This is an automated email from the git hooks/post-receive script. yoh pushed a commit to annotated tag v0.1 in repository python-mne.
commit 879debc2bc9c635da801f2acfb9a2d5385a315d5 Author: Alexandre Gramfort <[email protected]> Date: Thu Apr 14 17:41:04 2011 -0400 MISC : s/from_/from/g + some pep8 --- mne/fiff/meas_info.py | 80 +++++++++++++++++++++++++-------------------------- mne/fiff/tag.py | 2 +- mne/fiff/write.py | 2 +- mne/forward.py | 32 +++++++++++---------- mne/inverse.py | 4 +-- mne/transforms.py | 62 ++++++++++++++++++++------------------- 6 files changed, 93 insertions(+), 89 deletions(-) diff --git a/mne/fiff/meas_info.py b/mne/fiff/meas_info.py index 61c4b29..52898a6 100755 --- a/mne/fiff/meas_info.py +++ b/mne/fiff/meas_info.py @@ -41,16 +41,16 @@ def read_meas_info(fid, tree): # Find the desired blocks meas = dir_tree_find(tree, FIFF.FIFFB_MEAS) if len(meas) == 0: - raise ValueError, 'Could not find measurement data' + raise ValueError('Could not find measurement data') if len(meas) > 1: - raise ValueError, 'Cannot read more that 1 measurement data' + raise ValueError('Cannot read more that 1 measurement data') meas = meas[0] meas_info = dir_tree_find(meas, FIFF.FIFFB_MEAS_INFO) if len(meas_info) == 0: - raise ValueError, 'Could not find measurement info' + raise ValueError('Could not find measurement info') if len(meas_info) > 1: - raise ValueError, 'Cannot read more that 1 measurement info' + raise ValueError('Cannot read more that 1 measurement info') meas_info = meas_info[0] # Read measurement info @@ -88,72 +88,72 @@ def read_meas_info(fid, tree): elif kind == FIFF.FIFF_COORD_TRANS: tag = read_tag(fid, pos) cand = tag.data - if cand['from_'] == FIFF.FIFFV_COORD_DEVICE and \ - cand['to'] == FIFF.FIFFV_COORD_HEAD: # XXX : from + if cand['from'] == FIFF.FIFFV_COORD_DEVICE and \ + cand['to'] == FIFF.FIFFV_COORD_HEAD: dev_head_t = cand - elif cand['from_'] == FIFF.FIFFV_MNE_COORD_CTF_HEAD and \ + elif cand['from'] == FIFF.FIFFV_MNE_COORD_CTF_HEAD and \ cand['to'] == FIFF.FIFFV_COORD_HEAD: ctf_head_t = cand # Check that we have everything we need if nchan is None: - raise ValueError, 'Number of channels in not defined' + raise ValueError('Number of channels in not defined') if sfreq is None: - raise ValueError, 'Sampling frequency is not defined' + raise ValueError('Sampling frequency is not defined') if len(chs) == 0: - raise ValueError, 'Channel information not defined' + raise ValueError('Channel information not defined') if len(chs) != nchan: - raise ValueError, 'Incorrect number of channel definitions found' + raise ValueError('Incorrect number of channel definitions found') if dev_head_t is None or ctf_head_t is None: hpi_result = dir_tree_find(meas_info, FIFF.FIFFB_HPI_RESULT) if len(hpi_result) == 1: hpi_result = hpi_result[0] for k in range(hpi_result.nent): - kind = hpi_result.directory[k].kind - pos = hpi_result.directory[k].pos - if kind == FIFF.FIFF_COORD_TRANS: + kind = hpi_result.directory[k].kind + pos = hpi_result.directory[k].pos + if kind == FIFF.FIFF_COORD_TRANS: tag = read_tag(fid, pos) - cand = tag.data; - if cand.from_ == FIFF.FIFFV_COORD_DEVICE and \ - cand.to == FIFF.FIFFV_COORD_HEAD: # XXX: from - dev_head_t = cand; - elif cand.from_ == FIFF.FIFFV_MNE_COORD_CTF_HEAD and \ - cand.to == FIFF.FIFFV_COORD_HEAD: - ctf_head_t = cand; + cand = tag.data + if cand['from'] == FIFF.FIFFV_COORD_DEVICE and \ + cand['to'] == FIFF.FIFFV_COORD_HEAD: + dev_head_t = cand + elif cand['from'] == FIFF.FIFFV_MNE_COORD_CTF_HEAD and \ + cand['to'] == FIFF.FIFFV_COORD_HEAD: + ctf_head_t = cand # Locate the Polhemus data - isotrak = dir_tree_find(meas_info,FIFF.FIFFB_ISOTRAK) + isotrak = dir_tree_find(meas_info, FIFF.FIFFB_ISOTRAK) if len(isotrak): isotrak = isotrak[0] else: if len(isotrak) == 0: - raise ValueError, 'Isotrak not found' + raise ValueError('Isotrak not found') if len(isotrak) > 1: - raise ValueError, 'Multiple Isotrak found' + raise ValueError('Multiple Isotrak found') dig = [] if len(isotrak) == 1: for k in range(isotrak.nent): - kind = isotrak.directory[k].kind; - pos = isotrak.directory[k].pos; + kind = isotrak.directory[k].kind + pos = isotrak.directory[k].pos if kind == FIFF.FIFF_DIG_POINT: - tag = read_tag(fid,pos); + tag = read_tag(fid, pos) dig.append(tag.data) dig[-1]['coord_frame'] = FIFF.FIFFV_COORD_HEAD # Locate the acquisition information - acqpars = dir_tree_find(meas_info, FIFF.FIFFB_DACQ_PARS); + acqpars = dir_tree_find(meas_info, FIFF.FIFFB_DACQ_PARS) acq_pars = None acq_stim = None if len(acqpars) == 1: acqpars = acqpars[0] for k in range(acqpars.nent): kind = acqpars.directory[k].kind - pos = acqpars.directory[k].pos + pos = acqpars.directory[k].pos if kind == FIFF.FIFF_DACQ_PARS: tag = read_tag(fid, pos) acq_pars = tag.data @@ -174,9 +174,9 @@ def read_meas_info(fid, tree): # Put the data together # if tree.id is not None: - info = dict(file_id=tree.id) + info = dict(file_id=tree.id) else: - info = dict(file_id=None) + info = dict(file_id=None) # Make the most appropriate selection for the measurement id if meas_info.parent_id is None: @@ -191,12 +191,12 @@ def read_meas_info(fid, tree): else: info['meas_id'] = meas_info.id else: - info['meas_id'] = meas_info.parent_id; + info['meas_id'] = meas_info.parent_id if meas_date is None: - info['meas_date'] = [info['meas_id']['secs'], info['meas_id']['usecs']] + info['meas_date'] = [info['meas_id']['secs'], info['meas_id']['usecs']] else: - info['meas_date'] = meas_date + info['meas_date'] = meas_date info['nchan'] = nchan info['sfreq'] = sfreq @@ -205,7 +205,7 @@ def read_meas_info(fid, tree): # Add the channel information and make a list of channel names # for convenience - info['chs'] = chs; + info['chs'] = chs info['ch_names'] = [ch.ch_name for ch in chs] # @@ -214,11 +214,12 @@ def read_meas_info(fid, tree): info['dev_head_t'] = dev_head_t info['ctf_head_t'] = ctf_head_t if dev_head_t is not None and ctf_head_t is not None: - info['dev_ctf_t'] = info['dev_head_t'] - info['dev_ctf_t'].to = info['ctf_head_t'].from_ # XXX : see if better name - info['dev_ctf_t'].trans = np.dot(np.inv(ctf_head_t.trans), info.dev_ctf_t.trans) + info['dev_ctf_t'] = info['dev_head_t'] + info['dev_ctf_t']['to'] = info['ctf_head_t']['from'] + info['dev_ctf_t']['trans'] = np.dot(np.inv(ctf_head_t['trans']), + info['dev_ctf_t']['trans']) else: - info['dev_ctf_t'] = [] + info['dev_ctf_t'] = [] # All kinds of auxliary stuff info['dig'] = dig @@ -299,4 +300,3 @@ def write_meas_info(fid, info): end_block(fid, FIFF.FIFFB_MNE_BAD_CHANNELS) end_block(fid, FIFF.FIFFB_MEAS_INFO) - diff --git a/mne/fiff/tag.py b/mne/fiff/tag.py index de91909..d3652ae 100755 --- a/mne/fiff/tag.py +++ b/mne/fiff/tag.py @@ -235,7 +235,7 @@ def read_tag(fid, pos=None): tag.data['coord_frame'] = 0 elif tag.type == FIFF.FIFFT_COORD_TRANS_STRUCT: tag.data = Bunch() - tag.data['from_'] = int(np.fromfile(fid, dtype=">i4", count=1)) + tag.data['from'] = int(np.fromfile(fid, dtype=">i4", count=1)) tag.data['to'] = int(np.fromfile(fid, dtype=">i4", count=1)) rot = np.fromfile(fid, dtype=">f4", count=9).reshape(3, 3) move = np.fromfile(fid, dtype=">f4", count=3) diff --git a/mne/fiff/write.py b/mne/fiff/write.py index d96b6ff..51e0f61 100755 --- a/mne/fiff/write.py +++ b/mne/fiff/write.py @@ -184,7 +184,7 @@ def write_coord_trans(fid, trans): fid.write(np.array(FIFFT_COORD_TRANS_STRUCT, dtype='>i4').tostring()) fid.write(np.array(data_size, dtype='>i4').tostring()) fid.write(np.array(FIFFV_NEXT_SEQ, dtype='>i4').tostring()) - fid.write(np.array(trans['from_'], dtype='>i4').tostring()) + fid.write(np.array(trans['from'], dtype='>i4').tostring()) fid.write(np.array(trans['to'], dtype='>i4').tostring()) # The transform... diff --git a/mne/forward.py b/mne/forward.py index d5ba2ce..28b08a2 100755 --- a/mne/forward.py +++ b/mne/forward.py @@ -22,19 +22,21 @@ def _block_diag(A, n): You have to try it on a matrix to see what it's doing. - % If A is not sparse, then returns a sparse block diagonal "bd", - % diagonalized from the - % elements in "A". - % "A" is ma x na, comprising bdn=(na/"n") blocks of submatrices. - % Each submatrix is ma x "n", and these submatrices are - % placed down the diagonal of the matrix. - % - % If A is already sparse, then the operation is reversed, yielding - # a block - % row matrix, where each set of n columns corresponds to a block element - % from the block diagonal. - % - % Routine uses NO for-loops for speed considerations. + If A is not sparse, then returns a sparse block diagonal "bd", + diagonalized from the + elements in "A". + "A" is ma x na, comprising bdn=(na/"n") blocks of submatrices. + Each submatrix is ma x "n", and these submatrices are + placed down the diagonal of the matrix. + + If A is already sparse, then the operation is reversed, yielding + a block + row matrix, where each set of n columns corresponds to a block element + from the block diagonal. + + Routine uses NO for-loops for speed considerations. + + XXX : format doc """ from scipy import sparse @@ -294,10 +296,10 @@ def read_forward_solution(fname, force_fixed=False, surf_ori=False, raise ValueError, 'MRI/head coordinate transformation not found' else: mri_head_t = tag.data; - if (mri_head_t['from_'] != FIFF.FIFFV_COORD_MRI or + if (mri_head_t['from'] != FIFF.FIFFV_COORD_MRI or mri_head_t['to'] != FIFF.FIFFV_COORD_HEAD): mri_head_t = invert_transform(mri_head_t) - if (mri_head_t['from_'] != FIFF.FIFFV_COORD_MRI + if (mri_head_t['from'] != FIFF.FIFFV_COORD_MRI or mri_head_t['to'] != FIFF.FIFFV_COORD_HEAD): fid.close() raise ValueError, 'MRI/head coordinate transformation not ' \ diff --git a/mne/inverse.py b/mne/inverse.py index e563b61..e7a596d 100755 --- a/mne/inverse.py +++ b/mne/inverse.py @@ -199,10 +199,10 @@ def read_inverse_operator(fname): raise ValueError('MRI/head coordinate transformation not found') else: mri_head_t = tag.data - if mri_head_t['from_'] != FIFF.FIFFV_COORD_MRI or \ + if mri_head_t['from'] != FIFF.FIFFV_COORD_MRI or \ mri_head_t['to'] != FIFF.FIFFV_COORD_HEAD: mri_head_t = invert_transform(mri_head_t) - if mri_head_t['from_'] != FIFF.FIFFV_COORD_MRI or \ + if mri_head_t['from'] != FIFF.FIFFV_COORD_MRI or \ mri_head_t['to'] != FIFF.FIFFV_COORD_HEAD: fid.close() raise