ECOv003-L2T-STARS 1.0.0__tar.gz

ecov003_l2t_stars-1.0.0/.github/workflows/python-publish.yml

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+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

ecov003_l2t_stars-1.0.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/
+
+.vscode
+
+.DS_Store
+
+data/

ecov003_l2t_stars-1.0.0/ECOSTRESS Granule Download.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Using `ECOv002-CMR` package to retrieve ECOSTRESS granules as inputs using the Common Metadata Repository (CMR) API. Using `ECOv002-L2T-STARS` package to run the product generating executable (PGE)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "from ECOv002_CMR import download_ECOSTRESS_granule\n",
+    "from ECOv002_L2T_STARS import generate_L2T_STARS_runconfig, L2T_STARS"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Disable logger output in notebook"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import logging\n",
+    "\n",
+    "logging.getLogger().handlers = []"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Set working directory"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "working_directory = \"data\""
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Retrieve LST LSTE granule from CMR API for target date"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "L2T_LSTE_granule = download_ECOSTRESS_granule(\n",
+    "    product=\"L2T_LSTE\", \n",
+    "    orbit=35800,\n",
+    "    scene=3,\n",
+    "    tile=\"11SPS\", \n",
+    "    aquisition_date=\"2024-10-29\",\n",
+    "    parent_directory=working_directory\n",
+    ")\n",
+    "\n",
+    "L2T_LSTE_granule"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Load and display preview of surface temperature"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "L2T_LSTE_granule.ST_C"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Retrieve L2T STARS granule from CMR API as prior"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "L2T_STARS_granule = download_ECOSTRESS_granule(\n",
+    "    product=\"L2T_STARS\", \n",
+    "    tile=\"11SPS\", \n",
+    "    aquisition_date=\"2024-10-22\",\n",
+    "    parent_directory=working_directory\n",
+    ")\n",
+    "\n",
+    "L2T_STARS_granule"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Load and display preview of vegetation index"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "L2T_STARS_granule.NDVI"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Generate XML run-config file for L2T STARS PGE run"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "runconfig_filename = generate_L2T_STARS_runconfig(\n",
+    "    L2T_LSTE_filename=L2T_LSTE_granule.product_filename,\n",
+    "    prior_L2T_STARS_filename=L2T_STARS_granule.product_filename,\n",
+    "    working_directory=working_directory\n",
+    ")\n",
+    "\n",
+    "runconfig_filename"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with open(runconfig_filename, \"r\") as f:\n",
+    "    print(f.read())"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "exit_code = L2T_STARS(runconfig_filename=runconfig_filename, use_VNP43NRT=False)\n",
+    "exit_code"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "ECOv002-L2T-STARS",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

ecov003_l2t_stars-1.0.0/ECOv003_L2T_STARS/BRDF/BRDF.py

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+from os.path import join, abspath, dirname
+import warnings
+import numpy as np
+from numpy import where, isnan, logical_not, nanmean, nan, logical_or, loadtxt, digitize, arange
+
+
+def statistical_radiative_transport(SZA, AOT):
+    filename = join(abspath(dirname(__file__)), 'statistical_radiative_transport.txt')
+
+    data = loadtxt(filename)
+
+    sza_index = digitize(SZA, arange(0, 90, 1)[:-1])
+    aot_index = digitize(AOT, arange(0, 1, 0.02)[:-1])
+
+    SRT = data[sza_index, aot_index]
+
+    return SRT
+
+
+def bidirectional_reflectance(white_sky_albedo, black_sky_albedo, SZA, AOT):
+    warnings.filterwarnings('ignore')
+
+    # constrain aerosol optical thickness
+    # AOT = where(AOT >= 0.98, 0.97, AOT)
+    # AOT = where(AOT < 0.02, 0.02, AOT)
+    # AOT = where(isnan(AOT), 0.1, AOT)
+    AOT = np.clip(AOT, 0.1, 0.97)
+    AOT_mean = np.nanmean(AOT)
+    AOT = np.where(np.isnan(AOT), AOT_mean, AOT)
+
+    # constrain SZA
+    SZA = where(
+        logical_or(SZA <= 0, SZA > 90),
+        nanmean(where(
+            logical_not(logical_or(SZA <= 0, SZA > 90)),
+            SZA,
+            nan
+        )),
+        SZA
+    )
+
+    warnings.resetwarnings()
+
+    # gap-fill SZA with constant 45 degrees
+    SZA = where(isnan(SZA), 45, SZA)
+
+    # lookup statistical radiative transport
+    SRT = statistical_radiative_transport(SZA, AOT)
+
+    warnings.filterwarnings('ignore')
+
+    # cloud filter albedo
+    blue_sky_albedo = white_sky_albedo * SRT + black_sky_albedo * (1 - SRT)
+
+    warnings.resetwarnings()
+
+    return blue_sky_albedo

