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Move Beam group to Sonar/Beam_group1 and Beam_power to Sonar/Beam_power #574

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merged 15 commits into from
Mar 12, 2022
Merged

Move Beam group to Sonar/Beam_group1 and Beam_power to Sonar/Beam_power #574

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429b251
Move Beam group to Sonar/Beam
emiliom Jan 29, 2022
0cf9509
Move Beam group to Sonar/Beam
emiliom Jan 30, 2022
894b588
echodata tests now work with new nc test file
emiliom Jan 30, 2022
82cdefe
echodata tests now work with new nc test file
emiliom Jan 30, 2022
3693fe0
Merge branch 'beam_group' of github.com:emiliom/echopype into beam_group
emiliom Jan 30, 2022
9c3a39a
Fix harmless mistake in a comment, in test
emiliom Jan 30, 2022
1ad41dd
Run TestEchodata on new nc file within the standard folder structure …
emiliom Feb 1, 2022
79df08d
Merge dev into beam_group
emiliom Mar 4, 2022
810b673
Update test_echodata with sonar/beam nc and zarr datasets
emiliom Mar 5, 2022
8b13e16
Rename groups Sonar/Beam to Sonar/Beam_group1 and Beam_power to Sonar…
emiliom Mar 5, 2022
473758b
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 5, 2022
ceebca2
Add new beam group variables to Sonar group
emiliom Mar 9, 2022
f2f4ebf
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 9, 2022
37c4501
Changed Beam_power to Beam_group2 and updated Beam group descriptions
emiliom Mar 12, 2022
775c960
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 12, 2022
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198 changes: 0 additions & 198 deletions echopype/convert/add_ancillary.py
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12 changes: 7 additions & 5 deletions echopype/convert/api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,8 @@

NMEA_SENTENCE_DEFAULT = ["GGA", "GLL", "RMC"]

BEAM_SUBGROUP_DEFAULT = "Beam_group1"


def to_file(
echodata: EchoData,
Expand Down Expand Up @@ -132,7 +134,7 @@ def _save_groups_to_file(echodata, output_path, engine, compress=True):
engine=engine,
)

# Beam group
# /Sonar/Beam_groupX group
if echodata.sonar_model == "AD2CP":
io.save_file(
echodata.beam.chunk(
Expand All @@ -143,7 +145,7 @@ def _save_groups_to_file(echodata, output_path, engine, compress=True):
path=output_path,
mode="a",
engine=engine,
group="Beam",
group=f"Sonar/{BEAM_SUBGROUP_DEFAULT}",
compression_settings=COMPRESSION_SETTINGS[engine] if compress else None,
)
else:
Expand All @@ -157,7 +159,7 @@ def _save_groups_to_file(echodata, output_path, engine, compress=True):
path=output_path,
mode="a",
engine=engine,
group="Beam",
group=f"Sonar/{BEAM_SUBGROUP_DEFAULT}",
compression_settings=COMPRESSION_SETTINGS[engine] if compress else None,
)
if echodata.beam_power is not None:
Expand All @@ -171,7 +173,7 @@ def _save_groups_to_file(echodata, output_path, engine, compress=True):
path=output_path,
mode="a",
engine=engine,
group="Beam_power",
group="Sonar/Beam_group2",
compression_settings=COMPRESSION_SETTINGS[engine] if compress else None,
)

Expand Down Expand Up @@ -446,7 +448,7 @@ def open_raw(
echodata.nmea = setgrouper.set_nmea()
echodata.provenance = setgrouper.set_provenance()
echodata.sonar = setgrouper.set_sonar()
# Beam_power group only exist if EK80 has both complex and power/angle data
# Beam_group2 group only exist if EK80 has both complex and power/angle data
if sonar_model in ["EK80", "ES80", "EA640"]:
echodata.beam, echodata.beam_power = setgrouper.set_beam()
else:
Expand Down
10 changes: 5 additions & 5 deletions echopype/convert/convert_combine.py
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ def perform_combination(sonar_model, input_paths, output_path, engine):
# TODO: there should be compression option for the combined file too...

