coronagraphoto 1.0.0__tar.gz

coronagraphoto-1.0.0/.github/dependabot.yml

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+version: 2
+updates:
+    - package-ecosystem: "github-actions"
+      directory: "/"
+      schedule:
+          interval: "monthly"

coronagraphoto-1.0.0/.github/workflows/publish-to-pypi.yml

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+name: Publish to PyPI
+
+on: push
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.x"
+    - name: Install pypa/build
+      run: >-
+        python3 -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python distribution to PyPI
+    if: startsWith(github.ref, 'refs/tags/')
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/coronagraphoto
+    permissions:
+      id-token: write
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

coronagraphoto-1.0.0/.github/workflows/release-please.yml

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+on:
+  push:
+    branches:
+      - main
+
+permissions:
+  contents: write
+  pull-requests: write
+
+name: release-please
+
+jobs:
+  release-please:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: google-github-actions/release-please-action@v4
+        with:
+          # this assumes that you have created a personal access token
+          # (PAT) and configured it as a GitHub action secret named
+          # `MY_RELEASE_PLEASE_TOKEN` (this secret name is not important).
+          token: ${{ secrets.MY_RELEASE_PLEASE_TOKEN }}
+          # this is a built-in strategy in release-please, see "Action Inputs"
+          # for more options
+          release-type: simple

coronagraphoto-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/#use-with-ide
+.pdm.toml
+
+# 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/
+
+input/
+!input/settings/example.toml

coronagraphoto-1.0.0/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.5.0"
+    hooks:
+      - id: trailing-whitespace
+      - id: name-tests-test
+      - id: end-of-file-fixer
+      - id: no-commit-to-branch
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.4
+    hooks:
+      # Run the linter.
+      - id: ruff
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format
+  - repo: https://github.com/compilerla/conventional-pre-commit
+    rev: v3.1.0
+    hooks:
+      - id: conventional-pre-commit
+        stages: [commit-msg]
+        args: []

coronagraphoto-1.0.0/CHANGELOG.md

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+# Changelog
+
+## 1.0.0 (2024-03-22)
+
+
+### Bug Fixes
+
+* adding dependabot ([5a7fe8e](https://github.com/CoreySpohn/coronagraphoto/commit/5a7fe8e613a436155293495a44fb121d98819f16))
+* Adding workflow ([4f020b2](https://github.com/CoreySpohn/coronagraphoto/commit/4f020b26ce70578127a3560af6947c1d43b1dfaf))
+* Commenting out not implemented code ([49d9b0a](https://github.com/CoreySpohn/coronagraphoto/commit/49d9b0a40beb106a432fe501d4f5d01459162e41))
+* fixing more ruff linting things ([1dbb5e9](https://github.com/CoreySpohn/coronagraphoto/commit/1dbb5e90553949a5d9d186df91868a4f48c3ea0a))
+* hatch version control ([a1f342c](https://github.com/CoreySpohn/coronagraphoto/commit/a1f342ce8b883076205bb832bbdd9f964bede3fa))
+* Linting ([bca15f0](https://github.com/CoreySpohn/coronagraphoto/commit/bca15f0e096ce67466117c92d0cc6487ea11010e))
+* removing the problem files for ruff ([41911c1](https://github.com/CoreySpohn/coronagraphoto/commit/41911c1f86c455dd560d054ff65ceeb843c76619))
+* Still more annoying linting ([7022c05](https://github.com/CoreySpohn/coronagraphoto/commit/7022c05ec4c1ecf7f0859803a0fc47198a11939c))

coronagraphoto-1.0.0/LICENSE

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+MIT License
+
+Copyright (c) 2023 Corey Spohn
+
+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.

coronagraphoto-1.0.0/PKG-INFO

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+Metadata-Version: 2.3
+Name: coronagraphoto
+Version: 1.0.0
+Summary: A python library to simulate coronagraphic observations of exoplanets.
+Project-URL: Homepage, https://github.com/CoreySpohn/coronagraphoto
+Project-URL: Issues, https://github.com/CoreySpohn/coronagraphoto/issues
+Author-email: Corey Spohn <corey.a.spohn@nasa.gov>
+License: MIT License
+        
+        Copyright (c) 2023 Corey Spohn
+        
+        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.
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Requires-Python: >=3.9
+Requires-Dist: astropy
+Requires-Dist: exoverses
+Requires-Dist: lod-unit
+Requires-Dist: matplotlib
+Requires-Dist: numba
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: photutils
+Requires-Dist: synphot
+Requires-Dist: tqdm
+Requires-Dist: xarray
+Description-Content-Type: text/markdown
+
+# coronagraphoto
+A library to simulate observations based on
+1. An astrophysical scene (from [ExoVista](https://github.com/alexrhowe/ExoVista))
+2. A coronagraph (from a [yield input package](https://starkspace.com/yield_standards.pdf))
+3. An observation scenario

