water-column-sonar-annotation 26.1.8__tar.gz

water_column_sonar_annotation-26.1.8/LICENSE

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+MIT License
+
+Copyright (c) 2024 Cooperative Institutes, Coastal and Marine Geophysics
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

water_column_sonar_annotation-26.1.8/PKG-INFO

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+Metadata-Version: 2.4
+Name: water-column-sonar-annotation
+Version: 26.1.8
+Summary: Processing Tool for Working with Water Column Sonar Annotations
+Author-email: Rudy Klucik <rudy.klucik@noaa.gov>
+Maintainer-email: Rudy Klucik <rudy.klucik@noaa.gov>
+License-Expression: MIT
+Project-URL: Homepage, https://echo.fish
+Project-URL: Repository, https://github.com/CI-CMG/water-column-sonar-annotation
+Project-URL: Documentation, https://github.com/CI-CMG/water-column-sonar-annotation
+Project-URL: Issues, https://github.com/CI-CMG/water-column-sonar-annotation/issues
+Keywords: ocean,sonar,water column
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: build
+Requires-Dist: fiona
+Requires-Dist: folium
+Requires-Dist: geopandas
+Requires-Dist: netcdf4
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: pandas-stubs
+Requires-Dist: pooch
+Requires-Dist: pvlib
+Requires-Dist: pyarrow
+Requires-Dist: pyogrio
+Requires-Dist: python-dotenv
+Requires-Dist: s3fs
+Requires-Dist: scipy
+Requires-Dist: shapely
+Requires-Dist: setuptools
+Requires-Dist: timezonefinder
+Requires-Dist: xarray
+Requires-Dist: zarr
+Dynamic: license-file
+
+# Water Column Sonar Annotation
+
+Tool for converting EVR files to annotated regions of interest in parquet format
+
+![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/CI-CMG/water-column-sonar-annotation/test_action.yaml)
+![PyPI - Implementation](https://img.shields.io/pypi/v/water-column-sonar-annotation) ![GitHub code size in bytes](https://img.shields.io/github/languages/code-size/CI-CMG/water-column-sonar-annotation) ![GitHub repo size](https://img.shields.io/github/repo-size/CI-CMG/water-column-sonar-annotation)
+
+# Setting up the Python Environment
+
+> Python 3.12.12
+
+# Installing Dependencies
+
+```
+source .venv/bin/activate
+
+uv pip install --upgrade pip
+
+uv pip install -r pyproject.toml --all-extras
+
+uv run pre-commit install
+```
+
+# Pytest
+
+```
+uv run pytest tests -W ignore::DeprecationWarning
+```
+
+or
+> uv run pytest tests/cruise --cov=water_column_sonar_annotation --cov-report term-missing
+
+```
+uv run pre-commit install --allow-missing-config
+# or
+uv run pre-commit install
+```
+
+# Test Coverage
+
+TODO
+
+# Tag a Release
+
+Step 1 --> increment the semantic version in the zarr_manager.py "metadata" & the "pyproject.toml"
+
+```commandline
+git tag -a v26.1.0 -m "Releasing v26.1.0"
+git push origin --tags
+gh release create v26.1.0
+```
+
+# To Publish To PROD
+
+```commandline
+uv build --no-sources
+uv publish
+```
+
+# UV Debugging
+
+```
+uv lock --check
+uv lock
+uv sync --extra dev
+#uv run pytest tests
+```
+
+## Annotation format
+
+- https://roboflow.com/formats/coco-json
+- https://www.v7labs.com/blog/coco-dataset-guide

water_column_sonar_annotation-26.1.8/README.md

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+# Water Column Sonar Annotation
+
+Tool for converting EVR files to annotated regions of interest in parquet format
+
+![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/CI-CMG/water-column-sonar-annotation/test_action.yaml)
+![PyPI - Implementation](https://img.shields.io/pypi/v/water-column-sonar-annotation) ![GitHub code size in bytes](https://img.shields.io/github/languages/code-size/CI-CMG/water-column-sonar-annotation) ![GitHub repo size](https://img.shields.io/github/repo-size/CI-CMG/water-column-sonar-annotation)
+
+# Setting up the Python Environment
+
+> Python 3.12.12
+
+# Installing Dependencies
+
+```
+source .venv/bin/activate
+
+uv pip install --upgrade pip
+
+uv pip install -r pyproject.toml --all-extras
+
+uv run pre-commit install
+```
+
+# Pytest
+
+```
+uv run pytest tests -W ignore::DeprecationWarning
+```
+
+or
+> uv run pytest tests/cruise --cov=water_column_sonar_annotation --cov-report term-missing
+
+```
+uv run pre-commit install --allow-missing-config
+# or
+uv run pre-commit install
+```
+
+# Test Coverage
+
+TODO
+
+# Tag a Release
+
+Step 1 --> increment the semantic version in the zarr_manager.py "metadata" & the "pyproject.toml"
+
+```commandline
+git tag -a v26.1.0 -m "Releasing v26.1.0"
+git push origin --tags
+gh release create v26.1.0
+```
+
+# To Publish To PROD
+
+```commandline
+uv build --no-sources
+uv publish
+```
+
+# UV Debugging
+
+```
+uv lock --check
+uv lock
+uv sync --extra dev
+#uv run pytest tests
+```
+
+## Annotation format
+
+- https://roboflow.com/formats/coco-json
+- https://www.v7labs.com/blog/coco-dataset-guide

