Drop beam dimension

echopype/calibrate/cal_params.py

@@ -352,8 +352,8 @@ def get_cal_params_AZFP(beam: xr.DataArray, vend: xr.DataArray, user_dict: dict)
         if v is None:
             # Params from Sonar/Beam_group1
             if p == "equivalent_beam_angle":
-                # equivalent_beam_angle has dims: channel, ping_time, beam --> only need channel
-                out_dict[p] = beam[p].isel(ping_time=0, beam=0).drop(["ping_time", "beam"])
+                # equivalent_beam_angle has dims: channel, ping_time --> only need channel
+                out_dict[p] = beam[p].isel(ping_time=0).drop("ping_time")
 
             # Params from Vendor_specific group
             elif p in ["EL", "DS", "TVR", "VTX", "Sv_offset"]:
@@ -497,9 +497,14 @@ def _get_fs():
                         )
                     elif p == "equivalent_beam_angle":
                         # scaled according to frequency ratio
-                        out_dict[p] = beam[p].isel(beam=0).drop("beam") + 20 * np.log10(
-                            beam["frequency_nominal"] / freq_center
-                        )
+                        if "beam" in beam[p].dims:
+                            out_dict[p] = beam[p].isel(beam=0).drop("beam") + 20 * np.log10(
+                                beam["frequency_nominal"] / freq_center
+                            )
+                        else:
+                            out_dict[p] = beam[p] + 20 * np.log10(
+                                beam["frequency_nominal"] / freq_center
+                            )
                     elif p == "gain_correction":
                         # interpolate or pull from narrowband table
                         out_dict[p] = _get_interp_da(

echopype/calibrate/calibrate_azfp.py

@@ -70,9 +70,8 @@ def _cal_power_samples(self, cal_type, **kwargs):
         EL = (
             self.cal_params["EL"]
             - 2.5 / a
-            + self.echodata["Sonar/Beam_group1"]["backscatter_r"].squeeze("beam", drop=True)
-            / (26214 * a)
-        )  # eq.(5)  # has beam dim due to backscatter_r
+            + self.echodata["Sonar/Beam_group1"]["backscatter_r"] / (26214 * a)
+        )  # eq.(5)
 
         if cal_type == "Sv":
             # eq.(9)

echopype/calibrate/calibrate_ek.py

@@ -124,9 +124,12 @@ def _cal_power_samples(self, cal_type: str) -> xr.Dataset:
         if "time1" in out.coords:
             out = out.drop("time1")
 
-        # Squeeze out the beam dim
-        # doing it here because both out and self.cal_params["equivalent_beam_angle"] has beam dim
-        return out.squeeze("beam", drop=True)
+        # Squeeze out the beam dim, if present.
+        # Doing it here because both out and self.cal_params["equivalent_beam_angle"] have` beam dim
+        if "beam" in out.dims:
+            return out.squeeze("beam", drop=True)
+        else:
+            return out
 
 
 class CalibrateEK60(CalibrateEK):
@@ -250,7 +253,7 @@ def __init__(
             # use true center frequency to interpolate for various cal params
             self.freq_center = (beam["frequency_start"] + beam["frequency_end"]).sel(
                 channel=self.chan_sel
-            ).isel(beam=0).drop("beam") / 2
+            ) / 2
         else:
             # use nominal channel frequency for CW pulse
             self.freq_center = beam["frequency_nominal"].sel(channel=self.chan_sel)

echopype/convert/set_groups_azfp.py

@@ -19,13 +19,18 @@ class SetGroupsAZFP(SetGroupsBase):
     # these sets are applied to all Sonar/Beam_groupX groups.
 
     # Variables that need only the beam dimension added to them.
-    beam_only_names = {"backscatter_r"}
+    beam_only_names = set()
 
     # Variables that need only the ping_time dimension added to them.
-    ping_time_only_names = {"sample_interval", "transmit_duration_nominal"}
+    ping_time_only_names = {
+        "sample_interval",
+        "transmit_duration_nominal",
+        "equivalent_beam_angle",
+        "gain_correction",
+    }
 
     # Variables that need beam and ping_time dimensions added to them.
-    beam_ping_time_names = {"equivalent_beam_angle", "gain_correction"}
+    beam_ping_time_names = set()
 
     beamgroups_possible = [
         {

echopype/convert/set_groups_ek60.py

@@ -24,14 +24,16 @@ class SetGroupsEK60(SetGroupsBase):
     # in converting from v0.5.x to v0.6.0. The values within
     # these sets are applied to all Sonar/Beam_groupX groups.
 
