MRG: Use new nirscout test data location (mne-tools#8122)

* Use new nirscout test data location

* Add tests to viz

* Add support for nirstart 15.3

* Use latest testing data

* Update testing hash

* Update links to data creation

mne/channels/tests/test_interpolation.py

@@ -255,7 +255,7 @@ def test_interpolation_ctf_comp():
 def test_interpolation_nirs():
     """Test interpolating bad nirs channels."""
     fname = op.join(data_path(download=False),
-                    'NIRx', 'nirx_15_2_recording_w_overlap')
+                    'NIRx', 'nirscout', 'nirx_15_2_recording_w_overlap')
     raw_intensity = read_raw_nirx(fname, preload=False)
     raw_od = optical_density(raw_intensity)
     sci = scalp_coupling_index(raw_od)

mne/datasets/utils.py

@@ -240,7 +240,7 @@ def _data_path(path=None, force_update=False, update_path=True, download=True,
     path = _get_path(path, key, name)
     # To update the testing or misc dataset, push commits, then make a new
     # release on GitHub. Then update the "releases" variable:
-    releases = dict(testing='0.100', misc='0.6')
+    releases = dict(testing='0.103', misc='0.6')
     # And also update the "md5_hashes['testing']" variable below.
 
     # To update any other dataset, update the data archive itself (upload
@@ -327,7 +327,7 @@ def _data_path(path=None, force_update=False, update_path=True, download=True,
         sample='12b75d1cb7df9dfb4ad73ed82f61094f',
         somato='ea825966c0a1e9b2f84e3826c5500161',
         spm='9f43f67150e3b694b523a21eb929ea75',
-        testing='deb175669c3489c1fef582f72d3d6017',
+        testing='f7753da1b277d5ccf79da83b0854bcb7',
         multimodal='26ec847ae9ab80f58f204d09e2c08367',
         fnirs_motor='c4935d19ddab35422a69f3326a01fef8',
         opm='370ad1dcfd5c47e029e692c85358a374',

mne/io/nirx/nirx.py

@@ -73,7 +73,7 @@ def __init__(self, fname, preload=False, verbose=None):
             fname = op.dirname(op.abspath(fname))
 
         if not op.isdir(fname):
-            raise RuntimeError('The path you specified does not exist.')
+            raise FileNotFoundError('The path you specified does not exist.')
 
         # Check if required files exist and store names for later use
         files = dict()
@@ -107,8 +107,7 @@ def __init__(self, fname, preload=False, verbose=None):
         hdr.read_string(hdr_str)
 
         # Check that the file format version is supported
-        if not any(item == hdr['GeneralInfo']['NIRStar'] for item in
-                   ["\"15.0\"", "\"15.2\""]):
+        if hdr['GeneralInfo']['NIRStar'] not in ['"15.0"', '"15.2"', '"15.3"']:
             raise RuntimeError('MNE does not support this NIRStar version'
                                ' (%s)' % (hdr['GeneralInfo']['NIRStar'],))
         if "NIRScout" not in hdr['GeneralInfo']['Device']:

mne/io/nirx/tests/test_nirx.py

@@ -21,11 +21,14 @@
 from mne.io.constants import FIFF
 
 fname_nirx_15_0 = op.join(data_path(download=False),
-                          'NIRx', 'nirx_15_0_recording')
+                          'NIRx', 'nirscout', 'nirx_15_0_recording')
 fname_nirx_15_2 = op.join(data_path(download=False),
-                          'NIRx', 'nirx_15_2_recording')
+                          'NIRx', 'nirscout', 'nirx_15_2_recording')
 fname_nirx_15_2_short = op.join(data_path(download=False),
-                                'NIRx', 'nirx_15_2_recording_w_short')
+                                'NIRx', 'nirscout',
+                                'nirx_15_2_recording_w_short')
+fname_nirx_15_3_short = op.join(data_path(download=False),
+                                'NIRx', 'nirscout', 'nirx_15_3_recording')
 
 
 @requires_testing_data
@@ -42,7 +45,7 @@ def test_nirx_hdr_load():
 @requires_testing_data
 def test_nirx_missing_warn():
     """Test reading NIRX files when missing data."""
-    with pytest.raises(RuntimeError, match='The path you'):
+    with pytest.raises(FileNotFoundError, match='The path you'):
         read_raw_nirx(fname_nirx_15_2_short + "1", preload=True)
 
 
@@ -157,6 +160,89 @@ def test_nirx_15_2_short():
         mni_locs[21], [0.0388, -0.0477, 0.0932], atol=allowed_dist_error)
 
