ENH: Smaller test dataset (150MB)

.gitignore

@@ -28,10 +28,11 @@ memmap*.dat
 tmp-*.w
 tmtags
 auto_examples
-MNE-sample-data*
-MNE-spm-face*
 MNE-eegbci-data*
+MNE-sample-data*
 MNE-somato-data*
+MNE-spm-face*
+MNE-testing-data*
 MEGSIM*
 build
 coverage

.travis.yml

@@ -37,8 +37,6 @@ install:
       fi;
     - pip install -q coverage coveralls nose-timer > /dev/null
     # Suppress the parallel outputs for logging cleanliness
-    - export MNE_LOGGING_LEVEL=warning
-    - export MNE_SKIP_SAMPLE_DATASET_TESTS=1
     # Skip tests that require large downloads over the network to save bandwith
     # usage as travis workers are stateless and therefore traditional local
     # disk caching does not work.
@@ -49,6 +47,11 @@ install:
     - for script in $myscripts; do mne $script --help >/dev/null; done;
     - SRC_DIR=$(pwd)
     - cd ~
+    # Trigger download of testing data
+    - python -c 'import mne; mne.datasets.testing.data_path()'
+    # Set up tests
+    - export MNE_LOGGING_LEVEL=warning
+    - export MNE_SKIP_SAMPLE_DATASET_TESTS=1
     - MNE_DIR=$(python -c 'import mne;print(mne.__path__[0])')
     - ln -s ${SRC_DIR}/mne/io/tests/data ${MNE_DIR}/io/tests/data
     - ln -s ${SRC_DIR}/mne/io/bti/tests/data ${MNE_DIR}/io/bti/tests/data

Makefile

@@ -33,6 +33,9 @@ inplace:
 sample_data: $(CURDIR)/examples/MNE-sample-data/MEG/sample/sample_audvis_raw.fif
 	@echo "Target needs sample data"
 
+testing_data:
+	@python -c "import mne; mne.datasets.testing.data_path(verbose=True);"
+
 $(CURDIR)/examples/MNE-sample-data/MEG/sample/sample_audvis_raw.fif:
 	wget -c ftp://surfer.nmr.mgh.harvard.edu/pub/data/MNE-sample-data-processed.tar.gz
 	tar xvzf MNE-sample-data-processed.tar.gz
@@ -48,23 +51,23 @@ test-no-sample: in
 	$(NOSETESTS) mne
 
 
-test-no-sample-with-coverage: in
+test-no-sample-with-coverage: in testing_data
 	rm -rf coverage .coverage
 	@MNE_SKIP_SAMPLE_DATASET_TESTS=true \
 	$(NOSETESTS) --with-coverage --cover-package=mne --cover-html --cover-html-dir=coverage
 
-test-doc: sample_data
+test-doc: sample_data testing_data
 	$(NOSETESTS) --with-doctest --doctest-tests --doctest-extension=rst doc/ doc/source/
 
-test-coverage: sample_data
+test-coverage: sample_data testing_data
 	rm -rf coverage .coverage
 	$(NOSETESTS) --with-coverage --cover-package=mne --cover-html --cover-html-dir=coverage
 
-test-profile: sample_data
+test-profile: sample_data testing_data
 	$(NOSETESTS) --with-profile --profile-stats-file stats.pf mne
 	hotshot2dot stats.pf | dot -Tpng -o profile.png
 
