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commit 2da38029badc5162db3163cf45fe9ad9b19c33b5 Author: Alexandre Gramfort <[email protected]> Date: Fri Jan 14 17:04:27 2011 -0500 splitting fif and MNE --- AUTHORS.rst | 3 ++- MANIFEST.in | 4 ++-- README.rst | 7 +++---- examples/compute_mne_inverse.py | 2 +- examples/read_bem_surfaces.py | 2 +- examples/read_cov.py | 7 ++++--- examples/read_epochs.py | 9 +++++---- examples/read_events.py | 21 ++++++++------------- examples/read_evoked.py | 2 +- examples/read_forward.py | 4 ++-- examples/read_inverse.py | 4 ++-- examples/read_raw.py | 4 ++-- examples/read_stc.py | 4 ++-- examples/read_write_raw.py | 20 ++++++++++---------- {fiff => mne}/__init__.py | 9 +-------- {fiff => mne}/bem_surfaces.py | 14 +++++++++----- {fiff => mne}/cov.py | 23 +++++++++++++---------- {fiff => mne}/epochs.py | 6 ++++-- {fiff => mne}/event.py | 11 ++++++----- {fiff => mne/fiff}/__init__.py | 7 ------- {fiff => mne/fiff}/bunch.py | 0 {fiff => mne/fiff}/channels.py | 4 ++++ {fiff => mne/fiff}/constants.py | 5 +++++ {fiff => mne/fiff}/ctf.py | 4 ++++ {fiff => mne/fiff}/diff.py | 4 ++++ {fiff => mne/fiff}/evoked.py | 4 ++++ {fiff => mne/fiff}/matrix.py | 5 +++++ {fiff => mne/fiff}/meas_info.py | 4 ++++ {fiff => mne/fiff}/open.py | 5 +++++ {fiff => mne/fiff}/pick.py | 5 +++++ {fiff => mne/fiff}/proj.py | 5 +++++ {fiff => mne/fiff}/raw.py | 5 +++++ {fiff => mne/fiff}/tag.py | 4 ++++ mne/fiff/tests/__init__.py | 0 {fiff => mne/fiff}/tests/test_evoked.py | 9 ++++----- {fiff => mne/fiff}/tests/test_raw.py | 20 +++++++++++--------- {fiff => mne/fiff}/tree.py | 4 ++++ {fiff => mne/fiff}/write.py | 4 ++++ {fiff => mne}/forward.py | 17 +++++++++++------ {fiff => mne}/inverse.py | 28 +++++++++++++++++----------- {fiff => mne}/source_space.py | 12 ++++++++---- {fiff => mne}/stc.py | 4 ++++ mne/tests/__init__.py | 0 {fiff => mne}/tests/test_bem_surfaces.py | 6 +++--- {fiff => mne}/tests/test_cov.py | 14 +++++++------- {fiff => mne}/tests/test_event.py | 11 +++++------ {fiff => mne}/tests/test_forward.py | 7 +++---- {fiff => mne}/tests/test_inverse.py | 5 ++--- {fiff => mne}/tests/test_stc.py | 9 ++++----- setup.cfg | 2 +- setup.py | 15 +++++++-------- 51 files changed, 227 insertions(+), 157 deletions(-) diff --git a/AUTHORS.rst b/AUTHORS.rst index b4742d5..1a7b32f 100644 --- a/AUTHORS.rst +++ b/AUTHORS.rst @@ -3,4 +3,5 @@ Authors ======= - * Alexandre Gramfort <[email protected]> 2010 + * Alexandre Gramfort <[email protected]> 2011 + * Matti Hamalainen <[email protected]> 2011 diff --git a/MANIFEST.in b/MANIFEST.in index 4d6d738..228d8e2 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,5 +1,5 @@ include *.rst -include fiff/__init__.py +include mne/__init__.py recursive-include doc * recursive-include examples * -recursive-include fiff *.py +recursive-include mne *.py diff --git a/README.rst b/README.rst index d57af32..40506e1 100644 --- a/README.rst +++ b/README.rst @@ -3,8 +3,7 @@ About ===== -pyfiff is a python module for reading and writing the fif files -produced by Neuromag MEG systems. +MNE is a python module for processing MEG and EEG data; It is mainly a reimplementation of the Matlab code written by Matti Hämäläinen. @@ -46,11 +45,11 @@ GIT You can check the latest sources with the command:: - git clone git://github.com/agramfort/pyfiff.git + git clone git://github.com/mne/mne.git or if you have write privileges:: - git clone [email protected]/agramfort/pyfiff.git + git clone [email protected]/mne/mne.git Bugs ---- diff --git a/examples/compute_mne_inverse.py b/examples/compute_mne_inverse.py index 9673d69..1690acd 100644 --- a/examples/compute_mne_inverse.py +++ b/examples/compute_mne_inverse.py @@ -2,7 +2,7 @@ """ print __doc__ -import fiff +from mne import fiff fname_inv = 'MNE-sample-data/MEG/sample/sample_audvis-ave-7-meg-inv.fif' fname_data = 'MNE-sample-data/MEG/sample/sample_audvis-ave.fif' diff --git a/examples/read_bem_surfaces.py b/examples/read_bem_surfaces.py index d6567b0..ae39890 100644 --- a/examples/read_bem_surfaces.py +++ b/examples/read_bem_surfaces.py @@ -2,7 +2,7 @@ """ print __doc__ -import fiff +from mne import fiff fname = 'MNE-sample-data/subjects/sample/bem/sample-5120-bem-sol.fif' diff --git