coronagraphoto-1.0.0/README.md

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+# coronagraphoto
+A library to simulate observations based on
+1. An astrophysical scene (from [ExoVista](https://github.com/alexrhowe/ExoVista))
+2. A coronagraph (from a [yield input package](https://starkspace.com/yield_standards.pdf))
+3. An observation scenario

coronagraphoto-1.0.0/input/settings/example.toml

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+#####################
+# ObservingScenario #
+#####################
+[general]
+diameter = { value = 8.4, unit = 'm' }
+exposure_time = { value = 5, unit = 'hr' }
+frame_time = { value = 30, unit = 'min' }
+
+# Annoying astropy.time uses "val" and astropy.unit uses "value"
+start_time = { val = 2000, format = 'decimalyear' }
+
+[spectral_information]
+central_wavelength = { value = 500, unit = 'nm' }
+spectral_resolution = 100
+# bandpass
+
+[detector]
+# The size of the detector in pixels
+shape = [300, 300]
+# The pixel scale of the detector pixels
+pixel_scale = { value = 0.1, unit = 'arcsec' }
+
+############
+# Settings #
+############
+
+[sources]
+# When true, the code will include the source in the simulation
+star = false
+planets = true
+disk = false
+
+[output]
+# If true, the code returns all the frames individually (keyed as "time"). If
+# false, the code sums all the frames together.
+frames = true
+# If true, the observation separates out the counted photons by
+# "spectral_wavelength(nm)". If false, the observation returns the total
+spectrum = false
+# If true, the output includes the counted photons for each source. If false,
+# the output includes the total counted photons.
+sources = false
+
+[precision]
+[precision.wavelength]
+# When true, the code will recalculate the flux of each source for each
+# wavelength in the bandpass
+flux = false
+# When true, the code will recalculate the transmission of the bandpass for
+# each wavelength
+transmission = false
+
+[precision.time_invariance]
+# When true, the code will reuse the count rate from the initial exposure for
+# all subsequent exposures (frames)
+planets = false
+star = true
+disk = true

coronagraphoto-1.0.0/pyproject.toml

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+[build-system]
+requires = ['hatchling', "hatch-fancy-pypi-readme", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+[project]
+name = "coronagraphoto"
+description = "A python library to simulate coronagraphic observations of exoplanets."
+authors = [{ name = "Corey Spohn", email = "corey.a.spohn@nasa.gov" }]
+dynamic = ['readme', 'version']
+requires-python = ">=3.9"
+license = { file = "LICENSE" }
+classifiers = [
+  "Development Status :: 3 - Alpha",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: MIT License",
+  "Programming Language :: Python :: 3",
+  "Topic :: Scientific/Engineering :: Astronomy",
+]
+dependencies = [
+  "astropy",
+  "exoverses",
+  "lod_unit",
+  "matplotlib",
+  "numpy",
+  "numba",
+  "pandas",
+  "photutils",
+  "synphot",
+  "tqdm",
+  "xarray",
+]
+
+[tool.hatch.version]
+source = "vcs"
+
+[project.urls]
+Homepage = "https://github.com/CoreySpohn/coronagraphoto"
+Issues = "https://github.com/CoreySpohn/coronagraphoto/issues"
+
+[tool.hatch.metadata.hooks.fancy-pypi-readme]
+content-type = "text/markdown"
+
+[[tool.hatch.metadata.hooks.fancy-pypi-readme.fragments]]
+path = "README.md"