-test-mem: in sample_data
+test-mem: in sample_data testing_data
 	ulimit -v 1097152 && $(NOSETESTS)
 
 trailing-spaces:
@@ -91,3 +94,4 @@ manpages:
 			help2man -n "$$descr" --no-discard-stderr --no-info --version-string "$(uver)" ./$$f \
 			>| ../build/manpages/$$f.1; \
 	done
+

mne/datasets/__init__.py

@@ -6,3 +6,4 @@
 from . import spm_face
 from . import eegbci
 from . import somato
+from . import testing

mne/datasets/testing/__init__.py

@@ -0,0 +1,4 @@
+"""MNE sample dataset
+"""
+
+from ._testing import data_path

mne/datasets/testing/_testing.py

@@ -0,0 +1,19 @@
+# Authors: Alexandre Gramfort <[email protected]>
+#          Martin Luessi <[email protected]>
+#          Eric Larson <[email protected]>
+# License: BSD Style.
+
+from ...utils import verbose
+from ..utils import _data_path, _doc
+
+
+@verbose
+def data_path(path=None, force_update=False, update_path=True,
+              download=True, verbose=None):
+    return _data_path(path=path, force_update=force_update,
+                      update_path=update_path, name='testing',
+                      download=download,
+                      verbose=verbose)
+
+data_path.__doc__ = _doc.format(name='testing',
+                                conf='MNE_DATASETS_TESTING_PATH')

mne/datasets/utils.py

@@ -68,7 +68,9 @@ def _data_path(path=None, force_update=False, update_path=True,
     """
     key = {'sample': 'MNE_DATASETS_SAMPLE_PATH',
            'spm': 'MNE_DATASETS_SPM_FACE_PATH',
-           'somato': 'MNE_DATASETS_SOMATO_PATH',}[name]
+           'somato': 'MNE_DATASETS_SOMATO_PATH',
+           'testing': 'MNE_DATASETS_TESTING_PATH',
+           }[name]
 
     if path is None:
         # use an intelligent guess if it's not defined
@@ -95,30 +97,33 @@ def _data_path(path=None, force_update=False, update_path=True,
                         os.mkdir(path)
                 except OSError:
                     raise OSError("User does not have write permissions "
-                                  "at '%s', try giving the path as an argument "
-                                  "to data_path() where user has write "
+                                  "at '%s', try giving the path as an argument"
+                                  " to data_path() where user has write "
                                   "permissions, for ex:data_path"
                                   "('/home/xyz/me2/')" % (path))
 
     if not isinstance(path, string_types):
         raise ValueError('path must be a string or None')
     if name == 'sample':
         archive_name = "MNE-sample-data-processed.tar.gz"
-        url = "ftp://surfer.nmr.mgh.harvard.edu/pub/data/MNE/" + archive_name
         folder_name = "MNE-sample-data"
-        folder_path = op.join(path, folder_name)
+        url = "ftp://surfer.nmr.mgh.harvard.edu/pub/data/MNE/" + archive_name
     elif name == 'spm':
         archive_name = 'MNE-spm-face.tar.bz2'
-        url = 'ftp://surfer.nmr.mgh.harvard.edu/pub/data/MNE/' + archive_name
         folder_name = "MNE-spm-face"
-        folder_path = op.join(path, folder_name)
+        url = 'ftp://surfer.nmr.mgh.harvard.edu/pub/data/MNE/' + archive_name
     elif name == 'somato':
         archive_name = 'MNE-somato-data.tar.gz'
-        url = 'ftp://surfer.nmr.mgh.harvard.edu/pub/data/MNE/' + archive_name
         folder_name = "MNE-somato-data"
-        folder_path = op.join(path, folder_name)
+        url = 'ftp://surfer.nmr.mgh.harvard.edu/pub/data/MNE/' + archive_name
+    elif name == 'testing':
+        archive_name = 'MNE-testing-data.tar.gz'
+        folder_name = 'MNE-testing-data'
+        url = 'https://lester.ilabs.uw.edu/files/' + archive_name
     else:
         raise ValueError('Sorry, the dataset "%s" is not known.' % name)
+    folder_path = op.join(path, folder_name)
+
     rm_archive = False
     martinos_path = '/cluster/fusion/sample_data/' + archive_name
     neurospin_path = '/neurospin/tmp/gramfort/' + archive_name

