_ratio = 0
ll1 = l1_ratio
if model_name == 'struct_pca':
ltv = global_pen * tv_ratio
ll1 = l1_ratio * global_pen * (1 - tv_ratio)
ll2 = (1 - l1_ratio) * global_pen * (1 - tv_ratio)
assert (np.allclose(ll1 + ll2 + ltv, global_pen))
X_train = GLOBAL.DATA_RESAMPLED["X"][0]
n, p = X_train.shape
X_test = GLOBAL.DATA_RESAMPLED["X"][1]
# A matrices
Atv = GLOBAL.A
N_COMP = GLOBAL.N_COMP
# Fit model
if model_name == 'pca':
model = sklearn.decomposition.PCA(n_components=N_COMP)
if model_name == 'sparse_pca':
model = sklearn.decomposition.SparsePCA(n_components=N_COMP, alpha=ll1)
if model_name == 'struct_pca':
model = pca_tv.PCA_L1_L2_TV(n_components=N_COMP,
l1=ll1,
l2=ll2,
ltv=ltv,
Atv=Atv,
criterion="frobenius",
eps=1e-6,
max_iter=100,
inner_max_iter=int(1e4),
output=False)
model.fit(X_train)
# Save the projectors
if (model_name == 'pca') or (model_name == 'sparse_pca'):
V = model.components_.T
if model_name == 'struct_pca':
V = model.V
# Project train & test data
if (model_name == 'pca') or (model_name == 'sparse_pca'):
X_train_transform = model.transform(X_train)
X_test_transform = model.transform(X_test)
if (model_name == 'struct_pca'):
X_train_transform, _ = model.transform(X_train)
X_test_transform, _ = model.transform(X_test)
# Reconstruct train & test data
# For SparsePCA or PCA, the formula is: UV^t (U is given by transform)
# For StructPCA this is implemented in the predict method (which uses
# transform)
if (model_name == 'pca') or (model_name == 'sparse_pca'):
X_train_predict = np.dot(X_train_transform, V.T)
X_test_predict = np.dot(X_test_transform, V.T)
if (model_name == 'struct_pca'):
X_train_predict = model.predict(X_train)
X_test_predict = model.predict(X_test)
# Compute Frobenius norm between original and recontructed datasets
frobenius_train = np.linalg.norm(X_train - X_train_predict, 'fro')
frobenius_test = np.linalg.norm(X_test - X_test_predict, 'fro')
print(frobenius_test)
# Compute explained variance ratio
evr_train = metrics.adjusted_explained_variance(X_train_transform)
evr_train /= np.var(X_train, axis=0).sum()
evr_test = metrics.adjusted_explained_variance(X_test_transform)
evr_test /= np.var(X_test, axis=0).sum()
# Remove predicted values (they are huge)
del X_train_predict, X_test_predict
ret = dict(frobenius_train=frobenius_train,
frobenius_test=frobenius_test,
components=V,
X_train_transform=X_train_transform,
X_test_transform=X_test_transform,
evr_train=evr_train,
evr_test=evr_test)
output_collector.collect(key, ret)
ltv = global_pen * tv_ratio
ll1 = l1_ratio * global_pen * (1 - tv_ratio)
ll2 = (1 - l1_ratio) * global_pen * (1 - tv_ratio)
assert (np.allclose(ll1 + ll2 + ltv, global_pen))
#Compute A and mask
masks = []
INPUT_OBJECT_MASK_FILE_FORMAT = "mask_{o}.npy"
for i in range(3):
filename = INPUT_OBJECT_MASK_FILE_FORMAT.format(o=i)
masks.append(np.load(filename))
im_shape = config["im_shape"]
Atv = nesterov_tv.A_from_shape(im_shape)
########################################
snapshot = AlgorithmSnapshot(
'/neurospin/brainomics/2014_pca_struct/lambda_max/',
saving_period=1).save_conesta
mod = pca_tv.PCA_L1_L2_TV(n_components=3,
l1=ll1,
l2=ll2,
ltv=ltv,