a/examples/read_cov.py b/examples/read_cov.py index 0ffead2..142867a 100644 --- a/examples/read_cov.py +++ b/examples/read_cov.py @@ -2,18 +2,19 @@ """ print __doc__ -import fiff +import mne +from mne import fiff fname = 'MNE-sample-data/MEG/sample/sample_audvis-cov.fif' # Reading fid, tree, _ = fiff.fiff_open(fname) cov_type = 1 -cov = fiff.read_cov(fid, tree, cov_type) +cov = mne.read_cov(fid, tree, cov_type) fid.close() # Writing -fiff.write_cov_file('cov.fif', cov) +mne.write_cov_file('cov.fif', cov) print "covariance matrix size: %s x %s" % cov['data'].shape diff --git a/examples/read_epochs.py b/examples/read_epochs.py index 311eaa9..4e47659 100644 --- a/examples/read_epochs.py +++ b/examples/read_epochs.py @@ -5,7 +5,8 @@ print __doc__ # Authors : Alexandre Gramfort, [email protected] # Matti Hamalainen, [email protected] -import fiff +import mne +from mne import fiff ############################################################################### # Set parameters @@ -18,7 +19,7 @@ pick_all = True # Setup for reading the raw data raw = fiff.setup_read_raw(raw_fname) -events = fiff.read_events(event_name) +events = mne.read_events(event_name) if pick_all: # Pick all @@ -29,10 +30,10 @@ else: want_meg = True want_eeg = False want_stim = False - picks = fiff.fiff_pick_types(raw['info'], want_meg, want_eeg, want_stim, + picks = fiff.pick_types(raw['info'], want_meg, want_eeg, want_stim, include, raw['info']['bads']) -data, times, channel_names = fiff.read_epochs(raw, events, event_id, +data, times, channel_names = mne.read_epochs(raw, events, event_id, tmin, tmax, picks=picks) # for epoch in data: diff --git a/examples/read_events.py b/examples/read_events.py index 14157be..0064295 100644 --- a/examples/read_events.py +++ b/examples/read_events.py @@ -2,21 +2,16 @@ """ print __doc__ -import fiff +import mne fname = 'MNE-sample-data/MEG/sample/sample_audvis_raw-eve.fif' -event_list = fiff.read_events(fname) -fiff.write_events('events.fif', event_list) -event_list2 = fiff.read_events(fname) +# Reading events +events = mne.read_events(fname) -from scipy import linalg -print linalg.norm(event_list - event_list2) +# Writing events +mne.write_events('events.fif', events) -# ############################################################################### -# # Show MEG data -# import pylab as pl -# pl.plot(times, data.T) -# pl.xlabel('time (ms)') -# pl.ylabel('MEG data (T)') -# pl.show() +for ind, before, after in events[:5]: + print "At sample %d stim channel went from %d to %d" % ( + ind, before, after) diff --git a/examples/read_evoked.py b/examples/read_evoked.py index 1aae8f2..0b5ad10 100644 --- a/examples/read_evoked.py +++ b/examples/read_evoked.py @@ -2,7 +2,7 @@ """ print __doc__ -import fiff +from mne import fiff fname = 'MNE-sample-data/MEG/sample/sample_audvis-ave.fif' diff --git a/examples/read_forward.py b/examples/read_forward.py index 5312a93..725b3b3 100644 --- a/examples/read_forward.py +++ b/examples/read_forward.py @@ -2,12 +2,12 @@ """ print __doc__ -import fiff +import mne # fname = 'MNE-sample-data/MEG/sample/sample_audvis-ave-7-fwd.fif' fname = 'sm01a5-ave-oct-6-fwd.fif' -data = fiff.read_forward_solution(fname) +data = mne.read_forward_solution(fname) leadfield = data['sol']['data'] print "Leadfield size : %d x %d" % leadfield.shape diff --git a/examples/read_inverse.py b/examples/read_inverse.py index 940a786..7d6b359 100644 --- a/examples/read_inverse.py +++ b/examples/read_inverse.py @@ -2,11 +2,11 @@ """ print __doc__ -import fiff +import mne fname = 'MNE-sample-data/MEG/sample/sample_audvis-ave-7-meg-inv.fif' -inv = fiff.read_inverse_operator(fname) +inv = mne.read_inverse_operator(fname) print "Method: %s" % inv['methods'] print "fMRI prior: %s" % inv['fmri_prior'] diff --git a/examples/read_raw.py b/examples/read_raw.py index 82314dc..ca650ad 100644 --- a/examples/read_raw.py +++ b/examples/read_raw.py @@ -2,8 +2,7 @@ """ print __doc__ -import pylab as pl -import fiff +from mne import fiff fname = 'MNE-sample-data/MEG/sample/sample_audvis_raw.fif' @@ -19,6 +18,7 @@ raw.close() ############################################################################### # Show MEG data +import pylab as pl pl.close('all') pl.plot(times, data.T) pl.xlabel('time (s)') diff --git a/examples/read_stc.py b/examples/read_stc.py index e3fd2ed..d3032fd 100644 --- a/examples/read_stc.py +++ b/examples/read_stc.py @@ -5,11 +5,11 @@ reconstructions """ print __doc__ -import fiff +import mne fname = 'MNE-sample-data/MEG/sample/sample_audvis-ave-7-meg-lh.stc' -stc = fiff.read_stc(fname) +stc = mne.read_stc(fname) n_vertices, n_samples = stc['data'].shape print "tmin : %s (s)" % stc['tmin'] diff --git a/examples/read_write_raw.py b/examples/read_write_raw.py index 7e5df88..3a38cb2 100644 --- a/examples/read_write_raw.py +++ b/examples/read_write_raw.py @@ -5,8 +5,7 @@ Read and write raw data in 60-sec blocks print __doc__ from math import ceil -import fiff - +from mne import fiff infile = 'MNE-sample-data/MEG/sample/sample_audvis_raw.fif' outfile = 'sample_audvis_small_raw.fif' @@ -31,30 +30,31 @@ outfid, cals = fiff.start_writing_raw(outfile, raw['info'], picks) # # Set up the reading parameters # -from_ = raw['first_samp'] -to = raw['last_samp'] +start = raw['first_samp'] +stop = raw['last_samp'] + 1 quantum_sec = 10 quantum = int(ceil(quantum_sec * raw['info']['sfreq'])) # # To read the whole file at once set # -# quantum = to - from_ + 1; +# quantum = stop - start # # # Read and write all the data # first_buffer = True -for first in range(from_, to, quantum): - last = first + quantum - if last > to: - last = to +for first in range(start, stop, quantum): + last = start + quantum + if last >= stop: + last = stop try: - data, times = fiff.read_raw_segment(raw, first, last, picks) + data, times = raw[picks, first:last] except Exception as inst: raw['fid'].close() outfid.close() print inst + print 'Writing ... ', fiff.write_raw_buffer(outfid, data, cals) print '[done]' diff --git a/fiff/__init__.py b/mne/__init__.py similarity index 51% copy from fiff/__init__.py copy to mne/__init__.py index 25ddfe2..331369d 100644 --- a/fiff/__init__.py +++ b/mne/__init__.py @@ -1,17 +1,10 @@ __version__ = '0.1.git' -from .constants import FIFF -from .open import fiff_open -from .evoked import read_evoked, write_evoked from .cov import read_cov, write_cov, write_cov_file -from .raw import setup_read_raw, read_raw_segment, read_raw_segment_times, \ - start_writing_raw, write_raw_buffer, finish_writing_raw from .event import read_events, write_events from .forward import read_forward_solution from .stc import read_stc, write_stc from .bem_surfaces import read_bem_surfaces from .inverse import read_inverse_operator, compute_inverse -from .pick import pick_types -from .meas_info import get_current_comp from .epochs import read_epochs - +import fiff diff --git a/fiff/bem_surfaces.py b/mne/bem_surfaces.py similarity index 96% rename from fiff/bem_surfaces.py rename to mne/bem_surfaces.py index a1fdbe8..b878914 100644 --- a/fiff/bem_surfaces.py +++ b/mne/bem_surfaces.py @@ -1,11 +1,15 @@ -import numpy as np +# Author: Alexandre Gramfort <[email protected]> +# +# License: BSD Style. -from .constants import FIFF -from .open import fiff_open -from .tree import dir_tree_find -from .tag import find_tag +import numpy as np from scipy import linalg +from .fiff.constants import FIFF +from .fiff.open import fiff_open +from .fiff.tree import dir_tree_find +from .fiff.tag import find_tag + # # These fiff definitions are not needed elsewhere # diff --git a/fiff/cov.py b/mne/cov.py similarity index 92% rename from fiff/cov.py rename to mne/cov.py index 5cb19f6..4b2aa04 100644 --- a/fiff/cov.py +++ b/mne/cov.py @@ -1,11 +1,19 @@ +# Author: Alexandre Gramfort <[email protected]> +# +# License: BSD Style. + import os import numpy as np -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 .fiff.constants import FIFF +from .fiff.tag import find_tag +from .fiff.tree import dir_tree_find +from .fiff.proj import read_proj +from .fiff.channels import _read_bad_channels + +from .fiff.write import start_block, end_block, write_int, write_name_list, \ + write_double, write_float_matrix, start_file, end_file +from .fiff.proj import write_proj def read_cov(fid, node, cov_kind): @@ -120,11 +128,6 @@ def read_cov(fid, node, cov_kind): ############################################################################### # Writing -from .write import