From 6fabec2800607ec8dd58110bdc8e8199ff541b76 Mon Sep 17 00:00:00 2001
From: Robert Luke <hello@robertluke.net>
Date: Tue, 23 Mar 2021 10:30:44 +1100
Subject: [PATCH 1/7] Add more sanity checks for fnirs data

---
 mne/preprocessing/nirs/__init__.py            |   2 +-
 mne/preprocessing/nirs/_optical_density.py    |   3 +
 mne/preprocessing/nirs/_tddr.py               |   2 +
 mne/preprocessing/nirs/nirs.py                |  22 +++-
 .../nirs/tests/test_beer_lambert_law.py       |   2 +-
 mne/preprocessing/nirs/tests/test_nirs.py     | 122 +++++++++++++++++-
 6 files changed, 147 insertions(+), 6 deletions(-)

diff --git a/mne/preprocessing/nirs/__init__.py b/mne/preprocessing/nirs/__init__.py
index 6734cf53573..f101867f789 100644
--- a/mne/preprocessing/nirs/__init__.py
+++ b/mne/preprocessing/nirs/__init__.py
@@ -8,7 +8,7 @@
 
 from .nirs import (short_channels, source_detector_distances,
                    _check_channels_ordered, _channel_frequencies,
-                   _fnirs_check_bads, _fnirs_spread_bads)
+                   _fnirs_check_bads, _fnirs_spread_bads, _channel_chromophore)
 from ._optical_density import optical_density
 from ._beer_lambert_law import beer_lambert_law
 from ._scalp_coupling_index import scalp_coupling_index
diff --git a/mne/preprocessing/nirs/_optical_density.py b/mne/preprocessing/nirs/_optical_density.py
index 1efa72377a5..feb4ebb6637 100644
--- a/mne/preprocessing/nirs/_optical_density.py
+++ b/mne/preprocessing/nirs/_optical_density.py
@@ -10,6 +10,7 @@
 from ...io.constants import FIFF
 from ...utils import _validate_type, warn
 from ...io.pick import _picks_to_idx
+from ..nirs import _channel_frequencies, _check_channels_ordered
 
 
 def optical_density(raw):
@@ -27,6 +28,8 @@ def optical_density(raw):
     """
     raw = raw.copy().load_data()
     _validate_type(raw, BaseRaw, 'raw')
+    _check_channels_ordered(raw, np.unique(_channel_frequencies(raw)))
+
     picks = _picks_to_idx(raw.info, 'fnirs_cw_amplitude')
     data_means = np.mean(raw.get_data(), axis=1)
 
diff --git a/mne/preprocessing/nirs/_tddr.py b/mne/preprocessing/nirs/_tddr.py
index e4daa039188..935a0b98d5a 100644
--- a/mne/preprocessing/nirs/_tddr.py
+++ b/mne/preprocessing/nirs/_tddr.py
@@ -10,6 +10,7 @@
 from ...io import BaseRaw
 from ...utils import _validate_type, verbose
 from ...io.pick import _picks_to_idx
+from ..nirs import _channel_frequencies, _check_channels_ordered
 
 
 @verbose
@@ -42,6 +43,7 @@ def temporal_derivative_distribution_repair(raw, *, verbose=None):
     """
     raw = raw.copy().load_data()
     _validate_type(raw, BaseRaw, 'raw')
+    _check_channels_ordered(raw, np.unique(_channel_frequencies(raw)))
 
     if not len(pick_types(raw.info, fnirs='fnirs_od')):
         raise RuntimeError('TDDR should be run on optical density data.')
diff --git a/mne/preprocessing/nirs/nirs.py b/mne/preprocessing/nirs/nirs.py
index 28dabd1cfdb..6fb7ae38349 100644
--- a/mne/preprocessing/nirs/nirs.py
+++ b/mne/preprocessing/nirs/nirs.py
@@ -65,9 +65,19 @@ def _channel_frequencies(raw):
         freqs[ii] = raw.info['chs'][ii]['loc'][9]
     return freqs
 