Atv=Atv,
criterion="frobenius",
eps=1e-4,
max_iter=100,
inner_max_iter=int(1e4),
output=True,
callback=snapshot)
mod.fit(X[:250, :])
def mapper(key, output_collector):
import mapreduce as GLOBAL # access to global variables:
model_name, global_pen, struct_ratio, l1_ratio = key
if model_name == 'pca':
global_pen = struct_ratio = l1_ratio = 0
if model_name == 'sparse_pca':
global_pen = struct_ratio = 0
ll1 = l1_ratio
if model_name == 'struct_pca':
ltv = global_pen * struct_ratio
ll1 = l1_ratio * global_pen * (1 - struct_ratio)
ll2 = (1 - l1_ratio) * global_pen * (1 - struct_ratio)
assert (np.allclose(ll1 + ll2 + ltv, global_pen))
if model_name == 'graphNet_pca':
lgn = global_pen * struct_ratio
ll1 = l1_ratio * global_pen * (1 - struct_ratio)
ll2 = (1 - l1_ratio) * global_pen * (1 - struct_ratio)
assert (np.allclose(ll1 + ll2 + lgn, global_pen))
X_train = GLOBAL.DATA_RESAMPLED["X"][0]
n, p = X_train.shape
X_test = GLOBAL.DATA_RESAMPLED["X"][1]
# A matrices
A = GLOBAL.A
N_COMP = GLOBAL.N_COMP
# Fit model
if model_name == 'pca':
model = sklearn.decomposition.PCA(n_components=N_COMP)
if model_name == 'sparse_pca':
model = sklearn.decomposition.SparsePCA(n_components=N_COMP, alpha=ll1)
if model_name == 'struct_pca':
model = pca_tv.PCA_L1_L2_TV(n_components=N_COMP,
l1=ll1,
l2=ll2,
ltv=ltv,
Atv=A,
criterion="frobenius",
eps=1e-6,
max_iter=100,
inner_max_iter=int(1e3),
output=False)
if model_name == 'graphNet_pca':
A = sparse.vstack(A)
model = pca_struct.PCAGraphNet(n_components=N_COMP,
l1=ll1,
l2=ll2,
lgn=lgn,
Agn=A,
criterion="frobenius",
eps=1e-6,
max_iter=500,
output=False)
model.fit(X_train)
# Save the projectors
if (model_name == 'pca') or (model_name == 'sparse_pca'):
V = model.components_.T
if (model_name == 'struct_pca') or (model_name == 'graphNet_pca'):
V = model.V
# Project train & test data
if (model_name == 'pca') or (model_name == 'sparse_pca'):
X_train_transform = model.transform(X_train)
X_test_transform = model.transform(X_test)
if (model_name == 'struct_pca') or (model_name == 'graphNet_pca'):
X_train_transform, _ = model.transform(X_train)
X_test_transform, _ = model.transform(X_test)
# Reconstruct train & test data
# For SparsePCA or PCA, the formula is: UV^t (U is given by transform)
# For StructPCA this is implemented in the predict method (which uses
# transform)
if (model_name == 'pca') or (model_name == 'sparse_pca'):
X_train_predict = np.dot(X_train_transform, V.T)
X_test_predict = np.dot(X_test_transform, V.T)
if (model_name == 'struct_pca') or (model_name == 'graphNet_pca'):
X_train_predict = model.predict(X_train)
X_test_predict = model.predict(X_test)
# Compute Frobenius norm between original and recontructed datasets
frobenius_train = np.linalg.norm(X_train - X_train_predict, 'fro')
frobenius_test = np.linalg.norm(X_test - X_test_predict, 'fro')
print(frobenius_test)
del X_train_predict, X_test_predict
ret = dict(frobenius_train=frobenius_train,
frobenius_test=frobenius_test,
components=V,
X_train_transform=X_train_transform,
X_test_transform=X_test_transform)
output_collector.collect(key, ret)
def mapper(key, output_collector):