 
+@requires_testing_data
+def test_nirx_15_3_short():
+    """Test reading NIRX files."""
+    raw = read_raw_nirx(fname_nirx_15_3_short, preload=True)
+
+    # Test data import
+    assert raw._data.shape == (26, 220)
+    assert raw.info['sfreq'] == 12.5
+
+    # Test channel naming
+    assert raw.info['ch_names'][:4] == ["S1_D2 760", "S1_D2 850",
+                                        "S1_D9 760", "S1_D9 850"]
+    assert raw.info['ch_names'][24:26] == ["S5_D13 760", "S5_D13 850"]
+
+    # Test frequency encoding
+    assert raw.info['chs'][0]['loc'][9] == 760
+    assert raw.info['chs'][1]['loc'][9] == 850
+
+    # Test info import
+    assert raw.info['subject_info'] == dict(
+        sex=0, first_name="testMontage\\0ATestMontage")
+
+    # Test distance between optodes matches values from
+    # https://github.com/mne-tools/mne-testing-data/pull/72
+    allowed_distance_error = 0.001
+    distances = source_detector_distances(raw.info)
+    assert_allclose(distances[::2], [
+        0.0304, 0.0078, 0.0310, 0.0086, 0.0416,
+        0.0072, 0.0389, 0.0075, 0.0558, 0.0562,
+        0.0561, 0.0565, 0.0077], atol=allowed_distance_error)
+
+    # Test which channels are short
+    # These are the ones marked as red at
+    # https://github.com/mne-tools/mne-testing-data/pull/72
+    is_short = short_channels(raw.info)
+    assert_array_equal(is_short[:9:2], [False, True, False, True, False])
+    is_short = short_channels(raw.info, threshold=0.003)
+    assert_array_equal(is_short[:3:2], [False, False])
+    is_short = short_channels(raw.info, threshold=50)
+    assert_array_equal(is_short[:3:2], [True, True])
+
+    # Test trigger events
+    assert_array_equal(raw.annotations.description, ['4.0', '2.0', '1.0'])
+
+    # Test location of detectors
+    # The locations of detectors can be seen in the first
+    # figure on this page...
+    # https://github.com/mne-tools/mne-testing-data/pull/72
+    # And have been manually copied below
+    allowed_dist_error = 0.0002
+    locs = [ch['loc'][6:9] for ch in raw.info['chs']]
+    head_mri_t, _ = _get_trans('fsaverage', 'head', 'mri')
+    mni_locs = apply_trans(head_mri_t, locs)
+
+    assert raw.info['ch_names'][0][3:5] == 'D2'
+    assert_allclose(
+        mni_locs[0], [-0.0841, -0.0464, -0.0129], atol=allowed_dist_error)
+
+    assert raw.info['ch_names'][4][3:5] == 'D1'
+    assert_allclose(
+        mni_locs[4], [0.0846, -0.0142, -0.0156], atol=allowed_dist_error)
+
+    assert raw.info['ch_names'][8][3:5] == 'D3'
+    assert_allclose(
+        mni_locs[8], [0.0207, -0.1062, 0.0484], atol=allowed_dist_error)
+
+    assert raw.info['ch_names'][12][3:5] == 'D4'
+    assert_allclose(
+        mni_locs[12], [-0.0196, 0.0821, 0.0275], atol=allowed_dist_error)
+
+    assert raw.info['ch_names'][16][3:5] == 'D5'
+    assert_allclose(
+        mni_locs[16], [-0.0360, 0.0276, 0.0778], atol=allowed_dist_error)
+
+    assert raw.info['ch_names'][19][3:5] == 'D6'
+    assert_allclose(
+        mni_locs[19], [0.0388, -0.0477, 0.0932], atol=allowed_dist_error)
+
+    assert raw.info['ch_names'][21][3:5] == 'D7'
+    assert_allclose(
+        mni_locs[21], [-0.0394, -0.0483, 0.0928], atol=allowed_dist_error)
+
+
 @requires_testing_data
 def test_encoding(tmpdir):
     """Test NIRx encoding."""

mne/io/snirf/tests/test_snirf.py

@@ -16,7 +16,7 @@
                                  'snirf_1_3_nirx_15_2_recording_w_short.snirf')
 
 fname_original = op.join(data_path(download=False),
-                         'NIRx', 'nirx_15_2_recording_w_short')
+                         'NIRx', 'nirscout', 'nirx_15_2_recording_w_short')
 