+def _channel_chromophore(raw):
+    """Return the chromophore of each channel."""
+    # Only valid for fNIRS data after conversion to haemoglobin
+    picks = _picks_to_idx(raw.info, ['hbo', 'hbr'],
+                          exclude=[], allow_empty=True)
+    chroma = []
+    for ii in picks:
+        chroma.append(raw.ch_names[ii].split(" ")[1])
+    return chroma
+
 
 def _check_channels_ordered(raw, freqs):
-    """Check channels followed expected fNIRS format."""
+    """Check channels follow expected fNIRS format."""
     # Every second channel should be same SD pair
     # and have the specified light frequencies.
     picks = _picks_to_idx(raw.info, ['fnirs_cw_amplitude', 'fnirs_od'],
@@ -77,6 +87,13 @@ def _check_channels_ordered(raw, freqs):
             'NIRS channels not ordered correctly. An even number of NIRS '
             'channels is required. %d channels were provided: %r'
             % (len(raw.ch_names), raw.ch_names))
+
+    all_freqs = [raw.info["chs"][ii]["loc"][9] for ii in picks]
+    if np.any(np.isnan(all_freqs)):
+        raise ValueError(
+            'NIRS channels is missing wavelength information in the info["chs"]'
+            f'structure. The encoded wavelengths are {all_freqs}.')
+
     for ii in picks[::2]:
         ch1_name_info = re.match(r'S(\d+)_D(\d+) (\d+)',
                                  raw.info['chs'][ii]['ch_name'])
@@ -101,7 +118,8 @@ def _check_channels_ordered(raw, freqs):
            (int(ch2_name_info.groups()[2]) != freqs[1]):
             raise ValueError(
                 'NIRS channels not ordered correctly. Channels must be ordered'
-                ' as source detector pairs with frequencies: %d & %d'
+                ' as source detector pairs with alternating'
+                ' frequencies: %d & %d'
                 % (freqs[0], freqs[1]))
 
     return picks
diff --git a/mne/preprocessing/nirs/tests/test_beer_lambert_law.py b/mne/preprocessing/nirs/tests/test_beer_lambert_law.py
index 2e52d80cf5f..aca6c3d218c 100644
--- a/mne/preprocessing/nirs/tests/test_beer_lambert_law.py
+++ b/mne/preprocessing/nirs/tests/test_beer_lambert_law.py
@@ -70,7 +70,7 @@ def test_beer_lambert_unordered_errors():
 
     # Test that an error is thrown if inconsistent frequencies used in data
     raw_od.info['chs'][2]['loc'][9] = 770.0
-    with pytest.raises(ValueError, match='pairs with frequencies'):
+    with pytest.raises(ValueError, match='with alternating frequencies'):
         beer_lambert_law(raw_od)
 
 
diff --git a/mne/preprocessing/nirs/tests/test_nirs.py b/mne/preprocessing/nirs/tests/test_nirs.py
index 3a85589ef1c..be49666a5bc 100644
--- a/mne/preprocessing/nirs/tests/test_nirs.py
+++ b/mne/preprocessing/nirs/tests/test_nirs.py
@@ -10,12 +10,13 @@
 import numpy as np
 from numpy.testing import assert_array_equal
 
+from mne import create_info
 from mne.datasets.testing import data_path
-from mne.io import read_raw_nirx
+from mne.io import read_raw_nirx, RawArray
 from mne.preprocessing.nirs import (optical_density, beer_lambert_law,
                                     _fnirs_check_bads, _fnirs_spread_bads,
                                     _check_channels_ordered,
-                                    _channel_frequencies)
+                                    _channel_frequencies, _channel_chromophore)
 from mne.io.pick import _picks_to_idx
 
 from mne.datasets import testing
@@ -158,6 +159,8 @@ def test_fnirs_channel_naming_and_order_readers(fname):
     raw = read_raw_nirx(fname)
     freqs = np.unique(_channel_frequencies(raw))
     assert_array_equal(freqs, [760, 850])
+    chroma = np.unique(_channel_chromophore(raw))
+    assert len(chroma) == 0
 
     picks = _check_channels_ordered(raw, freqs)
     assert len(picks) == len(raw.ch_names)  # as all fNIRS only data
@@ -182,9 +185,124 @@ def test_fnirs_channel_naming_and_order_readers(fname):
     raw = optical_density(raw)
     freqs = np.unique(_channel_frequencies(raw))
     assert_array_equal(freqs, [760, 850])
+    chroma = np.unique(_channel_chromophore(raw))
+    assert len(chroma) == 0
     picks = _check_channels_ordered(raw, freqs)
     assert len(picks) == len(raw.ch_names)  # as all fNIRS only data
 