import mapreduce as GLOBAL # access to global variables:
model_name, global_pen, tv_ratio, l1_ratio = key
if model_name == 'pca':
# Force the key
global_pen = tv_ratio = l1_ratio = 0
# if model_name == 'sparse_pca':
# # Force the key
# ltv = 1e-6
# ll1 = l1_ratio * global_pen
# ll2 = (1 - l1_ratio) * global_pen * (1 - tv_ratio)
if model_name == 'sparse_pca':
global_pen = tv_ratio = 0
ll1=l1_ratio
if model_name == 'struct_pca':
ltv = global_pen * tv_ratio
ll1 = l1_ratio * global_pen * (1 - tv_ratio)
ll2 = (1 - l1_ratio) * global_pen * (1 - tv_ratio)
assert(np.allclose(ll1 + ll2 + ltv, global_pen))
X_train = GLOBAL.DATA_RESAMPLED["X"][0]
print (X_train.shape)
n, p = X_train.shape
X_test = GLOBAL.DATA_RESAMPLED["X"][1]
# A matrices
Atv = GLOBAL.Atv
# Fit model
if model_name == 'pca':
model = sklearn.decomposition.PCA(n_components=N_COMP)
# if model_name == 'sparse_pca':
# model = pca_tv.PCA_L1_L2_TV(n_components=N_COMP,
# l1=ll1, l2=ll2, ltv=ltv,
# Atv=Atv,
# criterion="frobenius",
# eps=1e-6,
# max_iter=100,
# inner_max_iter=int(1e4),
# output=False)
if model_name == 'sparse_pca':
model = sklearn.decomposition.SparsePCA(n_components=N_COMP,alpha=ll1)
if model_name == 'struct_pca':
model = pca_tv.PCA_L1_L2_TV(n_components=N_COMP,
l1=ll1, l2=ll2, ltv=ltv,
Atv=Atv,
criterion="frobenius",
eps=1e-6,
max_iter=100,
inner_max_iter=int(1e4),
output=True)
t0 = time.clock()
t0 = time.clock()
model.fit(X_train)
t1 = time.clock()
_time = t1 - t0
#print "X_test", GLOBAL.DATA["X"][1].shape
# Save the projectors
if (model_name == 'pca') or (model_name == 'sparse_pca'):
V = model.components_.T
if model_name == 'struct_pca' :
V = model.V
# Project train & test data
if (model_name == 'pca') or (model_name == 'sparse_pca'):
X_train_transform = model.transform(X_train)
X_test_transform = model.transform(X_test)
if (model_name == 'struct_pca') :
X_train_transform, _ = model.transform(X_train)
X_test_transform, _ = model.transform(X_test)
# Reconstruct train & test data
# For SparsePCA or PCA, the formula is: UV^t (U is given by transform)
# For StructPCA this is implemented in the predict method (which uses
# transform)
if (model_name == 'pca') or (model_name == 'sparse_pca'):
X_train_predict = np.dot(X_train_transform, V.T)
X_test_predict = np.dot(X_test_transform, V.T)
if (model_name == 'struct_pca') :
X_train_predict = model.predict(X_train)
X_test_predict = model.predict(X_test)
# Compute Frobenius norm between original and recontructed datasets
frobenius_train = np.linalg.norm(X_train - X_train_predict, 'fro')
frobenius_test = np.linalg.norm(X_test - X_test_predict, 'fro')
print (frobenius_test )
# Compute explained variance ratio
evr_train = metrics.adjusted_explained_variance(X_train_transform)
evr_train /= np.var(X_train, axis=0).sum()
evr_test = metrics.adjusted_explained_variance(X_test_transform)
evr_test /= np.var(X_test, axis=0).sum()
# Remove predicted values (they are huge)
del X_train_predict, X_test_predict
# Compute geometric metrics and norms of components
TV = parsimony.functions.nesterov.tv.TotalVariation(1, A=Atv)
l0 = np.zeros((N_COMP,))
l1 = np.zeros((N_COMP,))
l2 = np.zeros((N_COMP,))