water_column_sonar_annotation-26.1.8/pyproject.toml

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+[project]
+name = "water-column-sonar-annotation"
+version = "26.1.8"
+authors = [
+    { name = "Rudy Klucik", email = "rudy.klucik@noaa.gov" },
+]
+maintainers = [
+    { name = "Rudy Klucik", email = "rudy.klucik@noaa.gov" },
+]
+description = "Processing Tool for Working with Water Column Sonar Annotations"
+keywords = ["ocean", "sonar", "water column"]
+readme = "README.md"
+requires-python = ">=3.12"
+license = "MIT"
+license-files = ["LICENSE"]
+
+# uv sync --all-groups --upgrade
+dependencies = [
+    "build",
+    "fiona",
+    "folium",
+    "geopandas",
+    "netcdf4",
+    "numpy",
+    "pandas",
+    "pandas-stubs",
+    "pooch",
+    "pvlib",
+    "pyarrow",
+    "pyogrio",
+    "python-dotenv",
+    "s3fs", # problem here, uv finds the wrong one
+    "scipy",
+    "shapely",
+    "setuptools",
+    "timezonefinder",
+    #    "wheel",
+    "xarray",
+    "zarr",
+]
+
+# uv sync --all-groups --upgrade
+[dependency-groups]
+dev = [
+    "bandit[toml]",
+    "build",
+    "pooch",
+    "pre-commit",
+    "pytest",
+    "pytest-cov",
+    "ruff",
+    "tqdm",
+]
+
+[project.urls]
+Homepage = "https://echo.fish"
+Repository = "https://github.com/CI-CMG/water-column-sonar-annotation"
+Documentation = "https://github.com/CI-CMG/water-column-sonar-annotation"
+Issues = "https://github.com/CI-CMG/water-column-sonar-annotation/issues"
+
+[tool.bandit]
+exclude_dirs = ["tests"]
+
+[tool.pre-commit-hooks.bandit]
+exclude = ["*/tests/*"]
+
+[tool.setuptools.packages.find]
+exclude = ["data*"]

water_column_sonar_annotation-26.1.8/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

water_column_sonar_annotation-26.1.8/tests/astronomical/test_astronomical_manager.py