+    # Check on haemoglobin data
     raw = beer_lambert_law(raw)
     freqs = np.unique(_channel_frequencies(raw))
     assert len(freqs) == 0
+    assert len(_channel_chromophore(raw)) == len(raw.ch_names)
+    chroma = np.unique(_channel_chromophore(raw))
+    assert_array_equal(chroma, ["hbo", "hbr"])
+
+
+def test_fnirs_channel_naming_and_order_custom_raw():
+    """Ensure fNIRS channel checking on manually created data."""
+    data = np.random.normal(size=(6, 10))
+
+    # Start with a correctly named raw intensity dataset
+    # These are the steps required to build an fNIRS Raw object from scratch
+    ch_names = ['S1_D1 760', 'S1_D1 850', 'S2_D1 760', 'S2_D1 850',
+                'S3_D1 760', 'S3_D1 850']
+    ch_types = np.repeat("fnirs_cw_amplitude", 6)
+    info = create_info(ch_names=ch_names, ch_types=ch_types, sfreq=1.0)
+    raw = RawArray(data, info, verbose=True)
+    freqs = np.tile([760, 850], 3)
+    for idx, f in enumerate(freqs):
+        raw.info["chs"][idx]["loc"][9] = f
+
+    freqs = np.unique(_channel_frequencies(raw))
+    picks = _check_channels_ordered(raw, freqs)
+    assert len(picks) == len(raw.ch_names)
+    assert len(picks) == 6
+
+    # Different systems use different frequencies, so ensure that works
+    ch_names = ['S1_D1 920', 'S1_D1 850', 'S2_D1 920', 'S2_D1 850',
+                'S3_D1 920', 'S3_D1 850']
+    ch_types = np.repeat("fnirs_cw_amplitude", 6)
+    info = create_info(ch_names=ch_names, ch_types=ch_types, sfreq=1.0)
+    raw = RawArray(data, info, verbose=True)
+    freqs = np.tile([920, 850], 3)
+    for idx, f in enumerate(freqs):
+        raw.info["chs"][idx]["loc"][9] = f
+
+    picks = _check_channels_ordered(raw, [920, 850])
+    assert len(picks) == len(raw.ch_names)
+    assert len(picks) == 6
+
+    # Catch expected errors
+
+    # The frequencies named in the channel names must match the info loc field
+    ch_names = ['S1_D1 760', 'S1_D1 850', 'S2_D1 760', 'S2_D1 850',
+                'S3_D1 760', 'S3_D1 850']
+    ch_types = np.repeat("fnirs_cw_amplitude", 6)
+    info = create_info(ch_names=ch_names, ch_types=ch_types, sfreq=1.0)
+    raw = RawArray(data, info, verbose=True)
+    freqs = np.tile([920, 850], 3)
+    for idx, f in enumerate(freqs):
+        raw.info["chs"][idx]["loc"][9] = f
+    with pytest.raises(ValueError, match='name and NIRS frequency do not'):
+        _check_channels_ordered(raw, [920, 850])
+
+    # Catch if someone doesnt set the info field
+    ch_names = ['S1_D1 760', 'S1_D1 850', 'S2_D1 760', 'S2_D1 850',
+                'S3_D1 760', 'S3_D1 850']
+    ch_types = np.repeat("fnirs_cw_amplitude", 6)
+    info = create_info(ch_names=ch_names, ch_types=ch_types, sfreq=1.0)
+    raw = RawArray(data, info, verbose=True)
+    with pytest.raises(ValueError, match='missing wavelength information'):
+        _check_channels_ordered(raw, [920, 850])
+
+    # I have seen data encoded not in alternating frequency, but blocked.
+    ch_names = ['S1_D1 760', 'S2_D1 760', 'S3_D1 760',
+                'S1_D1 850', 'S2_D1 850', 'S3_D1 850']
+    ch_types = np.repeat("fnirs_cw_amplitude", 6)
+    info = create_info(ch_names=ch_names, ch_types=ch_types, sfreq=1.0)
+    raw = RawArray(data, info, verbose=True)
+    freqs = np.repeat([760, 850], 3)
+    for idx, f in enumerate(freqs):
+        raw.info["chs"][idx]["loc"][9] = f
+    with pytest.raises(ValueError, match='channels not ordered correctly'):
+        _check_channels_ordered(raw, [760, 850])
+    # and this is how you would fix the ordering, then it should pass
+    raw.pick(picks=[0, 3, 1, 4, 2, 5])
+    _check_channels_ordered(raw, [760, 850])
+
+
+def test_fnirs_channel_naming_and_order_custom_optical_density():
+    """Ensure fNIRS channel checking on manually created data."""
+    data = np.random.normal(size=(6, 10))
+
+    # Start with a correctly named raw intensity dataset
+    # These are the steps required to build an fNIRS Raw object from scratch
+    ch_names = ['S1_D1 760', 'S1_D1 850', 'S2_D1 760', 'S2_D1 850',
+                'S3_D1 760', 'S3_D1 850']
+    ch_types = np.repeat("fnirs_od", 6)
+    info = create_info(ch_names=ch_names, ch_types=ch_types, sfreq=1.0)
+    raw = RawArray(data, info, verbose=True)
+    freqs = np.tile([760, 850], 3)
+    for idx, f in enumerate(freqs):
+        raw.info["chs"][idx]["loc"][9] = f
+
+    freqs = np.unique(_channel_frequencies(raw))
+    picks = _check_channels_ordered(raw, freqs)
+    assert len(picks) == len(raw.ch_names)
+    assert len(picks) == 6
+
+    # Check block naming for optical density
+    ch_names = ['S1_D1 760', 'S2_D1 760', 'S3_D1 760',
+                'S1_D1 850', 'S2_D1 850', 'S3_D1 850']
+    ch_types = np.repeat("fnirs_od", 6)
+    info = create_info(ch_names=ch_names, ch_types=ch_types, sfreq=1.0)
+    raw = RawArray(data, info, verbose=True)
+    freqs = np.repeat([760, 850], 3)
+    for idx, f in enumerate(freqs):
+        raw.info["chs"][idx]["loc"][9] = f
+    with pytest.raises(ValueError, match='channels not ordered correctly'):
+        _check_channels_ordered(raw, [760, 850])
+    # and this is how you would fix the ordering, then it should pass
+    raw.pick(picks=[0, 3, 1, 4, 2, 5])
+    _check_channels_ordered(raw, [760, 850])
\ No newline at end of file

