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commit 81a34e9fb1a25e702936496e518675e68d7ca098 Author: Alexandre Gramfort <[email protected]> Date: Tue Feb 15 16:34:36 2011 -0500 ENH : better handling of sample dataset --- examples/plot_compute_mne_inverse.py | 8 +++--- examples/plot_estimate_covariance_matrix.py | 5 ++-- examples/plot_read_epochs.py | 10 +++---- examples/plot_read_evoked.py | 5 ++-- examples/plot_read_forward.py | 5 ++-- examples/plot_read_noise_covariance_matrix.py | 5 ++-- examples/plot_read_raw_data.py | 5 ++-- examples/plot_read_stc.py | 5 ++-- examples/plot_topography.py | 5 ++-- examples/plot_whiten_forward_solution.py | 11 ++++--- examples/plot_whitened_evoked_data.py | 8 +++--- examples/read_bem_surfaces.py | 6 ++-- examples/read_events.py | 5 ++-- examples/read_inverse.py | 5 +++- examples/read_write_raw.py | 4 ++- examples/stats/plot_sensor_permutation_test.py | 8 +++--- examples/time_frequency/plot_time_frequency.py | 8 +++--- mne/datasets/__init__.py | 0 mne/datasets/sample/__init__.py | 40 ++++++++++++++++++++++++++ mne/layouts/layout.py | 3 ++ mne/tests/test_bem_surfaces.py | 8 +++--- mne/tests/test_forward.py | 7 +++-- mne/tests/test_inverse.py | 8 ++++-- mne/tests/test_stc.py | 7 +++-- 24 files changed, 119 insertions(+), 62 deletions(-) diff --git a/examples/plot_compute_mne_inverse.py b/examples/plot_compute_mne_inverse.py index 45500ed..0fe1320 100644 --- a/examples/plot_compute_mne_inverse.py +++ b/examples/plot_compute_mne_inverse.py @@ -18,11 +18,11 @@ import os import numpy as np import pylab as pl import mne +from mne.datasets import sample -fname_inv = os.environ['MNE_SAMPLE_DATASET_PATH'] -fname_inv += '/MEG/sample/sample_audvis-meg-oct-6-meg-inv.fif' -fname_data = os.environ['MNE_SAMPLE_DATASET_PATH'] -fname_data += '/MEG/sample/sample_audvis-ave.fif' +data_path = sample.data_path('.') +fname_inv = data_path + '/MEG/sample/sample_audvis-meg-oct-6-meg-inv.fif' +fname_data = data_path + '/MEG/sample/sample_audvis-ave.fif' setno = 0 snr = 3.0 diff --git a/examples/plot_estimate_covariance_matrix.py b/examples/plot_estimate_covariance_matrix.py index 06b247c..128db46 100644 --- a/examples/plot_estimate_covariance_matrix.py +++ b/examples/plot_estimate_covariance_matrix.py @@ -13,9 +13,10 @@ print __doc__ import os import mne from mne import fiff +from mne.datasets import sample -fname = os.environ['MNE_SAMPLE_DATASET_PATH'] -fname += '/MEG/sample/sample_audvis_raw.fif' +data_path = sample.data_path('.') +fname = data_path + '/MEG/sample/sample_audvis_raw.fif' raw = fiff.setup_read_raw(fname) diff --git a/examples/plot_read_epochs.py b/examples/plot_read_epochs.py index 98cfcbb..239ec95 100644 --- a/examples/plot_read_epochs.py +++ b/examples/plot_read_epochs.py @@ -20,15 +20,13 @@ import numpy as np import mne from mne import fiff +from mne.datasets import sample +data_path = sample.data_path('.') ############################################################################### # Set parameters -raw_fname = os.environ['MNE_SAMPLE_DATASET_PATH'] -# raw_fname += '/MEG/sample/sample_audvis_raw.fif' -raw_fname += '/MEG/sample/sample_audvis_filt-0-40_raw.fif' -event_fname = os.environ['MNE_SAMPLE_DATASET_PATH'] -# event_fname += '/MEG/sample/sample_audvis_raw-eve.fif' -event_fname += '/MEG/sample/sample_audvis_filt-0-40_raw-eve.fif' +raw_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw.fif' +event_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw-eve.fif' event_id = 1 tmin = -0.2 tmax = 0.5 diff --git a/examples/plot_read_evoked.py b/examples/plot_read_evoked.py index f48e5e5..3e8634a 100644 --- a/examples/plot_read_evoked.py +++ b/examples/plot_read_evoked.py @@ -12,9 +12,10 @@ print __doc__ import os from mne import fiff +from mne.datasets import sample +data_path = sample.data_path('.') -fname = os.environ['MNE_SAMPLE_DATASET_PATH'] -fname += '/MEG/sample/sample_audvis-ave.fif' +fname = data_path + '/MEG/sample/sample_audvis-ave.fif' # Reading data = fiff.read_evoked(fname, setno=0, baseline=(None, 0)) diff --git a/examples/plot_read_forward.py b/examples/plot_read_forward.py index caa8338..797f8a9 100644 --- a/examples/plot_read_forward.py +++ b/examples/plot_read_forward.py @@ -11,9 +11,10 @@ print __doc__ import os import mne +from mne.datasets import sample +data_path = sample.data_path('.') -fname = os.environ['MNE_SAMPLE_DATASET_PATH'] -fname += '/MEG/sample/sample_audvis-meg-oct-6-fwd.fif' +fname = data_path + '/MEG/sample/sample_audvis-meg-oct-6-fwd.fif' fwd = mne.read_forward_solution(fname) leadfield = fwd['sol']['data'] diff --git a/examples/plot_read_noise_covariance_matrix.py b/examples/plot_read_noise_covariance_matrix.py index 3547017..2be0830 100644 --- a/examples/plot_read_noise_covariance_matrix.py +++ b/examples/plot_read_noise_covariance_matrix.py @@ -11,9 +11,10 @@ print __doc__ import os import mne +from mne.datasets import sample -fname = os.environ['MNE_SAMPLE_DATASET_PATH'] -fname += '/MEG/sample/sample_audvis-cov.fif' +data_path = sample.data_path('.') +fname = data_path + '/MEG/sample/sample_audvis-cov.fif' cov = mne.Covariance(kind='full') cov.load(fname) diff --git a/examples/plot_read_raw_data.py b/examples/plot_read_raw_data.py index 9e585bd..fee5580 100644 --- a/examples/plot_read_raw_data.py +++ b/examples/plot_read_raw_data.py @@ -11,9 +11,10 @@ print __doc__ import os from mne import fiff +from mne.datasets import sample +data_path = sample.data_path('.') -fname = os.environ['MNE_SAMPLE_DATASET_PATH'] -fname += '/MEG/sample/sample_audvis_raw.fif' +fname = data_path + '/MEG/sample/sample_audvis_raw.fif' raw = fiff.setup_read_raw(fname) diff --git a/examples/plot_read_stc.py b/examples/plot_read_stc.py index f35f06e..d8b7778 100644 --- a/examples/plot_read_stc.py +++ b/examples/plot_read_stc.py @@ -15,9 +15,10 @@ print __doc__ import os import numpy as np import mne +from mne.datasets import sample -fname = os.environ['MNE_SAMPLE_DATASET_PATH'] -fname += '/MEG/sample/sample_audvis-meg-lh.stc' +data_path = sample.data_path('.') +fname = data_path + '/MEG/sample/sample_audvis-meg-lh.stc' stc = mne.read_stc(fname) diff --git a/examples/plot_topography.py b/examples/plot_topography.py index 2c736af..939ec8e 100644 --- a/examples/plot_topography.py +++ b/examples/plot_topography.py @@ -17,9 +17,10 @@ import pylab as pl from mne import fiff from mne.layouts import Layout from mne.viz import plot_topo +from mne.datasets import sample +data_path = sample.data_path('.') -fname = os.environ['MNE_SAMPLE_DATASET_PATH'] -fname += '/MEG/sample/sample_audvis-ave.fif' +fname = data_path + '/MEG/sample/sample_audvis-ave.fif' # Reading data = fiff.read_evoked(fname, setno=0, baseline=(None, 0)) diff --git a/examples/plot_whiten_forward_solution.py b/examples/plot_whiten_forward_solution.py index 0faa4a4..4899da8 100644 --- a/examples/plot_whiten_forward_solution.py +++ b/examples/plot_whiten_forward_solution.py @@ -12,13 +12,12 @@ print __doc__ import os import mne from mne import fiff +from mne.datasets import sample -fwd_fname = os.environ['MNE_SAMPLE_DATASET_PATH'] -fwd_fname += '/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif' -ave_fname = os.environ['MNE_SAMPLE_DATASET_PATH'] -ave_fname += '/MEG/sample/sample_audvis-ave.fif' -cov_fname = os.environ['MNE_SAMPLE_DATASET_PATH'] -cov_fname += '/MEG/sample/sample_audvis-cov.fif' +data_path = sample.data_path('.') +fwd_fname = data_path + '/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif' +ave_fname = data_path + '/MEG/sample/sample_audvis-ave.fif' +cov_fname = data_path + '/MEG/sample/sample_audvis-cov.fif' # Reading ave = fiff.read_evoked(ave_fname, setno=0, baseline=(None, 0)) diff --git a/examples/plot_whitened_evoked_data.py b/examples/plot_whitened_evoked_data.py index 58e677a..1228f77 100644 --- a/examples/plot_whitened_evoked_data.py +++ b/examples/plot_whitened_evoked_data.py @@ -13,11 +13,11 @@ print __doc__ import os import mne from mne import fiff +from mne.datasets import sample -fname = os.environ['MNE_SAMPLE_DATASET_PATH'] -fname += '/MEG/sample/sample_audvis-ave.fif' -cov_fname = os.environ['MNE_SAMPLE_DATASET_PATH'] -cov_fname += '/MEG/sample/sample_audvis-cov.fif' +data_path = sample.data_path('.') +fname = data_path + '/MEG/sample/sample_audvis-ave.fif' +cov_fname = data_path + '/MEG/sample/sample_audvis-cov.fif' # Reading ave = fiff.read_evoked(fname, setno=0, baseline=(None, 0)) diff --git a/examples/read_bem_surfaces.py b/examples/read_bem_surfaces.py index ad9dcf4..dcd3b28 100644 --- a/examples/read_bem_surfaces.py +++ b/examples/read_bem_surfaces.py @@ -10,10 +10,10 @@ Reading BEM surfaces from a forward solution print __doc__ import mne +from mne.datasets import sample - -fname = os.environ['MNE_SAMPLE_DATASET_PATH'] -fname += '/subjects/sample/bem/sample-5120-5120-5120-bem-sol.fif' +data_path = sample.data_path('.') +fname = data_path + '/subjects/sample/bem/sample-5120-5120-5120-bem-sol.fif' surfaces = mne.read_bem_surfaces(fname) diff --git a/examples/read_events.py b/examples/read_events.py index 0c5b1bf..cc3fc1f 100644 --- a/examples/read_events.py +++ b/examples/read_events.py @@ -11,9 +11,10 @@ print __doc__ import os import mne +from mne.datasets import sample -fname = os.environ['MNE_SAMPLE_DATASET_PATH'] -fname += '/MEG/sample/sample_audvis_raw-eve.fif' +data_path = sample.data_path('.') +fname = data_path + '/MEG/sample/sample_audvis_raw-eve.fif' # Reading events events = mne.read_events(fname) diff --git a/examples/read_inverse.py b/examples/read_inverse.py index 9515503..5663155 100644 --- a/examples/read_inverse.py +++ b/examples/read_inverse.py @@ -10,8 +10,11 @@ Reading an inverse operator print __doc__ import mne +from mne.datasets import sample -fname = 'MNE-sample-data/MEG/sample/sample_audvis-meg-oct-6-meg-inv.fif' +data_path = sample.data_path('.') +fname = data_path +fname += 'MNE-sample-data/MEG/sample/sample_audvis-meg-oct-6-meg-inv.fif' inv = mne.read_inverse_operator(fname) diff --git a/examples/read_write_raw.py b/examples/read_write_raw.py index 09293ee..6d23be4 100644 --- a/examples/read_write_raw.py +++ b/examples/read_write_raw.py @@ -14,8 +14,10 @@ print __doc__ import os from math import ceil from mne import fiff +from mne.datasets import sample -infile = os.environ['MNE_SAMPLE_DATASET_PATH'] +data_path = sample.data_path('.') +infile = data_path infile += '/MEG/sample/sample_audvis_raw.fif' outfile = 'sample_audvis_small_raw.fif' diff --git a/examples/stats/plot_sensor_permutation_test.py b/examples/stats/plot_sensor_permutation_test.py index dcc2484..557b50d 100644 --- a/examples/stats/plot_sensor_permutation_test.py +++ b/examples/stats/plot_sensor_permutation_test.py @@ -21,13 +21,13 @@ import numpy as np import mne from mne import fiff from mne.stats import permutation_t_test +from mne.datasets import sample ############################################################################### # Set parameters -raw_fname = os.environ['MNE_SAMPLE_DATASET_PATH'] -raw_fname += '/MEG/sample/sample_audvis_filt-0-40_raw.fif' -event_fname = os.environ['MNE_SAMPLE_DATASET_PATH'] -event_fname += '/MEG/sample/sample_audvis_filt-0-40_raw-eve.fif' +data_path = sample.data_path('..') +raw_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw.fif' +event_fname = data_path + '/MEG/sample/sample_audvis_filt-0-40_raw-eve.fif' event_id = 1 tmin = -0.2 tmax = 0.5 diff --git a/examples/time_frequency/plot_time_frequency.py b/examples/time_frequency/plot_time_frequency.py index bb03ae2..f5209c3 100644 --- a/examples/time_frequency/plot_time_frequency.py +++ b/examples/time_frequency/plot_time_frequency.py @@ -20,13 +20,13 @@ import numpy as np import mne from mne import fiff from mne import time_frequency +from mne.datasets import sample ############################################################################### # Set parameters -raw_fname = os.environ['MNE_SAMPLE_DATASET_PATH'] -raw_fname += '/MEG/sample/sample_audvis_raw.fif' -event_fname = os.environ['MNE_SAMPLE_DATASET_PATH'] -event_fname += '/MEG/sample/sample_audvis_raw-eve.fif' +data_path = sample.data_path('..') +raw_fname = data_path + '/MEG/sample/sample_audvis_raw.fif' +event_fname = data_path + '/MEG/sample/sample_audvis_raw-eve.fif' event_id = 1 tmin = -0.2 tmax = 0.5 diff --git a/mne/datasets/__init__.py b/mne/datasets/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/mne/datasets/sample/__init__.py b/mne/datasets/sample/__init__.py new file mode 100644 index 0000000..9aa2703 --- /dev/null +++ b/mne/datasets/sample/__init__.py @@ -0,0 +1,40 @@ +# Author: Alexandre Gramfort <[email protected]> +# License: BSD Style. + +import os +import os.path as op + +def data_path(path='.'): + """Get path to local copy of Sample dataset + + Parameters + ---------- + dir : string + Location of where to look for the sample dataset. + If not set. The data will be automatically downloaded in + the local folder. + """ + archive_name = "MNE-sample-data-processed.tar.gz" + url = "ftp://surfer.nmr.mgh.harvard.edu/pub/data/"; + archive_name + folder_name = "MNE-sample-data-processed" + + martinos_path = '/homes/6/gramfort/cluster/work/data/MNE-sample-data-processed.tar.gz' + + if not os.path.exists(op.join(path, folder_name)): + if os.path.exists(martinos_path): + archive_name = martinos_path + elif not os.path.exists(archive_name): + import urllib + print "Downloading data, please Wait (600 MB)..." + print url + opener = urllib.urlopen(url) + open(archive_name, 'wb').write(opener.read()) + print + + import tarfile + print "Decompressiong the archive: " + archive_name + tarfile.open(archive_name, "r:gz").extractall(path=path) + print + + path = op.join(path, folder_name) + return