mne/forward/tests/test_field_interpolation.py

@@ -6,7 +6,7 @@
 
 from mne.forward import _make_surface_mapping, make_field_map
 from mne.surface import get_meg_helmet_surf, get_head_surf
-from mne.datasets import sample
+from mne.datasets import testing
 from mne.forward._lead_dots import (_comp_sum_eeg, _comp_sums_meg,
                                     _get_legen_table,
                                     _get_legen_lut_fast,
@@ -19,9 +19,9 @@
 base_dir = op.join(op.dirname(__file__), '..', '..', 'io', 'tests', 'data')
 evoked_fname = op.join(base_dir, 'test-ave.fif')
 
-data_path = sample.data_path(download=False)
+data_path = testing.data_path()
 trans_fname = op.join(data_path, 'MEG', 'sample',
-                      'sample_audvis_raw-trans.fif')
+                      'sample_audvis_trunc-trans.fif')
 subjects_dir = op.join(data_path, 'subjects')
 
 
@@ -90,7 +90,6 @@ def test_legendre_table():
         assert_allclose(n_fact1, n_fact2)
 
 
-@sample.requires_sample_data
 def test_make_field_map_eeg():
     """Test interpolation of EEG field onto head
     """
@@ -111,7 +110,7 @@ def test_make_field_map_eeg():
     fmd = make_field_map(evoked, trans_fname=trans_fname,
                          subject='sample', subjects_dir=subjects_dir)
     assert_true(len(fmd) == 1)
-    assert_array_equal(fmd[0]['data'].shape, (2562, 59))  # maps data onto surf
+    assert_array_equal(fmd[0]['data'].shape, (162, 59))  # maps data onto surf
     assert_true(len(fmd[0]['ch_names']), 59)
 
 

mne/forward/tests/test_forward.py

@@ -7,7 +7,7 @@
 from numpy.testing import (assert_array_almost_equal, assert_equal,
                            assert_array_equal, assert_allclose)
 
-from mne.datasets import sample
+from mne.datasets import testing
 from mne.io import Raw
 from mne import (read_forward_solution, apply_forward, apply_forward_raw,
                  average_forward_solutions, write_forward_solution,
@@ -18,17 +18,17 @@
 from mne.forward import (restrict_forward_to_stc, restrict_forward_to_label,
                          Forward)
 
-data_path = sample.data_path(download=False)
-fname = op.join(data_path, 'MEG', 'sample', 'sample_audvis-meg-oct-6-fwd.fif')
+data_path = testing.data_path()
 fname_meeg = op.join(data_path, 'MEG', 'sample',
-                     'sample_audvis-meg-eeg-oct-6-fwd.fif')
+                     'sample_audvis_trunc-meg-eeg-oct-4-fwd.fif')
 
 fname_raw = op.join(op.dirname(__file__), '..', '..', 'io', 'tests', 'data',
                     'test_raw.fif')
 
 fname_evoked = op.join(op.dirname(__file__), '..', '..', 'io', 'tests',
                        'data', 'test-ave.fif')
-fname_mri = op.join(data_path, 'MEG', 'sample', 'sample_audvis_raw-trans.fif')
+fname_mri = op.join(data_path, 'MEG', 'sample',
+                    'sample_audvis_trunc-trans.fif')
 subjects_dir = os.path.join(data_path, 'subjects')
 fname_src = op.join(subjects_dir, 'sample', 'bem', 'sample-oct-6-src.fif')
 temp_dir = _TempDir()
@@ -52,7 +52,6 @@ def compare_forwards(f1, f2):
     assert_equal(f1['surf_ori'], f2['surf_ori'])
 
 
-@sample.requires_sample_data
 def test_convert_forward():
     """Test converting forward solution between different representations
     """
@@ -83,61 +82,49 @@ def test_convert_forward():
     compare_forwards(fwd, fwd_new)
 