From 0d66ab95c0fbe7873e5ad182847ef048ac74cfe6 Mon Sep 17 00:00:00 2001
From: Robert Luke <hello@robertluke.net>
Date: Tue, 23 Mar 2021 10:55:02 +1100
Subject: [PATCH 2/7] Add description of fnirs fields

---
 mne/preprocessing/nirs/nirs.py             |  5 ++--
 mne/preprocessing/nirs/tests/test_nirs.py  |  2 +-
 tutorials/io/plot_30_reading_fnirs_data.py | 34 +++++++++++++++++++---
 3 files changed, 34 insertions(+), 7 deletions(-)

diff --git a/mne/preprocessing/nirs/nirs.py b/mne/preprocessing/nirs/nirs.py
index 6fb7ae38349..eea96594fa8 100644
--- a/mne/preprocessing/nirs/nirs.py
+++ b/mne/preprocessing/nirs/nirs.py
@@ -65,6 +65,7 @@ def _channel_frequencies(raw):
         freqs[ii] = raw.info['chs'][ii]['loc'][9]
     return freqs
 
+
 def _channel_chromophore(raw):
     """Return the chromophore of each channel."""
     # Only valid for fNIRS data after conversion to haemoglobin
@@ -91,8 +92,8 @@ def _check_channels_ordered(raw, freqs):
     all_freqs = [raw.info["chs"][ii]["loc"][9] for ii in picks]
     if np.any(np.isnan(all_freqs)):
         raise ValueError(
-            'NIRS channels is missing wavelength information in the info["chs"]'
-            f'structure. The encoded wavelengths are {all_freqs}.')
+            'NIRS channels is missing wavelength information in the'
+            f'info["chs"] structure. The encoded wavelengths are {all_freqs}.')
 