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+import numpy as np
+
+from water_column_sonar_annotation.astronomical import AstronomicalManager
+
+
+#######################################################
+def setup_module():
+    print("setup")
+
+
+def teardown_module():
+    print("teardown")
+
+
+def test_get_solar_azimuth():
+    astronomical_manager = AstronomicalManager()
+    # https://www.suncalc.org/#/39.9812,-105.2495,13/2026.01.26/11:52/1/3
+    azimuth_noon = astronomical_manager.get_solar_azimuth(
+        iso_time="2026-01-26T19:00:00Z",  # noon
+        latitude=39.9674884,  # Boulder
+        longitude=-105.2532602,
+    )
+    assert np.isclose(azimuth_noon, 31.38)  # 15)
+
+    azimuth_sunset = astronomical_manager.get_solar_azimuth(
+        iso_time="2026-01-26T00:00:00Z",  # sunset
+        latitude=39.9674884,
+        longitude=-105.2532602,
+    )
+    assert np.isclose(azimuth_sunset, 1.25)  # 27)
+
+
+def test_get_solar_azimuth_boulder_2pm():
+    # 2026-01-29 @2pm is UTC: "2026-01-29T21:02:23Z"
+    astronomical_manager = AstronomicalManager()
+    # https://www.suncalc.org/#/39.9812,-105.2495,13/2026.01.26/11:52/1/3
+    azimuth_noon = astronomical_manager.get_solar_azimuth(
+        iso_time="2026-01-29T21:02:23Z",  # 2pm
+        latitude=39.9674884,  # Boulder
+        longitude=-105.2532602,
+    )
+    assert np.isclose(azimuth_noon, 27.01)
+
+
+### PHASE OF DAY ###
+# { 'dawn': 1, 'day': 2, 'dusk': 3, 'night': 4 }
+def test_phase_of_day_at_noon():
+    astronomical_manager = AstronomicalManager()
+    phase = astronomical_manager.phase_of_day(
+        iso_time="2026-01-27T19:00:00Z",  # noon
+        latitude=39.9674884,  # Boulder
+        longitude=-105.2532602,
+    )
+    assert phase == 2
+
+
+def test_phase_of_day_at_midnight():
+    astronomical_manager = AstronomicalManager()
+    phase = astronomical_manager.phase_of_day(
+        iso_time="2026-01-28T07:00:00Z",
+        latitude=39.9674884,  # Boulder
+        longitude=-105.2532602,
+    )
+    assert phase == 4
+
+
+def test_phase_of_day_before_sunset():
+    astronomical_manager = AstronomicalManager()
+    phase = astronomical_manager.phase_of_day(
+        # sunset is at 5:13pm on jan 27th, per https://psl.noaa.gov/boulder/boulder.sunset.html
+        iso_time="2026-01-28T00:09:00Z",  # sunset @ 5:13pm, nautical sunset @6:16pm
+        latitude=39.9674884,  # Boulder
+        longitude=-105.2532602,
+    )
+    assert phase == 2  # day
+
+
+def test_phase_of_day_after_sunset():
+    astronomical_manager = AstronomicalManager()
+    phase = astronomical_manager.phase_of_day(
+        # sunset is at 5:13pm on jan 27th, per https://psl.noaa.gov/boulder/boulder.sunset.html
+        iso_time="2026-01-28T00:10:00Z",  # sunset @ 5:13pm, nautical sunset @6:16pm
+        latitude=39.9674884,  # Boulder
+        longitude=-105.2532602,
+    )
+    assert phase == 3  # dusk
+
+
+def test_phase_of_day_before_nautical_sunset():
+    astronomical_manager = AstronomicalManager()
+    # an hour'ish later is nautical sunset
+    phase_before_nautical_sunset = astronomical_manager.phase_of_day(
+        iso_time="2026-01-28T01:15:00Z",  # sunset @5:13pm, nautical sunset @6:16pm
+        latitude=39.9674884,  # Boulder
+        longitude=-105.2532602,
+    )
+    assert phase_before_nautical_sunset == 3  # dusk
+
+
+def test_phase_of_day_after_nautical_sunset():
+    astronomical_manager = AstronomicalManager()
+    phase_after_nautical_sunset = astronomical_manager.phase_of_day(
+        iso_time="2026-01-28T01:17:00Z",  # sunset @5:13pm, nautical sunset @6:16pm
+        latitude=39.9674884,  # Boulder
+        longitude=-105.2532602,
+    )
+    assert phase_after_nautical_sunset == 4  # night
+
+
+def test_phase_of_day_before_sunrise():
+    astronomical_manager = AstronomicalManager()
+    phase_at_sunrise = astronomical_manager.phase_of_day(
+        iso_time="2026-01-27T14:13:00Z",  # sunrise @7:13am, nautical sunrise @6:12am
+        latitude=39.9674884,  # Boulder
+        longitude=-105.2532602,
+    )
+    assert phase_at_sunrise == 1  # dusk
+
+
+def test_phase_of_day_after_sunrise():
+    astronomical_manager = AstronomicalManager()
+    phase_at_sunrise = astronomical_manager.phase_of_day(
+        iso_time="2026-01-27T14:20:00Z",  # sunrise @7:13am, nautical sunrise @6:12am
+        latitude=39.9674884,  # Boulder
+        longitude=-105.2532602,
+    )
+    assert phase_at_sunrise == 2  # day
+
+
+def test_phase_of_day_before_nautical_sunrise():
+    astronomical_manager = AstronomicalManager()
+    # about an hour before is nautical sunrise
+    phase_before_nautical_sunrise = astronomical_manager.phase_of_day(
+        iso_time="2026-01-27T13:12:00Z",  # sunrise @7:13am, nautical sunrise @6:12am
+        latitude=39.9674884,  # Boulder
+        longitude=-105.2532602,
+    )
+    assert phase_before_nautical_sunrise == 4  # night
+
+
+def test_phase_of_day_after_nautical_sunrise():
+    astronomical_manager = AstronomicalManager()
+    phase = astronomical_manager.phase_of_day(
+        iso_time="2026-01-27T14:13:00Z",  # sunrise @7:13am, nautical sunrise @6:12am
+        latitude=39.9674884,  # Boulder
+        longitude=-105.2532602,
+    )
+    assert phase == 1