tv = np.zeros((N_COMP,))
for i in range(N_COMP):
# Norms
l0[i] = np.linalg.norm(V[:, i], 0)
l1[i] = np.linalg.norm(V[:, i], 1)
l2[i] = np.linalg.norm(V[:, i], 2)
tv[i] = TV.f(V[:, i])
ret = dict(frobenius_train=frobenius_train,
frobenius_test=frobenius_test,
components=V,
X_train_transform=X_train_transform,
X_test_transform=X_test_transform,
evr_train=evr_train,
evr_test=evr_test,
l0=l0,
l1=l1,
l2=l2,
tv=tv,
time=_time)
output_collector.collect(key, ret)
global_pen=0.01
l1_ratio=0.5
tv_ratio=0.5
ll1, ll2, ltv = compute_coefs_from_ratios(global_pen,tv_ratio,l1_ratio)
start_vector = start_vectors.RandomStartVector(seed=24)
MODELS["SparsePCA"] = \
sklearn.decomposition.SparsePCA(n_components=N_COMP,alpha=1)
MODELS["ElasticNetPCA"] = \
pca_tv.PCA_L1_L2_TV(n_components=N_COMP,
l1=ll1, l2=ll2, ltv=1e-6,
Atv=Atv,
criterion="frobenius",
eps=1e-6,
max_iter=100,
inner_max_iter=int(1e4),
output=False,start_vector=start_vector)
MODELS["SPCATV"] = \
pca_tv.PCA_L1_L2_TV(n_components=N_COMP,
l1=ll1, l2=ll2, ltv=ltv,
Atv=Atv,
criterion="frobenius",
eps=1e-6,
max_iter=100,
inner_max_iter=int(1e4),
output=False,start_vector=start_vector)
###############################################################################
# pending
ll1, ll2, ltv = 0.05 * 0.025937425654559931, 1, 0.003
key_pca_enettv = "pca_enettv_%.4f_%.3f_%.3f" % (ll1, ll2, ltv)
## key_pca_enettv = CHOICE
key = key_pca_enettv
print(OUTPUT_DIR.format(key=key))
if not (os.path.exists(OUTPUT_DIR.format(key=key))):
os.makedirs(OUTPUT_DIR.format(key=key))
model = pca_tv.PCA_L1_L2_TV(n_components=N_COMP,
l1=ll1,
l2=ll2,
ltv=ltv,
Atv=A,
criterion="frobenius",
eps=1e-6,
max_iter=100,
inner_max_iter=inner_max_iter,
verbose=True)
t0 = time.clock()
model.fit(X)
model.l1_max(X)
t1 = time.clock()
_time = t1 - t0
print("Time TOT(s)", _time)
# Save results
#model.U, model.d, model.V = m["U"], m["d"], m["V"]
PC, d = model.transform(X)
def mapper(key, output_collector):
import mapreduce as GLOBAL # access to global variables:
# GLOBAL.DATA
# GLOBAL.DATA ::= {"X":[Xtrain, ytrain], "y":[Xtest, ytest]}
# key: list of parameters
model_name, global_pen, tv_ratio, l1_ratio = key
if model_name == 'pca':
# Force the key
global_pen = tv_ratio = l1_ratio = 0
if model_name == 'struct_pca':
ll1, ll2, ltv = compute_coefs_from_ratios(global_pen, tv_ratio,
l1_ratio)
# This should not happen
if ll1 > GLOBAL.l1_max:
raise ValueError
X_train = GLOBAL.DATA_RESAMPLED["X"][0]
n, p = X_train.shape
X_test = GLOBAL.DATA_RESAMPLED["X"][1]
# A matrices
Atv = GLOBAL.Atv
# Fit model
if model_name == 'pca':
model = sklearn.decomposition.PCA(n_components=GLOBAL.N_COMP)
if model_name == 'struct_pca':
model = pca_tv.PCA_L1_L2_TV(n_components=GLOBAL.N_COMP,
l1=ll1,
l2=ll2,
ltv=ltv,
Atv=Atv,
criterion="frobenius",
eps=1e-6,
max_iter=100,
inner_max_iter=int(1e4),
output=False)
t0 = time.clock()
model.fit(X_train)
t1 = time.clock()
_time = t1 - t0
#print "X_test", GLOBAL.DATA["X"][1].shape
# Save the projectors
if (model_name == 'pca'):
components = model.components_.T
if model_name == 'struct_pca':
components = model.V
# Threshold components
thresh_components = np.empty(components.shape)
