pax_global_header00006660000000000000000000000064152704151000014505gustar00rootroot0000000000000052 comment=aeccedb0f93e1d3520a81d0b21a3dd50e3a2627a sncosmo-extinction-aeccedb/000077500000000000000000000000001527041510000162605ustar00rootroot00000000000000sncosmo-extinction-aeccedb/.gitattributes000066400000000000000000000004321527041510000211520ustar00rootroot00000000000000# Check out text files with LF line endings on every platform, so that the # mixed-line-ending hook does not fight core.autocrlf=true on Windows. * text=auto eol=lf # Leave vendored code and test data byte for byte as upstream supplied them. extern/** -text tests/testdata/** -text sncosmo-extinction-aeccedb/.github/000077500000000000000000000000001527041510000176205ustar00rootroot00000000000000sncosmo-extinction-aeccedb/.github/dependabot.yml000066400000000000000000000022021527041510000224440ustar00rootroot00000000000000version: 2 updates: - package-ecosystem: github-actions directory: / schedule: interval: monthly # Wait a week before updating to a new release. cooldown: default-days: 7 groups: actions: patterns: - "*" # Dependabot only looks for updates that support Python 3.10, the oldest # version in requires-python, and it applies each update to every Python # version. So it never updates the packages that uv.lock locks at newer # versions for newer Pythons, such as numpy and matplotlib, and an update # for Python 3.10 to one of them downgrades it on the newer Pythons. Run # `uv lock --upgrade` to update them. - package-ecosystem: uv directory: / schedule: interval: monthly # Wait a week before updating to a new release. cooldown: default-days: 7 groups: python-packages: patterns: - "*" - package-ecosystem: pre-commit directory: / schedule: interval: monthly # Wait a week before updating to a new release. cooldown: default-days: 7 groups: hooks: patterns: - "*" sncosmo-extinction-aeccedb/.github/workflows/000077500000000000000000000000001527041510000216555ustar00rootroot00000000000000sncosmo-extinction-aeccedb/.github/workflows/test.yml000066400000000000000000000074351527041510000233700ustar00rootroot00000000000000# This workflow uses uv to install the locked dependencies from uv.lock and # run the tests, and uses prek to run the hooks in .pre-commit-config.yaml. name: Test on: push: # Pull requests from dependabot run the tests through pull_request, so # do not run them again for the pushes to the dependabot branches. A # branch filter alone would also stop the runs for tags, so list them. branches-ignore: - "dependabot/**" tags: - "**" pull_request: permissions: contents: read jobs: test: strategy: matrix: python: ["3.10", "3.11", "3.12", "3.13", "3.14", "3.14t", "3.15", "3.15t"] fail-fast: false runs-on: ubuntu-latest name: Test on python ${{ matrix.python }} steps: - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: persist-credentials: false - name: Setup Python id: setup-python uses: actions/setup-python@6d4fd22b20465ccc0f7354476588e8df7c9ca0e0 # v7.1.0 with: python-version: ${{ matrix.python }} allow-prereleases: true check-latest: true - name: Setup uv uses: astral-sh/setup-uv@07a047e608db84b3d8c06cd9a7c7dcc9c355c18e # v10.3.2 with: # setup-uv keys the cache on `python --version`, which is the same # for the default and the free-threaded builds. cache-suffix: ${{ matrix.python }} - name: Run tests # Use the Python from setup-python, which also supplies pre-releases. # Install only the test group, which is all that the tests need. The # docs and dev tools would add about 35 packages to every job. env: UV_PYTHON: ${{ steps.setup-python.outputs.python-path }} run: uv run --locked --no-default-groups --group test pytest build: runs-on: ubuntu-latest name: Build the sdist and a wheel from it steps: - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: persist-credentials: false - name: Setup uv uses: astral-sh/setup-uv@07a047e608db84b3d8c06cd9a7c7dcc9c355c18e # v10.3.2 with: cache-suffix: build - name: Build the sdist, and a wheel from the sdist # Without --sdist or --wheel, uv builds the wheel from the sdist, not # from the checkout, so this fails when MANIFEST.in leaves out a file # that the build needs. The test job uses an editable install. # Python 3.11 makes the cp311-abi3 wheel that the release builds. run: uv build --python 3.11 - name: Check that the wheel uses only the stable ABI of Python 3.11 run: uvx abi3audit@0.0.26 --strict --report dist/*.whl - name: Test the wheel with the newest dependencies # Do not use uv.lock here, so that a new numpy release that breaks # extinction fails CI. Dependabot does not update numpy in uv.lock, # see .github/dependabot.yml. Use a newer Python than the build, to # test that the abi3 wheel works there. run: uv run --isolated --no-project --python 3.14 --with pytest --with dist/*.whl pytest lint: runs-on: ubuntu-latest name: Run prek hooks steps: - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: persist-credentials: false - name: Setup uv uses: astral-sh/setup-uv@07a047e608db84b3d8c06cd9a7c7dcc9c355c18e # v10.3.2 - name: Run prek uses: j178/prek-action@44924fe9ef4a6f88253c4b6b1bf11c689d3ce53d # v3.1.0 with: # Use the newest prek whose checksum this version of the action # knows, so that the download is verified. The default, latest, # follows each new prek release at once and skips the check. prek-version: latest-known sncosmo-extinction-aeccedb/.github/workflows/upload_to_pypi.yml000066400000000000000000000054141527041510000254330ustar00rootroot00000000000000name: Build and upload to PyPI on: release: types: [published] workflow_dispatch: permissions: contents: read jobs: build_wheels: name: Build wheels on ${{ matrix.os }} runs-on: ${{ matrix.os }} strategy: matrix: os: [ubuntu-latest, ubuntu-26.04-arm, windows-latest, windows-11-arm, macos-latest] steps: - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: persist-credentials: false - name: Build wheels # For very recent Python versions, wheels from e.g. numpy might not be # available yet which can cause the build to fail. Keep going, and upload # the wheels that were built before the failure stopped cibuildwheel. # On Linux, cibuildwheel copies the wheels out of the manylinux # container, and then out of the musllinux one, only after all of the # builds in it pass, so a failure loses every wheel of that container, # and a manylinux failure also stops the musllinux builds. continue-on-error: true uses: pypa/cibuildwheel@f9b966cfadf4109556cadc5bb39ddb72d0ce664e # v4.3.5 with: # The build[uv] frontend of cibuildwheel needs uv on Windows and macOS. extras: uv - uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2 with: name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }} path: ./wheelhouse/*.whl # Fail when this runner built no wheels, so that the release is not # uploaded to PyPI without them. if-no-files-found: error build_sdist: name: Build source distribution runs-on: ubuntu-latest steps: - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 with: persist-credentials: false - uses: astral-sh/setup-uv@07a047e608db84b3d8c06cd9a7c7dcc9c355c18e # v10.3.2 with: enable-cache: false - name: Build sdist # Without --sdist, uv also builds a wheel from the sdist, which checks # that the sdist builds. Only the sdist is uploaded. run: uv build - uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2 with: name: cibw-sdist path: dist/*.tar.gz upload_pypi: name: Upload to PyPI needs: [build_wheels, build_sdist] runs-on: ubuntu-latest permissions: id-token: write if: startsWith(github.ref, 'refs/tags/v') steps: - uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8.0.2 with: pattern: cibw-* path: dist merge-multiple: true - uses: pypa/gh-action-pypi-publish@7245906fb61fa33a13554f9d5fb856fe61758086 # v1.14.3 sncosmo-extinction-aeccedb/.gitignore000066400000000000000000000016011527041510000202460ustar00rootroot00000000000000# Byte-compiled / optimized / DLL files __pycache__/ *.py[cod] *$py.class # C extensions *.so # Cython-generated files *.c # Distribution / packaging .Python env/ build/ develop-eggs/ dist/ downloads/ eggs/ .eggs/ lib/ lib64/ parts/ sdist/ var/ *.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/ .coverage .coverage.* .cache nosetests.xml coverage.xml *,cover .hypothesis/ .pytest_cache/ # Translations *.mo *.pot # Django stuff: *.log # Sphinx documentation docs/_build/ docs/api/ # PyBuilder target/ #Ipython Notebook .ipynb_checkpoints # emacs *~ # Pipenv Pipfile Pipfile.lock # uv .venv/ .ruff_cache/ sncosmo-extinction-aeccedb/.pre-commit-config.yaml000066400000000000000000000032511527041510000225420ustar00rootroot00000000000000# Run with prek (https://github.com/j178/prek) or pre-commit: # uv tool install prek # a hook installed with uvx breaks after uv cache clean # prek install # run the hooks on each commit # prek run -a # run the hooks on all files # Leave vendored code and test data byte for byte as upstream supplied them. exclude: ^(extern|tests/testdata)/ repos: - repo: https://github.com/pre-commit/pre-commit-hooks rev: v6.0.0 hooks: - id: check-toml - id: check-yaml - id: end-of-file-fixer # Use LF line endings, not CRLF. - id: mixed-line-ending args: [--fix=lf] - id: trailing-whitespace - repo: https://github.com/astral-sh/ruff-pre-commit rev: v0.17.3 hooks: - id: ruff-check args: [--fix] - id: ruff-format - repo: https://github.com/astral-sh/uv-pre-commit rev: 0.13.6 hooks: # Make sure that uv.lock agrees with pyproject.toml. - id: uv-lock - repo: local hooks: - id: ty name: ty check # ty reads the stub in src/, so do not install the project, which # compiles the extension and needs a C compiler. uv.lock installs # numpy 2.2 on Python 3.10 and newer numpy on newer Python, and their # stubs differ, so always check with Python 3.10, in a temporary # environment that leaves .venv alone. entry: uv run --isolated --locked --only-group dev --python 3.10 ty check language: system pass_filenames: false # Run on every commit, not only when Python files change: a change to # pyproject.toml or uv.lock, or a deletion, can change the result. always_run: true sncosmo-extinction-aeccedb/.python-version000066400000000000000000000000051527041510000212600ustar00rootroot000000000000003.14 sncosmo-extinction-aeccedb/.readthedocs.yaml000066400000000000000000000013301527041510000215040ustar00rootroot00000000000000version: 2 build: os: ubuntu-24.04 tools: # Keep this the same as .python-version: uv sync would otherwise replace # the environment of Read the Docs with one for that Python version. python: "3.14" sphinx: configuration: docs/conf.py fail_on_warning: false python: install: # Read the Docs runs `uv sync --group docs`, which installs the versions # in uv.lock. It cannot pass --no-default-groups, so uv also installs the # default dev group, which includes docs. conf.py imports extinction to # read the version, and the plot directives call into it, so this also # installs the project with its compiled extension. - method: uv command: sync groups: - docs sncosmo-extinction-aeccedb/CITATION.cff000066400000000000000000000016411527041510000201540ustar00rootroot00000000000000cff-version: 1.2.0 message: If you use extinction, please cite it using these metadata. title: extinction abstract: Python Fast interstellar dust extinction laws in Python repository-code: https://github.com/sncosmo/extinction license: MIT doi: 10.5281/zenodo.804966 authors: - given-names: Kyle family-names: Barbary affiliation: University of California, Berkeley orcid: https://orcid.org/0000-0002-2532-3696 - given-names: Luke family-names: Shingles affiliation: GSI, Darmstadt orcid: https://orcid.org/0000-0002-5738-1612 - given-names: Jeremy family-names: Lusk affiliation: University of Central Arkansas orcid: https://orcid.org/0000-0001-6843-1278 - given-names: Kyle family-names: Boone affiliation: University of Washington orcid: https://orcid.org/0000-0002-5828-6211 - given-names: Benjamin family-names: Rose affiliation: Baylor University orcid: https://orcid.org/0000-0002-1873-8973 sncosmo-extinction-aeccedb/LICENSE000066400000000000000000000021101527041510000172570ustar00rootroot00000000000000The MIT License (MIT) Copyright (c) 2016 Kyle Barbary and contributors 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. sncosmo-extinction-aeccedb/MANIFEST.in000066400000000000000000000005311527041510000200150ustar00rootroot00000000000000include README.md include LICENSE include setup.py include pyproject.toml recursive-include src *.pyx *.pyi py.typed # setup.py regenerates the C from the .pyx on every build, so do not ship it. exclude src/extinction/_extinction.c include extern/bs.