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Merged
mihaic merged 33 commits into from
Jul 13, 2017
Merged

changed behavior of rand_seed in BRSA #239

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Jul 13, 2017
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Jul 13, 2017
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changed random_state behavior according to sklearn guideline
Jul 13, 2017
65ad272
add doc_string for random_state_
Jul 13, 2017
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22 changes: 13 additions & 9 deletions brainiak/reprsimil/brsa.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,14 +30,12 @@
import scipy
import scipy.optimize
import scipy.stats
import warnings
import time
from sklearn.base import BaseEstimator
from sklearn.utils import assert_all_finite
from sklearn.utils import assert_all_finite, check_random_state
import logging
import brainiak.utils.utils as utils
import scipy.spatial.distance as spdist
warnings.filterwarnings('ignore')


logger = logging.getLogger(__name__)
Expand Down Expand Up @@ -141,8 +139,11 @@ class BRSA(BaseEstimator):
We use 'BFGS' as a default. Users can try other optimizer
coming with scipy.optimize.minimize, or a custom
optimizer.
rand_seed : int, default: 0
Seed for initializing the random number generator.
random_state : RandomState or an int seed. Default: None
A random number generator instance to define the state of
the random permutations generator whenever the module
needs to generate random number (e.g., initial parameter
of the Cholesky factor).

Attributes
----------
Expand Down Expand Up @@ -172,14 +173,17 @@ class BRSA(BaseEstimator):
beta0_: array, shape=[n_nureg, voxels]
The loading weights of each voxel for the shared time courses
not captured by the design matrix.
random_state_: `RandomState`
Random number generator initialized using random_state.

"""

def __init__(
self, n_iter=50, rank=None, GP_space=False, GP_inten=False,
tol=2e-3, auto_nuisance=True, n_nureg=6, verbose=False,
eta=0.0001, space_smooth_range=None, inten_smooth_range=None,
tau_range=10.0, init_iter=20, optimizer='BFGS', rand_seed=0):
tau_range=10.0, init_iter=20, optimizer='BFGS',
random_state=None):
self.n_iter = n_iter
self.rank = rank
self.GP_space = GP_space
Expand All @@ -203,7 +207,7 @@ def __init__(
# When imposing smoothness prior, fit the model without this
# prior for this number of iterations.
self.optimizer = optimizer
self.rand_seed = rand_seed
self.random_state = random_state
return

def fit(self, X, design, nuisance=None, scan_onsets=None, coords=None,
Expand Down Expand Up @@ -686,7 +690,7 @@ def _fit_RSA_UV(self, X, Y, X0,
n_C = np.size(X, axis=1)
l_idx = np.tril_indices(n_C)

np.random.seed(self.rand_seed)
self.random_state_ = check_random_state(self.random_state)

@mihaic mihaic Jul 13, 2017

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Please document this attribute in the class docstring. Could be something like this:

random_state_: `RandomState`
    Random number generator initialized using random_state

@lcnature lcnature Jul 13, 2017

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Thanks. Just added exactly this text.

# setting random seed
t_start = time.time()

Expand Down Expand Up @@ -932,7 +936,7 @@ def _initial_fit_singpara(self, XTX, XTDX, XTFX,

# (3) random initialization

current_vec_U_chlsk_l = np.random.randn(n_l)
current_vec_U_chlsk_l = self.random_state_.randn(n_l)
# vectorized version of L, Cholesky factor of U, the shared
# covariance matrix of betas across voxels.

Expand Down