 
-@sample.requires_sample_data
 def test_io_forward():
     """Test IO for forward solutions
     """
-    # test M/EEG
-    fwd_meeg = read_forward_solution(fname_meeg)
-    assert_true(isinstance(fwd_meeg, Forward))
-    leadfield = fwd_meeg['sol']['data']
-    assert_equal(leadfield.shape, (366, 22494))
-    assert_equal(len(fwd_meeg['sol']['row_names']), 366)
-    fname_temp = op.join(temp_dir, 'test-fwd.fif')
-    write_forward_solution(fname_temp, fwd_meeg, overwrite=True)
-
-    fwd_meeg = read_forward_solution(fname_temp)
-    assert_allclose(leadfield, fwd_meeg['sol']['data'])
-    assert_equal(len(fwd_meeg['sol']['row_names']), 366)
-
-    # now do extensive tests with MEG
-    fwd = read_forward_solution(fname)
-    fwd = read_forward_solution(fname, surf_ori=True)
+    # do extensive tests with MEEG
+    n_src = 1533
+    fwd = read_forward_solution(fname_meeg)
+    assert_true(isinstance(fwd, Forward))
+    fwd = read_forward_solution(fname_meeg, surf_ori=True)
     leadfield = fwd['sol']['data']
-    assert_equal(leadfield.shape, (306, 22494))
-    assert_equal(len(fwd['sol']['row_names']), 306)
+    assert_equal(leadfield.shape, (366, n_src))
+    assert_equal(len(fwd['sol']['row_names']), 366)
     fname_temp = op.join(temp_dir, 'test-fwd.fif')
     write_forward_solution(fname_temp, fwd, overwrite=True)
 
-    fwd = read_forward_solution(fname, surf_ori=True)
+    fwd = read_forward_solution(fname_meeg, surf_ori=True)
     fwd_read = read_forward_solution(fname_temp, surf_ori=True)
     leadfield = fwd_read['sol']['data']
-    assert_equal(leadfield.shape, (306, 22494))
-    assert_equal(len(fwd_read['sol']['row_names']), 306)
-    assert_equal(len(fwd_read['info']['chs']), 306)
+    assert_equal(leadfield.shape, (366, n_src))
+    assert_equal(len(fwd_read['sol']['row_names']), 366)
+    assert_equal(len(fwd_read['info']['chs']), 366)
     assert_true('dev_head_t' in fwd_read['info'])
     assert_true('mri_head_t' in fwd_read)
     assert_array_almost_equal(fwd['sol']['data'], fwd_read['sol']['data'])
 
-    fwd = read_forward_solution(fname, force_fixed=True)
+    fwd = read_forward_solution(fname_meeg, force_fixed=True)
     leadfield = fwd['sol']['data']
-    assert_equal(leadfield.shape, (306, 22494 / 3))
-    assert_equal(len(fwd['sol']['row_names']), 306)
-    assert_equal(len(fwd['info']['chs']), 306)
+    assert_equal(leadfield.shape, (366, n_src / 3))
+    assert_equal(len(fwd['sol']['row_names']), 366)
+    assert_equal(len(fwd['info']['chs']), 366)
     assert_true('dev_head_t' in fwd['info'])
     assert_true('mri_head_t' in fwd)
     assert_true(fwd['surf_ori'])
 
     # test warnings on bad filenames
+    fwd = read_forward_solution(fname_meeg)
     with warnings.catch_warnings(record=True) as w:
         warnings.simplefilter('always')
         fwd_badname = op.join(temp_dir, 'test-bad-name.fif.gz')
-        write_forward_solution(fwd_badname, fwd_meeg)
+        write_forward_solution(fwd_badname, fwd)
         read_forward_solution(fwd_badname)
     assert_true(len(w) == 2)
 
 
-@sample.requires_sample_data
 def test_apply_forward():
     """Test projection of source space data to sensor space
     """
@@ -147,7 +134,7 @@ def test_apply_forward():
     sfreq = 10.0
     t_start = 0.123
 