thresholds = np.empty((GLOBAL.N_COMP, ))
for k in range(GLOBAL.N_COMP):
thresh_comp, t = array_utils.arr_threshold_from_norm2_ratio(
components[:, k], .99)
thresh_components[:, k] = thresh_comp
thresholds[k] = t
# Project train & test data
if (model_name == 'pca'):
X_train_transform = model.transform(X_train)
X_test_transform = model.transform(X_test)
if (model_name == 'struct_pca'):
X_train_transform, _ = model.transform(X_train)
X_test_transform, _ = model.transform(X_test)
# Reconstruct train & test data
# For PCA, the formula is: UV^t (U is given by transform)
# For StructPCA this is implemented in the predict method (which uses
# transform)
if (model_name == 'pca'):
X_train_predict = np.dot(X_train_transform, components.T)
X_test_predict = np.dot(X_test_transform, components.T)
if (model_name == 'struct_pca'):
X_train_predict = model.predict(X_train)
X_test_predict = model.predict(X_test)
# Compute Frobenius norm between original and recontructed datasets
frobenius_train = np.linalg.norm(X_train - X_train_predict, 'fro')
frobenius_test = np.linalg.norm(X_test - X_test_predict, 'fro')
# Compute geometric metrics and norms of components
TV = parsimony.functions.nesterov.tv.TotalVariation(1, A=Atv)
l0 = np.zeros((GLOBAL.N_COMP, ))
l1 = np.zeros((GLOBAL.N_COMP, ))
l2 = np.zeros((GLOBAL.N_COMP, ))
tv = np.zeros((GLOBAL.N_COMP, ))
recall = np.zeros((GLOBAL.N_COMP, ))
precision = np.zeros((GLOBAL.N_COMP, ))
fscore = np.zeros((GLOBAL.N_COMP, ))
for i in range(GLOBAL.N_COMP):
# Norms
l0[i] = np.linalg.norm(components[:, i], 0)
l1[i] = np.linalg.norm(components[:, i], 1)
l2[i] = np.linalg.norm(components[:, i], 2)
tv[i] = TV.f(components[:, i])
# Compute explained variance ratio
evr_train = metrics.adjusted_explained_variance(X_train_transform)
evr_train /= np.var(X_train, axis=0).sum()
evr_test = metrics.adjusted_explained_variance(X_test_transform)
evr_test /= np.var(X_test, axis=0).sum()
ret = dict(frobenius_train=frobenius_train,
frobenius_test=frobenius_test,
components=components,
thresh_components=thresh_components,
thresholds=thresholds,
X_train_transform=X_train_transform,
X_test_transform=X_test_transform,
X_train_predict=X_train_predict,
X_test_predict=X_test_predict,
recall=recall,
precision=precision,
fscore=fscore,
evr_train=evr_train,
evr_test=evr_test,
l0=l0,
l1=l1,
l2=l2,
tv=tv,
time=_time)
output_collector.collect(key, ret)
)
########################################################################
#explained variance
import pca_tv
N_COMP = 5
import parsimony
Atv = parsimony.functions.nesterov.tv.A_from_mask(babel_mask.get_data())
X = T_hallu
print("# explained variance #############################################")
#fh = open(os.path.join(OUTPUT_DIR.format(key=key), "pca_enettv_info.txt"), "a")
mod = pca_tv.PCA_L1_L2_TV(n_components=N_COMP,
l1=0.1,
l2=0.1,
ltv=0.1,
Atv=Atv,
criterion="frobenius",
eps=1e-6,
max_iter=100,
inner_max_iter=1000)
mod.U, mod.V = projections, components
rsquared = np.zeros((N_COMP))
for j in range(N_COMP):
mod.n_components = j + 1
X_predict = mod.predict(X)
sse = np.sum((X - X_predict)**2)
ssX = np.sum(X**2)
rsquared[j] = 1 - sse / ssX