     for ii in picks[::2]:
         ch1_name_info = re.match(r'S(\d+)_D(\d+) (\d+)',
diff --git a/mne/preprocessing/nirs/tests/test_nirs.py b/mne/preprocessing/nirs/tests/test_nirs.py
index be49666a5bc..246e03b624b 100644
--- a/mne/preprocessing/nirs/tests/test_nirs.py
+++ b/mne/preprocessing/nirs/tests/test_nirs.py
@@ -305,4 +305,4 @@ def test_fnirs_channel_naming_and_order_custom_optical_density():
         _check_channels_ordered(raw, [760, 850])
     # and this is how you would fix the ordering, then it should pass
     raw.pick(picks=[0, 3, 1, 4, 2, 5])
-    _check_channels_ordered(raw, [760, 850])
\ No newline at end of file
+    _check_channels_ordered(raw, [760, 850])
diff --git a/tutorials/io/plot_30_reading_fnirs_data.py b/tutorials/io/plot_30_reading_fnirs_data.py
index 1bb8d851ea0..5d64be52d3b 100644
--- a/tutorials/io/plot_30_reading_fnirs_data.py
+++ b/tutorials/io/plot_30_reading_fnirs_data.py
@@ -68,9 +68,35 @@
 A channel is formed by source-detector pairs.
 MNE stores the location of the channels, sources, and detectors.
 
-
-.. warning:: Information about device light wavelength is stored in
-             channel names. Manual modification of channel names is not
-             recommended.
+.. warning:: Manual modification of channel names and info fields is not
+             recommended. fNIRS data is encoded in MNE using a combination
+             of the channel name and the info structure. Additionally, there
+             is an expected order of channels that must be maintained. Any
+             change to the expected structure will cause an error.
+             
+             Channels names must follow the structure
+             ``S#_D# value``
+             where S# is the source number (e.g. S12 for source 12),
+             D# is the detector number (e.g. D4 for detector 4),
+             and the value is either the light wavelength if the data type is
+             raw intensity or optical density, or the chromophore type if the
+             data is hbo or hbr. For example ``S1_D2 760`` is valid as is
+             ``S11_D1 850`` and ``S1_D2 hbo`` and ``S1_D2 hbr``. However,
+             these examples are not valid ``D1_S2 hbo``, ``S1_D2_760``.
+             
+             Channels with the same source-detector pairing must be stored
+             in consecutive order. For example
+             ``["S11_D2 hbo", "S11_D2 hbr", "S1_D2 hbo", "S11_D2 hbr"]``
+             is acceptable, but 
+             ``["S11_D2 hbo", "S1_D2 hbo", "S11_D2 hbr", "S11_D2 hbr"]``
+             is not. Further, the order of type must be maintained for all
+             fNIRS channels so the following is not valid
+             ``["S11_D2 hbo", "S11_D2 hbr", "S1_D2 hbr", "S11_D2 hbo"]``.
+             
+             For raw amplitude measurements and for optical density data
+             the wavelength information must be stored in
+             ``info["chs"][ii]["loc"][9]``
+             and it must match the channel name. For example the channel
+             ``S11_D2 760`` must have the value 760 stored in the loc[9] field.
 
 """  # noqa:E501

From 0312f8d3e753c5d50e0640a8d8b8e04e4f7cbebd Mon Sep 17 00:00:00 2001
From: Robert Luke <hello@robertluke.net>
Date: Tue, 23 Mar 2021 10:59:02 +1100
Subject: [PATCH 3/7] whitespace

---
 tutorials/io/plot_30_reading_fnirs_data.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tutorials/io/plot_30_reading_fnirs_data.py b/tutorials/io/plot_30_reading_fnirs_data.py
index 5d64be52d3b..c16ba5f8c66 100644
--- a/tutorials/io/plot_30_reading_fnirs_data.py
+++ b/tutorials/io/plot_30_reading_fnirs_data.py
@@ -73,7 +73,7 @@
              of the channel name and the info structure. Additionally, there
              is an expected order of channels that must be maintained. Any
              change to the expected structure will cause an error.
-             
+
              Channels names must follow the structure
              ``S#_D# value``
              where S# is the source number (e.g. S12 for source 12),
@@ -83,16 +83,16 @@
              data is hbo or hbr. For example ``S1_D2 760`` is valid as is
              ``S11_D1 850`` and ``S1_D2 hbo`` and ``S1_D2 hbr``. However,
              these examples are not valid ``D1_S2 hbo``, ``S1_D2_760``.
-             
+
              Channels with the same source-detector pairing must be stored
              in consecutive order. For example
              ``["S11_D2 hbo", "S11_D2 hbr", "S1_D2 hbo", "S11_D2 hbr"]``
-             is acceptable, but 
+             is acceptable, but
              ``["S11_D2 hbo", "S1_D2 hbo", "S11_D2 hbr", "S11_D2 hbr"]``
              is not. Further, the order of type must be maintained for all
              fNIRS channels so the following is not valid
              ``["S11_D2 hbo", "S11_D2 hbr", "S1_D2 hbr", "S11_D2 hbo"]``.
-             
+
              For raw amplitude measurements and for optical density data
              the wavelength information must be stored in
              ``info["chs"][ii]["loc"][9]``

