This is an automated email from the git hooks/post-receive script. yoh pushed a commit to tag 0.4 in repository python-mne.
commit ced9b64b4505ffe8c7e6d9cf4cb0196bf489ee85 Author: Alexandre Gramfort <[email protected]> Date: Fri Mar 9 12:49:39 2012 +0100 API : cleanup Covariance which now restricted to noise cov --- mne/cov.py | 36 ++++++++++++------------------------ mne/fiff/constants.py | 2 +- 2 files changed, 13 insertions(+), 25 deletions(-) diff --git a/mne/cov.py b/mne/cov.py index e91acba..a0f981c 100644 --- a/mne/cov.py +++ b/mne/cov.py @@ -14,6 +14,7 @@ from .fiff.write import start_file, end_file from .fiff.proj import make_projector from .fiff import fiff_open from .fiff.pick import pick_types, channel_indices_by_type +from .fiff.constants import FIFF from .epochs import _is_good @@ -37,9 +38,6 @@ class Covariance(object): fname: string The name of the raw file - kind: 'full' | 'diagonal' - The type of covariance. - Attributes ---------- data : 2D array of shape [n_channels x n_channels] @@ -52,24 +50,13 @@ class Covariance(object): Number of degrees of freedom i.e. number of time points used """ - _kind_to_id = dict(full=1, sparse=2, diagonal=3) # XXX : check - _id_to_kind = {1: 'full', 2: 'sparse', 3: 'diagonal'} # XXX : check - - def __init__(self, fname, kind='full'): - self.kind = kind - + def __init__(self, fname): if fname is None: return - if self.kind in Covariance._kind_to_id: - cov_kind = Covariance._kind_to_id[self.kind] - else: - raise ValueError('Unknown type of covariance. ' - 'Choose between full, sparse or diagonal.') - # Reading fid, tree, _ = fiff_open(fname) - cov = fiff.read_cov(fid, tree, cov_kind) + cov = fiff.read_cov(fid, tree, FIFF.FIFFV_MNE_NOISE_COV) fid.close() self._cov = cov @@ -90,8 +77,7 @@ class Covariance(object): end_file(fid) def __repr__(self): - s = "kind : %s" % self.kind - s += ", size : %s x %s" % self.data.shape + s = "size : %s x %s" % self.data.shape s += ", data : %s" % self.data return "Covariance (%s)" % s @@ -121,7 +107,7 @@ class Covariance(object): # IO def read_cov(fname): - """Read covariance from a FIF file. + """Read a noise covariance from a FIF file. Parameters ---------- @@ -130,11 +116,12 @@ def read_cov(fname): Returns ------- - projs: list - The list of projection vectors. + cov: Covariance + The noise covariance matrix. """ return Covariance(fname) + ############################################################################### # Estimate from data @@ -232,8 +219,9 @@ def compute_raw_data_covariance(raw, tmin=None, tmax=None, tstep=0.2, eigvec = None # Store structure for fif - cov._cov = dict(kind=1, diag=False, dim=len(data), names=cov.ch_names, - data=data, projs=copy.deepcopy(raw.info['projs']), + cov._cov = dict(kind=FIFF.FIFFV_MNE_NOISE_COV, diag=False, dim=len(data), + names=cov.ch_names, data=data, + projs=copy.deepcopy(raw.info['projs']), bads=raw.info['bads'], nfree=n_samples, eig=eig, eigvec=eigvec) @@ -314,7 +302,7 @@ def write_cov(fname, cov): The name of the file cov: Covariance - The noise covariance + The noise covariance matrix """ cov.save(fname) diff --git a/mne/fiff/constants.py b/mne/fiff/constants.py index c46258d..cfd757b 100644 --- a/mne/fiff/constants.py +++ b/mne/fiff/constants.py @@ -326,7 +326,7 @@ FIFF.FIFFV_MNE_SOURCE_COV = 2 FIFF.FIFFV_MNE_FMRI_PRIOR_COV = 3 FIFF.FIFFV_MNE_SIGNAL_COV = 4 # This will be potentially employed in beamformers FIFF.FIFFV_MNE_DEPTH_PRIOR_COV = 5 # The depth weighting prior -FIFF.FIFFV_MNE_ORIENT_PRIOR_COV = 6 # The orientation prior +FIFF.FIFFV_MNE_ORIENT_PRIOR_COV = 6 # The orientation prior # # Source space types (values of FIFF_MNE_SOURCE_SPACE_TYPE) # -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-mne.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