water_column_sonar_annotation-26.1.8/tests/conftest.py

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+from pathlib import Path
+
+import pooch
+import pytest
+
+HERE = Path(__file__).parent.absolute()
+TEST_DATA_FOLDER = HERE / "test_resources"
+
+HB1906_DATA = pooch.create(
+    path=pooch.os_cache("water-column-sonar-annotation"),
+    base_url="https://github.com/CI-CMG/water-column-sonar-annotation/releases/download/v26.1.0/",
+    retry_if_failed=1,
+    registry={
+        "HB201906_BOTTOMS.zip": "sha256:20609581493ea3326c1084b6868e02aafbb6c0eae871d946f30b8b5f0e7ba059",
+        "HB201906_EVR.zip": "sha256:ceed912a25301be8f1b8f91e134d0ca4cff717f52b6623a58677832fd60c2990",
+        #
+        # "ne_50m_coastline.shp": "sha256:797d675af9613f80b51ab6049fa32e589974d7a97c6497ca56772965f179ed26",
+        # "ne_50m_coastline.shx": "sha256:0ff1792f2d16b58246d074215edd9d12fa280880ecaad61a91b9382fee854065",
+        #
+        "ne_10m_coastline.shp": "sha256:459a4a97c09db19aadf5244026612de9d43748be27f83a360242b99f7fabb3c1",
+        "ne_10m_coastline.shx": "sha256:f873afee7f56779ce52253f740ec251c2f12244aea911dc40f0a85d75de8d5f2",
+    },
+)
+
+
+def fetch_raw_files():
+    HB1906_DATA.fetch(fname="HB201906_BOTTOMS.zip", progressbar=True)
+    HB1906_DATA.fetch(fname="HB201906_EVR.zip", progressbar=True)
+
+    # HB1906_DATA.fetch(fname="ne_50m_coastline.shp", progressbar=True)
+    # HB1906_DATA.fetch(fname="ne_50m_coastline.shx", progressbar=True)
+
+    HB1906_DATA.fetch(fname="ne_10m_coastline.shp", progressbar=True)
+    HB1906_DATA.fetch(fname="ne_10m_coastline.shx", progressbar=True)
+
+    file_name = HB1906_DATA.fetch(fname="HB201906_EVR.zip", progressbar=True)
+
+    """
+    water-column-sonar-annotation user$ ls /Users/user/Library/Caches/water-column-sonar-annotation
+    HB201906_BOTTOMS.zip	HB201906_EVR.zip	ne_10m_coastline.shp	ne_10m_coastline.shx
+    """
+    return Path(file_name).parent
+
+
+@pytest.fixture(scope="session")
+def test_path():
+    return {
+        "DATA_TEST_PATH": fetch_raw_files(),
+    }
+
+
+# """
+# Folder locations in mac and windows:
+#
+# Windows
+# C:\Users\<user>\AppData\Local\echopype\Cache\2024.12.23.10.10
+#
+# MacOS
+# /Users//Library/Caches/echopype/2024.12.23.10.10
+# """

