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commit 3c98f6ec105c34bef231118edc00c5bd156fcb42 Author: Alexandre Gramfort <[email protected]> Date: Thu Dec 30 18:00:23 2010 -0500 more on doc --- examples/read_stc.py | 23 ++++++++++------------- fiff/channels.py | 14 ++++---------- fiff/cov.py | 52 +++++++++++++++++++++++++++++----------------------- fiff/ctf.py | 6 +++--- fiff/event.py | 15 +++++++++------ fiff/evoked.py | 35 +++++++++++++++++++++++------------ fiff/forward.py | 16 ++++++++-------- fiff/inverse.py | 10 +++++----- fiff/matrix.py | 14 ++++++-------- fiff/meas_info.py | 4 ++-- 10 files changed, 99 insertions(+), 90 deletions(-) diff --git a/examples/read_stc.py b/examples/read_stc.py index 96bd266..e3fd2ed 100644 --- a/examples/read_stc.py +++ b/examples/read_stc.py @@ -1,4 +1,7 @@ -"""Reading a raw file segment +"""Reading an STC file + +STC files contain activations on cortex ie. source +reconstructions """ print __doc__ @@ -7,16 +10,10 @@ import fiff fname = 'MNE-sample-data/MEG/sample/sample_audvis-ave-7-meg-lh.stc' stc = fiff.read_stc(fname) -fiff.write_stc("tmp.stc", stc) -stc2 = fiff.read_stc("tmp.stc") - -from scipy import linalg -print linalg.norm(stc['data'] - stc2['data']) -# n_vertices, n_samples = stc['data'].shape -# print "tmin : %s (s)" % stc['tmin'] -# print "tstep : %s" % stc['tstep'] -# print "tmax : %s (s)" % (stc['tmin'] + stc['tstep'] * n_samples) -# print "stc data size: %s (nb of vertices) x %s (nb of samples)" % ( -# n_vertices, n_samples) -# +n_vertices, n_samples = stc['data'].shape +print "tmin : %s (s)" % stc['tmin'] +print "tstep : %s" % stc['tstep'] +print "tmax : %s (s)" % (stc['tmin'] + stc['tstep'] * n_samples) +print "stc data size: %s (nb of vertices) x %s (nb of samples)" % ( + n_vertices, n_samples) diff --git a/fiff/channels.py b/fiff/channels.py index dae6504..01ec9ba 100644 --- a/fiff/channels.py +++ b/fiff/channels.py @@ -3,16 +3,10 @@ from .tag import find_tag from .constants import FIFF -def read_bad_channels(fid, node): - """ - % - % [bads] = fiff_read_bad_channels(fid,node) - % - % Reas the bad channel list from a node if it exists - % - % fid - The file id - % node - The node of interest - % +def _read_bad_channels(fid, node): + """Read bad channels + + It returns the list of channel's names. """ nodes = dir_tree_find(node, FIFF.FIFFB_MNE_BAD_CHANNELS) diff --git a/fiff/cov.py b/fiff/cov.py index 237b9c3..2d4529d 100644 --- a/fiff/cov.py +++ b/fiff/cov.py @@ -5,22 +5,28 @@ from .constants import FIFF from .tag import find_tag from .tree import dir_tree_find from .proj import read_proj -from .channels import read_bad_channels +from .channels import _read_bad_channels def read_cov(fid, node, cov_kind): - """ - % - % [cov] = mne_read_cov(fid, node, kind) - % - % Reads a covariance matrix from a fiff file - % - % fid - an open file descriptor - % node - look for the matrix in here - % cov_kind - what kind of a covariance matrix do we want? - % - """ + """Read a noise covariance matrix + + Parameters + ---------- + fid: file + The file descriptor + + node: dict + The node in the FIF tree + + cov_kind: int + The type of covariance. XXX : clarify + Returns + ------- + data: dict + The noise covariance + """ # Find all covariance matrices covs = dir_tree_find(node, FIFF.FIFFB_MNE_COV) if len(covs) == 0: @@ -99,7 +105,7 @@ def read_cov(fid, node, cov_kind): projs = read_proj(fid, this) # Read the bad channel list - bads = read_bad_channels(fid, this) + bads = _read_bad_channels(fid, this) # Put it together cov = dict(kind=cov_kind, diag=diagmat, dim=dim, names=names, @@ -120,6 +126,7 @@ from .proj import write_proj def write_cov(fid, cov): + """ % % @@ -178,16 +185,15 @@ def write_cov(fid, cov): def write_cov_file(fname, cov): - """ - % - % function mne_write_cov_file(name,cov) - % - % Write a complete fif file containing a covariance matrix - % - % fname filename - % cov the covariance matrix to write - % - % + """Write a noise covariance matrix + + Parameters + ---------- + fname: string + The name of the file + + cov: dict + The noise covariance """ fid = start_file(fname) diff --git a/fiff/ctf.py b/fiff/ctf.py index f5c7461..6fa9a96 100644 --- a/fiff/ctf.py +++ b/fiff/ctf.py @@ -9,10 +9,10 @@ def hex2dec(s): return int(s, 16) -def read_named_matrix(fid, node, matkind): +def _read_named_matrix(fid, node, matkind): """ % - % [mat] = fiff_read_named_matrix(fid,node) + % [mat] = fiff__read_named_matrix(fid,node) % % Read named matrix from the given node % @@ -96,7 +96,7 @@ def read_ctf_comp(fid, node, chs): for node in comps: # Read the data we need - mat = read_named_matrix(fid, node, FIFF.FIFF_MNE_CTF_COMP_DATA) + mat = _read_named_matrix(fid, node, FIFF.FIFF_MNE_CTF_COMP_DATA) for p in range(node.nent): kind = node.dir[p].kind pos = node.dir[p].pos diff --git a/fiff/event.py b/fiff/event.py index fcac9a6..a4d6672 100644 --- a/fiff/event.py +++ b/fiff/event.py @@ -53,12 +53,15 @@ def read_events(filename): def write_events(filename, event_list): - """ - % - % mne_write_events(filename,eventlist) - % - % Write an event list into a fif file - % + """Write events to file + + Parameters + ---------- + filename: string + name of the fif file + + events: array, shape (n_events, 3) + The list of events """ # Start writing... fid = start_file(filename) diff --git a/fiff/evoked.py b/fiff/evoked.py index 013c481..5038f2d 100644 --- a/fiff/evoked.py +++ b/fiff/evoked.py @@ -8,13 +8,23 @@ from .meas_info import read_meas_info def read_evoked(fname, setno=0): - """ - [data] = fiff_read_evoked(fname,setno) + """Read an evoked dataset - Read one evoked data set + Parameters + ---------- + fname: string + The file name. - """ + setno: int + The index of the evoked dataset to read. FIF + file can contain multiple datasets. + Returns + ------- + data: dict + The evoked dataset + + """ if setno < 0: raise ValueError, 'Data set selector must be positive' @@ -220,14 +230,15 @@ from .ctf import write_ctf_comp def write_evoked(name, data): - """ - % - % function fiff_write_evoked(name,data) - % - % name filename - % data the data structure returned from fiff_read_evoked - % - % + """Write an evoked dataset to a file + + Parameters + ---------- + name: string + The file name. + + data: dict + The evoked dataset obtained with read_evoked """ # Create the file and save the essentials diff --git a/fiff/forward.py b/fiff/forward.py index 456fdf5..87a014c 100644 --- a/fiff/forward.py +++ b/fiff/forward.py @@ -5,10 +5,10 @@ from scipy import linalg from .constants import FIFF from .open import fiff_open from .tree import dir_tree_find -from .channels import read_bad_channels +from .channels import _read_bad_channels from .tag import find_tag from .source_space import read_source_spaces, find_source_space_hemi -from .matrix import read_named_matrix, transpose_named_matrix +from .matrix import _read_named_matrix, _transpose_named_matrix def _block_diag(A, n): @@ -152,17 +152,17 @@ def _read_one(fid, node): one['nchan'] = tag.data try: - one['sol'] = read_named_matrix(fid, node, + one['sol'] = _read_named_matrix(fid, node, FIFF.FIFF_MNE_FORWARD_SOLUTION) - one['sol'] = transpose_named_matrix(one['sol']) + one['sol'] = _transpose_named_matrix(one['sol']) except