From ea906973dcc7f87fb8a7682155feb00aaa10fc5a Mon Sep 17 00:00:00 2001
From: Robert Luke <hello@robertluke.net>
Date: Tue, 23 Mar 2021 11:20:48 +1100
Subject: [PATCH 4/7] Text tweaks

---
 mne/preprocessing/nirs/tests/test_nirs.py  |  2 +-
 tutorials/io/plot_30_reading_fnirs_data.py | 10 ++++++----
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/mne/preprocessing/nirs/tests/test_nirs.py b/mne/preprocessing/nirs/tests/test_nirs.py
index 246e03b624b..55845521f0b 100644
--- a/mne/preprocessing/nirs/tests/test_nirs.py
+++ b/mne/preprocessing/nirs/tests/test_nirs.py
@@ -247,7 +247,7 @@ def test_fnirs_channel_naming_and_order_custom_raw():
     with pytest.raises(ValueError, match='name and NIRS frequency do not'):
         _check_channels_ordered(raw, [920, 850])
 
-    # Catch if someone doesnt set the info field
+    # Catch if someone doesn't set the info field
     ch_names = ['S1_D1 760', 'S1_D1 850', 'S2_D1 760', 'S2_D1 850',
                 'S3_D1 760', 'S3_D1 850']
     ch_types = np.repeat("fnirs_cw_amplitude", 6)
diff --git a/tutorials/io/plot_30_reading_fnirs_data.py b/tutorials/io/plot_30_reading_fnirs_data.py
index c16ba5f8c66..e92c1722fd6 100644
--- a/tutorials/io/plot_30_reading_fnirs_data.py
+++ b/tutorials/io/plot_30_reading_fnirs_data.py
@@ -74,7 +74,7 @@
              is an expected order of channels that must be maintained. Any
              change to the expected structure will cause an error.
 
-             Channels names must follow the structure
+             Channel names must follow the structure
              ``S#_D# value``
              where S# is the source number (e.g. S12 for source 12),
              D# is the detector number (e.g. D4 for detector 4),
@@ -86,17 +86,19 @@
 
              Channels with the same source-detector pairing must be stored
              in consecutive order. For example
-             ``["S11_D2 hbo", "S11_D2 hbr", "S1_D2 hbo", "S11_D2 hbr"]``
+             ``["S11_D2 hbo", "S11_D2 hbr", "S1_D2 hbo", "S1_D2 hbr"]``
              is acceptable, but
-             ``["S11_D2 hbo", "S1_D2 hbo", "S11_D2 hbr", "S11_D2 hbr"]``
+             ``["S11_D2 hbo", "S1_D2 hbo", "S11_D2 hbr", "S1_D2 hbr"]``
              is not. Further, the order of type must be maintained for all
              fNIRS channels so the following is not valid
-             ``["S11_D2 hbo", "S11_D2 hbr", "S1_D2 hbr", "S11_D2 hbo"]``.
+             ``["S11_D2 hbo", "S11_D2 hbr", "S1_D2 hbr", "S1_D2 hbo"]``.
 
              For raw amplitude measurements and for optical density data
              the wavelength information must be stored in
              ``info["chs"][ii]["loc"][9]``
              and it must match the channel name. For example the channel
              ``S11_D2 760`` must have the value 760 stored in the loc[9] field.
+             There is no such requirement for hbo and hbr data as they have
+             a dedicated channel type.
 
 """  # noqa:E501

From a54f79adcea5513aa848062b6c097f93e59cc899 Mon Sep 17 00:00:00 2001
From: Robert Luke <hello@robertluke.net>
Date: Tue, 23 Mar 2021 11:21:44 +1100
Subject: [PATCH 5/7] Text tweaks

---
 tutorials/io/plot_30_reading_fnirs_data.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tutorials/io/plot_30_reading_fnirs_data.py b/tutorials/io/plot_30_reading_fnirs_data.py
index e92c1722fd6..eaf2eda5249 100644
--- a/tutorials/io/plot_30_reading_fnirs_data.py
+++ b/tutorials/io/plot_30_reading_fnirs_data.py
@@ -97,7 +97,7 @@
              the wavelength information must be stored in
              ``info["chs"][ii]["loc"][9]``
              and it must match the channel name. For example the channel
-             ``S11_D2 760`` must have the value 760 stored in the loc[9] field.
+             ``S11_D2 760`` must have the value 760 stored in the ``loc[9]`` field.
              There is no such requirement for hbo and hbr data as they have
              a dedicated channel type.
 