+    # 2023-05-25 note: We have decided to remove the beam dimension from EK60,
+    # where it was added as a length-1 dimension only to more closely match
+    # the SONAR-netCDF4 v1 convention. For the time being, we are retaining the
+    # infrastructure that adds this dimension, but updating the variables lists.
+
     # Variables that need only the beam dimension added to them.
-    beam_only_names = {"backscatter_r", "angle_athwartship", "angle_alongship"}
+    beam_only_names = set()
 
     # Variables that need only the ping_time dimension added to them.
-    ping_time_only_names = {"beam_type"}
-
-    # Variables that need beam and ping_time dimensions added to them.
-    beam_ping_time_names = {
+    ping_time_only_names = {
         "beam_direction_x",
         "beam_direction_y",
         "beam_direction_z",
@@ -45,6 +47,9 @@ class SetGroupsEK60(SetGroupsBase):
         "gain_correction",
     }
 
+    # Variables that need beam and ping_time dimensions added to them.
+    beam_ping_time_names = set()
+
     beamgroups_possible = [
         {
             "name": "Beam_group1",

echopype/convert/set_groups_ek80.py

@@ -27,20 +27,11 @@ class SetGroupsEK80(SetGroupsBase):
     # these sets are applied to all Sonar/Beam_groupX groups.
 
     # Variables that need only the beam dimension added to them.
-    beam_only_names = {
-        "backscatter_r",
-        "backscatter_i",
-        "angle_athwartship",
-        "angle_alongship",
-        "frequency_start",
-        "frequency_end",
-    }
+    beam_only_names = set()
 
     # Variables that need only the ping_time dimension added to them.
-    ping_time_only_names = {"beam_type"}
-
-    # Variables that need beam and ping_time dimensions added to them.
-    beam_ping_time_names = {
+    ping_time_only_names = {
+        "beam_type",
         "beam_direction_x",
         "beam_direction_y",
         "beam_direction_z",
@@ -53,6 +44,9 @@ class SetGroupsEK80(SetGroupsBase):
         "beamwidth_twoway_athwartship",
     }
 
+    # Variables that need beam and ping_time dimensions added to them.
+    beam_ping_time_names = set()
+
     beamgroups_possible = [
         {
             "name": "Beam_group1",

echopype/tests/calibrate/test_cal_params_integration.py

@@ -110,9 +110,7 @@ def test_cal_params_intake_EK80_BB_complex(ek80_cal_path):
     beam = ed["Sonar/Beam_group1"].sel(channel=chan_sel)
     vend = ed["Vendor_specific"].sel(channel=chan_sel)
     freq_center = (
-        (beam["frequency_start"] + beam["frequency_end"])
-        .sel(channel=chan_sel).isel(beam=0).drop("beam") / 2
-    )
+        (beam["frequency_start"] + beam["frequency_end"]).sel(channel=chan_sel) / 2)
     cal_params_manual = ep.calibrate.cal_params.get_cal_params_EK(
         "BB", freq_center, beam, vend, {"gain_correction": gain_freq_dep}
     )

echopype/tests/calibrate/test_ecs_integration.py

@@ -154,7 +154,7 @@ def test_ecs_intake_ek80_BB_complex(ek80_path, ecs_path):
     chan_w_BB_param = "WBT 549762-15 ES70-7C_ES"
     freq_center = (
         (beam["frequency_start"] + beam["frequency_end"]) / 2
-    ).sel(channel=chan_w_BB_param).isel(beam=0).drop_vars(["beam", "channel"])
+    ).sel(channel=chan_w_BB_param).drop_vars(["channel"])
 
     for p_name in [
         "gain_correction", "angle_offset_alongship", "angle_offset_athwartship",

echopype/tests/convert/test_convert_azfp.py

@@ -60,7 +60,7 @@ def test_convert_azfp_01a_matlab_raw(azfp_path):
         np.array(
             [ds_matlab_output['Output'][0]['N'][fidx] for fidx in range(4)]
         ),
-        echodata["Sonar/Beam_group1"].backscatter_r.isel(beam=0).drop_vars('beam').values,
+        echodata["Sonar/Beam_group1"].backscatter_r.values,
     )
 
     # Test vendor group
@@ -128,7 +128,7 @@ def test_convert_azfp_01a_raw_echoview(azfp_path):
     echodata = open_raw(
         raw_file=azfp_01a_path, sonar_model='AZFP', xml_path=azfp_xml_path
     )
-    assert np.array_equal(test_power, echodata["Sonar/Beam_group1"].backscatter_r.isel(beam=0).drop_vars('beam')) # noqa
+    assert np.array_equal(test_power, echodata["Sonar/Beam_group1"].backscatter_r)
 
