Add missing, mandatory Beam_groupX variables (#1103)

* Add missing, mandatory Beam_group beam_stabilisation and non_quantitative_processing, as scalars * Add mandatory Beam_groupX sample_time_offset to replace the now redundant (for EK60/80) range_sample_offset
OSOceanAcoustics · Aug 3, 2023 · e0e84f0 · e0e84f0
1 parent 8d80c35
commit e0e84f0
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Showing 4 changed files with 78 additions and 4 deletions.
diff --git a/echopype/convert/set_groups_azfp.py b/echopype/convert/set_groups_azfp.py
@@ -382,6 +382,34 @@ def set_beam(self) -> List[xr.Dataset]:
                         "valid_min": 0.0,
                     },
                 ),
+                "beam_stabilisation": (
+                    [],
+                    np.array(0, np.byte),
+                    {
+                        "long_name": "Beam stabilisation applied (or not)",
+                        "flag_values": [0, 1],
+                        "flag_meanings": ["not stabilised", "stabilised"],
+                    },
+                ),
+                "non_quantitative_processing": (
+                    [],
+                    np.array(0, np.int16),
+                    {
+                        "long_name": "Presence or not of non-quantitative processing applied"
+                        " to the backscattering data (sonar specific)",
+                        "flag_values": [0],
+                        "flag_meanings": ["None"],
+                    },
+                ),
+                "sample_time_offset": (
+                    [],
+                    0.0,
+                    {
+                        "long_name": "Time offset that is subtracted from the timestamp"
+                        " of each sample",
+                        "units": "s",
+                    },
+                ),
             },
             coords={
                 "channel": (

diff --git a/echopype/convert/set_groups_ek60.py b/echopype/convert/set_groups_ek60.py
@@ -596,6 +596,25 @@ def set_beam(self) -> List[xr.Dataset]:
                         ],
                     },
                 ),
+                "beam_stabilisation": (
+                    [],
+                    np.array(0, np.byte),
+                    {
+                        "long_name": "Beam stabilisation applied (or not)",
+                        "flag_values": [0, 1],
+                        "flag_meanings": ["not stabilised", "stabilised"],
+                    },
+                ),
+                "non_quantitative_processing": (
+                    [],
+                    np.array(0, np.int16),
+                    {
+                        "long_name": "Presence or not of non-quantitative processing applied"
+                        " to the backscattering data (sonar specific)",
+                        "flag_values": [0],
+                        "flag_meanings": ["None"],
+                    },
+                ),
             },
             coords={
                 "channel": (

diff --git a/echopype/convert/set_groups_ek80.py b/echopype/convert/set_groups_ek80.py
@@ -592,6 +592,25 @@ def _assemble_ds_ping_invariant(self, params, data_type):
                     ["channel"],
                     beam_params["transceiver_software_version"],
                 ),
+                "beam_stabilisation": (
+                    [],
+                    np.array(0, np.byte),
+                    {
+                        "long_name": "Beam stabilisation applied (or not)",
+                        "flag_values": [0, 1],
+                        "flag_meanings": ["not stabilised", "stabilised"],
+                    },
+                ),
+                "non_quantitative_processing": (
+                    [],
+                    np.array(0, np.int16),
+                    {
+                        "long_name": "Presence or not of non-quantitative processing applied"
+                        " to the backscattering data (sonar specific)",
+                        "flag_values": [0],
+                        "flag_meanings": ["None"],
+                    },
+                ),
             },
             coords={
                 "channel": (
@@ -921,10 +940,17 @@ def _assemble_ds_common(self, ch, range_sample_size):
                         "flag_meanings": ["CW", "FM", "FMD"],
                     },
                 ),
-                "range_sample_offset": (
+                "sample_time_offset": (
                     ["ping_time"],
-                    np.array(self.parser_obj.ping_data_dict["offset"][ch], dtype=int),
-                    {"long_name": "First sample number"},
+                    (
+                        np.array(self.parser_obj.ping_data_dict["offset"][ch])
+                        * np.array(self.parser_obj.ping_data_dict["sample_interval"][ch])
+                    ),
+                    {
+                        "long_name": "Time offset that is subtracted from the timestamp"
+                        " of each sample",
+                        "units": "s",
+                    },
                 ),
             },
             coords={

diff --git a/echopype/utils/coding.py b/echopype/utils/coding.py
@@ -43,7 +43,8 @@
     "cal_channel_id": np.str_,
     "beam": np.str_,
     "channel_mode": np.byte,
-    "range_sample_offset": np.int32,
+    "beam_stabilisation": np.byte,
+    "non_quantitative_processing": np.int16,
 }  # channel name  # beam name
 
 PREFERRED_CHUNKS = "preferred_chunks"