[med-svn] [python-mne] 63/376: adding sample test raw fif dataset updating corresponding tests
Yaroslav Halchenko
debian at onerussian.com
Fri Nov 27 17:22:08 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 588aba1a35fb448978872f179d479839448352fd
Author: Alexandre Gramfort <alexandre.gramfort at inria.fr>
Date: Wed Feb 2 12:20:55 2011 -0500
adding sample test raw fif dataset
updating corresponding tests
---
mne/fiff/tests/data/process_raw.sh | 13 +++++++++
mne/fiff/tests/data/test-ave.fif | Bin 0 -> 5546473 bytes
mne/fiff/tests/data/test-cov.fif | Bin 0 -> 541025 bytes
mne/fiff/tests/data/test-eve.fif | Bin 0 -> 543 bytes
mne/fiff/tests/data/test.ave | 49 +++++++++++++++++++++++++++++++
mne/fiff/tests/data/test.cov | 55 +++++++++++++++++++++++++++++++++++
mne/fiff/tests/data/test_raw-eve.fif | Bin 0 -> 927 bytes
mne/fiff/tests/data/test_raw.fif | Bin 0 -> 13852290 bytes
mne/fiff/tests/test_evoked.py | 6 ++--
mne/fiff/tests/test_raw.py | 6 ++--
mne/tests/test_cov.py | 4 +--
mne/tests/test_epochs.py | 9 +++---
mne/tests/test_event.py | 6 ++--
13 files changed, 129 insertions(+), 19 deletions(-)
diff --git a/mne/fiff/tests/data/process_raw.sh b/mne/fiff/tests/data/process_raw.sh
new file mode 100755
index 0000000..2db2d95
--- /dev/null
+++ b/mne/fiff/tests/data/process_raw.sh
@@ -0,0 +1,13 @@
+#!/usr/bin/env bash
+
+# Generate events
+mne_process_raw --raw test_raw.fif \
+ --eventsout test-eve.fif
+
+# Averaging
+mne_process_raw --raw test_raw.fif --lowpass 40 --projoff \
+ --saveavetag -ave --ave test.ave
+
+# Compute the noise covariance matrix
+mne_process_raw --raw test_raw.fif --lowpass 40 --projoff \
+ --savecovtag -cov --cov test.cov
diff --git a/mne/fiff/tests/data/test-ave.fif b/mne/fiff/tests/data/test-ave.fif
new file mode 100644
index 0000000..0ff74c8
Binary files /dev/null and b/mne/fiff/tests/data/test-ave.fif differ
diff --git a/mne/fiff/tests/data/test-cov.fif b/mne/fiff/tests/data/test-cov.fif
new file mode 100644
index 0000000..1a2da11
Binary files /dev/null and b/mne/fiff/tests/data/test-cov.fif differ
diff --git a/mne/fiff/tests/data/test-eve.fif b/mne/fiff/tests/data/test-eve.fif
new file mode 100644
index 0000000..d3cc74d
Binary files /dev/null and b/mne/fiff/tests/data/test-eve.fif differ
diff --git a/mne/fiff/tests/data/test.ave b/mne/fiff/tests/data/test.ave
new file mode 100644
index 0000000..be6ba6a
--- /dev/null
+++ b/mne/fiff/tests/data/test.ave
@@ -0,0 +1,49 @@
+#
+# These are comments
+#
+average {
+#
+# Output files
+#
+# outfile test-ave.fif
+# logfile test-ave.log
+# eventfile test.eve
+#
+# Rejection values
+#
+ gradReject 4000e-13
+ magReject 4e-12
+ eegReject 0e-6
+ eogReject 150e-6
+#
+# Category specifications
+#
+ category {
+ name "Left Auditory"
+ event 1
+ tmin -0.2
+ tmax 0.5
+ color 1 1 0
+ }
+ category {
+ name "Right Auditory"
+ event 2
+ tmin -0.2
+ tmax 0.5
+ color 1 0 0
+ }
+ category {
+ name "Left visual"
+ event 3
+ tmin -0.2
+ tmax 0.5
+ color 0 1 0
+ }
+ category {
+ name "Right visual"
+ event 4
+ tmin -0.2
+ tmax 0.5
+ color 0.5 0.8 1
+ }
+}
diff --git a/mne/fiff/tests/data/test.cov b/mne/fiff/tests/data/test.cov
new file mode 100644
index 0000000..1f9fae2
--- /dev/null
+++ b/mne/fiff/tests/data/test.cov
@@ -0,0 +1,55 @@
+#
+# These are comments
+#
+cov {
+#
+# Output files
+#
+ outfile sample_audvis-cov.fif
+ logfile sample_audvis-cov.log
+#
+# Rejection values
+#
+ gradReject 4000e-13
+ magReject 4e-12
+ eegReject 40e-6
+ eogReject 150e-6
+#
+# What to include in the covariance matrix?