def coerce_type(ds, group):
if group == "Beam":
if group == "Sonar/Beam_group1":
if sonar_model == "EK80":
ds["transceiver_software_version"] = ds[
"transceiver_software_version"
Expand Down Expand Up @@ -91,15 +91,15 @@ def coerce_type(ds, group):
# with nicely monotonically varying ping_time/location_time/mru_time.
# However we know there are lots of problems with pings going backward in time for EK60/EK80 files,
# and we will need to clean up data before calling merge.
# Combine Beam
# Combine /Sonar/Beam_group1
with xr.open_mfdataset(
input_paths,
group="Beam",
group="Sonar/Beam_group1",
concat_dim="ping_time",
data_vars="minimal",
engine=engine,
) as ds_beam:
coerce_type(ds_beam, "Beam")
coerce_type(ds_beam, "Sonar/Beam_group1")
io.save_file(
ds_beam.chunk(
{
Expand All @@ -110,7 +110,7 @@ def coerce_type(ds, group):
path=output_path,
mode="a",
engine=engine,
group="Beam",
group="Sonar/Beam_group1",
)

# Combine Environment group
Expand Down
15 changes: 13 additions & 2 deletions echopype/convert/set_groups_azfp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,13 @@ class SetGroupsAZFP(SetGroupsBase):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)

self._beamgroups = [
{
"name": "Beam_group1",
"descr": "contains backscatter power (uncalibrated) and other beam or channel-specific data.",
}
]

def set_env(self) -> xr.Dataset:
"""Set the Environment group."""
# TODO Look at why this cannot be encoded without the modifications
Expand Down Expand Up @@ -44,6 +51,11 @@ def set_env(self) -> xr.Dataset:

def set_sonar(self) -> xr.Dataset:
"""Set the Sonar group."""

# Add beam_group_name and beam_group_descr variables sharing a common dimension (beam),
# using the information from self._beamgroups
ds = xr.Dataset(self._beam_groups_vars())

# Assemble sonar group dictionary
sonar_dict = {
"sonar_manufacturer": "ASL Environmental Sciences",
Expand All @@ -53,9 +65,8 @@ def set_sonar(self) -> xr.Dataset:
"sonar_software_version": "1.4",
"sonar_type": "echosounder",
}
# Save
ds = xr.Dataset()
ds = ds.assign_attrs(sonar_dict)

return ds

def set_platform(self) -> xr.Dataset:
Expand Down
23 changes: 22 additions & 1 deletion echopype/convert/set_groups_base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,9 @@ def __init__(
self.compression_settings = COMPRESSION_SETTINGS[self.engine]

self._varattrs = sonarnetcdf_1.yaml_dict["variable_and_varattributes"]
# self._beamgroups must be a list of dicts, eg:
# [{"name":"Beam_group1", "descr":"contains complex backscatter data and other beam or channel-specific data."}]
self._beamgroups = []

# TODO: change the set_XXX methods to return a dataset to be saved
# in the overarching save method
Expand Down Expand Up @@ -94,7 +97,7 @@ def set_sonar(self) -> xr.Dataset:

@abc.abstractmethod
def set_beam(self) -> xr.Dataset:
"""Set the Beam group."""
"""Set the /Sonar/Beam group."""
raise NotImplementedError

@abc.abstractmethod
Expand Down Expand Up @@ -200,3 +203,21 @@ def _parse_NMEA(self):
)

return location_time, msg_type, lat, lon

def _beam_groups_vars(self):
"""Stage beam_group_name and beam_group_descr variables sharing a common dimension
to be inserted in the Sonar group"""
beam_groups_vars = {
"beam_group_name": (
["beam"],
[di["name"] for di in self._beamgroups],
{"long_name": "Beam group name"},
),
"beam_group_descr": (
["beam"],
[di["descr"] for di in self._beamgroups],
{"long_name": "Beam group description"},
),
}

return beam_groups_vars
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I like this! :D

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