water_column_sonar_annotation-26.1.8/tests/cruise/test_cruise_manager.py

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+import numpy as np
+import pytest
+
+from water_column_sonar_annotation.cruise import CruiseManager
+
+
+#######################################################
+def setup_module():
+    print("setup")
+
+
+def teardown_module():
+    print("teardown")
+
+
+@pytest.fixture
+def process_cruise_path(test_path):
+    return test_path["DATA_TEST_PATH"]
+
+
+#######################################################
+# def test_get_cruise_bottom_nan(process_cruise_path, tmp_path):
+#     cruise_manager = CruiseManager()
+#     cruise = cruise_manager.get_cruise()
+#     # count of non-nan values np.count_nonzero(~np.isnan(cruise.bottom.values)) / cruise.Sv.shape[1]
+#     assert len(cruise.Sv.shape) == 3
+
+
+def test_get_cruise(process_cruise_path, tmp_path):
+    cruise_manager = CruiseManager()
+    cruise = cruise_manager.get_cruise()
+    assert len(cruise.Sv.shape) == 3
+
+
+def test_get_coordinates():
+    """This only gets the depth over the interval, need to calculate the 'altitude'"""
+    cruise_manager = CruiseManager()
+    lat, lon = cruise_manager.get_coordinates(
+        start_time="2019-10-16T16:20:00",
+        end_time="2019-10-16T16:30:00",
+    )
+    assert np.isclose(lat, 41.48177)
+    assert np.isclose(lon, -68.50478)
+
+
+def test_get_depth():
+    """This only gets the depth over the interval, need to calculate the 'altitude'"""
+    cruise_manager = CruiseManager()
+    depth_value = cruise_manager.get_depth(
+        start_time="2019-10-16T16:20:00",
+        end_time="2019-10-16T16:50:00",
+    )
+    assert np.isclose(depth_value, 96.36)  # 96.356674
+
+
+def test_get_altitude():
+    """This gets the distance from EVR to the bottom"""
+    cruise_manager = CruiseManager()
+    altitude_value = cruise_manager.get_altitude(
+        start_time="2019-10-16T16:20:00",
+        end_time="2019-10-16T16:50:00",
+        bbox_max=80.0,
+    )
+    # bottom is at 96.356674
+    # setting the bbox at 80.
+    assert np.isclose(altitude_value, 16.36)  # 96.356674
+
+
+def test_get_altitude_nan_bottom():
+    """This gets the distance from EVR to the bottom when there are nan values"""
+    cruise_manager = CruiseManager()
+    altitude_value = cruise_manager.get_altitude(
+        start_time="2019-09-26T10:02:39.03",
+        end_time="2019-09-26T10:02:40.00",
+        bbox_max=10.0,
+    )
+    assert np.isclose(altitude_value, 0.0)
+
+
+# get_gps

water_column_sonar_annotation-26.1.8/tests/geospatial/test_geospatial_manager.py

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+import numpy as np
+import pytest
+
+from water_column_sonar_annotation.geospatial import GeospatialManager
+
+
+#######################################################
+def setup_module():
+    print("setup")
+
+
+def teardown_module():
+    print("teardown")
+
+
+@pytest.fixture
+def process_check_distance_from_coastline(test_path):
+    return test_path["DATA_TEST_PATH"]
+
+
+#######################################################
+def test_check_distance_from_coastline(process_check_distance_from_coastline, tmp_path):
+    geospatial_manager = GeospatialManager()
+    # Point in middle of atlantic https://wktmap.com/?ab28cbae
+    distance = geospatial_manager.check_distance_from_coastline(
+        latitude=51.508742,
+        longitude=-30.410156,
+        shapefile_path=process_check_distance_from_coastline,
+    )
+    # assert np.isclose(distance, 1_236_212.37356)  # 1,200 km
+    assert np.isclose(distance, 1_233_910.720702243)
+
+
+def test_check_distance_from_coastline_woods_hole(
+    process_check_distance_from_coastline, tmp_path
+):
+    geospatial_manager = GeospatialManager()
+    # Point in middle of woods hole vineyard sound: https://wktmap.com/?9b405aa9
+    distance = geospatial_manager.check_distance_from_coastline(
+        latitude=41.494692,
+        longitude=-70.647926,
+        shapefile_path=process_check_distance_from_coastline,
+    )
+    # The sound is 5 km across
+    # assert np.isclose(distance, 4_457.0347)  # 4.5 km --> should be 2.5 km?
+    assert np.isclose(distance, 3_093)  # 3_093.3015 km is close enough
+
+
+def test_get_local_time():
+    geospatial_manager = GeospatialManager()
+    local_time = geospatial_manager.get_local_time(
+        iso_time="2026-01-26T20:35:00Z",
+        latitude=51.508742,
+        longitude=-30.410156,
+    )
+    assert local_time == "2026-01-26T18:35:00-02:00"
+
+
+def test_get_local_hour_of_day():
+    geospatial_manager = GeospatialManager()
+    local_hour_of_day = geospatial_manager.get_local_hour_of_day(
+        iso_time="2026-01-26T20:35:00Z",
+        latitude=51.508742,
+        longitude=-30.410156,
+    )
+    assert local_hour_of_day == 18
+
+
+def test_get_month_of_year_january():
+    geospatial_manager = GeospatialManager()
+    month_of_year = geospatial_manager.get_month_of_year(
+        iso_time="2026-01-26T20:35:00Z",
+        latitude=51.508742,
+        longitude=-30.410156,
+    )
+    assert month_of_year == 1
+
+
+def test_get_month_of_year_july():
+    geospatial_manager = GeospatialManager()
+    month_of_year = geospatial_manager.get_month_of_year(
+        iso_time="2026-07-13T12:00:00Z",
+        latitude=51.508742,
+        longitude=-30.410156,
+    )
+    assert month_of_year == 7