+#
+ def {
+ name "Left Auditory"
+ event 1
+ tmin -0.2
+ tmax 0.0
+ basemin -0.2
+ basemax 0
+ }
+ def {
+ name "Right Auditory"
+ event 2
+ ignore 0
+ tmin -0.2
+ tmax 0.0
+ basemin -0.2
+ basemax 0
+ }
+ def {
+ name "Left visual"
+ event 3
+ ignore 0
+ tmin -0.2
+ tmax 0.0
+ basemin -0.2
+ basemax 0
+ }
+ def {
+ name "Right visual"
+ event 4
+ ignore 0
+ tmin -0.2
+ tmax 0.0
+ basemin -0.2
+ basemax 0
+ }
+}
diff --git a/mne/fiff/tests/data/test_raw-eve.fif b/mne/fiff/tests/data/test_raw-eve.fif
new file mode 100644
index 0000000..f81fd0d
Binary files /dev/null and b/mne/fiff/tests/data/test_raw-eve.fif differ
diff --git a/mne/fiff/tests/data/test_raw.fif b/mne/fiff/tests/data/test_raw.fif
new file mode 100644
index 0000000..35d068a
Binary files /dev/null and b/mne/fiff/tests/data/test_raw.fif differ
diff --git a/mne/fiff/tests/test_evoked.py b/mne/fiff/tests/test_evoked.py
index ba25e80..c69b55a 100644
--- a/mne/fiff/tests/test_evoked.py
+++ b/mne/fiff/tests/test_evoked.py
@@ -5,11 +5,9 @@ from numpy.testing import assert_array_almost_equal, assert_equal
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',
- 'sample_audvis-ave.fif')
+fname = op.join(op.dirname(__file__), 'data', 'test-ave.fif')
-def test_io_cov():
+def test_io_evoked():
"""Test IO for noise covariance matrices
"""
data = read_evoked(fname)
diff --git a/mne/fiff/tests/test_raw.py b/mne/fiff/tests/test_raw.py
index 42fea76..6629183 100644
--- a/mne/fiff/tests/test_raw.py
+++ b/mne/fiff/tests/test_raw.py
@@ -8,9 +8,7 @@ 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',
- 'sample_audvis_raw.fif')
+fname = op.join(op.dirname(__file__), 'data', 'test_raw.fif')
def test_io_raw():
"""Test IO for raw data
@@ -22,7 +20,7 @@ def test_io_raw():
meg_channels_idx = [k for k in range(nchan) if ch_names[k][:3]=='MEG']
meg_channels_idx = meg_channels_idx[:5]
- data, times = read_raw_segment_times(raw, start=100, stop=115,
+ data, times = read_raw_segment_times(raw, start=45, stop=50,
sel=meg_channels_idx)
# Writing
diff --git a/mne/tests/test_cov.py b/mne/tests/test_cov.py
index 0bad2fb..ac86811 100644
--- a/mne/tests/test_cov.py
+++ b/mne/tests/test_cov.py
@@ -6,9 +6,7 @@ from numpy.testing import assert_array_almost_equal
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',
- 'sample_audvis-cov.fif')
+fname = op.join(op.dirname(__file__), '..', 'fiff', 'tests', 'data', 'test-cov.fif')
def test_io_cov():
"""Test IO for noise covariance matrices
diff --git a/mne/tests/test_epochs.py b/mne/tests/test_epochs.py
index cc67544..af5ee6b 100644
--- a/mne/tests/test_epochs.py
+++ b/mne/tests/test_epochs.py
@@ -8,11 +8,10 @@ import os.path as op
import mne
from mne import fiff
-MNE_SAMPLE_DATASET_PATH = os.getenv('MNE_SAMPLE_DATASET_PATH')
-raw_fname = op.join(MNE_SAMPLE_DATASET_PATH, 'MEG', 'sample',
- 'sample_audvis_raw.fif')
-event_name = op.join(MNE_SAMPLE_DATASET_PATH, 'MEG', 'sample',
- 'sample_audvis_raw-eve.fif')
+raw_fname = op.join(op.dirname(__file__), '..', 'fiff', 'tests', 'data',
+ 'test_raw.fif')
+event_name = op.join(op.dirname(__file__), '..', 'fiff', 'tests', 'data',
+ 'test-eve.fif')
def test_read_epochs():
diff --git a/mne/tests/test_event.py b/mne/tests/test_event.py
index eaefc87..d51496a 100644
--- a/mne/tests/test_event.py
+++ b/mne/tests/test_event.py
@@ -5,9 +5,9 @@ from numpy.testing import assert_array_almost_equal
import mne
-MNE_SAMPLE_DATASET_PATH = os.getenv('MNE_SAMPLE_DATASET_PATH')
-fname = op.join(MNE_SAMPLE_DATASET_PATH, 'MEG', 'sample',
- 'sample_audvis_raw-eve.fif')
+
+fname = op.join(op.dirname(__file__), '..', 'fiff', 'tests', 'data',
+ 'test-eve.fif')
def test_io_cov():
--
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