 
 @requires_testing_data

mne/preprocessing/tests/test_beer_lambert_law.py

@@ -18,11 +18,12 @@
 
 
 fname_nirx_15_0 = op.join(data_path(download=False),
-                          'NIRx', 'nirx_15_0_recording')
+                          'NIRx', 'nirscout', 'nirx_15_0_recording')
 fname_nirx_15_2 = op.join(data_path(download=False),
-                          'NIRx', 'nirx_15_2_recording')
+                          'NIRx', 'nirscout', 'nirx_15_2_recording')
 fname_nirx_15_2_short = op.join(data_path(download=False),
-                                'NIRx', 'nirx_15_2_recording_w_short')
+                                'NIRx', 'nirscout',
+                                'nirx_15_2_recording_w_short')
 
 
 @testing.requires_testing_data
@@ -88,7 +89,8 @@ def test_beer_lambert_v_matlab():
     raw._data *= 1e6  # Scale to uM for comparison to MATLAB
 
     matlab_fname = op.join(data_path(download=False),
-                           'NIRx', 'validation', 'nirx_15_0_recording_bl.mat')
+                           'NIRx', 'nirscout', 'validation',
+                           'nirx_15_0_recording_bl.mat')
     matlab_data = read_mat(matlab_fname)
 
     for idx in range(raw.get_data().shape[0]):

mne/preprocessing/tests/test_nirs.py

@@ -16,11 +16,12 @@
 from mne.datasets import testing
 
 fname_nirx_15_0 = op.join(data_path(download=False),
-                          'NIRx', 'nirx_15_0_recording')
+                          'NIRx', 'nirscout', 'nirx_15_0_recording')
 fname_nirx_15_2 = op.join(data_path(download=False),
-                          'NIRx', 'nirx_15_2_recording')
+                          'NIRx', 'nirscout', 'nirx_15_2_recording')
 fname_nirx_15_2_short = op.join(data_path(download=False),
-                                'NIRx', 'nirx_15_2_recording_w_short')
+                                'NIRx', 'nirscout',
+                                'nirx_15_2_recording_w_short')
 
 
 @testing.requires_testing_data

mne/preprocessing/tests/test_optical_density.py

@@ -17,7 +17,7 @@
 
 
 fname_nirx = op.join(data_path(download=False),
-                     'NIRx', 'nirx_15_2_recording_w_short')
+                     'NIRx', 'nirscout', 'nirx_15_2_recording_w_short')
 
 
 @testing.requires_testing_data

mne/preprocessing/tests/test_scalp_coupling_index.py

@@ -17,11 +17,12 @@
 from mne.datasets import testing
 
 fname_nirx_15_0 = op.join(data_path(download=False),
-                          'NIRx', 'nirx_15_0_recording')
+                          'NIRx', 'nirscout', 'nirx_15_0_recording')
 fname_nirx_15_2 = op.join(data_path(download=False),
-                          'NIRx', 'nirx_15_2_recording')
+                          'NIRx', 'nirscout', 'nirx_15_2_recording')
 fname_nirx_15_2_short = op.join(data_path(download=False),
-                                'NIRx', 'nirx_15_2_recording_w_short')
+                                'NIRx', 'nirscout',
+                                'nirx_15_2_recording_w_short')
 
 
 @testing.requires_testing_data

mne/preprocessing/tests/test_temporal_derivative_distribution_repair.py

@@ -14,7 +14,7 @@
 
 
 fname_nirx_15_2 = op.join(data_path(download=False),
-                          'NIRx', 'nirx_15_2_recording')
+                          'NIRx', 'nirscout', 'nirx_15_2_recording')
 
 
 @testing.requires_testing_data

mne/viz/tests/conftest.py

@@ -34,7 +34,7 @@ def fnirs_evoked():
 def fnirs_epochs():
     """Create an fnirs epoch structure."""
     fname = op.join(data_path(download=False),
-                    'NIRx', 'nirx_15_2_recording_w_overlap')
+                    'NIRx', 'nirscout', 'nirx_15_2_recording_w_overlap')
     raw_intensity = read_raw_nirx(fname, preload=False)
     raw_od = optical_density(raw_intensity)
     raw_haemo = beer_lambert_law(raw_od)

mne/viz/tests/test_3d.py

@@ -54,7 +54,8 @@
                     'sample-oct-6-src.fif')
 dip_fname = op.join(data_dir, 'MEG', 'sample', 'sample_audvis_trunc_set1.dip')
 ctf_fname = op.join(data_dir, 'CTF', 'testdata_ctf.ds')
-nirx_fname = op.join(data_dir, 'NIRx', 'nirx_15_2_recording_w_short')
+nirx_fname = op.join(data_dir, 'NIRx', 'nirscout',
+                     'nirx_15_2_recording_w_short')
 
 io_dir = op.join(op.abspath(op.dirname(__file__)), '..', '..', 'io')
 base_dir = op.join(io_dir, 'tests', 'data')