[med-svn] [python-mne] 32/376: splitting fif and MNE
Yaroslav Halchenko
debian at onerussian.com
Fri Nov 27 17:22:01 UTC 2015
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 2da38029badc5162db3163cf45fe9ad9b19c33b5
Author: Alexandre Gramfort <alexandre.gramfort at inria.fr>
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 <gramfort at nmr.mgh.harvard.edu> 2010
+ * Alexandre Gramfort <gramfort at nmr.mgh.harvard.edu> 2011
+ * Matti Hamalainen <msh at nmr.mgh.harvard.edu> 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 git at github.com/agramfort/pyfiff.git
+ git clone git at github.com/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, gramfort at nmr.mgh.harvard.edu
# Matti Hamalainen, msh at nmr.mgh.harvard.edu
-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 <gramfort at nmr.mgh.harvard.edu>
+#
+# 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 <gramfort at nmr.mgh.harvard.edu>
+#
+# 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, gramfort at nmr.mgh.harvard.edu
-# Matti Hamalainen, msh at nmr.mgh.harvard.edu
+# Author: Alexandre Gramfort <gramfort at nmr.mgh.harvard.edu>
+#
+# 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 <gramfort at nmr.mgh.harvard.edu>
+#
# 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 <gramfort at nmr.mgh.harvard.edu>
+#
+# 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 <gramfort at nmr.mgh.harvard.edu>
+# Matti Hamalainen <msh at nmr.mgh.harvard.edu>
+#
+# 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 <gramfort at nmr.mgh.harvard.edu>
+#
+# 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 <gramfort at nmr.mgh.harvard.edu>
+#
+# 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 <gramfort at nmr.mgh.harvard.edu>
+#
+# 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 <gramfort at nmr.mgh.harvard.edu>
+# Matti Hamalainen <msh at nmr.mgh.harvard.edu>
+#
+# 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 <gramfort at nmr.mgh.harvard.edu>
+#
+# 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 <gramfort at nmr.mgh.harvard.edu>
+# Matti Hamalainen <msh at nmr.mgh.harvard.edu>
+#
+# 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 <gramfort at nmr.mgh.harvard.edu>
+# Matti Hamalainen <msh at nmr.mgh.harvard.edu>
+#
+# 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 <gramfort at nmr.mgh.harvard.edu>
+# Matti Hamalainen <msh at nmr.mgh.harvard.edu>
+#
+# 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 <gramfort at nmr.mgh.harvard.edu>
+# Matti Hamalainen <msh at nmr.mgh.harvard.edu>
+#
+# 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 <gramfort at nmr.mgh.harvard.edu>
+#
+# 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 <gramfort at nmr.mgh.harvard.edu>
+#
+# 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 <gramfort at nmr.mgh.harvard.edu>
+#
+# 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 <gramfort at nmr.mgh.harvard.edu>
+#
+# 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 <gramfort at nmr.mgh.harvard.edu>
+#
+# 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 <gramfort at nmr.mgh.harvard.edu>
+#
+# 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 <gramfort at nmr.mgh.harvard.edu>
+#
+# 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 <gramfort at nmr.mgh.harvard.edu>
+# Copyright (C) 2011 Alexandre Gramfort <gramfort at nmr.mgh.harvard.edu>
-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 = 'gramfort at nmr.mgh.harvard.edu'
-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',
--
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