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Centralize/generalize declaration of convention attributes #493

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merged 6 commits into from
Dec 3, 2021
Merged

Centralize/generalize declaration of convention attributes #493

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4911751
update_platform missing variable attributes
emiliom Nov 13, 2021
5afcf4f
Centralize declaration of convention attributes in new module
emiliom Nov 13, 2021
fd0c72d
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 14, 2021
8e61062
Merge branch 'dev' into generalize_conv
emiliom Dec 3, 2021
84f7685
Update set_groups_azfp.py
emiliom Dec 3, 2021
6449630
Update set_groups_ek80.py
emiliom Dec 3, 2021
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3 changes: 2 additions & 1 deletion echopype/convert/set_groups_azfp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,9 @@
import numpy as np
import xarray as xr

from ..echodata.convention.attrs import DEFAULT_BEAM_COORD_ATTRS
from ..utils.coding import set_encodings
from .set_groups_base import DEFAULT_BEAM_COORD_ATTRS, SetGroupsBase
from .set_groups_base import SetGroupsBase


class SetGroupsAZFP(SetGroupsBase):
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16 changes: 0 additions & 16 deletions echopype/convert/set_groups_base.py
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Expand Up @@ -10,22 +10,6 @@

DEFAULT_CHUNK_SIZE = {"range_bin": 25000, "ping_time": 2500}

# TODO: Move to a new utility module in, say, echodata.convention
DEFAULT_BEAM_COORD_ATTRS = {
"frequency": {
"long_name": "Transducer frequency",
"standard_name": "sound_frequency",
"units": "Hz",
"valid_min": 0.0,
},
"ping_time": {
"long_name": "Timestamp of each ping",
"standard_name": "time",
"axis": "T",
},
"range_bin": {"long_name": "Along-range bin (sample) number, base 0"},
}


class SetGroupsBase(abc.ABC):
"""Base class for saving groups to netcdf or zarr from echosounder data files."""
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54 changes: 13 additions & 41 deletions echopype/convert/set_groups_ek60.py
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Expand Up @@ -6,10 +6,15 @@
import xarray as xr
from _echopype_version import version as ECHOPYPE_VERSION

from ..echodata.convention.attrs import (
DEFAULT_BEAM_COORD_ATTRS,
DEFAULT_PLATFORM_COORD_ATTRS,
DEFAULT_PLATFORM_VAR_ATTRS,
)
from ..utils.coding import set_encodings

# fmt: off
from .set_groups_base import DEFAULT_BEAM_COORD_ATTRS, DEFAULT_CHUNK_SIZE, SetGroupsBase
from .set_groups_base import DEFAULT_CHUNK_SIZE, SetGroupsBase

# fmt: on

Expand Down Expand Up @@ -183,34 +188,20 @@ def set_platform(self, NMEA_only=False) -> xr.Dataset:
"latitude": (
["location_time"],
lat,
{
"long_name": "Platform latitude",
"standard_name": "latitude",
"units": "degrees_north",
"valid_range": (-90.0, 90.0),
},
DEFAULT_PLATFORM_VAR_ATTRS["latitude"],
),
"longitude": (
["location_time"],
lon,
{
"long_name": "Platform longitude",
"standard_name": "longitude",
"units": "degrees_east",
"valid_range": (-180.0, 180.0),
},
DEFAULT_PLATFORM_VAR_ATTRS["longitude"],
),
"sentence_type": (["location_time"], msg_type),
},
coords={
"location_time": (
["location_time"],
location_time,
{
"axis": "T",
"long_name": "Timestamps for NMEA position datagrams",
"standard_name": "time",
},
DEFAULT_PLATFORM_COORD_ATTRS["location_time"],
)
},
)
Expand All @@ -235,41 +226,22 @@ def set_platform(self, NMEA_only=False) -> xr.Dataset:
"pitch": (
["ping_time"],
self.parser_obj.ping_data_dict["pitch"][ch],
{
"long_name": "Platform pitch",
"standard_name": "platform_pitch_angle",
"units": "arc_degree",
"valid_range": (-90.0, 90.0),
},
DEFAULT_PLATFORM_VAR_ATTRS["pitch"],
),
"roll": (
["ping_time"],
self.parser_obj.ping_data_dict["roll"][ch],
{
"long_name": "Platform roll",
"standard_name": "platform_roll_angle",
"units": "arc_degree",
"valid_range": (-90.0, 90.0),
},
DEFAULT_PLATFORM_VAR_ATTRS["roll"],
),
"heave": (
["ping_time"],
self.parser_obj.ping_data_dict["heave"][ch],
{
"long_name": "Platform heave",
"standard_name": "platform_heave_angle",
"units": "arc_degree",
"valid_range": (-90.0, 90.0),
},
DEFAULT_PLATFORM_VAR_ATTRS["heave"],
),
"water_level": (
["ping_time"],
self.parser_obj.ping_data_dict["transducer_depth"][ch],
{
"long_name": "z-axis distance from the platform coordinate system "
"origin to the sonar transducer",
"units": "m",
},
DEFAULT_PLATFORM_VAR_ATTRS["water_level"],
),
},
coords={
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3 changes: 2 additions & 1 deletion echopype/convert/set_groups_ek80.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,9 @@
import numpy as np
import xarray as xr