* include extern/bsplines.pxi recursive-include tests * global-exclude __pycache__/* *.py[cod] sncosmo-extinction-aeccedb/README.md000066400000000000000000000007611527041510000175430ustar00rootroot00000000000000extinction ========== *Fast interstellar dust extinction laws in Python* [![Test](https://github.com/sncosmo/extinction/actions/workflows/test.yml/badge.svg)](https://github.com/sncosmo/extinction/actions/workflows/test.yml) [![PyPI](https://img.shields.io/pypi/v/extinction.svg?style=flat-square)](https://pypi.python.org/pypi/extinction) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.804967.svg)](https://doi.org/10.5281/zenodo.804967) documentation: http://extinction.readthedocs.io/ sncosmo-extinction-aeccedb/benchmark.py000077500000000000000000000121701527041510000205700ustar00rootroot00000000000000#!/usr/bin/env python import sys import timeit from typing import Any args = sys.argv[1:] if len(args) == 0: args = ["ccm89", "fitzpatrick99", "apply"] benchmarks: list[dict[str, Any]] if "ccm89" in args: setup = """ import numpy from extinction import {name} wave = numpy.logspace(numpy.log10({minwave}), numpy.log10({maxwave}), {size:d}) """ stmt = "{name}(wave, 1.0, 3.1)" benchmarks = [ { "name": "ccm89", "minwave": 1000.0, "maxwave": 30000.0, "size": 10, "nloops": 1000000, }, { "name": "ccm89", "minwave": 1000.0, "maxwave": 30000.0, "size": 100, "nloops": 100000, }, { "name": "ccm89", "minwave": 1000.0, "maxwave": 30000.0, "size": 1000, "nloops": 10000, }, { "name": "ccm89", "minwave": 1000.0, "maxwave": 30000.0, "size": 10000, "nloops": 1000, }, { "name": "odonnell94", "minwave": 1000.0, "maxwave": 30000.0, "size": 100, "nloops": 100000, }, { "name": "ccm89", "minwave": 1000.0, "maxwave": 1e4 / 8, "size": 100, "nloops": 100000, }, { "name": "ccm89", "minwave": 1e4 / 8, "maxwave": 1e4 / 3.3, "size": 100, "nloops": 100000, }, { "name": "ccm89", "minwave": 1e4 / 3.3, "maxwave": 1e4 / 1.1, "size": 100, "nloops": 100000, }, { "name": "ccm89", "minwave": 1e4 / 1.1, "maxwave": 1e4 / 0.3, "size": 100, "nloops": 100000, }, ] for b in benchmarks: times = timeit.repeat( stmt.format(**b), setup=setup.format(**b), repeat=3, number=b["nloops"] ) b["time"] = min(times) / b["nloops"] * 1e6 print( "{name:5s} wave=[{minwave: 7.1f}, {maxwave: 7.1f}] size={size:5d} {time:8.2f}us".format( **b ) ) print() if "fitzpatrick99" in args: # ----------------------------------------------------------------------- # Fitzpatrick init setup = """ import numpy from extinction import Fitzpatrick99 """ stmt = "Fitzpatrick99(3.1)" nloops = 10000 times = timeit.repeat(stmt, setup=setup, repeat=3, number=nloops) t = min(times) / nloops * 1e6 print(f"F99 init {t:8.2f}us") # ------------------------------------------------------------------------ # Fitzpatrick fast method setup = """ import numpy from extinction import Fitzpatrick99 wave = numpy.logspace(numpy.log10({minwave}), numpy.log10({maxwave}), {size:d}) f = Fitzpatrick99(3.1) """ stmt = "f(wave, 1.0)" benchmarks = [ {"minwave": 1000.0, "maxwave": 30000.0, "size": 10, "nloops": 10000}, {"minwave": 1000.0, "maxwave": 30000.0, "size": 100, "nloops": 10000}, {"minwave": 1000.0, "maxwave": 30000.0, "size": 1000, "nloops": 10000}, {"minwave": 1000.0, "maxwave": 30000.0, "size": 10000, "nloops": 1000}, {"minwave": 1000.0, "maxwave": 2700.0, "size": 1000, "nloops": 10000}, {"minwave": 2700.0, "maxwave": 30000.0, "size": 1000, "nloops": 10000}, ] for b in benchmarks: times = timeit.repeat( stmt.format(**b), setup=setup.format(**b), repeat=3, number=b["nloops"] ) b["time"] = min(times) / b["nloops"] * 1e6 print( "Fitzpatrick99 call wave=[{minwave: 7.1f}, {maxwave: 7.1f}] size={size:5d} {time:8.2f}us".format( **b ) ) if "apply" in args: setup = """ import numpy from extinction import apply ext = numpy.ones({size:d}) flux = numpy.ones({size:d}) """ stmt = "apply(ext, flux, inplace={inplace!r})" benchmarks = [ {"size": 10, "nloops": 100000, "inplace": True}, {"size": 10, "nloops": 100000, "inplace": False}, {"size": 100, "nloops": 100000, "inplace": True}, {"size": 100, "nloops": 100000, "inplace": False}, {"size": 1000, "nloops": 10000, "inplace": False}, ] for b in benchmarks: times = timeit.repeat( stmt.format(**b), setup=setup.format(**b), repeat=3, number=b["nloops"] ) b["time"] = min(times) / b["nloops"] * 1e6 print("apply size={size:5d} inplace={inplace!r} {time:8.2f}us".format(**b)) # def benchmark(f, args, repeat=3): # """Time `f(*args)`, repeat `repeat` times and return the best time.""" # # number = 1 # times = [] # # # determine number of times to run the loop. # while number < 10**9: # t0 = time.time() # for i in range(number): # f(*args) # t = time.time() - t0 # # if t > 0.1: # break # # number *= 10 # # # run the loop `number` times sncosmo-extinction-aeccedb/docs/000077500000000000000000000000001527041510000172105ustar00rootroot00000000000000sncosmo-extinction-aeccedb/docs/Makefile000066400000000000000000000151541527041510000206560ustar00rootroot00000000000000# Makefile for Sphinx documentation # # You can set these variables from the command line. 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The pseudo-XML files are in $(BUILDDIR)/pseudoxml." sncosmo-extinction-aeccedb/docs/conf.py000066400000000000000000000070761527041510000205210ustar00rootroot00000000000000# # build requires sphinx_rtd_theme and numpydoc. import os import sys import extinction # ensure that plot helper is on the path sys.path.insert(0, os.path.dirname(os.path.abspath(__file__))) # generate api directory if it doesn't already exist if not os.path.exists("api"): os.mkdir("api") # -- General configuration ------------------------------------------------ intersphinx_mapping = { "python": ("https://docs.python.org/3/", None), "numpy": ("https://numpy.org/doc/stable/", None), } extensions = [ "sphinx.ext.autodoc", "sphinx.ext.autosummary", "sphinx.ext.intersphinx", "sphinx.ext.mathjax", "numpydoc", "matplotlib.sphinxext.plot_directive", ] numpydoc_show_class_members = False autosummary_generate = True autoclass_content = "class" autodoc_default_options = {"members": True} # The suffix of source filenames. source_suffix = ".rst" # The master toctree document. master_doc = "index" # General information about the project. project = "extinction" copyright = "2016, Kyle Barbary and contributors" # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # THe short X.Y version. version = ".".join(extinction.__version__.split(".")[0:2]) # The full version, including alpha/beta/rc tags. release = extinction.__version__ # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. exclude_patterns = ["_build"] # The reST default role (used for this markup: `text`) to use for all # documents. default_role = "obj" # The name of the Pygments (syntax highlighting) style to use. pygments_style = "sphinx" # -- Options for HTML output ---------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. html_theme = "sphinx_rtd_theme" # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = [] # Output file base name for HTML help builder. htmlhelp_basename = "extinctiondoc" # -- Options for LaTeX output --------------------------------------------- latex_elements = { # The paper size ('letterpaper' or 'a4paper'). #'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). #'pointsize': '10pt', # Additional stuff for the LaTeX preamble. #'preamble': '', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ ("index", "extinction.tex", "extinction Documentation", "Kyle Barbary", "manual"), ] # -- Options for manual page output --------------------------------------- # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [("index", "extinction", "extinction Documentation", ["Kyle Barbary"], 1)] # -- Options for Texinfo output ------------------------------------------- # Grouping the document tree into Texinfo files. List of tuples # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ ( "index", "extinction", "extinction Documentation", "Kyle Barbary", "extinction", "One line description of project.", "Miscellaneous", ), ] sncosmo-extinction-aeccedb/docs/extinction_plot.py000066400000000000000000000034341527041510000230100ustar00rootroot00000000000000"""Plot extinction functions for comparison""" import matplotlib.pyplot as plt from matplotlib import rcParams from mpl_toolkits.axes_grid1 import make_axes_locatable rcParams["font.family"] = "serif" def extinction_figure( wave, a_lambda, residual_from, residual_lims=(-0.1, 0.4), title_text="$R_V = 3.1$" ): names = list(a_lambda.keys()) # consistent ordering between panels fig = plt.figure(figsize=(8.5, 6.0)) ax = plt.axes() for name in names: plt.plot(wave, a_lambda[name], label=name) plt.axvline(x=2700.0, ls=":", c="k") plt.axvline(x=3030.3030, ls=":", c="k") plt.axvline(x=9090.9091, ls=":", c="k") plt.axvspan(wave[0], 1150.0, fc="0.8", ec="none", zorder=-1000) plt.axvspan(1150.0, 1250.0, fc="0.9", ec="none", zorder=-1000) plt.text( 0.65, 0.95, title_text, transform=ax.transAxes, va="top", ha="right", size="x-large", ) plt.ylabel(r"Extinction ($A(\lambda)$ / $A_V$)") plt.legend() plt.setp(ax.get_xticklabels(), visible=False) divider = make_axes_locatable(ax) axresid = divider.append_axes("bottom", size=2.0, pad=0.2, sharex=ax) for name in names: plt.plot(wave, a_lambda[name] - a_lambda[residual_from]) plt.axvline(x=2700.0, ls=":", c="k") plt.axvline(x=3030.3030, ls=":", c="k") plt.axvline(x=9090.9091, ls=":", c="k") plt.axvspan(wave[0], 1150.0, fc="0.8", ec="none", zorder=-1000) plt.axvspan(1150.0, 1250.0, fc="0.9", ec="none", zorder=-1000) plt.xlim(wave[0], wave[-1]) plt.ylim(ymin=residual_lims[0], ymax=residual_lims[1]) plt.ylabel("residual from " + residual_from) plt.xlabel(r"Wavelength ($\mathrm{\AA}$)") ax.set_xscale("log") axresid.set_xscale("log") plt.tight_layout() return fig sncosmo-extinction-aeccedb/docs/index.rst000066400000000000000000000141031527041510000210500ustar00rootroot00000000000000extinction ========== *Fast interstellar dust extinction laws in Python* Cython-optimized implementations of empirical dust exitinction laws found in the literature. Installation ------------ Using conda:: conda install -c conda-forge extinction Using pip (requires a C compiler):: pip install extinction Extinction depends on numpy. **Development version / source code:** https://github.com/sncosmo/extinction Usage ----- **Functions:** .. autosummary:: :toctree: api extinction.ccm89 extinction.odonnell94 extinction.calzetti00 extinction.fitzpatrick99 extinction.fm07 extinction.apply extinction.remove **Classes:** .. autosummary:: :toctree: api extinction.Fitzpatrick99 **Examples:** Get extinction in magnitudes at a set of wavelengths for various dust laws:: >>> import numpy as np >>> import extinction >>> wave = np.array([2000., 4000., 8000.]) # wavelength in Angstroms # Cardelli, Clayton & Mathis (1989) with A_V = 1 and R_V = 3.1 >>> extinction.ccm89(wave, 1.0, 3.1) array([ 2.84252644, 1.4645557 , 0.59748901]) # extinction in magnitudes # O'Donnell (1994) >>> extinction.odonnell94(wave, 1.0, 3.1) array([ 2.84252644, 1.42617802, 0.60793495]) # Fitzpatrick (1999) >>> extinction.fitzpatrick99(wave, 1.0, 3.1) array([ 2.76225609, 1.79674653, 1.42325373]) The Fitzpatrick & Massa (2007) function has a fixed :math:`R_V` of 3.1:: >>> extinction.fm07(wave, 1.0) array([ 2.90478329, 1.42645161, 0.54703201]) All extinction laws accept a ``unit`` keyword to change the interpretation of the wavelength array from Angstroms to inverse microns:: >>> wave = np.array([5., 2.5, 1.25]) # wavelength in inverse microns >>> extinction.ccm89(wave, 1.0, 3.1, unit='invum') array([ 2.84252644, 1.4645557 , 0.59748901]) # extinction in magnitudes Redden or deredden .................. To "redden" or "deredden" flux values by some amount, use the ``apply`` and ``remove`` convenience functions:: >>> from extinction import ccm89, apply >>> flux = np.ones(3) # "redden" flux by A_V = 1.0 >>> apply(ccm89(wave, 1.0, 3.1), flux) array([ 0.07294397, 0.25952412, 0.5767723 ]) # "deredden" flux by A_V = 1.0 >>> remove(ccm89(wave, 1.0, 3.1), flux) array([ 13.70915145, 3.85320647, 1.73378645]) Comparison of functions ....................... .. plot:: import numpy as np import extinction from extinction_plot import extinction_figure wave = np.logspace(np.log10(910.), np.log10(30000.), 2000) a_lambda = {'ccm89': extinction.ccm89(wave, 1.0, 3.1), 'odonnell94': extinction.odonnell94(wave, 1.0, 3.1), 'fitzpatrick99': extinction.fitzpatrick99(wave, 1.0), 'fm07': extinction.fm07(wave, 1.0)} extinction_figure(wave, a_lambda, 'fitzpatrick99') R_V dependence of odonnell94 ............................ .. plot:: from collections import OrderedDict import numpy as np import extinction from extinction_plot import extinction_figure wave = np.logspace(np.log10(910.), np.log10(30000.), 2000) a_lambda = OrderedDict([ ('$R_V$ = 2.1', extinction.odonnell94(wave, 1.0, 2.1)), ('$R_V$ = 2.6', extinction.odonnell94(wave, 1.0, 2.6)), ('$R_V$ = 3.1', extinction.odonnell94(wave, 1.0, 3.1)), ('$R_V$ = 3.6', extinction.odonnell94(wave, 1.0, 3.6)), ('$R_V$ = 4.1', extinction.odonnell94(wave, 1.0, 4.1)) ]) extinction_figure(wave, a_lambda, '$R_V$ = 3.1', residual_lims=(-0.2, 0.6), title_text='odonnell94') R_V dependence of Fitzpatrick99 ............................... .. plot:: from collections import OrderedDict import numpy as np import extinction from extinction_plot import extinction_figure wave = np.logspace(np.log10(910.), np.log10(30000.), 2000) a_lambda = OrderedDict([ ('$R_V$ = 2.1', extinction.Fitzpatrick99(2.1)(wave, 1.0)), ('$R_V$ = 2.6', extinction.Fitzpatrick99(2.6)(wave, 1.0)), ('$R_V$ = 3.1', extinction.Fitzpatrick99(3.1)(wave, 1.0)), ('$R_V$ = 3.6', extinction.Fitzpatrick99(3.6)(wave, 1.0)), ('$R_V$ = 4.1', extinction.Fitzpatrick99(4.1)(wave, 1.0)) ]) extinction_figure(wave, a_lambda, '$R_V$ = 3.1', residual_lims=(-0.2, 0.6), title_text='Fitzpatrick99') A note on parameterization .......................... Most extinction laws here have two parameters: :math:`A_V` and :math:`R_V`. :math:`A_V` is a simply a linear scaling parameter; that is: ``ccm89(wave, 2.0, 3.1)`` is the same as ``2.0 * ccm89(wave, 1.0, 3.1)``. :math:`R_V` changes the *shape* of the extinction curve, rather than just the amplitude. Traditionally, the meaning ascribed to these parameters was that :math:`A_V` is the extinction in the *V* band, and :math:`R_V` describes the ratio of total to selective extinction: :math:`R_V = A_V / E(B-V)`, where :math:`E(B-V)` is the difference in extinction between the *B* and *V* bands. While this is approximately correct, the *measured* extinction of a source in actual *B* and *V* bandpasses will generally depend on the source spectrum and the shape of the specific bandpasses. Therefore, the :math:`A_V` and :math:`R_V` that are parameters in our extinction law will not correspond perfectly to measured *B* and *V* extinctions. So, in the context of these extinction laws, it is best to think of :math:`A_V` and :math:`R_V` as simply parameters that describe the amplitude and shape of the wavelength dependence, rather than corresponding directly to measured magnitudes. Finally, for a given shape of the extinction curve (described by :math:`R_V`), one can equally well use :math:`E(B-V)` as a linear scaling parameter in place of :math:`A_V`, with the equivalence :math:`E(B-V) = A_V / R_V`. Note that the above caution applies here: :math:`E(B-V)` should be considered simply a parameter describing amplitude of extinction; it will not correspond exactly to a difference in measured *B* and *V* extinctions. License and Credits ------------------- The license is MIT. Part of this code originated in the specutils package. sncosmo-extinction-aeccedb/extern/000077500000000000000000000000001527041510000175655ustar00rootroot00000000000000sncosmo-extinction-aeccedb/extern/README.md000066400000000000000000000001231527041510000210400ustar00rootroot00000000000000# external code Fetched using `fetch.sh` from https://github.com/kbarbary/bsplinessncosmo-extinction-aeccedb/extern/bs.c000066400000000000000000001147351527041510000203500ustar00rootroot00000000000000#include #include #include #include #if defined(_MSC_VER) #define INLINE _inline // __inline in newer versions #define RESTRICT __restrict #else #define INLINE inline #define RESTRICT restrict #endif //----------------------------------------------------------------------------- // debug stuff (remove later) #include void print_a_and_b(double first[5], double last[5], double *A, double *b, int M) { int i; printf("\nfirst: [ %f %f %f %f %f ]\n", first[0], first[1], first[2], first[3], first[4]); for (i=0; i= values[i] and x= values[n-1]. //----------------------------------------------------------------------------- // Linear search starting from guess that // values[start] <= x < values[start+1]. static int find_index_from(double *values, int n, double x, int start) { int i; if (start <= -1) { // search down i = 0; while (i < n && x >= values[i]) i++; return i-1; } else if (start >= n-1) { // search down i = n - 1; while (i > -1 && x < values[i]) i--; return i; } else if (x >= values[start]) { // search up i = start + 1; while (i < n && x >= values[i]) i++; return i-1; } else { // search down i = start - 1; while (i > -1 && x < values[i]) i--; return i; } } // find index using binary search static int find_index_binary(double *values, int n, double x) { int lo, hi, mid; lo = 0; hi = n; mid = n/2; if (x < values[0]) return -1; if (x >= values[n-1]) return n-1; while (hi - lo > 1) { if (x >= values[mid]) lo = mid; else hi = mid; mid = lo + (hi - lo) / 2; } return mid; } static int is_monotonic(bs_array x) { int i; int ok; ok = 1; for (i=1; i= x.data[(i-1)*x.stride]); } return ok; } static int min_points(bs_bctype left, bs_bctype right) { // one additional point needed for each not-a-knot condition. return 2 + (left == BS_NOTAKNOT) + (right == BS_NOTAKNOT); } //----------------------------------------------------------------------------- // knots & constants //----------------------------------------------------------------------------- // fill spline knots based on x array (includes padding on either // end of array). static double* alloc_knots(bs_array x) { int N; double *knots; int i; N = x.size; knots = malloc((N + 5) * sizeof(double)); // move pointer past initial two-element padding. knots += 2; // copy x into main part of knots for (i=0; i < N; i++) knots[i] = x.data[i * x.stride]; // fill padded area before beginning knots[-2] = knots[0] - 2.0 * (knots[1] - knots[0]); knots[-1] = knots[0] - 1.0 * (knots[1] - knots[0]); // fill padded area after end. knots[N] = knots[N-1] + 1.0 * (knots[N-1] - knots[N-2]); knots[N+1] = knots[N-1] + 2.0 * (knots[N-1] - knots[N-2]); knots[N+2] = knots[N-1] + 3.0 * (knots[N-1] - knots[N-2]); return knots; } static void free_knots(double *knots) { free(knots - 2); } // constants used when evaluating a spline. // constants + 4*i is a pointer to the four constants used // when evaluating the spline in the range knots[i] <= x < knots[i+1]. static double* alloc_constants(double *knots, int n) { int i; double *constants; constants = malloc(4 * n * sizeof(double)); for (i=0; i0; i--) { b[i] -= b[i+1] * A[3*i+2]; } // first row is different b[0] -= b[1] * A[1] + b[2] * A[2]; } */ //----------------------------------------------------------------------------- // solve() // // Solve A * x = b for x. The solution is stored in b. // // A is a matrix like this: // // | x x x x x | // | x x x | // | x x x | // | ... | // | x x x | // | x x x | // | x x x | // | x x x x x | // // A is stored compactly in 3*n elements, with row i corresponding to A[3*i], // with the exception of the first and last rows which are passed in // separately because they are too large to be stored this way. // // Note that the first 3 and last 3 elements of A are initially empty as // these row values are stored in `first` and `last`. In fact the last 3 // elements of A are not used at all. // //----------------------------------------------------------------------------- typedef struct { double *first; double *rows; // first + 5 double *last; // first + 5 + 3*(M-1) } banded_matrix; // allocate storate for a banded matrix. // M is total number of rows, including first and last. static banded_matrix alloc_banded_matrix(int M) { double* first = malloc((5 + 3*(M-1) + 5) * sizeof(double)); banded_matrix m = {first, first + 5, first + 5 + 3*(M-1)}; return m; } static void free_banded_matrix(banded_matrix A) { free(A.first); A.first = NULL; A.rows = NULL; A.last = NULL; } static void copy_banded_matrix(banded_matrix dst, banded_matrix src, int M) { size_t nbytes = (10 + 3*(M-1)) * sizeof(double); memcpy(dst.first, src.first, nbytes); } static void solve(banded_matrix mat, double* RESTRICT b, int n) { int i; double tmp; double* RESTRICT first = mat.first; double* RESTRICT A = mat.rows; double* RESTRICT last = mat.last; // rows 1, 2, 3: divide by first non-zero // // x x x x x | y x x x x x | y // x x x | y 1 x x | y // x x x | y --> 1 x x | y // x x x | y 1 x x | y for (i=1; i<4; i++) { b[i] /= A[3*i]; A[3*i+2] /= A[3*i]; A[3*i+1] /= A[3*i]; A[3*i] = 1.0; } // eliminate first two elements of first row and divide by first non-zero. // // x x x x x | y 0 0 1 x x | y // 1 x x | y 1 x x | y // 1 x x | y --> 1 x x | y // 1 x x | y 1 x x | y b[0] -= first[0] * b[1]; first[2] -= first[0] * A[3*1+2]; first[1] -= first[0] * A[3*1+1]; first[0] = 0.0; b[0] -= first[1] * b[2]; first[3] -= first[1] * A[3*2+2]; first[2] -= first[1] * A[3*2+1]; first[1] = 0.0; b[0] /= first[2]; first[4] /= first[2]; first[3] /= first[2]; first[2] = 1.0; // reduce row 3 // // 0 0 1 x x | y 0 0 1 x x | y // 1 x x | y 1 x x | y // 1 x x | y --> 1 x x | y // 1 x x | y 0 1 x | y b[3] -= A[3*3+0] * b[0]; A[3*3+2] -= A[3*3+0] * first[4]; A[3*3+1] -= A[3*3+0] * first[3]; A[3*3+0] = 0.0; b[3] /= A[3*3+1]; A[3*3+2] /= A[3*3+1]; A[3*3+1] = 1.0; // permute first three rows: // 0 0 1 x x | y 1 x x | y // 1 x x | y 1 x x | y // 1 x x | y --> 1 x x | y // 0 1 x | y 0 1 x | y tmp = b[0]; b[0] = b[1]; A[3*0+0] = A[3*1+0]; A[3*0+1] = A[3*1+1]; A[3*0+2] = A[3*1+2]; b[1] = b[2]; A[3*1+0] = A[3*2+0]; A[3*1+1] = A[3*2+1]; A[3*1+2] = A[3*2+2]; b[2] = tmp; A[3*2+0] = first[2]; A[3*2+1] = first[3]; A[3*2+2] = first[4]; // reduce rest of the middle rows for (i=4; i=3; i--) { b[i] -= b[i+1] * A[3*i+2]; } // we now have: // 1 x x | y // 1 x x | y // 1 x x | y // 1 | y // 1 | y // ... // // eliminate the remaining elements. b[2] -= b[3] * A[3*2+1] + b[4] * A[3*2+2]; b[1] -= b[2] * A[3*1+1] + b[3] * A[3*1+2]; b[0] -= b[1] * A[3*0+1] + b[2] * A[3*0+2]; } //----------------------------------------------------------------------------- // finding coefficients //----------------------------------------------------------------------------- static void notaknot_row(double *consts, int i, double row[5]) { int j; double buf[4]; d3b3nonzeros(i-1, consts, row); d3b3nonzeros(i, consts, buf); row[4] = 0.0; for (j=0; j<4; j++) { row[j+1] -= buf[j]; } } static void fill_banded_matrix(banded_matrix A, double* RESTRICT knots, double* RESTRICT consts, int N, bs_bctype bctypes[2]) { int i; double* RESTRICT first = A.first; double* RESTRICT rows = A.rows; double* RESTRICT last = A.last; // Left boundary condition switch (bctypes[0]) { case BS_DERIV1: db3nonzeros(knots[0], 0, knots, consts, first); first[3] = first[4] = 0.0; break; case BS_DERIV2: d2b3nonzeros(knots[0], 0, knots, consts, first); first[3] = first[4] = 0.0; break; case BS_NOTAKNOT: notaknot_row(consts, 1, first); } // fill rows 1 through M-1 with values of b_{i-3}, b_{i-2}, b{i-1} // at knot i. for (i=0; i1; i--) last[i] = last[i-2]; last[0] = last[1] = 0.0; break; case BS_DERIV2: d2b3nonzeros(knots[N-1], N-1, knots, consts, last); for (i=4; i>1; i--) last[i] = last[i-2]; last[0] = last[1] = 0.0; break; case BS_NOTAKNOT: notaknot_row(consts, N-2, last); } } // Find spline coefficients along one dimension. // knots and consts are as belong to a spline. // A should be allocated with M = values.size + 2. // coeffs should be size M. static void find_1d_coefficients(banded_matrix A, bs_array values, double bcvalues[2], double* RESTRICT coeffs) { int i; int N = values.size; int M = N+2; coeffs[0] = bcvalues[0]; for (i=0; iknots = alloc_knots(x); spline->n = N; spline->exts = exts; spline->consts = alloc_constants(spline->knots, N); spline->coeffs = malloc(M * sizeof(double)); A = alloc_banded_matrix(M); fill_banded_matrix(A, spline->knots, spline->consts, N, bctypes); bcvalues[0] = (bcs.left.type == BS_NOTAKNOT) ? 