     # check convention-required variables in the Platform group
     check_platform_required_scalar_vars(echodata)
@@ -145,10 +145,10 @@ def test_convert_azfp_01a_different_ranges(azfp_path):
     )
     assert echodata["Sonar/Beam_group1"].backscatter_r.sel(channel='55030-125-1').dropna(
         'range_sample'
-    ).shape == (360, 438, 1)
+    ).shape == (360, 438)
     assert echodata["Sonar/Beam_group1"].backscatter_r.sel(channel='55030-769-4').dropna(
         'range_sample'
-    ).shape == (360, 135, 1)
+    ).shape == (360, 135)
 
     # check convention-required variables in the Platform group
     check_platform_required_scalar_vars(echodata)

echopype/tests/convert/test_convert_ek60.py

@@ -69,7 +69,7 @@ def test_convert_ek60_matlab_raw(ek60_path):
             ds_matlab['rawData'][0]['pings'][0]['power'][0][fidx]
             for fidx in range(5)
         ],
-        echodata["Sonar/Beam_group1"].backscatter_r.isel(beam=0).transpose(
+        echodata["Sonar/Beam_group1"].backscatter_r.transpose(
             'channel', 'range_sample', 'ping_time'
         ),
         rtol=0,
@@ -82,7 +82,7 @@ def test_convert_ek60_matlab_raw(ek60_path):
                 ds_matlab['rawData'][0]['pings'][0][angle][0][fidx]
                 for fidx in range(5)
             ],
-            echodata["Sonar/Beam_group1"]['angle_' + angle].isel(beam=0).transpose(
+            echodata["Sonar/Beam_group1"]['angle_' + angle].transpose(
                 'channel', 'range_sample', 'ping_time'
             ),
         )
@@ -121,8 +121,7 @@ def test_convert_ek60_echoview_raw(ek60_path):
             echodata["Sonar/Beam_group1"].backscatter_r.isel(
                 channel=sorted_freq_ind[fidx],
                 ping_time=slice(None, 10),
-                range_sample=slice(1, None),
-                beam=0
+                range_sample=slice(1, None)
             ),
             atol=9e-6,
             rtol=atol,

echopype/tests/convert/test_convert_ek80.py

@@ -189,8 +189,7 @@ def test_convert_ek80_cw_power_angle_echoview(ek80_path):
         test_power = pd.read_csv(file, delimiter=';').iloc[:, 13:].values
         assert np.allclose(
             test_power,
-            echodata["Sonar/Beam_group1"].backscatter_r.sel(channel=chan,
-                                            beam='1').dropna('range_sample'),
+            echodata["Sonar/Beam_group1"].backscatter_r.sel(channel=chan).dropna('range_sample'),
             rtol=0,
             atol=1.1e-5,
         )
@@ -216,15 +215,15 @@ def test_convert_ek80_cw_power_angle_echoview(ek80_path):
         for ping_idx in df_angle['Ping_index'].value_counts().index:
             assert np.allclose(
                 df_angle.loc[df_angle['Ping_index'] == ping_idx, ' Major'],
-                major.sel(channel=chan, beam='1')
+                major.sel(channel=chan)
                 .isel(ping_time=ping_idx)
                 .dropna('range_sample'),
                 rtol=0,
                 atol=5e-5,
             )
             assert np.allclose(
                 df_angle.loc[df_angle['Ping_index'] == ping_idx, ' Minor'],
-                minor.sel(channel=chan, beam='1')
+                minor.sel(channel=chan)
                 .isel(ping_time=ping_idx)
                 .dropna('range_sample'),
                 rtol=0,

echopype/tests/echodata/test_echodata.py

@@ -459,12 +459,16 @@ def test_nan_range_entries(range_check_files):
             echodata, env_params=None, cal_params=None, ecs_file=None, waveform_mode="BB", encode_mode="complex",
         )
         range_output = cal_obj.range_meter
-        nan_locs_backscatter_r = ~echodata["Sonar/Beam_group1"].backscatter_r.isel(beam=0).drop("beam").isnull()
+        if "beam" in echodata["Sonar/Beam_group1"].dims:
+            nan_locs_backscatter_r = ~echodata["Sonar/Beam_group1"].backscatter_r.isel(beam=0).drop(
+                "beam").isnull()
+        else:
+            nan_locs_backscatter_r = ~echodata["Sonar/Beam_group1"].backscatter_r.isnull()
     else:
         ds_Sv = echopype.calibrate.compute_Sv(echodata)
         cal_obj = CalibrateEK60(echodata, env_params={}, cal_params=None, ecs_file=None)
         range_output = cal_obj.range_meter
-        nan_locs_backscatter_r = ~echodata["Sonar/Beam_group1"].backscatter_r.isel(beam=0).drop("beam").isnull()
+        nan_locs_backscatter_r = ~echodata["Sonar/Beam_group1"].backscatter_r.isnull()
 
     nan_locs_Sv_range = ~ds_Sv.echo_range.isnull()
     nan_locs_range = ~range_output.isnull()