path diff --git a/mne/layouts/layout.py b/mne/layouts/layout.py index e73bba4..8eac6b4 100644 --- a/mne/layouts/layout.py +++ b/mne/layouts/layout.py @@ -8,7 +8,10 @@ class Layout(object): """Sensor layouts""" def __init__(self, kind='Vectorview-all'): """ + Parameters + ---------- kind : 'Vectorview-all' | 'CTF-275' | 'Vectorview-grad' | 'Vectorview-mag' + Type of layout """ lout_fname = op.join(op.dirname(__file__), kind + '.lout') diff --git a/mne/tests/test_bem_surfaces.py b/mne/tests/test_bem_surfaces.py index 1703fc9..59e3c26 100644 --- a/mne/tests/test_bem_surfaces.py +++ b/mne/tests/test_bem_surfaces.py @@ -1,13 +1,13 @@ -import os import os.path as op -import numpy as np from numpy.testing import assert_array_almost_equal import mne +from mne.datasets import sample -MNE_SAMPLE_DATASET_PATH = os.getenv('MNE_SAMPLE_DATASET_PATH') -fname = op.join(MNE_SAMPLE_DATASET_PATH, 'subjects', 'sample', 'bem', +examples_folder = op.join(op.dirname(__file__), '..', '..', 'examples') +data_path = sample.data_path(examples_folder) +fname = op.join(data_path, 'subjects', 'sample', 'bem', 'sample-5120-5120-5120-bem-sol.fif') def test_io_bem_surfaces(): diff --git a/mne/tests/test_forward.py b/mne/tests/test_forward.py index 5f2f85c..5bf55ba 100644 --- a/mne/tests/test_forward.py +++ b/mne/tests/test_forward.py @@ -4,10 +4,11 @@ import os.path as op from numpy.testing import assert_array_almost_equal, assert_equal import mne +from mne.datasets import sample -MNE_SAMPLE_DATASET_PATH = os.getenv('MNE_SAMPLE_DATASET_PATH') -fname = op.join(MNE_SAMPLE_DATASET_PATH, 'MEG', 'sample', - 'sample_audvis-meg-oct-6-fwd.fif') +examples_folder = op.join(op.dirname(__file__), '..', '..', 'examples') +data_path = sample.data_path(examples_folder) +fname = op.join(data_path, 'MEG', 'sample', 'sample_audvis-meg-oct-6-fwd.fif') def test_io_forward(): """Test IO for forward solutions diff --git a/mne/tests/test_inverse.py b/mne/tests/test_inverse.py index a41d0c3..840e02c 100644 --- a/mne/tests/test_inverse.py +++ b/mne/tests/test_inverse.py @@ -5,11 +5,13 @@ import numpy as np from numpy.testing import assert_array_almost_equal, assert_equal import mne +from mne.datasets import sample -MNE_SAMPLE_DATASET_PATH = os.getenv('MNE_SAMPLE_DATASET_PATH') -fname_inv = op.join(MNE_SAMPLE_DATASET_PATH, 'MEG', 'sample', +examples_folder = op.join(op.dirname(__file__), '..', '..', 'examples') +data_path = sample.data_path(examples_folder) +fname_inv = op.join(data_path, 'MEG', 'sample', 'sample_audvis-meg-oct-6-meg-inv.fif') -fname_data = op.join(MNE_SAMPLE_DATASET_PATH, 'MEG', 'sample', +fname_data = op.join(data_path, 'MEG', 'sample', 'sample_audvis-ave.fif') def test_io_inverse(): diff --git a/mne/tests/test_stc.py b/mne/tests/test_stc.py index 634d4d6..8eece25 100644 --- a/mne/tests/test_stc.py +++ b/mne/tests/test_stc.py @@ -4,10 +4,11 @@ import os.path as op from numpy.testing import assert_array_almost_equal import mne +from mne.datasets import sample -MNE_SAMPLE_DATASET_PATH = os.getenv('MNE_SAMPLE_DATASET_PATH') -fname = op.join(MNE_SAMPLE_DATASET_PATH, 'MEG', 'sample', - 'sample_audvis-meg-lh.stc') +examples_folder = op.join(op.dirname(__file__), '..', '..', 'examples') +data_path = sample.data_path(examples_folder) +fname = op.join(data_path, 'MEG', 'sample', 'sample_audvis-meg-lh.stc') def test_io_stc(): -- 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