start_block, end_block, write_int, write_name_list, \ - write_double, write_float_matrix, start_file, end_file -from .proj import write_proj - - def write_cov(fid, cov): """Write a noise covariance matrix diff --git a/fiff/epochs.py b/mne/epochs.py similarity index 97% rename from fiff/epochs.py rename to mne/epochs.py index 38bd8f0..c9aeb04 100644 --- a/fiff/epochs.py +++ b/mne/epochs.py @@ -1,5 +1,7 @@ -# Authors : Alexandre Gramfort, [email protected] -# Matti Hamalainen, [email protected] +# Author: Alexandre Gramfort <[email protected]> +# +# License: BSD Style. + import numpy as np import fiff diff --git a/fiff/event.py b/mne/event.py similarity index 87% rename from fiff/event.py rename to mne/event.py index a4d6672..4f7fa6a 100644 --- a/fiff/event.py +++ b/mne/event.py @@ -2,13 +2,14 @@ """ # Author: Alexandre Gramfort <[email protected]> +# # License: BSD Style. -from .constants import FIFF -from .tree import dir_tree_find -from .tag import read_tag -from .open import fiff_open -from .write import write_int, start_block, start_file, end_block, end_file +from .fiff.constants import FIFF +from .fiff.tree import dir_tree_find +from .fiff.tag import read_tag +from .fiff.open import fiff_open +from .fiff.write import write_int, start_block, start_file, end_block, end_file def read_events(filename): diff --git a/fiff/__init__.py b/mne/fiff/__init__.py similarity index 52% rename from fiff/__init__.py rename to mne/fiff/__init__.py index 25ddfe2..f85d4d6 100644 --- a/fiff/__init__.py +++ b/mne/fiff/__init__.py @@ -3,15 +3,8 @@ __version__ = '0.1.git' from .constants import FIFF from .open import fiff_open from .evoked import read_evoked, write_evoked -from .cov import read_cov, write_cov, write_cov_file from .raw import setup_read_raw, read_raw_segment, read_raw_segment_times, \ start_writing_raw, write_raw_buffer, finish_writing_raw -from .event import read_events, write_events -from .forward import read_forward_solution -from .stc import read_stc, write_stc -from .bem_surfaces import read_bem_surfaces -from .inverse import read_inverse_operator, compute_inverse from .pick import pick_types from .meas_info import get_current_comp -from .epochs import read_epochs diff --git a/fiff/bunch.py b/mne/fiff/bunch.py similarity index 100% rename from fiff/bunch.py rename to mne/fiff/bunch.py diff --git a/fiff/channels.py b/mne/fiff/channels.py similarity index 88% rename from fiff/channels.py rename to mne/fiff/channels.py index 31aaa03..8c057be 100644 --- a/fiff/channels.py +++ b/mne/fiff/channels.py @@ -1,3 +1,7 @@ +# Author: Alexandre Gramfort <[email protected]> +# +# License: BSD Style. + from .tree import dir_tree_find from .tag import find_tag from .constants import FIFF diff --git a/fiff/constants.py b/mne/fiff/constants.py similarity index 99% rename from fiff/constants.py rename to mne/fiff/constants.py index 21c916f..42fafe5 100644 --- a/fiff/constants.py +++ b/mne/fiff/constants.py @@ -1,3 +1,8 @@ +# Author: Alexandre Gramfort <[email protected]> +# Matti Hamalainen <[email protected]> +# +# License: BSD Style. + from bunch import Bunch FIFF = Bunch() diff --git a/fiff/ctf.py b/mne/fiff/ctf.py similarity index 98% rename from fiff/ctf.py rename to mne/fiff/ctf.py index fe1c59a..e64e9d5 100644 --- a/fiff/ctf.py +++ b/mne/fiff/ctf.py @@ -1,3 +1,7 @@ +# Author: Alexandre Gramfort <[email protected]> +# +# License: BSD Style. + import numpy as np from .constants import FIFF diff --git a/fiff/diff.py b/mne/fiff/diff.py similarity index 92% rename from fiff/diff.py rename to mne/fiff/diff.py index 4b18c40..88e4f61 100644 --- a/fiff/diff.py +++ b/mne/fiff/diff.py @@ -1,3 +1,7 @@ +# Author: Alexandre Gramfort <[email protected]> +# +# License: BSD Style. + import numpy as np def is_equal(first, second): diff --git a/fiff/evoked.py b/mne/fiff/evoked.py similarity index 99% rename from fiff/evoked.py rename to mne/fiff/evoked.py index eaf7ab4..09c1152 100644 --- a/fiff/evoked.py +++ b/mne/fiff/evoked.py @@ -1,3 +1,7 @@ +# Author: Alexandre Gramfort <[email protected]> +# +# License: BSD Style. + import numpy as np from .constants import FIFF diff --git a/fiff/matrix.py b/mne/fiff/matrix.py similarity index 93% rename from fiff/matrix.py rename to mne/fiff/matrix.py index 3eb82d0..8f61d4d 