ValueError('MRI/head coordinate transformation ' diff --git a/mne/transforms.py b/mne/transforms.py index 80912aa..5de385d 100755 --- a/mne/transforms.py +++ b/mne/transforms.py @@ -2,44 +2,46 @@ import copy import numpy as np from scipy import linalg -from .fiff import FIFF - +# from .fiff import FIFF def invert_transform(trans): """Invert a transformation between coordinate systems """ itrans = copy.copy(trans) - aux = itrans['from_'] - itrans['from_'] = itrans['to'] + aux = itrans['from'] + itrans['from'] = itrans['to'] itrans['to'] = aux itrans['trans'] = linalg.inv(itrans['trans']) return itrans def transform_source_space_to(src, dest, trans): - """ - % - % [res] = mne_transform_source_space_to(src,dest,trans) - % - % Transform source space data to the desired coordinate system - % - % fname - The name of the file - % include - Include these channels (optional) - % exclude - Exclude these channels (optional) - % + """Transform source space data to the desired coordinate system + + Parameters + ---------- + src : dict + Source space + dest : dict + destination coordinate system + trans : dict + Transformation - XXX + Returns + ------- + res : dict + Transformed source space """ if src['coord_frame'] == dest: res = src return res - if trans['to'] == src['coord_frame'] and trans['from_'] == dest: + if trans['to'] == src['coord_frame'] and trans['from'] == dest: trans = invert_transform(trans) - elif trans['from_'] != src['coord_frame'] or trans['to'] != dest: - raise ValueError, 'Cannot transform the source space using this ' \ - 'coordinate transformation' + elif trans['from'] != src['coord_frame'] or trans['to'] != dest: + raise ValueError('Cannot transform the source space using this ' + 'coordinate transformation') t = trans['trans'][:3,:] res = src @@ -62,26 +64,26 @@ def transform_source_space_to(src, dest, trans): # % loc which remains to reflect the original data read from the fif file # % # % -# +# # XXX # """ -# +# # res = copy.copy(chs) -# +# # count = 0 # t = trans['trans'] # for ch in res: # if (ch['kind'] == FIFF.FIFFV_MEG_CH # or ch['kind'] == FIFF.FIFFV_REF_MEG_CH): -# if (ch['coord_frame'] == trans['from_'] +# if (ch['coord_frame'] == trans['from'] # and ch['coil_trans'] is not None): # ch['coil_trans'] = np.dot(t, ch['coil_trans']) # ch['coord_frame'] = trans['to'] # count += 1 -# +# # if count > 0: # print '\t%d MEG channel locations transformed' % count -# +# # return res, count @@ -96,11 +98,11 @@ def transform_source_space_to(src, dest, trans): # % NOTE: Only the eeg_loc field is modified by this routine, not # % loc which remains to reflect the original data read from the fif file # % -# +# # XXX # """ # res = copy.copy(chs) -# +# # count = 0 # # # # Output unaugmented vectors from the transformation @@ -108,7 +110,7 @@ def transform_source_space_to(src, dest, trans): # t = trans['trans'][:3,:] # for ch in res: # if ch['kind'] == FIFF.FIFFV_EEG_CH: -# if (ch['coord_frame'] == trans['from_'] +# if (ch['coord_frame'] == trans['from'] # and ch['eeg_loc'] is not None): # # # # Transform the augmented EEG location vectors @@ -118,8 +120,8 @@ def transform_source_space_to(src, dest, trans): # np.r_[ch['eeg_loc'][:,p], 1]) # count += 1 # ch['coord_frame'] = trans['to'] -# +# # if count > 0: # print '\t%d EEG electrode locations transformed\n' % count -# +# # return res, count -- 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