from ..echodata.convention.attrs import DEFAULT_BEAM_COORD_ATTRS
from ..utils.coding import set_encodings
from .set_groups_base import DEFAULT_BEAM_COORD_ATTRS, SetGroupsBase
from .set_groups_base import SetGroupsBase


class SetGroupsEK80(SetGroupsBase):
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65 changes: 65 additions & 0 deletions echopype/echodata/convention/attrs.py
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@@ -0,0 +1,65 @@
"""
Define convention-based global, coordinate and variable attributes
in one place for consistent reuse
"""

DEFAULT_BEAM_COORD_ATTRS = {
"frequency": {
"long_name": "Transducer frequency",
"standard_name": "sound_frequency",
"units": "Hz",
"valid_min": 0.0,
},
"ping_time": {
"long_name": "Timestamp of each ping",
"standard_name": "time",
"axis": "T",
},
"range_bin": {"long_name": "Along-range bin (sample) number, base 0"},
}

DEFAULT_PLATFORM_COORD_ATTRS = {
"location_time": {
"axis": "T",
"long_name": "Timestamps for NMEA datagrams",
"standard_name": "time",
}
}

DEFAULT_PLATFORM_VAR_ATTRS = {
"latitude": {
"long_name": "Platform latitude",
"standard_name": "latitude",
"units": "degrees_north",
"valid_range": (-90.0, 90.0),
},
"longitude": {
"long_name": "Platform longitude",
"standard_name": "longitude",
"units": "degrees_east",
"valid_range": (-180.0, 180.0),
},
"pitch": {
"long_name": "Platform pitch",
"standard_name": "platform_pitch_angle",
"units": "arc_degree",
"valid_range": (-90.0, 90.0),
},
"roll": {
"long_name": "Platform roll",
"standard_name": "platform_roll_angle",
"units": "arc_degree",
"valid_range": (-90.0, 90.0),
},
"heave": {
"long_name": "Platform heave",
"standard_name": "platform_heave_angle",
"units": "arc_degree",
"valid_range": (-90.0, 90.0),
},
"water_level": {
"long_name": "z-axis distance from the platform coordinate system "
"origin to the sonar transducer",
"units": "m",
},
}
10 changes: 1 addition & 9 deletions echopype/echodata/echodata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@
from ..utils.repr import HtmlTemplate
from ..utils.uwa import calc_sound_speed
from .convention import _get_convention
from .convention.attrs import DEFAULT_PLATFORM_COORD_ATTRS

XARRAY_ENGINE_MAP: Dict["FileFormatHint", "EngineHint"] = {
".nc": "netcdf4",
Expand All @@ -30,15 +31,6 @@
"EK80": 0,
}

# TODO: Move to a new utility module in, say, echodata.convention
DEFAULT_PLATFORM_COORD_ATTRS = {
"location_time": {
"axis": "T",
"long_name": "Timestamps for NMEA datagrams",
"standard_name": "time",
}
}


class EchoData:
"""Echo data model class for handling raw converted data,
Expand Down