0.0 : bcs.left.value; bcvalues[1] = (bcs.right.type == BS_NOTAKNOT) ? 0.0 : bcs.right.value; find_1d_coefficients(A, y, bcvalues, spline->coeffs); free_banded_matrix(A); *out = spline; return BS_OK; } void bs_spline1d_free(bs_spline1d* spline) { if (spline != NULL) { free_knots(spline->knots); free(spline->consts); free(spline->coeffs); free(spline); } } bs_errorcode bs_spline1d_eval(bs_spline1d *spline, bs_array x, bs_array out) { int i; int j; double xval; double b3vals[4]; // for first index, it could be anywhere, so use binary search i = find_index_binary(spline->knots, spline->n, x.data[0]); for (j=0; jknots, spline->n, xval, i); // index outside left boundary if (i == -1) { switch (spline->exts.left.type) { case BS_EXTRAPOLATE: i = 0; break; case BS_CONSTANT: i = 0; xval = spline->knots[0]; break; case BS_VALUE: out.data[j * out.stride] = spline->exts.left.value; continue; case BS_RAISE: return BS_DOMAINERROR; } } // index outside right boundary else if (i == spline->n - 1) { switch (spline->exts.right.type) { case BS_EXTRAPOLATE: i = spline->n - 2; break; case BS_CONSTANT: i = spline->n-2; xval = spline->knots[spline->n-1]; break; case BS_VALUE: out.data[j * out.stride] = spline->exts.right.value; continue; case BS_RAISE: return BS_DOMAINERROR; } } // if we get this far, we're either extrapolating or xval is in range. b3nonzeros(xval, i, spline->knots, spline->consts, b3vals); out.data[j*out.stride] = (spline->coeffs[i] * b3vals[0] + spline->coeffs[i+1] * b3vals[1] + spline->coeffs[i+2] * b3vals[2] + spline->coeffs[i+3] * b3vals[3]); } return BS_OK; } //----------------------------------------------------------------------------- // spline2d //----------------------------------------------------------------------------- // get the i-th bc value static double get_bcarray_value(bs_bcarray bc, int i) { return (bc.type == BS_NOTAKNOT) ? 0.0 : bc.data[i * bc.stride]; } static int bcarray_size_match(bs_bcarray bc, int size) { // if not-a-knot, value is not used, so size is OK. return (bc.type == BS_NOTAKNOT) ? 1 : (bc.size == size); } bs_errorcode bs_spline2d_create(bs_array x, bs_array y, bs_array2d z, bs_bcarray_pair xbcs, bs_bcarray_pair ybcs, bs_exts xexts, bs_exts yexts, bs_spline2d **out) { int i, j; int nx, mx, ny, my; bs_bctype bctypes[2] = {ybcs.left.type, ybcs.right.type}; double bcvalues[2]; bs_spline2d* spline; double *coeffs; banded_matrix A, Awork; bs_array zslice, coeffs_slice; double *buf; *out = NULL; // In case of error, ensure that output pointer is NULL. if ((x.size != z.sizes[0]) || (y.size != z.sizes[1])) return BS_SIZEMISMATCH; if (!is_monotonic(x) || !is_monotonic(y)) return BS_NOTMONOTONIC; if ((x.size < min_points(xbcs.left.type, xbcs.right.type)) || (y.size < min_points(ybcs.left.type, ybcs.right.type))) return BS_TOOFEWPOINTS; // check if boundary condition sizes match x and y sizes. if (!(bcarray_size_match(xbcs.left, y.size) && bcarray_size_match(xbcs.right, y.size) && bcarray_size_match(ybcs.left, x.size) && bcarray_size_match(ybcs.left, x.size))) return BS_BCSIZEMISMATCH; spline = malloc(sizeof(bs_spline2d)); nx = x.size; mx = nx + 2; ny = y.size; my = ny + 2; spline->xknots = alloc_knots(x); spline->xconsts = alloc_constants(spline->xknots, nx); spline->nx = nx; spline->xexts = xexts; spline->yknots = alloc_knots(y); spline->yconsts = alloc_constants(spline->yknots, ny); spline->ny = ny; spline->yexts = yexts; coeffs = malloc(mx * my * sizeof(double)); // find coefficients along y (fast axis) A = alloc_banded_matrix(my); Awork = alloc_banded_matrix(my); fill_banded_matrix(A, spline->yknots, spline->yconsts, spline->ny, bctypes); for (i=0; ixknots, spline->xconsts, spline->nx, bctypes); buf = malloc(mx * sizeof(double)); for (i=0; icoeffs = coeffs; *out = spline; return BS_OK; } void bs_spline2d_free(bs_spline2d* spline) { if (spline != NULL) { free_knots(spline->xknots); free(spline->xconsts); free_knots(spline->yknots); free(spline->yconsts); free(spline->coeffs); free(spline); } } bs_errorcode bs_spline2d_eval(bs_spline2d *spline, bs_array x, bs_array y, bs_array2d out) { // for first index, it could be anywhere, so use binary search int i = find_index_binary(spline->xknots, spline->nx, x.data[0]); int j0 = find_index_binary(spline->yknots, spline->ny, y.data[0]); int j, k, l; int my = spline->ny + 2; // for indexing coeffs. double xb3vals[4]; double yb3vals[4]; double xval, yval; for (k=0; kxknots, spline->nx, xval, i); // index outside left boundary if (i == -1) { switch (spline->xexts.left.type) { case BS_EXTRAPOLATE: i = 0; break; case BS_CONSTANT: i = 0; xval = spline->xknots[0]; break; case BS_VALUE: for (l=0; lxexts.left.value; } continue; case BS_RAISE: return BS_DOMAINERROR; } } // index outside right boundary else if (i == spline->nx - 1) { switch (spline->xexts.right.type) { case BS_EXTRAPOLATE: i = spline->nx - 2; break; case BS_CONSTANT: i = spline->nx - 2; xval = spline->xknots[spline->nx-1]; break; case BS_VALUE: for (l=0; lxexts.right.value; } continue; case BS_RAISE: return BS_DOMAINERROR; } } // get basis function values for x coordinate b3nonzeros(xval, i, spline->xknots, spline->xconsts, xb3vals); // x value is in range (or extrapolating); loop over y values: j = j0; for (l=0; lyknots, spline->ny, yval, j); // index outside left boundary if (j == -1) { switch (spline->yexts.left.type) { case BS_EXTRAPOLATE: j = 0; break; case BS_CONSTANT: j = 0; yval = spline->yknots[0]; break; case BS_VALUE: out.data[k * out.strides[0] + l * out.strides[1]] = spline->yexts.left.value; continue; case BS_RAISE: return BS_DOMAINERROR; } } // index outside right boundary else if (j == spline->ny - 1) { switch (spline->yexts.right.type) { case BS_EXTRAPOLATE: j = spline->ny - 2; break; case BS_CONSTANT: j = spline->ny - 2; yval = spline->yknots[spline->ny-1]; break; case BS_VALUE: out.data[k * out.strides[0] + l * out.strides[1]] = spline->yexts.right.value; continue; case BS_RAISE: return BS_DOMAINERROR; } } // get basis function values for y coordinate b3nonzeros(yval, j, spline->yknots, spline->yconsts, yb3vals); out.data[k * out.strides[0] + l * out.strides[1]] = (spline->coeffs[(i )*my+j] * xb3vals[0] * yb3vals[0] + spline->coeffs[(i )*my+j+1] * xb3vals[0] * yb3vals[1] + spline->coeffs[(i )*my+j+2] * xb3vals[0] * yb3vals[2] + spline->coeffs[(i )*my+j+3] * xb3vals[0] * yb3vals[3] + spline->coeffs[(i+1)*my+j] * xb3vals[1] * yb3vals[0] + spline->coeffs[(i+1)*my+j+1] * xb3vals[1] * yb3vals[1] + spline->coeffs[(i+1)*my+j+2] * xb3vals[1] * yb3vals[2] + spline->coeffs[(i+1)*my+j+3] * xb3vals[1] * yb3vals[3] + spline->coeffs[(i+2)*my+j] * xb3vals[2] * yb3vals[0] + spline->coeffs[(i+2)*my+j+1] * xb3vals[2] * yb3vals[1] + spline->coeffs[(i+2)*my+j+2] * xb3vals[2] * yb3vals[2] + spline->coeffs[(i+2)*my+j+3] * xb3vals[2] * yb3vals[3] + spline->coeffs[(i+3)*my+j] * xb3vals[3] * yb3vals[0] + spline->coeffs[(i+3)*my+j+1] * xb3vals[3] * yb3vals[1] + spline->coeffs[(i+3)*my+j+2] * xb3vals[3] * yb3vals[2] + spline->coeffs[(i+3)*my+j+3] * xb3vals[3] * yb3vals[3]); } } return BS_OK; } //----------------------------------------------------------------------------- // uspline1d //----------------------------------------------------------------------------- static void fill_banded_matrix_u(banded_matrix A, int N, double didx, bs_bctype bctypes[2]) { int i, j; // values, first and second derivatives of b3_{i-3}, b3_{i-2}, b3_{i-1} // at knot i. const double b3vals[3] = {1.0/6.0, 2.0/3.0, 1.0/6.0}; const double db3vals[3] = {-0.5 * didx, 0.0, 0.5 * didx}; const double d2b3vals[3] = {didx * didx, -2.0 * didx * didx, didx * didx}; const double notaknot_row[5] = {-1.0, 4.0, -6.0, 4.0, -1.0}; // Left boundary condition switch (bctypes[0]) { case BS_DERIV1: for (i=0; i<3; i++) A.first[i] = db3vals[i]; A.first[3] = A.first[4] = 0.0; break; case BS_DERIV2: for (i=0; i<3; i++) A.first[i] = d2b3vals[i]; A.first[3] = A.first[4] = 0.0; break; case BS_NOTAKNOT: for (i=0; i<5; i++) A.first[i] = notaknot_row[i]; } // rows for (i=0; ix = x; spline->didx = didx; spline->n = N; spline->exts = exts; b = malloc(M * sizeof(double)); A = alloc_banded_matrix(M); fill_banded_matrix_u(A, N, didx, bctypes); // fill RHS b[0] = (bcs.left.type == BS_NOTAKNOT)? 0.0: bcs.left.value; b[M-1] = (bcs.right.type == BS_NOTAKNOT)? 0.0: bcs.right.value; for (i=0; icoeffs = b; *out = spline; return BS_OK; } void bs_uspline1d_free(bs_uspline1d* spline) { if (spline != NULL) { free(spline->coeffs); free(spline); } } bs_errorcode bs_uspline1d_eval(bs_uspline1d *spline, bs_array x, bs_array out) { int i, j; double xval; double xfloor; double b3vals[4]; for (j=0; jx.min) * spline->didx; xfloor = floor(xval); i = (int)xfloor; // index outside left boundary if (i < 0) { switch (spline->exts.left.type) { case BS_EXTRAPOLATE: i = 0; xfloor = 0.0; break; case BS_CONSTANT: i = 0; xfloor = 0.0; xval = 0.0; break; case BS_VALUE: out.data[j * out.stride] = spline->exts.left.value; continue; case BS_RAISE: return BS_DOMAINERROR; } } // index outside right boundary else if (i >= spline->n-1) { switch (spline->exts.right.type) { case BS_EXTRAPOLATE: i = spline->n - 2; xfloor = i; break; case BS_CONSTANT: i = spline->n - 2; xfloor = i; xval = xfloor+1.0; break; case BS_VALUE: out.data[j * out.stride] = spline->exts.right.value; continue; case BS_RAISE: return BS_DOMAINERROR; } } // if we get this far, we're evaluating the spline b3unonzeros(xval - xfloor, b3vals); out.data[j*out.stride] = (spline->coeffs[i] * b3vals[0] + spline->coeffs[i+1] * b3vals[1] + spline->coeffs[i+2] * b3vals[2] + spline->coeffs[i+3] * b3vals[3]); } return BS_OK; } sncosmo-extinction-aeccedb/extern/bs.h000066400000000000000000000067341527041510000203540ustar00rootroot00000000000000#ifndef BS_H #define BS_H //----------------------------------------------------------------------------- // Error codes //----------------------------------------------------------------------------- typedef enum { BS_OK = 0, BS_OUTOFMEMORY = 1, BS_DOMAINERROR = 2, BS_NOTMONOTONIC = 3, BS_SIZEMISMATCH = 4, BS_BCSIZEMISMATCH = 5, BS_TOOFEWPOINTS = 6, } bs_errorcode; //----------------------------------------------------------------------------- // Input data types //----------------------------------------------------------------------------- typedef struct { double *data; int size; int stride; } bs_array; typedef struct { double *data; int sizes[2]; int strides[2]; } bs_array2d; typedef struct { double min; // inclusive double max; // inclusive } bs_range; //----------------------------------------------------------------------------- // Boundary conditions //----------------------------------------------------------------------------- typedef enum {BS_DERIV1, BS_DERIV2, BS_NOTAKNOT} bs_bctype; typedef struct { bs_bctype type; double value; } bs_bc; typedef struct { bs_bc left; bs_bc right; } bs_bcs; // array boundary conditions for spline2d. typedef struct { bs_bctype type; double *data; int size; int stride; } bs_bcarray; typedef struct { bs_bcarray left; bs_bcarray right; } bs_bcarray_pair; //----------------------------------------------------------------------------- // out-of-domain behavior ("extension") //----------------------------------------------------------------------------- typedef enum {BS_EXTRAPOLATE, BS_CONSTANT, BS_VALUE, BS_RAISE} bs_exttype; typedef struct { bs_exttype type; double value; } bs_ext; typedef struct { bs_ext left; bs_ext right; } bs_exts; //----------------------------------------------------------------------------- // 1-d splines //----------------------------------------------------------------------------- typedef struct { double *knots; double *consts; double *coeffs; int n; bs_exts exts; } bs_spline1d; bs_errorcode bs_spline1d_create(bs_array x, bs_array y, bs_bcs bcs, bs_exts exts, bs_spline1d **out); bs_errorcode bs_spline1d_eval(bs_spline1d *spline, bs_array x, bs_array out); void bs_spline1d_free(bs_spline1d *spline); typedef struct { bs_range x; double didx; double *coeffs; int n; bs_exts exts; } bs_uspline1d; bs_errorcode bs_uspline1d_create(bs_range x, bs_array y, bs_bcs bcs, bs_exts exts, bs_uspline1d **out); bs_errorcode bs_uspline1d_eval(bs_uspline1d *spline, bs_array x, bs_array out); void bs_uspline1d_free(bs_uspline1d *spline); //----------------------------------------------------------------------------- // 2-d splines //----------------------------------------------------------------------------- typedef struct { double *xknots; double *xconsts; double *yknots; double *yconsts; double *coeffs; int nx; int ny; bs_exts xexts; bs_exts yexts; } bs_spline2d; bs_errorcode bs_spline2d_create(bs_array x, bs_array y, bs_array2d z, bs_bcarray_pair xbcs, bs_bcarray_pair ybcs, bs_exts xexts, bs_exts yexts, bs_spline2d **out); bs_errorcode bs_spline2d_eval(bs_spline2d *spline, bs_array x, bs_array y, bs_array2d out); void bs_spline2d_free(bs_spline2d *spline); #endif sncosmo-extinction-aeccedb/extern/bsplines.pxi000066400000000000000000000101301527041510000221210ustar00rootroot00000000000000cdef extern from "bs.h": ctypedef enum bs_errorcode: BS_OK = 0 BS_OUTOFMEMORY = 1 BS_DOMAINERROR = 2 BS_NOTMONOTONIC = 3 BS_SIZEMISMATCH = 4 BS_BCSIZEMISMATCH = 5 BS_TOOFEWPOINTS = 6 ctypedef struct bs_array: double *data int size int stride ctypedef struct bs_array2d: double *data int sizes[2] int strides[2] ctypedef struct bs_range: double min double max ctypedef enum bs_bctype: BS_DERIV1 BS_DERIV2 BS_NOTAKNOT ctypedef struct bs_bc: bs_bctype type double value ctypedef struct bs_bcs: bs_bc left bs_bc right ctypedef enum bs_exttype: BS_EXTRAPOLATE BS_CONSTANT BS_VALUE BS_RAISE ctypedef struct bs_ext: bs_exttype type double value ctypedef struct bs_exts: bs_ext left bs_ext right ctypedef struct bs_spline1d: double *knots double *coeffs int n ctypedef struct bs_bcarray: bs_bctype type double *data int size int stride ctypedef struct bs_bcarray_pair: bs_bcarray left bs_bcarray right bs_errorcode bs_spline1d_create(bs_array x, bs_array y, bs_bcs bcs, bs_exts exts, bs_spline1d **out) bs_errorcode bs_spline1d_eval(bs_spline1d *spline, bs_array x, bs_array out) void bs_spline1d_free(bs_spline1d *spline) ctypedef struct bs_spline2d: double *xknots double *xconsts double *yknots double *yconsts double *coeffs int nx int ny bs_exts xexts bs_exts yexts bs_errorcode bs_spline2d_create(bs_array x, bs_array y, bs_array2d z, bs_bcarray_pair xbcs, bs_bcarray_pair ybcs, bs_exts xexts, bs_exts yexts, bs_spline2d **out) bs_errorcode bs_spline2d_eval(bs_spline2d *spline, bs_array x, bs_array y, bs_array2d out) void bs_spline2d_free(bs_spline2d *spline) ctypedef struct bs_uspline1d: bs_range x double didx double *coeffs int n bs_exts exts bs_errorcode bs_uspline1d_create(bs_range x, bs_array y, bs_bcs bcs, bs_exts exts, bs_uspline1d **out) bs_errorcode bs_uspline1d_eval(bs_uspline1d *spline, bs_array x, bs_array out) void bs_uspline1d_free(bs_uspline1d *spline) #------------------------------------------------------------------------------ # helpers class DomainError(Exception): """Raised when spline input(s) are outside spline boundaries.""" pass cdef int assert_ok(bs_errorcode code) except -1: """raise an exception if the error code is not OK""" if code == BS_OK: return 0 elif code == BS_OUTOFMEMORY: raise MemoryError() elif code == BS_DOMAINERROR: raise DomainError() elif code == BS_NOTMONOTONIC: raise ValueError("input array(s) not monotonically increasing") elif code == BS_SIZEMISMATCH: raise ValueError("input array size mismatch") elif code == BS_BCSIZEMISMATCH: raise ValueError("boundary condition size mismatch") elif code == BS_TOOFEWPOINTS: raise ValueError("Too few points in input array. required: 2 + (1 for each not-a-knot condition)") else: raise Exception("unrecognized error") cdef inline bs_array to_bs_array(const double[:] x): # bs_array is also used for outputs, so its pointer is not const. # bs_spline1d_eval only reads its input array. return bs_array(&x[0], x.shape[0], x.strides[0]//sizeof(double)) cdef inline bs_array2d to_bs_array2d(double[:, :] x): cdef bs_array2d out out.data = &x[0, 0] out.sizes[0] = x.shape[0] out.sizes[1] = x.shape[1] out.strides[0] = x.strides[0] // sizeof(double) out.strides[1] = x.strides[1] // sizeof(double) return out sncosmo-extinction-aeccedb/extern/fetch.sh000077500000000000000000000003651527041510000212210ustar00rootroot00000000000000#!/bin/sh COMMIT_HASH=2f14aa748f200290400307b40116787a0dbf5d43 URL=https://raw.githubusercontent.com/kbarbary/bsplines wget -nc ${URL}/${COMMIT_HASH}/src/bs.c wget -nc ${URL}/${COMMIT_HASH}/src/bs.h wget -nc ${URL}/${COMMIT_HASH}/bsplines.pxi sncosmo-extinction-aeccedb/pyproject.toml000066400000000000000000000070111527041510000211730ustar00rootroot00000000000000[build-system] requires = [ "setuptools>=77", # 3.1 is the first release that honours the freethreading_compatible # directive in extinction.pyx; earlier versions silently ignore it and # emit a module that re-enables the GIL on free-threaded interpreters. "Cython>=3.1", "numpy>=2", ] build-backend = "setuptools.build_meta" [project] name = "extinction" description = "Fast interstellar dust extinction laws" readme = "README.md" license = "MIT" license-files = ["LICENSE"] authors = [{ name = "Kyle Barbary", email = "kylebarbary@gmail.com" }] requires-python = ">=3.10" # Wheels are built against numpy 2, which stays ABI compatible back to 1.19.3. dependencies = ["numpy>=1.19.3"] dynamic = ["version"] classifiers = [ "Development Status :: 5 - Production/Stable", "Intended Audience :: Science/Research", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", "Programming Language :: Python :: 3.13", "Programming Language :: Python :: 3.14", "Programming Language :: Python :: 3.15", "Programming Language :: Python :: Free Threading :: 3 - Stable", "Topic :: Scientific/Engineering :: Astronomy", ] [dependency-groups] test = ["pytest"] docs = ["matplotlib", "numpydoc", "sphinx", "sphinx-rtd-theme"] dev = [ { include-group = "test" }, { include-group = "docs" }, "ty", # The build requirements, so that ty can check setup.py. The ty hook does # not install the project, so numpy here is also what ty uses for the # stub and the tests. "Cython>=3.1", "numpy>=2", "setuptools>=77", ] [project.urls] Homepage = "https://github.com/sncosmo/extinction" Documentation = "https://extinction.readthedocs.io" Source = "https://github.com/sncosmo/extinction" [tool.setuptools] package-dir = { "" = "src" } [tool.setuptools.packages.find] where = ["src"] # PEP 561 marker and stubs for the compiled module. [tool.setuptools.package-data] extinction = ["py.typed", "*.pyi"] # The Cython source belongs in the sdist, not in binary wheels; now that it # lives inside the package directory, MANIFEST.in would otherwise pull it in. # setup.py regenerates the C next to it on every build, so neither the sdist # (see MANIFEST.in) nor the wheels ship the C. [tool.setuptools.exclude-package-data] extinction = ["*.pyx", "*.c"] [tool.pytest.ini_options] testpaths = ["tests"] [tool.ruff] extend-exclude = ["extern"] # uv rebuilds the project only when one of these changes, and this list # replaces the default one. Add the Cython and C sources, so that `uv run` and # `uv sync` rebuild the compiled extension after they change. Also rebuild # when .venv is created again: the editable install builds the extension in # src/extinction, outside .venv, and `git clean -fdx` deletes both. [tool.uv] cache-keys = [ { file = "pyproject.toml" }, { file = "setup.py" }, { file = "src/extinction/*.pyx" }, { file = "extern/*" }, { dir = ".venv" }, ] [tool.cibuildwheel] build-frontend = "build[uv]" # numpy has no Windows ARM64 wheels for Python 3.10, and its source build fails # on windows-11-arm. cibuildwheel would stop there, before it builds the wheels # for the newer Python versions. skip = ["cp310-win_arm64"] # setup.py builds a cp311-abi3 wheel on Python 3.11. cibuildwheel then does # not build again for the later Python versions with the GIL: it tests the # abi3 wheel on each of them. test-groups = ["test"] test-command = "pytest {project}/tests" sncosmo-extinction-aeccedb/setup.py000077500000000000000000000073751527041510000200110ustar00rootroot00000000000000#!/usr/bin/env python import importlib.machinery import os import re import sys import sysconfig import numpy from Cython.Build import cythonize from setuptools import setup from setuptools.command.build_ext import build_ext from setuptools.extension import Extension here = os.path.dirname(os.path.abspath(__file__)) # Everything except the version and the extension itself lives in # pyproject.toml. Synchronize the version from code. fname = os.path.join("src", "extinction", "_extinction.pyx") with open(fname, encoding="utf-8") as f: version = re.findall(r"__version__ = \"(.*?)\"", f.read())[0] # Build Cython extension source_files = [fname, os.path.join("extern", "bs.c")] depends_files = [os.path.join("extern", "bs.h"), os.path.join("extern", "bsplines.pxi")] include_dirs = [numpy.get_include(), "extern"] # MSVC does not understand -std=c11 and only warns about it. extra_compile_args = [] if sys.platform == "win32" else ["-std=c11"] # Pin the numpy C API level, so that a future numpy removing an already # deprecated API is a compile error here rather than a surprise at runtime. define_macros = [("NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION")] # From Python 3.11, build for the stable ABI (abi3), so that one wheel works # on Python 3.11 and all later versions with the GIL. The typed memoryviews # need the buffer protocol, which is in the limited API only from 3.11, so # Python 3.10 gets its own wheel. The free-threaded builds also get their own # wheels: their stable ABI (abi3t, from 3.15) needs support in Cython first. # PyPy and GraalPy do not implement the whole limited API, and a module built # for it there fails to import, so build for their own ABI. limited_api = ( sys.implementation.name == "cpython" and sys.version_info >= (3, 11) and not sysconfig.get_config_var("Py_GIL_DISABLED") ) if limited_api: define_macros.append(("Py_LIMITED_API", "0x030B0000")) extensions = [ Extension( "extinction._extinction", source_files, include_dirs=include_dirs, depends=depends_files, define_macros=define_macros, extra_compile_args=extra_compile_args, py_limited_api=limited_api, ) ] class cythonize_build_ext(build_ext): """Generate the C when the extension is built. Cythonizing at the top level of setup.py would also run it for each call that only reads the metadata or makes the sdist. """ def run(self): for ext in self.extensions: # `include "extern/bsplines.pxi"` in the .pyx resolves against the # project root, not the directory holding the .pyx. Always # regenerate the C, which depends on the numpy .pxd of the build # environment: uv links build environments from its cache with # old mtimes, so Cython's timestamp check can reuse a .c made for # another numpy, which then fails to compile. (cythonized,) = cythonize( [ext], language_level=3, include_path=[here], force=True ) ext.sources = cythonized.sources super().run() if self.inplace and limited_api: # A build for this Python without the limited API leaves a module # with a version-specific suffix, which Python imports before the # new abi3 one, so remove it. for ext in self.extensions: stale = os.path.join(here, "src", *ext.name.split(".")) stale += importlib.machinery.EXTENSION_SUFFIXES[0] if os.path.exists(stale): os.remove(stale) setup( version=version, ext_modules=extensions, cmdclass={"build_ext": cythonize_build_ext}, # Tag the wheel cp311-abi3. options={"bdist_wheel": {"py_limited_api": "cp311"}} if limited_api else {}, ) sncosmo-extinction-aeccedb/src/000077500000000000000000000000001527041510000170475ustar00rootroot00000000000000sncosmo-extinction-aeccedb/src/extinction/000077500000000000000000000000001527041510000212335ustar00rootroot00000000000000sncosmo-extinction-aeccedb/src/extinction/__init__.py000066400000000000000000000005751527041510000233530ustar00rootroot00000000000000"""Interstellar dust extinction functions.""" from extinction._extinction import ( Fitzpatrick99, __version__, apply, calzetti00, ccm89, fitzpatrick99, fm07, odonnell94, remove, ) __all__ = [ "Fitzpatrick99", "__version__", "apply", "calzetti00", "ccm89", "fitzpatrick99", "fm07", "odonnell94", "remove", ] sncosmo-extinction-aeccedb/src/extinction/_extinction.pyi000066400000000000000000000030021527041510000242740ustar00rootroot00000000000000from typing import Literal, TypeAlias import numpy as np from numpy.typing import ArrayLike, NDArray __version__: str __all__ = [ "Fitzpatrick99", "apply", "calzetti00", "ccm89", "fitzpatrick99", "fm07", "odonnell94", "remove", ] _Unit: TypeAlias = Literal["aa", "invum"] _Array: TypeAlias = NDArray[np.float64] def ccm89( wave: _Array, a_v: float, r_v: float, unit: _Unit = ..., out: _Array | None = ..., ) -> _Array: ... def odonnell94( wave: _Array, a_v: float, r_v: float, unit: _Unit = ..., out: _Array | None = ..., ) -> _Array: ... def calzetti00( wave: _Array, a_v: float, r_v: float, unit: _Unit = ..., out: _Array | None = ..., ) -> _Array: ... def fitzpatrick99( wave: _Array, a_v: float, r_v: float = ..., unit: _Unit = ..., ) -> _Array: ... def fm07(wave: _Array, a_v: float, unit: _Unit = ...) -> _Array: ... class Fitzpatrick99: # cdef readonly in the extension: assignment raises AttributeError. @property def r_v(self) -> float: ... def __init__(self, r_v: float = ...) -> None: ... def __call__(self, wave: _Array, a_v: float, unit: _Unit = ...) -> _Array: ... # Unlike the wavelength arguments above, which go through typed memoryviews, # these are plain numpy arithmetic and accept any array-like of any dtype. def apply(extinction: ArrayLike, flux: ArrayLike, inplace: bool = ...) -> _Array: ... def remove(extinction: ArrayLike, flux: ArrayLike, inplace: bool = ...) -> _Array: ... sncosmo-extinction-aeccedb/src/extinction/_extinction.pyx000066400000000000000000000611451527041510000243270ustar00rootroot00000000000000#!python #cython: boundscheck=False, wraparound=False, initializedcheck=False, cdivision=True, freethreading_compatible=True """Interstellar dust extinction functions.""" import numpy as np cimport numpy as np __version__ = "0.4.10" __all__ = ['ccm89', 'odonnell94', 'Fitzpatrick99', 'fitzpatrick99', 'fm07', 'calzetti00', 'apply', 'remove'] # We use some C code for Cubic splines in the Fitzpatrick99 and fm07 functions. # There are two reasons for using this over something from scipy: # # First, Fitzpatrick99 specifies "natural" boundary conditions on the splines, # but in scipy.interpolate, this can only be achieved using the CubicSpline # class, which is new in scipy v0.18 (a bit too recent). # # Second, this C code is significantly faster than CubicSpline. include "extern/bsplines.pxi" # ------------------------------------------------------------------------------ # Utility functions for converting wavelength units cdef double aa_to_invum(double x): """Convert Angstroms to inverse microns""" return 1e4 / x cdef double noop(double x): return x ctypedef double (*scalar_func)(double) # ----------------------------------------------------------------------------- # Cardelli, Clayton & Mathis (1989) cdef inline void ccm89ab_ir_invum(double x, double *a, double *b): """ccm89 a, b parameters for 0.3 < x < 1.1 (infrared)""" cdef double y y = x**1.61 a[0] = 0.574 * y b[0] = -0.527 * y cdef inline void ccm89ab_opt_invum(double x, double *a, double *b): """ccm89 a, b parameters for 1.1 < x < 3.3 (optical)""" cdef double y y = x - 1.82 a[0] = ((((((0.329990*y - 0.77530)*y + 0.01979)*y + 0.72085)*y - 0.02427)*y - 0.50447)*y + 0.17699)*y + 1.0 b[0] = ((((((-2.09002*y + 5.30260)*y - 0.62251)*y - 5.38434)*y + 1.07233)*y + 2.28305)*y + 1.41338)*y cdef inline void ccm89ab_uv_invum(double x, double *a, double *b): """ccm89 a, b parameters for 3.3 < x < 8.0 (ultraviolet)""" cdef double y, y2, y3 y = x - 4.67 a[0] = 1.752 - 0.316*x - (0.104 / (y*y + 0.341)) y = x - 4.62 b[0] = -3.090 + 1.825*x + (1.206 / (y*y + 0.263)) if x > 5.9: y = x - 5.9 y2 = y * y y3 = y2 * y a[0] += -0.04473*y2 - 0.009779*y3 b[0] += 0.2130*y2 + 0.1207*y3 cdef inline void ccm89ab_fuv_invum(double x, double *a, double *b): """ccm89 a, b parameters for 8 < x < 11 (far-UV)""" cdef double y, y2, y3 y = x - 8. y2 = y * y y3 = y2 * y a[0] = -0.070*y3 + 0.137*y2 - 0.628*y - 1.073 b[0] = 0.374*y3 - 0.420*y2 + 4.257*y + 13.670 cdef inline void ccm89ab_invum(double x, double *a, double *b): """ccm89 a, b parameters for 0.3 < x < 11 in microns^-1""" if x < 1.1: ccm89ab_ir_invum(x, a, b) elif x < 3.3: ccm89ab_opt_invum(x, a, b) elif x < 8.: ccm89ab_uv_invum(x, a, b) else: ccm89ab_fuv_invum(x, a, b) def ccm89(const double[:] wave, double a_v, double r_v, unit='aa', np.ndarray out=None): """ccm89(wave, a_v, r_v, unit='aa', out=None) Cardelli, Clayton & Mathis (1989) extinction function. The parameters given in the original paper [1]_ are used. The claimed validity is 1250 Angstroms to 3.3 microns. Parameters ---------- wave : numpy.ndarray (1-d) Wavelengths or wavenumbers. a_v : float Scaling parameter, A_V: extinction in magnitudes at characteristic V band wavelength. r_v : float Ratio of total to selective extinction, A_V / E(B-V). unit : {'aa', 'invum'}, optional Unit of wave: 'aa' (Angstroms) or 'invum' (inverse microns). out : np.ndarray, optional If specified, store output values in this array. It must be a 1-d float64 array with the same length as wave. Returns ------- Extinction in magnitudes at each input wavelength. Raises ------ ValueError If out is not a 1-d float64 array with the same length as wave. Notes ----- In Cardelli, Clayton & Mathis (1989) the mean R_V-dependent extinction law, is parameterized as .. math:: = a(x) + b(x) / R_V where the coefficients a(x) and b(x) are functions of wavelength. At a wavelength of approximately 5494.5 angstroms (a characteristic wavelength for the V band), a(x) = 1 and b(x) = 0, so that A(5494.5 angstroms) = A_V. This function returns .. math:: A(\lambda) = A_V (a(x) + b(x) / R_V) References ---------- .. [1] Cardelli, J. A., Clayton, G. C., & Mathis, J. S. 1989, ApJ, 345, 245 """ cdef: size_t i size_t n = wave.shape[0] double a = 0.0 double b = 0.0 if out is None: out = np.empty(n, dtype=np.float64) else: if out.ndim != 1 or out.shape[0] != wave.shape[0]: raise ValueError("out must be a 1-d array with the same length as wave") if out.dtype != np.float64: raise ValueError("out must have dtype float64") cdef scalar_func convert_wave if unit == 'aa': convert_wave = &aa_to_invum elif unit == 'invum': convert_wave = &noop else: raise ValueError("unrecognized unit") cdef double[:] out_view = out for i in range(n): ccm89ab_invum(convert_wave(wave[i]), &a, &b) out_view[i] = a_v * (a + b / r_v) return out # ----------------------------------------------------------------------------- # O'Donnell (1994) cdef inline void od94ab_opt_invum(double x, double *a, double *b): """od94 a, b parameters for 1.1 < x < 3.3 (optical)""" cdef double y y = x - 1.82 a[0] = (((((((-0.505*y + 1.647)*y - 0.827)*y - 1.718)*y + 1.137)*y + 0.701)*y - 0.609)*y + 0.104)*y + 1.0 b[0] = (((((((3.347*y - 10.805)*y + 5.491)*y + 11.102)*y - 7.985)*y - 3.989)*y + 2.908)*y + 1.952)*y cdef inline void od94ab_invum(double x, double *a, double *b): """od94 a, b parameters for 0.3 < x < 11 in microns^-1""" if x < 1.1: ccm89ab_ir_invum(x, a, b) elif x < 3.3: od94ab_opt_invum(x, a, b) elif x < 8.: ccm89ab_uv_invum(x, a, b) else: ccm89ab_fuv_invum(x, a, b) def odonnell94(const double[:] wave, double a_v, double r_v, unit='aa', np.ndarray out=None): """odonnell94(wave, a_v, r_v, unit='aa', out=None) O'Donnell (1994) extinction function. Like Cardelli, Clayton, & Mathis (1989) [1]_ but using the O'Donnell (1994) [2]_ optical coefficients between 3030 A and 9091 A. Parameters ---------- wave : numpy.ndarray (1-d) Wavelengths or wavenumbers. a_v : float Scaling parameter, A_V: extinction in magnitudes at characteristic V band wavelength. r_v : float Ratio of total to selective extinction, A_V / E(B-V). unit : {'aa', 'invum'}, optional Unit of wave: 'aa' (Angstroms) or 'invum' (inverse microns). out : np.ndarray, optional If specified, store output values in this array. It must be a 1-d float64 array with the same length as wave. Returns ------- Extinction in magnitudes at each input wavelength. Raises ------ ValueError If out is not a 1-d float64 array with the same length as wave. Notes ----- This function matches the Goddard IDL astrolib routine CCM_UNRED. From the documentation for that routine: 1. The CCM curve shows good agreement with the Savage & Mathis (1979) [3]_ ultraviolet curve shortward of 1400 A, but is probably preferable between 1200 and 1400 A. 2. Curve is extrapolated between 912 and 1000 A as suggested by Longo et al. (1989) [4]_ 3. Valencic et al. (2004) [5]_ revise the ultraviolet CCM curve (3.3 -- 8.0 um^-1). But since their revised curve does not connect smoothly with longer and shorter wavelengths, it is not included here. References ---------- .. [1] Cardelli, J. A., Clayton, G. C., & Mathis, J. S. 1989, ApJ, 345, 245 .. [2] O'Donnell, J. E. 1994, ApJ, 422, 158O .. [3] Savage & Mathis 1979, ARA&A, 17, 73 .. [4] Longo et al. 1989, ApJ, 339,474 .. [5] Valencic et al. 2004, ApJ, 616, 912 """ cdef: size_t i size_t n = wave.shape[0] double a = 0.0 double b = 0.0 if out is None: out = np.empty(n, dtype=np.float64) else: if out.ndim != 1 or out.shape[0] != wave.shape[0]: raise ValueError("out must be a 1-d array with the same length as wave") if out.dtype != np.float64: raise ValueError("out must have dtype float64") cdef scalar_func convert_wave if unit == 'aa': convert_wave = &aa_to_invum elif unit == 'invum': convert_wave = &noop else: raise ValueError("unrecognized unit") cdef double[:] out_view = out for i in range(n): od94ab_invum(convert_wave(wave[i]), &a, &b) out_view[i] = a_v * (a + b / r_v) return out # ----------------------------------------------------------------------------- # Fitzpatrick (1999) DEF F99_X0 = 4.596 DEF F99_GAMMA = 0.99 DEF F99_C3 = 3.23 DEF F99_C4 = 0.41 DEF F99_C5 = 5.9 DEF F99_X02 = F99_X0 * F99_X0 DEF F99_GAMMA2 = F99_GAMMA * F99_GAMMA cdef inline double f99_uv_invum(double x, double a_v, double r_v): """f99 extinction for x < 1e4/2700 microns^-1""" cdef double c1, c2, d, x2, y, y2, rv2, k c2 = -0.824 + 4.717 / r_v c1 = 2.030 - 3.007 * c2 x2 = x * x y = x2 - F99_X02 d = x2 / (y * y + x2 * F99_GAMMA2) k = c1 + c2 * x + F99_C3 * d if x >= F99_C5: y = x - F99_C5 y2 = y * y k += F99_C4 * (0.5392 * y2 + 0.05644 * y2 * y) return a_v * (1. + k / r_v) cdef double *_F99_XKNOTS = [0.0, 1.e4 / 26500., 1.e4 / 12200., 1.e4 / 6000., 1.e4 / 5470., 1.e4 / 4670., 1.e4 / 4110., 1.e4 / 2700., 1.e4 / 2600.] cdef void _f99_kknots(double *xknots, double r_v, double *out): """Fill knot k values in Fitzpatrick 99 for given R_V. xknots and out should be arrays of length 9.""" cdef double c1, c2, d, x, x2, y, rv2 cdef int i c2 = -0.824 + 4.717 / r_v c1 = 2.030 - 3.007 * c2 rv2 = r_v * r_v out[0] = -r_v out[1] = 0.26469 * r_v/3.1 - r_v out[2] = 0.82925 * r_v/3.1 - r_v out[3] = -0.422809 + 1.00270*r_v + 2.13572e-04*rv2 - r_v out[4] = -5.13540e-02 + 1.00216 * r_v - 7.35778e-05*rv2 - r_v out[5] = 0.700127 + 1.00184*r_v - 3.32598e-05*rv2 - r_v out[6] = (1.19456 + 1.01707*r_v - 5.46959e-03*rv2 + 7.97809e-04 * rv2 * r_v - 4.45636e-05 * rv2*rv2 - r_v) for i in range(7,9): x2 = xknots[i] * xknots[i] y = (x2 - F99_X02) d = x2 / (y * y + x2 * F99_GAMMA2) out[i] = c1 + c2*xknots[i] + F99_C3 * d cdef class Fitzpatrick99(object): """Fitzpatrick (1999) dust extinction function for arbitrary R_V. An instance of this class is a callable that can be used as ``f(wave, a_v)`` where ``wave`` is a 1-d array of wavelengths and ``a_v`` is a scalar value. Parameters ---------- r_v : float, optional R_V value. Default is 3.1. Examples -------- Create a callable that gives the extinction law for a given ``r_v`` and use it: >>> f = Fitzpatrick99(3.1) >>> f(np.array([3000., 4000.]), 1.) array([ 1.79939955, 1.42338583]) """ cdef bs_spline1d *spline # pointer to c struct cdef readonly double r_v def __cinit__(self, double r_v=3.1): self.r_v = r_v cdef double *kknots = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] _f99_kknots(_F99_XKNOTS, r_v, kknots) cdef bs_bcs bcs cdef bs_exts exts cdef bs_errorcode code bcs.left.type = BS_DERIV2 bcs.left.value = 0.0 bcs.right.type = BS_DERIV2 bcs.right.value = 0.0 exts.left.type = BS_VALUE exts.left.value = 0.0 exts.right.type = BS_VALUE exts.right.value = 0.0 code = bs_spline1d_create(bs_array(_F99_XKNOTS, 9, 1), bs_array(kknots, 9, 1), bcs, exts, &self.spline) assert_ok(code) def __call__(self, np.ndarray wave not None, double a_v, unit='aa'): cdef const double[:] wave_view cdef double[:] out_view cdef double r_v = self.r_v cdef double ebv = a_v / r_v cdef size_t i cdef size_t n cdef bs_errorcode code # translate `wave` to inverse microns if unit == 'invum': pass elif unit == 'aa': wave = 1e4 / wave else: raise ValueError("unrecognized unit") n = wave.shape[0] out = np.empty(n, dtype=np.float64) wave_view = wave out_view = out # Optical/IR spline: evaluate at all wavelengths; we will overwrite # the UV points afterwards. These are outside the spline range, so # they don't actually take too much time to evaluate. # (outview actually holds "k" after this call; see below) code = bs_spline1d_eval(self.spline, to_bs_array(wave_view), to_bs_array(out_view)) assert_ok(code) # Analytic function in the UV (< 2700 Angstroms). for i in range(n): # for optical/IR, `out` is actually k, but we wanted # a_v/r_v * (k+r_v), so we adjust here. if wave_view[i] < 3.7037037037037037: # 1e4 / 2700 out_view[i] = ebv * (out_view[i] + r_v) # for UV, we overwrite the array with the UV function value. else: out_view[i] = f99_uv_invum(wave_view[i], a_v, r_v) return out def __dealloc__(self): bs_spline1d_free(self.spline) # functional interface for Fitzpatrick (1999) with R_V = 3.1 _fitzpatrick99_fixed = Fitzpatrick99(3.1) def fitzpatrick99(wave, a_v, r_v=3.1, unit='aa'): """fitzpatrick99(wave, a_v, r_v=3.1, unit='aa') Fitzpatrick (1999) dust extinction function. Fitzpatrick (1999) [1]_ model which relies on the parametrization of Fitzpatrick & Massa (1990) [2]_ in the UV (below 2700 A) and spline fitting in the optical and IR. This function is defined from 910 A to 6 microns, but note the claimed validity goes down only to 1150 A. The optical spline points are not taken from F99 Table 4, but rather updated versions from E. Fitzpatrick (this matches the Goddard IDL astrolib routine FM_UNRED). Parameters ---------- wave : numpy.ndarray (1-d) Input wavelengths or wavenumbers (see units). a_v : float Total V-band extinction in magnitudes. r_v : float Ratio of total to selective extinction, A_V / E(B-V). unit : {'aa', 'invum'}, optional Wavelength units: Angstroms or inverse microns. Returns ------- Extinction in magnitudes at each input wavelength. References ---------- .. [1] Fitzpatrick, E. L. 1999, PASP, 111, 63 .. [2] Fitzpatrick, E. L. & Massa, D. 1990, ApJS, 72, 163 """ if r_v == 3.1: return _fitzpatrick99_fixed(wave, a_v, unit=unit) else: return Fitzpatrick99(r_v)(wave, a_v, unit=unit) # ----------------------------------------------------------------------------- # Fitzpatrick & Massa 2007 DEF FM07_X0 = 4.592 DEF FM07_GAMMA = 0.922 DEF FM07_C1 = -0.175 DEF FM07_C2 = 0.807 DEF FM07_C3 = 2.991 DEF FM07_C4 = 0.319 DEF FM07_C5 = 6.097 DEF FM07_X02 = FM07_X0 * FM07_X0 DEF FM07_GAMMA2 = FM07_GAMMA * FM07_GAMMA DEF FM07_R_V = 3.1 # Fixed for the time being (used in fm07kknots) # Used for wave < 2700. cdef inline double fm07_uv_invum(double x, double a_v): """fm07 for x < 1e4/2700 microns^-1 (ultraviolet)""" cdef double d, x2, y, k x2 = x * x y = x2 - FM07_X02 d = x2 / (y*y + x2 * FM07_GAMMA2) k = FM07_C1 + FM07_C2 * x + FM07_C3 * d if x > FM07_C5: y = x - FM07_C5 k += FM07_C4 * y * y return a_v * (1. + k / FM07_R_V) cdef void _fm07_kknots(double *xknots, double *out): """Return k knots given xknots for fm07. (Could be a static array)""" cdef double d cdef int i for i in range(0, 5): out[i] = (-0.83 + 0.63*FM07_R_V) * xknots[i]**1.84 - FM07_R_V out[5] = 0.0 out[6] = 1.322 out[7] = 2.055 for i in range(8, 10): d = xknots[i]**2 / ((xknots[i]**2 - FM07_X02)**2 + xknots[i]**2 * FM07_GAMMA2) out[i] = FM07_C1 + FM07_C2 * xknots[i] + FM07_C3 * d cdef double *_FM07_XKNOTS = [0., 0.25, 0.50, 0.75, 1., 1.e4 / 5530., 1.e4 / 4000., 1.e4 / 3300., 1.e4 / 2700., 1.e4 / 2600.] cdef double *_FM07_KKNOTS = [0., 0., 0., 0., 0., 0., 0., 0., 0., 0.] _fm07_kknots(_FM07_XKNOTS, _FM07_KKNOTS) def fm07(np.ndarray wave not None, double a_v, unit='aa'): """fm07(wave, a_v, unit='aa') Fitzpatrick & Massa (2007) extinction model for R_V = 3.1. The Fitzpatrick & Massa (2007) [1]_ model, which has a slightly different functional form from that of Fitzpatrick (1999) [3]_ (`extinction_f99`). Fitzpatrick & Massa (2007) claim it is preferable, although it is unclear if signficantly so (Gordon et al. 2009 [2]_). Defined from 910 A to 6 microns. Parameters ---------- wave : numpy.ndarray (1-d) Wavelengths or wavenumbers. a_v : float Scaling parameter, A_V: extinction in magnitudes at characteristic V band wavelength. unit : {'aa', 'invum'}, optional Unit of wave: 'aa' (Angstroms) or 'invum' (inverse microns). References ---------- .. [1] Fitzpatrick, E. L. & Massa, D. 2007, ApJ, 663, 320 .. [2] Gordon, K. D., Cartledge, S., & Clayton, G. C. 2009, ApJ, 705, 1320 .. [3] Fitzpatrick, E. L. 1999, PASP, 111, 63 """ cdef const double[:] wave_view cdef double[:] out_view cdef double ebv = a_v / FM07_R_V cdef size_t i cdef size_t n # translate `wave` to inverse microns if unit == 'invum': pass elif unit == 'aa': wave = 1e4 / wave else: raise ValueError("unrecognized unit") # create the spline (we do this here rather than globally so we can # deallocate it.) cdef bs_spline1d* spline cdef bs_bcs bcs cdef bs_exts exts cdef bs_errorcode code bcs.left.type = BS_DERIV2 bcs.left.value = 0.0 bcs.right.type = BS_DERIV2 bcs.right.value = 0.0 exts.left.type = BS_VALUE exts.left.value = 0.0 exts.right.type = BS_VALUE exts.right.value = 0.0 code = bs_spline1d_create(bs_array(_FM07_XKNOTS, 10, 1), bs_array(_FM07_KKNOTS, 10, 1), bcs, exts, &spline) assert_ok(code) n = wave.shape[0] out = np.empty(n, dtype=np.float64) wave_view = wave out_view = out # Optical/IR spline: evaluate at all wavelengths; we will overwrite # the UV points afterwards. These are outside the spline range, so # they don't actually take too much time to evaluate. # (outview actually holds "k" after this call; see below) code = bs_spline1d_eval(spline, to_bs_array(wave_view), to_bs_array(out_view)) assert_ok(code) bs_spline1d_free(spline) # Analytic function in the UV (< 2700 Angstroms). for i in range(n): # for optical/IR, `out` is actually k, but we wanted # a_v/r_v * (k+r_v), so we adjust here. if wave_view[i] < 3.7037037037037037: # 1e4 / 2700 out_view[i] = ebv * (out_view[i] + FM07_R_V) # for UV, we overwrite the array with the UV function value. else: out_view[i] = fm07_uv_invum(wave_view[i], a_v) return out # ----------------------------------------------------------------------------- # Calzetti 2000 # http://adsabs.harvard.edu/abs/2000ApJ...533..682C cdef inline double calzetti00k_uv_invum(double x): """calzetti00 `k` for 0.12 microns < wave < 0.63 microns (UV/optical), x in microns^-1""" return 2.659 * (((0.011*x - 0.198)*x + 1.509)*x - 2.156) cdef inline double calzetti00k_ir_invum(double x): """calzetti00 `k` for 0.63 microns < wave < 2.2 microns (optical/IR), x in microns^-1""" return 2.659 * (1.040*x - 1.857) cdef inline double calzetti00_invum(double x, double r_v): cdef double k if x > 1.5873015873015872: # 1. / 0.63 k = calzetti00k_uv_invum(x) else: k = calzetti00k_ir_invum(x) return 1.0 + k / r_v def calzetti00(const double[:] wave, double a_v, double r_v, unit='aa', np.ndarray out=None): """calzetti00(wave, a_v, r_v, unit='aa', out=None) Calzetti (2000) extinction function. Calzetti et al. (2000, ApJ 533, 682) developed a recipe for dereddening the spectra of galaxies where massive stars dominate the radiation output, valid between 0.12 to 2.2 microns. They estimate :math:`R_V = 4.05 \pm 0.80` from optical-IR observations of 4 starburst galaxies. Parameters ---------- wave : numpy.ndarray (1-d) Wavelengths or wavenumbers. a_v : float Scaling parameter, A_V: extinction in magnitudes at characteristic V band wavelength. r_v : float Ratio of total to selective extinction, A_V / E(B-V). unit : {'aa', 'invum'}, optional Unit of wave: 'aa' (Angstroms) or 'invum' (inverse microns). out : np.ndarray, optional If specified, store output values in this array. It must be a 1-d float64 array with the same length as wave. Returns ------- Extinction in magnitudes at each input wavelength. Raises ------ ValueError If out is not a 1-d float64 array with the same length as wave. """ cdef: size_t i size_t n = wave.shape[0] double a = 0.0 double b = 0.0 if out is None: out = np.empty(n, dtype=np.float64) else: if out.ndim != 1 or out.shape[0] != wave.shape[0]: raise ValueError("out must be a 1-d array with the same length as wave") if out.dtype != np.float64: raise ValueError("out must have dtype float64") cdef scalar_func convert_wave if unit == 'aa': convert_wave = &aa_to_invum elif unit == 'invum': convert_wave = &noop else: raise ValueError("unrecognized unit") cdef double[:] out_view = out for i in range(n): out_view[i] = a_v * calzetti00_invum(convert_wave(wave[i]), r_v) return out # ------------------------------------------------------------------------------ # convenience functions for applying/removing extinction to/from flux # values, optionally in-place. It turns out that pure Python is about as # fast as C here. def apply(extinction, flux, inplace=False): """apply(extinction, flux, inplace=False) Apply extinction to flux values. This is a convenience function to perform "reddening" of flux values. It simply performs ``flux * 10**(-0.4 * extinction)``: flux is decreased (for positive extinction values). Parameters ---------- extinction : numpy.ndarray (1-d) Extinction in magnitudes. (Positive extinction values decrease flux values.) flux : numpy.ndarray Flux values. inplace : bool, optional Whether to perform the operation in-place on the flux array. If True, the return value is a reference to the input flux array. Returns ------- new_flux : numpy.ndarray (1-d) Flux values with extinction applied. """ trans = 10.**(-0.4 * extinction) if inplace: flux *= trans return flux else: return flux * trans # ------------------------------------------------------------------------------ # convenience function for removing extinction from flux values, optionally # in-place. (It turns out that this isn't really faster than just doing it # in pure python...) def remove(extinction, flux, inplace=False): """remove(extinction, flux, inplace=False) Remove extinction from flux values. This is a convenience function to "deredden" fluxes. It simply performs ``flux * 10**(0.4 * extinction)``: flux is increased (for positive extinction values). Parameters ---------- extinction : numpy.ndarray (1-d) Extinction in magnitudes. flux : numpy.ndarray Flux values. inplace : bool, optional Whether to perform the operation in-place on the flux array. If True, the return value is a reference to the input flux array. Returns ------- new_flux : numpy.ndarray (1-d) Flux values with extinction removed. """ trans = 10.**(0.4 * extinction) if inplace: flux *= trans return flux else: return flux * trans sncosmo-extinction-aeccedb/src/extinction/py.typed000066400000000000000000000000001527041510000227200ustar00rootroot00000000000000sncosmo-extinction-aeccedb/tests/000077500000000000000000000000001527041510000174225ustar00rootroot00000000000000sncosmo-extinction-aeccedb/tests/test_extinction.py000077500000000000000000000160571527041510000232330ustar00rootroot00000000000000#!