From d42951dcd0f4eb89ffc376befeba5a35a6c680b1 Mon Sep 17 00:00:00 2001
From: Robert Luke <hello@robertluke.net>
Date: Tue, 23 Mar 2021 12:02:14 +1100
Subject: [PATCH 6/7] Remove tutorial text and defer to discussion in #9141

---
 tutorials/io/plot_30_reading_fnirs_data.py | 35 ++--------------------
 1 file changed, 3 insertions(+), 32 deletions(-)

diff --git a/tutorials/io/plot_30_reading_fnirs_data.py b/tutorials/io/plot_30_reading_fnirs_data.py
index eaf2eda5249..21c0f0f7b1d 100644
--- a/tutorials/io/plot_30_reading_fnirs_data.py
+++ b/tutorials/io/plot_30_reading_fnirs_data.py
@@ -68,37 +68,8 @@
 A channel is formed by source-detector pairs.
 MNE stores the location of the channels, sources, and detectors.
 
-.. warning:: Manual modification of channel names and info fields is not
-             recommended. fNIRS data is encoded in MNE using a combination
-             of the channel name and the info structure. Additionally, there
-             is an expected order of channels that must be maintained. Any
-             change to the expected structure will cause an error.
-
-             Channel names must follow the structure
-             ``S#_D# value``
-             where S# is the source number (e.g. S12 for source 12),
-             D# is the detector number (e.g. D4 for detector 4),
-             and the value is either the light wavelength if the data type is
-             raw intensity or optical density, or the chromophore type if the
-             data is hbo or hbr. For example ``S1_D2 760`` is valid as is
-             ``S11_D1 850`` and ``S1_D2 hbo`` and ``S1_D2 hbr``. However,
-             these examples are not valid ``D1_S2 hbo``, ``S1_D2_760``.
-
-             Channels with the same source-detector pairing must be stored
-             in consecutive order. For example
-             ``["S11_D2 hbo", "S11_D2 hbr", "S1_D2 hbo", "S1_D2 hbr"]``
-             is acceptable, but
-             ``["S11_D2 hbo", "S1_D2 hbo", "S11_D2 hbr", "S1_D2 hbr"]``
-             is not. Further, the order of type must be maintained for all
-             fNIRS channels so the following is not valid
-             ``["S11_D2 hbo", "S11_D2 hbr", "S1_D2 hbr", "S1_D2 hbo"]``.
-
-             For raw amplitude measurements and for optical density data
-             the wavelength information must be stored in
-             ``info["chs"][ii]["loc"][9]``
-             and it must match the channel name. For example the channel
-             ``S11_D2 760`` must have the value 760 stored in the ``loc[9]`` field.
-             There is no such requirement for hbo and hbr data as they have
-             a dedicated channel type.
+.. warning:: Information about device light wavelength is stored in
+             channel names. Manual modification of channel names is not
+             recommended.
 
 """  # noqa:E501

From 016434c63e62cf996aeb7ec53f848addcd5eb296 Mon Sep 17 00:00:00 2001
From: Robert Luke <hello@robertluke.net>
Date: Tue, 23 Mar 2021 12:02:56 +1100
Subject: [PATCH 7/7] Line missing

---
 tutorials/io/plot_30_reading_fnirs_data.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tutorials/io/plot_30_reading_fnirs_data.py b/tutorials/io/plot_30_reading_fnirs_data.py
index 21c0f0f7b1d..1bb8d851ea0 100644
--- a/tutorials/io/plot_30_reading_fnirs_data.py
+++ b/tutorials/io/plot_30_reading_fnirs_data.py
@@ -68,6 +68,7 @@
 A channel is formed by source-detector pairs.
 MNE stores the location of the channels, sources, and detectors.
 
+
 .. warning:: Information about device light wavelength is stored in
              channel names. Manual modification of channel names is not
              recommended.