modify occurences of ppf to reflect changes in beer_lambert_law

scholzri · scholzri · commit cc5fe31c4482 · 2024-02-16T23:58:06.000+01:00
diff --git a/mne/channels/tests/test_interpolation.py b/mne/channels/tests/test_interpolation.py
@@ -323,7 +323,7 @@ def test_interpolation_nirs():
     raw_od.interpolate_bads()
     assert raw_od.info["bads"] == []
     assert bad_0_std_pre_interp > np.std(raw_od._data[bad_0])
-    raw_haemo = beer_lambert_law(raw_od, ppf=6)
+    raw_haemo = beer_lambert_law(raw_od, ppf=(6.0, 6.0))
     raw_haemo.info["bads"] = raw_haemo.ch_names[2:4]
     assert raw_haemo.info["bads"] == ["S1_D2 hbo", "S1_D2 hbr"]
     raw_haemo.interpolate_bads()
diff --git a/mne/channels/tests/test_standard_montage.py b/mne/channels/tests/test_standard_montage.py
@@ -201,7 +201,7 @@ def test_set_montage_artinis_basic():
     old_info_od = raw_od.info.copy()
     raw.set_montage(montage_octamon)
     raw_od.set_montage(montage_octamon)
-    raw_hb = beer_lambert_law(raw_od, ppf=6)  # montage needed for BLL
+    raw_hb = beer_lambert_law(raw_od, ppf=(6.0, 6.0))  # montage needed for BLL
     # Check that the montage was actually modified
     assert_raises(
         AssertionError,
diff --git a/mne/io/hitachi/tests/test_hitachi.py b/mne/io/hitachi/tests/test_hitachi.py
@@ -228,7 +228,7 @@ def test_hitachi_basic(
     assert_allclose(distances, want, atol=0.0)
     raw_od_bad = optical_density(raw)
     with pytest.warns(RuntimeWarning, match="will be zero"):
-        beer_lambert_law(raw_od_bad, ppf=6)
+        beer_lambert_law(raw_od_bad, ppf=(6.0, 6.0))
     # bad distances (too big)
     if versions[0] == "1.18" and len(fnames) == 1:
         need = sum(([f"S{ii}", f"D{ii}"] for ii in range(1, 9)), [])[:-1]
@@ -239,7 +239,7 @@ def test_hitachi_basic(
         raw.set_montage(mon)
         raw_od_bad = optical_density(raw)
         with pytest.warns(RuntimeWarning, match="greater than 10 cm"):
-            beer_lambert_law(raw_od_bad, ppf=6)
+            beer_lambert_law(raw_od_bad, ppf=(6.0, 6.0))
     # good distances
     mon = make_standard_montage("standard_1020")
     if versions[0] == "1.18":
@@ -306,7 +306,7 @@ def test_hitachi_basic(
     assert_array_less(peaks, 1, err_msg="TDDR too big")
     # HbO/HbR
     raw_tddr.set_montage(mon)
-    raw_h = beer_lambert_law(raw_tddr, ppf=6)
+    raw_h = beer_lambert_law(raw_tddr, ppf=(6.0, 6.0))
     data = raw_h.get_data("fnirs")
     assert np.isfinite(data).all()
     assert data.shape == (n_ch - 4, n_times)
diff --git a/mne/io/snirf/tests/test_snirf.py b/mne/io/snirf/tests/test_snirf.py
@@ -98,7 +98,7 @@ def test_basic_reading_and_min_process(fname):
     if "fnirs_cw_amplitude" in raw:
         raw = optical_density(raw)
     if "fnirs_od" in raw:
-        raw = beer_lambert_law(raw, ppf=6)
+        raw = beer_lambert_law(raw, ppf=(6.0, 6.0))
     assert "hbo" in raw
     assert "hbr" in raw
 
diff --git a/mne/preprocessing/nirs/tests/test_scalp_coupling_index.py b/mne/preprocessing/nirs/tests/test_scalp_coupling_index.py
@@ -76,6 +76,6 @@ def test_scalp_coupling_index(fname, fmt, tmp_path):
     assert_allclose(sci[8:12], 0, atol=1e-10)
 
     # Ensure function errors if wrong type is passed in
-    raw = beer_lambert_law(raw, ppf=6)
+    raw = beer_lambert_law(raw, ppf=(6.0, 6.0))
     with pytest.raises(RuntimeError, match="Scalp"):
         scalp_coupling_index(raw)
diff --git a/mne/viz/conftest.py b/mne/viz/conftest.py
@@ -42,7 +42,7 @@ def fnirs_epochs():
     """Create an fnirs epoch structure."""
     raw_intensity = read_raw_nirx(fname_nirx, preload=False)
     raw_od = optical_density(raw_intensity)
-    raw_haemo = beer_lambert_law(raw_od, ppf=6.0)
+    raw_haemo = beer_lambert_law(raw_od, ppf=(6.0, 6.0))
     evts, _ = events_from_annotations(raw_haemo, event_id={"1.0": 1})
     evts_dct = {"A": 1}
     tn, tx = -1, 2
diff --git a/tutorials/preprocessing/70_fnirs_processing.py b/tutorials/preprocessing/70_fnirs_processing.py
@@ -140,7 +140,7 @@
 # Next we convert the optical density data to haemoglobin concentration using
 # the modified Beer-Lambert law.
 
-raw_haemo = mne.preprocessing.nirs.beer_lambert_law(raw_od, ppf=0.1)
+raw_haemo = mne.preprocessing.nirs.beer_lambert_law(raw_od, ppf=(0.6, 0.6))
 raw_haemo.plot(n_channels=len(raw_haemo.ch_names), duration=500, show_scrollbars=False)
 
 