-    fwd = read_forward_solution(fname, force_fixed=True)
+    fwd = read_forward_solution(fname_meeg, force_fixed=True)
     fwd = pick_types_forward(fwd, meg=True)
     assert_true(isinstance(fwd, Forward))
 
@@ -183,7 +170,6 @@ def test_apply_forward():
         assert_array_almost_equal(times[-1], t_start + (n_times - 1) / sfreq)
 
 
-@sample.requires_sample_data
 def test_restrict_forward_to_stc():
     """Test restriction of source space to source SourceEstimate
     """
@@ -193,7 +179,7 @@ def test_restrict_forward_to_stc():
     sfreq = 10.0
     t_start = 0.123
 
-    fwd = read_forward_solution(fname, force_fixed=True)
+    fwd = read_forward_solution(fname_meeg, force_fixed=True)
     fwd = pick_types_forward(fwd, meg=True)
 
     vertno = [fwd['src'][0]['vertno'][0:15], fwd['src'][1]['vertno'][0:5]]
@@ -209,7 +195,7 @@ def test_restrict_forward_to_stc():
     assert_equal(fwd_out['src'][0]['vertno'], fwd['src'][0]['vertno'][0:15])
     assert_equal(fwd_out['src'][1]['vertno'], fwd['src'][1]['vertno'][0:5])
 
-    fwd = read_forward_solution(fname, force_fixed=False)
+    fwd = read_forward_solution(fname_meeg, force_fixed=False)
     fwd = pick_types_forward(fwd, meg=True)
 
     vertno = [fwd['src'][0]['vertno'][0:15], fwd['src'][1]['vertno'][0:5]]
@@ -225,11 +211,10 @@ def test_restrict_forward_to_stc():
     assert_equal(fwd_out['src'][1]['vertno'], fwd['src'][1]['vertno'][0:5])
 
 
-@sample.requires_sample_data
 def test_restrict_forward_to_label():
     """Test restriction of source space to label
     """
-    fwd = read_forward_solution(fname, force_fixed=True)
+    fwd = read_forward_solution(fname_meeg, force_fixed=True)
     fwd = pick_types_forward(fwd, meg=True)
 
     label_path = op.join(data_path, 'MEG', 'sample', 'labels')
@@ -252,7 +237,7 @@ def test_restrict_forward_to_label():
     assert_equal(fwd_out['src'][0]['vertno'], src_sel_lh)
     assert_equal(fwd_out['src'][1]['vertno'], src_sel_rh)
 
-    fwd = read_forward_solution(fname, force_fixed=False)
+    fwd = read_forward_solution(fname_meeg, force_fixed=False)
     fwd = pick_types_forward(fwd, meg=True)
 
     label_path = op.join(data_path, 'MEG', 'sample', 'labels')
@@ -277,12 +262,11 @@ def test_restrict_forward_to_label():
     assert_equal(fwd_out['src'][1]['vertno'], src_sel_rh)
 
 
-@sample.requires_sample_data
 @requires_mne
 def test_average_forward_solution():
     """Test averaging forward solutions
     """
-    fwd = read_forward_solution(fname)
+    fwd = read_forward_solution(fname_meeg)
     # input not a list
     assert_raises(TypeError, average_forward_solutions, 1)
     # list is too short
@@ -305,7 +289,7 @@ def test_average_forward_solution():
     fwd_copy['sol']['data'] *= 0.5
     fname_copy = op.join(temp_dir, 'copy-fwd.fif')
     write_forward_solution(fname_copy, fwd_copy, overwrite=True)
-    cmd = ('mne_average_forward_solutions', '--fwd', fname, '--fwd',
+    cmd = ('mne_average_forward_solutions', '--fwd', fname_meeg, '--fwd',
            fname_copy, '--out', fname_copy)
     run_subprocess(cmd)