diff --git a/.github/workflows/pytest.yaml b/.github/workflows/pytest.yaml new file mode 100644 index 0000000..13dedfe --- /dev/null +++ b/.github/workflows/pytest.yaml @@ -0,0 +1,55 @@ +name: Run Tests +on: + pull_request: + push: + branches: + - main + +jobs: + unit-tests: + name: Run Tests + runs-on: ubuntu-latest + strategy: + matrix: + # Select the Python versions to test against + os: [ubuntu-latest, macos-latest] + python-version: ["3.10", "3.11"] + fail-fast: true + steps: + - name: Check out the code + uses: actions/checkout@v3.5.2 + with: + fetch-depth: 1 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + + # Install Poetry + - name: Install Poetry + uses: snok/install-poetry@v1.3.3 + with: + version: 1.4.0 + + # Configure Poetry to use the virtual environment in the project + - name: Setup Poetry + run: | + poetry config virtualenvs.in-project true + + # Install the dependencies + - name: Install Package + run: | + poetry install --with tests + + # Run the unit tests and build the coverage report + - name: Run Tests + run: poetry run pytest -v --cov=./rs_tools --cov-report=xml:./coverage.xml + + - name: Upload code coverage + uses: codecov/codecov-action@v3 + with: + token: ${{ secrets.CODECOV_TOKEN }} + file: ./coverage.xml + name: rs_tools + flags: unittests + env_vars: OS,PYTHON \ No newline at end of file diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..2068519 --- /dev/null +++ b/.gitignore @@ -0,0 +1,149 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +pip-wheel-metadata/ +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/ + +# 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 +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +.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 + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow +__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/ + +# exclude data from source control by default +datasets/* +!datasets/.gitkeep +*.pckl +*.pkl +*.pickle +.vscode/settings.json +.idea/.gitignore +.idea/jaxsw.iml +.idea/misc.xml +.idea/modules.xml +.idea/vcs.xml +.idea/inspectionProfiles/profiles_settings.xml +.jupyter/desktop-settings.json +.jupyter/desktop-workspaces/default-37a8.jupyterlab-workspace +*.DS_STORE +\outputs/ +\jbook/_build/ +\_build/ +\.idea/ \ No newline at end of file diff --git a/.project-root b/.project-root new file mode 100644 index 0000000..e69de29 diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..9c8f3ea --- /dev/null +++ b/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright {yyyy} {name of copyright owner} + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. \ No newline at end of file diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..4917d9d --- /dev/null +++ b/Makefile @@ -0,0 +1,36 @@ +.PHONY: conda format style types black test link check notebooks +.DEFAULT_GOAL = help + +PYTHON = python +VERSION = 3.10 +NAME = py_name +ROOT = ./ +PIP = pip +CONDA = conda +SHELL = bash +PKGROOT = finitevolx + + +help: ## Display this help + @awk 'BEGIN {FS = ":.*##"; printf "\nUsage:\n make \033[36m\033[0m\n"} /^[a-zA-Z_-]+:.*?##/ { printf " \033[36m%-15s\033[0m %s\n", $$1, $$2 } /^##@/ { printf "\n\033[1m%s\033[0m\n", substr($$0, 5) } ' $(MAKEFILE_LIST) + + +##@ Formatting +black: ## Format code in-place using black. + black ${PKGROOT}/ -l 79 . + +isort: ## Format imports in-place using isort. + isort ${PKGROOT}/ + + +format: ## Code styling - black, isort + black ${PKGROOT}/ -l 100 . + @printf "\033[1;34mBlack passes!\033[0m\n\n" + isort ${PKGROOT}/ + @printf "\033[1;34misort passes!\033[0m\n\n" + +##@ Testing +test: ## Test code using pytest. + @printf "\033[1;34mRunning tests with pytest...\033[0m\n\n" + pytest -v finitevolx + @printf "\033[1;34mPyTest passes!