coronagraphoto-1.0.0/sim_star_cor.py

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+from pathlib import Path
+
+import astropy.units as u
+import matplotlib.colors as colors
+import matplotlib.pyplot as plt
+import numpy as np
+from astropy.time import Time
+from exoverses.exovista.system import ExovistaSystem
+from synphot import SpectralElement
+from synphot.models import Gaussian1D
+
+from coronagraphoto import Coronagraph, Observation, ObservingScenario, Settings
+
+# Input files
+scene = Path("input/scenes/999-HIP_-TYC_SUN-mv_4.83-L_1.00-d_10.00-Teff_5778.00.fits")
+time = Time(2000, format="decimalyear")
+wavelength = 500 * u.nm
+frac_bandwidth = 0.15
+bandpass = SpectralElement(
+    Gaussian1D,
+    mean=wavelength,
+    stddev=frac_bandwidth * wavelength / np.sqrt(2 * np.pi),
+)
+
+# high_fid = {"bandpass": bandpass}
+base = "input/observing_scenarios/example.toml"
+med_fid = {
+    "diameter": 8 * u.m,
+    "central_wavelength": wavelength,
+    "start_time": time,
+    "exposure_time": 48 * u.hr,
+    "frame_time": 1 * u.hr,
+    "bandpass": bandpass,
+    "spectral_resolution": 100,
+}
+# low_fid = {
+#     "diameter": 8 * u.m,
+#     "wavelength": wavelength,
+#     "time": time,
+#     "exposure_time": 48 * u.hr,
+#     "include_star": True,
+#     "include_planets": True,
+#     "include_disk": True,
+#     "bandpass": bandpass,
+#     "return_spectrum": False,
+#     "return_frames": False,
+#     "return_sources": False,
+#     "wavelength_resolved_flux": False,
+#     "wavelength_resolved_transmission": False,
+# }
+# high_fid_scen = ObservingScenario(base, overwrite=high_fid)
+# med_fid_scen = ObservingScenario(med_fid)
+# low_fid_scen = ObservingScenario(low_fid)
+
+# Initialize coronagraph object.
+# Load ExoVista scene
+settings = Settings(base)
+observing_scenario = ObservingScenario(base, custom_scenario=med_fid)
+system = ExovistaSystem(scene)
+
+coronagraph_dir1 = Path("input/coronagraphs/LUVOIR-B-VC6_timeseries/")
+# coronagraph_dir2 = Path(
+#     "input/coronagraphs/LUVOIR-A_APLC_18bw_medFPM_2021-05-07_Dyn10pm-nostaticabb/"
+# )
+cdirs = [coronagraph_dir1]
+
+# Loop over coronagraphs and simulate observations
+for cdir in cdirs:
+    coro = Coronagraph(cdir)
+    obs = Observation(coro, system, observing_scenario, settings)
+    # obs = observation.Observation(coro, system, med_fid_scen)
+    obs.create_count_rates()
+    image = obs.count_photons()
+    fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(12, 6))
+    ax1.imshow(
+        obs.planet_count_rate.squeeze().value, norm=colors.LogNorm(), origin="lower"
+    )
+    ax2.imshow(
+        obs.planet_count_rate.squeeze().value, norm=colors.LogNorm(), origin="lower"
+    )
+    plt.show()
+    # fig, ax = plt.subplots(1, 1, figsize=(6, 6))
+    # ax.imshow(
+    #     obs.planet_count_rate[1].value - obs.planet_count_rate[0].value,
+    #     norm=colors.LogNorm(),
+    #     origin="lower",
+    # )
+
+    # start = datetime.datetime.now()
+    # obs.create_count_rates()
+    # obs.count_photons()
+    # print(f"High fidelity: {datetime.datetime.now() - start}")
+
+    # obs.load_observing_scenario(med_fid_scen)
+    # start = datetime.datetime.now()
+    # obs.create_count_rates()
+    # obs.count_photons()
+    # print(f"Medium fidelity: {datetime.datetime.now() - start}")
+    #
+    # obs.load_observing_scenario(low_fid_scen)
+    # start = datetime.datetime.now()
+    # obs.create_count_rates()
+    # obs.count_photons()
+    # print(f"Low fidelity: {datetime.datetime.now() - start}")
+    #
+    # plt.imshow(obs.data["total"], norm=colors.LogNorm(), origin="lower")
+    # x_loc = obs.system.planets[4]._x_pix[0] - obs.system.star._x_pix[0]
+    # y_loc = obs.system.planets[4]._y_pix[0] - obs.system.star._y_pix[0]
+    # plt.scatter(y_loc.value, x_loc.value, marker="x", color="r")
+    # plt.scatter(120, 120, marker="x", color="g")
+    # plt.show()
+    #
+    # obs.snr_check(np.arange(1, 100, 1) * u.hr)
+    #
+    # # re.render(system, coro, observing_scenario, obs)
+    # plt.close("all")

coronagraphoto-1.0.0/src/coronagraphoto/__init__.py

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+__all__ = [
+    "Coronagraph",
+    "logger",
+    "Observation",
+    "Observations",
+    "ObservingScenario",
+    "Settings",
+    "util",
+]
+
+from .coronagraph import Coronagraph
+from .logger import logger
+from .observation import Observation
+from .observations import Observations
+from .observing_scenario import ObservingScenario
+from .settings import Settings
+from . import util