From 51a6f851c8719cb4633ff8cfa6fa71cecc42f197 Mon Sep 17 00:00:00 2001
From: Lloyd Izard <76954858+LOCEANlloydizard@users.noreply.github.com>
Date: Mon, 29 Jun 2026 21:52:11 -0700
Subject: [PATCH] Fix channel-frequency mapping in compute_MVBS

---
 echopype/commongrid/api.py                    | 29 +++++++++++--
 .../tests/commongrid/test_commongrid_api.py   | 41 +++++++++++++++++++
 2 files changed, 66 insertions(+), 4 deletions(-)

diff --git a/echopype/commongrid/api.py b/echopype/commongrid/api.py
index c5fcc4ddc..546d98b15 100644
--- a/echopype/commongrid/api.py
+++ b/echopype/commongrid/api.py
@@ -183,9 +183,18 @@ def compute_MVBS(
     prov_dict = echopype_prov_attrs(process_type="processing")
     prov_dict["processing_function"] = "commongrid.compute_MVBS"
     ds_MVBS = ds_MVBS.assign_attrs(prov_dict)
-    ds_MVBS["frequency_nominal"] = ds_Sv["frequency_nominal"]  # re-attach frequency_nominal
-    ds_MVBS["channel"] = ds_Sv["channel"]  # re-attach channel
 
+    # Preserve the channel order returned by compute_raw_MVBS and align
+    # frequency_nominal to that order.
+    freq = ds_Sv["frequency_nominal"]
+
+    if "ping_time" in freq.dims:
+        freq = freq.isel(ping_time=0, drop=True)
+
+    if "channel" in ds_MVBS.dims:
+        ds_MVBS["frequency_nominal"] = freq.sel(channel=ds_MVBS["channel"])
+    else:
+        ds_MVBS["frequency_nominal"] = freq
     ds_MVBS = insert_input_processing_level(ds_MVBS, input_ds=ds_Sv)
 
     return ds_MVBS
@@ -259,7 +268,12 @@ def compute_MVBS_index_binning(ds_Sv, range_sample_num=100, ping_num=100):
     prov_dict = echopype_prov_attrs(process_type="processing")
     prov_dict["processing_function"] = "commongrid.compute_MVBS_index_binning"
     ds_MVBS = ds_MVBS.assign_attrs(prov_dict)
-    ds_MVBS["frequency_nominal"] = ds_Sv["frequency_nominal"]  # re-attach frequency_nominal
+    freq = ds_Sv["frequency_nominal"]
+
+    if "ping_time" in freq.dims:
+        freq = freq.isel(ping_time=0, drop=True)
+
+    ds_MVBS["frequency_nominal"] = freq
 
     ds_MVBS = insert_input_processing_level(ds_MVBS, input_ds=ds_Sv)
 
@@ -387,8 +401,15 @@ def compute_NASC(
 
     # Set ping time binning information
     ds_NASC["ping_time"] = (["distance"], raw_NASC["ping_time"].data, ds_Sv["ping_time"].attrs)
+    freq = ds_Sv["frequency_nominal"]
+
+    if "ping_time" in freq.dims:
+        freq = freq.isel(ping_time=0, drop=True)
 
-    ds_NASC["frequency_nominal"] = ds_Sv["frequency_nominal"]  # re-attach frequency_nominal
+    if "channel" in ds_NASC.dims:
+        ds_NASC["frequency_nominal"] = freq.sel(channel=ds_NASC["channel"])
+    else:
+        ds_NASC["frequency_nominal"] = freq
 
     # Attach attributes
     _set_var_attrs(
diff --git a/echopype/tests/commongrid/test_commongrid_api.py b/echopype/tests/commongrid/test_commongrid_api.py
index 63ce2ebc2..0b7367314 100644
--- a/echopype/tests/commongrid/test_commongrid_api.py
+++ b/echopype/tests/commongrid/test_commongrid_api.py
@@ -91,6 +91,37 @@ def test__groupby_x_along_channels(request, range_var, lat_lon):
     assert f"{range_var}_bins" in sv_mean.dims
 
 
+@pytest.mark.unit
+def test_compute_MVBS_preserves_channel_frequency_mapping_with_2d_frequency_nominal(
+    mock_Sv_dataset_regular,
+):
+    ds_Sv = mock_Sv_dataset_regular.copy()
+
+    # Force AZFP-like metadata: frequency_nominal(ping_time, channel)
+    freq_values = xr.DataArray(
+        np.tile(np.array([120000.0, 200000.0]), (ds_Sv.sizes["ping_time"], 1)),
+        dims=("ping_time", "channel"),
+        coords={
+            "ping_time": ds_Sv["ping_time"],
+            "channel": ds_Sv["channel"],
+        },
+    )
+    ds_Sv["frequency_nominal"] = freq_values
+
+    ds_MVBS = ep.commongrid.compute_MVBS(
+        ds_Sv,
+        range_bin="2m",
+        ping_time_bin="1s",
+    )
+
+    expected_freq = ds_Sv["frequency_nominal"].isel(ping_time=0).sel(
+        channel=ds_MVBS["channel"]
+    )
+
+    assert ds_MVBS["frequency_nominal"].dims == ("channel",)
+    assert np.array_equal(ds_MVBS["frequency_nominal"].values, expected_freq.values)
+
+
 # NASC Tests
 @pytest.mark.integration
 @pytest.mark.parametrize("compute_mvbs", [True, False])
@@ -300,6 +331,16 @@ def test_compute_MVBS(test_data_samples):
     ping_time_bin = "20s"
     ds_MVBS = ep.commongrid.compute_MVBS(Sv, ping_time_bin=ping_time_bin)
     assert ds_MVBS is not None
+    freq = Sv["frequency_nominal"]
+
+    if "ping_time" in freq.dims:
+        freq = freq.isel(ping_time=0, drop=True)
+
+    expected_freq = freq.sel(channel=ds_MVBS["channel"])
+    assert np.array_equal(
+        ds_MVBS["frequency_nominal"].values,
+        expected_freq.values,
+    )
 
     # Test to see if ping_time was resampled correctly
     expected_ping_time = (