\033[0m\n\n" \ No newline at end of file diff --git a/README.md b/README.md new file mode 100644 index 0000000..f37470b --- /dev/null +++ b/README.md @@ -0,0 +1,35 @@ +# A minimal library for preprocessing remote sensing data for machine learning applications (In Progress) +[![CodeFactor](https://www.codefactor.io/repository/github/jejjohnson/rs_tools/badge)](https://www.codefactor.io/repository/github/jejjohnson/rs_tools) +[![codecov](https://codecov.io/gh/jejjohnson/rs_tools/branch/main/graph/badge.svg?token=YGPQQEAK91)](https://codecov.io/gh/jejjohnson/rs_tools) + +> This package has some simple, minimal preprocessing of helio-data to make it machine learning ready. + + + + +--- +## Installation + +We can install it directly through pip + +```bash +pip install git+https://github.com/jejjohnson/rs_tools +``` + +We also use poetry for the development environment. + +```bash +git clone https://github.com/jejjohnson/rs_tools.git +cd rs_tools +conda create -n rs_tools python=3.11 poetry +poetry install +``` + + + +--- +## References + +**Software** + +* 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"ipython-genutils (==0.2.0)", "jedi (==0.16)", "jinja2 (==3.0.0)", "jupyter-client (==6.1.5)", "jupyter-client (==7.0.0)", "jupyter-core (==4.7.0)", "nbconvert (==6.0.0)", "nbconvert (==6.1.0)", "pyflakes (==2.2.0)", "tomli (==0.2.0)"] +tests = ["pytest (>=4.6.0)", "pytest (>=4.6.0)", "pytest (>=6.2.5)", "pytest-cov (>=3.0.0)", "typing (>=3.7.4)"] +tests-binary = ["cmake", "cmake", "ninja", "ninja", "pybind11", "pybind11", "scikit-build", "scikit-build"] +tests-binary-strict = ["cmake (==3.21.2)", "cmake (==3.25.0)", "ninja (==1.10.2)", "ninja (==1.11.1)", "pybind11 (==2.10.3)", "pybind11 (==2.7.1)", "scikit-build (==0.11.1)", "scikit-build (==0.16.1)"] +tests-strict = ["pytest (==4.6.0)", "pytest (==4.6.0)", "pytest (==6.2.5)", "pytest-cov (==3.0.0)", "typing (==3.7.4)"] + +[[package]] +name = "zipp" +version = "3.17.0" +description = "Backport of pathlib-compatible object wrapper for zip files" +optional = false +python-versions = ">=3.8" +files = [ + {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"}, + {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"}, +] + +[package.extras] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] + +[metadata] +lock-version = "2.0" +python-versions = ">=3.10,<3.12" +content-hash = "c30028691ea0d69e2557532fee66a35ab45a8b2436775455aa94f0012af12db7" diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..65e040f --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,182 @@ +[tool.poetry] +name = "rs-tools" +version = "0.0.1" +description = "Remote Sensing Tools" +authors = [ + "Juan Emmanuel Johnson ", +] +license = "MIT" +readme = "README.md" +repository = "https://github.com/jejjohnson/rs_tools" +keywords = ["rasterio", "remote sensing"] +classifiers = [ + "Topic :: Scientific/Engineering", + "Topic :: Software Development :: Libraries", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.10", + "Operating System :: MACOS/Linux", + "Natural Language :: English", + "License :: OSI Approved :: MIT License", + "Intended Audience :: Science/Research", + "Development Status :: 2 - Pre-Alpha copy", + +] + +[tool.poetry.dependencies] +python = ">=3.10,<3.12" +beartype = "^0.13.1" +rastervision-core = "^0.21.3" + + +[tool.poetry.group.test.dependencies] +pytest = "^7.3.1" +pytest-cov = "^4.0.0" +pytest-pretty = "^1.1.1" +pytest-xdist = "^3.2.1" +networkx = "^3.0" +coverage = "^7.2.2" +absolufy-imports = "^0.3.1" +xdoctest = "^1.1.1" +mktestdocs = "^0.2.1" + +[tool.poetry.group.dev.dependencies] +black = "^23.1.0" +isort = "^5.12.0" +pylint = "^2.17.1" +nox = "^2022.11.21" +ruff = "^0.0.259" +flax = "^0.6.8" +pre-commit = "^3.2.2" +nbstripout = "^0.6.1" +pydocstyle = "^6.3.0" +codespell = "^2.2.4" +asv = "^0.6.0" +interrogate = "^1.5.0" + + +[tool.poetry.group.exp.dependencies] +wandb = "^0.15.0" +loguru = "^0.7.0" +hydra-core = "^1.3.2" +matplotlib = "^3.7.1" +seaborn = "^0.12.2" +autoroot = "^1.0.0" + +[tool.poetry.group.jlab.dependencies] +ipykernel = "^6.22.0" +autoroot = "^1.0.0" + +[tool.poetry.group.docs.dependencies] +linkify-it-py = "^2.0.0" +jinja2 = "^3.1.2" +matplotlib = "^3.7.1" +ipython = "^8.11.0" +ipykernel = "^6.22.0" +watermark = "^2.3.1" +jupytext = "^1.14.5" +mkdocs = "^1.4.2" +mkdocs-material = "^9.1.8" +pymdown-extensions = "^9.11" +mknotebooks = "^0.7.1" +pygments = "^2.15.1" +mkdocs-bibtex = "^2.8.16" +mkdocs-jupyter = "^0.24.1" +mdx-truly-sane-lists = "^1.3" +pytkdocs = "^0.16.1" +mkdocs-gen-files = "^0.5.0" +mkdocs-literate-nav = "^0.6.0" +mkdocs-git-authors-plugin = "^0.7.0" +mkdocstrings = { version = "^0.21.2", extras = ["python"] } +markdown-katex = "^202112.1034" + + + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" + + +[tool.pytest.ini_options] # https://docs.pytest.org/en/latest/reference/reference.html#ini-options-ref +# addopts = "--color=yes --doctest-modules --exitfirst --failed-first --strict-config --strict-markers --typeguard-packages=my_package --verbosity=2 --junitxml=reports/pytest.xml" +filterwarnings = ["error", "ignore::DeprecationWarning"] +testpaths = ["rs_tools"] +xfail_strict = true + + +[tool.ruff] # https://github.com/charliermarsh/ruff +fix = true +cache-dir = "~/.cache/ruff" +dummy-variable-rgx = "^_$" +exclude = ["docs/"] +ignore-init-module-imports = true +line-length = 88 +select = [ + # pyflakes + "F", + # pycodestyle + "E", + "W", + # flake8-2020 + "YTT", + # flake8-bugbear + "B", + # flake8-quotes + "Q", + # pylint + "PLE", + "PLR", + "PLW", + # misc lints + "PIE", + # flake8-pyi + "PYI", + # tidy imports + "TID", + # implicit string concatenation + "ISC", +] +ignore = [ + # space before : (needed for how black formats slicing) + # "E203", # not yet implemented + # module level import not at top of file + "E402", + # do not assign a lambda expression, use a def + "E731", + "E501", + "PGH001", + "RET504", + "S101", + "F722", + 'PLR2004', + "PLR0913", +] +unfixable = ["ERA001", "F401", "F841", "T201", "T203"] +src = ["rs_tools"] +target-version = "py38" + +[tool.black] # https://black.readthedocs.io/en/stable/usage_and_configuration/the_basics.html#configuration-via-a-file +line-length = 88 +target-version = ["py38"] + + +[tool.isort] +profile = "black" +combine_as_imports = true +force_sort_within_sections = true +force_grid_wrap = 2 +skip = 'docs' + +[tool.coverage.report] # https://coverage.readthedocs.io/en/latest/config.html#report +fail_under = 50 +precision = 1 +show_missing = true +skip_covered = true + +[tool.coverage.run] # https://coverage.readthedocs.io/en/latest/config.html#run +branch = true +command_line = "--module pytest" +data_file = "reports/.coverage" +source = ["src"] + +[tool.coverage.xml] # https://coverage.readthedocs.io/en/latest/config.html#xml +output = "reports/coverage.xml" diff --git a/rs_tools/__init__.py b/rs_tools/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/rs_tools/_src/__init__.py b/rs_tools/_src/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/rs_tools/_src/data/__init__.py b/rs_tools/_src/data/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/rs_tools/_src/data/goes/__init__.py b/rs_tools/_src/data/goes/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/rs_tools/_src/data/modis/__init__.py b/rs_tools/_src/data/modis/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/rs_tools/_src/geoprocessing/__init__.py b/rs_tools/_src/geoprocessing/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/rs_tools/_src/preprocessing/__init__.py