ecov003_l2t_stars-1.0.0/ECOv003_L2T_STARS/BRDF/SZA.py

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+from typing import Union
+
+import numpy as np
+from rasters import Raster, RasterGeometry
+
+
+def day_angle_rad_from_doy(doy):
+    """
+    This function calculates day angle in radians from day of year between 1 and 365.
+    """
+    return (2 * np.pi * (doy - 1)) / 365
+
+
+def solar_dec_deg_from_day_angle_rad(day_angle_rad):
+    """
+    This function calculates solar declination in degrees from day angle in radians.
+    """
+    return (0.006918 - 0.399912 * np.cos(day_angle_rad) + 0.070257 * np.sin(day_angle_rad) - 0.006758 * np.cos(
+        2 * day_angle_rad) + 0.000907 * np.sin(2 * day_angle_rad) - 0.002697 * np.cos(
+        3 * day_angle_rad) + 0.00148 * np.sin(
+        3 * day_angle_rad)) * (180 / np.pi)
+
+
+def SZA_deg_from_lat_dec_hour(latitude, solar_dec_deg, hour):
+    """
+    This function calculates solar zenith angle from longitude, solar declination, and solar time.
+    SZA calculated by this function matching SZA provided by MOD07 to within 0.4 degrees.
+
+    :param latitude: latitude in degrees
+    :param solar_dec_deg: solar declination in degrees
+    :param hour: solar time in hours
+    :return: solar zenith angle in degrees
+    """
+    # convert angles to radians
+    latitude_rad = np.radians(latitude)
+    solar_dec_rad = np.radians(solar_dec_deg)
+    hour_angle_deg = hour * 15.0 - 180.0
+    hour_angle_rad = np.radians(hour_angle_deg)
+    sza_rad = np.arccos(
+        np.sin(latitude_rad) * np.sin(solar_dec_rad) + np.cos(latitude_rad) * np.cos(solar_dec_rad) * np.cos(
+            hour_angle_rad))
+    sza_deg = np.degrees(sza_rad)
+
+    return sza_deg
+
+
+def calculate_SZA(day_of_year: Union[Raster, float], hour_of_day: Union[Raster, float], geometry: RasterGeometry) -> Raster:
+    """
+    Calculates solar zenith angle at latitude and solar apparent time.
+    :param lat: latitude in degrees
+    :param dec: solar declination in degrees
+    :param hour: hour of day
+    :return: solar zenith angle in degrees
+    """
+    day_angle = (2 * np.pi * (day_of_year - 1)) / 365
+    lat = np.radians(geometry.lat)
+    dec = np.radians((0.006918 - 0.399912 * np.cos(day_angle) + 0.070257 * np.sin(day_angle) - 0.006758 * np.cos(
+        2 * day_angle) + 0.000907 * np.sin(2 * day_angle) - 0.002697 * np.cos(3 * day_angle) + 0.00148 * np.sin(
+        3 * day_angle)) * (180 / np.pi))
+    hour_angle = np.radians(hour_of_day * 15.0 - 180.0)
+    SZA = np.degrees(np.arccos(np.sin(lat) * np.sin(dec) + np.cos(lat) * np.cos(dec) * np.cos(hour_angle)))
+    SZA = Raster(SZA, geometry=geometry)
+
+    return SZA
+

ecov003_l2t_stars-1.0.0/ECOv003_L2T_STARS/BRDF/__init__.py

@@ -0,0 +1 @@
+from .BRDF import *

ecov003_l2t_stars-1.0.0/ECOv003_L2T_STARS/BRDF/statistical_radiative_transport.txt

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ecov003_l2t_stars-1.0.0/ECOv003_L2T_STARS/BRDF/version.txt

@@ -0,0 +1 @@
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