Exception as inst: fid.close() raise 'Forward solution data not found (%s)' % inst try: - one['sol_grad'] = read_named_matrix(fid, node, + one['sol_grad'] = _read_named_matrix(fid, node, FIFF.FIFF_MNE_FORWARD_SOLUTION_GRAD) - one['sol_grad'] = transpose_named_matrix(one['sol_grad']) + one['sol_grad'] = _transpose_named_matrix(one['sol_grad']) except Exception as inst: one['sol_grad'] = None @@ -206,7 +206,7 @@ def read_forward_solution(fname, force_fixed=False, surf_ori=False, Returns ------- - fwt: dict + fwd: dict The forward solution """ @@ -240,7 +240,7 @@ def read_forward_solution(fname, force_fixed=False, surf_ori=False, fwd = None # Bad channel list - bads = read_bad_channels(fid, tree) + bads = _read_bad_channels(fid, tree) print '\t%d bad channels read' % len(bads) diff --git a/fiff/inverse.py b/fiff/inverse.py index 6ce1fac..7ed16e6 100644 --- a/fiff/inverse.py +++ b/fiff/inverse.py @@ -1,7 +1,7 @@ from .constants import FIFF from .open import fiff_open from .tag import find_tag -from .matrix import read_named_matrix, transpose_named_matrix +from .matrix import _read_named_matrix, _transpose_named_matrix from .cov import read_cov from .proj import read_proj from .tree import dir_tree_find @@ -103,19 +103,19 @@ def read_inverse_operator(fname): # inv['eigen_leads_weighted'] = False try: - inv['eigen_leads'] = read_named_matrix(fid, invs, FIFF.FIFF_MNE_INVERSE_LEADS) + inv['eigen_leads'] = _read_named_matrix(fid, invs, FIFF.FIFF_MNE_INVERSE_LEADS) except: inv['eigen_leads_weighted'] = True try: - inv.eigen_leads = read_named_matrix(fid,invs,FIFF.FIFF_MNE_INVERSE_LEADS_WEIGHTED); + inv.eigen_leads = _read_named_matrix(fid,invs,FIFF.FIFF_MNE_INVERSE_LEADS_WEIGHTED); except Exception as inst: raise ValueError, '%s' % inst # # Having the eigenleads as columns is better for the inverse calculations # - inv['eigen_leads'] = transpose_named_matrix(inv['eigen_leads']) + inv['eigen_leads'] = _transpose_named_matrix(inv['eigen_leads']) try: - inv['eigen_fields'] = read_named_matrix(fid, invs, FIFF.FIFF_MNE_INVERSE_FIELDS) + inv['eigen_fields'] = _read_named_matrix(fid, invs, FIFF.FIFF_MNE_INVERSE_FIELDS) except Exception as inst: raise ValueError, '%s' % inst diff --git a/fiff/matrix.py b/fiff/matrix.py index ce51a4c..3eb82d0 100644 --- a/fiff/matrix.py +++ b/fiff/matrix.py @@ -2,7 +2,7 @@ from .constants import FIFF from .tag import find_tag, has_tag -def transpose_named_matrix(mat): +def _transpose_named_matrix(mat): """Transpose mat inplace (no copy) """ mat['nrow'] = mat['ncol'] @@ -13,13 +13,11 @@ def transpose_named_matrix(mat): return mat -def read_named_matrix(fid, node, matkind): - """ - % - % [mat] = fiff_read_named_matrix(fid,node) - % - % Read named matrix from the given node - % +def _read_named_matrix(fid, node, matkind): + """Read named matrix from the given node + + XXX + """ # Descend one level if necessary diff --git a/fiff/meas_info.py b/fiff/meas_info.py index 9858fed..1e7d6e8 100644 --- a/fiff/meas_info.py +++ b/fiff/meas_info.py @@ -6,7 +6,7 @@ from .constants import FIFF from .tag import read_tag from .proj import read_proj from .ctf import read_ctf_comp -from .channels import read_bad_channels +from .channels import _read_bad_channels def read_meas_info(source, tree=None): @@ -187,7 +187,7 @@ def read_meas_info(source, tree=None): comps = read_ctf_comp(fid, meas_info, chs) # Load the bad channel list - bads = read_bad_channels(fid, meas_info) + bads = _read_bad_channels(fid, meas_info) # # Put the data together -- 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