100644 --- a/fiff/matrix.py +++ b/mne/fiff/matrix.py @@ -1,3 +1,8 @@ +# Author: Alexandre Gramfort <[email protected]> +# Matti Hamalainen <[email protected]> +# +# License: BSD Style. + from .constants import FIFF from .tag import find_tag, has_tag diff --git a/fiff/meas_info.py b/mne/fiff/meas_info.py similarity index 98% rename from fiff/meas_info.py rename to mne/fiff/meas_info.py index 144a7ca..c1edc6e 100644 --- a/fiff/meas_info.py +++ b/mne/fiff/meas_info.py @@ -1,3 +1,7 @@ +# Author: Alexandre Gramfort <[email protected]> +# +# License: BSD Style. + import numpy as np from .tree import dir_tree_find diff --git a/fiff/open.py b/mne/fiff/open.py similarity index 92% rename from fiff/open.py rename to mne/fiff/open.py index 7cb57d7..9c0fed7 100644 --- a/fiff/open.py +++ b/mne/fiff/open.py @@ -1,3 +1,8 @@ +# Author: Alexandre Gramfort <[email protected]> +# Matti Hamalainen <[email protected]> +# +# License: BSD Style. + from .tag import read_tag_info, read_tag from .tree import make_dir_tree from .constants import FIFF diff --git a/fiff/pick.py b/mne/fiff/pick.py similarity index 96% rename from fiff/pick.py rename to mne/fiff/pick.py index 31dd241..5d5abbe 100644 --- a/fiff/pick.py +++ b/mne/fiff/pick.py @@ -1,3 +1,8 @@ +# Author: Alexandre Gramfort <[email protected]> +# Matti Hamalainen <[email protected]> +# +# License: BSD Style. + from copy import copy import numpy as np diff --git a/fiff/proj.py b/mne/fiff/proj.py similarity index 98% rename from fiff/proj.py rename to mne/fiff/proj.py index 010307f..788b895 100644 --- a/fiff/proj.py +++ b/mne/fiff/proj.py @@ -1,3 +1,8 @@ +# Author: Alexandre Gramfort <[email protected]> +# Matti Hamalainen <[email protected]> +# +# License: BSD Style. + from math import sqrt import numpy as np from scipy import linalg diff --git a/fiff/raw.py b/mne/fiff/raw.py similarity index 99% rename from fiff/raw.py rename to mne/fiff/raw.py index d9eb0c9..cc3d030 100644 --- a/fiff/raw.py +++ b/mne/fiff/raw.py @@ -1,3 +1,8 @@ +# Author: Alexandre Gramfort <[email protected]> +# Matti Hamalainen <[email protected]> +# +# License: BSD Style. + from math import floor, ceil import numpy as np diff --git a/fiff/tag.py b/mne/fiff/tag.py similarity index 99% rename from fiff/tag.py rename to mne/fiff/tag.py index 6cd766f..021636b 100644 --- a/fiff/tag.py +++ b/mne/fiff/tag.py @@ -1,3 +1,7 @@ +# Author: Alexandre Gramfort <[email protected]> +# +# License: BSD Style. + import struct import numpy as np diff --git a/mne/fiff/tests/__init__.py b/mne/fiff/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/fiff/tests/test_evoked.py b/mne/fiff/tests/test_evoked.py similarity index 87% rename from fiff/tests/test_evoked.py rename to mne/fiff/tests/test_evoked.py index 52e7178..ba25e80 100644 --- a/fiff/tests/test_evoked.py +++ b/mne/fiff/tests/test_evoked.py @@ -1,10 +1,9 @@ import os import os.path as op -import numpy as np from numpy.testing import assert_array_almost_equal, assert_equal -import fiff +from .. import read_evoked, write_evoked MNE_SAMPLE_DATASET_PATH = os.getenv('MNE_SAMPLE_DATASET_PATH') fname = op.join(MNE_SAMPLE_DATASET_PATH, 'MEG', 'sample', @@ -13,10 +12,10 @@ fname = op.join(MNE_SAMPLE_DATASET_PATH, 'MEG', 'sample', def test_io_cov(): """Test IO for noise covariance matrices """ - data = fiff.read_evoked(fname) + data = read_evoked(fname) - fiff.write_evoked('evoked.fif', data) - data2 = fiff.read_evoked('evoked.fif') + write_evoked('evoked.fif', data) + data2 = read_evoked('evoked.fif') print assert_array_almost_equal(data['evoked']['epochs'], data2['evoked']['epochs']) diff --git a/fiff/tests/test_raw.py b/mne/fiff/tests/test_raw.py similarity index 73% rename from fiff/tests/test_raw.py rename to mne/fiff/tests/test_raw.py index 84f6aa2..42fea76 100644 --- a/fiff/tests/test_raw.py +++ b/mne/fiff/tests/test_raw.py @@ -4,7 +4,9 @@ import os.path as op from numpy.testing import assert_array_almost_equal, assert_equal from math import ceil -import fiff +from .. import setup_read_raw, read_raw_segment_times, pick_types, \ + start_writing_raw, write_raw_buffer, finish_writing_raw + MNE_SAMPLE_DATASET_PATH = os.getenv('MNE_SAMPLE_DATASET_PATH') fname = op.join(MNE_SAMPLE_DATASET_PATH, 'MEG', 'sample', @@ -13,14 +15,14 @@ fname = op.join(MNE_SAMPLE_DATASET_PATH, 'MEG', 'sample', def test_io_raw(): """Test IO for raw data """ - raw = fiff.setup_read_raw(fname) + raw = setup_read_raw(fname) nchan = raw['info']['nchan'] ch_names = raw['info']['ch_names'] meg_channels_idx = [k for k in range(nchan) if ch_names[k][:3]=='MEG'] meg_channels_idx = meg_channels_idx[:5] - data, times = fiff.read_raw_segment_times(raw, start=100, stop=115, + data, times = read_raw_segment_times(raw, start=100, stop=115, sel=meg_channels_idx) # Writing @@ -31,13 +33,13 @@ def test_io_raw(): want_stim = False include = ['STI 014'] - picks = fiff.pick_types(raw['info'], meg=want_meg, eeg=want_eeg, + picks = pick_types(raw['info'], meg=want_meg, eeg=want_eeg, stim=want_stim, include=include, exclude=raw['info']['bads']) print "Number of picked channels : %d" % len(picks) - outfid, cals = fiff.start_writing_raw('raw.fif', raw['info'], picks) + outfid, cals = start_writing_raw('raw.fif', raw['info'], picks) # # Set up the reading parameters # @@ -50,18 +52,18 @@ def test_io_raw(): # for first in range(start, stop, quantum): last = first + quantum - if last > stop: + if last >= stop: last = stop try: - data, times = fiff.read_raw_segment(raw, first, last, picks) + data, times = raw[picks, first:last] except Exception as inst: raw['fid'].close() outfid.close() print inst - fiff.write_raw_buffer(outfid, data, cals) + write_raw_buffer(outfid, data, cals) print '[done]' - fiff.finish_writing_raw(outfid) + finish_writing_raw(outfid) raw['fid'].close() diff --git a/fiff/tree.py b/mne/fiff/tree.py similarity index 98% rename from fiff/tree.py rename to mne/fiff/tree.py index 86b23c1..9c2b92a 100644 --- a/fiff/tree.py +++ b/mne/fiff/tree.py @@ -1,3 +1,7 @@ +# Author: Alexandre Gramfort <[email protected]> +# +# License: BSD Style. + from .bunch import Bunch from .tag import read_tag diff --git a/fiff/write.py b/mne/fiff/write.py similarity index 99% rename from fiff/write.py rename to mne/fiff/write.py index a0091b8..20144bf 100644 --- a/fiff/write.py +++ b/mne/fiff/write.py @@ -1,3 +1,7 @@ +# Author: Alexandre Gramfort <[email protected]> +# +# License: BSD Style. + import time import array import numpy as np diff --git a/fiff/forward.py b/mne/forward.py similarity index 97% rename from fiff/forward.py rename to mne/forward.py index 6a7b2cc..c8922e5 100644 --- a/fiff/forward.py +++ b/mne/forward.py @@ -1,14 +1,19 @@ +# Author: Alexandre Gramfort <[email protected]> +# +# License: BSD Style. + import copy import numpy as np 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 .tag import find_tag +from .fiff.constants import FIFF +from .fiff.open import fiff_open +from .fiff.tree import dir_tree_find +from .fiff.channels import _read_bad_channels +from .fiff.tag import find_tag +from .fiff.matrix import _read_named_matrix, _transpose_named_matrix + from .source_space import read_source_spaces, find_source_space_hemi -from .matrix import _read_named_matrix, _transpose_named_matrix def _block_diag(A, n): diff --git a/fiff/inverse.py b/mne/inverse.py similarity index 96% rename from fiff/inverse.py rename to mne/inverse.py index b18c67d..77317d2 100644 --- a/fiff/inverse.py +++ b/mne/inverse.py @@ -1,18 +1,24 @@ +# Author: Alexandre Gramfort <[email protected]> +# +# License: BSD Style. + from math import sqrt import numpy as np -from .constants import FIFF -from .open import fiff_open -from .tag import find_tag -from .matrix import _read_named_matrix, _transpose_named_matrix -from .cov import read_cov -from .proj import read_proj, make_projector -from .tree import dir_tree_find +from .fiff.constants import FIFF +from .fiff.open import fiff_open +from .fiff.tag import find_tag +from .fiff.matrix import _read_named_matrix, _transpose_named_matrix +from .fiff.cov import read_cov +from .fiff.proj import read_proj, make_projector +from .fiff.tree import dir_tree_find +from .fiff.evoked import read_evoked +from .fiff.pick import pick_channels_evoked + from .source_space import read_source_spaces, find_source_space_hemi -from .forward import _invert_transform, _transform_source_space_to -from .evoked import read_evoked -from .pick import pick_channels_evoked -from .forward import _block_diag +from .forward import _invert_transform, _transform_source_space_to, \ + _block_diag + def read_inverse_operator(fname): """Read the inverse operator decomposition from a FIF file diff --git a/fiff/source_space.py b/mne/source_space.py similarity index 97% rename from fiff/source_space.py rename to mne/source_space.py index fc8daaa..1b10c8d 100644 --- a/fiff/source_space.py +++ b/mne/source_space.py @@ -1,10 +1,14 @@ +# Author: Alexandre Gramfort <[email protected]> +# +# License: BSD Style. + from math import sqrt import numpy as np -from .constants import FIFF -from .tree import dir_tree_find -from .tag import find_tag -from .open import fiff_open +from .fiff.constants import FIFF +from .fiff.tree import dir_tree_find +from .fiff.tag import find_tag +from .fiff.open import fiff_open def patch_info(nearest): diff --git a/fiff/stc.py b/mne/stc.py similarity index 96% rename from fiff/stc.py rename to mne/stc.py index cb662ae..cb9c4e5 100644 --- a/fiff/stc.py +++ b/mne/stc.py @@ -1,3 +1,7 @@ +# Author: Alexandre Gramfort <[email protected]> +# +# License: BSD Style. + import numpy as np diff --git a/mne/tests/__init__.py b/mne/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/fiff/tests/test_bem_surfaces.py b/mne/tests/test_bem_surfaces.py similarity index 77% rename from fiff/tests/test_bem_surfaces.py rename to mne/tests/test_bem_surfaces.py index a8588a4..2579b8e 100644 --- a/fiff/tests/test_bem_surfaces.py +++ b/mne/tests/test_bem_surfaces.py @@ -4,7 +4,7 @@ import os.path as op import numpy as np from numpy.testing import assert_array_almost_equal -import fiff +import mne MNE_SAMPLE_DATASET_PATH = os.getenv('MNE_SAMPLE_DATASET_PATH') fname = op.join(MNE_SAMPLE_DATASET_PATH, 'subjects', 'sample', 'bem', @@ -13,6 +13,6 @@ fname = op.join(MNE_SAMPLE_DATASET_PATH, 'subjects', 'sample', 'bem', def test_io_bem_surfaces(): """Testing reading of bem surfaces """ - surf = fiff.read_bem_surfaces(fname, add_geom=False) - surf = fiff.read_bem_surfaces(fname, add_geom=True) + surf = mne.read_bem_surfaces(fname, add_geom=False) + surf = mne.read_bem_surfaces(fname, add_geom=True) print "Number of surfaces : %d" % len(surf) diff --git a/fiff/tests/test_cov.py b/mne/tests/test_cov.py similarity index 56% rename from fiff/tests/test_cov.py rename to mne/tests/test_cov.py index 79ceba5..0bad2fb 100644 --- a/fiff/tests/test_cov.py +++ b/mne/tests/test_cov.py @@ -1,10 +1,10 @@ import os import os.path as op -import numpy as np from numpy.testing import assert_array_almost_equal -import fiff +import mne +from ..fiff import fiff_open MNE_SAMPLE_DATASET_PATH = os.getenv('MNE_SAMPLE_DATASET_PATH') fname = op.join(MNE_SAMPLE_DATASET_PATH, 'MEG', 'sample', @@ -13,15 +13,15 @@ fname = op.join(MNE_SAMPLE_DATASET_PATH, 'MEG', 'sample', def test_io_cov(): """Test IO for noise covariance matrices """ - fid, tree, _ = fiff.fiff_open(fname) + fid, tree, _ = fiff_open(fname) cov_type = 1 - cov = fiff.read_cov(fid, tree, cov_type) + cov = mne.read_cov(fid, tree, cov_type) fid.close() - fiff.write_cov_file('cov.fif', cov) + mne.write_cov_file('cov.fif', cov) - fid, tree, _ = fiff.fiff_open('cov.fif') - cov2 = fiff.read_cov(fid, tree, cov_type) + fid, tree, _ = fiff_open('cov.fif') + cov2 = mne.read_cov(fid, tree, cov_type) fid.close() print assert_array_almost_equal(cov['data'], cov2['data']) \ No newline at end of file diff --git a/fiff/tests/test_event.py b/mne/tests/test_event.py similarity index 61% rename from fiff/tests/test_event.py rename to mne/tests/test_event.py index 5b224fc..eaefc87 100644 --- a/fiff/tests/test_event.py +++ b/mne/tests/test_event.py @@ -1,10 +1,9 @@ import os import os.path as op -import numpy as np from numpy.testing import assert_array_almost_equal -import fiff +import mne MNE_SAMPLE_DATASET_PATH = os.getenv('MNE_SAMPLE_DATASET_PATH') fname = op.join(MNE_SAMPLE_DATASET_PATH, 'MEG', 'sample', @@ -14,7 +13,7 @@ fname = op.join(MNE_SAMPLE_DATASET_PATH, 'MEG', 'sample', def test_io_cov(): """Test IO for noise covariance matrices """ - event_list = fiff.read_events(fname) - fiff.write_events('events.fif', event_list) - event_list2 = fiff.read_events(fname) - assert_array_almost_equal(event_list, event_list2) + events = mne.read_events(fname) + mne.write_events('events.fif', events) + events2 = mne.read_events(fname) + assert_array_almost_equal(events, events2) diff --git a/fiff/tests/test_forward.py b/mne/tests/test_forward.py similarity index 74% rename from fiff/tests/test_forward.py rename to mne/tests/test_forward.py index 4693c0f..dd67505 100644 --- a/fiff/tests/test_forward.py +++ b/mne/tests/test_forward.py @@ -1,10 +1,9 @@ import os import os.path as op -import numpy as np from numpy.testing import assert_array_almost_equal, assert_equal -import fiff +import mne MNE_SAMPLE_DATASET_PATH = os.getenv('MNE_SAMPLE_DATASET_PATH') fname = op.join(MNE_SAMPLE_DATASET_PATH, 'MEG', 'sample', @@ -13,6 +12,6 @@ fname = op.join(MNE_SAMPLE_DATASET_PATH, 'MEG', 'sample', def test_io_forward(): """Test IO for forward solutions """ - fwd = fiff.read_forward_solution(fname) - fwd = fiff.read_forward_solution(fname, force_fixed=True) + fwd = mne.read_forward_solution(fname) + fwd = mne.read_forward_solution(fname, force_fixed=True) leadfield = fwd['sol']['data'] diff --git a/fiff/tests/test_inverse.py b/mne/tests/test_inverse.py similarity index 83% rename from fiff/tests/test_inverse.py rename to mne/tests/test_inverse.py index 748d43e..be20ccd 100644 --- a/fiff/tests/test_inverse.py +++ b/mne/tests/test_inverse.py @@ -1,10 +1,9 @@ import os import os.path as op -import numpy as np from numpy.testing import assert_array_almost_equal, assert_equal -import fiff +import mne MNE_SAMPLE_DATASET_PATH = os.getenv('MNE_SAMPLE_DATASET_PATH') fname = op.join(MNE_SAMPLE_DATASET_PATH, 'MEG', 'sample', @@ -13,4 +12,4 @@ fname = op.join(MNE_SAMPLE_DATASET_PATH, 'MEG', 'sample', def test_io_forward(): """Test IO for inverse operator """ - fwd = fiff.read_inverse_operator(fname) + fwd = mne.read_inverse_operator(fname) diff --git a/fiff/tests/test_stc.py b/mne/tests/test_stc.py similarity index 81% rename from fiff/tests/test_stc.py rename to mne/tests/test_stc.py index 9ece422..02c5a23 100644 --- a/fiff/tests/test_stc.py +++ b/mne/tests/test_stc.py @@ -1,10 +1,9 @@ import os import os.path as op -import numpy as np from numpy.testing import assert_array_almost_equal, assert_equal -import fiff +import mne MNE_SAMPLE_DATASET_PATH = os.getenv('MNE_SAMPLE_DATASET_PATH') fname = op.join(MNE_SAMPLE_DATASET_PATH, 'MEG', 'sample', @@ -13,10 +12,10 @@ fname = op.join(MNE_SAMPLE_DATASET_PATH, 'MEG', 'sample', def test_io_stc(): """Test IO for STC files """ - stc = fiff.read_stc(fname) + stc = mne.read_stc(fname) - fiff.write_stc("tmp.stc", stc) - stc2 = fiff.read_stc("tmp.stc") + mne.write_stc("tmp.stc", stc) + stc2 = mne.read_stc("tmp.stc") assert_array_almost_equal(stc['data'], stc2['data']) assert_array_almost_equal(stc['tmin'], stc2['tmin']) diff --git a/setup.cfg b/setup.cfg index 6cec9dd..bcd477b 100644 --- a/setup.cfg +++ b/setup.cfg @@ -6,5 +6,5 @@ test = nosetests [nosetests] detailed-errors = 1 with-doctest = 1 -cover-package = fiff +cover-package = mne diff --git a/setup.py b/setup.py index b9b78b1..624b309 100644 --- a/setup.py +++ b/setup.py @@ -1,20 +1,20 @@ #! /usr/bin/env python # -# Copyright (C) 2010 Alexandre Gramfort <[email protected]> +# Copyright (C) 2011 Alexandre Gramfort <[email protected]> -descr = """A set of python functions to read and write Neuromag FIF files.""" +descr = """MNE python project for MEG and EEG data analysis.""" import os -DISTNAME = 'pyfiff' -DESCRIPTION = 'Functions to read and write Neuromag FIF files.' +DISTNAME = 'mne' +DESCRIPTION = 'MNE python project for MEG and EEG data analysis' LONG_DESCRIPTION = descr MAINTAINER = 'Alexandre Gramfort' MAINTAINER_EMAIL = '[email protected]' -URL = 'http://github.com/agramfort/pyfiff' -LICENSE = 'To be determined' # XXX -DOWNLOAD_URL = 'http://github.com/agramfort/pyfiff' +URL = 'http://github.com/mne/mne' +LICENSE = 'BSD' +DOWNLOAD_URL = 'http://github.com/mne/mne' VERSION = '0.1.git' import setuptools # we are using a setuptools namespace @@ -39,7 +39,6 @@ if __name__ == "__main__": ['Intended Audience :: Science/Research', 'Intended Audience :: Developers', 'License :: OSI Approved', - 'Programming Language :: C', 'Programming Language :: Python', 'Topic :: Software Development', 'Topic :: Scientific/Engineering', -- 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