/usr/bin/env py.test import os import numpy as np from numpy.testing import assert_allclose import extinction # Resolve test data relative to this file so the suite can be run from any # working directory, including against an installed wheel. TESTDATA_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), "testdata") def test_ccm89(): # NOTE: Test is only to precision of 0.016 because there is a discrepancy # of 0.014 for the B band wavelength of unknown origin (and up to 0.002 in # other bands). # # Note that a and b can be obtained with: # b = ccm89(wave, 0.) # a = ccm89(wave, 1.) - b # # These differ from the values tablulated in the original paper. # Could be due to floating point errors in the original paper? # # U, B, V, R, I, J, H, K band effective wavelengths from CCM '89 table 3 x_inv_microns = np.array([2.78, 2.27, 1.82, 1.43, 1.11, 0.80, 0.63, 0.46]) wave = 1.0e4 / x_inv_microns # A(lambda)/A(V) for R_V = 3.1 from Table 3 of CCM '89 ref_values = np.array([1.569, 1.337, 1.000, 0.751, 0.479, 0.282, 0.190, 0.114]) assert_allclose(extinction.ccm89(wave, 1.0, 3.1), ref_values, rtol=0.016, atol=0.0) def test_odonnell94(): # NOTE: The tabulated values go to 0.001, but the test is only for matching # at the 0.005 level, because there is currently a discrepancy up to 0.0047 # of unknown origin. # # Tests od94() at Rv = 3.1 against the widely used values tabulated in # Schlegel, Finkbeiner and Davis (1998) # http://adsabs.harvard.edu/abs/1998ApJ...500..525S # # This is tested by evaluating the extinction curve at a (given) # effective wavelength, since these effective wavelengths: # "... represent(s) that wavelength on the extinction curve # with the same extinction as the full passband." # # The test does not include UKIRT L' (which, at 3.8 microns) is # beyond the range of wavelengths allowed by the function # or the APM b_J filter which is defined in a non-standard way. # # The SFD98 tabulated values go to 1e-3, so we should be able to match at # that level. # fmt: off wave = np.array([3372., 4404., 5428., 6509., 8090., 3683., 4393., 5519., 6602., 8046., 12660., 16732., 22152., 5244., 6707., 7985., 9055., 6993., 3502., 4676., 4127., 4861., 5479., 3546., 4925., 6335., 7799., 9294., 3047., 4711., 5498., 6042., 7068., 8066., 4814., 6571., 8183.]) ref_values = np.array([1.664, 1.321, 1.015, 0.819, 0.594, 1.521, 1.324, 0.992, 0.807, 0.601, 0.276, 0.176, 0.112, 1.065, 0.793, 0.610, 0.472, 0.755, 1.602, 1.240, 1.394, 1.182, 1.004, 1.579, 1.161, 0.843, 0.639, 0.453, 1.791, 1.229, 0.996, 0.885, 0.746, 0.597, 1.197, 0.811, 0.580]) # fmt: on assert_allclose( extinction.odonnell94(wave, 1.0, 3.1), ref_values, rtol=0.0051, atol=0.0 ) def test_fitzpatrick99_knots(): """Test that knots match values in Fitzpatrick (1999) Table 3 for fitzpatrick99 function (with R_V = 3.1)""" wave = np.array( [np.inf, 26500.0, 12200.0, 6000.0, 5470.0, 4670.0, 4110.0, 2700.0, 2600.0] ) x = np.array([0.0, 0.377, 0.820, 1.667, 1.828, 2.141, 2.433, 3.704, 3.846]) # A(lambda) values for E(B-V) = 1 or A_V = 3.1 ref_values = np.array([0.0, 0.265, 0.829, 2.688, 3.055, 3.806, 4.315, 6.265, 6.591]) assert_allclose( extinction.fitzpatrick99(wave, 3.1, unit="aa"), ref_values, rtol=0.0, atol=0.001 ) # atol = 0.002 because the input values are less precise (e.g., 0.377 # rather than 1.e4 / 26500.) assert_allclose( extinction.fitzpatrick99(x, 3.1, unit="invum"), ref_values, rtol=0.0, atol=0.002 ) def test_fitzpatrick99_rv_knots(): """Test that Fitzpatrick function has the right R_V dependence at the knots.""" wave = np.array([26500.0, 12200.0, 6000.0, 5470.0, 4670.0, 4110.0]) # "the IR points at 1/lambda < 1 invum are simply scaled by R/3.1" # "the optical points are vertically offset by an amount R - 3.1 , with # slight corrections made to preserve the normalization" for r in [1.0, 2.0, 3.0, 4.0, 5.0, 6.0]: # `expected` gives expected A(lambda) for E(B-V) = 1 (A_V = R) expected = [ r / 3.1 * 0.265, # Table 3 scaled by R/3.1 r / 3.1 * 0.829, # Table 3 scaled by R/3.1 -0.426 + 1.0044 * r, # Table 4 -0.050 + 1.0016 * r, # Table 4 0.701 + 1.0016 * r, # Table 4 1.208 + 1.0032 * r - 0.00033 * r**2, # Table 4 ] result = extinction.Fitzpatrick99(r)(wave, r) # Note that we don't expect an exact match because, as noted in the # code, "the optical spline points are not taken from F99 table 4, # but rather updated versions from E. Fitzpatrick (matching the IDL # astrolib routine FM_UNRED). assert_allclose(result, expected, rtol=0.003) def test_fitzpatrick99_idl(): """Test that result matches implementation in IDL procedure FM_UNRED""" for r_v in (2.3, 3.1, 4.0, 5.3): fname = os.path.join(TESTDATA_DIR, f"fm_unred_{r_v:3.1f}.dat") wave, a_lambda_ref = np.loadtxt(fname, unpack=True) a_lambda = extinction.Fitzpatrick99(r_v)(wave, 1.0) assert_allclose(a_lambda, a_lambda_ref, rtol=0.00005) def test_fitzpatrick99_r_v(): """Test that we can access the `r_v` attribute.""" f = extinction.Fitzpatrick99() assert f.r_v == 3.1 f = extinction.Fitzpatrick99(2.1) assert f.r_v == 2.1 def test_fitzpatrick99_func(): """Check passing R_V.""" wave = np.array([2000.0, 30000.0]) for r_v in (3.1, 4.0): assert np.all( extinction.Fitzpatrick99(r_v)(wave, 1.0) == extinction.fitzpatrick99(wave, 1.0, r_v) ) def test_fm07(): # The dtype makes the type float64 with the numpy 2.2 stubs too, which the # lock installs on Python 3.10, so that ty accepts the call to fm07. wave = np.arange(3000.0, 9000.0, 1000, dtype=np.float64) # from running the code; we're just checking that results don't change! ref_values = [ 1.84192286, 1.42645161, 1.13842341, 0.88843179, 0.69226384, 0.54709373, ] assert_allclose(extinction.fm07(wave, 1.0), ref_values) def test_calzetti00(): """Test calzetti against another translation of the same base code""" wave = np.array([2000.0, 4000.0, 8000.0]) flux = np.ones(3) new_flux = extinction.apply(extinction.calzetti00(wave, -1.0, 3.1), flux) # derived using Julia version of IDL calz_unred ref_values = np.array([10.5288, 3.88153, 1.61769]) assert_allclose(new_flux, ref_values, atol=0.0001) sncosmo-extinction-aeccedb/tests/test_out.py000066400000000000000000000042661527041510000216520ustar00rootroot00000000000000"""The documented output array must receive and return the calculated values.""" from functools import partial import numpy as np import pytest from numpy.testing import assert_array_equal import extinction LAWS = [ partial(extinction.ccm89, r_v=3.1), partial(extinction.odonnell94, r_v=3.1), partial(extinction.calzetti00, r_v=4.05), ] @pytest.mark.parametrize("law", LAWS) @pytest.mark.parametrize("unit", ["aa", "invum"]) @pytest.mark.parametrize("step", [1, 2, -1]) def test_out(law, unit, step): wave = np.array([2000.0, 4000.0, 8000.0]) if unit == "invum": wave = 1.0e4 / wave original = wave.copy() expected = law(wave, 1.0, unit=unit) backing = np.full(wave.size * abs(step), -1.0) out = backing[::step] assert law(wave, 1.0, unit=unit, out=out) is out assert_array_equal(out, expected) assert_array_equal(wave, original) if step == 2: assert_array_equal(backing[1::2], -1.0) @pytest.mark.parametrize("law", LAWS) @pytest.mark.parametrize("unit", ["aa", "invum"]) def test_out_can_alias_wavelengths(law, unit): wave = np.array([2000.0, 4000.0, 8000.0]) if unit == "invum": wave = 1.0e4 / wave expected = law(wave.copy(), 1.0, unit=unit) assert law(wave, 1.0, unit=unit, out=wave) is wave assert_array_equal(wave, expected) @pytest.mark.parametrize("law", LAWS) @pytest.mark.parametrize("size", [0, 2, 4]) def test_out_wrong_length(law, size): # The loop writes len(wave) values without bounds checks, so this check # must not be an assert, which `python -O` skips. wave = np.array([2000.0, 4000.0, 8000.0]) backing = np.full(8, -1.0) with pytest.raises(ValueError, match="same length as wave"): law(wave, 1.0, out=backing[:size]) assert_array_equal(backing, -1.0) @pytest.mark.parametrize("law", LAWS) @pytest.mark.parametrize( ("shape", "dtype"), [((1, 3), np.float64), (3, np.float32), (3, [("a", np.float64)])], ids=["2d", "float32", "structured"], ) def test_out_wrong_ndim_or_dtype(law, shape, dtype): wave = np.array([2000.0, 4000.0, 8000.0]) with pytest.raises(ValueError, match="out must"): law(wave, 1.0, out=np.zeros(shape, dtype=dtype)) sncosmo-extinction-aeccedb/tests/test_readonly.py000066400000000000000000000020451527041510000226510ustar00rootroot00000000000000"""Input wavelengths need not be writable; output arrays still must be.""" from functools import partial import numpy as np import pytest from numpy.testing import assert_array_equal import extinction LAWS = [ partial(extinction.ccm89, r_v=3.1), partial(extinction.odonnell94, r_v=3.1), partial(extinction.calzetti00, r_v=4.05), extinction.fitzpatrick99, extinction.Fitzpatrick99(4.0), extinction.fm07, ] @pytest.mark.parametrize("law", LAWS) @pytest.mark.parametrize("unit", ["aa", "invum"]) @pytest.mark.parametrize("step", [1, 2, -1]) def test_readonly_wavelengths(law, unit, step): wave = np.array([1500.0, 2000.0, 3000.0, 4000.0, 5500.0, 9000.0]) if unit == "invum": wave = 1.0e4 / wave wave = wave[::step] expected = law(wave.copy(), 1.0, unit=unit) original = wave.copy() wave.flags.writeable = False actual = law(wave, 1.0, unit=unit) assert_array_equal(actual, expected) assert_array_equal(wave, original) assert not wave.flags.writeable assert actual.flags.writeable sncosmo-extinction-aeccedb/tests/testdata/000077500000000000000000000000001527041510000212335ustar00rootroot00000000000000sncosmo-extinction-aeccedb/tests/testdata/README.md000066400000000000000000000005001527041510000225050ustar00rootroot00000000000000Test data --------- This directory contains comparison files used in the tests. These outputs from running the IDL procedure `FM_UNRED` from the IDL Astro library: http://idlastro.gsfc.nasa.gov/ftp/pro/astro/ (`FM_UNRED` also requires the `CSPLINE` procedure.) The script used to generate the output is included here. sncosmo-extinction-aeccedb/tests/testdata/fm_unred_2.3.dat000066400000000000000000000124301527041510000241060ustar00rootroot00000000000000 1000.00 7.94421 1019.85 7.59781 1040.10 7.27403 1060.75 6.97145 1081.81 6.68871 1103.28 6.42455 1125.19 6.17778 1147.53 5.94731 1170.31 5.73211 1193.54 5.53122 1217.24 5.34375 1241.40 5.16887 1266.05 5.00581 1291.18 4.85387 1316.82 4.71239 1342.96 4.58078 1369.62 4.45850 1396.81 4.34507 1424.54 4.24006 1452.82 4.14313 1481.67 4.05396 1511.08 3.97234 1541.08 3.89814 1571.68 3.83131 1602.88 3.77192 1634.70 3.72020 1667.16 3.67655 1700.25 3.64155 1734.01 3.61454 1768.43 3.59610 1803.54 3.58819 1839.35 3.59330 1875.86 3.61449 1913.10 3.65526 1951.09 3.71893 1989.82 3.80714 2029.32 3.91664 2069.61 4.03432 2110.70 4.13307 2152.60 4.17544 2195.34 4.13146 2238.92 3.99958 2283.37 3.80789 2328.70 3.59403 2374.93 3.38638 2422.08 3.19915 2470.17 3.03622 2519.21 2.89621 2569.22 2.77581 2620.23 2.67149 2672.25 2.58009 2725.30 2.49643 2779.41 2.41715 2834.58 2.34391 2890.86 2.27609 2948.25 2.21313 3006.78 2.15452 3066.48 2.09980 3127.35 2.04854 3189.44 2.00033 3252.76 1.95481 3317.34 1.91167 3383.20 1.87059 3450.36 1.83130 3518.86 1.79356 3588.72 1.75714 3659.97 1.72184 3732.63 1.68747 3806.73 1.65386 3882.31 1.62087 3959.38 1.58836 4037.99 1.55622 4118.16 1.52434 4199.91 1.49253 4283.29 1.46040 4368.33 1.42754 4455.05 1.39361 4543.50 1.35830 4633.70 1.32134 4725.69 1.28255 4819.51 1.24218 4915.19 1.20085 5012.77 1.15908 5112.29 1.11735 5213.78 1.07609 5317.29 1.03569 5422.86 0.996474 5530.52 0.958739 5640.31 0.922606 5752.29 0.888073 5866.49 0.855133 5982.96 0.823770 6101.73 0.793961 6222.87 0.765628 6346.41 0.738682 6472.41 0.713036 6600.90 0.688611 6731.95 0.665332 6865.60 0.643129 7001.90 0.621937 7140.91 0.601695 7282.68 0.582344 7427.26 0.563831 7574.72 0.546106 7725.09 0.529122 7878.46 0.512833 8034.87 0.497201 8194.39 0.482184 8357.07 0.467748 8522.98 0.453859 8692.18 0.440485 8864.75 0.427595 9040.74 0.415164 9220.23 0.403164 9403.28 0.391572 9589.96 0.380365 9780.35 0.369522 9974.52 0.359023 10172.5 0.348849 10374.5 0.338983 10580.5 0.329409 10790.5 0.320112 11004.7 0.311078 11223.2 0.302292 11446.0 0.293743 11673.3 0.285420 11905.0 0.277312 12141.4 0.269407 12382.4 0.261698 12628.2 0.254182 12878.9 0.246855 13134.6 0.239718 13395.4 0.232768 13661.3 0.226003 13932.5 0.219421 14209.1 0.213019 14491.2 0.206796 14778.9 0.200747 15072.3 0.194871 15371.5 0.189163 15676.7 0.183622 15987.9 0.178243 16305.4 0.173024 16629.1 0.167961 16959.2 0.163051 17295.9 0.158291 17639.3 0.153676 17989.4 0.149205 18346.6 0.144872 18710.8 0.140676 19082.3 0.136612 19461.1 0.132678 19847.5 0.128869 20241.5 0.125183 20643.4 0.121617 21053.2 0.118166 21471.2 0.114829 21897.4 0.111601 22332.2 0.108480 22775.5 0.105463 23227.7 0.102547 23688.8 0.0997283 24159.1 0.0970047 24638.8 0.0943733 25127.9 0.0918315 25626.7 0.0893764 26135.5 0.0870052 26654.4 0.0847156 27183.5 0.0825048 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0.0441818 49026.6 0.0432741 50000.0 0.0423868 sncosmo-extinction-aeccedb/tests/testdata/run.pro000066400000000000000000000016251527041510000225650ustar00rootroot00000000000000 pro run minwave = 1000 maxwave = 50000 n = 200 ; create log-spaced wavelength vector minexp = alog10(minwave) maxexp = alog10(maxwave) step = (maxexp - minexp) / (n-1) exps = minexp + step * findgen(n) wave = 10.^exps ; create a "flat" flux vector flux = wave * 0.0 + 1.0 r_vs = [2.3, 3.1, 4.0, 5.3] fnames = ['fm_unred_2.3.dat', 'fm_unred_3.1.dat', 'fm_unred_4.0.dat', 'fm_unred_5.3.dat'] for i = 0, n_elements(r_vs) - 1 do begin a_v = 1.0 r_v = r_vs(i) ebv = a_v / r_v fm_unred, wave, flux, -ebv, flux_new, R_V=r_v ;Redden (negative E(B-V)) ; fm_unred does `result = flux * 10.^(0.4*curve)` where is scaled by input ; undo it to get the curve a_lambda = -2.5 * alog10(flux_new) data = fltarr(2, n_elements(wave)) data(0,*) = wave data(1,*) = a_lambda openw, 1, fnames(i) printf, 1, data close, 1 endfor end 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