b/rs_tools/_src/preprocessing/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/scripts/goes.py b/scripts/goes.py new file mode 100644 index 0000000..a23cfdb --- /dev/null +++ b/scripts/goes.py @@ -0,0 +1,95 @@ +import shutil +from datetime import datetime, timedelta +from pathlib import Path +import numpy as np +import pandas as pd +import s3fs +import os +import argparse +from tqdm import tqdm +import multiprocessing +from concurrent.futures import ThreadPoolExecutor, as_completed, wait + +"""GOES data downloader from AWS S3 bucket inspired by goes2go from https://github.com/blaylockbk/goes2go""" + +fs = s3fs.S3FileSystem(anon=True) + +class GOESDownloader: + def __init__(self, base_path): + self.base_path = base_path + self.dirs = ["G16", "G17", "G18"] + #self.product = product + [os.makedirs(os.path.join(base_path, dir), exist_ok=True) for dir in self.dirs] + #os.makedirs(os.path.join(base_path, self.satellite, self.product), exist_ok=True) + + def download(self, df, base_path): + """Download the files from a DataFrame listing with multithreading""" + + for i in tqdm(range(len(df))): + #file_path = os.path.join(base_path, df.satellite[i], df.product_mode[i], "%s.nc" % df.start[i].isoformat("T", timespec='seconds')) + fs.get(df.file[i], os.path.join(base_path, df.satellite[i], df.product_mode[i], "%s.nc" % df.start[i].isoformat("T", timespec='seconds'))) + + def goes_file_df(self, satellite, product, start, end, bands=None, refresh=True): + + start = pd.to_datetime(start) + end = pd.to_datetime(end) + + DATES = pd.date_range(f"{start:%Y-%m-%d %H:00}", f"{end:%Y-%m-%d %H:00}", freq="1H") + files = [] + for DATE in DATES: + files += fs.ls(f"{satellite}/{product}/{DATE:%Y/%j/%H/}", refresh=refresh) + + # Build a table of the files + # -------------------------- + df = pd.DataFrame(files, columns=["file"]) + df[["product_mode", "satellite", "start", "end", "creation"]] = ( + df["file"].str.rsplit("_", expand=True, n=5).loc[:, 1:] + ) + + if product.startswith("ABI"): + product_mode = df.product_mode.str.rsplit("-", n=1, expand=True) + df["product"] = product_mode[0] + df["mode_bands"] = product_mode[1] + + mode_bands = df.mode_bands.str.split("C", expand=True) + df["mode"] = mode_bands[0].str[1:].astype(int) + try: + df["band"] = mode_bands[1].astype(int) + except: + # No channel data + df["band"] = None + + # Filter files by band number + if bands is not None: + if not hasattr(bands, "__len__"): + bands = [bands] + df = df.loc[df.band.isin(bands)] + + df["start"] = pd.to_datetime(df.start, format="s%Y%j%H%M%S%f") + df["end"] = pd.to_datetime(df.end, format="e%Y%j%H%M%S%f") + df["creation"] = pd.to_datetime(df.creation, format="c%Y%j%H%M%S%f.nc") + + #Filter files by requested time range + df = df.loc[df.start >= start].loc[df.end <= end].reset_index(drop=True) + + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description='Download GOES data') + parser.add_argument('--download_dir', type=str, help='path to the download directory.') + parser.add_argument('--n_workers', type=str, help='number of parallel threads.', required=False, default=4) + + args = parser.parse_args() + # base_path = args.download_dir + # n_workers = args.n_workers + # satellite = args.satellite + # product = args.product + base_path = '/Users/christophschirninger/PycharmProjects/MDRAIT_ITI/GOES' + + download_util = GOESDownloader(base_path=base_path) + start_date = datetime(2022, 1, 1) + end_date = datetime(2022, 1, 2) + product = ["ABI-L2-ACHAF", "ABI-L2-ACHTF", "ABI-L2-ACMF"] + + dataframe = download_util.goes_file_df(satellite="noaa-goes16", product=product[0], start=start_date, end=end_date, bands=None, + refresh=True) + download_util.download(dataframe, base_path) \ No newline at end of file